Molecular characterization of integrons and their associated gene cassettes in multidrug-resistant enterobacteriaceae isolates from environmental sources and the exploration of antibiotic combination against some resistant strains
- Fadare, Folake Temitope https://orcid.org/0000-0001-5779-9798
- Authors: Fadare, Folake Temitope https://orcid.org/0000-0001-5779-9798
- Date: 2023
- Subjects: Enterobacteriaceae , Molecular microbiology , Enterobacteria
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/27809 , vital:69942
- Description: Globally, the increasing rate of antimicrobial resistance against our currently available drugs has been a serious public concern. Due to the selective nature of antibiotics, bacteria are expected to develop resistance against them over time, but the current scourge of antimicrobial resistance is aggravated by factors other than the expected evolutionary trend. The use and overuse of antibiotics in clinical and agricultural contexts have led to the fast rise of multidrug-resistant MDR microorganisms. A scenario that necessitates an upsurge in the clinical failures observed with our current drug arsenals is expected to rise if left unchecked. One of the significant drivers implicated in the spread of antimicrobial resistance genes is the integrons. These are mobile genetic elements found on pathogenicity islands, transposons, and plasmids, easing their distribution among various bacteria. They are considered efficient gene expression systems that naturally capture, integrate gene cassettes GCs and immediately express the captured antimicrobial resistance genes on the GCs due to the inherent promoters on their structures. Integrons have been known to confer resistance against most classes of antibiotics. These include all known β-lactams, chloramphenicol, trimethoprim, erythromycin, aminoglycosides, quinolones, streptothricin, lincomycin, rifampicin, fosfomycin, and antiseptics of the quaternary ammonium compound family. They have been detected in bacterial populations under direct or indirect antibiotic pressure in clinical, agricultural, and environmental contexts. The emergence of MDR in Enterobacteriaceae is a critical public health issue that has attracted the World Health Organization WHO, which classified them as one of the critical priority pathogens urgently requiring new antibiotics. The resistance phenomenon has proven most of the current antibiotics ineffective, further compounded by the slow pace of the discovery of new antibiotics, necessitating the hunt for new, practical remedies. One of such is the exploration of synergy among existing antibiotics. Two medications combined have a higher impact, thereby allowing current antibiotics to be salvaged for use in treating MDR bacteria, even if the bacteria are resistant against one or both antibiotics separately. Hence, this research focused on the occurrence and prevalence of multidrug resistance and the characterization of integrons and their associated gene cassettes in members of Enterobacteriaceae, including Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Escherichia coli, and Citrobacter spp. recovered from animal droppings, rivers, and effluents of hospital and wastewater treatment plants in Eastern Cape Province, South Africa. The inhibitory effect of combining two drugs belonging to different antibiotic classes to obtain a possible potentiating effect against some multidrug-resistant Enterobacteriaceae isolates harbouring integrons were examined and studied. The isolates were identified using the conventional molecular Polymerase Chain Reaction with specific primers. The antimicrobial resistance profile and the production of Extended-spectrum and metallo β-lactamase were detected using disk diffusion technique DDT, double-disk synergy test DDST, and ethylenediaminetetraacetic acid EDTA tests, respectively. The PCR-based screening method, DNA sequencing analyses, and restriction fragment length polymorphism RFLP were used to characterize the integrons and their associated GCs. Furthermore, Enterobacterial Repetitive Intergenic Consensus ERIC PCR determined the genotypic relationships between some specific species. The various antibiotics' minimum inhibitory concentration MIC was determined using the broth microdilution, while the checkerboard method was used to determine the fractional inhibitory concentration indices FICIs. The time-kill assays TKAs were further used to confirm the synergism observed from the checkerboard assays. Most of the isolates were resistant against most antibiotics tested and were considered MDR. The least resistance was observed against imipenem, a carbapenem, one of the drugs of last resort. Also present were the ESBL and MBL producers, with a few isolates co-producing the enzymes. A high prevalence of integrons was observed in the isolates, with class 1 integrons being the most frequently detected. Some isolates co-harboured the intI1 and intI2 genes and were classified as class1 plus 2 integrons. Although Citrobacter spp. had the least number of isolates among the Enterobacteriaceae studied, it harboured the most diverse gene cassette arrays. The various gene cassette arrays were identified as follows: For Klebsiella spp. Aac 6 Ib, aadA1 dfrA1, and dfrA1 sat2; for Citrobacter spp., dfrA5 aac3 Ib, aac6 ib, aadA1dfrA1 aadA1, aadA1-dfrA1, aadA5 dfrA17, and dfrA21-aac3-Ib; for E. coli dfrA21- aac-3-Ib, dfrA5-aac-3-Ib, aadA1 dfrA1, and aadA5 dfrA17 and for E. cloacae aadA1 dfrA1, dfrA7 dfrA21 dfrA5 aac 3 Ib, and dfrA1 sat2. The GC array dfrA1 sat2 was the only array detected in class 2 integrons which are analogous to that found in Tn7, dfrA1-sat2-aadA1, with the deletion of the last GC aadA1. These detected GCs confer resistance against aminoglycosides, including streptomycin and spectinomycin, and trimethoprim, further increasing the resistance spectrum of the bacterial species harbouring them. The detection of integrons and their associated GC and the presence of these β-lactamases is also associated with coresistance against other classes of antibiotics by bacterial species harbouring them, further limiting treatment options. The checkerboard assays combining antibiotics against these drug-resistant integron harbouring Enterobacteriaceae revealed that 26.3 percent 10 over 38 of the interactions were categorized as synergistic, while 73.7 percent 28 over 38 were indifferent. None of the combinations was antagonistic. The TKAs revealed all the synergistic interactions as bactericidal. Therefore, the combinations of gentamicin with tetracycline, ciprofloxacin, and ceftazidime against Multidrug-resistant MDR Klebsiella pneumoniae; tetracycline-ceftazidime combination against MDR Escherichia coli, colistin combinations with ceftazidime and gentamicin, and tetracycline-gentamicin combinations against MDR Citrobacter freundii may be future therapeutic alternatives. , Thesis (MSci) -- Faculty of Science and Agriculture, 2023
- Full Text:
- Date Issued: 2023
- Authors: Fadare, Folake Temitope https://orcid.org/0000-0001-5779-9798
- Date: 2023
- Subjects: Enterobacteriaceae , Molecular microbiology , Enterobacteria
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/27809 , vital:69942
- Description: Globally, the increasing rate of antimicrobial resistance against our currently available drugs has been a serious public concern. Due to the selective nature of antibiotics, bacteria are expected to develop resistance against them over time, but the current scourge of antimicrobial resistance is aggravated by factors other than the expected evolutionary trend. The use and overuse of antibiotics in clinical and agricultural contexts have led to the fast rise of multidrug-resistant MDR microorganisms. A scenario that necessitates an upsurge in the clinical failures observed with our current drug arsenals is expected to rise if left unchecked. One of the significant drivers implicated in the spread of antimicrobial resistance genes is the integrons. These are mobile genetic elements found on pathogenicity islands, transposons, and plasmids, easing their distribution among various bacteria. They are considered efficient gene expression systems that naturally capture, integrate gene cassettes GCs and immediately express the captured antimicrobial resistance genes on the GCs due to the inherent promoters on their structures. Integrons have been known to confer resistance against most classes of antibiotics. These include all known β-lactams, chloramphenicol, trimethoprim, erythromycin, aminoglycosides, quinolones, streptothricin, lincomycin, rifampicin, fosfomycin, and antiseptics of the quaternary ammonium compound family. They have been detected in bacterial populations under direct or indirect antibiotic pressure in clinical, agricultural, and environmental contexts. The emergence of MDR in Enterobacteriaceae is a critical public health issue that has attracted the World Health Organization WHO, which classified them as one of the critical priority pathogens urgently requiring new antibiotics. The resistance phenomenon has proven most of the current antibiotics ineffective, further compounded by the slow pace of the discovery of new antibiotics, necessitating the hunt for new, practical remedies. One of such is the exploration of synergy among existing antibiotics. Two medications combined have a higher impact, thereby allowing current antibiotics to be salvaged for use in treating MDR bacteria, even if the bacteria are resistant against one or both antibiotics separately. Hence, this research focused on the occurrence and prevalence of multidrug resistance and the characterization of integrons and their associated gene cassettes in members of Enterobacteriaceae, including Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Escherichia coli, and Citrobacter spp. recovered from animal droppings, rivers, and effluents of hospital and wastewater treatment plants in Eastern Cape Province, South Africa. The inhibitory effect of combining two drugs belonging to different antibiotic classes to obtain a possible potentiating effect against some multidrug-resistant Enterobacteriaceae isolates harbouring integrons were examined and studied. The isolates were identified using the conventional molecular Polymerase Chain Reaction with specific primers. The antimicrobial resistance profile and the production of Extended-spectrum and metallo β-lactamase were detected using disk diffusion technique DDT, double-disk synergy test DDST, and ethylenediaminetetraacetic acid EDTA tests, respectively. The PCR-based screening method, DNA sequencing analyses, and restriction fragment length polymorphism RFLP were used to characterize the integrons and their associated GCs. Furthermore, Enterobacterial Repetitive Intergenic Consensus ERIC PCR determined the genotypic relationships between some specific species. The various antibiotics' minimum inhibitory concentration MIC was determined using the broth microdilution, while the checkerboard method was used to determine the fractional inhibitory concentration indices FICIs. The time-kill assays TKAs were further used to confirm the synergism observed from the checkerboard assays. Most of the isolates were resistant against most antibiotics tested and were considered MDR. The least resistance was observed against imipenem, a carbapenem, one of the drugs of last resort. Also present were the ESBL and MBL producers, with a few isolates co-producing the enzymes. A high prevalence of integrons was observed in the isolates, with class 1 integrons being the most frequently detected. Some isolates co-harboured the intI1 and intI2 genes and were classified as class1 plus 2 integrons. Although Citrobacter spp. had the least number of isolates among the Enterobacteriaceae studied, it harboured the most diverse gene cassette arrays. The various gene cassette arrays were identified as follows: For Klebsiella spp. Aac 6 Ib, aadA1 dfrA1, and dfrA1 sat2; for Citrobacter spp., dfrA5 aac3 Ib, aac6 ib, aadA1dfrA1 aadA1, aadA1-dfrA1, aadA5 dfrA17, and dfrA21-aac3-Ib; for E. coli dfrA21- aac-3-Ib, dfrA5-aac-3-Ib, aadA1 dfrA1, and aadA5 dfrA17 and for E. cloacae aadA1 dfrA1, dfrA7 dfrA21 dfrA5 aac 3 Ib, and dfrA1 sat2. The GC array dfrA1 sat2 was the only array detected in class 2 integrons which are analogous to that found in Tn7, dfrA1-sat2-aadA1, with the deletion of the last GC aadA1. These detected GCs confer resistance against aminoglycosides, including streptomycin and spectinomycin, and trimethoprim, further increasing the resistance spectrum of the bacterial species harbouring them. The detection of integrons and their associated GC and the presence of these β-lactamases is also associated with coresistance against other classes of antibiotics by bacterial species harbouring them, further limiting treatment options. The checkerboard assays combining antibiotics against these drug-resistant integron harbouring Enterobacteriaceae revealed that 26.3 percent 10 over 38 of the interactions were categorized as synergistic, while 73.7 percent 28 over 38 were indifferent. None of the combinations was antagonistic. The TKAs revealed all the synergistic interactions as bactericidal. Therefore, the combinations of gentamicin with tetracycline, ciprofloxacin, and ceftazidime against Multidrug-resistant MDR Klebsiella pneumoniae; tetracycline-ceftazidime combination against MDR Escherichia coli, colistin combinations with ceftazidime and gentamicin, and tetracycline-gentamicin combinations against MDR Citrobacter freundii may be future therapeutic alternatives. , Thesis (MSci) -- Faculty of Science and Agriculture, 2023
- Full Text:
- Date Issued: 2023
Evaluation of antimicrobial combination therapy options for the management of integron-mediated multidrug resistance in enterococcus species and acinetobacter baumannii from aquatic environment in the Eastern Cape Province, South Africa
- Authors: Ola, Adeniji Oluwaseun
- Date: 2022-04
- Subjects: Enterococcus , Aquatic biodiversity , Acinetobacter
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/27776 , vital:69467
- Description: Infectious diseases caused by multidrug-resistant MDR pathogens, such as Acinetobacter baumannii and Enterococcus spp., is an increasing worldwide problem. For treating these diseases, antibiotics are usually the first choice. But organisms develop resistance as a result of drug abuse, continuous use of antibiotics and release of antibiotics into the environment. These have prompted MDR's development, making even the most active drugs ineffective. Transposons, plasmids and integrons are the most effective mobile genetic elements that promote acquisition and spread of resistance determinants. Integrons carrying various arrays of resistance gene cassettes are principally helpful for epidemiological studies of these disease-causing organisms. Alternative treatments, such as using drugs in combination or with adjuvants and nanoparticles therapy, have been documented. Nanoparticles have the potential requirements for qualifying as antibacterial agents. In addition to their antimicrobial activities, nanoparticles can be used together with antibiotics for more enhanced antimicrobial activity In this study, Acinetobacter baumanni, Enterococcus faecium and Enterococcus faecalis were recovered from the aquatic environment in the Eastern Cape Province, South Africa with a standard microbiological method. Their antibiotic sensitivity testing was carried out using Kirby Bauer disk diffusion and microdilution methods. A high occurrence of class-1 integrons was discovered in MDR A. baumanni, with the internal variable containing aadA1, aadA5 and aadA2 genes, which confer resistance for streptomycin and spectinomycin, aac 6Ib for amikacin/ tobramycin and dfrA17 genes for trimethoprim. Similarly, class1 integron was detected in Enterococcus, without the presence of gene cassette. The checkerboard assay and time-kill assay were used to test for the effect of the combination of the antibiotic. The impact of colistin combined with quinolones (ciprofloxacin) with the Fractional inhibitory concentration index FICs 0.31 indicated synergistic effects against MDR A baumanni. However, when colistin was combined with meropenem and ceftazidime, additive effects with FIC, ranging from 0.52 to 1 were observed. In addition, a combination of gentamicin MIC 4 μgml with vancomycin MIC 256 μgml antibiotics against vancomycin-resistant Enterococcus faecalis showed antibacterial activity. In contrast, the combination of ciprofloxacin 1 μgml with Ampicillin 16 μgml antibiotics against Enterococcus faecalis showed a bacteriostatic effect. The initial inoculum declined by 100 percentage when gentamicin was combined with vancomycin at a concentration of 4 and 128 μgml MIC respectively, for about 2 h following the treatment for MDR E. faecium. Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction ERIC PCR analyses of the studied pathogens revealed great genetic diversity, suggesting the various sources of environmental contamination. Silver nanoparticles AgNPs and zinc oxide nanoparticles ZnO NPs were chemically synthesized using a precipitation method and characterized using energy dispersive Xray analysis EDX, scanning electron microscopy SEM, Fourier transforms infrared spectroscopic analysis FTIR and transmission electron microscopy TEM. The characterization results showed the synthesis of 43.37 nm and 21.03 nm nanoparticles of zinc oxide and silver origins, correspondingly, with distinct morphology, as revealed in TEM. The size, stability and functional groups of the nanoparticles produced were revealed using EDX and FTIR. Zinc oxide nanoparticles were cytotoxic against Vero cell lines at the tested concentrations, whereas AgNPs had no cytotoxic effect at lower concentrations. Acinetobacter baumanni, Enterococcus faecium and Enterococcus faecalis were with MIC in the range of 0.0390.078mgml for silver nanoparticles. Zinc oxide nanoparticles were explicitly active against Enterococcus species gram-positive with MIC of 1.25 5 mgml. Both studied nanoparticles exhibited profound synergistic and additive activities against all the investigated MDR pathogens. These findings demonstrate good antibacterial potential of the nanoparticles against drug-resistant strains and open a new arena of antimicrobials for medical treatment. , Thesis (MSc) -- Faculty of Science and Agriculture, 2022
- Full Text:
- Date Issued: 2022-04
- Authors: Ola, Adeniji Oluwaseun
- Date: 2022-04
- Subjects: Enterococcus , Aquatic biodiversity , Acinetobacter
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/27776 , vital:69467
- Description: Infectious diseases caused by multidrug-resistant MDR pathogens, such as Acinetobacter baumannii and Enterococcus spp., is an increasing worldwide problem. For treating these diseases, antibiotics are usually the first choice. But organisms develop resistance as a result of drug abuse, continuous use of antibiotics and release of antibiotics into the environment. These have prompted MDR's development, making even the most active drugs ineffective. Transposons, plasmids and integrons are the most effective mobile genetic elements that promote acquisition and spread of resistance determinants. Integrons carrying various arrays of resistance gene cassettes are principally helpful for epidemiological studies of these disease-causing organisms. Alternative treatments, such as using drugs in combination or with adjuvants and nanoparticles therapy, have been documented. Nanoparticles have the potential requirements for qualifying as antibacterial agents. In addition to their antimicrobial activities, nanoparticles can be used together with antibiotics for more enhanced antimicrobial activity In this study, Acinetobacter baumanni, Enterococcus faecium and Enterococcus faecalis were recovered from the aquatic environment in the Eastern Cape Province, South Africa with a standard microbiological method. Their antibiotic sensitivity testing was carried out using Kirby Bauer disk diffusion and microdilution methods. A high occurrence of class-1 integrons was discovered in MDR A. baumanni, with the internal variable containing aadA1, aadA5 and aadA2 genes, which confer resistance for streptomycin and spectinomycin, aac 6Ib for amikacin/ tobramycin and dfrA17 genes for trimethoprim. Similarly, class1 integron was detected in Enterococcus, without the presence of gene cassette. The checkerboard assay and time-kill assay were used to test for the effect of the combination of the antibiotic. The impact of colistin combined with quinolones (ciprofloxacin) with the Fractional inhibitory concentration index FICs 0.31 indicated synergistic effects against MDR A baumanni. However, when colistin was combined with meropenem and ceftazidime, additive effects with FIC, ranging from 0.52 to 1 were observed. In addition, a combination of gentamicin MIC 4 μgml with vancomycin MIC 256 μgml antibiotics against vancomycin-resistant Enterococcus faecalis showed antibacterial activity. In contrast, the combination of ciprofloxacin 1 μgml with Ampicillin 16 μgml antibiotics against Enterococcus faecalis showed a bacteriostatic effect. The initial inoculum declined by 100 percentage when gentamicin was combined with vancomycin at a concentration of 4 and 128 μgml MIC respectively, for about 2 h following the treatment for MDR E. faecium. Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction ERIC PCR analyses of the studied pathogens revealed great genetic diversity, suggesting the various sources of environmental contamination. Silver nanoparticles AgNPs and zinc oxide nanoparticles ZnO NPs were chemically synthesized using a precipitation method and characterized using energy dispersive Xray analysis EDX, scanning electron microscopy SEM, Fourier transforms infrared spectroscopic analysis FTIR and transmission electron microscopy TEM. The characterization results showed the synthesis of 43.37 nm and 21.03 nm nanoparticles of zinc oxide and silver origins, correspondingly, with distinct morphology, as revealed in TEM. The size, stability and functional groups of the nanoparticles produced were revealed using EDX and FTIR. Zinc oxide nanoparticles were cytotoxic against Vero cell lines at the tested concentrations, whereas AgNPs had no cytotoxic effect at lower concentrations. Acinetobacter baumanni, Enterococcus faecium and Enterococcus faecalis were with MIC in the range of 0.0390.078mgml for silver nanoparticles. Zinc oxide nanoparticles were explicitly active against Enterococcus species gram-positive with MIC of 1.25 5 mgml. Both studied nanoparticles exhibited profound synergistic and additive activities against all the investigated MDR pathogens. These findings demonstrate good antibacterial potential of the nanoparticles against drug-resistant strains and open a new arena of antimicrobials for medical treatment. , Thesis (MSc) -- Faculty of Science and Agriculture, 2022
- Full Text:
- Date Issued: 2022-04
Genetic diversity, resistance profile of HIV and risk assessment of mother-to-child transmission in pregnant women on anti-retroviral therapy in the Eastern Cape, South Africa
- Authors: Adeniyi, Oladele Vincent
- Date: 2018-12
- Subjects: Antiretroviral agents , AIDS (Disease) in infants
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/19817 , vital:43254
- Description: Despite the initiation of life-long ART in HIV-infected pregnant women, the rate and determinants of infant HIV transmission are not known, especially in the poor resource settings of the Eastern Cape, South Africa. Maternal anti-retroviral therapy (ART) is crucial for elimination of mother-to-child transmission (MTCT) of HIV. However, the inevitable risks of emergence of HIV drug resistance poses significant threat to achieving this goal of HIV-free generation and keeping mothers alive. Also, it is unclear if women with high viral load at delivery have acquired clinically relevant mutations, which could confer resistance to the ART, thus, further increasing the risks of motherto- child transmission of HIV-drug resistance strains. In addition to the gaps identified in the prevention of mother-to-child transmission (PMTCT) context, the understanding of regional epidemics is crucial to the broader epidemiological profiling of HIV infections in the country. Despite the rapid influx of foreign nationals to South African and Eastern Cape Province, there has not been any molecular epidemiological studies profiling the HIV diversity in the Eastern Cape. , Thesis (PhD) (Microbiology) -- University of Fort Hare, 2018
- Full Text:
- Date Issued: 2018-12
- Authors: Adeniyi, Oladele Vincent
- Date: 2018-12
- Subjects: Antiretroviral agents , AIDS (Disease) in infants
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/19817 , vital:43254
- Description: Despite the initiation of life-long ART in HIV-infected pregnant women, the rate and determinants of infant HIV transmission are not known, especially in the poor resource settings of the Eastern Cape, South Africa. Maternal anti-retroviral therapy (ART) is crucial for elimination of mother-to-child transmission (MTCT) of HIV. However, the inevitable risks of emergence of HIV drug resistance poses significant threat to achieving this goal of HIV-free generation and keeping mothers alive. Also, it is unclear if women with high viral load at delivery have acquired clinically relevant mutations, which could confer resistance to the ART, thus, further increasing the risks of motherto- child transmission of HIV-drug resistance strains. In addition to the gaps identified in the prevention of mother-to-child transmission (PMTCT) context, the understanding of regional epidemics is crucial to the broader epidemiological profiling of HIV infections in the country. Despite the rapid influx of foreign nationals to South African and Eastern Cape Province, there has not been any molecular epidemiological studies profiling the HIV diversity in the Eastern Cape. , Thesis (PhD) (Microbiology) -- University of Fort Hare, 2018
- Full Text:
- Date Issued: 2018-12
Incidence of porcine circovirus type 2 and porcine parvoviruses in swine herds of some communities in Eastern Cape, South Africa
- Authors: Afolabi, Kayode Olayinka
- Date: 2018
- Subjects: Swine -- Diseases Swine -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/9691 , vital:34820
- Description: Porcine circovirus type 2 (PCV2) is one of the swine pathogens of global economic importance. Since its first detection in early 1990s as the main etiologic agent of porcine multisystemic wasting syndrome (PMWS) and many other porcine circovirus-associated diseases (PCVAD), the virus has been extensively studied and has been found to be present in virtually all the pig producing countries of the world. As a viral pathogen that brings about clinical diseases aided by co-infecting pathogens, the involvement of many other viral agents including porcine parvoviruses (PPVs) have caught the attention of stakeholders worldwide. However, no surveillance study of the viral pathogens has been carried out in South Africa as there are little or no information on their prevalence in the swine herds of the country. This present study therefore aimed at detection and molecular characterization of PCV2 and PPVs in swine herds of some selected communities in Eastern Cape Province, South Africa. A total of 375 field samples were collected from seven commercial and communal farms from three District Municipalities of Eastern Cape, South Africa between 2015 and 2016. Structured questionnaires were also administered to each farm at the time of sample collection to obtain some important information relating to health status and farm management practices in the sampled farms. With the aid of conventional PCR method, 339 samples were initially screened for the presence of PCV2; positive amplicons were sequenced and obtained partial genomes of the virus were preliminarily analyzed. In order to obtain the complete genomes of the virus, four overlapping primer pairs were used to amplify the full-genome of PCV2 from the initial positive samples; amplified genomes were sequenced using the Sanger methods, sequenced PCV2 genomes were assembled and characterized. Furthermore, the prevalences of some designated PPVs in the sampled farms were obtained using 110 samples randomly selected from the previously archived samples and screened with 6 different primer pairs specific for the detection of 7 PPVs. All the amplified parvoviruses’ genomes were sequenced; their sequenced partial genomes were subsequently base-culled and analysed. The data obtained revealed that 54/339 (15.93 percent) samples from the swine herds were positive for PCV2; whereas the degree of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6 to 60 percent. The majority 15/17 (88 percent) of the analyzed partial sequences were found clustering with other PCV2b strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genotype in the initial screening and analysis. Furthermore, 15 complete PCV2 genomes were successfully amplified, sequenced and assembled. NJ and ML phylogenetic analysis of the complete ORF2 gene and full genomes unanimously showed 11 of the assembled genomes belonging to genotype PCV2b. Another 3 of the characterized sequences formed clade with other reference mutant PCV2b and PCV2b subtype 1C (PCV2d) strains from different parts of the world. The last sequence however, clustered with other reference strains belonging to PCV2 intermediate clade 2 (PCV2-IM2) recently identified in a global PCV2 strains phylogenetic analysis. Other genetic analyses including multiple sequence alignment and p-distance analysis also confirmed the outcomes of the phylogenetic analyses of the complete capsid gene and fullgenomes of the virus. On the other hand, the findings of the molecular profiling for PPVs showed that all the screened parvoviruses were present in the study area, having prevalence of 29.1 percent (PPV1), 21.8 percent (PPV2), 5.5 percent (PPV3), 43.6 percent (PPV4), 21.8 percent (PBo-likeV) and 44.6 percent for PBoV1 and PBoV2. Double infection of the screened PPVs was observed to be very rampant among the pigs as high as 20/110 (18.2 percent) for PPV2/PPV4 and PPV4/PBoV; followed by 19/110 (17.3 percent) of the samples for PPV1/PPV4 and PPV1/PBoV. Three of the viruses were found simultaneously in 19 of the screened samples representing 17.3 percent, whereas 8 (7.3 percent) samples were positive for four of the viruses. Phylogenetic analyses of PPV1, PPV2 and PBoVs 1 and 2 were conducted with two major clades homologous for each of them. This is the first report of PCV2 in swine herds of the Province and the first detection of PCV2b, PCV2d and PCV2-IM2 strains in South African swine herds. It follows the first reported case of PCV2a in an outbreak of porcine multisystemic wasting syndrome (PMWS) in Gauteng Province, South Africa over two decades ago. Also, this is the first major epidemiologic study on PPVs in the country following the initial case study of 1975. These findings confirmed the presence of the allimportant viral pathogens among pigs and also give preliminary insights into the possibility of co-infections of the pathogens in the studied area. This could however result in a serious large scale outbreak of devastating disease(s) associated with the viral pathogens, thereby ultimately resulting in huge economic losses if no appropriate measures are taken to effectively curb their spread across the country.
- Full Text:
- Date Issued: 2018
- Authors: Afolabi, Kayode Olayinka
- Date: 2018
- Subjects: Swine -- Diseases Swine -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/9691 , vital:34820
- Description: Porcine circovirus type 2 (PCV2) is one of the swine pathogens of global economic importance. Since its first detection in early 1990s as the main etiologic agent of porcine multisystemic wasting syndrome (PMWS) and many other porcine circovirus-associated diseases (PCVAD), the virus has been extensively studied and has been found to be present in virtually all the pig producing countries of the world. As a viral pathogen that brings about clinical diseases aided by co-infecting pathogens, the involvement of many other viral agents including porcine parvoviruses (PPVs) have caught the attention of stakeholders worldwide. However, no surveillance study of the viral pathogens has been carried out in South Africa as there are little or no information on their prevalence in the swine herds of the country. This present study therefore aimed at detection and molecular characterization of PCV2 and PPVs in swine herds of some selected communities in Eastern Cape Province, South Africa. A total of 375 field samples were collected from seven commercial and communal farms from three District Municipalities of Eastern Cape, South Africa between 2015 and 2016. Structured questionnaires were also administered to each farm at the time of sample collection to obtain some important information relating to health status and farm management practices in the sampled farms. With the aid of conventional PCR method, 339 samples were initially screened for the presence of PCV2; positive amplicons were sequenced and obtained partial genomes of the virus were preliminarily analyzed. In order to obtain the complete genomes of the virus, four overlapping primer pairs were used to amplify the full-genome of PCV2 from the initial positive samples; amplified genomes were sequenced using the Sanger methods, sequenced PCV2 genomes were assembled and characterized. Furthermore, the prevalences of some designated PPVs in the sampled farms were obtained using 110 samples randomly selected from the previously archived samples and screened with 6 different primer pairs specific for the detection of 7 PPVs. All the amplified parvoviruses’ genomes were sequenced; their sequenced partial genomes were subsequently base-culled and analysed. The data obtained revealed that 54/339 (15.93 percent) samples from the swine herds were positive for PCV2; whereas the degree of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6 to 60 percent. The majority 15/17 (88 percent) of the analyzed partial sequences were found clustering with other PCV2b strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genotype in the initial screening and analysis. Furthermore, 15 complete PCV2 genomes were successfully amplified, sequenced and assembled. NJ and ML phylogenetic analysis of the complete ORF2 gene and full genomes unanimously showed 11 of the assembled genomes belonging to genotype PCV2b. Another 3 of the characterized sequences formed clade with other reference mutant PCV2b and PCV2b subtype 1C (PCV2d) strains from different parts of the world. The last sequence however, clustered with other reference strains belonging to PCV2 intermediate clade 2 (PCV2-IM2) recently identified in a global PCV2 strains phylogenetic analysis. Other genetic analyses including multiple sequence alignment and p-distance analysis also confirmed the outcomes of the phylogenetic analyses of the complete capsid gene and fullgenomes of the virus. On the other hand, the findings of the molecular profiling for PPVs showed that all the screened parvoviruses were present in the study area, having prevalence of 29.1 percent (PPV1), 21.8 percent (PPV2), 5.5 percent (PPV3), 43.6 percent (PPV4), 21.8 percent (PBo-likeV) and 44.6 percent for PBoV1 and PBoV2. Double infection of the screened PPVs was observed to be very rampant among the pigs as high as 20/110 (18.2 percent) for PPV2/PPV4 and PPV4/PBoV; followed by 19/110 (17.3 percent) of the samples for PPV1/PPV4 and PPV1/PBoV. Three of the viruses were found simultaneously in 19 of the screened samples representing 17.3 percent, whereas 8 (7.3 percent) samples were positive for four of the viruses. Phylogenetic analyses of PPV1, PPV2 and PBoVs 1 and 2 were conducted with two major clades homologous for each of them. This is the first report of PCV2 in swine herds of the Province and the first detection of PCV2b, PCV2d and PCV2-IM2 strains in South African swine herds. It follows the first reported case of PCV2a in an outbreak of porcine multisystemic wasting syndrome (PMWS) in Gauteng Province, South Africa over two decades ago. Also, this is the first major epidemiologic study on PPVs in the country following the initial case study of 1975. These findings confirmed the presence of the allimportant viral pathogens among pigs and also give preliminary insights into the possibility of co-infections of the pathogens in the studied area. This could however result in a serious large scale outbreak of devastating disease(s) associated with the viral pathogens, thereby ultimately resulting in huge economic losses if no appropriate measures are taken to effectively curb their spread across the country.
- Full Text:
- Date Issued: 2018
Development communication for water conservation in rural and peri-urban communities : a study of three district municipalities in Eastern Cape, South Africa
- Onyenankeya, Kevin Uwaecheghi
- Authors: Onyenankeya, Kevin Uwaecheghi
- Date: 2017
- Subjects: Communication in rural development -- South Africa -- Eastern Cape Water conservation -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/8397 , vital:32562
- Description: South Africa continues to ramp up public campaigns to rein in escalating water demand amid dwindling and erratic supply. One of the objectives of the campaign is to reduce water demand in urban areas to 15 precent by 2030 through water conservation and water demand management strategies. While the water conservation drive continue to gain traction among commercial and urban water users, it does not appear to resonate with rural and peri-urban residents. Using the pragmatic convergent parallel mixed methods approach consisting of the quantitative and qualitative methods such as survey, focus groups, and indepth-interviews and observation, this study explored the water conservation attitudes, behaviour and intentions of rural and peri-urban respondents in four Eastern Cape communities in South Africa, and to determine if any factors influence their attitudes and behaviour. The study also attempted to determine whether a dialogic approach to communication about water conservation is likely to lead to positive change in attitude and behaviour. The questionnaires were distributed personally by researcher and trained assistants but respondents were left to complete the questionnaires at their convenience and in their own pace but within a negotiated period of five working days. The collected data were analysed using both parametric and non-parametric methods. The nonparametric methods used include thematic analysis. Transcripts of focus group and individual interviews were coded using Nvivo, while quantitative data was analysed in SPSS and presented in simple frequency and cross tabulation. Regression analysis was used to establish the influence of attitude, subjective norm and perceived behavioural control on water conservation intention. Results revealed respondents consider water conservation important and are favourably disposed to conserving water. Although peri-urban and rural residents considered water important and would want to make effort to conserve water in the future, not all considered water conservation an overarching social priority and, as a result, are generally passive or indifferent to water conservation. The indifference appears to be underpinned by residents’ beliefs about water. Further analysis showed that peri-urban residents have stronger positive attitude towards water conservation and greater intent and commitment towards water conservation than their rural counterpart. Attitude, subjective norm and behavioural control emerged as significant factors influencing water conservation intentions of respondents. The findings suggest that water curtailment behaviours were the prevalent water conservation activities rural and peri-urban residents engaged in, while water efficiency behaviours was very poor among the population. Factors such as cost, need, knowledge and locus of control had significant influence on residents’ water conservation behaviour and intentions, especially in purchasing or installing water efficient appliances. The study found no significant relationship between sociodemographic such as age, level of education and home tenure on resident’s water conservation behaviour or intentions. The findings indicate that many rural and peri-urban communities do not have adequate information on water conservation, what to do, how to do it and why it should be done and this affects their water conservation behaviour. It was also found that engaging residents through participatory dialogue is effective in raising awareness and stimulating interest in water saving activities. The study concludes that rural and peri-urban residents are yet to develop a social ethic of water conservation. The study highlights the need for concerted education and awareness campaign around water issues so as to build community knowledge and support for water conservation. But to encourage residents to make adjustment in deep-rooted “beliefs, habits, or practices” and change to a sustainable water use behaviour in the face of scarce water supplies and increasing demand, requires not just communication to inform and persuade, but also development communication to foster mutual understanding and collective action.
- Full Text:
- Date Issued: 2017
- Authors: Onyenankeya, Kevin Uwaecheghi
- Date: 2017
- Subjects: Communication in rural development -- South Africa -- Eastern Cape Water conservation -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/8397 , vital:32562
- Description: South Africa continues to ramp up public campaigns to rein in escalating water demand amid dwindling and erratic supply. One of the objectives of the campaign is to reduce water demand in urban areas to 15 precent by 2030 through water conservation and water demand management strategies. While the water conservation drive continue to gain traction among commercial and urban water users, it does not appear to resonate with rural and peri-urban residents. Using the pragmatic convergent parallel mixed methods approach consisting of the quantitative and qualitative methods such as survey, focus groups, and indepth-interviews and observation, this study explored the water conservation attitudes, behaviour and intentions of rural and peri-urban respondents in four Eastern Cape communities in South Africa, and to determine if any factors influence their attitudes and behaviour. The study also attempted to determine whether a dialogic approach to communication about water conservation is likely to lead to positive change in attitude and behaviour. The questionnaires were distributed personally by researcher and trained assistants but respondents were left to complete the questionnaires at their convenience and in their own pace but within a negotiated period of five working days. The collected data were analysed using both parametric and non-parametric methods. The nonparametric methods used include thematic analysis. Transcripts of focus group and individual interviews were coded using Nvivo, while quantitative data was analysed in SPSS and presented in simple frequency and cross tabulation. Regression analysis was used to establish the influence of attitude, subjective norm and perceived behavioural control on water conservation intention. Results revealed respondents consider water conservation important and are favourably disposed to conserving water. Although peri-urban and rural residents considered water important and would want to make effort to conserve water in the future, not all considered water conservation an overarching social priority and, as a result, are generally passive or indifferent to water conservation. The indifference appears to be underpinned by residents’ beliefs about water. Further analysis showed that peri-urban residents have stronger positive attitude towards water conservation and greater intent and commitment towards water conservation than their rural counterpart. Attitude, subjective norm and behavioural control emerged as significant factors influencing water conservation intentions of respondents. The findings suggest that water curtailment behaviours were the prevalent water conservation activities rural and peri-urban residents engaged in, while water efficiency behaviours was very poor among the population. Factors such as cost, need, knowledge and locus of control had significant influence on residents’ water conservation behaviour and intentions, especially in purchasing or installing water efficient appliances. The study found no significant relationship between sociodemographic such as age, level of education and home tenure on resident’s water conservation behaviour or intentions. The findings indicate that many rural and peri-urban communities do not have adequate information on water conservation, what to do, how to do it and why it should be done and this affects their water conservation behaviour. It was also found that engaging residents through participatory dialogue is effective in raising awareness and stimulating interest in water saving activities. The study concludes that rural and peri-urban residents are yet to develop a social ethic of water conservation. The study highlights the need for concerted education and awareness campaign around water issues so as to build community knowledge and support for water conservation. But to encourage residents to make adjustment in deep-rooted “beliefs, habits, or practices” and change to a sustainable water use behaviour in the face of scarce water supplies and increasing demand, requires not just communication to inform and persuade, but also development communication to foster mutual understanding and collective action.
- Full Text:
- Date Issued: 2017
Evaluation of some pharmaceutical and personal care products and pesticide residues in selected wastewater treatment plants and receiving watersheds in Eastern Cape, South Africa
- Ademoyegun, Olufemi Temitope
- Authors: Ademoyegun, Olufemi Temitope
- Date: 2017
- Subjects: Emerging contaminants in water -- South Africa -- Eastern Cape Water treatment plants -- Waste disposal -- South Africa -- Eastern Cape Organic compounds -- Environmental aspects -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/2922 , vital:28138
- Description: Emerging organic contaminants (EOCs) have been the focus of global environmental research for over three decades. EOCs have caused widespread concern due to their extensive use. As EOCs were designed to correct, enhance or protect a specific physiological, their target effects in humans and/or farm stocks are relatively well known and documented. However, there is limited knowledge about their unintended effects in the environment. To address the occurrence, distribution and fate of EOCs in the environment, efficient and reliable analytical methods are needed. The relatively low concentration, high polarity, and thermal lability of some EOCs, together with their interaction with complex environmental matrices, make their analysis challenging. Sample preparation followed by GC or HPLC separation and mass spectrometry (MS) detection has become the standard approach for evaluating EOCs in environmental samples. Physicochemical properties of EOCs range from highly water-soluble (hydrophylic) to highly water-insoluble (hydrophobic). Two groups of these EOCs were considered for study in this work. Pharmaceutical and personal care products (PPCPs) were comprehensively studied in five wastewater treatment plants and their receiving watersheds in Amathole districts in Eastern C ape, South Africa. PPCPs have been widely reported in wastewater influents, effluents, receiving rivers and biosolids, but reports of their occurrence in all these matrixes have been limited by the difficulty of analysis. Therefore, a comprehensive validation of methods was carried out on the influents, effluents, sludge and soil from the irrigated golf course where the effluent of one of the study sites was being used for over three decades now for irrigation. In all, thirteen PPCPs from five therapeutic groups were selected for study in this work because of their administering rate and availability of analytical instrument. Good limit of detection (LOD) and limit of quantification (LOQ) were achieved for the method used. The LOD for the aqueous Three different technologies were employed for the treatment of wastewater in the five selected wastewater treatment plants (WWTPs) and study was carried out to evaluate their ability to eliminate the selected compounds from the influents to the effluents using statistical analysis (ANOVA) at p<0.05 on the percentage removal rate across the three plants. The results had shown eight of the compounds having no significant difference among the treatment operations, whereas the remaining five compounds varied significantly among the treatment technologies under investigation. Principal component analysis was performed on the concentration of PPCPs, their removal rate and also on the physicochemical and treatment operation parameters. Hydraulic retention time (HRT) had correlation coefficient, r = 0.90 with the concentration of PPCPs and removal rates. Furthermore, occurrences, seasonal variation, mean concentration distribution pattern of the compounds, and temporal evaluation of the mean concentration of the pharmaceutical compounds in the five WWTPs during one year of sampling were considered. The results revealed that five products which were diclofenac, ibuprofen, paracetamol, triclosan and diethyl toluamide (DDET) were predominant among the PPCPs in all the WWTPs. The removal efficiency was highest in caffeine with 96 percent, and the lowest was obtained with carbamazepine (4 percent). Risk quotient of the concentration of PPCPs in the effluents and receiving waters was determined to assess their chronic toxicity at three trophic levels: fish, algae and matrixes studied ranged from 0.01 μg/L to 0.25 μg/L, and the LOQ from 0.02 μg/L to 0.78 μg/L. In the solid matrixes, LOD varied from 0.01 ng/g to 0.65 ng/g, and the LOQ between 0.08 ng/g and 5.17 ng/g. Better recovery efficiency was obtained with this mixture of solvents, acetone: dichloromethane (1:1), for the recovery of the five therapeutic groups in the solid matrixes using ultrasonication- assisted techniques. The results show percentage recovery values ranging from 68.8 percent to 107.5 percent diaphian. According to the environmental risk assessment results, ibuprofen and triclosan were found to be the most critical compounds due to their high risk quotient values. These findings will, therefore, help in the future evaluation of the efficiency of different treatment technologies in the removal of various PPCPs from the wastewater and their sustainable management in the aquatic resources in Eastern Cape, South Africa. For the lipophilic organochlorine pesticides (OCPs), the limits of detection (LODs) of the tested congeners varied from 0.04 ng/g (α-BHC) to 0.49 ng/g (endosulfan sulfate) and the limits of quantification ranging from 0.22 ng/g (aldrin) to 2.17 ng/g (δ-BHC).
- Full Text:
- Date Issued: 2017
- Authors: Ademoyegun, Olufemi Temitope
- Date: 2017
- Subjects: Emerging contaminants in water -- South Africa -- Eastern Cape Water treatment plants -- Waste disposal -- South Africa -- Eastern Cape Organic compounds -- Environmental aspects -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/2922 , vital:28138
- Description: Emerging organic contaminants (EOCs) have been the focus of global environmental research for over three decades. EOCs have caused widespread concern due to their extensive use. As EOCs were designed to correct, enhance or protect a specific physiological, their target effects in humans and/or farm stocks are relatively well known and documented. However, there is limited knowledge about their unintended effects in the environment. To address the occurrence, distribution and fate of EOCs in the environment, efficient and reliable analytical methods are needed. The relatively low concentration, high polarity, and thermal lability of some EOCs, together with their interaction with complex environmental matrices, make their analysis challenging. Sample preparation followed by GC or HPLC separation and mass spectrometry (MS) detection has become the standard approach for evaluating EOCs in environmental samples. Physicochemical properties of EOCs range from highly water-soluble (hydrophylic) to highly water-insoluble (hydrophobic). Two groups of these EOCs were considered for study in this work. Pharmaceutical and personal care products (PPCPs) were comprehensively studied in five wastewater treatment plants and their receiving watersheds in Amathole districts in Eastern C ape, South Africa. PPCPs have been widely reported in wastewater influents, effluents, receiving rivers and biosolids, but reports of their occurrence in all these matrixes have been limited by the difficulty of analysis. Therefore, a comprehensive validation of methods was carried out on the influents, effluents, sludge and soil from the irrigated golf course where the effluent of one of the study sites was being used for over three decades now for irrigation. In all, thirteen PPCPs from five therapeutic groups were selected for study in this work because of their administering rate and availability of analytical instrument. Good limit of detection (LOD) and limit of quantification (LOQ) were achieved for the method used. The LOD for the aqueous Three different technologies were employed for the treatment of wastewater in the five selected wastewater treatment plants (WWTPs) and study was carried out to evaluate their ability to eliminate the selected compounds from the influents to the effluents using statistical analysis (ANOVA) at p<0.05 on the percentage removal rate across the three plants. The results had shown eight of the compounds having no significant difference among the treatment operations, whereas the remaining five compounds varied significantly among the treatment technologies under investigation. Principal component analysis was performed on the concentration of PPCPs, their removal rate and also on the physicochemical and treatment operation parameters. Hydraulic retention time (HRT) had correlation coefficient, r = 0.90 with the concentration of PPCPs and removal rates. Furthermore, occurrences, seasonal variation, mean concentration distribution pattern of the compounds, and temporal evaluation of the mean concentration of the pharmaceutical compounds in the five WWTPs during one year of sampling were considered. The results revealed that five products which were diclofenac, ibuprofen, paracetamol, triclosan and diethyl toluamide (DDET) were predominant among the PPCPs in all the WWTPs. The removal efficiency was highest in caffeine with 96 percent, and the lowest was obtained with carbamazepine (4 percent). Risk quotient of the concentration of PPCPs in the effluents and receiving waters was determined to assess their chronic toxicity at three trophic levels: fish, algae and matrixes studied ranged from 0.01 μg/L to 0.25 μg/L, and the LOQ from 0.02 μg/L to 0.78 μg/L. In the solid matrixes, LOD varied from 0.01 ng/g to 0.65 ng/g, and the LOQ between 0.08 ng/g and 5.17 ng/g. Better recovery efficiency was obtained with this mixture of solvents, acetone: dichloromethane (1:1), for the recovery of the five therapeutic groups in the solid matrixes using ultrasonication- assisted techniques. The results show percentage recovery values ranging from 68.8 percent to 107.5 percent diaphian. According to the environmental risk assessment results, ibuprofen and triclosan were found to be the most critical compounds due to their high risk quotient values. These findings will, therefore, help in the future evaluation of the efficiency of different treatment technologies in the removal of various PPCPs from the wastewater and their sustainable management in the aquatic resources in Eastern Cape, South Africa. For the lipophilic organochlorine pesticides (OCPs), the limits of detection (LODs) of the tested congeners varied from 0.04 ng/g (α-BHC) to 0.49 ng/g (endosulfan sulfate) and the limits of quantification ranging from 0.22 ng/g (aldrin) to 2.17 ng/g (δ-BHC).
- Full Text:
- Date Issued: 2017
Removal rate of endocrine disruptors (phthalates and phenolic compounds) in effluents of selected wastewater treatment plants operated under different treatment technologies in the Eastern Cape, South Africa
- Authors: Salaudeen, Taofeek Gbenga
- Date: 2017
- Subjects: Water -- Purification Phenols
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/8552 , vital:33113
- Description: The presence of phthalate esters (PAEs) and certain phenolic compounds widely known as endocrine disruptors in environmental waters such as treated wastewaters constitutes health hazard to human and aquatic lives. Unfortunately, wastewater treatment plants (WWTPs) only partially remove these synthetic chemical compounds from wastewater. In order to forestall the health challenge faced by rural dwellers, which rely on surface water for their daily needs, the present study embarked on investigating these endocrine disruptors in Municipal wastewater in the Amathole and Buffalo Districts in the Eastern Cape, South Africa and their removal rate by different WWTP technologies. One WWTP each from Adelaide, Alice, Bedford, Berlin and Seymour, using activated sludge (AS), trickling filter (TF), and oxidation pond (OP) technology were randomly selected. Some physicochemical parameters of these wastewaters were determined on-site using standard methods and the extraction method for endocrine disrupting chemicals (EDCs) in water was validated using solid phase extraction (SPE). Extracts were analysed using gas chromatography-mass spectrometer (GC-MS). Nine phenolic compounds; phenol (PH), 2-chlorophenol (2-CP), 2,4-dimethylphenol (2,4-DMP), 2,4-dichlorophenol (2,4-DCP), 4-chloro-3-methylphenol (4-C-3MP), 2-nitrophenol (2-NP), 4-nitrophenol (4-NP), pentachlorophenol (PCP), 2,4,6-trichlorophenol (2,4,6-TCP) and six priority PAEs namely; dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP), benzyl butyl phthalate (BBP), di(2-ethyl hexyl) phthalate (DEHP), and di-n-octyl phthalate (DOP) were the investigated EDCs. PAEs were extracted from dried sludge samples in an ultrasonic bath using dichloromethane. Some physicochemical parameters of the wastewater assessed revealed that treatment processes of AS, TF, and OP reduced turbidity, total suspended solids (TSS), total dissolved solids (TDS), and electrical conductivity (EC) while dissolved oxygen (DO) was increased. There was no significant influence on temperature and pH across the sampling points. Except for turbidity, the quality of effluent released mostly falls within South Africa standard limits for domestic and recreational water. The nine phenolic compounds were detected across the sampling points for all the WWTPs at different frequencies. The prominent phenolic compounds were 2-NP, 4-C-3MP, PCP, and 2,4-DMP with concentrations ranging from 3.3 (2,4-DMP) – 83.0 μgL-1 (4-C-3MP) in the influents. However, their concentrations in the effluents and receiving water bodies were below tolerable limits of 5 μgL-1 set by the US Environmental Protection Agency (USEPA) and the European Union (EU) for domestic use. The removal capacities of the WWTPs varied between 33 and 96 percent. The six PAEs were detected in all water samples from all the WWTPs. DBP was the most abundant compound in all the sampling points and sometimes DEHP in some receiving waters. The maximum detection for DBP in influent, effluent, downstream and sludge were 2,488 μgL-1 (Alice), 26.47 μgL-1 (Adelaide), 115.3 μgL-1 (Seymour) and 1,249 μg/g dw (Alice), respectively. DEHP was the highest detected PAE in the upstream 17.53 μgL-1 (Seymour). There was a notable reduction of all PAEs in the final effluent with a removal efficiency which varied as much as 61.9 – 99.5 percent except for AS in Seymour which operated a single tank system (27.3 - 93.7 percent). Removal mechanisms continued more on adsorption on settling particles and sludge than biodegradation as this study found a high positive correlation between TSS, turbidity and PAEs removal. The concentrations of PAEs detected in the receiving waters were above 1.3 and 3μgL-1 limit standard set by the EU and USEPA, respectively for DEHP in surface water. Similarly, the average concentrations of DBP, BBP, DEHP and DOP which vary as much as 25.97 (BBP) – 1249 μg/g d.w (DBP) in sludge samples were above EU legislation of 100 μg/g d.w. for agricultural use. AS technology, showed a better performance in the removal of PAEs (77 – 99 percent), followed by TF (76 – 98 percent) and OP (61 – 98 percent). In conclusion, the PAE concentration in the WWTP effluents impacted negatively on the receiving water bodies and sewage sludge unlike the phenolic compounds that were notably reduced below the acceptable limits. Perhaps, due to the meagre amounts of the phenolic compounds that was detected entering the WWTPs. In order to avert the potential health risk to aquatic organisms’ and rural dwellers, it is exigent that constituted authorities gather more information on micro-pollutants in the environment as a basis for regulations on the use of these dangerous chemicals in industries.
- Full Text:
- Date Issued: 2017
- Authors: Salaudeen, Taofeek Gbenga
- Date: 2017
- Subjects: Water -- Purification Phenols
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/8552 , vital:33113
- Description: The presence of phthalate esters (PAEs) and certain phenolic compounds widely known as endocrine disruptors in environmental waters such as treated wastewaters constitutes health hazard to human and aquatic lives. Unfortunately, wastewater treatment plants (WWTPs) only partially remove these synthetic chemical compounds from wastewater. In order to forestall the health challenge faced by rural dwellers, which rely on surface water for their daily needs, the present study embarked on investigating these endocrine disruptors in Municipal wastewater in the Amathole and Buffalo Districts in the Eastern Cape, South Africa and their removal rate by different WWTP technologies. One WWTP each from Adelaide, Alice, Bedford, Berlin and Seymour, using activated sludge (AS), trickling filter (TF), and oxidation pond (OP) technology were randomly selected. Some physicochemical parameters of these wastewaters were determined on-site using standard methods and the extraction method for endocrine disrupting chemicals (EDCs) in water was validated using solid phase extraction (SPE). Extracts were analysed using gas chromatography-mass spectrometer (GC-MS). Nine phenolic compounds; phenol (PH), 2-chlorophenol (2-CP), 2,4-dimethylphenol (2,4-DMP), 2,4-dichlorophenol (2,4-DCP), 4-chloro-3-methylphenol (4-C-3MP), 2-nitrophenol (2-NP), 4-nitrophenol (4-NP), pentachlorophenol (PCP), 2,4,6-trichlorophenol (2,4,6-TCP) and six priority PAEs namely; dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP), benzyl butyl phthalate (BBP), di(2-ethyl hexyl) phthalate (DEHP), and di-n-octyl phthalate (DOP) were the investigated EDCs. PAEs were extracted from dried sludge samples in an ultrasonic bath using dichloromethane. Some physicochemical parameters of the wastewater assessed revealed that treatment processes of AS, TF, and OP reduced turbidity, total suspended solids (TSS), total dissolved solids (TDS), and electrical conductivity (EC) while dissolved oxygen (DO) was increased. There was no significant influence on temperature and pH across the sampling points. Except for turbidity, the quality of effluent released mostly falls within South Africa standard limits for domestic and recreational water. The nine phenolic compounds were detected across the sampling points for all the WWTPs at different frequencies. The prominent phenolic compounds were 2-NP, 4-C-3MP, PCP, and 2,4-DMP with concentrations ranging from 3.3 (2,4-DMP) – 83.0 μgL-1 (4-C-3MP) in the influents. However, their concentrations in the effluents and receiving water bodies were below tolerable limits of 5 μgL-1 set by the US Environmental Protection Agency (USEPA) and the European Union (EU) for domestic use. The removal capacities of the WWTPs varied between 33 and 96 percent. The six PAEs were detected in all water samples from all the WWTPs. DBP was the most abundant compound in all the sampling points and sometimes DEHP in some receiving waters. The maximum detection for DBP in influent, effluent, downstream and sludge were 2,488 μgL-1 (Alice), 26.47 μgL-1 (Adelaide), 115.3 μgL-1 (Seymour) and 1,249 μg/g dw (Alice), respectively. DEHP was the highest detected PAE in the upstream 17.53 μgL-1 (Seymour). There was a notable reduction of all PAEs in the final effluent with a removal efficiency which varied as much as 61.9 – 99.5 percent except for AS in Seymour which operated a single tank system (27.3 - 93.7 percent). Removal mechanisms continued more on adsorption on settling particles and sludge than biodegradation as this study found a high positive correlation between TSS, turbidity and PAEs removal. The concentrations of PAEs detected in the receiving waters were above 1.3 and 3μgL-1 limit standard set by the EU and USEPA, respectively for DEHP in surface water. Similarly, the average concentrations of DBP, BBP, DEHP and DOP which vary as much as 25.97 (BBP) – 1249 μg/g d.w (DBP) in sludge samples were above EU legislation of 100 μg/g d.w. for agricultural use. AS technology, showed a better performance in the removal of PAEs (77 – 99 percent), followed by TF (76 – 98 percent) and OP (61 – 98 percent). In conclusion, the PAE concentration in the WWTP effluents impacted negatively on the receiving water bodies and sewage sludge unlike the phenolic compounds that were notably reduced below the acceptable limits. Perhaps, due to the meagre amounts of the phenolic compounds that was detected entering the WWTPs. In order to avert the potential health risk to aquatic organisms’ and rural dwellers, it is exigent that constituted authorities gather more information on micro-pollutants in the environment as a basis for regulations on the use of these dangerous chemicals in industries.
- Full Text:
- Date Issued: 2017
Assessment of the flocculating efficiency of bioflocculant produced by bacillus sp. Aemreg4 isolated from Tyhume river, Eastern Cape, South Africa
- Authors: Ntsangani, Nozipho
- Date: 2016
- Subjects: Flocculants
- Language: English
- Type: Thesis , Masters , MSc (Biochemistry)
- Identifier: vital:11357 , http://hdl.handle.net/10353/d1021324
- Description: Bioflocculants are flocculating substances produced by microorganisms during growth and have recently received considerable attention from researchers; due to their biodegradability, non-toxicity and lack of secondary pollution from degradation intermediates. This study evaluated the efficiency of bioflocculant produced by Bacillus sp. AEMREG4 isolated from Tyhume River. The bacterial identification was through 16S rDNA sequencing; nucleotide sequences were deposited in GenBank as Bacillus sp. AEMREG4 with an Accession number KP406729. The optimum culture conditions for bioflocculant production were an inoculum size of 4% (v/v) and starch as well as yeast extract as sole carbon and nitrogen sources respectively. The addition of CaCl2 enhanced the flocculating activity, at a wide range of pH 4-10 and the highest flocculating activity was reached at an initial pH 8 (80%). A bioflocculant yield of 0.78 g was recovered from 1 L of culture broth. The optimum flocculating activity of 78% was reached at the lowest bioflocculant dosage of 0.1 mg/ml and the presence of divalent cations (Ca2+, Mn2+ and Mg2+) as well as a trivalent cation (Al3+) enhanced flocculating activity. The purified bioflocculant retained more than 70% flocculating activity when subjected to heating at 100 °C for 1 h and maximum flocculating activity of 83% was achieved at both acidic and basic pH values of 3 and 10 respectively. Chemical analysis showed that the bioflocculant is predominantly polysaccharide. The Fourier transform infrared (FTIR) spectrum revealed the presence of carboxyl, hydroxyl and methoxyl groups as the functional moieties and the scanning electron microscopy (SEM) imaging of the purified bioflocculant showed its morphological structure as rod-shaped which contributes to its high flocculating efficiency. The high flocculation activity displayed by this bioflocculant indicates its potential suitability for industrial application.Keywords: Bioflocculant, Bacillus sp. AEMREG4, flocculating activity.
- Full Text:
- Date Issued: 2016
- Authors: Ntsangani, Nozipho
- Date: 2016
- Subjects: Flocculants
- Language: English
- Type: Thesis , Masters , MSc (Biochemistry)
- Identifier: vital:11357 , http://hdl.handle.net/10353/d1021324
- Description: Bioflocculants are flocculating substances produced by microorganisms during growth and have recently received considerable attention from researchers; due to their biodegradability, non-toxicity and lack of secondary pollution from degradation intermediates. This study evaluated the efficiency of bioflocculant produced by Bacillus sp. AEMREG4 isolated from Tyhume River. The bacterial identification was through 16S rDNA sequencing; nucleotide sequences were deposited in GenBank as Bacillus sp. AEMREG4 with an Accession number KP406729. The optimum culture conditions for bioflocculant production were an inoculum size of 4% (v/v) and starch as well as yeast extract as sole carbon and nitrogen sources respectively. The addition of CaCl2 enhanced the flocculating activity, at a wide range of pH 4-10 and the highest flocculating activity was reached at an initial pH 8 (80%). A bioflocculant yield of 0.78 g was recovered from 1 L of culture broth. The optimum flocculating activity of 78% was reached at the lowest bioflocculant dosage of 0.1 mg/ml and the presence of divalent cations (Ca2+, Mn2+ and Mg2+) as well as a trivalent cation (Al3+) enhanced flocculating activity. The purified bioflocculant retained more than 70% flocculating activity when subjected to heating at 100 °C for 1 h and maximum flocculating activity of 83% was achieved at both acidic and basic pH values of 3 and 10 respectively. Chemical analysis showed that the bioflocculant is predominantly polysaccharide. The Fourier transform infrared (FTIR) spectrum revealed the presence of carboxyl, hydroxyl and methoxyl groups as the functional moieties and the scanning electron microscopy (SEM) imaging of the purified bioflocculant showed its morphological structure as rod-shaped which contributes to its high flocculating efficiency. The high flocculation activity displayed by this bioflocculant indicates its potential suitability for industrial application.Keywords: Bioflocculant, Bacillus sp. AEMREG4, flocculating activity.
- Full Text:
- Date Issued: 2016
Distribution of Escherichia coli O157:H7 in irrigation water, drinking water troughs, dairy wastewater and rectal swabs from three dairy farms in Amathole district municipality, Eastern Cape, South Africa
- Myataza, Asive https://orcid.org/0000-0001-5483-122X
- Authors: Myataza, Asive https://orcid.org/0000-0001-5483-122X
- Date: 2016
- Subjects: Escherichia coli O157:H7 , Irrigation water
- Language: English
- Type: Master's theses
- Identifier: http://hdl.handle.net/10353/24150 , vital:62397
- Description: Escherichia coli belongs to the genus Escherichia which has five species, including E. hermanii, E. fergusonii, E. vulneris, E. blattae and E. coli (Willshaw et al., 2001). Some E. coli strains are pathogenic, and such strains are differentiated into different pathotypes based on the virulence factors they possess, mechanisms of pathogenesis, clinical manifestation and serotyping of their somatic, flagella and capsule (O, H and K) antigens; while some are nonpathogenic (Dikobe et al., 2011). These strains have been grouped into major pathotypes namely: enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), enteroaggregative E. coli (EAEC), diffusely adherent E. coli (DAEC), enterohaemorrhagic E. coli (EHEC), uropathogenic E. coli (UPEC) and neonatal meningitis E.coli (NMEC) (Willshaw et al., 2001; Villegas-sepulveda et al., 2003; Kaper et al., 2004; Bugarel et al., 2011). Members of EPEC pathotype are Shiga-toxin producing (STEC) organisms, with E. coli O157:H7 serotype being recognized as the most frequent STEC serotype linked to diseases in human (Barkocy-Gallagher et al., 2001; Coombes et al., 2011; Dikobe et al., 2011; Jacob et al., 2013). E. coli O157:H7 is the major cause of haemorrhagic diarrhoea and haemolytic uremic syndrome (UHS) in humans, due to the production of Shiga-toxins that are similar to Shigella toxins (Villegas-sepulveda et al., 2003; Ngwa et al., 2013). These toxins are coded by genes which allow them to penetrate small intestines of human and animals (Chern et al., 2011). Dairy products and cattle are the major reservoirs of haemorrhagic E. coli O157: H7 (Elder et al., 2000; Elmali et al., 2005; Ayaz et al., 2014). Haemorrhagic E. coli O157:H7 is carried mostly in the gastrointestinal tracts of cows and other ruminants (Gun et al., 2003)and it is transmitted through ingestion of contaminated food and water, or through direct and indirect contact with infected cows and other ruminants and/or via a person to person transmission (Lahti et al., 2003). Almost 70percent of countries in the world use poorly treated water for irrigation; this is inclusive of developing countries, which lack well developed means of adequate water treatment due to unavailable financial resources (Gerba et al., 2011). Most communities in the Eastern Cape Province of South Africa are rural with poor water supply with majority of them relying on ground and surface waters that are impacted by insufficiently treated municipal water (which may harbour many pathogens) for domestic purposes (Ateba et al., 2008). Cows may contaminate drinking, recreational and irrigation waters with faecal matters or through direct contact with water (Solomon et al., 2002; Chern et al., 2011). A number of countries with water shortage tend to use insufficiently treated water for irrigation, leading to further contamination of irrigated crops (Fatoki et al., 2001). This has all resulted to elevated levels of E. coli O157:H7 related disease outbreaks and deaths of humans (Olsen et al., 2002). , Thesis (MSc) -- Faculty of Science and Agriculture, 2016
- Full Text:
- Date Issued: 2016
- Authors: Myataza, Asive https://orcid.org/0000-0001-5483-122X
- Date: 2016
- Subjects: Escherichia coli O157:H7 , Irrigation water
- Language: English
- Type: Master's theses
- Identifier: http://hdl.handle.net/10353/24150 , vital:62397
- Description: Escherichia coli belongs to the genus Escherichia which has five species, including E. hermanii, E. fergusonii, E. vulneris, E. blattae and E. coli (Willshaw et al., 2001). Some E. coli strains are pathogenic, and such strains are differentiated into different pathotypes based on the virulence factors they possess, mechanisms of pathogenesis, clinical manifestation and serotyping of their somatic, flagella and capsule (O, H and K) antigens; while some are nonpathogenic (Dikobe et al., 2011). These strains have been grouped into major pathotypes namely: enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), enteroaggregative E. coli (EAEC), diffusely adherent E. coli (DAEC), enterohaemorrhagic E. coli (EHEC), uropathogenic E. coli (UPEC) and neonatal meningitis E.coli (NMEC) (Willshaw et al., 2001; Villegas-sepulveda et al., 2003; Kaper et al., 2004; Bugarel et al., 2011). Members of EPEC pathotype are Shiga-toxin producing (STEC) organisms, with E. coli O157:H7 serotype being recognized as the most frequent STEC serotype linked to diseases in human (Barkocy-Gallagher et al., 2001; Coombes et al., 2011; Dikobe et al., 2011; Jacob et al., 2013). E. coli O157:H7 is the major cause of haemorrhagic diarrhoea and haemolytic uremic syndrome (UHS) in humans, due to the production of Shiga-toxins that are similar to Shigella toxins (Villegas-sepulveda et al., 2003; Ngwa et al., 2013). These toxins are coded by genes which allow them to penetrate small intestines of human and animals (Chern et al., 2011). Dairy products and cattle are the major reservoirs of haemorrhagic E. coli O157: H7 (Elder et al., 2000; Elmali et al., 2005; Ayaz et al., 2014). Haemorrhagic E. coli O157:H7 is carried mostly in the gastrointestinal tracts of cows and other ruminants (Gun et al., 2003)and it is transmitted through ingestion of contaminated food and water, or through direct and indirect contact with infected cows and other ruminants and/or via a person to person transmission (Lahti et al., 2003). Almost 70percent of countries in the world use poorly treated water for irrigation; this is inclusive of developing countries, which lack well developed means of adequate water treatment due to unavailable financial resources (Gerba et al., 2011). Most communities in the Eastern Cape Province of South Africa are rural with poor water supply with majority of them relying on ground and surface waters that are impacted by insufficiently treated municipal water (which may harbour many pathogens) for domestic purposes (Ateba et al., 2008). Cows may contaminate drinking, recreational and irrigation waters with faecal matters or through direct contact with water (Solomon et al., 2002; Chern et al., 2011). A number of countries with water shortage tend to use insufficiently treated water for irrigation, leading to further contamination of irrigated crops (Fatoki et al., 2001). This has all resulted to elevated levels of E. coli O157:H7 related disease outbreaks and deaths of humans (Olsen et al., 2002). , Thesis (MSc) -- Faculty of Science and Agriculture, 2016
- Full Text:
- Date Issued: 2016
Evaluation of the incidence of enteric viruses, Vibrio species and Escherichia coli pathotypes in effluents of two wastewater treatment plants located in Keiskammahoek and Stutterheim in the Eastern Cape Province of South Africa
- Authors: Adefisoye, Martins Ajibade
- Date: 2016
- Subjects: Escherichia coli -- South Africa -- Eastern Cape Water -- Purification -- South Africa -- Eastern Cape Effluent quality -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10353/3165 , vital:28328
- Description: South Africa is currently experiencing water shortage crisis, a challenge that has been attributed not only to the scarcity of freshwater, but also to fast degrading water quality. Factors such as rapid urbanisation, population and economic growth, climate change as well as poor operational and maintenance of many of the exisiting water/wastewater treatment facilities have been acknowledged as important contributors to degrading water quality in the country. Untreated or inadequately treated discharged wastewater effluents constitute point source pollution to many freshwater environments in South Africa. Hence, it becomes imperative to evaluate wastewater discharges in other to protect the scarce freshwater resource, the environment and public health. Over a twelve-month sampling period (September 2012 to August 2013), we assessed the bacteriological, virological and physicochemical qualities of the discharged final effluents of two wastewater treatment facilities in the Eastern Cape Province of South Africa. For the physicochemical assessment, a total of 144 final effluent samples were collected from both the final effluent tanks (FE) and the discharge points (DP) of the treatment facilities. Physicochemical parameters including pH, temperature, turbidity, total dissolved solids (TDS), dissolved oxygen (DO), electrical conductivity (EC) and free chlorine concentration were determined on site while biological oxygen demand (BOD), nitrate (NO3-), nitrite (NO2-), phosphate (PO4-) and chemical oxygen demand (COD) were determined in the laboratory. The bacteriological analysis of the samples was done using standard membrane filtration (MF) technique. Bacterial group assessed included: faecal indicator bacteria (faecal coliforms and E. coli) and Vibrio species, while the antibiotic susceptibility profiles of selected E. coli and Vibrio species isolates against some selected antibiotics commonly used in human therapy and veterinary medicine were determind using the standard agar-disc diffusion method. The occurrence and concentrations of human enteric viruses including: human adenovirus (HAdV), hepatitis A virus (HAV) and rotavirus (RoV) in the samples were determined by TaqMan-based real-time polymerase chain reaction (qPCR) following concentration by adsorption-elution method. The physicochemical characteristics of the samples ranged as follows: pH (6.5 – 7.6), TDS (95 – 171 mg/L), EC (134 – 267 μS/cm), temperature (12 – 27 °C), turbidity (1.5 – 65.7 mg/L), free chlorine (0.08 – 0.72 mg/L), DO (2.06 – 9.81 mg/L), BOD (0.13 – 9.81 mg/L), NO3- (0 – 21.5 mg/L), NO2- (0 – 0.72 mg/L), PO4- (0 – 18.3 mg/L) and COD (27 – 680 mg/L). Some of the characteristic such as pH, TDS, EC, temperature, nitrite and DO (on most instances) complied with recommended guidelines. Other characteristics, however, including turbidity, BOD, nitrate, phosphate and COD fell short of the recommended guidelines. All the 48 samples analysed for bacteriological qualities tested positive for the presence of the bacterial groups with significant (P≤0.05) seasonal variation in their densities. Faecal coliforms were detected in counts ranging from 1 CFU/100ml to 2.7 × 104 CFU/100ml. Presumptive E. coli counts ranged generally between 1 CFU/100ml – 1.4 × 105 CFU/100ml while counts of presumptive Vibrio species ranged between 4 CFU/100ml – 1.4 × 104 CFU/100ml. Molecular identification of the presumptive isolates by polymerase chain reactions PCR gave positive reaction rates of 76.2 percent (381/500) and 69.8 percent (279/400) for E.coli and Vibrio species respectively. The antibiotic susceptibility profiling of 205 PCR-confirmed Vibiro isolates against 18 commomly used antibiotics showed resistance frequencies ranging from 0.5 percent (imipenem) to 96.1 percent (penicillin G) at recommended breakpoint concentrations. Eighty-one percent (166/205) of the Vibrio isolates showed multidrug resistance (resistance to 3 or more antibiotics) with the most common multiple antibiotic resistance phenotype (MARP) being AP-T-TM-SMX-PG-NI-PB, occurring in 8 isolates.
- Full Text:
- Date Issued: 2016
- Authors: Adefisoye, Martins Ajibade
- Date: 2016
- Subjects: Escherichia coli -- South Africa -- Eastern Cape Water -- Purification -- South Africa -- Eastern Cape Effluent quality -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10353/3165 , vital:28328
- Description: South Africa is currently experiencing water shortage crisis, a challenge that has been attributed not only to the scarcity of freshwater, but also to fast degrading water quality. Factors such as rapid urbanisation, population and economic growth, climate change as well as poor operational and maintenance of many of the exisiting water/wastewater treatment facilities have been acknowledged as important contributors to degrading water quality in the country. Untreated or inadequately treated discharged wastewater effluents constitute point source pollution to many freshwater environments in South Africa. Hence, it becomes imperative to evaluate wastewater discharges in other to protect the scarce freshwater resource, the environment and public health. Over a twelve-month sampling period (September 2012 to August 2013), we assessed the bacteriological, virological and physicochemical qualities of the discharged final effluents of two wastewater treatment facilities in the Eastern Cape Province of South Africa. For the physicochemical assessment, a total of 144 final effluent samples were collected from both the final effluent tanks (FE) and the discharge points (DP) of the treatment facilities. Physicochemical parameters including pH, temperature, turbidity, total dissolved solids (TDS), dissolved oxygen (DO), electrical conductivity (EC) and free chlorine concentration were determined on site while biological oxygen demand (BOD), nitrate (NO3-), nitrite (NO2-), phosphate (PO4-) and chemical oxygen demand (COD) were determined in the laboratory. The bacteriological analysis of the samples was done using standard membrane filtration (MF) technique. Bacterial group assessed included: faecal indicator bacteria (faecal coliforms and E. coli) and Vibrio species, while the antibiotic susceptibility profiles of selected E. coli and Vibrio species isolates against some selected antibiotics commonly used in human therapy and veterinary medicine were determind using the standard agar-disc diffusion method. The occurrence and concentrations of human enteric viruses including: human adenovirus (HAdV), hepatitis A virus (HAV) and rotavirus (RoV) in the samples were determined by TaqMan-based real-time polymerase chain reaction (qPCR) following concentration by adsorption-elution method. The physicochemical characteristics of the samples ranged as follows: pH (6.5 – 7.6), TDS (95 – 171 mg/L), EC (134 – 267 μS/cm), temperature (12 – 27 °C), turbidity (1.5 – 65.7 mg/L), free chlorine (0.08 – 0.72 mg/L), DO (2.06 – 9.81 mg/L), BOD (0.13 – 9.81 mg/L), NO3- (0 – 21.5 mg/L), NO2- (0 – 0.72 mg/L), PO4- (0 – 18.3 mg/L) and COD (27 – 680 mg/L). Some of the characteristic such as pH, TDS, EC, temperature, nitrite and DO (on most instances) complied with recommended guidelines. Other characteristics, however, including turbidity, BOD, nitrate, phosphate and COD fell short of the recommended guidelines. All the 48 samples analysed for bacteriological qualities tested positive for the presence of the bacterial groups with significant (P≤0.05) seasonal variation in their densities. Faecal coliforms were detected in counts ranging from 1 CFU/100ml to 2.7 × 104 CFU/100ml. Presumptive E. coli counts ranged generally between 1 CFU/100ml – 1.4 × 105 CFU/100ml while counts of presumptive Vibrio species ranged between 4 CFU/100ml – 1.4 × 104 CFU/100ml. Molecular identification of the presumptive isolates by polymerase chain reactions PCR gave positive reaction rates of 76.2 percent (381/500) and 69.8 percent (279/400) for E.coli and Vibrio species respectively. The antibiotic susceptibility profiling of 205 PCR-confirmed Vibiro isolates against 18 commomly used antibiotics showed resistance frequencies ranging from 0.5 percent (imipenem) to 96.1 percent (penicillin G) at recommended breakpoint concentrations. Eighty-one percent (166/205) of the Vibrio isolates showed multidrug resistance (resistance to 3 or more antibiotics) with the most common multiple antibiotic resistance phenotype (MARP) being AP-T-TM-SMX-PG-NI-PB, occurring in 8 isolates.
- Full Text:
- Date Issued: 2016
Assessment of bioflocculant production by two marine bacteria isolated from the bottom sediment of marine Algoa Bay
- Authors: Ntozonke, Ncedo
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11298 , http://hdl.handle.net/10353/d1021290
- Description: Bioflocculants are polymers, mostly, of microbial origin which floc out suspended particles from liquid medium. The ability of these biopolymers to remove suspended particles from solutions is termed bioflocculation, and the efficiency of flocculation activities depends on the characteristics of the flocculants. In comparison with conventionally used flocculants, bioflocculants have the advantage of being safe (no toxic effects known), biodegradable and harmlessness to the environment. The study assessed production of bioflocculant by two marine bacteria from the bottom sediment of marine environment. The 16S rDNA was used for identification, and the two bacteria species were identified as Enterococcus hirae and Bacillus thuringiensis. Factors affecting the production and activity of the bioflocculants produced by these two organisms were studied. The bacteria optimally produced bioflocculant with fructose (91.7%) and urea (91%) as sole carbon and nitrogen sources respectively. Mg2+ (87%) and Ca2+ (86%), likewise, served as best cation sources on the production of the bioflocculant at pH 5(93%). Additionally, the flocculating activity of the bioflocculant increased with the addition of Mg2+ (81%) and Na+ (81%), and the highest flocculating activity was at pH 5 of the kaolin clay. The Fourier transform infrared spectroscopy (FTIR) shows that the bioflocculant is a glycoprotein. The second bacterium (Bacillus thuringiensis) produced bioflocculant optimally when the media had mixed nitrogen sources (Urea, ammonium chloride and tryptone (67%)) and glucose (85.65%) as a sole carbon source, also Ca2+ (74.6%) was the best cation that induced the production of bioflocculant. After purification, the bioflocculant flocculated optimally in alkaline pH 12 (81%) in the presence of Mn2+ (73%) and Ca2+ (72.8%). Chemical analysis of the bioflocculant revealed it to be a polysaccharide. Both bioflocculants flocculate efficiently and can be used to replace synthetic flocculants in water treatment, wastewater, in downstream processing, and processing of food and chemicals and other industrial uses of flocculants. Challenges though (i) are to develop conditions for large scale production of the bioflocculant, (ii) to do further characterization of the both bioflocculants (iii) to assess the bioflocculants for treatments of water/wastewater, and to apply it in various industrial processes.
- Full Text:
- Date Issued: 2015
- Authors: Ntozonke, Ncedo
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11298 , http://hdl.handle.net/10353/d1021290
- Description: Bioflocculants are polymers, mostly, of microbial origin which floc out suspended particles from liquid medium. The ability of these biopolymers to remove suspended particles from solutions is termed bioflocculation, and the efficiency of flocculation activities depends on the characteristics of the flocculants. In comparison with conventionally used flocculants, bioflocculants have the advantage of being safe (no toxic effects known), biodegradable and harmlessness to the environment. The study assessed production of bioflocculant by two marine bacteria from the bottom sediment of marine environment. The 16S rDNA was used for identification, and the two bacteria species were identified as Enterococcus hirae and Bacillus thuringiensis. Factors affecting the production and activity of the bioflocculants produced by these two organisms were studied. The bacteria optimally produced bioflocculant with fructose (91.7%) and urea (91%) as sole carbon and nitrogen sources respectively. Mg2+ (87%) and Ca2+ (86%), likewise, served as best cation sources on the production of the bioflocculant at pH 5(93%). Additionally, the flocculating activity of the bioflocculant increased with the addition of Mg2+ (81%) and Na+ (81%), and the highest flocculating activity was at pH 5 of the kaolin clay. The Fourier transform infrared spectroscopy (FTIR) shows that the bioflocculant is a glycoprotein. The second bacterium (Bacillus thuringiensis) produced bioflocculant optimally when the media had mixed nitrogen sources (Urea, ammonium chloride and tryptone (67%)) and glucose (85.65%) as a sole carbon source, also Ca2+ (74.6%) was the best cation that induced the production of bioflocculant. After purification, the bioflocculant flocculated optimally in alkaline pH 12 (81%) in the presence of Mn2+ (73%) and Ca2+ (72.8%). Chemical analysis of the bioflocculant revealed it to be a polysaccharide. Both bioflocculants flocculate efficiently and can be used to replace synthetic flocculants in water treatment, wastewater, in downstream processing, and processing of food and chemicals and other industrial uses of flocculants. Challenges though (i) are to develop conditions for large scale production of the bioflocculant, (ii) to do further characterization of the both bioflocculants (iii) to assess the bioflocculants for treatments of water/wastewater, and to apply it in various industrial processes.
- Full Text:
- Date Issued: 2015
Assessment of the quality indices and prevalence of Escherichia coli pathotypes in selected rivers of Osun state, Southwestern Nigeria
- Authors: Titilawo, Osuolale Yinka
- Date: 2015
- Language: English
- Type: Thesis , Doctoral , PhD (Microbiology)
- Identifier: vital:11295 , http://hdl.handle.net/10353/d1021274
- Description: Surface waters are important freshwater sources used for domestic, industrial, agricultural and recreational activities, and the availability of good quality freshwater is indispensable for preventing water-borne diseases and improving quality of life especially in communities that lack pipe-borne water. Water samples were collected from ten rivers at different locations in Osun State, Southwestern Nigeria. A total of 12 physicochemical parameters, counts of total coliforms (TC) and Escherichia coli isolates were determined using standard analytical procedures. Confirmed Escherichia coli isolates (n=300) were assessed for the presence of 10 virulence genes (VGs) associated with Escherichia coli strains causing intestinal and extra-intestinal infections. The recovered Escherichia coli isolates were elucidated for their antibiogram profiling by disk diffusion method and the resistant isolates were further profiled for their genotypic antimicrobial resistance by polymerase chain reaction technique. The physicochemical qualities ranged as follows: pH (6.9 - 7.6), temperature (26 – 29 ºC), turbidity (2.28 – 9.46 NTU), electrical conductivity (229 – 581 μS/cm), nitrate (0.03 – 0.05 mg/L), nitrite (0.00 – 0.01 mg/L), sulphate (3.33 – 20.33 mg/L), chloride ions (7.83 – 27.33 mg/L), dissolved oxygen (4.23 – 5.57 mg/L), total dissolved solids (56 – 184 mg/L), total hardness (78 – 519 mg/L) and alkalinity (50.67 – 146.67 mg/L). Statistical analysis showed that pH, temperature, electrical conductivities, nitrates, nitrites, chloride, dissolved oxygen, total dissolved solid, total hardness and alkalinity were significantly different (P < 0.05), whereas turbidity and sulphate were not significantly different (P ˃ 0.05) from each parameter with respect to sampling sites. While the VG lt for enterotoxigenic E. coli had the highest prevalence of 45%, the enteropathogenic E. coli genes eae and bfp were detected in 6% and 4% of the isolates respectively. The VGs stx1 and stx2 specific for the enterohemorrhagic E. coli pathotypes were equally detected in 7% and 1% of the isolates respectively. Also, the VG eagg harboured by enteroaggregative pathotype and diffusely-adherent E. coli VG daaE were detected in 2% and 4% of the isolates respectively and enteroinvasive E. coli VG ipaH was not detected. In addition, the VGs papC for uropathogenic and ibeA for neonatal meningitis were frequently detected in 19% and 3% of isolates respectively. While all the isolates tested were susceptible to imipenem, meropenem, amikacin and gatilofloxacin, others were variously susceptible, and resistant as follows; ciprofloxacin (96%), kanamycin (95%), neomycin (92%), streptomycin (84%), chloramphenicol (73%), nalidixic acid (66%), nitrofuratoin (64%), gentamycin (63%), doxycycline (58%), cefepime (57%), tetracycline (49%) and cephalothin (42%). Conversely, all the isolates were resistant to sulphamethoxazole, and high levels of resistance were equally observed against amoxycillin (59%), ampicilin (57%) and cefuroxime (40%). Cefepime, cephalothin, cefuroxime, nalidixic acid, nitrofuratoin, chloramphenicol and tetracycline were not significantly different in their effect against the isolates from all locations (P > 0.05), whereas the resistance profile of the isolates against gentamycin, ciprofloxacin, sulphamethoxazole, ampicillin and amoxicillin were significantly different (P < 0.05). Amikacin, kanamycin, streptomycin, meropenem, imipenem and gatilofloxacin were statistically excluded from the analysis since all tested isolates showed total susceptibility to these antimicrobials. The multiple antibiotic resistance indexing ranged from 0.50 to 0.80 for all the sampling locations and exceeded the threshold value of 0.2. Prevalence and distributions of the 19 resistance determinants assessed were obtained as follows; [sulfonamides (sulI (8%), sulII (41%)], [beta-lactams; (ampC 22%; blaTEM, (21%), blaZ (18%),], [tetracyclines (tetA (24%), tetB (23%), tetC (18%), tetD (78%), tetK (15%), tetM, (10%)], [phenicols; (catI (37%), catII (28%), cmlA1 (19%)] and [aminoglycosides; (aacC2 (8%), aphA1 (80%), aphA2 (80%), aadA (79%) and strA (38%)]. The Pearson chi square exact test revealed many strong significant associations among ampC, blaTEM, blaZ and tetA genes with some determinants screened. In the same vein, a grand total of 366 resistance gene fingerprints were spotted across the sampling locations and among the resistant pathotypes, the modal prevalent gene prints were found among the ETEC strains in 148 (40%), being the predominant pathotype observed, followed by UPEC strains 80 (22%) while the lowest was the least occurring EAEC pathotype 14 (4%). While some physicochemical parameters exceeded prescribed standards for drinking water, some fell within. The total coliforms obtained in all the sampling sites were above the acceptable limits. Findings reveal the presence of diarrhoeagenic and non-diarrhoeagenic E. coli in the selected rivers and suggest a potential public health risk as the rivers are important resources for domestic, recreational and livelihood usage by their host communities. The multiple drug resistance indexing signifies isolates and pathotypes of high antimicrobial usage origin. An increase in the antimicrobial resistance signatures towards conventionally used antibiotics as observed in this study necessitates for safe water supply, adequate sanitation facilities and proper surveillance programs towards the monitoring of antimicrobial resistance determinants in water-bodies. Generally, results from this study indicate that the river waters are not suitable for consumption, domestic or recreational use and re-echo the importance of safeguarding the freshwater resources of Southwestern Nigeria.
- Full Text:
- Date Issued: 2015
- Authors: Titilawo, Osuolale Yinka
- Date: 2015
- Language: English
- Type: Thesis , Doctoral , PhD (Microbiology)
- Identifier: vital:11295 , http://hdl.handle.net/10353/d1021274
- Description: Surface waters are important freshwater sources used for domestic, industrial, agricultural and recreational activities, and the availability of good quality freshwater is indispensable for preventing water-borne diseases and improving quality of life especially in communities that lack pipe-borne water. Water samples were collected from ten rivers at different locations in Osun State, Southwestern Nigeria. A total of 12 physicochemical parameters, counts of total coliforms (TC) and Escherichia coli isolates were determined using standard analytical procedures. Confirmed Escherichia coli isolates (n=300) were assessed for the presence of 10 virulence genes (VGs) associated with Escherichia coli strains causing intestinal and extra-intestinal infections. The recovered Escherichia coli isolates were elucidated for their antibiogram profiling by disk diffusion method and the resistant isolates were further profiled for their genotypic antimicrobial resistance by polymerase chain reaction technique. The physicochemical qualities ranged as follows: pH (6.9 - 7.6), temperature (26 – 29 ºC), turbidity (2.28 – 9.46 NTU), electrical conductivity (229 – 581 μS/cm), nitrate (0.03 – 0.05 mg/L), nitrite (0.00 – 0.01 mg/L), sulphate (3.33 – 20.33 mg/L), chloride ions (7.83 – 27.33 mg/L), dissolved oxygen (4.23 – 5.57 mg/L), total dissolved solids (56 – 184 mg/L), total hardness (78 – 519 mg/L) and alkalinity (50.67 – 146.67 mg/L). Statistical analysis showed that pH, temperature, electrical conductivities, nitrates, nitrites, chloride, dissolved oxygen, total dissolved solid, total hardness and alkalinity were significantly different (P < 0.05), whereas turbidity and sulphate were not significantly different (P ˃ 0.05) from each parameter with respect to sampling sites. While the VG lt for enterotoxigenic E. coli had the highest prevalence of 45%, the enteropathogenic E. coli genes eae and bfp were detected in 6% and 4% of the isolates respectively. The VGs stx1 and stx2 specific for the enterohemorrhagic E. coli pathotypes were equally detected in 7% and 1% of the isolates respectively. Also, the VG eagg harboured by enteroaggregative pathotype and diffusely-adherent E. coli VG daaE were detected in 2% and 4% of the isolates respectively and enteroinvasive E. coli VG ipaH was not detected. In addition, the VGs papC for uropathogenic and ibeA for neonatal meningitis were frequently detected in 19% and 3% of isolates respectively. While all the isolates tested were susceptible to imipenem, meropenem, amikacin and gatilofloxacin, others were variously susceptible, and resistant as follows; ciprofloxacin (96%), kanamycin (95%), neomycin (92%), streptomycin (84%), chloramphenicol (73%), nalidixic acid (66%), nitrofuratoin (64%), gentamycin (63%), doxycycline (58%), cefepime (57%), tetracycline (49%) and cephalothin (42%). Conversely, all the isolates were resistant to sulphamethoxazole, and high levels of resistance were equally observed against amoxycillin (59%), ampicilin (57%) and cefuroxime (40%). Cefepime, cephalothin, cefuroxime, nalidixic acid, nitrofuratoin, chloramphenicol and tetracycline were not significantly different in their effect against the isolates from all locations (P > 0.05), whereas the resistance profile of the isolates against gentamycin, ciprofloxacin, sulphamethoxazole, ampicillin and amoxicillin were significantly different (P < 0.05). Amikacin, kanamycin, streptomycin, meropenem, imipenem and gatilofloxacin were statistically excluded from the analysis since all tested isolates showed total susceptibility to these antimicrobials. The multiple antibiotic resistance indexing ranged from 0.50 to 0.80 for all the sampling locations and exceeded the threshold value of 0.2. Prevalence and distributions of the 19 resistance determinants assessed were obtained as follows; [sulfonamides (sulI (8%), sulII (41%)], [beta-lactams; (ampC 22%; blaTEM, (21%), blaZ (18%),], [tetracyclines (tetA (24%), tetB (23%), tetC (18%), tetD (78%), tetK (15%), tetM, (10%)], [phenicols; (catI (37%), catII (28%), cmlA1 (19%)] and [aminoglycosides; (aacC2 (8%), aphA1 (80%), aphA2 (80%), aadA (79%) and strA (38%)]. The Pearson chi square exact test revealed many strong significant associations among ampC, blaTEM, blaZ and tetA genes with some determinants screened. In the same vein, a grand total of 366 resistance gene fingerprints were spotted across the sampling locations and among the resistant pathotypes, the modal prevalent gene prints were found among the ETEC strains in 148 (40%), being the predominant pathotype observed, followed by UPEC strains 80 (22%) while the lowest was the least occurring EAEC pathotype 14 (4%). While some physicochemical parameters exceeded prescribed standards for drinking water, some fell within. The total coliforms obtained in all the sampling sites were above the acceptable limits. Findings reveal the presence of diarrhoeagenic and non-diarrhoeagenic E. coli in the selected rivers and suggest a potential public health risk as the rivers are important resources for domestic, recreational and livelihood usage by their host communities. The multiple drug resistance indexing signifies isolates and pathotypes of high antimicrobial usage origin. An increase in the antimicrobial resistance signatures towards conventionally used antibiotics as observed in this study necessitates for safe water supply, adequate sanitation facilities and proper surveillance programs towards the monitoring of antimicrobial resistance determinants in water-bodies. Generally, results from this study indicate that the river waters are not suitable for consumption, domestic or recreational use and re-echo the importance of safeguarding the freshwater resources of Southwestern Nigeria.
- Full Text:
- Date Issued: 2015
Characterization of some virulence and antibiotic resistance genes of Staphylococcus aureus isolated from cases of Bovine Mastitis in Nkonkobe Municipality, Eastern Cape Province, RSA
- Authors: Pekana, Abongile
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11293 , http://hdl.handle.net/10353/d1021133
- Description: Staphylococcus aureus is one of the predominant causative agents of mastitis disease in dairy herds. Mastitis disease has a negative impact in the economic losses in the dairy sector across the globe. The aim of this study is to detect some of the virulence genes in the S. aureus isolated from 400 milk samples of subclinical and clinical mastitis dairy cows in Fort Hare dairy farm and Middle Drift dairy farm in Alice in the Eastern Cape province of South Africa. In addition antibiotic resistance pattern and antibiotic resistance genes were investigated. Gram-staining, oxidase test, catalase test and API Staph kit were preliminary biochemical tests used for the identification of S. aureus isolates. The MALDI-TOF-MS was also used for further identification. Polymerase chain reaction was performed of genes encoding antibiotic resistance as well as clumping (clfA), coagulase (coa) gene, toxic shock syndrome (tsst), exfoliative toxin A and B (eta and etb), and the gene segment encoding the immunoglobulin G binding region and X region of protein gene spa. A total of 20 (5%) S. aureus strains obtained from 400 milk samples from the two farms were subjected to 16 antibiotics for antibiotic susceptibility testing. In Middle Drift dairy farm 11 (5.5%) isolates were obtained from 200 samples and 9 (4.5%) isolates were obtained in Fort Hare dairy farm from 200 samples. A large percent of the isolates were resistant to penicillin G (60%), followed by trimethoprim (60%) and tetracycline (60%), trimethoprim-sulfamethaxazole (55%), telithroprim (55%) and doxycycline (45%). Most of the isolates were sensitive to several (50-85%) antibiotics. Of the twenty isolates tested 12 samples contained the penicillin antibiotic resistance gene (blaZ gene), 8 samples contained at least one aminoglycoside-modifying enzyme gene (AME gene); the (aac(6’)/aph(2’’) gene and no amplification occurred for aph(3’)-IIIa and ant(4’)-Ia) genes. In the case of the tetracycline antibiotic resistance gene (tetK and tetM), 2 samples contained tetM and a single sample contained tetK gene. No amplification was observed for the erythromycin antibiotic resistance genes (ermA, ermB, ermC, Mef and msrA). All the samples tested were negative for the expression of toxic syndrome gene (tsst), etb, and Immunoglobulin G binding region. However, amplification of the clumping factor was observed in 7 (35%) isolates of S. aureus, exfoliative toxin (eta) expressed 4(20%) isolates; coagulase gene (coa) yielded six DNA bands of six differences sizes from 16 (80%) isolates. A total of four different bands size were expressed for the spa X region from 12 (60%) isolates. The data obtained in this study suggests that poor hygienic practices and inadequate management practices are responsible for the increase in Staphylococcus aureus isolation. The high resistance of S. aureus to antibiotics and the distribution of virulence genes contribute in bovine mastitis in these farms may cause health problems in the community consuming raw milk purchased from these farms.
- Full Text:
- Date Issued: 2015
- Authors: Pekana, Abongile
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11293 , http://hdl.handle.net/10353/d1021133
- Description: Staphylococcus aureus is one of the predominant causative agents of mastitis disease in dairy herds. Mastitis disease has a negative impact in the economic losses in the dairy sector across the globe. The aim of this study is to detect some of the virulence genes in the S. aureus isolated from 400 milk samples of subclinical and clinical mastitis dairy cows in Fort Hare dairy farm and Middle Drift dairy farm in Alice in the Eastern Cape province of South Africa. In addition antibiotic resistance pattern and antibiotic resistance genes were investigated. Gram-staining, oxidase test, catalase test and API Staph kit were preliminary biochemical tests used for the identification of S. aureus isolates. The MALDI-TOF-MS was also used for further identification. Polymerase chain reaction was performed of genes encoding antibiotic resistance as well as clumping (clfA), coagulase (coa) gene, toxic shock syndrome (tsst), exfoliative toxin A and B (eta and etb), and the gene segment encoding the immunoglobulin G binding region and X region of protein gene spa. A total of 20 (5%) S. aureus strains obtained from 400 milk samples from the two farms were subjected to 16 antibiotics for antibiotic susceptibility testing. In Middle Drift dairy farm 11 (5.5%) isolates were obtained from 200 samples and 9 (4.5%) isolates were obtained in Fort Hare dairy farm from 200 samples. A large percent of the isolates were resistant to penicillin G (60%), followed by trimethoprim (60%) and tetracycline (60%), trimethoprim-sulfamethaxazole (55%), telithroprim (55%) and doxycycline (45%). Most of the isolates were sensitive to several (50-85%) antibiotics. Of the twenty isolates tested 12 samples contained the penicillin antibiotic resistance gene (blaZ gene), 8 samples contained at least one aminoglycoside-modifying enzyme gene (AME gene); the (aac(6’)/aph(2’’) gene and no amplification occurred for aph(3’)-IIIa and ant(4’)-Ia) genes. In the case of the tetracycline antibiotic resistance gene (tetK and tetM), 2 samples contained tetM and a single sample contained tetK gene. No amplification was observed for the erythromycin antibiotic resistance genes (ermA, ermB, ermC, Mef and msrA). All the samples tested were negative for the expression of toxic syndrome gene (tsst), etb, and Immunoglobulin G binding region. However, amplification of the clumping factor was observed in 7 (35%) isolates of S. aureus, exfoliative toxin (eta) expressed 4(20%) isolates; coagulase gene (coa) yielded six DNA bands of six differences sizes from 16 (80%) isolates. A total of four different bands size were expressed for the spa X region from 12 (60%) isolates. The data obtained in this study suggests that poor hygienic practices and inadequate management practices are responsible for the increase in Staphylococcus aureus isolation. The high resistance of S. aureus to antibiotics and the distribution of virulence genes contribute in bovine mastitis in these farms may cause health problems in the community consuming raw milk purchased from these farms.
- Full Text:
- Date Issued: 2015
Evaluation of the quality indices of the final effluents of two wastewater treatment plants in buffalo City Metropolitan Municipality in the Eastern Cape Province
- Authors: Osuolale, Olayinka O
- Date: 2015
- Language: English
- Type: Thesis , Doctoral , PhD (Microbiology)
- Identifier: vital:11292 , http://hdl.handle.net/10353/d1021079
- Description: Waste waters can be sources of pollution to surface water and the environment with severe implications for public health. Most treatment plants in the Buffalo City Municipality in the Eastern Cape Province discharge their treated effluent into the surface waters which directly and indirectly impacts on the quality of surface waters in the region. The objective of this study was to determine the microbiological and physicochemical qualities of the final effluents of two wastewater treatment plants in the Buffalo City Municipality in the Eastern Cape Province of South Africa over a period of 12 months (September 2012 to August 2013). The qualities of the final effluents of WW-Ama Wastewater Treatment Plant with respect to phosphate (3.9 mg/l - 20.6 mg/l), free chlorine (0.05 mg/l - 0.71 mg/l), chemical oxygen demand (COD) (4.7 mg/l - 211 mg/l), and faecal coliform (0 - 2.92 × 104 CFU/100 ml) were not in compliance with the permissible limits set for effluent discharged to surface water by South Africa guidelines for effluent discharge. Other physicochemical parameters like biological oxygen demand (BOD) (2.2 mg/l - 9.0 mg/l), total dissolve solid (TDS) (253 mg/l - 336.3 mg/l) and turbidity (4.8 NTU - 43.20 NTU) with no SA regulatory set limits were compared to other regulatory standards and they do not comply with the limits. Also, at the second WWTP’s, the WW-Dim Treatment Plant effluent quality for free chlorine (0.06 mg/l - 7.2 mg/l), BOD (0.1 mg/l - 7.4 mg/l), and turbidity (4.02 NTU - 24.3 NTU) also did not comply. For microbiological qualities, counts of presumptive E. coli and Vibrio ranged between 0 - 2.92 × PROFESSOR ANTHONY I. OKOHAntibiogram of the bacterial isolates were determined using the disk diffusion method. A total of 107 confirmed E. coli and 100 confirmed Vibrio spp. were used for this assay. Results of antibiotic sensitivity test revealed that 63.6% of the E. coli isolates were resistance to ampicillin while 49.5% were resistant to tetracycline and cephalothin. The least resistances were observed against gentamicin (3.7%) and cefotaxime (1.9%). No resistance was observed against meropenem. For the Vibrio spp, resistance was most frequently observed against tetracycline (38%) ampicillin (26%), chloramphenicol (16%), cefotaxime (14%), trimethoprim-sulfamethoxazole (13%) and the least resistance observed was against ciprofloxacin (1%). This study demonstrates that poorly treated wastewater effluent can be a source of eutrophic water with high nutrient levels and pathogenic bacteria and enteric viruses as well as antibiotic resistance determinants that could impact negatively on human health. The finding of this study also suggests that WWTPs have to be properly monitored and controlled to ensure compliance to set guidelines. This could be attained through the application of appropriate treatment processes, which will help to minimize possible dangers to public environment health.
- Full Text:
- Date Issued: 2015
- Authors: Osuolale, Olayinka O
- Date: 2015
- Language: English
- Type: Thesis , Doctoral , PhD (Microbiology)
- Identifier: vital:11292 , http://hdl.handle.net/10353/d1021079
- Description: Waste waters can be sources of pollution to surface water and the environment with severe implications for public health. Most treatment plants in the Buffalo City Municipality in the Eastern Cape Province discharge their treated effluent into the surface waters which directly and indirectly impacts on the quality of surface waters in the region. The objective of this study was to determine the microbiological and physicochemical qualities of the final effluents of two wastewater treatment plants in the Buffalo City Municipality in the Eastern Cape Province of South Africa over a period of 12 months (September 2012 to August 2013). The qualities of the final effluents of WW-Ama Wastewater Treatment Plant with respect to phosphate (3.9 mg/l - 20.6 mg/l), free chlorine (0.05 mg/l - 0.71 mg/l), chemical oxygen demand (COD) (4.7 mg/l - 211 mg/l), and faecal coliform (0 - 2.92 × 104 CFU/100 ml) were not in compliance with the permissible limits set for effluent discharged to surface water by South Africa guidelines for effluent discharge. Other physicochemical parameters like biological oxygen demand (BOD) (2.2 mg/l - 9.0 mg/l), total dissolve solid (TDS) (253 mg/l - 336.3 mg/l) and turbidity (4.8 NTU - 43.20 NTU) with no SA regulatory set limits were compared to other regulatory standards and they do not comply with the limits. Also, at the second WWTP’s, the WW-Dim Treatment Plant effluent quality for free chlorine (0.06 mg/l - 7.2 mg/l), BOD (0.1 mg/l - 7.4 mg/l), and turbidity (4.02 NTU - 24.3 NTU) also did not comply. For microbiological qualities, counts of presumptive E. coli and Vibrio ranged between 0 - 2.92 × PROFESSOR ANTHONY I. OKOHAntibiogram of the bacterial isolates were determined using the disk diffusion method. A total of 107 confirmed E. coli and 100 confirmed Vibrio spp. were used for this assay. Results of antibiotic sensitivity test revealed that 63.6% of the E. coli isolates were resistance to ampicillin while 49.5% were resistant to tetracycline and cephalothin. The least resistances were observed against gentamicin (3.7%) and cefotaxime (1.9%). No resistance was observed against meropenem. For the Vibrio spp, resistance was most frequently observed against tetracycline (38%) ampicillin (26%), chloramphenicol (16%), cefotaxime (14%), trimethoprim-sulfamethoxazole (13%) and the least resistance observed was against ciprofloxacin (1%). This study demonstrates that poorly treated wastewater effluent can be a source of eutrophic water with high nutrient levels and pathogenic bacteria and enteric viruses as well as antibiotic resistance determinants that could impact negatively on human health. The finding of this study also suggests that WWTPs have to be properly monitored and controlled to ensure compliance to set guidelines. This could be attained through the application of appropriate treatment processes, which will help to minimize possible dangers to public environment health.
- Full Text:
- Date Issued: 2015
Isolation and characterisation of lignocellulose degrading bacteria from Tyume River in the Eastern Cape Province, South Africa
- Authors: Tembisa, Papiyana Ayavuya
- Date: 2015
- Subjects: Lignocellulose -- Biodegradation -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Waterborne infection -- South Africa -- Eastern Cape , Bacteriophages -- South Africa -- Eastern Cape , Sediments (Geology) -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11299 , http://hdl.handle.net/10353/d1021293 , Lignocellulose -- Biodegradation -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Waterborne infection -- South Africa -- Eastern Cape , Bacteriophages -- South Africa -- Eastern Cape , Sediments (Geology) -- South Africa -- Eastern Cape
- Description: This study focuses on the isolation and characterization of bacteria from lignocellulosic biomass obtained from the sediments of the Tyume River in Alice, Eastern Cape and to determine those bacterial isolates with good potential for modification and decomposition of lignocellulosic biomass for industrial application. Several bacterial isolates were recovered and screened for ability to degrade various lignocellulosic materials. Nine of the isolates were positive for lignocellulolytic activity. Four isolates were cellulase positive and six were xylanase positive. Moreover, one isolate (SB1) was positive for both xylanase and cellulase activities and showed the best hydrolysis zone on solid media. This isolate was then chosen as the best and identified molecularly. The 16S rDNA sequence analysis indicated that SB1 was a Bacillus cereus species. Factors affecting the cellulose and xylanase enzyme production by the organisms were studied. The organisms produced the enzymes maximally at earlier hours of incubation (12-30 hr) and optimally at acidic pH (3-5) and at moderate temperatures (35-45ºC). SB1 appears to hold promise in the decomposition of lignocellulosic wastes.
- Full Text:
- Date Issued: 2015
- Authors: Tembisa, Papiyana Ayavuya
- Date: 2015
- Subjects: Lignocellulose -- Biodegradation -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Waterborne infection -- South Africa -- Eastern Cape , Bacteriophages -- South Africa -- Eastern Cape , Sediments (Geology) -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11299 , http://hdl.handle.net/10353/d1021293 , Lignocellulose -- Biodegradation -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Waterborne infection -- South Africa -- Eastern Cape , Bacteriophages -- South Africa -- Eastern Cape , Sediments (Geology) -- South Africa -- Eastern Cape
- Description: This study focuses on the isolation and characterization of bacteria from lignocellulosic biomass obtained from the sediments of the Tyume River in Alice, Eastern Cape and to determine those bacterial isolates with good potential for modification and decomposition of lignocellulosic biomass for industrial application. Several bacterial isolates were recovered and screened for ability to degrade various lignocellulosic materials. Nine of the isolates were positive for lignocellulolytic activity. Four isolates were cellulase positive and six were xylanase positive. Moreover, one isolate (SB1) was positive for both xylanase and cellulase activities and showed the best hydrolysis zone on solid media. This isolate was then chosen as the best and identified molecularly. The 16S rDNA sequence analysis indicated that SB1 was a Bacillus cereus species. Factors affecting the cellulose and xylanase enzyme production by the organisms were studied. The organisms produced the enzymes maximally at earlier hours of incubation (12-30 hr) and optimally at acidic pH (3-5) and at moderate temperatures (35-45ºC). SB1 appears to hold promise in the decomposition of lignocellulosic wastes.
- Full Text:
- Date Issued: 2015
Isolation and molecular characterization of Bacillus cereus from cow’s raw milk
- Authors: Lukanji, Zinathi , Ndip, R N
- Date: 2015
- Subjects: Milk contamination -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Foodborne diseases -- Molecular diagnosis -- South Africa -- Eastern Cape , Dairy products -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11296 , http://hdl.handle.net/10353/d1021284 , Milk contamination -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Foodborne diseases -- Molecular diagnosis -- South Africa -- Eastern Cape , Dairy products -- South Africa -- Eastern Cape
- Description: Bacillus cereus is a group of ubiquitous facultative anaerobic spore forming Gram-positive rods commonly found in soil. It has been detected and implicated in several contaminated food products and raw milk in dairy farms and it causes foodborne gastroenteritis by producing several toxins. This study is aimed at characterizing virulence determinants of B. cereus from cow‟s raw milk. A total of 400 raw milk samples were collected in Fort Hare Dairy Trust and Middledrift Dairy Farm; and cultured on Polymyxin pyruvate Egg-Yolk Mannitol Bromothymol Agar (PEMBA) for 48 hours at 37°C. DNA was isolated from the isolates and 16S rDNA was amplified and sent to Central Analytical Laboratory for sequencing. The gyrB gene of B. cereus was also used to confirm the identity of the isolates. Antibiotic susceptibility profiles of the isolates together with virulence genes were investigated. Multilocus Sequence typing was used to investigate the genetic relatedness of some selected isolates. Furthermore, spores of the isolates were produced, harvested and their concentrations determined. All (100%) of the isolates were identified as having a 96-99% similarity to B. cereus, B. thuringiensis and B. anthracis using sequencing; while gyrB gene was observed in all (100%) of the isolates. Three virulence genes nheA, nheB, nheC encoding for non haemolysin enterotoxin were amplified in all (100%) the isolates. All (100%) of the isolates were susceptible to doxycycline, gentamycin, tetracycline, ciprofloxacin, chloramphenicol and streptomycin. Resistance to rifampicin and penicillin G was predominant with equal rate of 100%, while susceptibility to erythromycin, clindamycin and doxycycline ranged from 60% to 100%. The selected isolates were related and are descendants of the same ancestor. All (100%) the isolates produced spores. The B. cereus isolates contain virulence genes, has multiple antibiotic drug resistance and produce spores, which poses a health risk to the public and cannot be used as probiotics.
- Full Text:
- Date Issued: 2015
- Authors: Lukanji, Zinathi , Ndip, R N
- Date: 2015
- Subjects: Milk contamination -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Foodborne diseases -- Molecular diagnosis -- South Africa -- Eastern Cape , Dairy products -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11296 , http://hdl.handle.net/10353/d1021284 , Milk contamination -- South Africa -- Eastern Cape , Bacillus (Bacteria) -- South Africa -- Eastern Cape , Foodborne diseases -- Molecular diagnosis -- South Africa -- Eastern Cape , Dairy products -- South Africa -- Eastern Cape
- Description: Bacillus cereus is a group of ubiquitous facultative anaerobic spore forming Gram-positive rods commonly found in soil. It has been detected and implicated in several contaminated food products and raw milk in dairy farms and it causes foodborne gastroenteritis by producing several toxins. This study is aimed at characterizing virulence determinants of B. cereus from cow‟s raw milk. A total of 400 raw milk samples were collected in Fort Hare Dairy Trust and Middledrift Dairy Farm; and cultured on Polymyxin pyruvate Egg-Yolk Mannitol Bromothymol Agar (PEMBA) for 48 hours at 37°C. DNA was isolated from the isolates and 16S rDNA was amplified and sent to Central Analytical Laboratory for sequencing. The gyrB gene of B. cereus was also used to confirm the identity of the isolates. Antibiotic susceptibility profiles of the isolates together with virulence genes were investigated. Multilocus Sequence typing was used to investigate the genetic relatedness of some selected isolates. Furthermore, spores of the isolates were produced, harvested and their concentrations determined. All (100%) of the isolates were identified as having a 96-99% similarity to B. cereus, B. thuringiensis and B. anthracis using sequencing; while gyrB gene was observed in all (100%) of the isolates. Three virulence genes nheA, nheB, nheC encoding for non haemolysin enterotoxin were amplified in all (100%) the isolates. All (100%) of the isolates were susceptible to doxycycline, gentamycin, tetracycline, ciprofloxacin, chloramphenicol and streptomycin. Resistance to rifampicin and penicillin G was predominant with equal rate of 100%, while susceptibility to erythromycin, clindamycin and doxycycline ranged from 60% to 100%. The selected isolates were related and are descendants of the same ancestor. All (100%) the isolates produced spores. The B. cereus isolates contain virulence genes, has multiple antibiotic drug resistance and produce spores, which poses a health risk to the public and cannot be used as probiotics.
- Full Text:
- Date Issued: 2015
Prevalence and antibiogram of some swine associated Shiga toxin producing Escherichia coli Serogroups and Salmonella species in Nkonkobe Municipality, Eastern Cape Province, South Africa
- Authors: Iwu, Chinwe Juliana
- Date: 2015
- Subjects: Escherichia coli -- South Africa -- Eastern Cape , Salmonella infections -- South Africa -- Eastern Cape , Water -- Pollution -- Environmental aspects -- South Africa -- Eastern Cape , Escherichia coli infections -- South Africa -- Eastern Cape , Water quality management -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11294 , http://hdl.handle.net/10353/d1021273 , Escherichia coli -- South Africa -- Eastern Cape , Salmonella infections -- South Africa -- Eastern Cape , Water -- Pollution -- Environmental aspects -- South Africa -- Eastern Cape , Escherichia coli infections -- South Africa -- Eastern Cape , Water quality management -- South Africa -- Eastern Cape
- Description: Gastrointestinal illnesses have continually become a global public health issue. Exposure to zoonotic food borne pathogens such as Salmonella and diarrhoegenic E. coli either by direct or indirect contact through the consumption of food producing animals is likely an important mode of infection to humans. More so, the use of antibiotics in farm animals similar to those used in humans can select for resistance in bacteria frequently harboured by them. These resistant strains can be passed on to humans through contaminated meat products and water leading to resistant infections with consequences such as prolonged illnesses, treatment failures, and increased morbidity and mortality. In animals, these can lead to reduced productivity. Monitoring the level of resistance among bacteria from animal isolates will help in generating data that could be used to create awareness of their presence in the environment and aid in preventing a potential epidemic in the community. In this study, we investigated the prevalence and antimicrobial resistance profile of Escherichia coli serogroups and Salmonella species in faecal samples collected from pigs in Nkonkobe Municipality in the Eastern Cape Province, South Africa between April – July, 2014. A total of 310 presumptive Shiga toxin producing Escherichia coli (STEC) were confirmed as E. coli spp using polymerase chain reaction (PCR) technique by amplification of the uidA gene, out of which 179 (58%) were confirmed positive. Approximately, serogrougs O157:H7, O145 and O26 made up 24% (n=43), 8% (n=14) and 20% (n=35) of the E. coli population respectively. Only E. coli O26 was positive for stx2 gene in 31% of the isolates harbouring the gene, while the other serogroups were non-pathogenic. Susceptibility of the isolates to 18 antibiotics was carried out in vitro by the standardized agar disc-diffusion method. All the isolates were susceptible to imipenem. Similarly, a relatively high susceptibility was observed in norfloxacin (83-100%), ciprofloxacin (63-100%), gentamycin (77-100%), and chloramphenicol (77-100%). However, all the isolates were resistant to tetracycline and its long acting counterpart oxytetracycline. Resistances observed against other antimicrobials are as follows: ampicillin (84-91%), streptomycin (14-100%), erythromycin (91-100%), ceftazidime (35%). Multiple antimicrobial resistance patterns and indices ranged from 3 to 12 and 0.2 to 0.7 to respectively. Genes encoding resistances to ampicillin (ampC), streptomycin (strA) and tetracycline (tetA) were frequently detected in 50-100%, 22-29% and 40-86% of the resistant isolates respectively. In the other arm of the dissertation, two hundred and fifty eight presumptive isolates of Salmonella were recovered from the faecal samples of pigs. Specific primers targeting serogroups A, B, C1, C2, and D were used to delineate the isolates into different serogroups using PCR. Only serogroup A (n=48) was detected. These isolates were examined for antimicrobial susceptibility by disc diffusion method using 18 antibiotics. The results showed that a large proportion of the isolates were resistant to tetracycline (100%), oxytetracycline (100%), ampicillin (75%), sulphamethoxazole/trimethoprim (75%) and streptomycin (75%). Majority of the isolates exhibited multidrug resistances with the predominant multiple antibiotic resistance (MAR) phenotype being against eleven antibiotics. A high multiple antibiotic resistance (MAR) index in a range of 0.3- 0.6 was observed. The incidence of genes encoding resistance against tetracycline (tetA), streptomycin (stra), and ampicillin (ampC) were 54%, 44% and 61% respectively. These findings reveal that pigs within the Nkonkobe Municipality in the Eastern Cape Province could harbour Shiga toxins and multidrug resistant serogroups of E. coli as well as resistant Salmonella which could be transmitted to humans through the food chain. To ensure public health safety, continuous monitoring and sufficient sanitation in swine industries must be ensured.
- Full Text:
- Date Issued: 2015
- Authors: Iwu, Chinwe Juliana
- Date: 2015
- Subjects: Escherichia coli -- South Africa -- Eastern Cape , Salmonella infections -- South Africa -- Eastern Cape , Water -- Pollution -- Environmental aspects -- South Africa -- Eastern Cape , Escherichia coli infections -- South Africa -- Eastern Cape , Water quality management -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11294 , http://hdl.handle.net/10353/d1021273 , Escherichia coli -- South Africa -- Eastern Cape , Salmonella infections -- South Africa -- Eastern Cape , Water -- Pollution -- Environmental aspects -- South Africa -- Eastern Cape , Escherichia coli infections -- South Africa -- Eastern Cape , Water quality management -- South Africa -- Eastern Cape
- Description: Gastrointestinal illnesses have continually become a global public health issue. Exposure to zoonotic food borne pathogens such as Salmonella and diarrhoegenic E. coli either by direct or indirect contact through the consumption of food producing animals is likely an important mode of infection to humans. More so, the use of antibiotics in farm animals similar to those used in humans can select for resistance in bacteria frequently harboured by them. These resistant strains can be passed on to humans through contaminated meat products and water leading to resistant infections with consequences such as prolonged illnesses, treatment failures, and increased morbidity and mortality. In animals, these can lead to reduced productivity. Monitoring the level of resistance among bacteria from animal isolates will help in generating data that could be used to create awareness of their presence in the environment and aid in preventing a potential epidemic in the community. In this study, we investigated the prevalence and antimicrobial resistance profile of Escherichia coli serogroups and Salmonella species in faecal samples collected from pigs in Nkonkobe Municipality in the Eastern Cape Province, South Africa between April – July, 2014. A total of 310 presumptive Shiga toxin producing Escherichia coli (STEC) were confirmed as E. coli spp using polymerase chain reaction (PCR) technique by amplification of the uidA gene, out of which 179 (58%) were confirmed positive. Approximately, serogrougs O157:H7, O145 and O26 made up 24% (n=43), 8% (n=14) and 20% (n=35) of the E. coli population respectively. Only E. coli O26 was positive for stx2 gene in 31% of the isolates harbouring the gene, while the other serogroups were non-pathogenic. Susceptibility of the isolates to 18 antibiotics was carried out in vitro by the standardized agar disc-diffusion method. All the isolates were susceptible to imipenem. Similarly, a relatively high susceptibility was observed in norfloxacin (83-100%), ciprofloxacin (63-100%), gentamycin (77-100%), and chloramphenicol (77-100%). However, all the isolates were resistant to tetracycline and its long acting counterpart oxytetracycline. Resistances observed against other antimicrobials are as follows: ampicillin (84-91%), streptomycin (14-100%), erythromycin (91-100%), ceftazidime (35%). Multiple antimicrobial resistance patterns and indices ranged from 3 to 12 and 0.2 to 0.7 to respectively. Genes encoding resistances to ampicillin (ampC), streptomycin (strA) and tetracycline (tetA) were frequently detected in 50-100%, 22-29% and 40-86% of the resistant isolates respectively. In the other arm of the dissertation, two hundred and fifty eight presumptive isolates of Salmonella were recovered from the faecal samples of pigs. Specific primers targeting serogroups A, B, C1, C2, and D were used to delineate the isolates into different serogroups using PCR. Only serogroup A (n=48) was detected. These isolates were examined for antimicrobial susceptibility by disc diffusion method using 18 antibiotics. The results showed that a large proportion of the isolates were resistant to tetracycline (100%), oxytetracycline (100%), ampicillin (75%), sulphamethoxazole/trimethoprim (75%) and streptomycin (75%). Majority of the isolates exhibited multidrug resistances with the predominant multiple antibiotic resistance (MAR) phenotype being against eleven antibiotics. A high multiple antibiotic resistance (MAR) index in a range of 0.3- 0.6 was observed. The incidence of genes encoding resistance against tetracycline (tetA), streptomycin (stra), and ampicillin (ampC) were 54%, 44% and 61% respectively. These findings reveal that pigs within the Nkonkobe Municipality in the Eastern Cape Province could harbour Shiga toxins and multidrug resistant serogroups of E. coli as well as resistant Salmonella which could be transmitted to humans through the food chain. To ensure public health safety, continuous monitoring and sufficient sanitation in swine industries must be ensured.
- Full Text:
- Date Issued: 2015
Antibiogram profiling of Escherichia coli pathotypes isolated from Kat River and Fort Beaufort abstraction water
- Authors: Nontongana, Nolonwabo
- Date: 2014
- Subjects: Escherichia coli infections -- South Africa -- Eastern Cape , Water -- Pollution -- Environmental aspects -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11289 , http://hdl.handle.net/10353/d1019820 , Escherichia coli infections -- South Africa -- Eastern Cape , Water -- Pollution -- Environmental aspects -- South Africa -- Eastern Cape
- Description: Escherichia coli (E. coli) is a widespread species that includes a broad variety of strains, ranging from highly pathogenic strains causing worldwide outbreaks of severe disease to virulent isolates which are part of the normal intestinal flora or which are well characterized and safe laboratory strains. The pathogenicity of a given E. coli strain is mainly determined by specific virulence factors which include adhesins, invasins, toxins and capsule. The aim of this study was to evaluate the prevalence and antibiogram profiles of E. coli pathotypes previously isolated from Kat River and Fort Beaufort abstraction water. A total of 171 E. coli isolates showed at least one pathogenic determinant among the isolated 278 E. coli. The other 107 isolates were negative for the tested virulence genes. All 278 presumptive isolates tested positive for the UidA gene, and were therefore classified as non-categorized pathogenic E. coli. The 171 pathogenic isolates had at least one characteristic gene of pathogenic E. coli and were identified and classified as enteropathogenic E. coli (6%), enterotoxigenicE. coli (131), uropathogenic E. coli (6), neonatal meningitis E. coli (14), diffusely adherent E. coli (1) and enterohaemrrhagic E. coli (1). Interestingly, no virulence genes were detected for the enteroinvasive E. coli and the enteroaggregative E. coli. The antibiotic resistance profiles for all isolates that were identified as E. coli showed 100% resistance to penicillin G, 98% resistance to ampicillin, 38% resistance to trimethoprim-sulphamethoxazole and 8% resistance to streptomycin. Multiple antibacterial resistance (MAR) was also observed, where 44% of the isolates were resistant to three antibiotics and 8% resistant to four antibiotics. The results of this study showed the Kat River and Fort Beaufort abstraction water are reservoirs of pathogenic strains of E. coli which harbour antibiotic resistance determinants that can cause serious health risks to the people in the surrounding communities.
- Full Text:
- Date Issued: 2014
- Authors: Nontongana, Nolonwabo
- Date: 2014
- Subjects: Escherichia coli infections -- South Africa -- Eastern Cape , Water -- Pollution -- Environmental aspects -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11289 , http://hdl.handle.net/10353/d1019820 , Escherichia coli infections -- South Africa -- Eastern Cape , Water -- Pollution -- Environmental aspects -- South Africa -- Eastern Cape
- Description: Escherichia coli (E. coli) is a widespread species that includes a broad variety of strains, ranging from highly pathogenic strains causing worldwide outbreaks of severe disease to virulent isolates which are part of the normal intestinal flora or which are well characterized and safe laboratory strains. The pathogenicity of a given E. coli strain is mainly determined by specific virulence factors which include adhesins, invasins, toxins and capsule. The aim of this study was to evaluate the prevalence and antibiogram profiles of E. coli pathotypes previously isolated from Kat River and Fort Beaufort abstraction water. A total of 171 E. coli isolates showed at least one pathogenic determinant among the isolated 278 E. coli. The other 107 isolates were negative for the tested virulence genes. All 278 presumptive isolates tested positive for the UidA gene, and were therefore classified as non-categorized pathogenic E. coli. The 171 pathogenic isolates had at least one characteristic gene of pathogenic E. coli and were identified and classified as enteropathogenic E. coli (6%), enterotoxigenicE. coli (131), uropathogenic E. coli (6), neonatal meningitis E. coli (14), diffusely adherent E. coli (1) and enterohaemrrhagic E. coli (1). Interestingly, no virulence genes were detected for the enteroinvasive E. coli and the enteroaggregative E. coli. The antibiotic resistance profiles for all isolates that were identified as E. coli showed 100% resistance to penicillin G, 98% resistance to ampicillin, 38% resistance to trimethoprim-sulphamethoxazole and 8% resistance to streptomycin. Multiple antibacterial resistance (MAR) was also observed, where 44% of the isolates were resistant to three antibiotics and 8% resistant to four antibiotics. The results of this study showed the Kat River and Fort Beaufort abstraction water are reservoirs of pathogenic strains of E. coli which harbour antibiotic resistance determinants that can cause serious health risks to the people in the surrounding communities.
- Full Text:
- Date Issued: 2014
Assessment of the anti-Listerial properties of Garcinia kola (Heckel) seeds
- Authors: Penduka, Dambudzo
- Date: 2014
- Subjects: Microbial sensitivity tests , Garcinia , Medicinal plants , Traditional medicine
- Language: English
- Type: Thesis , Doctoral , PhD (Microbiology)
- Identifier: vital:11278 , http://hdl.handle.net/10353/d1015527 , Microbial sensitivity tests , Garcinia , Medicinal plants , Traditional medicine
- Description: A follow-up of traditional medicinal plants uses is an important tool in highlighting their therapeutic potentials, as they have been found to be a source of a wide range of bioactive compounds that can be used as base compounds for new pharmaceutical drugs. This study therefore focuses on assessing the anti-Listerial properties of the seeds of Garcinia kola (Heckel) plant, which is a traditional medicinal plant of west and central African origin, and was and is still used to traditionally treat several ailments. Four different solvents crude extracts of the seeds were assessed for their anti-Listerial activities in-vitro, against a panel of 42 Listeria bacteria, which included Listeria monocytogenes, Listeria ivanovii and Listeria grayi species. At 10 mg/ml concentration the aqueous extract had activity against 29% of the test isolates while the other three crude extracts namely dichloromethane, n-hexane and the methanol extracts had activity against 45% of the test bacteria. The minimum inhibitory concentration (MIC) ranges of the extracts were 0.079-0.313 mg/ml for the dichloromethane extract; 0.079-0.625 mg/ml for the n-hexane extract; 0.157-0.625 mg/ml for the methanol extract; and 10->10 mg/ml for the aqueous extract. The minimum bactericidal concentration (MBC) ranges of the extracts were 0.625–10 mg/ml for both the n-hexane and the dichloromethane extract; 5-10 mg/ml for the methanol extract; and those for the aqueous extract were above 10 mg/ml against all the susceptible Listeria isolates. The rate of kill analysis was then determined for the three most active crude extracts that is excluding the aqueous extract and it was assessed against four representative Listeria species namely L. monocytogenes (LAL 8), L. grayi (LAL 15), L. ivanovii (LEL 30) and L. ivanovii (LEL 18). All the three extracts showed a general trend of being concentration and time dependent in their rate of kill profiles such that most bacteria cells were killed at the highest test concentration of 4× MIC value after the maximum exposure time of 2 h. The n-hexane, dichloromethane and methanol extracts were bactericidal against 4, 3 and 1 isolates out of the four test Listeria isolates respectively.
- Full Text:
- Date Issued: 2014
- Authors: Penduka, Dambudzo
- Date: 2014
- Subjects: Microbial sensitivity tests , Garcinia , Medicinal plants , Traditional medicine
- Language: English
- Type: Thesis , Doctoral , PhD (Microbiology)
- Identifier: vital:11278 , http://hdl.handle.net/10353/d1015527 , Microbial sensitivity tests , Garcinia , Medicinal plants , Traditional medicine
- Description: A follow-up of traditional medicinal plants uses is an important tool in highlighting their therapeutic potentials, as they have been found to be a source of a wide range of bioactive compounds that can be used as base compounds for new pharmaceutical drugs. This study therefore focuses on assessing the anti-Listerial properties of the seeds of Garcinia kola (Heckel) plant, which is a traditional medicinal plant of west and central African origin, and was and is still used to traditionally treat several ailments. Four different solvents crude extracts of the seeds were assessed for their anti-Listerial activities in-vitro, against a panel of 42 Listeria bacteria, which included Listeria monocytogenes, Listeria ivanovii and Listeria grayi species. At 10 mg/ml concentration the aqueous extract had activity against 29% of the test isolates while the other three crude extracts namely dichloromethane, n-hexane and the methanol extracts had activity against 45% of the test bacteria. The minimum inhibitory concentration (MIC) ranges of the extracts were 0.079-0.313 mg/ml for the dichloromethane extract; 0.079-0.625 mg/ml for the n-hexane extract; 0.157-0.625 mg/ml for the methanol extract; and 10->10 mg/ml for the aqueous extract. The minimum bactericidal concentration (MBC) ranges of the extracts were 0.625–10 mg/ml for both the n-hexane and the dichloromethane extract; 5-10 mg/ml for the methanol extract; and those for the aqueous extract were above 10 mg/ml against all the susceptible Listeria isolates. The rate of kill analysis was then determined for the three most active crude extracts that is excluding the aqueous extract and it was assessed against four representative Listeria species namely L. monocytogenes (LAL 8), L. grayi (LAL 15), L. ivanovii (LEL 30) and L. ivanovii (LEL 18). All the three extracts showed a general trend of being concentration and time dependent in their rate of kill profiles such that most bacteria cells were killed at the highest test concentration of 4× MIC value after the maximum exposure time of 2 h. The n-hexane, dichloromethane and methanol extracts were bactericidal against 4, 3 and 1 isolates out of the four test Listeria isolates respectively.
- Full Text:
- Date Issued: 2014
Assessment of the prevalence of faecal coliforms and Escherichia coli o157:h7 in the final effluents of two wastewater treatment plants in Amahlathi Local Municipality of Eastern Cape Province, South Africa
- Authors: Ajibade, Adefisoye Martins
- Date: 2014
- Subjects: Sewage disposal plants , Escherichia coli -- South Africa -- Eastern Cape , Escherichia coli O157:H7 , Escherichia coli , Effluent quality -- Testing , Whole effluent toxicity testing , Water -- Purification
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11283 , http://hdl.handle.net/10353/d1016166 , Sewage disposal plants , Escherichia coli -- South Africa -- Eastern Cape , Escherichia coli O157:H7 , Escherichia coli , Effluent quality -- Testing , Whole effluent toxicity testing , Water -- Purification
- Description: The production of final effluents that meet discharged requirements and guidelines remain a major challenge particularly in the developing world with the resultant problem of surface water pollution. This study assessed the physicochemical and microbiological qualities of two wastewater treatment works in the Eastern Cape Province of South Africa in terms of the prevalence of faecal coliforms and Escherichia coli O157:H7 over a five month period. All physicochemical and microbiological analyses were carried out using standard methods. Data were collected in triplicates and analysed statistically using IBM SPSS version 20.0. The ranges of some of the physicochemical parameters that complied with set guidelines include pH (6.7 – 7.6), TDS (107 – 171 mg/L), EC (168 – 266 μS/cm), Temperature (15 – 24oC), NO3- (0 – 8.2 mg/L), NO2- (0.14 – 0.71 mg/L) and PO4 (1.05 – 4.50 mg/L). Others including Turbidity (2.64 – 58.00 NTU), Free Cl (0.13 – 0.65 mg/L), DO (2.20 – 8.48 mg/L), BOD (0.13 – 6.85 mg/L) and COD (40 – 482 mg/L) did not comply with set guidelines. The microbiological parameters ranged 0 – 2.7 × 104 CFU/100 ml for FC and 0 – 9.3 × 103 for EHEC CFU/100 ml, an indication of non-compliance with set guidelines. Preliminary identification of 40 randomly selected presumptive enterohemorrhagic E. coli isolates by Gram’s staining and oxidase test shows 100% (all 40 selected isolates) to be Gram positive while 90% (36 randomly selected isolates) were oxidase negative. Statistical correlation between the physicochemical and the microbiological parameters were generally weak except in the case of free chlorine and DO where they showed inverse correlation with the microbiological parameters. The recovery of EHEC showed the inefficiency of the treatment processes to effectively inactivate the bacteria, and possibly other pathogenic bacteria that may be present in the treated wastewater. The assessment suggested the need for proper monitoring and a review of the treatment procedures used at these treatment works.
- Full Text:
- Date Issued: 2014
- Authors: Ajibade, Adefisoye Martins
- Date: 2014
- Subjects: Sewage disposal plants , Escherichia coli -- South Africa -- Eastern Cape , Escherichia coli O157:H7 , Escherichia coli , Effluent quality -- Testing , Whole effluent toxicity testing , Water -- Purification
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11283 , http://hdl.handle.net/10353/d1016166 , Sewage disposal plants , Escherichia coli -- South Africa -- Eastern Cape , Escherichia coli O157:H7 , Escherichia coli , Effluent quality -- Testing , Whole effluent toxicity testing , Water -- Purification
- Description: The production of final effluents that meet discharged requirements and guidelines remain a major challenge particularly in the developing world with the resultant problem of surface water pollution. This study assessed the physicochemical and microbiological qualities of two wastewater treatment works in the Eastern Cape Province of South Africa in terms of the prevalence of faecal coliforms and Escherichia coli O157:H7 over a five month period. All physicochemical and microbiological analyses were carried out using standard methods. Data were collected in triplicates and analysed statistically using IBM SPSS version 20.0. The ranges of some of the physicochemical parameters that complied with set guidelines include pH (6.7 – 7.6), TDS (107 – 171 mg/L), EC (168 – 266 μS/cm), Temperature (15 – 24oC), NO3- (0 – 8.2 mg/L), NO2- (0.14 – 0.71 mg/L) and PO4 (1.05 – 4.50 mg/L). Others including Turbidity (2.64 – 58.00 NTU), Free Cl (0.13 – 0.65 mg/L), DO (2.20 – 8.48 mg/L), BOD (0.13 – 6.85 mg/L) and COD (40 – 482 mg/L) did not comply with set guidelines. The microbiological parameters ranged 0 – 2.7 × 104 CFU/100 ml for FC and 0 – 9.3 × 103 for EHEC CFU/100 ml, an indication of non-compliance with set guidelines. Preliminary identification of 40 randomly selected presumptive enterohemorrhagic E. coli isolates by Gram’s staining and oxidase test shows 100% (all 40 selected isolates) to be Gram positive while 90% (36 randomly selected isolates) were oxidase negative. Statistical correlation between the physicochemical and the microbiological parameters were generally weak except in the case of free chlorine and DO where they showed inverse correlation with the microbiological parameters. The recovery of EHEC showed the inefficiency of the treatment processes to effectively inactivate the bacteria, and possibly other pathogenic bacteria that may be present in the treated wastewater. The assessment suggested the need for proper monitoring and a review of the treatment procedures used at these treatment works.
- Full Text:
- Date Issued: 2014