Isolation and characterization of E. coli and Campylobacter spp. from diarrhoeal samples collected from selected hospitals in Amathole District Municipality, Eastern Cape, South Africa
- Authors: Omolajaiye, Sunday Abraham
- Date: 2018
- Subjects: Escherichia coli infections Campylobacter infections Diarrhea
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/6213 , vital:29515
- Description: Approximately 2-4 billion cases of infectious diarrhoea occur every year, with the highest numbers recorded in sub-Saharan Africa. It remains the most common public health issue among children in developing nations. The purpose of this research was to unfold the prevalence of diarrhoeagenic E. coli and Campylobacter pathotypes as well as elucidate their antibiogram characteristics in diarrhoeal stool samples collected in some medical facilities in Eastern Cape Province, South Africa. Two hundred stool samples were collected from both inpatients and outpatients from male and females of all age groups attending selected medical facilities in the study area. Isolation and characterization of both organisms were done using culture based and molecular methods. Antibiotic susceptibility patterns of identified isolates were determined against a panel of 12 antimicrobial agents. One hundred and twenty presumptive E. coli isolates and 42 presumptive isolates of Campylobacter spp. Were isolated. Eighty-two percent (82 percent) of the presumptive E. coli isolates were confirmed as E. coli while 46.3 percent belonged to Campylobacter spp. Pathotyping of the diarrhoeagenic E. coli isolates by Polymerase chain reaction (PCR) showed the following prevalences: DAEC 43 (32 percent), EHEC 18 (17 percent), EIEC 11 (10 percent) and EPEC 18 (17 percent). EAEC and ETEC were not detected, while for Campylobacter spp. 37 (88 percent) were C. jejuni, and C. coli was not detected. A total of 12 (32.4 percent) of the confirmed Campylobacter jejuni isolates were found to possess the fliM gene, 9 (24.3 percent) possessed the flhA gene and only 6 (16.2 percent) harboured the gene flgE2. None were positive for the flaA, flab and flhB genes.The antibiotic resistance patterns observed among the E. coli isolates were high against ampicillin (98.1 percent), chloramphenicol (94.3 percent) and tetracycline (90.6 percent). For Campylobacter spp., resistance observed were: chloramphenicol (91.6 percent), tetracycline (25.2 percent), erythromycin (49.6 percent) and gentamycin (56.4 percent). A lesser resistance against imipenem (35.9 percent) and quinolone (ciprofloxacin) (45.5 percent) were exhibited by the E.coli isolates. 10.8 percent and 20.3 percent of the Campylobacter isolates were resistant to imipenem and ciprofloxacin respectively. The presence of chloramphenicol (CatA1) and tetracycline (tetA) resistance genes were detected in 94 percent and 89 percent of E. coli isolates respectively while 98 percent of Campylobacter spp. Harboured the catA1 resistance gene. It could be deduced from this study that E. coli and Campylobacter spp. are predomiant enteric pathogens as the etiologic agents of diarrhoea in the study community, and that their antimicrobial resistance is high in the study location. The need to develop strategies to prevent infection and control resistant organisms is evident.
- Full Text:
- Authors: Omolajaiye, Sunday Abraham
- Date: 2018
- Subjects: Escherichia coli infections Campylobacter infections Diarrhea
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/6213 , vital:29515
- Description: Approximately 2-4 billion cases of infectious diarrhoea occur every year, with the highest numbers recorded in sub-Saharan Africa. It remains the most common public health issue among children in developing nations. The purpose of this research was to unfold the prevalence of diarrhoeagenic E. coli and Campylobacter pathotypes as well as elucidate their antibiogram characteristics in diarrhoeal stool samples collected in some medical facilities in Eastern Cape Province, South Africa. Two hundred stool samples were collected from both inpatients and outpatients from male and females of all age groups attending selected medical facilities in the study area. Isolation and characterization of both organisms were done using culture based and molecular methods. Antibiotic susceptibility patterns of identified isolates were determined against a panel of 12 antimicrobial agents. One hundred and twenty presumptive E. coli isolates and 42 presumptive isolates of Campylobacter spp. Were isolated. Eighty-two percent (82 percent) of the presumptive E. coli isolates were confirmed as E. coli while 46.3 percent belonged to Campylobacter spp. Pathotyping of the diarrhoeagenic E. coli isolates by Polymerase chain reaction (PCR) showed the following prevalences: DAEC 43 (32 percent), EHEC 18 (17 percent), EIEC 11 (10 percent) and EPEC 18 (17 percent). EAEC and ETEC were not detected, while for Campylobacter spp. 37 (88 percent) were C. jejuni, and C. coli was not detected. A total of 12 (32.4 percent) of the confirmed Campylobacter jejuni isolates were found to possess the fliM gene, 9 (24.3 percent) possessed the flhA gene and only 6 (16.2 percent) harboured the gene flgE2. None were positive for the flaA, flab and flhB genes.The antibiotic resistance patterns observed among the E. coli isolates were high against ampicillin (98.1 percent), chloramphenicol (94.3 percent) and tetracycline (90.6 percent). For Campylobacter spp., resistance observed were: chloramphenicol (91.6 percent), tetracycline (25.2 percent), erythromycin (49.6 percent) and gentamycin (56.4 percent). A lesser resistance against imipenem (35.9 percent) and quinolone (ciprofloxacin) (45.5 percent) were exhibited by the E.coli isolates. 10.8 percent and 20.3 percent of the Campylobacter isolates were resistant to imipenem and ciprofloxacin respectively. The presence of chloramphenicol (CatA1) and tetracycline (tetA) resistance genes were detected in 94 percent and 89 percent of E. coli isolates respectively while 98 percent of Campylobacter spp. Harboured the catA1 resistance gene. It could be deduced from this study that E. coli and Campylobacter spp. are predomiant enteric pathogens as the etiologic agents of diarrhoea in the study community, and that their antimicrobial resistance is high in the study location. The need to develop strategies to prevent infection and control resistant organisms is evident.
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Quality indices of the Nahoon beach and canal in Buffalo City Metropolitan Municipality, Eastern Cape, South Africa
- Authors: Ebomah, Kingsley Ehi
- Date: 2017
- Subjects: Pathogenic bacteria -- South Africa -- Eastern Cape Water quality -- South Africa -- Eastern Cape -- Measurement Water -- Microbiology -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/8122 , vital:31525
- Description: Faecal indicator bacteria have long been recommended for usage in water quality monitoring of various water sources including surface water. A large number of people in different parts of the world often engage in recreational and other commercial activities at the various beaches along the coastal lines, most especially, during summer season and festive periods. It is generally assumed that beach water is safe all the times, however, there have been increasing reports of beach and other coastal water pollutions because of rising anthropogenic activities around coastal areas globally. The presence of pathogens in faecal contaminated beach water either directly or indirectly increases the risk of human exposure which may result in skin infections as well as the ingestion and transmission of multidrug resistant pathogens. Microorganisms may gain entry into beach water directly from improperly treated final effluents released by wastewater treatment plants and from agricultural runoffs and/or faulty drainages. The aim of this study was to evaluate the quality indices of the Nahoon Beach and canal waters in the Eastern Cape Province of South Africa. In order to achieve this aim, the objectives of this study were as follow: to determine the seasonal variations of the physicochemical characteristics of the Nahoon beach and canal waters, to assess the microbiological quality of the beach water by assessing the prevalence of potentially E. coli and Enterococcus species, and to evaluate the antibiogram profile of the E. coli pathotypes and Enterococci species recovered from the beach water samples. Water samples were collected bi-weekly for a period of twelve months, during which on-site physicochemical analyses were carried out. Bacteriological assessment was performed using the membrane filtration technique and the necessary incubation conditions were followed. Identification of the target organisms was done by molecular based methods using PCR (polymerase chain reaction) while antibiotic susceptibility testing was done using the disk diffusion method. During the spring season (August to October) and periods of festive activities (December, January and March), it was observed that turbidity was at its highest, consequently, influencing total dissolved solids and a rise in the values of pH and electrical conductivity. Microbiological qualities assessed follow the order: Escherichia coli (101 – 103 CFU/100ml) and Enterococcus (101 – 102 CFU/100 ml). The results show that 41.2percent (107/260) of the presumptive E. coli isolates were positive for uidA gene. A total of 73 out of 107 (68.2percent) PCR-confirmed E. coli isolates were observed to belong to different pathotypes while 59percent (102/172) of the presumptive Enterococcus strains isolated were positive for SodA gene (Enterococcus spp.). Out of 102 enterococci isolates, 45 strains were identified as species (E. faecalis and E. faecium) and these were subjected to antibiotic susceptibility testing. The E. coli strains exhibited a frequency of 100percent resistance against ampicillin while the Enterococcus strains also showed 100percent resistance against vancomycin and linezolid. Target genes eae 11 (10.3percent); ipaH 14 (13.1percent); ibeA 48 (44.9percent) that encode pathogenicity in E. coli were successfully amplified by PCR suggesting that the isolates are potentially pathogenic strains whereas Enterococcus spp. including Enterococcus faecalis 26 (25.5percent) and Enterococcus faecium 19 (18.6percent) were also identified in the water samples. In this study, the phenotypic antibiogram profiles of the E. coli isolates revealed that all 73 (100percent) of the pathotypes were resistant to ampicillin, 67 (91.8percent) were resistant to amikacin, gentamicin and ceftazidime while about 61 (83.6percent) and 51 (69.9percent) were resistant to tetracycline and ciprofloxacin as well as trimethoprim respectively. About 21.9percent (16) of the E. coli isolates exhibited multiple antibiotic resistances with 100percent being resistant to eight antibiotics whereas multiple antimicrobial resistances were observed in 14 (31percent) of the enterococci strains and the most predominant profile was the simultaneous resistance to ampicillin, penicillin and vancomycin. The results obtained in this study show that the beach water generally did not comply with the set guidelines. The results also suggest the possible survival and prevalence of potentially virulent E. coli as well as Enterococcus strains in the aquatic environment which may be a cause of concern for public health. Monitoring of the quality of surface water and antimicrobial resistance (AMR) in bacteria is of great importance and has clinical and human health significance. Nonetheless, this study underscores the need for more detailed study of other waterborne pathogens of health importance including enteric viruses to ascertain the safety of the beach for human use.
- Full Text:
- Authors: Ebomah, Kingsley Ehi
- Date: 2017
- Subjects: Pathogenic bacteria -- South Africa -- Eastern Cape Water quality -- South Africa -- Eastern Cape -- Measurement Water -- Microbiology -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/8122 , vital:31525
- Description: Faecal indicator bacteria have long been recommended for usage in water quality monitoring of various water sources including surface water. A large number of people in different parts of the world often engage in recreational and other commercial activities at the various beaches along the coastal lines, most especially, during summer season and festive periods. It is generally assumed that beach water is safe all the times, however, there have been increasing reports of beach and other coastal water pollutions because of rising anthropogenic activities around coastal areas globally. The presence of pathogens in faecal contaminated beach water either directly or indirectly increases the risk of human exposure which may result in skin infections as well as the ingestion and transmission of multidrug resistant pathogens. Microorganisms may gain entry into beach water directly from improperly treated final effluents released by wastewater treatment plants and from agricultural runoffs and/or faulty drainages. The aim of this study was to evaluate the quality indices of the Nahoon Beach and canal waters in the Eastern Cape Province of South Africa. In order to achieve this aim, the objectives of this study were as follow: to determine the seasonal variations of the physicochemical characteristics of the Nahoon beach and canal waters, to assess the microbiological quality of the beach water by assessing the prevalence of potentially E. coli and Enterococcus species, and to evaluate the antibiogram profile of the E. coli pathotypes and Enterococci species recovered from the beach water samples. Water samples were collected bi-weekly for a period of twelve months, during which on-site physicochemical analyses were carried out. Bacteriological assessment was performed using the membrane filtration technique and the necessary incubation conditions were followed. Identification of the target organisms was done by molecular based methods using PCR (polymerase chain reaction) while antibiotic susceptibility testing was done using the disk diffusion method. During the spring season (August to October) and periods of festive activities (December, January and March), it was observed that turbidity was at its highest, consequently, influencing total dissolved solids and a rise in the values of pH and electrical conductivity. Microbiological qualities assessed follow the order: Escherichia coli (101 – 103 CFU/100ml) and Enterococcus (101 – 102 CFU/100 ml). The results show that 41.2percent (107/260) of the presumptive E. coli isolates were positive for uidA gene. A total of 73 out of 107 (68.2percent) PCR-confirmed E. coli isolates were observed to belong to different pathotypes while 59percent (102/172) of the presumptive Enterococcus strains isolated were positive for SodA gene (Enterococcus spp.). Out of 102 enterococci isolates, 45 strains were identified as species (E. faecalis and E. faecium) and these were subjected to antibiotic susceptibility testing. The E. coli strains exhibited a frequency of 100percent resistance against ampicillin while the Enterococcus strains also showed 100percent resistance against vancomycin and linezolid. Target genes eae 11 (10.3percent); ipaH 14 (13.1percent); ibeA 48 (44.9percent) that encode pathogenicity in E. coli were successfully amplified by PCR suggesting that the isolates are potentially pathogenic strains whereas Enterococcus spp. including Enterococcus faecalis 26 (25.5percent) and Enterococcus faecium 19 (18.6percent) were also identified in the water samples. In this study, the phenotypic antibiogram profiles of the E. coli isolates revealed that all 73 (100percent) of the pathotypes were resistant to ampicillin, 67 (91.8percent) were resistant to amikacin, gentamicin and ceftazidime while about 61 (83.6percent) and 51 (69.9percent) were resistant to tetracycline and ciprofloxacin as well as trimethoprim respectively. About 21.9percent (16) of the E. coli isolates exhibited multiple antibiotic resistances with 100percent being resistant to eight antibiotics whereas multiple antimicrobial resistances were observed in 14 (31percent) of the enterococci strains and the most predominant profile was the simultaneous resistance to ampicillin, penicillin and vancomycin. The results obtained in this study show that the beach water generally did not comply with the set guidelines. The results also suggest the possible survival and prevalence of potentially virulent E. coli as well as Enterococcus strains in the aquatic environment which may be a cause of concern for public health. Monitoring of the quality of surface water and antimicrobial resistance (AMR) in bacteria is of great importance and has clinical and human health significance. Nonetheless, this study underscores the need for more detailed study of other waterborne pathogens of health importance including enteric viruses to ascertain the safety of the beach for human use.
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Evaluation of cellulase and xylanase production by two actinobacteria species belonging to the Micrococcus genus isolated from decaying lignocellulosic biomass
- Mmango-Kaseke, Ziyanda https://orcid.org/0000-0002-8936-1149
- Authors: Mmango-Kaseke, Ziyanda https://orcid.org/0000-0002-8936-1149
- Date: 2016-05
- Subjects: Lignocellulose , Biomass energy
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/24197 , vital:62442
- Description: Bacteria were isolated from sawdust and screened for cellulase and xylanase production on carboxyl methyl cellulose (CMC) and birchwood xylan agar. The bacteria showing halo forms around the colony were selected for further analyses and those isolates with the highest cumulative halozone size (isolate PLY1 and MLY10) were chosen for detailed studies. Evaluation of cellulase and xylanase production by saw dust actinobacterial species whose 16S rDNA nucleotide sequences were deposited in GenBank as Micrococcus luteus strain SAMRC-UFH3 with accession number KU171371 and Micrococcus yunnanensis strain SAMRC-UFH4 with accession number KU171372. Optimum culture conditions for the production of cellulase for respective axenic culture include incubation period (96 h), incubation temperature (25oC), agitation speed (50 rpm), and pH 5. For xylanase production, the optimum culture conditions in the presence of 1percent (w/v) birchwood xylan include incubation period (84 h), incubation temperature (25oC), agitation speed (200 rpm), and pH 10. For Micrococcus yunnanensis strain SAMRC-UFH4 cellulase production was optimal under such conditions as, incubation temperature (30oC), agitation speed (0 rpm), and pH 5, while xylanase production was optimal at, incubation temperature (30oC), agitation speed (150 rpm), and pH 10. The high cellulase and xylanase activity obtained from these isolates suggest suitability of the organisms as important candidates for commercial application. , Thesis (MSc) -- Faculty of Science and Agriculture, 2016
- Full Text:
- Authors: Mmango-Kaseke, Ziyanda https://orcid.org/0000-0002-8936-1149
- Date: 2016-05
- Subjects: Lignocellulose , Biomass energy
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/24197 , vital:62442
- Description: Bacteria were isolated from sawdust and screened for cellulase and xylanase production on carboxyl methyl cellulose (CMC) and birchwood xylan agar. The bacteria showing halo forms around the colony were selected for further analyses and those isolates with the highest cumulative halozone size (isolate PLY1 and MLY10) were chosen for detailed studies. Evaluation of cellulase and xylanase production by saw dust actinobacterial species whose 16S rDNA nucleotide sequences were deposited in GenBank as Micrococcus luteus strain SAMRC-UFH3 with accession number KU171371 and Micrococcus yunnanensis strain SAMRC-UFH4 with accession number KU171372. Optimum culture conditions for the production of cellulase for respective axenic culture include incubation period (96 h), incubation temperature (25oC), agitation speed (50 rpm), and pH 5. For xylanase production, the optimum culture conditions in the presence of 1percent (w/v) birchwood xylan include incubation period (84 h), incubation temperature (25oC), agitation speed (200 rpm), and pH 10. For Micrococcus yunnanensis strain SAMRC-UFH4 cellulase production was optimal under such conditions as, incubation temperature (30oC), agitation speed (0 rpm), and pH 5, while xylanase production was optimal at, incubation temperature (30oC), agitation speed (150 rpm), and pH 10. The high cellulase and xylanase activity obtained from these isolates suggest suitability of the organisms as important candidates for commercial application. , Thesis (MSc) -- Faculty of Science and Agriculture, 2016
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Assessment of the physicochemical and microbiological qualities of Tyume River in Amathole District in the Eastern Cape Province, South Africa
- Sibanda, Timothy https://orcid.org/0000-0002-6864-3796
- Authors: Sibanda, Timothy https://orcid.org/0000-0002-6864-3796
- Date: 2013-05
- Subjects: Water -- Purification , Sewage -- Purification
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/24465 , vital:62812
- Description: The bioflocculant-producing potentials of three marine bacteria isolated from the sediment samples of Algoa Bay in the Eastern Cape Province of South Africa were assessed. Analysis of the partial nucleotide sequence of the 16S rDNA of the bacteria revealed 99 percent, 99 percent, and 98 percent similarity to Cobetia sp. L222, Bacillus sp. A-5A, and Bacillus sp. HXG-C1 respectively and the sequence was deposited in GenBank as Cobetia sp. OAUIFE, Bacillus sp. MAYA and Bacillus sp. Gilbert (accession number JF799092, JF799093, and HQ537128 respectively). Cultivation condition studies for Cobetia sp. OAUIFE revealed that bioflocculant production was optimal with an inoculum size of 2 percent (v/v), initial pH of 6.0, Mn2+ as the metal ion, and glucose as the carbon source. Metal ions, including Na+, K+, Li+, Ca2+and Mg2+ stimulated bioflocculant production resulting in flocculating activity of above 90 percent. This crude bioflocculant is thermally stable, with about 78 percent of its flocculating activity remaining after heating at 100 oC for 25 min. Analysis of the purified bioflocculant revealed it to be an acidic extracellular polysaccharide. FTIR analysis revealed the presence of methoxyl, hydroxyl, and carboxyl - groups in the compound bioflocculant and SEM micrograph of the bioflocculant revealed a crystal-linear structure. On the other hand, bioflocculant production by Bacillus sp. MAYA was optimal when glucose (95.6 percent flocculating activity) and ammonium nitrate (83.3 percent flocculating activity) were used as carbon and nitrogen sources respectively; inoculum size was 2 percent (v/v); initial pH 6; and Ca2+ as coagulant aid. Chemical analysis of the purified bioflocculant shows that it is composed of uronic acid, neutral sugar and protein. FTIR analysis also revealed the presence of methoxyl, hydroxyl, carboxyl and amino- groups in this bioflocculant. The bioflocculant is thermostable with about 65.6 percent residual flocculating activity retained after heating the bioflocculant at 100 oC for 25 min. However bioflocculant production by Bacillus sp. Gilbert was optimal when sodium carbonate (95.2 percent flocculating activity) and potassium nitrate (76.6 percent flocculating activity) were used as carbon and nitrogen sources respectively; inoculum size was 3 percent (v/v); initial pH 9; and Al3+ as cation. The crude bioflocculant retained 44.2 percent residual flocculating activity after heating at 100 oC for 15 min. FTIR analysis reveals the presence of hydroxyl, carboxyl and methylene - groups in the compound bioflocculant. SEM micrograph of the bioflocculant revealed an amorphous compound. The consortia of these bacteria strains also produced bioflocculants with high flocculating activities which were highly efficient in removing turbidity and chemical oxygen demand (COD) from brewery wastewater, diary wastewater and river water. The bioflocculants from the consortia seemed better than traditional flocculants such as alum . The characteristics of the bioflocculant produced by the consortium of Cobetia sp. OAUIFE and Bacillus sp. MAYA showed that this extracellular bioflocculant, composed of 66percent uronic acid and 31percent protein and an optimum flocculation (90 percent) of kaolin suspension, when the dosage concentration was 0.8 mg/ml, under weak alkaline pH of 8, and Ca2+ as a coagulant aid. The bioflocculant is thermally stable, with a high residual flocculating activity of 86.7 percent, 89.3 percent and 87.0 percent after heating at 50 oC, 80 oC and 100 oC for 25 min respectively. The FTIR analysis of the bioflocculant indicated the presence of hydroxyl, amino, carbonyl and carboxyl functional groups. Scanning electron microscopy (SEM) image revealed a crystal-linear spongy-like bioflocculant structure and EDX analysis of the purified bioflocculant showed that the elemental composition in mass proportion of C,N,O,S and P was 6.67:6.23:37.55:0.38:4.42 (percent w/w). However, the characteristics of the bioflocculant produced by the consortium of Cobetia sp OAUIFE and Bacillus sp. Gilbert showed an optimum flocculation (90 percent) of kaolin suspension when the dosage concentration was 0.2 mg/ml, under neutral pH of 7, and Ca2+ as a coagulant aid. The FTIR analysis of the bioflocculant Tyume River water samples were collected monthly, over a 12-month period starting from August 2010 and ending in July 2011, and transported on ice to the Applied and Environmental Microbiology Research Group (AEMREG) Laboratory at the University of Fort Hare, Alice for analyses within 6 h of collection. Electrical conductivity (EC), total dissolved solids (TDS), temperature, pH and dissolved oxygen (DO) of water samples were determined in situ using a multi-parameter ion-specific meter. Concentrations of orthophosphate and total nitrogen (nitrate + nitrite) were determined by standard photometric methods. Total coliforms (TC), faecal coliforms (FC) and enterococci were determined by the membrane filtration method. Viruses in water samples were concentrated using the adsorption-elution method, followed by extraction of viral nucleic acids and purification done using commercially available kits. The concentrations of human enteric viruses in the river-water samples were estimated using quantitative PCR. RNA viruses were quantified in a two-step protocol where RNA was first transcribed into cDNA in a separate reverse-transcription step. Adenovirus species and serotypes were simultaneously detected using serotype-specific multiplex PCR. Norovirus genogroups GI and GII were detected by semi-nested PCR. The risk of infection associated with recreational and domestic use of the water was also estimated. Biochemical oxygen demand (BOD) levels fell within the stipulated BOD guideline of 10 mg/ℓ for surface waters where full contact use is allowed and ≤ 30 mg/ℓ where public access is prohibited, restricted, or infrequent. DO concentrations generally ranged between 7.47 mg/ℓ and 10.42 mg/ℓ, well within the target water quality requirements. The temperature regime ranged between 6°C and 28°C and for most sampling sites, the temperature regimes were within the acceptable limit of no risk (≤ 25°C) for domestic water uses in South Africa. EC ranged between 47 μS/cm and 408 μS/cm well within the South African target water quality EC guideline of 700 μS/cm though it was observed to increase as the river flowed through settlements. The pH in the period beginning September 2010 through to January 2011 was consistently below pH 9, but from February 2011 to June 2011 the pH significantly increased to between pH 10 and pH 11 at most sampling sites. Unpolluted waters normally show a pH of between 6.5 and 8.5. Most of the pH values observed in this study lie between pH 8.5 and pH 10.8 levels which are not far off from the upper level guideline of pH 9.0 for domestic use. Turbidity ranged between 6 NTU and 281 and fell short of the target water quality range (0 NTU to 1 NTU) of no risk for domestic water uses in South Africa. Monthly TDS values and EC values showed direct proportionality. TDS concentrations at all sites fell within the acceptable guideline of 0 mg/ℓ to 450 mg/ℓ of TDS for domestic use. Nutrient profiles were as follows: nitrate (0.18 mg/ℓ to 4.21 mg/ℓ); nitrite (0.02 mg/ℓ to 2.35 mg/ℓ); and orthophosphate (0.06 mg/ℓ to 2.72 mg/ℓ). The bacteriological qualities of the water were poor, exceeding the guideline of 200 CFU/100 mℓ and 33 CFU/100 mℓ for FC and enterococci respectively, for recreational water. FC counts also exceeded the 1 000 CFU/100 mℓ guideline for water used in fresh produce irrigation. Generally, higher counts of TC, FC and enterococci were recorded at the sampling sites located at the lower reaches of the river compared to the upper reaches. Adenovirus was detected in 31percent of the river samples in concentrations ranging between 1.0×100 genome copies/ℓ and 8.49×104 genome copies/ℓ. Serotyping showed the presence of species C adenovirus serotypes 1, 2, 6 and 7, and species F adenovirus serotype 41. The prevalence of norovirus was 4percent while rotavirus was detected in 4percent of river samples in concentrations ranging between 9×100 genome copies/ℓ and 5.64×103 genome copies/ℓ. Hepatitis A virus was detected in 13percent of river samples in concentrations ranging between1.67×103 and 1.64×104 genome copies/ℓ while enteroviruses were not detected. Detection of enteric viruses was inversely correlated to temperature. Risk analysis showed that both hepatitis A virus and adenovirus presented significantly higher risk of infection values compared to rotavirus in the case of ingestion of 10 mℓ or 100 mℓ of water from Tyume River while enteroviruses did not present any significant risk of infection. Tyume River water samples also did not conform to the US Environmental Protection Agency (US EPA) bacterial criteria of 200 CFU/100 mℓ faecal coliforms and 33 CFU/100 mℓ enterococci for bathing waters. Whereas the physicochemical parameters showed that Tyume River water was relatively clean, the bacteriological water quality was poor. Most of the microbiological contamination observed in this study (especially FIBs) can be blamed on inadequate sanitary infrastructure as we observed that open defecation is commonplace in this catchment, which also serves as a conduit for effluent discharges from wastewater-treatment facilities. Enteric viruses were detected along the course of the river in a sporadic pattern, generally not related to natural hydrological cycles and so we conclude that the presence of enteric viruses in the river is suggestive of the dynamics of the same in the host population. Even though the proportion of infective viruses was estimated in this study, fact remains that there is considerable risk of infection posed by the use of raw surface water for either domestic or recreational use. This study further confirmed the lack of correlation between faecal indicator bacteria and enteric virus occurrence in environmental waters, showing that assaying for enteric viruses in environmental waters remains the best method for determining the health risks associated with the use of faecally contaminated water. , Thesis (PhD) -- Faculty of Science and Agriculture, 2013
- Full Text:
- Authors: Sibanda, Timothy https://orcid.org/0000-0002-6864-3796
- Date: 2013-05
- Subjects: Water -- Purification , Sewage -- Purification
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/24465 , vital:62812
- Description: The bioflocculant-producing potentials of three marine bacteria isolated from the sediment samples of Algoa Bay in the Eastern Cape Province of South Africa were assessed. Analysis of the partial nucleotide sequence of the 16S rDNA of the bacteria revealed 99 percent, 99 percent, and 98 percent similarity to Cobetia sp. L222, Bacillus sp. A-5A, and Bacillus sp. HXG-C1 respectively and the sequence was deposited in GenBank as Cobetia sp. OAUIFE, Bacillus sp. MAYA and Bacillus sp. Gilbert (accession number JF799092, JF799093, and HQ537128 respectively). Cultivation condition studies for Cobetia sp. OAUIFE revealed that bioflocculant production was optimal with an inoculum size of 2 percent (v/v), initial pH of 6.0, Mn2+ as the metal ion, and glucose as the carbon source. Metal ions, including Na+, K+, Li+, Ca2+and Mg2+ stimulated bioflocculant production resulting in flocculating activity of above 90 percent. This crude bioflocculant is thermally stable, with about 78 percent of its flocculating activity remaining after heating at 100 oC for 25 min. Analysis of the purified bioflocculant revealed it to be an acidic extracellular polysaccharide. FTIR analysis revealed the presence of methoxyl, hydroxyl, and carboxyl - groups in the compound bioflocculant and SEM micrograph of the bioflocculant revealed a crystal-linear structure. On the other hand, bioflocculant production by Bacillus sp. MAYA was optimal when glucose (95.6 percent flocculating activity) and ammonium nitrate (83.3 percent flocculating activity) were used as carbon and nitrogen sources respectively; inoculum size was 2 percent (v/v); initial pH 6; and Ca2+ as coagulant aid. Chemical analysis of the purified bioflocculant shows that it is composed of uronic acid, neutral sugar and protein. FTIR analysis also revealed the presence of methoxyl, hydroxyl, carboxyl and amino- groups in this bioflocculant. The bioflocculant is thermostable with about 65.6 percent residual flocculating activity retained after heating the bioflocculant at 100 oC for 25 min. However bioflocculant production by Bacillus sp. Gilbert was optimal when sodium carbonate (95.2 percent flocculating activity) and potassium nitrate (76.6 percent flocculating activity) were used as carbon and nitrogen sources respectively; inoculum size was 3 percent (v/v); initial pH 9; and Al3+ as cation. The crude bioflocculant retained 44.2 percent residual flocculating activity after heating at 100 oC for 15 min. FTIR analysis reveals the presence of hydroxyl, carboxyl and methylene - groups in the compound bioflocculant. SEM micrograph of the bioflocculant revealed an amorphous compound. The consortia of these bacteria strains also produced bioflocculants with high flocculating activities which were highly efficient in removing turbidity and chemical oxygen demand (COD) from brewery wastewater, diary wastewater and river water. The bioflocculants from the consortia seemed better than traditional flocculants such as alum . The characteristics of the bioflocculant produced by the consortium of Cobetia sp. OAUIFE and Bacillus sp. MAYA showed that this extracellular bioflocculant, composed of 66percent uronic acid and 31percent protein and an optimum flocculation (90 percent) of kaolin suspension, when the dosage concentration was 0.8 mg/ml, under weak alkaline pH of 8, and Ca2+ as a coagulant aid. The bioflocculant is thermally stable, with a high residual flocculating activity of 86.7 percent, 89.3 percent and 87.0 percent after heating at 50 oC, 80 oC and 100 oC for 25 min respectively. The FTIR analysis of the bioflocculant indicated the presence of hydroxyl, amino, carbonyl and carboxyl functional groups. Scanning electron microscopy (SEM) image revealed a crystal-linear spongy-like bioflocculant structure and EDX analysis of the purified bioflocculant showed that the elemental composition in mass proportion of C,N,O,S and P was 6.67:6.23:37.55:0.38:4.42 (percent w/w). However, the characteristics of the bioflocculant produced by the consortium of Cobetia sp OAUIFE and Bacillus sp. Gilbert showed an optimum flocculation (90 percent) of kaolin suspension when the dosage concentration was 0.2 mg/ml, under neutral pH of 7, and Ca2+ as a coagulant aid. The FTIR analysis of the bioflocculant Tyume River water samples were collected monthly, over a 12-month period starting from August 2010 and ending in July 2011, and transported on ice to the Applied and Environmental Microbiology Research Group (AEMREG) Laboratory at the University of Fort Hare, Alice for analyses within 6 h of collection. Electrical conductivity (EC), total dissolved solids (TDS), temperature, pH and dissolved oxygen (DO) of water samples were determined in situ using a multi-parameter ion-specific meter. Concentrations of orthophosphate and total nitrogen (nitrate + nitrite) were determined by standard photometric methods. Total coliforms (TC), faecal coliforms (FC) and enterococci were determined by the membrane filtration method. Viruses in water samples were concentrated using the adsorption-elution method, followed by extraction of viral nucleic acids and purification done using commercially available kits. The concentrations of human enteric viruses in the river-water samples were estimated using quantitative PCR. RNA viruses were quantified in a two-step protocol where RNA was first transcribed into cDNA in a separate reverse-transcription step. Adenovirus species and serotypes were simultaneously detected using serotype-specific multiplex PCR. Norovirus genogroups GI and GII were detected by semi-nested PCR. The risk of infection associated with recreational and domestic use of the water was also estimated. Biochemical oxygen demand (BOD) levels fell within the stipulated BOD guideline of 10 mg/ℓ for surface waters where full contact use is allowed and ≤ 30 mg/ℓ where public access is prohibited, restricted, or infrequent. DO concentrations generally ranged between 7.47 mg/ℓ and 10.42 mg/ℓ, well within the target water quality requirements. The temperature regime ranged between 6°C and 28°C and for most sampling sites, the temperature regimes were within the acceptable limit of no risk (≤ 25°C) for domestic water uses in South Africa. EC ranged between 47 μS/cm and 408 μS/cm well within the South African target water quality EC guideline of 700 μS/cm though it was observed to increase as the river flowed through settlements. The pH in the period beginning September 2010 through to January 2011 was consistently below pH 9, but from February 2011 to June 2011 the pH significantly increased to between pH 10 and pH 11 at most sampling sites. Unpolluted waters normally show a pH of between 6.5 and 8.5. Most of the pH values observed in this study lie between pH 8.5 and pH 10.8 levels which are not far off from the upper level guideline of pH 9.0 for domestic use. Turbidity ranged between 6 NTU and 281 and fell short of the target water quality range (0 NTU to 1 NTU) of no risk for domestic water uses in South Africa. Monthly TDS values and EC values showed direct proportionality. TDS concentrations at all sites fell within the acceptable guideline of 0 mg/ℓ to 450 mg/ℓ of TDS for domestic use. Nutrient profiles were as follows: nitrate (0.18 mg/ℓ to 4.21 mg/ℓ); nitrite (0.02 mg/ℓ to 2.35 mg/ℓ); and orthophosphate (0.06 mg/ℓ to 2.72 mg/ℓ). The bacteriological qualities of the water were poor, exceeding the guideline of 200 CFU/100 mℓ and 33 CFU/100 mℓ for FC and enterococci respectively, for recreational water. FC counts also exceeded the 1 000 CFU/100 mℓ guideline for water used in fresh produce irrigation. Generally, higher counts of TC, FC and enterococci were recorded at the sampling sites located at the lower reaches of the river compared to the upper reaches. Adenovirus was detected in 31percent of the river samples in concentrations ranging between 1.0×100 genome copies/ℓ and 8.49×104 genome copies/ℓ. Serotyping showed the presence of species C adenovirus serotypes 1, 2, 6 and 7, and species F adenovirus serotype 41. The prevalence of norovirus was 4percent while rotavirus was detected in 4percent of river samples in concentrations ranging between 9×100 genome copies/ℓ and 5.64×103 genome copies/ℓ. Hepatitis A virus was detected in 13percent of river samples in concentrations ranging between1.67×103 and 1.64×104 genome copies/ℓ while enteroviruses were not detected. Detection of enteric viruses was inversely correlated to temperature. Risk analysis showed that both hepatitis A virus and adenovirus presented significantly higher risk of infection values compared to rotavirus in the case of ingestion of 10 mℓ or 100 mℓ of water from Tyume River while enteroviruses did not present any significant risk of infection. Tyume River water samples also did not conform to the US Environmental Protection Agency (US EPA) bacterial criteria of 200 CFU/100 mℓ faecal coliforms and 33 CFU/100 mℓ enterococci for bathing waters. Whereas the physicochemical parameters showed that Tyume River water was relatively clean, the bacteriological water quality was poor. Most of the microbiological contamination observed in this study (especially FIBs) can be blamed on inadequate sanitary infrastructure as we observed that open defecation is commonplace in this catchment, which also serves as a conduit for effluent discharges from wastewater-treatment facilities. Enteric viruses were detected along the course of the river in a sporadic pattern, generally not related to natural hydrological cycles and so we conclude that the presence of enteric viruses in the river is suggestive of the dynamics of the same in the host population. Even though the proportion of infective viruses was estimated in this study, fact remains that there is considerable risk of infection posed by the use of raw surface water for either domestic or recreational use. This study further confirmed the lack of correlation between faecal indicator bacteria and enteric virus occurrence in environmental waters, showing that assaying for enteric viruses in environmental waters remains the best method for determining the health risks associated with the use of faecally contaminated water. , Thesis (PhD) -- Faculty of Science and Agriculture, 2013
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