Surveillance study on pathogenic Acinetobacter species in freshwater environment of the Amathole and Chris Hani District Municipalities, Eastern Cape, South Africa
- Authors: Adewoyin, Mary Ayobami
- Date: 2019-09
- Subjects: Acinetobacter infections , Acinetobacter , Nosocomial infections
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/19836 , vital:43257
- Description: This study evaluates the occurrence of medically relevant Acinetobacter species in three rivers, namely; Keiskamma, Tyhume and Great Fish in the Eastern Cape Province, South Africa in one year sampling regime (April 2017 - March 2018). The physicochemical parameters (pH, temperature (TEM), electrical conductivity (EC), total dissolved solids (TDS), salinity (SAL), total suspended solids (TSS), turbidity (TBS), dissolved oxygen (DO) and biological oxygen demand (BOD)) of the water bodies were measured. The presumptive Acinetobacter species recovered from the freshwater resources were recorded and further confirmed using molecular techniques. Similarly, confirmed isolates were subjected to speciation using species-specific primer sets for A. baumannii and A. nosocomialis. Also, virulence genes namely; afa/draBC, epsA, fimH, OmpA, PAI, sfa/focDE, and traT in the two Acinetobacter species were also determined using molecular method. In addition, the antibiogram characteristics of A. baumannii and A. nosocomialis isolated from the water samples were determined using standard methods. The antibiotic susceptibility test was performed using a panel of 12 antibiotics belonging to the aminoglycosides (amikacin, AK and gentamicin, GM), β-lactam/β-lactamase-inhibitor combinations (piperacillin-tazobactam, PTZ), cephems (ceftazidime, CAZ, cefotaxime, CTX, and cefepime, CPM), carbapenems (imipenem, IMI and meropenem, MEM), fluoroquinolones (ciprofloxacin, CIP), folate pathway inhibitors (Trimethoprim/sulfamethoxazole, TS), lipopeptides (Polymyxin B, PB) and tetracyclines (tetracycline, TET). Similarly, antibiotic resistance genes (ARGs) present in the Acinetobacter isolates were investigated including aminoglycoside resistance genes (aacC2, aphA1 and aphA2), β-lactamases resistance genes (blaTEM, blaSHV, blaOXA-1-like, blaCTX-M(GROUP 1), blaCTX-M(GROUP 2), blaCTX-M(GROUP 9), blaVEB, blaGES, blaPER, blaCTX-M-8/-25, blaOXA-48-like, blaVIM, blaIMP and blaKPC), fluoroquinolones resistance genes (qnrA, qnrB, qnrC, qnrD and qnrS), sulfonamide resistance genes (sul1 and sul2), and tetracycline resistance genes (tetA, tetB, tetC, tetM, tetL and tetO). The pH, EC, TDS, SAL, TEMP, TSS, TBS, DO, and BOD for Tyhume River ranged as follows: 7.2-7.7, 125-141 μS/cm, 62-71mg/L, 0.06- 0.07 PSU, 11.3-20.2oC, 30.0-89.6 mg/L, 35.0-96.0 NTU, 8.2-9.8 mg/L, 2.0-4.2 mg/L, while for Great Fish River, the parameters were 8.0-8.2, 274-369 μS/cm, 137-184mg/L, 0.13-0.18PSU, 12.7-22.3oC, 44.3-99.4 mg/L, 48.0-214.0 NTU, 7.8-9.9 mg/L, 3.1- 4.9 mg/L, and at Keiskamma River they were 7.5-7.9, 153.2-285.0 μS/cm, 86-143 mg/L, 0.07-0.14 PSU, 11.0-21.4oC, 27.0- 55.6 mg/L, 31-61 NTU, 8.3-9.8 mg/L, 3.0-6.0 mg/L. A total of 1107 presumptive Acinetobacter spp. were recovered from the rivers sampled of which 428, 370 and 309 isolates were recovered from Tyhume, Great Fish and Keiskamma rivers respectively. However, only 844 was confirmed positive for the genus Acinetobacter and are recovered in the proportions 285 (77 percent), 219 (70.9 percent) and 340 (79 percent) from Great Fish, Keiskemma and Tyhume rivers respectively. Our finding revealed that 410 (48.58 percent) and 23 (2.7 percent) of the isolates were confirmed to be A. baumannii and A. nosocomalis respectively. Also, 308 (75.12 percent percent) A. baumannii and 3 (13.04 percent) A. nosocomialis isolates exhibited one or more virulence genes out of the seven tested, whereas 102 (24.88 percent) and 20 (86.95 percent) of the A. baumannii and A. nosocomialis isolates did not harbour any virulence gene. Additionally, OmpA was the most prevalent (p<0.05) virulence gene found in A. baumannii with 69 (45.10 percent), 52 (50.98 percent) and 77 (49.68 percent) isolates from Great Fish, Keiskamma and Tyhume rivers respectively. The rates of susceptibilities of A. baumannii and A. nosocomialis to the antibiotics followed the order; Piperacillin-tazobactam (72.8 percent ; 73.9 percent), Ceftazidime (70.5 percent ; 91.3 percent), Cefotaxime (16.8 percent ; 17.4 percent), Cefepime (88.5 percent ; 95.7 percent), Imipenem (95.9 percent ; 100 percent ), Meropenem (92.7 percent ; 91.3 percent), Amikacin (97.6 percent ; 91.3 percent), Gentamicin (89.8 percent ; 87 percent), Polymyxin B (84.4 percent ; 91.3 percent), Tetracycline (74.7 percent ; 78.3 percent), Ciprofloxacin (75.9 percent ; 78.3 percent) and Trimethoprim/sulfamethoxazole (74.0 percent ; 73.9 percent) respectively. Both A. baumannii and A. nosocomialis were highly susceptible to all the antimicrobials tested except cefotaxime where 64 percent and 78 percent intermediate responses were observed in the species. At least 10 isolates of A. baumannii were resistant against each of the antibiotics used. The modal multiple antibiotics resistance phenotypes (MARPs) for Acinetobacter spp. was MARP 3 (29.87 percent) and the least was MARP 10 and 11 (2.6 percent each). The antimicrobial resistance index (ARI) was higher at two sampling sites KE2 (0.33) and TY1 (0.22). Similarly, MARI showed that sampling sites KE2 was a hotspot for multidrug-resistant Acinetobacter spp. Of the five classes of ARGs studied, there was a widespread of β-lactamases (blaTEM) in the two Acinetobacter species, followed by sul2, which were detected in 67 (63.2 percent) and 44 (49.4 percent) isolates respectively, across the rivers studied. We conclude that aquatic resources of the study community are important reservoirs of pathogenic Acinetobacter species and antibiotic resistance determinants. The occurrence of clinically-important Acinetobacter species suggests possible contamination of these selected rivers which are consumed by humans and livestock, as well as being used for irrigation system, and this constitutes a risk to public health. It also shows that A. baumannii and A. nosocomialis can thrive in the aquatic environment. This study suggests that direct utilization of water from these sources for domestic and other purposes without any form of pre-treatment should be avoided. It is, therefore, necessary for regulatory authorities to monitor the release of domestic and industrial wastewater into these water bodies in order to prevent outbreaks of epidemics. , Thesis (PhD) (Microbiology) -- University of Fort Hare, 2019
- Full Text:
- Date Issued: 2019-09
- Authors: Adewoyin, Mary Ayobami
- Date: 2019-09
- Subjects: Acinetobacter infections , Acinetobacter , Nosocomial infections
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/19836 , vital:43257
- Description: This study evaluates the occurrence of medically relevant Acinetobacter species in three rivers, namely; Keiskamma, Tyhume and Great Fish in the Eastern Cape Province, South Africa in one year sampling regime (April 2017 - March 2018). The physicochemical parameters (pH, temperature (TEM), electrical conductivity (EC), total dissolved solids (TDS), salinity (SAL), total suspended solids (TSS), turbidity (TBS), dissolved oxygen (DO) and biological oxygen demand (BOD)) of the water bodies were measured. The presumptive Acinetobacter species recovered from the freshwater resources were recorded and further confirmed using molecular techniques. Similarly, confirmed isolates were subjected to speciation using species-specific primer sets for A. baumannii and A. nosocomialis. Also, virulence genes namely; afa/draBC, epsA, fimH, OmpA, PAI, sfa/focDE, and traT in the two Acinetobacter species were also determined using molecular method. In addition, the antibiogram characteristics of A. baumannii and A. nosocomialis isolated from the water samples were determined using standard methods. The antibiotic susceptibility test was performed using a panel of 12 antibiotics belonging to the aminoglycosides (amikacin, AK and gentamicin, GM), β-lactam/β-lactamase-inhibitor combinations (piperacillin-tazobactam, PTZ), cephems (ceftazidime, CAZ, cefotaxime, CTX, and cefepime, CPM), carbapenems (imipenem, IMI and meropenem, MEM), fluoroquinolones (ciprofloxacin, CIP), folate pathway inhibitors (Trimethoprim/sulfamethoxazole, TS), lipopeptides (Polymyxin B, PB) and tetracyclines (tetracycline, TET). Similarly, antibiotic resistance genes (ARGs) present in the Acinetobacter isolates were investigated including aminoglycoside resistance genes (aacC2, aphA1 and aphA2), β-lactamases resistance genes (blaTEM, blaSHV, blaOXA-1-like, blaCTX-M(GROUP 1), blaCTX-M(GROUP 2), blaCTX-M(GROUP 9), blaVEB, blaGES, blaPER, blaCTX-M-8/-25, blaOXA-48-like, blaVIM, blaIMP and blaKPC), fluoroquinolones resistance genes (qnrA, qnrB, qnrC, qnrD and qnrS), sulfonamide resistance genes (sul1 and sul2), and tetracycline resistance genes (tetA, tetB, tetC, tetM, tetL and tetO). The pH, EC, TDS, SAL, TEMP, TSS, TBS, DO, and BOD for Tyhume River ranged as follows: 7.2-7.7, 125-141 μS/cm, 62-71mg/L, 0.06- 0.07 PSU, 11.3-20.2oC, 30.0-89.6 mg/L, 35.0-96.0 NTU, 8.2-9.8 mg/L, 2.0-4.2 mg/L, while for Great Fish River, the parameters were 8.0-8.2, 274-369 μS/cm, 137-184mg/L, 0.13-0.18PSU, 12.7-22.3oC, 44.3-99.4 mg/L, 48.0-214.0 NTU, 7.8-9.9 mg/L, 3.1- 4.9 mg/L, and at Keiskamma River they were 7.5-7.9, 153.2-285.0 μS/cm, 86-143 mg/L, 0.07-0.14 PSU, 11.0-21.4oC, 27.0- 55.6 mg/L, 31-61 NTU, 8.3-9.8 mg/L, 3.0-6.0 mg/L. A total of 1107 presumptive Acinetobacter spp. were recovered from the rivers sampled of which 428, 370 and 309 isolates were recovered from Tyhume, Great Fish and Keiskamma rivers respectively. However, only 844 was confirmed positive for the genus Acinetobacter and are recovered in the proportions 285 (77 percent), 219 (70.9 percent) and 340 (79 percent) from Great Fish, Keiskemma and Tyhume rivers respectively. Our finding revealed that 410 (48.58 percent) and 23 (2.7 percent) of the isolates were confirmed to be A. baumannii and A. nosocomalis respectively. Also, 308 (75.12 percent percent) A. baumannii and 3 (13.04 percent) A. nosocomialis isolates exhibited one or more virulence genes out of the seven tested, whereas 102 (24.88 percent) and 20 (86.95 percent) of the A. baumannii and A. nosocomialis isolates did not harbour any virulence gene. Additionally, OmpA was the most prevalent (p<0.05) virulence gene found in A. baumannii with 69 (45.10 percent), 52 (50.98 percent) and 77 (49.68 percent) isolates from Great Fish, Keiskamma and Tyhume rivers respectively. The rates of susceptibilities of A. baumannii and A. nosocomialis to the antibiotics followed the order; Piperacillin-tazobactam (72.8 percent ; 73.9 percent), Ceftazidime (70.5 percent ; 91.3 percent), Cefotaxime (16.8 percent ; 17.4 percent), Cefepime (88.5 percent ; 95.7 percent), Imipenem (95.9 percent ; 100 percent ), Meropenem (92.7 percent ; 91.3 percent), Amikacin (97.6 percent ; 91.3 percent), Gentamicin (89.8 percent ; 87 percent), Polymyxin B (84.4 percent ; 91.3 percent), Tetracycline (74.7 percent ; 78.3 percent), Ciprofloxacin (75.9 percent ; 78.3 percent) and Trimethoprim/sulfamethoxazole (74.0 percent ; 73.9 percent) respectively. Both A. baumannii and A. nosocomialis were highly susceptible to all the antimicrobials tested except cefotaxime where 64 percent and 78 percent intermediate responses were observed in the species. At least 10 isolates of A. baumannii were resistant against each of the antibiotics used. The modal multiple antibiotics resistance phenotypes (MARPs) for Acinetobacter spp. was MARP 3 (29.87 percent) and the least was MARP 10 and 11 (2.6 percent each). The antimicrobial resistance index (ARI) was higher at two sampling sites KE2 (0.33) and TY1 (0.22). Similarly, MARI showed that sampling sites KE2 was a hotspot for multidrug-resistant Acinetobacter spp. Of the five classes of ARGs studied, there was a widespread of β-lactamases (blaTEM) in the two Acinetobacter species, followed by sul2, which were detected in 67 (63.2 percent) and 44 (49.4 percent) isolates respectively, across the rivers studied. We conclude that aquatic resources of the study community are important reservoirs of pathogenic Acinetobacter species and antibiotic resistance determinants. The occurrence of clinically-important Acinetobacter species suggests possible contamination of these selected rivers which are consumed by humans and livestock, as well as being used for irrigation system, and this constitutes a risk to public health. It also shows that A. baumannii and A. nosocomialis can thrive in the aquatic environment. This study suggests that direct utilization of water from these sources for domestic and other purposes without any form of pre-treatment should be avoided. It is, therefore, necessary for regulatory authorities to monitor the release of domestic and industrial wastewater into these water bodies in order to prevent outbreaks of epidemics. , Thesis (PhD) (Microbiology) -- University of Fort Hare, 2019
- Full Text:
- Date Issued: 2019-09
Perceptions Of School Based Support Teams About Providing Support To Foundation Phase Teachers In Two Butterworth Primary Schools, Eastern Cape
- Authors: Luningo, Mziwonke
- Date: 2017-11
- Subjects: School support teams
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/11260/6668 , vital:47202
- Description: The Policy on Inclusive Education acknowledges that all children can learn if they are given the necessary support. In order to achieve this goal, the Department of Education (DoE) introduced the establishment of School-Based Support Teams (SBSTs) whose main function is to support teaching and learning in schools. Nonetheless, there seems to be challenges on how to support learners experiencing barriers to learning among the members of the SBST. The aim of this study is to explore the perceptions of the SBSTs about providing support to the Foundation Phase (FP) teachers in two Butterworth Primary Schools in the Eastern Cape. This study used the qualitative mode of inquiry and a case study as a research design. Face-to face semi-structured interviews, observations and document analysis were used to collect the data from the SBSTs about their perceptions in providing support to the FP teachers. Data was analysed by identifying common themes. The findings revealed that the SBSTs do not have enough knowledge and skills on how to support the FP teachers. Some of the challenges they cited include inadequate training, lack of communication, overcrowding in classrooms, lack of support from the parents and from the Department of Education. In an attempt to alleviate the above raised challenges, a model has been proposed. , Thesis (D.Ed) -- Faculty of Education Sciences, 2020
- Full Text:
- Date Issued: 2017-11
- Authors: Luningo, Mziwonke
- Date: 2017-11
- Subjects: School support teams
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/11260/6668 , vital:47202
- Description: The Policy on Inclusive Education acknowledges that all children can learn if they are given the necessary support. In order to achieve this goal, the Department of Education (DoE) introduced the establishment of School-Based Support Teams (SBSTs) whose main function is to support teaching and learning in schools. Nonetheless, there seems to be challenges on how to support learners experiencing barriers to learning among the members of the SBST. The aim of this study is to explore the perceptions of the SBSTs about providing support to the Foundation Phase (FP) teachers in two Butterworth Primary Schools in the Eastern Cape. This study used the qualitative mode of inquiry and a case study as a research design. Face-to face semi-structured interviews, observations and document analysis were used to collect the data from the SBSTs about their perceptions in providing support to the FP teachers. Data was analysed by identifying common themes. The findings revealed that the SBSTs do not have enough knowledge and skills on how to support the FP teachers. Some of the challenges they cited include inadequate training, lack of communication, overcrowding in classrooms, lack of support from the parents and from the Department of Education. In an attempt to alleviate the above raised challenges, a model has been proposed. , Thesis (D.Ed) -- Faculty of Education Sciences, 2020
- Full Text:
- Date Issued: 2017-11
Perceptions of School Based Support Teams about Providing Support to Foundation Phase Teachers in Two Butterworth Primary Schools, Eastern Cape
- Authors: Luningo, Mziwonke
- Date: 2017-11
- Subjects: School Support Teams
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/11260/6653 , vital:47204
- Description: The Policy on Inclusive Education acknowledges that all children can learn if they are given the necessary support. In order to achieve this goal, the Department of Education (DoE) introduced the establishment of School-Based Support Teams (SBSTs) whose main function is to support teaching and learning in schools. Nonetheless, there seems to be challenges on how to support learners experiencing barriers to learning among the members of the SBST. The aim of this study is to explore the perceptions of the SBSTs about providing support to the Foundation Phase (FP) teachers in two Butterworth Primary Schools in the Eastern Cape. This study used the qualitative mode of inquiry and a case study as a research design. Face-to face semi-structured interviews, observations and document analysis were used to collect the data from the SBSTs about their perceptions in providing support to the FP teachers. Data was analysed by identifying common themes. The findings revealed that the SBSTs do not have enough knowledge and skills on how to support the FP teachers. Some of the challenges they cited include inadequate training, lack of communication, overcrowding in classrooms, lack of support from the parents and from the Department of Education. In an attempt to alleviate the above raised challenges, a model has been proposed. , Thesis (D.Ed) -- Faculty of Education Sciences, 2017
- Full Text:
- Date Issued: 2017-11
- Authors: Luningo, Mziwonke
- Date: 2017-11
- Subjects: School Support Teams
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/11260/6653 , vital:47204
- Description: The Policy on Inclusive Education acknowledges that all children can learn if they are given the necessary support. In order to achieve this goal, the Department of Education (DoE) introduced the establishment of School-Based Support Teams (SBSTs) whose main function is to support teaching and learning in schools. Nonetheless, there seems to be challenges on how to support learners experiencing barriers to learning among the members of the SBST. The aim of this study is to explore the perceptions of the SBSTs about providing support to the Foundation Phase (FP) teachers in two Butterworth Primary Schools in the Eastern Cape. This study used the qualitative mode of inquiry and a case study as a research design. Face-to face semi-structured interviews, observations and document analysis were used to collect the data from the SBSTs about their perceptions in providing support to the FP teachers. Data was analysed by identifying common themes. The findings revealed that the SBSTs do not have enough knowledge and skills on how to support the FP teachers. Some of the challenges they cited include inadequate training, lack of communication, overcrowding in classrooms, lack of support from the parents and from the Department of Education. In an attempt to alleviate the above raised challenges, a model has been proposed. , Thesis (D.Ed) -- Faculty of Education Sciences, 2017
- Full Text:
- Date Issued: 2017-11
Assessment of the water quality, incidence of enteric viruses and microbial risk in the Buffalo River in the Eastern Cape Province of South Africa
- Chigor, Vincent Nnamdigadi https://orcid.org/0000-0002-0811-4526
- Authors: Chigor, Vincent Nnamdigadi https://orcid.org/0000-0002-0811-4526
- Date: 2013-03
- Subjects: Water quality , Water -- Microbiology
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/24272 , vital:62596
- Description: Buffalo River is an important water resource in the Eastern Cape Province of South Africa. Over a 1-year period (August 2010–July 2011), the water quality and incidence of human enteric viruses (HEntVs) was assessed, using standard methods and molecular techniques and a total 72 composite water samples collected monthly from a total of 6 sites located on the river and three dams along its course. The sites were selected based on a number of factors including geographical location, anthropogenic activity/major water use, rural/urban status and access. A total of 13 physicochemical parameters were determined using the standard methods. The counts of faecal indicator bacteria (FIB) including total coliforms (TC), faecal coliforms (FC) and enterococci (ENT) were determined by the membrane filtration technique. HEntVs were concentrated using an adsorption-elution method based on cation (Al3+)-coated membrane filter. Real-time quantitative polymerase chain reaction (qPCR) was used for the detection and quantification of human adenoviruses (HAdV), and real-time reverse transcriptase-PCR (RT-qPCR) was used for the quantitative detection of hepatitis A virus (HAV), human rotaviruses (RoV) and enteroviruses (EnV). The detected HAdV were characterized by multiplex conventional/semi-nested PCR methods. The risks for human health constituted by exposure to the detected HEntVs at the six sites were evaluated by a static quantitative microbial risk assessment (QMRA) using both the exponential and beta-Poisson models. Water temperature ranged from 11 to 28oC, while pH varied from 6.6 to 10.7, and turbidity from 1.7 to 133 NTU. Electrical conductivity (EC), total dissolved solids (TDS) and salinity showed drastic variations (42.3-46693 μS/cm, 20.3–23350 mg/L and 0.02–33.8 PSU respectively). The concentrations of other parameters ranged as follows: chloride (3.7–168 mg/L); DO (6.9–11.1); BOD (0.6–9.4); COD (3.7–45.9); nitrite-nitrogen (0.02–0.21); nitrate-nitrogen (1–4.47); and orthophosphate (0.01–1.72). TC, FC and ENT counts were high and ranged from 1.9 × 102–3.8 × 107 cfu/100 mL, 0–3.0×105 cfu/100 mL and 0–5.3 × 105 cfu/100 mL for TC, FC and ENT respectively. Significantly (P<0.05) higher concentrations of FC and ENT were observed at the sampling sites located at the lower reaches of the river compared to the upper reaches. The FIB counts mostly exceeded the maximum limits recommended by national and international guidelines for safe fresh produce irrigation, domestic applications, full-contact recreation and livestock watering. Significant (P<0.01) positive correlations existed between TDS and salinity (r=0.921), between turbidity and each of TC (r=0.552) and FC (r=0.425), as well as between BOD and each of TC (r=0.282), FC (r=0.472) and ENT (r=0.552). Phosphate correlated positively with FC (r=0.424), and nitrate also with the same, FC (r=0.460). A strong positive correlation existed between FC and ENT (r=0.915). There existed a significant (P˂0.01) inverse correlation between enteric viruses and each of water temperature (r=-0.191) and pH (r=-0.234). No correlation could be deduced between enteric viruses and all the tested chemical and bacteriological parameters. HAV, HAdV, RoV and EnV were detected in 43.1percent, 34.7percent, 13.9percent and 9.7percent respectively of the total 72 water samples tested. Two or more viruses were detected in 22.2 percent of the samples. HAdV were detected at 5 of the 6 sampling sites with concentrations ranging from 1.2×101 genome copies (GC)/litre to 4.71×103 GC/litre. Epidemiologically important serotypes, Ad40/41 constituted 83.3percent, while Ad21 made up 16.7percent of all the HAdV detected. HAV was detected at all the sites in significantly (p < 0.05) varying concentrations that ranged from 1.5 × 101–1.9 × 105 GC/litre compared to RoV and EnV. Neither of RoV nor EnV was detected at any of the dams. The detected concentrations at the non-dam sites ranged from 2.5 × 101–2.1 × 103 GC/litre and 1.3 × 101–8.6 × 101 GC/litre for RoV and EnV respectively. The values for the estimated daily risks of enteric virus infection varied with sites and exposure scenario, and ranged from 7.31×10-3–1 (for HAdV), 4.23×10-2–6.54×10-1 (RoV), 2.32×10-4–1.73×10-1 (HAV) and 1.32×10-4–5.70×10-2 (EnV). The yearly risks of infection in individuals exposed to the river/dam water via drinking, recreational, domestic or irrigational activities were unacceptably high, exceeding the acceptable yearly risk of 0.01percent (10-4 infection/person/year) recommended by the USEPA for drinking water. The risks of illness and of death from infection ranged from 6.58×10-5–5.0×10-1 and 6.58×10-9–5.0×10-5 respectively. Data on the physicochemical and bacteriological parameters showed that the Buffalo River water quality was poor, and deteriorated in the plains compared to the upper reaches. These water quality data, the presence of enteric viruses and the QMRA data, that revealed unacceptably high risks of enteric virus infections, and of illness and mortality from the infections, show that the Buffalo River and its dams are contaminated waters that constitute significant public health hazards. Provision of adequate sanitary infrastructure will help prevent source water contamination, and public health education aimed at improving personal, household and community hygiene is imperative. Monitoring enteric viruses in rivers and source water dams is necessary and useful as a risk assessment tool for the exposed population. Future research should consider a comprehensive characterization of the detected viruses. This work is both a significant contribution to the molecular epidemiology of enteric viruses and the first report on molecular detection and quantification of enteric viruses in surface waters in the Eastern Cape. , Thesis (PhD) -- Faculty of Science and Agriculture, 2013
- Full Text:
- Date Issued: 2013-03
- Authors: Chigor, Vincent Nnamdigadi https://orcid.org/0000-0002-0811-4526
- Date: 2013-03
- Subjects: Water quality , Water -- Microbiology
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/24272 , vital:62596
- Description: Buffalo River is an important water resource in the Eastern Cape Province of South Africa. Over a 1-year period (August 2010–July 2011), the water quality and incidence of human enteric viruses (HEntVs) was assessed, using standard methods and molecular techniques and a total 72 composite water samples collected monthly from a total of 6 sites located on the river and three dams along its course. The sites were selected based on a number of factors including geographical location, anthropogenic activity/major water use, rural/urban status and access. A total of 13 physicochemical parameters were determined using the standard methods. The counts of faecal indicator bacteria (FIB) including total coliforms (TC), faecal coliforms (FC) and enterococci (ENT) were determined by the membrane filtration technique. HEntVs were concentrated using an adsorption-elution method based on cation (Al3+)-coated membrane filter. Real-time quantitative polymerase chain reaction (qPCR) was used for the detection and quantification of human adenoviruses (HAdV), and real-time reverse transcriptase-PCR (RT-qPCR) was used for the quantitative detection of hepatitis A virus (HAV), human rotaviruses (RoV) and enteroviruses (EnV). The detected HAdV were characterized by multiplex conventional/semi-nested PCR methods. The risks for human health constituted by exposure to the detected HEntVs at the six sites were evaluated by a static quantitative microbial risk assessment (QMRA) using both the exponential and beta-Poisson models. Water temperature ranged from 11 to 28oC, while pH varied from 6.6 to 10.7, and turbidity from 1.7 to 133 NTU. Electrical conductivity (EC), total dissolved solids (TDS) and salinity showed drastic variations (42.3-46693 μS/cm, 20.3–23350 mg/L and 0.02–33.8 PSU respectively). The concentrations of other parameters ranged as follows: chloride (3.7–168 mg/L); DO (6.9–11.1); BOD (0.6–9.4); COD (3.7–45.9); nitrite-nitrogen (0.02–0.21); nitrate-nitrogen (1–4.47); and orthophosphate (0.01–1.72). TC, FC and ENT counts were high and ranged from 1.9 × 102–3.8 × 107 cfu/100 mL, 0–3.0×105 cfu/100 mL and 0–5.3 × 105 cfu/100 mL for TC, FC and ENT respectively. Significantly (P<0.05) higher concentrations of FC and ENT were observed at the sampling sites located at the lower reaches of the river compared to the upper reaches. The FIB counts mostly exceeded the maximum limits recommended by national and international guidelines for safe fresh produce irrigation, domestic applications, full-contact recreation and livestock watering. Significant (P<0.01) positive correlations existed between TDS and salinity (r=0.921), between turbidity and each of TC (r=0.552) and FC (r=0.425), as well as between BOD and each of TC (r=0.282), FC (r=0.472) and ENT (r=0.552). Phosphate correlated positively with FC (r=0.424), and nitrate also with the same, FC (r=0.460). A strong positive correlation existed between FC and ENT (r=0.915). There existed a significant (P˂0.01) inverse correlation between enteric viruses and each of water temperature (r=-0.191) and pH (r=-0.234). No correlation could be deduced between enteric viruses and all the tested chemical and bacteriological parameters. HAV, HAdV, RoV and EnV were detected in 43.1percent, 34.7percent, 13.9percent and 9.7percent respectively of the total 72 water samples tested. Two or more viruses were detected in 22.2 percent of the samples. HAdV were detected at 5 of the 6 sampling sites with concentrations ranging from 1.2×101 genome copies (GC)/litre to 4.71×103 GC/litre. Epidemiologically important serotypes, Ad40/41 constituted 83.3percent, while Ad21 made up 16.7percent of all the HAdV detected. HAV was detected at all the sites in significantly (p < 0.05) varying concentrations that ranged from 1.5 × 101–1.9 × 105 GC/litre compared to RoV and EnV. Neither of RoV nor EnV was detected at any of the dams. The detected concentrations at the non-dam sites ranged from 2.5 × 101–2.1 × 103 GC/litre and 1.3 × 101–8.6 × 101 GC/litre for RoV and EnV respectively. The values for the estimated daily risks of enteric virus infection varied with sites and exposure scenario, and ranged from 7.31×10-3–1 (for HAdV), 4.23×10-2–6.54×10-1 (RoV), 2.32×10-4–1.73×10-1 (HAV) and 1.32×10-4–5.70×10-2 (EnV). The yearly risks of infection in individuals exposed to the river/dam water via drinking, recreational, domestic or irrigational activities were unacceptably high, exceeding the acceptable yearly risk of 0.01percent (10-4 infection/person/year) recommended by the USEPA for drinking water. The risks of illness and of death from infection ranged from 6.58×10-5–5.0×10-1 and 6.58×10-9–5.0×10-5 respectively. Data on the physicochemical and bacteriological parameters showed that the Buffalo River water quality was poor, and deteriorated in the plains compared to the upper reaches. These water quality data, the presence of enteric viruses and the QMRA data, that revealed unacceptably high risks of enteric virus infections, and of illness and mortality from the infections, show that the Buffalo River and its dams are contaminated waters that constitute significant public health hazards. Provision of adequate sanitary infrastructure will help prevent source water contamination, and public health education aimed at improving personal, household and community hygiene is imperative. Monitoring enteric viruses in rivers and source water dams is necessary and useful as a risk assessment tool for the exposed population. Future research should consider a comprehensive characterization of the detected viruses. This work is both a significant contribution to the molecular epidemiology of enteric viruses and the first report on molecular detection and quantification of enteric viruses in surface waters in the Eastern Cape. , Thesis (PhD) -- Faculty of Science and Agriculture, 2013
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- Date Issued: 2013-03
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