Potgieter, N.Traore, A. N.Kabue, J. P.Munzhedzi, Lutendo2021-02-032021-02-032020-03Munzhedzi, Lutendo (2020) Characterization of diarrhoeagenic escherichia coli and human norovirus from daycare centres in the Vhembe Region of the Limpopo Province. University of Venda, South Africa.<http://hdl.handle.net/11602/1666>.http://hdl.handle.net/11602/1666MSc (Microbiology)Department of MicrobiologyBACKGROUND: Child daycare centers (DCCs) host a variety of pathogenic enteric microorganisms which may be found in various areas within the compound. Enteric pathogens are the most common cause of diarrhoea worldwide in children under the age of 5 years and are a burden in developing countries with high numbers of diarrhoeal diseases leading to a high mortality rate. OBJECTIVE: To perform a pilot study to characterize diarrhoeagenic E. coli and Norovirus strains from child daycare centers in the Vhembe Region in Limpopo Province, South Africa. MATERIALS AND METHODS: Two daycare centers were randomly selected in the Vhembe District for this study. A total of 83 samples were collected from various areas within the daycare centers. For E. coli, the environmental and handwash samples were analysed using the Colilert®/ Quanti-tray® 2000 technique and stool samples were cultured on Eosin Methylene Blue agar: presumptive E. coli isolates were confirmed using three biochemical tests (Kliglers Iron Agar test, Indole test and Urease test). Total nucleic acid was extracted from presumptive E. coli isolates using a semiautomated method and DNA was used for further m-PCR confirmation. For human norovirus identification, environmental and handwash samples were subjected to membrane filtration and RNA was extracted using the semi-automated system. RNA was extracted from stool samples (clinical samples) using the Allprep® Powerfecal® RNA Kit. For detection of Norovirus, RNA extracts were subjected to the Seegene Allplex™ Gastrointestinal Full Panel Assay. Positive samples for Norovirus were amplified using a One-step Ahead RT-PCR followed by Sanger sequencing. Phylogenetic analysis was done using MEGA 7 software. RESULTS: E. coli was isolated from the environmental samples (10%), stool samples (100%), handwash samples of daycare workers (40%) and handwash samples of children (13.6%); several bacterial co-infections among pathotypes were observed. Norovirus prevalence in this study, was detected in 5% of handwash samples of the children, 10% from handwash samples of the workers and 27% were stool specimens. All detected samples were co-infection between bacterial pathotypes (90.4%) as well xi as bacterial-viral co-infections (9.6%). Norovirus genotype GII.1 was shown through sequencing of one positive sample. CONCLUSION: The study findings showed genetic diversity of E. coli in these settings. The phylogenetic analysis revealed NoV genotype GII.I capsid sequenced to share a common ancestor with previously reported strains associated with outbreaks of NoV globally. The high prevalence of E. coli and NoV detected in this study will aid in setting guidelines for hygiene in the DCC environment.1 online resource (xi, 87 leaves : color illustrations, color map)enUniversity of VendaE. coliUCTDDaycare centersNorovirusEnteric pathogensDissertationMunzhedzi L. Characterization of diarrhoeagenic escherichia coli and human norovirus from daycare centres in the Vhembe Region of the Limpopo Province. []. , 2020 [cited yyyy month dd]. Available from: http://hdl.handle.net/11602/1666Munzhedzi, L. (2020). <i>Characterization of diarrhoeagenic escherichia coli and human norovirus from daycare centres in the Vhembe Region of the Limpopo Province</i>. (). . Retrieved from http://hdl.handle.net/11602/1666Munzhedzi, Lutendo. <i>"Characterization of diarrhoeagenic escherichia coli and human norovirus from daycare centres in the Vhembe Region of the Limpopo Province."</i> ., , 2020. http://hdl.handle.net/11602/1666TY - Dissertation AU - Munzhedzi, Lutendo AB - BACKGROUND: Child daycare centers (DCCs) host a variety of pathogenic enteric microorganisms which may be found in various areas within the compound. Enteric pathogens are the most common cause of diarrhoea worldwide in children under the age of 5 years and are a burden in developing countries with high numbers of diarrhoeal diseases leading to a high mortality rate. OBJECTIVE: To perform a pilot study to characterize diarrhoeagenic E. coli and Norovirus strains from child daycare centers in the Vhembe Region in Limpopo Province, South Africa. MATERIALS AND METHODS: Two daycare centers were randomly selected in the Vhembe District for this study. A total of 83 samples were collected from various areas within the daycare centers. For E. coli, the environmental and handwash samples were analysed using the Colilert®/ Quanti-tray® 2000 technique and stool samples were cultured on Eosin Methylene Blue agar: presumptive E. coli isolates were confirmed using three biochemical tests (Kliglers Iron Agar test, Indole test and Urease test). Total nucleic acid was extracted from presumptive E. coli isolates using a semiautomated method and DNA was used for further m-PCR confirmation. For human norovirus identification, environmental and handwash samples were subjected to membrane filtration and RNA was extracted using the semi-automated system. RNA was extracted from stool samples (clinical samples) using the Allprep® Powerfecal® RNA Kit. For detection of Norovirus, RNA extracts were subjected to the Seegene Allplex™ Gastrointestinal Full Panel Assay. Positive samples for Norovirus were amplified using a One-step Ahead RT-PCR followed by Sanger sequencing. Phylogenetic analysis was done using MEGA 7 software. RESULTS: E. coli was isolated from the environmental samples (10%), stool samples (100%), handwash samples of daycare workers (40%) and handwash samples of children (13.6%); several bacterial co-infections among pathotypes were observed. Norovirus prevalence in this study, was detected in 5% of handwash samples of the children, 10% from handwash samples of the workers and 27% were stool specimens. All detected samples were co-infection between bacterial pathotypes (90.4%) as well xi as bacterial-viral co-infections (9.6%). Norovirus genotype GII.1 was shown through sequencing of one positive sample. CONCLUSION: The study findings showed genetic diversity of E. coli in these settings. The phylogenetic analysis revealed NoV genotype GII.I capsid sequenced to share a common ancestor with previously reported strains associated with outbreaks of NoV globally. The high prevalence of E. coli and NoV detected in this study will aid in setting guidelines for hygiene in the DCC environment. DA - 2020-03 DB - ResearchSpace DP - Univen KW - E. coli KW - Daycare centers KW - Norovirus KW - Enteric pathogens LK - https://univendspace.univen.ac.za PY - 2020 T1 - Characterization of diarrhoeagenic escherichia coli and human norovirus from daycare centres in the Vhembe Region of the Limpopo Province TI - Characterization of diarrhoeagenic escherichia coli and human norovirus from daycare centres in the Vhembe Region of the Limpopo Province UR - http://hdl.handle.net/11602/1666 ER -