Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa

dc.contributor.authorSmith, Anthony Marius
dc.contributor.authorRamudzulu, Masindi
dc.contributor.authorMunk, Patrick
dc.contributor.authorAvot, Baptiste J.P.
dc.contributor.authorEsterhuyse, Kerneels C.M.
dc.contributor.authorVan Blerk, Nico
dc.contributor.authorKwendaI, Stanford
dc.contributor.authorSekwadi, Phuti
dc.date.accessioned2025-05-22T12:35:11Z
dc.date.available2025-05-22T12:35:11Z
dc.date.issued2024-08-26
dc.descriptionDATA AVAILABILITY STATEMENT : All metagenomics sequencing data for samples can be found at the European Nucleotide Archive under BioProject number PRJEB70907.
dc.description.abstractOur 24-month study used metagenomics to investigate antimicrobial resistance (AMR) abundance in raw sewage from wastewater treatment works (WWTWs) in two municipalities in Gauteng Province, South Africa. At the AMR class level, data showed similar trends at all WWTWs, showing that aminoglycoside, beta-lactam, sulfonamide and tetracycline resistance was most abundant. AMR abundance differences were shown between municipalities, where Tshwane Metropolitan Municipality (TMM) WWTWs showed overall higher abundance of AMR compared to Ekurhuleni Metropolitan Municipality (EMM) WWTWs. Also, within each municipality, there were differing trends in AMR abundance. Notably, within TMM, certain AMR classes (macrolides and macrolides_streptogramin B) were in higher abundance at a WWTW serving an urban high-income area, while other AMR classes (aminoglycosides) were in higher abundance at a WWTW serving a semi-urban low income area. At the AMR gene level, all WWTWs samples showed the most abundance for the sul1 gene (encoding sulfonamide resistance). Following this, the next 14 most abundant genes encoded resistance to sulfonamides, aminoglycosides, macrolides, tetracyclines and beta-lactams. Notably, within TMM, some macrolide-encoding resistance genes (mefC, msrE, mphG and mphE) were in highest abundance at a WWTW serving an urban high-income area; while sul1, sul2 and tetC genes were in highest abundance at a WWTW serving a semi-urban low income area. Differential abundance analysis of AMR genes at WWTWs, following stratification of data by season, showed some notable variance in six AMR genes, of which blaKPC-2 and blaKPC-34 genes showed the highest prevalence of seasonal abundance differences when comparing data within a WWTW. The general trend was to see higher abundances of AMR genes in colder seasons, when comparing seasonal data within a WWTW. Our study investigated wastewater samples in only one province of South Africa, from WWTWs located within close proximity to one another. We would require a more widespread investigation at WWTWs distributed across all regions/provinces of South Africa, in order to describe a more comprehensive profile of AMR abundance across the country.
dc.description.departmentMedical Microbiology
dc.description.librarianam2025
dc.description.sdgSDG-03: Good health and well-being
dc.description.sponsorshipFUNDING : Research reported in this publication was supported by South African Medical Research Council (SAMRC) as a sub-grant received from the Bill and Melinda Gates Foundation.
dc.description.urihttps://journals.plos.org/plosone/
dc.identifier.citationSmith, A.M., Ramudzulu, M., Munk, P., Avot, B.J.P., Esterhuyse, K.C.M., Van Blerk, N., et al. (2024) Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa. PLoS ONE 19(8): e0309409. https://doi.org/10.1371/journal.pone.0309409.
dc.identifier.issn1932-6203 (online)
dc.identifier.other10.1371/journal.pone.0309409
dc.identifier.urihttp://hdl.handle.net/2263/102481
dc.language.isoen
dc.publisherPublic Library of Science
dc.rights© 2024 Smith et al. This is an open access article distributed under the terms of the Creative Commons Attribution License.
dc.subjectAntimicrobial resistance (AMR)
dc.subjectRaw sewage
dc.subjectWastewater treatment works (WWTW)
dc.subjectGauteng Province, South Africa
dc.subjectEkurhuleni Metropolitan Municipality (EMM)
dc.subjectTshwane Metropolitan Municipality (TMM)
dc.titleMetagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa
dc.typeArticle

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