{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T02:59:06Z","timestamp":1778295546950,"version":"3.51.4"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.15514.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,1,24]],"date-time":"2020-01-24T00:00:00Z","timestamp":1579824000000}}],"reference-count":43,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2020,1,24]],"date-time":"2020-01-24T00:00:00Z","timestamp":1579824000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/S004793\/1"],"award-info":[{"award-number":["MR\/S004793\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["204059"],"award-info":[{"award-number":["204059"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["109105"],"award-info":[{"award-number":["109105"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns4:p><ns4:bold>Background<\/ns4:bold>: Extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) threaten human health; and, in areas of sub-Saharan Africa (sSA) where carbapenems are not available, may render ESBL-E infections untreatable. Gut mucosal colonisation probably occurs before infection, making prevention of colonisation an attractive target for intervention, but the epidemiology of ESBL-E in sSA is poorly described.<\/ns4:p><ns4:p> <ns4:bold>Objectives<\/ns4:bold>: Describe ESBL-E colonisation prevalence in sSA and risk factors associated with colonisation.<\/ns4:p><ns4:p> <ns4:bold>Methods:<\/ns4:bold> Studies included were prospective cross-sectional or cohort studies reporting gut mucosal ESBL-E colonisation in any population in sSA. We searched PubMed and Scopus on 18 December 2018. We summarise the range of prevalence across sites and tabulated risk factors for colonisation. The protocol was registered (Prospero ID <ns4:ext-link xmlns:ns3=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" ns3:href=\"https:\/\/www.crd.york.ac.uk\/PROSPERO\/display_record.php?RecordID=123559\">CRD42019123559<\/ns4:ext-link>).<\/ns4:p><ns4:p> <ns4:bold>Results:<\/ns4:bold> From 2975 abstracts we identified 32 studies including a total of 8619 participants from a range of countries and settings. Six studies were longitudinal; no longitudinal studies followed patients beyond hospital discharge.\u00a0 Prevalence varied between 5 and 84% with a median of 31%, with a relationship to setting: pooled ESBL-E colonisation in community studies was 18% (95% CI 12 to 28, 12 studies); in studies recruiting people at admission to hospital colonisation was 32% (95% CI 24 to 41% 8 studies); and for inpatients, colonisation was 55% (95% CI 49 to 60%, 7 studies). Antimicrobial use was associated with increased risk of ESBL-E colonisation, and protected water sources or water treatment by boiling may reduce risk.<\/ns4:p><ns4:p> <ns4:bold>Conclusions:<\/ns4:bold> ESBL-E colonisation is common in sSA, but how people become carriers and why is not well understood. To inform the design of interventions to interrupt transmission in this setting requires longitudinal, community studies.<\/ns4:p>","DOI":"10.12688\/wellcomeopenres.15514.2","type":"journal-article","created":{"date-parts":[[2020,1,24]],"date-time":"2020-01-24T15:00:11Z","timestamp":1579878011000},"page":"160","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["Gut mucosal colonisation with extended-spectrum beta-lactamase producing Enterobacteriaceae in sub-Saharan Africa: a systematic review and meta-analysis"],"prefix":"10.12688","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3837-5188","authenticated-orcid":false,"given":"Joseph M.","family":"Lewis","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0259-9630","authenticated-orcid":false,"given":"Rebecca","family":"Lester","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0607-6941","authenticated-orcid":false,"given":"Paul","family":"Garner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4041-1405","authenticated-orcid":false,"given":"Nicholas A.","family":"Feasey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2020,1,24]]},"reference":[{"key":"ref-1","article-title":"Prioritization of pathogens to guide discovery, research and development of new antibiotics for drug-resistant bacterial infections, including 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in sub-Saharan Africa: a systematic review and meta-analysis (Version v1.0).","author":"J Lewis","year":"2019","journal-title":"Zenodo."}],"container-title":["Wellcome Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,21]],"date-time":"2020-10-21T17:20:09Z","timestamp":1603300809000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,24]]},"references-count":43,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.15514.2","relation":{},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,1,24]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.16981.r36859, Samuel Kariuki, Centre for Microbiology Research, Kenya Medical Research Institute\u00a0(KEMRI), Nairobi, Kenya, 06 Nov 2019, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v1#referee-response-36859","order":0,"name":"referee-response-36859","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Joseph Lewis<\/b>; \n<i>Posted: 23 Jan 2020<\/i>; We thank the reviewer for their review, and agree that the available data are scanty and it is not at all clear that the findings are generalisable across the diverse countries of sub-Saharan Africa, especially as some countries are over-represented in the dataset. We have amended the limitations section of our manuscript to highlight the lack of data and, in particular, that the role of animal to human transmission and HIV infection play in driving ESBL-E colonisation in sSA is unclear.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v2#referee-comment-4064","order":1,"name":"referee-comment-4064","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.16981.r37453, Vincent Richard, International Department, Institut Pasteur, Paris, France, 10 Jan 2020, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v1#referee-response-37453","order":2,"name":"referee-response-37453","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Joseph Lewis<\/b>; \n<i>Posted: 23 Jan 2020<\/i>; We thank the reviewer for their review, and agree that systematic WaSH interventions are likely crucial for tackling antimicrobial resistance in sSA.&nbsp;2943 studies were excluded at the abstract review stage, largely because they were not relevant to the subject of the review (i.e. were not concerned with ESBL-E carriage at all); others did not take place in sSA, or were review articles, case reports, or studies looking at invasive ESBL-E infection. Unfortunately we did not capture the reasons for rejection for each abstract.&nbsp;We agree that risk factors for ESBL-E carriage are likely to be context dependent across the diverse settings of sSA. We also agree that there are a number of risk factors (including livestock) that are not explored as potential drivers of ESBL-E carriage in the available studies, and hence their role is not clear. We have amended the limitations section to highlight this.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v2#referee-comment-4063","order":3,"name":"referee-comment-4063","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Joseph Lewis<\/b>; \n<i>Posted: 18 Oct 2020<\/i>; Analysis code for this manuscript is available at&nbsp;https:\/\/github.com\/joelewis101\/esbl_ssa","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-160\/v2#article-response-4392","order":4,"name":"article-response-4392","label":"Article Comment","group":{"name":"article-comments","label":"Article Comments"}},{"value":"JL and RL are supported by Wellcome Trust Clinical PhD Fellowships (109105z\/15\/a and University of Liverpool block award 347 [203919\/Z\/16\/Z] respectively). NF is funded by the Antimicrobial Resistance Cross-Council Initiative through a grant from the Medical Research Council, a Council of UK Research and Innovation, and the National Institute for Health Research. This award is part of the EDCTP2 programme supported by the European Union (Grant number MR\/S004793\/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":5,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}