{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:45:03Z","timestamp":1792025103915,"version":"4.4.0"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"4","funder":[{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Broad Agency Announcement","award":["FY2018-OADS-01"],"award-info":[{"award-number":["FY2018-OADS-01"]}]},{"name":"Broad Agency Announcement","award":["75D30118C02919"],"award-info":[{"award-number":["75D30118C02919"]}]},{"name":"Prevention of Healthcare Associated Infections"},{"DOI":"10.13039\/100016263","name":"Penn Center for AIDS Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016263","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P30 AI 045008"],"award-info":[{"award-number":["P30 AI 045008"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Although extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) are a global health challenge, molecular data from low- and middle-income countries are limited. We used whole-genome sequencing to characterize ESCrE in community and healthcare settings in Botswana.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Study isolates were collected from 3 hospitals and 6 outpatient clinics in Botswana, as well as from adults and children in the community. Enrollment occurred from 15 January to 4 September 2020 but was paused from 2 April to 21 May 2020 due to a countrywide coronavirus disease 2019 (COVID-19) lockdown. Isolates from rectal swab specimens obtained from participants testing positive for ESCrE underwent whole-genome sequencing. Genomic data were analyzed to characterize resistance genes, sequence types (STs), and exposures associated with putative interpersonal transmission.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Escherichia coli and Klebsiella pneumoniae ESCrE were diverse, represented by 87 and 49 STs, respectively, carrying 16 distinct extended-spectrum \u03b2-lactamase (ESBL) gene alleles. Twelve E. coli STs accounted for most isolates, with these common STs observed in both community and healthcare settings and increasing in the proportion after lockdown (from 61% to 80%). Examination of factors associated with harboring genetically similar E. coli revealed shared household and social networks across lockdown periods, with differences in shared hospital exposure and participant age between lockdown periods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Genomic characterization of ESCrE in Botswana revealed diverse STs carrying common ESBL genes, with overlapping STs among hospital and community participants consistent with intersecting transmission networks. Risk analysis of transmission supported the role of direct human contact, with the COVID-19 lockdown affecting the diversity of ESCrE and transmission pathways, highlighting the potential for behavioral changes to affect ESCrE spread.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/infdis\/jiag342","type":"journal-article","created":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:01:43Z","timestamp":1783382503000},"page":"e996-e1008","source":"Crossref","is-referenced-by-count":0,"title":["Diverse Genetic Lineages Spreading Across Healthcare and Community Boundaries Underlie Extended-Spectrum Cephalosporin-Resistant Enterobacterales Colonization Burden in Botswana"],"prefix":"10.1093","volume":"234","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8446-3114","authenticated-orcid":false,"given":"Tiffany","family":"Wan","sequence":"first","affiliation":[{"name":"Department of Microbiology & Immunology, University of Michigan Medical School , Ann Arbor, Michigan ,","place":["USA"]},{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan Medical School , Ann Arbor, Michigan ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4772-2409","authenticated-orcid":false,"given":"Ebbing","family":"Lautenbach","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania ,","place":["USA"]},{"name":"Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania ,","place":["USA"]},{"name":"Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naledi","family":"Mannathoko","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Botswana , Gaborone ,","place":["Botswana"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6051-0999","authenticated-orcid":false,"given":"Mosepele","family":"Mosepele","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, University of Botswana , Gaborone ,","place":["Botswana"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4682-8087","authenticated-orcid":false,"given":"Ashley","family":"Styczynski","sequence":"additional","affiliation":[{"name":"Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention (CDC) , Atlanta, Georgia ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gemma","family":"Parra","sequence":"additional","affiliation":[{"name":"Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention (CDC) , Atlanta, Georgia ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel M","family":"Smith","sequence":"additional","affiliation":[{"name":"Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention (CDC) , Atlanta, Georgia ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Gross","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania ,","place":["USA"]},{"name":"Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania ,","place":["USA"]},{"name":"Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leigh","family":"Cressman","sequence":"additional","affiliation":[{"name":"Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Jaskowiak-Barr","sequence":"additional","affiliation":[{"name":"Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 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