{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T17:17:12Z","timestamp":1791566232727,"version":"4.3.4"},"reference-count":52,"publisher":"Microbiology Society","issue":"3","license":[{"start":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T00:00:00Z","timestamp":1646092800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["109105z\/15\/a"],"award-info":[{"award-number":["109105z\/15\/a"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,1]]},"abstract":"\n Members of the\n \n \n Klebsiella pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n species complex, particularly\n \n \n K. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n subsp.\n \n \n pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n are antimicrobial resistance (AMR) associated pathogens of global importance, and polyvalent vaccines targeting\n \n \n Klebsiella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n O-antigens are in development. Whole-genome sequencing has provided insight into O-antigen distribution in the\n \n \n K. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n species complex\n ,<\/jats:italic>\n as well as population structure and virulence determinants, but genomes from sub-Saharan Africa are underrepresented in global sequencing efforts. We therefore carried out a genomic analysis of extended-spectrum beta-lactamase (ESBL)-producing\n \n \n K. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n species complex isolates colonizing adults in Blantyre, Malawi. We placed these isolates in a global genomic context, and compared colonizing to invasive isolates from the main public hospital in Blantyre. In total, 203 isolates from stool and rectal swabs from adults were whole-genome sequenced and compared to a publicly available multicounty collection and previously sequenced Malawian and Kenyan isolates from blood or sterile sites. We inferred phylogenetic relationships and analysed the diversity of genetic loci linked to AMR, virulence, capsule and LPS O-antigen (O-types). We find that the diversity of Malawian\n \n \n K. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n subsp.\n \n \n pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n isolates represents the species\u2019 population structure, but shows distinct local signatures concerning clonal expansions. Siderophore and hypermucoidy genes were more frequent in invasive versus colonizing isolates (present in 13\u200a% vs 1\u200a%) but still generally lacking in most invasive isolates. O-antigen population structure and distribution was similar in invasive and colonizing isolates, with O4 more common (14%) than in previously published studies (2\u20135\u200a%). We conclude that host factors, pathogen opportunity or alternate virulence loci not linked to invasive disease elsewhere are likely to be the major determinants of invasive disease in Malawi. Distinct ST and O-type distributions in Malawi highlight the need to sample locations where the burden of invasive\n \n \n Klebsiella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n disease is greatest to robustly define secular trends in\n \n \n Klebsiella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n diversity to assist in the development of a useful vaccine. Colonizing and invasive isolates in Blantyre are similar, hence O-typing of colonizing\n \n \n Klebsiella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n isolates may be a rapid and cost-effective approach to describe global diversity and guide vaccine development.\n <\/jats:p>","DOI":"10.1099\/mgen.0.000778","type":"journal-article","created":{"date-parts":[[2022,3,18]],"date-time":"2022-03-18T09:16:33Z","timestamp":1647594993000},"source":"Crossref","is-referenced-by-count":16,"title":["Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi"],"prefix":"10.1099","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3837-5188","authenticated-orcid":false,"given":"Joseph M.","family":"Lewis","sequence":"first","affiliation":[{"name":"Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi"},{"name":"Liverpool School of Tropical Medicine, Liverpool, UK"},{"name":"University of Liverpool, Liverpool, UK"},{"name":"Wellcome Sanger Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madalitso","family":"Mphasa","sequence":"additional","affiliation":[{"name":"Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Banda","sequence":"additional","affiliation":[{"name":"Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathew A.","family":"Beale","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Mallewa","sequence":"additional","affiliation":[{"name":"Kamuzu University of Health Sciences, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Heinz","sequence":"additional","affiliation":[{"name":"Liverpool School of Tropical Medicine, Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas R.","family":"Thomson","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, UK"},{"name":"Wellcome Sanger Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas A.","family":"Feasey","sequence":"additional","affiliation":[{"name":"Liverpool School of Tropical Medicine, Liverpool, UK"},{"name":"London School of Hygiene and Tropical Medicine, London, UK"},{"name":"Kamuzu University of Health Sciences, Blantyre, Malawi"},{"name":"Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cix270"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0315-1"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(19)30414-1"},{"key":"R4","volume-title":"Prioritization of Pathogens to Guide Discovery, Research and Development of New Antibiotics for Drug-Resistant Bacterial Infections, Including Tuberculosis","year":"2017"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa162"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1093\/jacamr\/dlab087"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1186\/s13756-020-00809-3"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(17)30394-8"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-021-00870-7"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1501049112"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000196"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00089-19"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-019-0706-y"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00001-19"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1080\/14760584.2019.1635460"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000073"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000102"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.01249"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00489-17"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0492-8"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1101\/2021.10.08.21264775"},{"key":"R22","article-title":"2018 Malawi Population and Housing Census Main Report","year":"2019","journal-title":"Zomba"},{"key":"R23","volume-title":"Consolidated Guidelines On the Use of Antiretroviral Drugs for Treating and Preventing HIV Infection: Recommendations for a Public Health Approach. 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