{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T15:51:59Z","timestamp":1786117919485,"version":"build-2736575974"},"reference-count":43,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,8,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Antimicrobial resistance, particularly to carbapenems, represents a major global public health threat. In Senegal, the increasing prevalence of carbapenem-resistant Gram-negative bacilli compromises the management of severe infections. This study, conducted between October 2022 and March 2024 at the Centre Hospitalier National Universitaire de Fann and the Institut Pasteur de Dakar, investigated 50 carbapenem-resistant bacterial isolates. Species identification was performed using Vitek 2 and MALDI-TOF MS, and antimicrobial susceptibility was assessed by disk diffusion testing. Whole-genome sequencing enabled the detection of resistance genes, plasmid replicons, and clonal lineages through MLST analysis. Among the 50 isolates, 35 (70%) carried at least one carbapenemase gene. The\n                      <jats:italic toggle=\"yes\">\n                        bla\n                        <jats:sub>NDM-5<\/jats:sub>\n                      <\/jats:italic>\n                      gene was the most frequent (15\/35; 42.9%), followed by\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic toggle=\"yes\">OXA-181<\/jats:italic>\n                      <\/jats:sub>\n                      (20.0%),\n                      <jats:italic toggle=\"yes\">\n                        bla\n                        <jats:sub>NDM-1<\/jats:sub>\n                      <\/jats:italic>\n                      (14.3%), and\n                      <jats:italic toggle=\"yes\">\n                        bla\n                        <jats:sub>OXA-484<\/jats:sub>\n                      <\/jats:italic>\n                      (11.4%). Co-occurrences of carbapenemase genes were observed (17.1%), including\n                      <jats:italic toggle=\"yes\">\n                        bla\n                        <jats:sub>NDM-5<\/jats:sub>\n                        + blaOXA\n                        <jats:sub>OXA-181<\/jats:sub>\n                        , bla\n                        <jats:sub>OXA-23<\/jats:sub>\n                        + blaOXA\n                        <jats:sub>OXA-68<\/jats:sub>\n                        ,\n                      <\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">\n                        bla\n                        <jats:sub>OXA-70<\/jats:sub>\n                        + blaOXA\n                        <jats:sub>OXA-420<\/jats:sub>\n                      <\/jats:italic>\n                      . These isolates extensively co-harbored other resistance determinants, most notably the\n                      <jats:italic toggle=\"yes\">\n                        bla\n                        <jats:sub>CTX-M-15<\/jats:sub>\n                      <\/jats:italic>\n                      extended-spectrum \u03b2-lactamase (ESBL) gene. Genes conferring high-level resistance to aminoglycosides (\n                      <jats:italic toggle=\"yes\">rmtB, armA<\/jats:italic>\n                      ) and quinolones [\n                      <jats:italic toggle=\"yes\">aac(6\u2032)-Ib-cr, qnrA, qnrB<\/jats:italic>\n                      ] were also identified. The predominant plasmid types were IncF (91.4%) and Col (62.9%). MLST analysis showed that, in this study collection (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 35),\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      ST410 (7\/35; 20.0%) and ST648 (3\/35; 8.6%), as well as\n                      <jats:italic toggle=\"yes\">Klebsiella pneumoniae<\/jats:italic>\n                      ST307 (3\/35; 8.6%) and ST147 (2\/35; 5.7%), were the most frequently detected sequence types. Notably, this study reports the first detection of the\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic toggle=\"yes\">VEB-6<\/jats:italic>\n                      <\/jats:sub>\n                      gene in Senegal. These findings highlight the circulation of multidrug-resistant clones harboring carbapenemase genes and underscore the urgent need to strengthen surveillance and infection control measures in Senegalese hospitals.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Carbapenem resistance among Gram-negative bacilli represents a global public health emergency, particularly in resource-limited settings where therapeutic options are scarce. In Senegal, data on the genetic mechanisms underlying this resistance remain limited. This study is among the few that have employed whole-genome sequencing to characterize carbapenemase-producing bacteria. The identification of high-risk clones, such as\n                        <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                        ST410 and\n                        <jats:italic toggle=\"yes\">Klebsiella pneumoniae<\/jats:italic>\n                        ST307, along with the first detection of the\n                        <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                        <jats:sub>\n                          <jats:italic toggle=\"yes\">VEB-6<\/jats:italic>\n                        <\/jats:sub>\n                        gene in Senegal, highlights the local spread of multidrug-resistant lineages. By combining phenotypic and genomic analyses, this research provides essential insights to strengthen genomic surveillance, optimize antibiotic use, and improve infection prevention and control strategies in Senegalese hospitals.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03704-25","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T13:02:54Z","timestamp":1784206974000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Whole-genome sequencing analysis of clinical carbapenemase-producing bacteria isolated in Dakar, Senegal"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-4388-3642","authenticated-orcid":true,"given":"Moustoifa","family":"Ibrahim","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04je6yw13","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Animal Biology, Faculty of Science and Technology, Cheikh Anta Diop University of Dakar","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheikh","family":"Ibrahima Lo","sequence":"additional","affiliation":[{"name":"Microbiology pole Institut Pasteur de Dakar","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatoumata","family":"Diallo","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04fp9fm22","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Bacteriology-Virology, National University Hospital Center of Fann","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Komla Mawunyo","family":"Dossouvi","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Genomics, Global Health Research Institute of Lom\u00e9","place":["Lom\u00e9, Togo"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ousmane","family":"Sadio","sequence":"additional","affiliation":[{"name":"Microbiology pole Institut Pasteur de Dakar","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adja Bousso","family":"Gueye","sequence":"additional","affiliation":[{"name":"Microbiology pole Institut Pasteur de Dakar","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5461-5623","authenticated-orcid":true,"given":"Moussa Moise","family":"Diagne","sequence":"additional","affiliation":[{"name":"Virology pole Institut Pasteur de Dakar","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Safi\u00e9tou","family":"Sanghe","sequence":"additional","affiliation":[{"name":"Virology pole Institut Pasteur de Dakar","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madiagne","family":"Der","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04fp9fm22","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Bacteriology-Virology, National University Hospital Center of Fann","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yakhya","family":"Dieye","sequence":"additional","affiliation":[{"name":"Microbiology pole Institut Pasteur de Dakar","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mouhamadou Lamine","family":"Dia","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04fp9fm22","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Bacteriology-Virology, National University Hospital Center of Fann","place":["Dakar, Senegal"]},{"id":[{"id":"https:\/\/ror.org\/04je6yw13","id-type":"ROR","asserted-by":"publisher"}],"name":"Faculty of Medicine, Pharmacy, and Dentistry, Cheikh Anta Diop University of Dakar","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","unstructured":"Guidelines for the prevention and control of carbapenem-resistant Enterobacteriaceae Acinetobacter baumannii and Pseudomonas aeruginosa in Health Care Facilities. 2017. https:\/\/www.who.int\/publications\/i\/item\/9789241550178."},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(24)01867-1"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-022-07548-3"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00001-07"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00102-19"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1155\/2019\/6736897"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28819-2"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01707-08"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx488"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-023-05745-7"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12941-023-00601-2"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01369-23"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.nmni.2015.11.009"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.18527\/2024112556"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1590\/1518-8345.1751.2935"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-53596-x"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens12080974"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12920-024-02016-0"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13756-019-0497-3"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics13010031"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2023.10.008"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.5897\/JBR2023.0360"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12920-024-02043-x"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-84754-w"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2021.10.011"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01773-13"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2023.e23368"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00021-18"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.70187"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.979558"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00964"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1562222"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhin.2024.04.014"},{"key":"e_1_3_4_35_2","unstructured":"Amara M Aubin G Caron F Cattoir V Dortet L Goutelle S Jeannot K Lepeule R Lina G Marchandin H M\u00e9rens A Ploy M-C Schramm F Varon E. 2022. Recommandations du Comit\u00e9 de l\u2019Antibiogramme de la Soci\u00e9t\u00e9 Fran\u00e7aise de Microbiologi. Paris France Soci\u00e9t\u00e9 Fran\u00e7aise de Microbiologie. https:\/\/www.sfm-microbiologie.org\/wp-content\/uploads\/2025\/07\/CASFM2022_V1.0-Juin.pdf."},{"key":"e_1_3_4_36_2","unstructured":"Amara M. 2023. Recommandations du Comit\u00e9 de l\u2019Antibiogramme de la Soci\u00e9t\u00e9 Fran\u00e7aise de Microbiologie. https:\/\/www.sfm-microbiologie.org\/wp-content\/uploads\/2023\/06\/CASFM2023_V1.0.pdf."},{"key":"e_1_3_4_37_2","unstructured":"Babraham Bioinformatics. 2025. FastQC a quality control tool for high throughput sequence data. https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc."},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.107"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.102"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty266"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0997-x"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-022-00738-y"},{"key":"e_1_3_4_43_2","unstructured":"GitHub - tseemann\/abricate::mag_right: Mass screening of contigs for antimicrobial and virulence genes. 2018. https:\/\/github.com\/tseemann\/abricate?utm."},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dks261"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03704-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03704-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T14:45:38Z","timestamp":1786027538000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.03704-25"}},"subtitle":[],"editor":[{"given":"Krisztina M.","family":"Papp-Wallace","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,4]]},"references-count":43,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8,4]]}},"alternative-id":["10.1128\/spectrum.03704-25"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.03704-25","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,4]]},"assertion":[{"value":"2025-11-14","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-04-02","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-16","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e03704-25"}}