{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:01:28Z","timestamp":1785420088476,"version":"3.56.0"},"reference-count":54,"publisher":"American Society for Microbiology","issue":"11","license":[{"start":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T00:00:00Z","timestamp":1762214400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T00:00:00Z","timestamp":1762214400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI50440, AI50440-S"],"award-info":[{"award-number":["AI50440, AI50440-S"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["HCT 44180"],"award-info":[{"award-number":["HCT 44180"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100003896","name":"Henry M. Jackson Foundation","doi-asserted-by":"publisher","award":["HU0001-19-2-0068"],"award-info":[{"award-number":["HU0001-19-2-0068"]}],"id":[{"id":"10.13039\/100003896","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,11,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      We investigated the trends and antimicrobial resistance (AMR) of\n                      <jats:italic toggle=\"yes\">Neisseria gonorrhoeae<\/jats:italic>\n                      (NG) in Kenya with whole-genome sequencing (WGS) of isolates collected in 2002\u20132009 (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 108) and 2020\u20132022 (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 110). Phenotypic AMR was confirmed by agar dilution. Predicted minimum inhibitory concentrations (MICs), multi-locus sequence typing (MLST), multi-antigen ST (NG-MAST), NG-STAR, and AMR genetic determinants were determined using WGS and detection of molecular markers. The WGS cgMLST typing used LIN codes. Resistance to penicillin, ciprofloxacin, and tetracycline was common throughout. In 2020\u20132022, azithromycin resistance (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 2) and cephalosporin alert values (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 5) were observed. Phylogenetic clusters were congruent with the LIN code lineage, though other typing schemes (MLST, NG-STAR, and NG-MAST) were not as consistent. There were major shifts over time in the lineages and genetic determinants. Circumcision and HIV status were associated with several AMR, housekeeping, metabolism, and iron acquisition genetic determinants. These findings highlight dynamic NG genomic trends, emerging macrolide resistance, and the value of WGS for surveillance. Behavioral and biological factors may contribute to AMR emergence and warrant further investigation.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>This work highlights the significant value of using whole-genome sequencing to track the evolution and epidemiology of gonorrhea over 20 years: (i) we documented the emergence of azithromycin resistance and cephalosporin reduced susceptibility and relationship to genetics of gonorrhea; (ii) by combining epidemiological and genetic data, we found that circumcision and HIV status were linked to specific genetic features of gonorrhea, including those tied to antibiotic resistance; and (iii) we used novel and traditional genetic typing methods to expand and refine the understanding of lineage shifts and genetic determinants, enhancing surveillance and intervention efforts. Some isolates had potential decreasing susceptibility for cephalosporins, highlighting the critical importance of ongoing surveillance and the opportunity for novel resistance gene identification. Studying how gonorrhea strains relate to a person\u2019s immune system, other bacteria (microbiome), and sexual networks could help us understand how certain strains spread and what the potential factors amplifying antimicrobial resistance are.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01586-25","type":"journal-article","created":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T15:07:10Z","timestamp":1759849630000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Genomic trends and emerging antimicrobial resistance in\n                    <i>Neisseria gonorrhoeae<\/i>\n                    over two decades in Kenya"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7926-2489","authenticated-orcid":true,"given":"Supriya D.","family":"Mehta","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02mpq6x41","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Epidemiology & Biostatistics, University of Illinois Chicago School of Public Health","place":["Chicago, USA"]},{"id":[{"id":"https:\/\/ror.org\/01k9xac83","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Infectious Disease Medicine, Rush University Medical College","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robyn","family":"Thorington","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/023xf2a37","id-type":"ROR","asserted-by":"publisher"}],"name":"National Microbiology Laboratory Branch, Public Health Agency of Canada","place":["Winnipeg, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter","family":"Agingu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02nmyab03","id-type":"ROR","asserted-by":"publisher"}],"name":"Nyanza Reproductive Health Society","place":["Kisumu, Kenya"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fredrick","family":"Otieno","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02nmyab03","id-type":"ROR","asserted-by":"publisher"}],"name":"Nyanza Reproductive Health Society","place":["Kisumu, Kenya"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia","family":"Unitt","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/052gg0110","id-type":"ROR","asserted-by":"publisher"}],"name":"Nuffield Department of Population Health, University of Oxford","place":["Oxford, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura K.","family":"Rusie","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01k9xac83","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Infectious Disease Medicine, Rush University Medical College","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriana","family":"Le Van","sequence":"additional","affiliation":[{"name":"Henry M. 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