{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T23:17:48Z","timestamp":1792624668913,"version":"4.5.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"4","funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1211806"],"award-info":[{"award-number":["OPP1211806"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Antimicrobial resistance (AMR) surveillance in low- and middle-income countries (LMICs) often relies on poorly resourced laboratory processes. Centralized sequencing was combined with cloud-based, open-source bioinformatics solutions for national AMR surveillance in Cambodia.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Blood cultures growing gram-negative bacteria were collected at 6 Cambodian hospitals (January 2021 to October 2022). Isolates were obtained from pure plate growth and shotgun DNA sequencing performed in country. Using public nucleotide and protein databases, reads were aligned for pathogen identification and AMR gene characterization. Multilocus sequence typing was performed on whole-genome assemblies and haplotype clusters compared against published genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Genes associated with acquired resistance to fluoroquinolones were identified in 59%, trimethoprim\/sulfamethoxazole in 45%, and aminoglycosides in 52% of 715 isolates. Extended-spectrum \u03b2-lactamase encoding genes were identified in 34% isolates, most commonly blaCTX-M-15, blaCTX-M-27, and blaCTX-M-55 in Escherichia coli sequence types 131 and 1193. Carbapenemase genes were identified in 12% isolates, most commonly blaOXA-23, blaNDM-1, blaOXA-58, and blaOXA-66 in Acinetobacter species. Phylogenetic analysis revealed clonal strains of Acinetobacter baumannii, representing suspected nosocomial outbreaks, and genetic clusters of quinolone-resistant typhoidal Salmonella and extended-spectrum \u03b2-lactamase E. coli cases suggesting community transmission.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>With accessible sequencing platforms and bioinformatics solutions, bacterial genomics can supplement AMR surveillance in LMICs.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/infdis\/jiae417","type":"journal-article","created":{"date-parts":[[2024,8,21]],"date-time":"2024-08-21T19:40:44Z","timestamp":1724269244000},"page":"859-869","source":"Crossref","is-referenced-by-count":4,"title":["Bacterial Genomics for National Antimicrobial Resistance Surveillance in Cambodia"],"prefix":"10.1093","volume":"232","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8293-3901","authenticated-orcid":false,"given":"Christina","family":"Yek","sequence":"first","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]},{"name":"Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases , Rockville, Maryland ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chanthap","family":"Lon","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3187-3691","authenticated-orcid":false,"given":"Sophana","family":"Chea","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sreyngim","family":"Lay","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng Heng","family":"Oum","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gechlang","family":"Tang","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chansothea","family":"Lon","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea R","family":"Pacheco","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian","family":"Drobish","sequence":"additional","affiliation":[{"name":"Critical Care Medicine Department, National Institutes of Health Clinical Center , Bethesda, Maryland ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reagan","family":"Stuehser","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sokna","family":"Ly","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ratanak","family":"Sath","sequence":"additional","affiliation":[{"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malin","family":"Srouen","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Preah Kossomak Hospital , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chamrouen","family":"Bin","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Siem Reap Hospital , Siem Reap ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chanthou","family":"Chak","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Takeo Provincial Hospital , Takeo ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sosorphea","family":"Seang","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Takeo Provincial Hospital , Takeo ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viso","family":"Srey","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, National Pediatric Hospital , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bunna","family":"Chhor","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, National Pediatric Hospital , Phnom Penh ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Somary","family":"Nhem","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Kampong Cham Provincial Hospital , Kampong Cham ,","place":["Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sivhour","family":"Chiek","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Battambang Provincial Referral Hospital , Battambang 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