{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T18:58:04Z","timestamp":1774551484381,"version":"3.50.1"},"reference-count":58,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T00:00:00Z","timestamp":1761177600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["218647"],"award-info":[{"award-number":["218647"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014035","name":"Armed Forces Health Surveillance Branch","doi-asserted-by":"publisher","award":["ProMIS P0089_24_KY"],"award-info":[{"award-number":["ProMIS P0089_24_KY"]}],"id":[{"id":"10.13039\/100014035","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosglobalpublichealth.org"],"crossmark-restriction":false},"short-container-title":["PLOS Glob Public Health"],"abstract":"<jats:p>\n                    Antimicrobial resistance (AMR) is a rising global health threat and estimated to cause 700,000 deaths annually. Although blood cultures (BCs) are the reference standard to diagnose bloodstream infections and inference of antimicrobial susceptibility testing (AST), the method could fail to differentiate bacteria with similar biochemical characteristics. This study compared phenotypic method (AST) and whole genome sequencing (WGS) in bacterial species identification and assessment of AMR. Blood samples came from children who had been prescribed antibiotics at admission at the county referral hospitals in western Kenya and around the Lake Victoria region. BCs and AST were performed on BD Bactec 9050 and Phoenix 100 respectively. Out of the 960 BCs, 17 isolates were useable and were evaluated by WGS on the Oxford Nanopore PromethION platform. BD Phoenix system identified the 17 bacteria isolates as: 4\n                    <jats:italic>\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                    <\/jats:italic>\n                    , 8\n                    <jats:italic>\n                      <jats:italic>Salmonella enterica<\/jats:italic>\n                    <\/jats:italic>\n                    serovar Typhi, 1 unspeciated\n                    <jats:italic>\n                      <jats:italic>Salmonella<\/jats:italic>\n                    <\/jats:italic>\n                    , 3\n                    <jats:italic>\n                      <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    <\/jats:italic>\n                    and 1\n                    <jats:italic>\n                      <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    <\/jats:italic>\n                    . WGS results differed from BCs in identifying the 9\n                    <jats:italic>\n                      <jats:italic>Salmonella<\/jats:italic>\n                    <\/jats:italic>\n                    species, with WGS identifying the species as\n                    <jats:italic>\n                      <jats:italic>Salmonella enterica<\/jats:italic>\n                    <\/jats:italic>\n                    serovar Typhimurium. Conversely, WGS detected AMR determinants in bacteria that AST had classified as susceptible. In conclusion, we caution that BCs may not be providing correct identity of\n                    <jats:italic>\n                      <jats:italic>Salmonella<\/jats:italic>\n                    <\/jats:italic>\n                    species. The observed discrepancies between phenotypic and genotypic markers of drug resistance highlight the challenges in interpreting and predicting the functional utility of AMR determinants.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgph.0004773","type":"journal-article","created":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T17:40:44Z","timestamp":1761241244000},"page":"e0004773","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgph.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Phenotypic markers misclassify isolates of Salmonella Typhimurium as S. Typhi, but were correctly identified by whole genome sequencing during a septicemia study in western Kenya"],"prefix":"10.1371","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-4993-0261","authenticated-orcid":true,"given":"Joseph","family":"Kaingu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4555-4480","authenticated-orcid":true,"given":"Kimita","family":"Gathii","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carolyne","family":"Kifude","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3249-2754","authenticated-orcid":true,"given":"James","family":"Nonoh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6730-512X","authenticated-orcid":true,"given":"Lillian","family":"Ogonda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amos","family":"Onditi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kirti","family":"Tiwari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2540-4397","authenticated-orcid":true,"given":"John","family":"Waitumbi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,10,23]]},"reference":[{"issue":"8","key":"pgph.0004773.ref001","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.3390\/antibiotics11081082","article-title":"Antimicrobial Resistance and Its Spread Is a Global Threat","volume":"11","author":"MM Aljeldah","year":"2022","journal-title":"Antibiotics (Basel)"},{"issue":"8","key":"pgph.0004773.ref002","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1080\/14740338.2022.2106368","article-title":"Tackling antimicrobial resistance across sub-Saharan Africa: current challenges and implications for the future","volume":"21","author":"B Godman","year":"2022","journal-title":"Expert Opin Drug Saf"},{"issue":"1","key":"pgph.0004773.ref003","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/s12887-019-1411-0","article-title":"Deciphering risk factors for blood stream infections, bacteria species and antimicrobial resistance profiles among children under five years of age in North-Western Tanzania: a multicentre study in a cascade of referral health care system","volume":"19","author":"J Seni","year":"2019","journal-title":"BMC Pediatr"},{"issue":"2","key":"pgph.0004773.ref004","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.ARBA-0009-2017","article-title":"Antimicrobial Resistance: a One Health Perspective","volume":"6","author":"SA McEwen","year":"2018","journal-title":"Microbiol Spectr"},{"issue":"20","key":"pgph.0004773.ref005","doi-asserted-by":"crossref","first-page":"3246","DOI":"10.3390\/diagnostics13203246","article-title":"Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria","volume":"13","author":"D Yamin","year":"2023","journal-title":"Diagnostics (Basel)"},{"key":"pgph.0004773.ref006","doi-asserted-by":"crossref","first-page":"29","DOI":"10.3184\/003685007780440521","article-title":"Current molecular techniques for the detection of microbial pathogens","volume":"90","author":"L Galluzzi","year":"2007","journal-title":"Sci Prog"},{"issue":"9","key":"pgph.0004773.ref007","doi-asserted-by":"crossref","first-page":"346","DOI":"10.3390\/bios11090346","article-title":"Advancement in Salmonella Detection Methods: From Conventional to Electrochemical-Based Sensing Detection","volume":"11","author":"MS Awang","year":"2021","journal-title":"Biosensors (Basel)"},{"key":"pgph.0004773.ref008","doi-asserted-by":"crossref","first-page":"2554","DOI":"10.3389\/fmicb.2019.02554","article-title":"Salmonella Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an in silico Platform Using Whole Genome Sequencing Data","volume":"10","author":"B Diep","year":"2019","journal-title":"Front Microbiol"},{"issue":"7","key":"pgph.0004773.ref009","doi-asserted-by":"crossref","first-page":"2018","DOI":"10.1128\/JCM.00313-13","article-title":"Next-generation antimicrobial susceptibility testing","volume":"51","author":"A van Belkum","year":"2013","journal-title":"J Clin Microbiol"},{"issue":"3","key":"pgph.0004773.ref010","doi-asserted-by":"crossref","first-page":"103582","DOI":"10.1016\/j.sjbs.2023.103582","article-title":"Conventional methods and future trends in antimicrobial susceptibility testing","volume":"30","author":"MA Salam","year":"2023","journal-title":"Saudi J Biol Sci"},{"issue":"6","key":"pgph.0004773.ref011","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.ARBA-0011-2017","article-title":"Molecular Methods for Detection of Antimicrobial Resistance","volume":"5","author":"MF Anjum","year":"2017","journal-title":"Microbiol Spectr"},{"key":"pgph.0004773.ref012","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/Spectrum.00954-21","article-title":"Comparison of four carbapenemase detection methods for bla KPC-2 variants","volume":"9","author":"L Ding","year":"2021","journal-title":"Microbiol Spectr"},{"issue":"3","key":"pgph.0004773.ref013","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0213865","article-title":"Performance and usability of Cepheid GeneXpert HIV-1 qualitative and quantitative assay in Kenya","volume":"14","author":"P Bwana","year":"2019","journal-title":"PLoS One"},{"issue":"11","key":"pgph.0004773.ref014","article-title":"Evaluation of GeneXpert vanA\/vanB in the early diagnosis of vancomycin-resistant enterococci infection","volume":"15","author":"Z-L Li","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pgph.0004773.ref015","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.01923-18","article-title":"Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates","volume":"63","author":"PD Tamma","year":"2018","journal-title":"Antimicrob Agents Chemother"},{"issue":"11","key":"pgph.0004773.ref016","article-title":"Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids","volume":"5","author":"TV Sydenham","year":"2019","journal-title":"Microb Genom"},{"issue":"3","key":"pgph.0004773.ref017","article-title":"Genome-Based Prediction of Bacterial Antibiotic Resistance","volume":"57","author":"M Su","year":"2019","journal-title":"J Clin Microbiol"},{"key":"pgph.0004773.ref018","doi-asserted-by":"crossref","first-page":"256","DOI":"10.12688\/wellcomeopenres.18289.1","article-title":"The CINAMR (Clinical Information Network-Antimicrobial Resistance) Project: A pilot microbial surveillance using hospitals linked to regional laboratories in Kenya: Study Protocol","volume":"7","author":"S Akech","year":"2022","journal-title":"Wellcome Open Res"},{"key":"pgph.0004773.ref019","unstructured":"GLASS. Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report 2021. 2021."},{"issue":"1","key":"pgph.0004773.ref020","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1093\/nar\/gkw1027","article-title":"Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform","volume":"45","author":"P-E Li","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pgph.0004773.ref021","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1186\/s12859-014-0366-2","article-title":"Rapid evaluation and quality control of next generation sequencing data with FaQCs","volume":"15","author":"C-C Lo","year":"2014","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"pgph.0004773.ref022","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"M Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"3","key":"pgph.0004773.ref023","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"DE Wood","year":"2014","journal-title":"Genome Biol"},{"issue":"1","key":"pgph.0004773.ref024","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/s41467-022-35713-4","article-title":"An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance","volume":"14","author":"NL Sherry","year":"2023","journal-title":"Nat Commun"},{"issue":"6","key":"pgph.0004773.ref025","article-title":"Curation of the AMRFinderPlus databases: applications, functionality and impact","volume":"8","author":"M Feldgarden","year":"2022","journal-title":"Microb Genom"},{"key":"pgph.0004773.ref026","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"BP Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"pgph.0004773.ref027","doi-asserted-by":"crossref","first-page":"804627","DOI":"10.3389\/fmicb.2022.804627","article-title":"One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings","volume":"13","author":"AR Rebelo","year":"2022","journal-title":"Front Microbiol"},{"key":"pgph.0004773.ref028","doi-asserted-by":"crossref","first-page":"711472","DOI":"10.3389\/fmicb.2021.711472","article-title":"Genotypic and Phenotypic Characterization of Antimicrobial Resistance Profiles in Non-typhoidal Salmonella enterica Strains Isolated From Cambodian Informal Markets","volume":"12","author":"CL Schwan","year":"2021","journal-title":"Front Microbiol"},{"issue":"1","key":"pgph.0004773.ref029","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1101\/gr.251678.119","article-title":"The EnteroBase user\u2019s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity","volume":"30","author":"Z Zhou","year":"2020","journal-title":"Genome Res"},{"key":"pgph.0004773.ref030","doi-asserted-by":"crossref","first-page":"0","DOI":"10.1093\/bioinformatics\/btae311","article-title":"Parsnp 2.0: scalable core-genome alignment for massive microbial datasets","volume":"40","author":"B Kille","year":"2024","journal-title":"Bioinformatics"},{"issue":"11","key":"pgph.0004773.ref031","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1186\/s13059-014-0524-x","article-title":"The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes","volume":"15","author":"TJ Treangen","year":"2014","journal-title":"Genome Biol"},{"key":"pgph.0004773.ref032","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"I Letunic","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pgph.0004773.ref033","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13756-019-0499-1","article-title":"Shifting trends and age distribution of ESKAPEEc resistance in bloodstream infection, Southwest China, 2012-2017","volume":"8","author":"S Yang","year":"2019","journal-title":"Antimicrob Resist Infect Control"},{"key":"pgph.0004773.ref034","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1186\/s12887-023-04343-0","article-title":"Blood culture versus antibiotic use for neonatal inpatients in 61 hospitals implementing with the NEST360 Alliance in Kenya, Malawi, Nigeria, and Tanzania: a cross-sectional study","volume":"23","author":"S Murless-Collins","year":"2023","journal-title":"BMC Pediatr"},{"issue":"2","key":"pgph.0004773.ref035","doi-asserted-by":"crossref","first-page":"71","DOI":"10.3390\/tropicalmed6020071","article-title":"Blood Culture Testing Outcomes among Non-Malarial Febrile Children at Antimicrobial Resistance Surveillance Sites in Uganda, 2017-2018","volume":"6","author":"R Kisame","year":"2021","journal-title":"Trop Med Infect Dis"},{"issue":"1","key":"pgph.0004773.ref036","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1186\/s12879-017-2862-2","article-title":"Bloodstream infections at a tertiary level paediatric hospital in South Africa","volume":"17","author":"H Lochan","year":"2017","journal-title":"BMC Infect Dis"},{"issue":"1","key":"pgph.0004773.ref037","doi-asserted-by":"crossref","first-page":"13824","DOI":"10.1038\/s41598-017-14244-9","article-title":"Comparison of four automated microbiology systems with 16S rRNA gene sequencing for identification of Chryseobacterium and Elizabethkingia species","volume":"7","author":"J-N Lin","year":"2017","journal-title":"Sci Rep"},{"key":"pgph.0004773.ref038","unstructured":"Phoenix TM Automated Microbiology System User\u2019s Manua l. 003342."},{"key":"pgph.0004773.ref039","unstructured":"Id CN, Id CV, Akoko J, et al. Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets. 2020;1\u201316."},{"issue":"2","key":"pgph.0004773.ref040","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1128\/CMR.00066-12","article-title":"Salmonella enterica serovar Typhimurium skills to succeed in the host: virulence and regulation","volume":"26","author":"A F\u00e0brega","year":"2013","journal-title":"Clin Microbiol Rev"},{"issue":"3","key":"pgph.0004773.ref041","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.aninu.2018.04.006","article-title":"Animals as sources of food-borne pathogens: A review","volume":"4","author":"N Heredia","year":"2018","journal-title":"Anim Nutr"},{"key":"pgph.0004773.ref042","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1146\/annurev-micro-091313-103739","article-title":"Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever","volume":"68","author":"G Dougan","year":"2014","journal-title":"Annu Rev Microbiol"},{"issue":"8","key":"pgph.0004773.ref043","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0008440","article-title":"High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya","volume":"14","author":"S Kariuki","year":"2020","journal-title":"PLoS Negl Trop Dis"},{"issue":"6","key":"pgph.0004773.ref044","doi-asserted-by":"crossref","first-page":"3133","DOI":"10.1128\/AAC.00078-15","article-title":"Ceftriaxone-resistant Salmonella enterica serotype typhimurium sequence type 313 from Kenyan patients is associated with the blaCTX-M-15 gene on a novel IncHI2 plasmid","volume":"59","author":"S Kariuki","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"key":"pgph.0004773.ref045","first-page":"50","article-title":"Antimicrobial Resistance Patterns of Bacterial Septicaemia Infecting Infants in Mbita Subcounty, Western Region of Kenya","volume":"10","author":"GH Sora","year":"2020","journal-title":"J Nat Sci Res"},{"key":"pgph.0004773.ref046","doi-asserted-by":"crossref","first-page":"2885","DOI":"10.2147\/IDR.S210961","article-title":"Molecular epidemiology and antimicrobial resistance of invasive non-typhoidal salmonella in China, 2007\u20132016","volume":"12","author":"Z Zhan","year":"2019","journal-title":"Infect Drug Resist"},{"issue":"2","key":"pgph.0004773.ref047","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0008991","article-title":"Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya","volume":"15","author":"JZ Kubicek-Sutherland","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"issue":"3","key":"pgph.0004773.ref048","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1111\/jam.13468","article-title":"Environmental Escherichia coli: ecology and public health implications-a review","volume":"123","author":"J Jang","year":"2017","journal-title":"J Appl Microbiol"},{"issue":"11","key":"pgph.0004773.ref049","doi-asserted-by":"crossref","first-page":"799","DOI":"10.3855\/jidc.1674","article-title":"A ten-year review of neonatal bloodstream infections in a tertiary private hospital in Kenya","volume":"5","author":"R Kohli-Kochhar","year":"2011","journal-title":"J Infect Dev Ctries"},{"key":"pgph.0004773.ref050","unstructured":"Kibaba PW, Louis H, Kering KK, et al. Antimicrobal susceptibility pattern of methicillin resistant Staphylococcus aureus isolated from pediatric clinical samples at Webuye District Hospital. 2017;74:238\u201350."},{"key":"pgph.0004773.ref051","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.11958","article-title":"Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya","volume":"9","author":"J Lord","year":"2021","journal-title":"PeerJ"},{"issue":"12","key":"pgph.0004773.ref052","doi-asserted-by":"crossref","first-page":"1726","DOI":"10.3390\/antibiotics11121726","article-title":"Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya","volume":"11","author":"BA Obanda","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"pgph.0004773.ref053","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/s13756-019-0673-5","article-title":"Bacterial pathogens and resistance causing community acquired paediatric bloodstream infections in low- and middle-income countries: a systematic review and meta-analysis","volume":"8","author":"N Droz","year":"2019","journal-title":"Antimicrob Resist Infect Control"},{"key":"pgph.0004773.ref054","doi-asserted-by":"crossref","unstructured":"Orucho VO, Nyangau MK. Antibiotic resistance of Streptococcus pneumonia serotypes in Kisii, Kenya Cyrus Orucho Ochoi Kisii Teaching and referral hospital. 2020;1\u201310.","DOI":"10.21203\/rs.2.13786\/v2"},{"issue":"12","key":"pgph.0004773.ref055","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"V Bortolaia","year":"2020","journal-title":"J Antimicrob Chemother"},{"issue":"1","key":"pgph.0004773.ref056","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.cmi.2016.11.012","article-title":"The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee","volume":"23","author":"MJ Ellington","year":"2017","journal-title":"Clin Microbiol Infect"},{"key":"pgph.0004773.ref057","unstructured":"WHO. GLASS Whole-Genome Sequencing for Surveillance of Antimicrobial Resistance. 2020."},{"key":"pgph.0004773.ref058","unstructured":"World Health Organization. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance. 2021. Available from: https:\/\/www.who.int\/publications\/i\/item\/9789240028173"}],"container-title":["PLOS Global Public Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgph.0004773","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T17:40:51Z","timestamp":1761241251000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgph.0004773"}},"subtitle":[],"editor":[{"given":"Stephanie","family":"van Wyk","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,10,23]]},"references-count":58,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2025,10,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgph.0004773","relation":{},"ISSN":["2767-3375"],"issn-type":[{"value":"2767-3375","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,23]]}}}