{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T19:21:34Z","timestamp":1785525694264,"version":"3.56.0"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"intramural funds"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Aims<\/jats:title>\n                  <jats:p>The use of metagenomics for pathogen identification in clinical practice has been limited. Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi, and antimicrobial resistance genes (ARGs).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods and results<\/jats:title>\n                  <jats:p>The method includes target enrichment, long-read sequencing, and automated bioinformatics. Evaluation of several tools and databases was undertaken across standard organisms (n\u00a0=\u00a012), clinical isolates (n\u00a0=\u00a0114), and blood samples from patients with suspected bloodstream infections (n\u00a0=\u00a033). The strategy used could offset the presence of host background DNA, error rates of long-read sequencing, and provide accurate and reproducible detection of pathogens. Eleven targets could be successfully tested in a single assay. Organisms could be confidently identified considering\u00a0\u226560% of best hits of a BLAST-based threshold of e-value 0.001 and a percent identity of\u00a0&amp;gt;80%. For ARGs, reads with percent identity of\u00a0&amp;gt;90% and\u00a0&amp;gt;60% overlap of the complete gene could be confidently annotated. A kappa of 0.83 was observed compared to standard diagnostic methods. Thus, a workflow for the direct-from-sample, on-site sequencing combined with automated genomics was demonstrated to be reproducible.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>NGS-based technologies overcome several limitations of current day diagnostics. Highly sensitive and comprehensive methods of pathogen screening are the need of the hour. We developed a framework for reliable, on-site, screening of pathogens.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jambio\/lxae037","type":"journal-article","created":{"date-parts":[[2024,2,13]],"date-time":"2024-02-13T02:08:37Z","timestamp":1707790117000},"source":"Crossref","is-referenced-by-count":5,"title":["An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG"],"prefix":"10.1093","volume":"135","author":[{"given":"Sanjana","family":"Kuruwa","sequence":"first","affiliation":[{"name":"HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amrutraj","family":"Zade","sequence":"additional","affiliation":[{"name":"HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanchi","family":"Shah","sequence":"additional","affiliation":[{"name":"HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rameez","family":"Moidu","sequence":"additional","affiliation":[{"name":"HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shailesh","family":"Lad","sequence":"additional","affiliation":[{"name":"HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chhaya","family":"Chande","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Sir J. J. Group of Hospitals , Mumbai 400008 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ameeta","family":"Joshi","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Sir J. J. Group of Hospitals , Mumbai 400008 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nilma","family":"Hirani","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Sir J. J. Group of Hospitals , Mumbai 400008 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaitali","family":"Nikam","sequence":"additional","affiliation":[{"name":"HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India"},{"name":"Thyrocare Technologies Pvt. Ltd , Navi Mumbai 400703 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjay","family":"Bhattacharya","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Tata Medical Center , 14, MAR(E-W), DH Block (Newtown), Action Area I, Newtown, Kolkata, Chakpachuria 700160 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aruna","family":"Poojary","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Breach Candy Hospital and Research Center , Mumbai 400026 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahua","family":"Kapoor","sequence":"additional","affiliation":[{"name":"HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7942-023X","authenticated-orcid":false,"given":"Kiran","family":"Kondabagil","sequence":"additional","affiliation":[{"name":"Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anirvan","family":"Chatterjee","sequence":"additional","affiliation":[{"name":"HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,2,12]]},"reference":[{"key":"2024022314524040800_bib2","first-page":"403","article-title":"Basic local alignment search tool","volume-title":"J Mol Biol\u00a0","author":"Altschul","year":"1990"},{"key":"2024022314524040800_bib3","doi-asserted-by":"crossref","first-page":"4118","DOI":"10.1111\/mec.17031","article-title":"Detecting and analysing intraspecific genetic variation with eDNA: from population genetics to species abundance","volume":"32","author":"Andres","year":"2023","journal-title":"Mol Ecol"},{"key":"2024022314524040800_bib4","doi-asserted-by":"crossref","first-page":"822402","DOI":"10.3389\/fmicb.2022.822402","article-title":"Ultrafast and cost-effective pathogen identification and resistance gene detection in a clinical setting using nanopore flongle sequencing","volume":"13","author":"Avershina","year":"2022","journal-title":"Front Microbiol"},{"key":"2024022314524040800_bib5","doi-asserted-by":"crossref","first-page":"292","DOI":"10.3390\/microorganisms10020292","article-title":"Correlation between phenotypic and in silico detection of antimicrobial resistance in Salmonella enterica in Canada using staramr","volume":"10","author":"Bharat","year":"2022","journal-title":"Microorganisms"},{"key":"2024022314524040800_bib6","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1038\/s41564-018-0349-6","article-title":"Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease","volume":"4","author":"Blauwkamp","year":"2019","journal-title":"Nat Microbiol"},{"key":"2024022314524040800_bib7","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob Agents Chemother"},{"key":"2024022314524040800_bib8","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.tube.2017.08.002","article-title":"Whole genome sequencing of clinical strains of Mycobacterium tuberculosis from Mumbai, India: a potential tool for determining drug-resistance and strain lineage","volume":"107","author":"Chatterjee","year":"2017","journal-title":"Tuberculosis"},{"key":"2024022314524040800_bib9","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.jare.2023.02.018","article-title":"Clinical evaluation of cell-free and cellular metagenomic next-generation sequencing of infected body fluids","volume":"55","author":"Chen","year":"2023","journal-title":"J Adv Res"},{"key":"2024022314524040800_bib10","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","article-title":"Clinical metagenomics","volume":"20","author":"Chiu","year":"2019","journal-title":"Nat Rev Genet"},{"key":"2024022314524040800_bib11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/CMR.00053-19","article-title":"Performance and application of 16S rRNA gene cycle sequencing for routine identification of bacteria in the clinical microbiology laboratory","volume":"33","author":"Church","year":"2020","journal-title":"Clin Microbiol Rev"},{"key":"2024022314524040800_bib12","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/s41592-022-01520-4","article-title":"Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data","volume":"19","author":"Curry","year":"2022","journal-title":"Nat Methods"},{"key":"2024022314524040800_bib15","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1590\/S1413-86702009000400010","article-title":"Rapid detection of vancomycin-resistant enterococci (VRE) in rectal samples from patients admitted to intensive care units","volume":"13","author":"d'Azevedo","year":"2009","journal-title":"Braz J Infect Dis"},{"key":"2024022314524040800_bib13","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1093\/jac\/dkp498","article-title":"Development of a set of multiplex PCR assays for the detection of genes encoding important \u03b2-lactamases in Enterobacteriaceae","volume":"65","author":"Dallenne","year":"2010","journal-title":"J Antimicrob Chemother"},{"key":"2024022314524040800_bib14","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"2024022314524040800_bib16","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: visualizing and processing long-read sequencing data","volume":"34","author":"De\u00a0Coster","year":"2018","journal-title":"Bioinformatics"},{"key":"2024022314524040800_bib55_154_194224","first-page":"16","article-title":"Sequencing DNA with nanopores: Troubles and biases","volume-title":"PLoS One","author":"Delahaye","year":"2021"},{"key":"2024022314524040800_bib17","doi-asserted-by":"crossref","first-page":"943859","DOI":"10.3389\/fcimb.2022.943859","article-title":"Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections","volume":"12","author":"Deng","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"key":"2024022314524040800_bib18","first-page":"mgen000832","article-title":"Curation of the AMRFinderPlus databases: applications, functionality and impact","volume":"8","author":"Feldgarden","year":"2022","journal-title":"Microb Genom"},{"key":"2024022314524040800_bib19","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1093\/cid\/ciab349","article-title":"Detection of pathogenic bacteria from septic patients using 16S Ribosomal RNA gene-targeted metagenomic sequencing","volume":"73","author":"Fida","year":"2021","journal-title":"Clin Infect Dis"},{"key":"2024022314524040800_bib20","doi-asserted-by":"crossref","first-page":"e0027022","DOI":"10.1128\/spectrum.00270-22","article-title":"Clinical performance of nanopore targeted sequencing for diagnosing infectious diseases","volume":"10","author":"Fu","year":"2022","journal-title":"Microbiol Spectr"},{"key":"2024022314524040800_bib21","doi-asserted-by":"crossref","first-page":"e0291620","DOI":"10.1128\/JCM.02916-20","article-title":"Metagenomic sequencing as a pathogen-agnostic clinical diagnostic tool for infectious diseases: a systematic review and meta-analysis of diagnostic test accuracy studies","volume":"59","author":"Govender","year":"2021","journal-title":"J Clin Microbiol"},{"key":"2024022314524040800_bib22","doi-asserted-by":"crossref","first-page":"e394","DOI":"10.1097\/CCM.0000000000003658","article-title":"Enhanced performance of next-generation sequencing diagnostics compared with standard of care microbiological diagnostics in patients suffering from septic shock","volume":"47","author":"Grumaz","year":"2019","journal-title":"Crit Care Med"},{"key":"2024022314524040800_bib23","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1146\/annurev-pathmechdis-012418-012751","article-title":"Clinical metagenomic next-generation sequencing for pathogen detection","volume":"14","author":"Gu","year":"2019","journal-title":"Annu Rev Pathol Mech Dis"},{"key":"2024022314524040800_bib24","doi-asserted-by":"crossref","first-page":"3233","DOI":"10.1128\/aem.63.8.3233-3241.1997","article-title":"Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients","volume":"63","author":"Heuer","year":"1997","journal-title":"Appl Environ Microbiol"},{"key":"2024022314524040800_bib25","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/s10096-019-03681-1","article-title":"The necessity to revise Koch\u2019s postulates and its application to infectious and non-infectious diseases: a mini-review","volume":"39","author":"Hosainzadegan","year":"2020","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"2024022314524040800_bib26","doi-asserted-by":"crossref","first-page":"e95567","DOI":"10.1371\/journal.pone.0095567","article-title":"Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia","volume":"9","author":"Hugerth","year":"2014","journal-title":"PLoS One"},{"key":"2024022314524040800_bib27","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.3390\/ijms23031395","article-title":"Application and challenge of 3rd generation sequencing for clinical bacterial studies","volume":"23","author":"Khedher","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2024022314524040800_bib28","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1186\/s13059-021-02344-9","article-title":"Next-generation microbiology: from comparative genomics to gene function","volume":"22","author":"Kobras","year":"2021","journal-title":"Genome Biol"},{"key":"2024022314524040800_bib29","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1016\/j.tim.2021.01.005","article-title":"Evolution of microbial genomics: conceptual shifts over a quarter century","volume":"29","author":"Koonin","year":"2021","journal-title":"Trends Microbiol"},{"key":"2024022314524040800_bib30","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1111\/j.1574-6968.2004.tb09534.x","article-title":"Diversity of genetic environment of blaCTX-M genes","volume":"234","author":"Lartigue","year":"2004","journal-title":"FEMS Microbiol Lett"},{"key":"2024022314524040800_bib31","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2024022314524040800_bib32","article-title":"The mobilome associated with Gram-negative bloodstream infections: a large-scale observational hybrid sequencing based study","author":"Lipworth","year":"2022","journal-title":"Medrxiv"},{"key":"2024022314524040800_bib33","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s43008-020-00033-z","article-title":"Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?","volume":"11","author":"L\u00fccking","year":"2020","journal-title":"IMA Fungus"},{"key":"2024022314524040800_bib34","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1038\/s41597-022-01762-z","article-title":"Benchmarking second and third-generation sequencing platforms for microbial metagenomics","volume":"9","author":"Meslier","year":"2022","journal-title":"Sci Data"},{"key":"2024022314524040800_bib35","doi-asserted-by":"crossref","first-page":"2240","DOI":"10.1128\/jcm.29.10.2240-2244.1991","article-title":"Identification of methicillin-resistant strains of Staphylococci by polymerase chain reaction","volume":"29","author":"Murakami","year":"1991","journal-title":"J Clin Microbiol"},{"key":"2024022314524040800_bib36","doi-asserted-by":"crossref","first-page":"303104","DOI":"10.1155\/2014\/303104","article-title":"Carbapenemase genes among multidrug resistant Gram negative clinical isolates from a tertiary hospital in Mwanza, Tanzania","volume":"2014","author":"Mushi","year":"2014","journal-title":"Biomed Res Int"},{"key":"2024022314524040800_bib37","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/ja.2015.68","article-title":"Development of a multiplex PCR system and its application in detection of blaSHV, blaTEM, blaCTX-M-1, blaCTX-M-9 and blaOXA-1 group genes in clinical Klebsiella pneumoniae and Escherichia coli strains","volume":"68","author":"Ogutu","year":"2015","journal-title":"J Antibiot"},{"key":"2024022314524040800_bib38","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.mimet.2009.07.008","article-title":"Identification of pathogenic bacteria in blood cultures: comparison between conventional and PCR methods","volume":"78","author":"Pechorsky","year":"2009","journal-title":"J Microbiol Methods"},{"key":"2024022314524040800_bib39","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1086\/512818","article-title":"Detection and identification of microorganisms by gene amplification and sequencing","volume":"44","author":"Petti","year":"2007","journal-title":"Clin Infect Dis"},{"key":"2024022314524040800_bib40","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1186\/s12879-021-06934-7","article-title":"The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with sepsis","volume":"21","author":"Ren","year":"2021","journal-title":"BMC Infect Dis"},{"key":"2024022314524040800_bib41","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.cmi.2017.11.001","article-title":"Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology","volume":"24","author":"Rossen","year":"2018","journal-title":"Clin Microbiol Infect"},{"key":"2024022314524040800_bib42","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1002\/jmv.22186","article-title":"Clinical evaluation of multiplex real-time PCR panels for rapid detection of respiratory viral infections","volume":"84","author":"Sanghavi","year":"2012","journal-title":"J Med Virol"},{"key":"2024022314524040800_bib43","doi-asserted-by":"crossref","first-page":"D10","DOI":"10.1093\/nar\/gkaa892","article-title":"Database resources of the National Center for Biotechnology Information","volume":"49","author":"Sayers","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024022314524040800_bib44","doi-asserted-by":"crossref","first-page":"e0215621","DOI":"10.1128\/jcm.02156-21","article-title":"Clinical metagenomic sequencing for species identification and antimicrobial resistance prediction in orthopedic device infection","volume":"60","author":"Street","year":"2022","journal-title":"J Clin Microbiol"},{"key":"2024022314524040800_bib45","doi-asserted-by":"crossref","first-page":"7622","DOI":"10.1038\/s41598-020-64616-x","article-title":"Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing","volume":"10","author":"Taxt","year":"2020","journal-title":"Sci Rep"},{"key":"2024022314524040800_bib1","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1056\/NEJMoa1800474","article-title":"Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing","volume":"379","author":"The CRyPTIC Consortium and the 100 000 Genomes Project","year":"2018","journal-title":"N Engl J Med"},{"key":"2024022314524040800_bib46","doi-asserted-by":"crossref","first-page":"1478","DOI":"10.1001\/jama.2020.2717","article-title":"Prevalence and outcomes of infection among patients in intensive care units in 2017","volume":"323","author":"Vincent","year":"2020","journal-title":"JAMA"},{"key":"2024022314524040800_bib47","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/S1473-3099(12)70277-3","article-title":"Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study","volume":"13","author":"Walker","year":"2013","journal-title":"Lancet Infect Dis"},{"key":"2024022314524040800_bib48","doi-asserted-by":"crossref","first-page":"e90053","DOI":"10.1371\/journal.pone.0090053","article-title":"Optimal eukaryotic 18S and universal 16S\/18S ribosomal RNA primers and their application in a study of symbiosis","volume":"9","author":"Wang","year":"2014","journal-title":"PLoS One"},{"key":"2024022314524040800_bib49","volume-title":"Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report [Internet]","author":"World Health Organisation","year":"2022"},{"key":"2024022314524040800_bib50","first-page":"385","article-title":"Plasmid-mediated colistin resistance gene mcr-1 in Escherichia coli and Klebsiella pneumoniae isolated from market retail fruits in Guangzhou, China","volume-title":"Infect Drug Resist","author":"Yang","year":"2019"},{"key":"2024022314524040800_bib51","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.cell.2019.07.010","article-title":"Benchmarking metagenomics tools for taxonomic classification","volume":"178","author":"Ye","year":"2019","journal-title":"Cell"},{"key":"2024022314524040800_bib52","first-page":"693","article-title":"Answers in hours\u201d: a prospective clinical study using nanopore sequencing for bile duct cultures","volume":"171","author":"Yonkus","year":"2022","journal-title":"Surgery (United States)"},{"key":"2024022314524040800_bib53","doi-asserted-by":"crossref","first-page":"606480","DOI":"10.1155\/2013\/606480","article-title":"Fungal and bacterial communities in the rhizosphere of pinus tabulaeformis related to the restoration of plantations and natural secondary forests in the loess plateau, Northwest China","volume":"2013","author":"Yu","year":"2013","journal-title":"Sci World J"},{"key":"2024022314524040800_bib54","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/j.jgar.2022.10.004","article-title":"Whole-genome sequencing of presumptive MDR-TB isolates from a tertiary healthcare setting in Mumbai","volume":"31","author":"Zade","year":"2022","journal-title":"J Glob Antimicrob Resist"}],"container-title":["Journal of Applied Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jambio\/advance-article-pdf\/doi\/10.1093\/jambio\/lxae037\/56666259\/lxae037.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jambio\/article-pdf\/135\/2\/lxae037\/56747413\/lxae037.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jambio\/article-pdf\/135\/2\/lxae037\/56747413\/lxae037.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,23]],"date-time":"2024-02-23T15:46:43Z","timestamp":1708703203000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jambio\/article\/doi\/10.1093\/jambio\/lxae037\/7606793"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,1]]},"references-count":55,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/jambio\/lxae037","relation":{},"ISSN":["1365-2672"],"issn-type":[{"value":"1365-2672","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,2]]},"published":{"date-parts":[[2024,2,1]]},"article-number":"lxae037"}}