{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T21:27:00Z","timestamp":1792445220884,"version":"4.5.0"},"reference-count":86,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,5,17]],"date-time":"2021-05-17T00:00:00Z","timestamp":1621209600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,5,17]],"date-time":"2021-05-17T00:00:00Z","timestamp":1621209600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access to genomic data for public health on a global scale. Here we present the Pathogenwatch scheme for\n                    <jats:italic>Salmonella enterica<\/jats:italic>\n                    serovar Typhi (\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi), a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data. We show that the clustering of\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are highly concordant with phenotypic susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from &gt;4,300 public genomes available in the application. Pathogenwatch provides an intuitive entry point to monitor of the emergence and spread of\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi high risk clones.\n                  <\/jats:p>","DOI":"10.1038\/s41467-021-23091-2","type":"journal-article","created":{"date-parts":[[2021,5,17]],"date-time":"2021-05-17T06:04:53Z","timestamp":1621231493000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":144,"title":["A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch"],"prefix":"10.1038","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2884-3857","authenticated-orcid":false,"given":"Silvia","family":"Argim\u00f3n","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Corin A.","family":"Yeats","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9954-841X","authenticated-orcid":false,"given":"Richard J.","family":"Goater","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khalil","family":"Abudahab","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9105-7760","authenticated-orcid":false,"given":"Benjamin","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony","family":"Underwood","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4162-0228","authenticated-orcid":false,"given":"Leonor","family":"S\u00e1nchez-Bus\u00f3","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa K.","family":"Wong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8887-3492","authenticated-orcid":false,"given":"Zoe A.","family":"Dyson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7297-1485","authenticated-orcid":false,"given":"Satheesh","family":"Nair","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1632-3045","authenticated-orcid":false,"given":"Se Eun","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6043-7170","authenticated-orcid":false,"given":"Florian","family":"Marks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew J.","family":"Page","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacqueline A.","family":"Keane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Baker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn E.","family":"Holt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gordon","family":"Dougan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Aanensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,17]]},"reference":[{"key":"23091_CR1","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1086\/649541","volume":"50","author":"JA Crump","year":"2010","unstructured":"Crump, J. A. & Mintz, E. D. Global trends in typhoid and paratyphoid fever. Clin. Infect. Dis. 50, 241\u2013246 (2010).","journal-title":"Clin. Infect. Dis."},{"key":"23091_CR2","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1016\/S0140-6736(13)62708-7","volume":"385","author":"J Wain","year":"2015","unstructured":"Wain, J., Hendriksen, R. S., Mikoleit, M. L., Keddy, K. H. & Ochiai, R. L. Typhoid fever. Lancet 385, 1136\u20131145 (2015).","journal-title":"Lancet"},{"key":"23091_CR3","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1038\/ng.3281","volume":"47","author":"VK Wong","year":"2015","unstructured":"Wong, V. K. et al. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies intercontinental and intracontinental transmission events. Nat. Genet. 47, 632\u2013639 (2015).","journal-title":"Nat. Genet."},{"key":"23091_CR4","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms12827","volume":"7","author":"VK Wong","year":"2016","unstructured":"Wong, V. K. et al. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nat. Commun. 7, 12827 (2016).","journal-title":"Nat. Commun."},{"key":"23091_CR5","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1038\/ng.195","volume":"40","author":"KE Holt","year":"2008","unstructured":"Holt, K. E. et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat. Genet. 40, 987\u2013993 (2008).","journal-title":"Nat. Genet."},{"key":"23091_CR6","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","volume":"75","author":"V Bortolaia","year":"2020","unstructured":"Bortolaia, V. et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother. 75, 3491\u20133500 (2020).","journal-title":"J. Antimicrob. Chemother."},{"key":"23091_CR7","doi-asserted-by":"crossref","unstructured":"Feldgarden, M. et al. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype\u2013phenotype correlations in a collection of isolates. Antimicrob. Agents Chemother. 63, 11 (2019).","DOI":"10.1128\/AAC.00483-19"},{"key":"23091_CR8","doi-asserted-by":"publisher","first-page":"e1007261","DOI":"10.1371\/journal.pgen.1007261","volume":"14","author":"NF Alikhan","year":"2018","unstructured":"Alikhan, N. F., Zhou, Z., Sergeant, M. J. & Achtman, M. A genomic overview of the population structure of Salmonella. PLoS Genet. 14, e1007261 (2018).","journal-title":"PLoS Genet."},{"key":"23091_CR9","first-page":"D606","volume":"48","author":"JJ Davis","year":"2020","unstructured":"Davis, J. J. et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 48, D606\u2013D612 (2020).","journal-title":"Nucleic Acids Res."},{"key":"23091_CR10","first-page":"2019","volume":"201-212","author":"RE Timme","year":"1918","unstructured":"Timme, R. E., Sanchez Leon, M. & Allard, M. W. Utilizing the public GenomeTrakr database for foodborne pathogen traceback. Methods Mol. Biol. 201-212, 2019 (1918).","journal-title":"Methods Mol. Biol."},{"key":"23091_CR11","doi-asserted-by":"publisher","first-page":"e0147101","DOI":"10.1371\/journal.pone.0147101","volume":"11","author":"CE Yoshida","year":"2016","unstructured":"Yoshida, C. E. et al. The Salmonella In Silico Typing Resource (SISTR): an open Web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. PLoS ONE 11, e0147101 (2016).","journal-title":"PLoS ONE"},{"key":"23091_CR12","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1101\/gr.251678.119","volume":"30","author":"Z Zhou","year":"2020","unstructured":"Zhou, Z. et al. The EnteroBase user\u2019s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res. 30, 138\u2013152 (2020).","journal-title":"Genome Res."},{"key":"23091_CR13","doi-asserted-by":"publisher","first-page":"e1002776","DOI":"10.1371\/journal.ppat.1002776","volume":"8","author":"M Achtman","year":"2012","unstructured":"Achtman, M. et al. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. PLoS Pathog. 8, e1002776 (2012).","journal-title":"PLoS Pathog."},{"key":"23091_CR14","unstructured":"Centre for Genomic Pathogen Surveillance. Pathogewatch S. Typhi video\u00a0https:\/\/vimeo.com\/542566630. Accessed 28 April 2021."},{"key":"23091_CR15","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","volume":"58","author":"A Carattoli","year":"2014","unstructured":"Carattoli, A. et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895\u20133903 (2014).","journal-title":"Antimicrob. Agents Chemother."},{"key":"23091_CR16","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1128\/JCM.02026-14","volume":"53","author":"RS Hendriksen","year":"2015","unstructured":"Hendriksen, R. S. et al. Genomic signature of multidrug-resistant Salmonella enterica serovar typhi isolates related to a massive outbreak in Zambia between 2010 and 2012. J. Clin. Microbiol. 53, 262\u2013272 (2015).","journal-title":"J. Clin. Microbiol."},{"key":"23091_CR17","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch S. Typhi 4389 public genomes collection https:\/\/pathogen.watch\/collection\/07lsscrbhu2x-public-genomes. Accessed 28 January 2021."},{"key":"23091_CR18","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch S. Typhi public collections https:\/\/pathogen.watch\/collections\/all?access=public&organismId=90370. Accessed 28 January 2021."},{"key":"23091_CR19","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."},{"key":"23091_CR20","doi-asserted-by":"crossref","unstructured":"Klemm, E. J. et al. Emergence of an extensively drug-resistant Salmonella enterica serovar typhi clone harboring a promiscuous plasmid encoding resistance to fluoroquinolones and third-generation cephalosporins. mBio 9, e00105-18\u00a0(2018).","DOI":"10.1128\/mBio.00105-18"},{"key":"23091_CR21","doi-asserted-by":"crossref","unstructured":"Pragasam, A. K. et al. Phylogenetic analysis indicates a longer term presence of the globally distributed H58 haplotype of Salmonella Typhi in Southern India. Clin. Infect. Dis. 71, 1856\u20131863 (2020).","DOI":"10.1093\/cid\/ciz1112"},{"key":"23091_CR22","doi-asserted-by":"crossref","unstructured":"Tanmoy, A. M. et al. Salmonella enterica serovar Typhi in Bangladesh: exploration of genomic diversity and antimicrobial Resistance. mBio 9, e02112\u201318\u00a0(2018).","DOI":"10.1128\/mBio.02112-18"},{"key":"23091_CR23","doi-asserted-by":"crossref","unstructured":"Hunt, M. et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb. Genomics 3, e000131\u00a0(2017).","DOI":"10.1099\/mgen.0.000131"},{"key":"23091_CR24","doi-asserted-by":"publisher","first-page":"e0006408","DOI":"10.1371\/journal.pntd.0006408","volume":"12","author":"CD Britto","year":"2018","unstructured":"Britto, C. D. et al. Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: antimicrobial resistance and implications for vaccine policy. PLoS Negl. Trop. Dis. 12, e0006408 (2018).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"23091_CR25","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","volume":"67","author":"E Zankari","year":"2012","unstructured":"Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640\u20132644 (2012).","journal-title":"J. Antimicrob. Chemother."},{"key":"23091_CR26","doi-asserted-by":"publisher","first-page":"e0007620","DOI":"10.1371\/journal.pntd.0007620","volume":"13","author":"DJ Ingle","year":"2019","unstructured":"Ingle, D. J. et al. Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. PLoS Negl. Trop. Dis. 13, e0007620 (2019).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"23091_CR27","doi-asserted-by":"publisher","first-page":"e14003","DOI":"10.7554\/eLife.14003","volume":"5","author":"D Pham Thanh","year":"2016","unstructured":"Pham Thanh, D. et al. A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure. Elife 5, e14003 (2016).","journal-title":"Elife"},{"key":"23091_CR28","doi-asserted-by":"crossref","unstructured":"Day, M. R. et al. Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi. J. Antimicrob. Chemother. 73, 365\u2013372 (2017).","DOI":"10.1093\/jac\/dkx379"},{"key":"23091_CR29","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1038\/35101607","volume":"413","author":"J Parkhill","year":"2001","unstructured":"Parkhill, J. et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413, 848\u2013852 (2001).","journal-title":"Nature"},{"key":"23091_CR30","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07370-z","volume":"9","author":"SE Park","year":"2018","unstructured":"Park, S. E. et al. The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Nat. Commun. 9, 5094 (2018).","journal-title":"Nat. Commun."},{"key":"23091_CR31","doi-asserted-by":"publisher","first-page":"e0007868","DOI":"10.1371\/journal.pntd.0007868","volume":"13","author":"Y Hooda","year":"2019","unstructured":"Hooda, Y. et al. Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance. PLoS Negl. Trop. Dis. 13, e0007868 (2019).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"23091_CR32","doi-asserted-by":"publisher","first-page":"e1752","DOI":"10.7717\/peerj.1752","volume":"4","author":"PM Ashton","year":"2016","unstructured":"Ashton, P. M. et al. Identification of Salmonella for public health surveillance using whole genome sequencing. PeerJ 4, e1752 (2016).","journal-title":"PeerJ"},{"key":"23091_CR33","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1016\/S0140-6736(05)67181-4","volume":"366","author":"MK Bhan","year":"2005","unstructured":"Bhan, M. K., Bahl, R. & Bhatnagar, S. Typhoid and paratyphoid fever. Lancet 366, 749\u2013762 (2005).","journal-title":"Lancet"},{"key":"23091_CR34","doi-asserted-by":"crossref","unstructured":"Engsbro, A. L. et al. Ceftriaxone-resistant Salmonella enterica serotype Typhi in a pregnant traveller returning from Karachi, Pakistan to Denmark, 2019. EuroSurveillance 24, 1900289 (2019).","DOI":"10.2807\/1560-7917.ES.2019.24.21.1900289"},{"key":"23091_CR35","doi-asserted-by":"publisher","first-page":"1976","DOI":"10.1093\/cid\/ciy032","volume":"66","author":"GS Godbole","year":"2018","unstructured":"Godbole, G. S., Day, M. R., Murthy, S., Chattaway, M. A. & Nair, S. First report of CTX-M-15 Salmonella Typhi from England. Clin. Infect. Dis. 66, 1976\u20131977 (2018).","journal-title":"Clin. Infect. Dis."},{"key":"23091_CR36","doi-asserted-by":"publisher","first-page":"e00492","DOI":"10.1016\/j.idcr.2019.e00492","volume":"15","author":"W Wong","year":"2019","unstructured":"Wong, W. et al. The first Canadian pediatric case of extensively drug-resistant Salmonella Typhi originating from an outbreak in Pakistan and its implication for empiric antimicrobial choices. IDCases 15, e00492 (2019).","journal-title":"IDCases"},{"key":"23091_CR37","first-page":"337","volume":"75","author":"CD Britto","year":"2020","unstructured":"Britto, C. D. et al. Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent. J. Antimicrob. Chemother. 75, 337\u2013341 (2020).","journal-title":"J. Antimicrob. Chemother."},{"key":"23091_CR38","doi-asserted-by":"crossref","unstructured":"Matono, T. et al. Emergence of resistance Mutations in Salmonella enterica serovar typhi against fluoroquinolones. Open Forum Infect. Dis. 4, ofx230 (2017).","DOI":"10.1093\/ofid\/ofx230"},{"key":"23091_CR39","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1093\/trstmh\/trz053","volume":"113","author":"KM Oo","year":"2019","unstructured":"Oo, K. M. et al. Molecular mechanisms of antimicrobial resistance and phylogenetic relationships of Salmonella enterica isolates from febrile patients in Yangon, Myanmar. Trans. R. Soc. Trop. Med. Hyg. 113, 641\u2013648 (2019).","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"23091_CR40","doi-asserted-by":"publisher","first-page":"e0004785","DOI":"10.1371\/journal.pntd.0004785","volume":"10","author":"D Pham Thanh","year":"2016","unstructured":"Pham Thanh, D. et al. The molecular and spatial epidemiology of typhoid fever in rural Cambodia. PLoS Negl. Trop. Dis. 10, e0004785 (2016).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"23091_CR41","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/nrg.2017.88","volume":"19","author":"JL Gardy","year":"2018","unstructured":"Gardy, J. L. & Loman, N. J. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat. Rev. Genet. 19, 9\u201320 (2018).","journal-title":"Nat. Rev. Genet."},{"key":"23091_CR42","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1016\/j.cmi.2016.11.012","volume":"23","author":"MJ Ellington","year":"2017","unstructured":"Ellington, M. J. et al. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST subcommittee. Clin. Microbiol. Infect. 23, 2\u201322 (2017).","journal-title":"Clin. Microbiol. Infect."},{"key":"23091_CR43","doi-asserted-by":"publisher","first-page":"2300","DOI":"10.1093\/jac\/dkw093","volume":"71","author":"M Doumith","year":"2016","unstructured":"Doumith, M. et al. Detection of the plasmid-mediated mcr-1 gene conferring colistin resistance in human and food isolates of Salmonella enterica and Escherichia coli in England and Wales. J. Antimicrob. Chemother. 71, 2300\u20132305 (2016).","journal-title":"J. Antimicrob. Chemother."},{"key":"23091_CR44","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1038\/nrg3226","volume":"13","author":"X Didelot","year":"2012","unstructured":"Didelot, X., Bowden, R., Wilson, D. J., Peto, T. E. A. & Crook, D. W. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet. 13, 601\u2013612 (2012).","journal-title":"Nat. Rev. Genet."},{"key":"23091_CR45","doi-asserted-by":"crossref","unstructured":"NIHR Global Health Research Unit on Genomic Surveillance of AMR. Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap. BMJ Glob. Health 5, e002244 (2020).","DOI":"10.1136\/bmjgh-2019-002244"},{"key":"23091_CR46","doi-asserted-by":"crossref","unstructured":"The COVID-19 Genomics UK (COG-UK). An integrated national scale SARS-CoV-2 genomic surveillance network. The Lancet Microbe1, E99-E100 (2020).","DOI":"10.1016\/S2666-5247(20)30054-9"},{"key":"23091_CR47","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1038\/538127a","volume":"538","author":"J Perkel","year":"2016","unstructured":"Perkel, J. Democratic databases: science on GitHub. Nature 538, 127\u2013128 (2016).","journal-title":"Nature"},{"key":"23091_CR48","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch private metadata https:\/\/cgps.gitbook.io\/pathogenwatch\/how-to-use-pathogenwatch\/private-metadata. Accessed 28 January 2021."},{"key":"23091_CR49","doi-asserted-by":"publisher","first-page":"S31","DOI":"10.1093\/cid\/ciy927","volume":"68","author":"AD Bentsi-Enchill","year":"2019","unstructured":"Bentsi-Enchill, A. D. & Hombach, J. Revised global typhoid vaccination policy. Clin. Infect. Dis. 68, S31\u2013S33 (2019).","journal-title":"Clin. Infect. Dis."},{"key":"23091_CR50","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/s41564-019-0651-y","volume":"5","author":"C Colijn","year":"2020","unstructured":"Colijn, C., Corander, J. & Croucher, N. J. Designing ecologically optimized pneumococcal vaccines using population genomics. Nat. Microbiol. 5, 473\u2013485 (2020).","journal-title":"Nat. Microbiol."},{"key":"23091_CR51","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1016\/S1473-3099(19)30297-X","volume":"19","author":"SW Lo","year":"2019","unstructured":"Lo, S. W. et al. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study. Lancet Infect. Dis. 19, 759\u2013769 (2019).","journal-title":"Lancet Infect. Dis."},{"key":"23091_CR52","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1128\/CMR.00002-15","volume":"28","author":"JA Crump","year":"2015","unstructured":"Crump, J. A., Sjolund-Karlsson, M., Gordon, M. A. & Parry, C. M. Epidemiology, clinical presentation, laboratory diagnosis, antimicrobial resistance, and antimicrobial management of invasive Salmonella infections. Clin. Microbiol Rev. 28, 901\u2013937 (2015).","journal-title":"Clin. Microbiol Rev."},{"key":"23091_CR53","unstructured":"Facebook Inc.\u00a0React https:\/\/reactjs.org\/. Accessed 28 January 2021."},{"key":"23091_CR54","unstructured":"Google.\u00a0Material Design Lite https:\/\/getmdl.io. Accessed 28 January 2021."},{"key":"23091_CR55","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Phylocanvas http:\/\/phylocanvas.org. Accessed 28 January 2021."},{"key":"23091_CR56","unstructured":"Agafonkin V.\u00a0Leaflet https:\/\/leafletjs.com\/. Accessed 28 January 2021."},{"key":"23091_CR57","unstructured":"Jacomy A. and Plique G.\u00a0Sigma http:\/\/sigmajs.org\/. Accessed 28 January 2021."},{"key":"23091_CR58","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput Biol. 19, 455\u2013477 (2012).","journal-title":"J. Comput Biol."},{"key":"23091_CR59","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch short-read assembly https:\/\/cgps.gitbook.io\/pathogenwatch\/technical-descriptions\/short-read-assembly. Accessed 28 January 2021."},{"key":"23091_CR60","first-page":"e000083","volume":"2","author":"AJ Page","year":"2016","unstructured":"Page, A. J. et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb. Genomics 2, e000083 (2016).","journal-title":"Microb. Genomics"},{"key":"23091_CR61","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"DR Zerbino","year":"2008","unstructured":"Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821\u2013829 (2008).","journal-title":"Genome Res."},{"key":"23091_CR62","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0997-x","volume":"17","author":"BD Ondov","year":"2016","unstructured":"Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).","journal-title":"Genome Biol."},{"key":"23091_CR63","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch speciator https:\/\/cgps.gitbook.io\/pathogenwatch\/technical-descriptions\/species-assignment\/speciator. Accessed 28 January 2021."},{"key":"23091_CR64","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch typhing methods https:\/\/cgps.gitbook.io\/pathogenwatch\/technical-descriptions\/typing-methods. Accessed 28 January 2021."},{"key":"23091_CR65","unstructured":"Warwick Medical School.\u00a0Enterobase allele ST search http:\/\/enterobase.warwick.ac.uk\/species\/senterica\/allele_st_search. Accessed 28 January 2021."},{"key":"23091_CR66","unstructured":"Warwick Medical School.\u00a0Enterobase cgMLST database http:\/\/enterobase.warwick.ac.uk\/species\/index\/senterica. Accessed 28 January 2021."},{"key":"23091_CR67","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch MLST https:\/\/cgps.gitbook.io\/pathogenwatch\/technical-descriptions\/typing-methods\/mlst. Accessed 28 January 2021."},{"key":"23091_CR68","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch cgMLST https:\/\/cgps.gitbook.io\/pathogenwatch\/technical-descriptions\/typing-methods\/cgmlst. Accessed 28 January 2021."},{"key":"23091_CR69","unstructured":"Holt K.\u00a0GenoTyphi https:\/\/github.com\/katholt\/genotyphi. Accessed 28 January 2021."},{"key":"23091_CR70","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch IncTyper https:\/\/cgps.gitbook.io\/pathogenwatch\/technical-descriptions\/inctyper. Accessed 28 January 2021."},{"key":"23091_CR71","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch S. Typhi core gene library https:\/\/gitlab.com\/cgps\/cgps-core-fp\/-\/tree\/master\/schemes\/90370. Accessed 28 January 2021."},{"key":"23091_CR72","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691\u20133693 (2015).","journal-title":"Bioinformatics"},{"key":"23091_CR73","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772\u2013780 (2013).","journal-title":"Mol. Biol. Evol."},{"key":"23091_CR74","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch core genome tree https:\/\/cgps.gitbook.io\/pathogenwatch\/technical-descriptions\/core-genome-tree. Accessed 28 January 2021."},{"key":"23091_CR75","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","volume":"27","author":"KP Schliep","year":"2011","unstructured":"Schliep, K. P. phangorn: phylogenetic analysis in R. Bioinformatics 27, 592\u2013593 (2011).","journal-title":"Bioinformatics"},{"key":"23091_CR76","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","volume":"35","author":"E Paradis","year":"2019","unstructured":"Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526\u2013528 (2019).","journal-title":"Bioinformatics"},{"key":"23091_CR77","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","volume":"22","author":"A Stamatakis","year":"2006","unstructured":"Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688\u20132690 (2006).","journal-title":"Bioinformatics"},{"key":"23091_CR78","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","volume":"5","author":"MN Price","year":"2010","unstructured":"Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).","journal-title":"PLoS ONE"},{"key":"23091_CR79","doi-asserted-by":"crossref","unstructured":"Jombart, T., Kendall, M., Almagro-Garcia, J. & Colijn, C. treespace: Statistical exploration of landscapes of phylogenetic trees. Mol. Ecol. Resour. 17, 1385\u20131392 (2017).","DOI":"10.1111\/1755-0998.12676"},{"key":"23091_CR80","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1093\/sysbio\/sys062","volume":"61","author":"DH Huson","year":"2012","unstructured":"Huson, D. H. & Scornavacca, C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061\u20131067 (2012).","journal-title":"Syst. Biol."},{"key":"23091_CR81","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch publication repository https:\/\/gitlab.com\/cgps\/pathogenwatch\/publications. Accessed 28 January 2021."},{"key":"23091_CR82","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1093\/comjnl\/16.1.30","volume":"16","author":"R Sibson","year":"1973","unstructured":"Sibson, R. SLINK: An optimally efficient algorithm for the single-link cluster method. Comput. J. 16, 30\u201334 (1973).","journal-title":"Comput. J."},{"key":"23091_CR83","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch S. Typhi AMR library https:\/\/gitlab.com\/cgps\/pathogenwatch\/amr-libraries\/-\/blob\/master\/90370.toml. Accessed 28 January 2021."},{"key":"23091_CR84","unstructured":"Centre for Genomic Pathogen Surveillance (CGPS).\u00a0Pathogenwatch AMR https:\/\/cgps.gitbook.io\/pathogenwatch\/technical-descriptions\/antimicrobial-resistance-prediction\/pw-amr. Accessed 28 January 2021."},{"key":"23091_CR85","unstructured":"Stevenson M.\u00a0epiR package https:\/\/www.rdocumentation.org\/packages\/epiR. Accessed 28 January 2021."},{"key":"23091_CR86","unstructured":"Clinical Laboratory Standards Institute. Performance Standards for Antimicrobial Susceptibility Testing.\u00a030th ed. CLSI supplement M100S.\u00a0(Clinical Laboratory Standards Institute, Wayne, PA, 2020)."}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-021-23091-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-021-23091-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-021-23091-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,2]],"date-time":"2022-12-02T07:10:55Z","timestamp":1669965055000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-021-23091-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,17]]},"references-count":86,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,12]]}},"alternative-id":["23091"],"URL":"https:\/\/doi.org\/10.1038\/s41467-021-23091-2","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.07.03.186692","asserted-by":"object"}]},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,17]]},"assertion":[{"value":"12 February 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 April 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 May 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"2879"}}