{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T17:10:54Z","timestamp":1793812254587,"version":"4.6.1"},"reference-count":57,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2021,3,29]],"date-time":"2021-03-29T00:00:00Z","timestamp":1616976000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,3,29]],"date-time":"2021-03-29T00:00:00Z","timestamp":1616976000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1119772"],"award-info":[{"award-number":["OPP1119772"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OP1191522"],"award-info":[{"award-number":["OP1191522"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Microbiol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Antimicrobial resistance in neonatal sepsis is rising, yet mechanisms of resistance that often spread between species via mobile genetic elements, ultimately limiting treatments in low- and middle-income countries (LMICs), are poorly characterized. The Burden of Antibiotic Resistance in Neonates from Developing Societies (BARNARDS) network was initiated to characterize the cause and burden of antimicrobial resistance in neonatal sepsis for seven LMICs in Africa and South Asia. A total of 36,285 neonates were enrolled in the BARNARDS study between November 2015 and December 2017, of whom 2,483 were diagnosed with culture-confirmed sepsis.\n                    <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                    (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009258) was the main cause of neonatal sepsis, with\n                    <jats:italic>Serratia marcescens<\/jats:italic>\n                    (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009151),\n                    <jats:italic>Klebsiella michiganensis<\/jats:italic>\n                    (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009117),\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200975) and\n                    <jats:italic>Enterobacter cloacae<\/jats:italic>\n                    complex (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200957) also detected. We present whole-genome sequencing, antimicrobial susceptibility and clinical data for 916 out of 1,038 neonatal sepsis isolates (97 isolates were not recovered from initial isolation at local sites). Enterobacterales (\n                    <jats:italic>K. pneumoniae, E. coli<\/jats:italic>\n                    and\n                    <jats:italic>E. cloacae<\/jats:italic>\n                    ) harboured multiple cephalosporin and carbapenem resistance genes. All isolated pathogens were resistant to multiple antibiotic classes, including those used to treat neonatal sepsis. Intraspecies diversity of\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    and\n                    <jats:italic>E. coli<\/jats:italic>\n                    indicated that multiple antibiotic-resistant lineages cause neonatal sepsis. Our results will underpin research towards better treatments for neonatal sepsis in LMICs.\n                  <\/jats:p>","DOI":"10.1038\/s41564-021-00870-7","type":"journal-article","created":{"date-parts":[[2021,3,29]],"date-time":"2021-03-29T12:03:18Z","timestamp":1617019398000},"page":"512-523","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":420,"title":["Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries"],"prefix":"10.1038","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5049-4481","authenticated-orcid":false,"given":"Kirsty","family":"Sands","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6819-927X","authenticated-orcid":false,"given":"Maria J.","family":"Carvalho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward","family":"Portal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn","family":"Thomson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Calie","family":"Dyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chinenye","family":"Akpulu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Andrews","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Ferreira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6934-2928","authenticated-orcid":false,"given":"David","family":"Gillespie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5987-5923","authenticated-orcid":false,"given":"Thomas","family":"Hender","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerenza","family":"Hood","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordan","family":"Mathias","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Milton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6188-5947","authenticated-orcid":false,"given":"Maria","family":"Nieto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khadijeh","family":"Taiyari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grace J.","family":"Chan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9243-2622","authenticated-orcid":false,"given":"Delayehu","family":"Bekele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Semaria","family":"Solomon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sulagna","family":"Basu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pinaki","family":"Chattopadhyay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suchandra","family":"Mukherjee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth","family":"Iregbu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatima","family":"Modibbo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stella","family":"Uwaezuoke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rabaab","family":"Zahra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haider","family":"Shirazi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adil","family":"Muhammad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Baptiste","family":"Mazarati","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aniceth","family":"Rucogoza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucie","family":"Gaju","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3165-5566","authenticated-orcid":false,"given":"Shaheen","family":"Mehtar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andre N. H.","family":"Bulabula","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9070-5247","authenticated-orcid":false,"given":"Andrew","family":"Whitelaw","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"BARNARDS Group","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4315-4096","authenticated-orcid":false,"given":"Timothy R.","family":"Walsh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,3,29]]},"reference":[{"key":"870_CR1","unstructured":"United Nations Inter-agency Group for Child Mortality Estimation. Levels & Trends in Child Mortality: Report 2018: Estimates Developed by the UN Inter-agency Group for Child Mortality Estimation (United Nations Children\u2019s Fund, 2018)."},{"key":"870_CR2","unstructured":"World Mortality 2019 (Department of Economic and Social Affairs, United Nations, 2019)."},{"key":"870_CR3","doi-asserted-by":"publisher","first-page":"101028","DOI":"10.1016\/j.siny.2019.101028","volume":"24","author":"V Shukla","year":"2019","unstructured":"Shukla, V., Mwenechanya, M. & Carlo, W. A. Dealing with neonatal emergencies in low-resource settings. Semin. Fetal Neonatal Med. 24, 101028 (2019).","journal-title":"Semin. Fetal Neonatal Med."},{"key":"870_CR4","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1080\/14787210.2020.1732818","volume":"18","author":"CR Popescu","year":"2020","unstructured":"Popescu, C. R. et al. Neonatal sepsis in low-income countries: epidemiology, diagnosis and prevention. Expert Rev. Anti. Infect. Ther. 18, 443\u2013452 (2020).","journal-title":"Expert Rev. Anti. Infect. Ther."},{"key":"870_CR5","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1097\/QCO.0000000000000371","volume":"30","author":"L Folgori","year":"2017","unstructured":"Folgori, L., Bielicki, J., Heath, P. T. & Sharland, M. Antimicrobial-resistant Gram-negative infections in neonates: burden of disease and challenges in treatment. Curr. Opin. Infect. Dis. 30, 281\u2013288 (2017).","journal-title":"Curr. Opin. Infect. Dis."},{"key":"870_CR6","first-page":"k5314","volume":"1","author":"MJ Sankar","year":"2019","unstructured":"Sankar, M. J. Neonatal sepsis in South Asia: huge burden and spiralling antimicrobial resistance. BMJ 1, k5314 (2019).","journal-title":"BMJ"},{"key":"870_CR7","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1086\/605473","volume":"200","author":"GL Darmstadt","year":"2010","unstructured":"Darmstadt, G. L. et al. Population-based incidence and etiology of community-acquired neonatal bacteremia in Mirzapur, Bangladesh: an observational study. J. Infect. Dis. 200, 906\u2013915 (2010).","journal-title":"J. Infect. Dis."},{"key":"870_CR8","doi-asserted-by":"publisher","first-page":"183","DOI":"10.2149\/tmh.2015-03","volume":"43","author":"O Peterside","year":"2015","unstructured":"Peterside, O., Pondei, K. & Akinbami, F. O. Bacteriological profile and antibiotic susceptibility pattern of neonatal sepsis at a teaching hospital in Bayelsa State, Nigeria. Trop. Med. Health 43, 183\u2013190 (2015).","journal-title":"Trop. Med. Health"},{"key":"870_CR9","first-page":"866","volume":"19","author":"O Ullah","year":"2016","unstructured":"Ullah, O. et al. Antibiotic sensitivity pattern of bacterial isolates of neonatal septicemia in Peshawar, Pakistan. Arch. Iran. Med. 19, 866\u2013869 (2016).","journal-title":"Arch. Iran. Med."},{"key":"870_CR10","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/s13756-019-0486-6","volume":"8","author":"A Sorsa","year":"2019","unstructured":"Sorsa, A., Fr\u00fch, J., St\u00f6tter, L. & Abdissa, S. Blood culture result profile and antimicrobial resistance pattern: a report from neonatal intensive care unit (NICU), Asella teaching and referral hospital, Asella, south East Ethiopia. Antimicrob. Resist. Infect. Control 8, 42 (2019).","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"870_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1097\/INF.0000000000000549","volume":"34","author":"DH Hamer","year":"2015","unstructured":"Hamer, D. H. et al. Etiology of bacteremia in young infants in six countries. Pediatr. Infect. Dis. J. 34, 1\u20138 (2015).","journal-title":"Pediatr. Infect. Dis. J."},{"key":"870_CR12","doi-asserted-by":"publisher","first-page":"e752","DOI":"10.1016\/S2214-109X(16)30148-6","volume":"4","author":"N Infection","year":"2016","unstructured":"Infection, N. & Denis, S. Characterisation and antimicrobial resistance of sepsis pathogens in neonates born in tertiary care centres in Delhi, India: a cohort study. Lancet Glob. Health 4, e752\u2013e760 (2016).","journal-title":"Lancet Glob. Health"},{"key":"870_CR13","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.1093\/cid\/ciy778","volume":"68","author":"R Farzana","year":"2019","unstructured":"Farzana, R., Jones, L. S., Rahman, A. & Andrey, D. O. Outbreak of hypervirulent multidrug-resistant Klebsiella variicola causing high mortality in neonates in Bangladesh. Clin. Infect. Dis. 68, 1225\u20131227 (2019).","journal-title":"Clin. Infect. Dis."},{"key":"870_CR14","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1099\/jmm.0.000947","volume":"68","author":"A Rohit","year":"2019","unstructured":"Rohit, A. et al. Whole-genome-based analysis reveals multiclone Serratia marcescens outbreaks in a non-neonatal intensive care unit setting in a tertiary care hospital in India. J. Med. Microbiol. 68, 616\u2013621 (2019).","journal-title":"J. Med. Microbiol."},{"key":"870_CR15","doi-asserted-by":"publisher","first-page":"638","DOI":"10.1097\/INF.0000000000002258","volume":"36","author":"L Wisgrill","year":"2019","unstructured":"Wisgrill, L. et al. Outbreak of yersiniabactin-producing Klebsiella pneumoniae in a neonatal intensive care unit. Pediatr. Infect. Dis. J. 36, 638\u2013642 (2019).","journal-title":"Pediatr. Infect. Dis. J."},{"key":"870_CR16","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1093\/cid\/ciu084","volume":"58","author":"MA Carl","year":"2014","unstructured":"Carl, M. A. et al. Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Class. Infect. Dis. 58, 1211\u20131218 (2014).","journal-title":"Class. Infect. Dis."},{"key":"870_CR17","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1016\/j.wombi.2017.10.012","volume":"31","author":"K Braye","year":"2018","unstructured":"Braye, K. et al. Effectiveness of intrapartum antibiotic prophylaxis for early-onset group B streptococcal infection: an integrative review. Women Birth 31, 244\u2013253 (2018).","journal-title":"Women Birth"},{"key":"870_CR18","doi-asserted-by":"publisher","first-page":"1219","DOI":"10.1016\/S1473-3099(19)30414-1","volume":"19","author":"U Okomo","year":"2019","unstructured":"Okomo, U. et al. Aetiology of invasive bacterial infection and antimicrobial resistance in neonates in sub-Saharan Africa: a systematic review and meta-analysis in line with the STROBE-NI reporting guidelines. Lancet Infect. Dis. 19, 1219\u20131234 (2019).","journal-title":"Lancet Infect. Dis."},{"key":"870_CR19","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1179\/2046905515Y.0000000029","volume":"35","author":"A Dramowski","year":"2015","unstructured":"Dramowski, A., Madide, A. & Bekker, A. Neonatal nosocomial bloodstream infections at a referral hospital in a middle-income country: burden, pathogens, antimicrobial resistance and mortality. Paediatr. Int. Child Health 35, 265\u2013272 (2015).","journal-title":"Paediatr. Int. Child Health"},{"key":"870_CR20","unstructured":"Breakpoint Tables for Interpretation of MICs and Zone Diameters Version 9.0 (European Committee on Antimicrobial Susceptibility Testing, 2019)."},{"key":"870_CR21","unstructured":"Guidance Document on Tigecycline Dosing in association with Revision of Breakpoints for Enterobacterales and Other Species With an \u201cIntermediate\u201d Category (European Committee on Antimicrobial Susceptibility Testing, 2018)."},{"key":"870_CR22","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1016\/j.ijmm.2018.06.012","volume":"308","author":"R Marando","year":"2018","unstructured":"Marando, R. et al. Predictors of the extended-spectrum-beta lactamases producing Enterobacteriaceae neonatal sepsis at a tertiary hospital, Tanzania. Int. J. Med. Microbiol. 308, 803\u2013811 (2018).","journal-title":"Int. J. Med. Microbiol."},{"key":"870_CR23","doi-asserted-by":"publisher","first-page":"E3574","DOI":"10.1073\/pnas.1501049112","volume":"112","author":"KE Holt","year":"2015","unstructured":"Holt, K. E. et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc. Natl Acad. Sci. USA 112, E3574\u2013E3581 (2015).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"870_CR24","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/j.mib.2019.06.004","volume":"51","author":"SJ Dunn","year":"2019","unstructured":"Dunn, S. J., Connor, C. & Mcnally, A. The evolution and transmission of multi-drug resistant Escherichia coli and Klebsiella pneumoniae: the complexity of clones and plasmids. Curr. Opin. Microbiol. 51, 51\u201356 (2019).","journal-title":"Curr. Opin. Microbiol."},{"key":"870_CR25","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1186\/s12879-016-1870-y","volume":"16","author":"J Yu","year":"2016","unstructured":"Yu, J. et al. Nosocomial outbreak of KPC-2- and NDM-1-producing Klebsiella pneumoniae in a neonatal ward: a retrospective study. BMC Infect. Dis. 16, 563 (2016).","journal-title":"BMC Infect. Dis."},{"key":"870_CR26","first-page":"468","volume":"43","author":"H Battikh","year":"2016","unstructured":"Battikh, H. et al. Clonal spread of colistin-resistant Klebsiella pneumoniae coproducing KPC and VIM carbapenemases in neonates at a Tunisian university hospital. Microb. Drug Resist. 43, 468\u2013472 (2016).","journal-title":"Microb. Drug Resist."},{"key":"870_CR27","first-page":"e000196","volume":"4","author":"MMC Lam","year":"2018","unstructured":"Lam, M. M. C. et al. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microb. Genom. 4, e000196 (2018).","journal-title":"Microb. Genom."},{"key":"870_CR28","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.1038\/ng.3145","volume":"46","author":"A Mentzer","year":"2014","unstructured":"Mentzer, A. et al. Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nat. Genet. 46, 1321\u20131326 (2014).","journal-title":"Nat. Genet."},{"key":"870_CR29","doi-asserted-by":"publisher","first-page":"e752","DOI":"10.1016\/S2214-109X(16)30148-6","volume":"4","author":"N Infection","year":"2016","unstructured":"Infection, N. & Denis, S. Characterisation and antimicrobial resistance of sepsis pathogens in neonates born in tertiary care centres in Delhi, India: a cohort study. Lancet Glob. Health 4, e752\u2013e760 (2016).","journal-title":"Lancet Glob. Health"},{"key":"870_CR30","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068\u20132069 (2014).","journal-title":"Bioinformatics"},{"key":"870_CR31","doi-asserted-by":"publisher","first-page":"1935","DOI":"10.2147\/IDR.S175584","volume":"11","author":"C Wang","year":"2018","unstructured":"Wang, C. Resistance phenotype and clinical molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae among pediatric patients in Shanghai. Infect. Drug Resist. 11, 1935\u20131943 (2018).","journal-title":"Infect. Drug Resist."},{"key":"870_CR32","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1111\/j.1469-0691.2012.03805.x","volume":"19","author":"S Breurec","year":"2013","unstructured":"Breurec, S. et al. Klebsiella pneumoniae resistant to third-generation cephalosporins in five African and two Vietnamese major towns: multiclonal population structure with two major international clonal groups, CG15 and CG258. Clin. Microbiol. Infect. 19, 349\u2013355 (2013).","journal-title":"Clin. Microbiol. Infect."},{"key":"870_CR33","first-page":"e000306","volume":"5","author":"M Hamidian","year":"2019","unstructured":"Hamidian, M. & Nigro, S. J.Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii. Microb. Genom. 5, e000306 (2019).","journal-title":"Microb. Genom."},{"key":"870_CR34","first-page":"e000086","volume":"2","author":"TR Connor","year":"2016","unstructured":"Connor, T. R. et al. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microb. Genom. 2, e000086 (2016).","journal-title":"Microb. Genom."},{"key":"870_CR35","unstructured":"Krueger, F. Trim Galore v.0.4.3 https:\/\/github.com\/FelixKrueger\/TrimGalore (The Babraham Institute, 2017)."},{"key":"870_CR36","unstructured":"Andrews, S. FastQC: a quality control tool for high throughput sequence data http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc (2009)."},{"key":"870_CR37","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels, P., Lundin, S. & Max, K. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047\u20133048 (2016).","journal-title":"Bioinformatics"},{"key":"870_CR38","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","volume":"27","author":"T Mago\u010d","year":"2011","unstructured":"Mago\u010d, T. & Salzberg, S. L.FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957\u20132963 (2011).","journal-title":"Bioinformatics"},{"key":"870_CR39","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":"870_CR40","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"870_CR41","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"870_CR42","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","volume":"9","author":"BJ Walker","year":"2014","unstructured":"Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).","journal-title":"PLoS ONE"},{"key":"870_CR43","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. Bioinformatics applications note genome analysis QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072\u20131075 (2013).","journal-title":"Bioinformatics"},{"key":"870_CR44","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1093\/nar\/gkh435","volume":"32","author":"S Mcginnis","year":"2004","unstructured":"Mcginnis, S. & Madden, T. L. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32, 20\u201325 (2004).","journal-title":"Nucleic Acids Res."},{"key":"870_CR45","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13073-014-0090-6","volume":"6","author":"M Inouye","year":"2014","unstructured":"Inouye, M. et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 6, 90 (2014).","journal-title":"Genome Med."},{"key":"870_CR46","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":"870_CR47","doi-asserted-by":"publisher","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","volume":"44","author":"L Chen","year":"2016","unstructured":"Chen, L., Zheng, D., Liu, B., Yang, J. & Jin, Q. VFDB 2016: hierarchical and refined dataset for big data analysis\u201410 years on. Nucleic Acids Res. 44, D694\u2013D697 (2016).","journal-title":"Nucleic Acids Res."},{"key":"870_CR48","unstructured":"Seemann, T. ABRicate v.0.9.7 https:\/\/github.com\/tseemann\/abricate (The University of Melbourne, 2019)."},{"key":"870_CR49","doi-asserted-by":"publisher","first-page":"e00483-19","DOI":"10.1128\/AAC.00483-19","volume":"63","author":"M Feldgarden","year":"2019","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, e00483-19 (2019).","journal-title":"Antimicrob. Agents Chemother."},{"key":"870_CR50","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":"870_CR51","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1186\/1471-2105-11-595","volume":"11","author":"KA Jolley","year":"2010","unstructured":"Jolley, K. A. & Maiden, M. C. J.BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11, 595 (2010).","journal-title":"BMC Bioinformatics"},{"key":"870_CR52","doi-asserted-by":"publisher","first-page":"e00197-18","DOI":"10.1128\/JCM.00197-18","volume":"56","author":"RR Wick","year":"2018","unstructured":"Wick, R. R., Heinz, E., Holt, K. E. & Wyres, K. L.Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes. J. Clin. Microbiol. 56, e00197-18 (2018).","journal-title":"J. Clin. Microbiol."},{"key":"870_CR53","doi-asserted-by":"publisher","first-page":"2410","DOI":"10.1128\/JCM.00008-15","volume":"53","author":"KG Joensen","year":"2015","unstructured":"Joensen, K. G., Tetzschner, A. M. M., Iguchi, A. & Aarestrup, F. M. Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J. Clin. Microbiol. 53, 2410\u20132426 (2015).","journal-title":"J. Clin. Microbiol."},{"key":"870_CR54","doi-asserted-by":"publisher","first-page":"1685","DOI":"10.1128\/JCM.00323-15","volume":"53","author":"S Zhang","year":"2015","unstructured":"Zhang, S. et al. Salmonella serotype determination utilizing high-throughput genome sequencing data. J. Clin. Microbiol. 53, 1685\u20131692 (2015).","journal-title":"J. Clin. Microbiol."},{"key":"870_CR55","first-page":"e000192","volume":"4","author":"J Beghain","year":"2018","unstructured":"Beghain, J., Bridier-Nahmias, A., Le Nagard, H., Denamur, E. & Clermont, O.ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microb. Genom. 4, e000192 (2018).","journal-title":"Microb. Genom."},{"key":"870_CR56","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":"870_CR57","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1093\/nar\/gkz239","volume":"47","author":"I Letunic","year":"2019","unstructured":"Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, 256\u2013259 (2019).","journal-title":"Nucleic Acids Res."}],"container-title":["Nature Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00870-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00870-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00870-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,29]],"date-time":"2023-01-29T23:43:51Z","timestamp":1675035831000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00870-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,3,29]]},"references-count":57,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2021,4]]}},"alternative-id":["870"],"URL":"https:\/\/doi.org\/10.1038\/s41564-021-00870-7","relation":{},"ISSN":["2058-5276"],"issn-type":[{"value":"2058-5276","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,3,29]]},"assertion":[{"value":"21 January 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 January 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 March 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"}}]}}