{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T10:49:20Z","timestamp":1778237360076,"version":"3.51.4"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2019,7,29]],"date-time":"2019-07-29T00:00:00Z","timestamp":1564358400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2019,7,29]],"date-time":"2019-07-29T00:00:00Z","timestamp":1564358400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Microbiol"],"DOI":"10.1038\/s41564-019-0492-8","type":"journal-article","created":{"date-parts":[[2019,7,29]],"date-time":"2019-07-29T16:02:59Z","timestamp":1564416179000},"page":"1919-1929","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":690,"title":["Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread"],"prefix":"10.1038","volume":"4","author":[{"given":"Sophia","family":"David","sequence":"first","affiliation":[]},{"given":"Sandra","family":"Reuter","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1512-6194","authenticated-orcid":false,"given":"Simon R.","family":"Harris","sequence":"additional","affiliation":[]},{"given":"Corinna","family":"Glasner","sequence":"additional","affiliation":[]},{"given":"Theresa","family":"Feltwell","sequence":"additional","affiliation":[]},{"given":"Silvia","family":"Argimon","sequence":"additional","affiliation":[]},{"given":"Khalil","family":"Abudahab","sequence":"additional","affiliation":[]},{"given":"Richard","family":"Goater","sequence":"additional","affiliation":[]},{"given":"Tommaso","family":"Giani","sequence":"additional","affiliation":[]},{"given":"Giulia","family":"Errico","sequence":"additional","affiliation":[]},{"given":"Marianne","family":"Aspbury","sequence":"additional","affiliation":[]},{"given":"Sara","family":"Sjunnebo","sequence":"additional","affiliation":[]},{"name":"the EuSCAPE Working Group","sequence":"additional","affiliation":[]},{"given":"Andi","family":"Koraqi","sequence":"additional","affiliation":[]},{"given":"Denada","family":"Lacej","sequence":"additional","affiliation":[]},{"given":"Petra","family":"Apfalter","sequence":"additional","affiliation":[]},{"given":"Rainer","family":"Hartl","sequence":"additional","affiliation":[]},{"given":"Youri","family":"Glupczynski","sequence":"additional","affiliation":[]},{"given":"Te-Din","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Tanya","family":"Strateva","sequence":"additional","affiliation":[]},{"given":"Yuliya","family":"Marteva-Proevska","sequence":"additional","affiliation":[]},{"given":"Arjana Tambic","family":"Andrasevic","sequence":"additional","affiliation":[]},{"given":"Iva","family":"Butic","sequence":"additional","affiliation":[]},{"given":"Despo","family":"Pieridou-Bagatzouni","sequence":"additional","affiliation":[]},{"given":"Panagiota","family":"Maikanti-Charalampous","sequence":"additional","affiliation":[]},{"given":"Jaroslav","family":"Hrabak","sequence":"additional","affiliation":[]},{"given":"Helena","family":"Zemlickova","sequence":"additional","affiliation":[]},{"given":"Anette","family":"Hammerum","sequence":"additional","affiliation":[]},{"given":"Lotte","family":"Jakobsen","sequence":"additional","affiliation":[]},{"given":"Marina","family":"Ivanova","sequence":"additional","affiliation":[]},{"given":"Anastasia","family":"Pavelkovich","sequence":"additional","affiliation":[]},{"given":"Jari","family":"Jalava","sequence":"additional","affiliation":[]},{"given":"Monica","family":"\u00d6sterblad","sequence":"additional","affiliation":[]},{"given":"Laurent","family":"Dortet","sequence":"additional","affiliation":[]},{"given":"Sophie","family":"Vaux","sequence":"additional","affiliation":[]},{"given":"Martin","family":"Kaase","sequence":"additional","affiliation":[]},{"given":"S\u00f6ren G.","family":"Gatermann","sequence":"additional","affiliation":[]},{"given":"Alkiviadis","family":"Vatopoulos","sequence":"additional","affiliation":[]},{"given":"Kyriaki","family":"Tryfinopoulou","sequence":"additional","affiliation":[]},{"given":"\u00c1kos","family":"T\u00f3th","sequence":"additional","affiliation":[]},{"given":"Laura","family":"J\u00e1nv\u00e1ri","sequence":"additional","affiliation":[]},{"given":"Teck Wee","family":"Boo","sequence":"additional","affiliation":[]},{"given":"Elaine","family":"McGrath","sequence":"additional","affiliation":[]},{"given":"Yehuda","family":"Carmeli","sequence":"additional","affiliation":[]},{"given":"Amos","family":"Adler","sequence":"additional","affiliation":[]},{"given":"Annalisa","family":"Pantosti","sequence":"additional","affiliation":[]},{"given":"Monica","family":"Monaco","sequence":"additional","affiliation":[]},{"given":"Lul","family":"Raka","sequence":"additional","affiliation":[]},{"given":"Arsim","family":"Kurti","sequence":"additional","affiliation":[]},{"given":"Arta","family":"Balode","sequence":"additional","affiliation":[]},{"given":"Mara","family":"Saule","sequence":"additional","affiliation":[]},{"given":"Jolanta","family":"Miciuleviciene","sequence":"additional","affiliation":[]},{"given":"Aiste","family":"Mierauskaite","sequence":"additional","affiliation":[]},{"given":"Monique","family":"Perrin-Weniger","sequence":"additional","affiliation":[]},{"given":"Paul","family":"Reichert","sequence":"additional","affiliation":[]},{"given":"Nina","family":"Nestorova","sequence":"additional","affiliation":[]},{"given":"Sonia","family":"Debattista","sequence":"additional","affiliation":[]},{"given":"Gordana","family":"Mijovic","sequence":"additional","affiliation":[]},{"given":"Milena","family":"Lopicic","sequence":"additional","affiliation":[]},{"given":"\u00d8rjan","family":"Samuelsen","sequence":"additional","affiliation":[]},{"given":"Bj\u00f8rg","family":"Haldorsen","sequence":"additional","affiliation":[]},{"given":"Dorota","family":"Zabicka","sequence":"additional","affiliation":[]},{"given":"Elzbieta","family":"Literacka","sequence":"additional","affiliation":[]},{"given":"Manuela","family":"Cani\u00e7a","sequence":"additional","affiliation":[]},{"given":"Vera","family":"Manageiro","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Kaftandzieva","sequence":"additional","affiliation":[]},{"given":"Elena","family":"Trajkovska-Dokic","sequence":"additional","affiliation":[]},{"given":"Maria","family":"Damian","sequence":"additional","affiliation":[]},{"given":"Brandusa","family":"Lixandru","sequence":"additional","affiliation":[]},{"given":"Zora","family":"Jelesic","sequence":"additional","affiliation":[]},{"given":"Anika","family":"Trudic","sequence":"additional","affiliation":[]},{"given":"Milan","family":"Niks","sequence":"additional","affiliation":[]},{"given":"Eva","family":"Schreterova","sequence":"additional","affiliation":[]},{"given":"Mateja","family":"Pirs","sequence":"additional","affiliation":[]},{"given":"Tjasa","family":"Cerar","sequence":"additional","affiliation":[]},{"given":"Jes\u00fas","family":"Oteo","sequence":"additional","affiliation":[]},{"given":"Bel\u00e9n","family":"Aracil","sequence":"additional","affiliation":[]},{"given":"Christian","family":"Giske","sequence":"additional","affiliation":[]},{"given":"Karin","family":"Sj\u00f6str\u00f6m","sequence":"additional","affiliation":[]},{"given":"Deniz","family":"G\u00fcr","sequence":"additional","affiliation":[]},{"given":"Asli","family":"Cakar","sequence":"additional","affiliation":[]},{"given":"Neil","family":"Woodford","sequence":"additional","affiliation":[]},{"given":"Katie","family":"Hopkins","sequence":"additional","affiliation":[]},{"given":"Camilla","family":"Wiuff","sequence":"additional","affiliation":[]},{"given":"Derek J.","family":"Brown","sequence":"additional","affiliation":[]},{"name":"the ESGEM Study Group","sequence":"additional","affiliation":[]},{"given":"Edward J.","family":"Feil","sequence":"additional","affiliation":[]},{"given":"Gian Maria","family":"Rossolini","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6688-0854","authenticated-orcid":false,"given":"David M.","family":"Aanensen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9971-522X","authenticated-orcid":false,"given":"Hajo","family":"Grundmann","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,7,29]]},"reference":[{"key":"492_CR1","unstructured":"Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics (World Health Organization, 2017)."},{"key":"492_CR2","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/S1473-3099(18)30605-4","volume":"19","author":"A Cassini","year":"2019","unstructured":"Cassini, A. et al. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis. Lancet Infect. Dis. 19, 56\u201366 (2019).","journal-title":"Lancet Infect. Dis."},{"key":"492_CR3","doi-asserted-by":"publisher","first-page":"e00204-11","DOI":"10.1128\/mBio.00204-11","volume":"2","author":"AJ Mathers","year":"2011","unstructured":"Mathers, A. J. et al. Molecular dissection of an outbreak of carbapenem-resistant Enterobacteriaceae reveals intergenus KPC carbapenemase transmission through a promiscuous plasmid. mBio 2, e00204-11 (2011).","journal-title":"mBio"},{"key":"492_CR4","doi-asserted-by":"publisher","first-page":"3025","DOI":"10.1093\/jac\/dkx264","volume":"72","author":"J Martin","year":"2017","unstructured":"Martin, J. et al. Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission. J. Antimicrob. Chemother. 72, 3025\u20133034 (2017).","journal-title":"J. Antimicrob. Chemother."},{"key":"492_CR5","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1128\/AAC.45.4.1151-1161.2001","volume":"45","author":"H Yigit","year":"2001","unstructured":"Yigit, H. et al. Novel carbapenem-hydrolyzing \u03b2-lactamase, KPC-1, from a carbapenem-resistant strain of Klebsiella pneumoniae. Antimicrob. Agents Chemother. 45, 1151\u20131161 (2001).","journal-title":"Antimicrob. Agents Chemother."},{"key":"492_CR6","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1128\/AAC.48.1.15-22.2004","volume":"48","author":"L Poirel","year":"2004","unstructured":"Poirel, L., Heritier, C., Tolun, V. & Nordmann, P. Emergence of oxacillinase-mediated resistance to imipenem in Klebsiella pneumoniae. Antimicrob. Agents Chemother. 48, 15\u201322 (2004).","journal-title":"Antimicrob. Agents Chemother."},{"key":"492_CR7","doi-asserted-by":"publisher","first-page":"5046","DOI":"10.1128\/AAC.00774-09","volume":"53","author":"D Yong","year":"2009","unstructured":"Yong, D. et al. Characterization of a new metallo-\u03b2-lactamase gene, bla\n                           NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob. Agents Chemother. 53, 5046\u20135054 (2009).","journal-title":"Antimicrob. Agents Chemother."},{"key":"492_CR8","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1016\/S1473-3099(13)70190-7","volume":"13","author":"LS Munoz-Price","year":"2013","unstructured":"Munoz-Price, L. S. et al. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect. Dis. 13, 785\u2013796 (2013).","journal-title":"Lancet Infect. Dis."},{"key":"492_CR9","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/S1473-3099(11)70059-7","volume":"11","author":"TR Walsh","year":"2011","unstructured":"Walsh, T. R., Weeks, J., Livermore, D. M. & Toleman, M. A. Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study. Lancet Infect. Dis. 11, 355\u2013362 (2011).","journal-title":"Lancet Infect. Dis."},{"key":"492_CR10","doi-asserted-by":"publisher","first-page":"16260","DOI":"10.1038\/nmicrobiol.2016.260","volume":"2","author":"Y Wang","year":"2017","unstructured":"Wang, Y. et al. Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production. Nat. Microbiol. 2, 16260 (2017).","journal-title":"Nat. Microbiol."},{"key":"492_CR11","doi-asserted-by":"publisher","first-page":"17","DOI":"10.2807\/1560-7917.ES.2015.20.45.30062","volume":"20","author":"B Albiger","year":"2015","unstructured":"Albiger, B. et al. Carbapenemase-producing Enterobacteriaceae in Europe: assessment by national experts from 38 countries, May 2015. Eurosurveillance 20, 17\u201334 (2015).","journal-title":"Eurosurveillance"},{"key":"492_CR12","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1007\/s10096-014-2249-x","volume":"34","author":"M Kazi","year":"2015","unstructured":"Kazi, M. et al. Molecular characterization of carbapenem-resistant Enterobacteriaceae at a tertiary care laboratory in Mumbai. Eur. J. Clin. Microbiol. Infect. Dis. 34, 467\u2013472 (2015).","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"492_CR13","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-016-1858-7","volume":"16","author":"A Singh-Moodley","year":"2016","unstructured":"Singh-Moodley, A. & Perovic, O. Antimicrobial susceptibility testing in predicting the presence of carbapenemase genes in Enterobacteriaceae in South Africa. BMC Infect. Dis. 16, 536 (2016).","journal-title":"BMC Infect. Dis."},{"key":"492_CR14","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/S1473-3099(16)30257-2","volume":"17","author":"H Grundmann","year":"2017","unstructured":"Grundmann, H. et al. Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study. Lancet Infect. Dis. 17, 153\u2013163 (2017).","journal-title":"Lancet Infect. Dis."},{"key":"492_CR15","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":"492_CR16","doi-asserted-by":"publisher","first-page":"e01057-17","DOI":"10.1128\/genomeA.01057-17","volume":"5","author":"SW Long","year":"2017","unstructured":"Long, S. W. et al. Whole-genome sequencing of a human clinical isolate of the novel species Klebsiella quasivariicola sp. nov. Genome Announc. 5, e01057-17 (2017).","journal-title":"Genome Announc."},{"key":"492_CR17","doi-asserted-by":"publisher","first-page":"4178","DOI":"10.1128\/JCM.43.8.4178-4182.2005","volume":"43","author":"L Diancourt","year":"2005","unstructured":"Diancourt, L., Passet, V., Verhoef, J., Grimont, P. A. & Brisse, S. Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J. Clin. Microbiol. 43, 4178\u20134182 (2005).","journal-title":"J. Clin. Microbiol."},{"key":"492_CR18","doi-asserted-by":"crossref","unstructured":"Aspbury, M. et al. Rapid statistical methods for inferring intra- and inter-hospital transmission of nosocomial pathogens from whole genome sequence data. Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/442319v1 (2018).","DOI":"10.1101\/442319"},{"key":"492_CR19","doi-asserted-by":"publisher","first-page":"e01355-14","DOI":"10.1128\/mBio.01355-14","volume":"5","author":"L Chen","year":"2014","unstructured":"Chen, L., Mathema, B., Pitout, J. D. D., DeLeo, F. R. & Kreiswirth, B. N. Epidemic Klebsiella pneumoniae ST258 is a hybrid strain. mBio 5, e01355-14 (2014).","journal-title":"mBio"},{"key":"492_CR20","doi-asserted-by":"publisher","first-page":"4943","DOI":"10.1128\/AAC.00296-11","volume":"55","author":"KM Papp-Wallace","year":"2011","unstructured":"Papp-Wallace, K. M., Endimiani, A., Taracila, M. A. & Bonomo, R. A. Carbapenems: past, present, and future. Antimicrob. Agents Chemother. 55, 4943\u20134960 (2011).","journal-title":"Antimicrob. Agents Chemother."},{"key":"492_CR21","doi-asserted-by":"publisher","first-page":"e00440-18","DOI":"10.1128\/mBio.00440-18","volume":"9","author":"TJB de Man","year":"2018","unstructured":"de Man, T. J. B. et al. Genomic analysis of a pan-resistant isolate of Klebsiella pneumoniae, United States 2016. mBio 9, e00440-18 (2018).","journal-title":"mBio"},{"key":"492_CR22","first-page":"15","volume":"3","author":"G Meletis","year":"2016","unstructured":"Meletis, G. Carbapenem resistance: overview of the problem and future perspectives. Ther. Adv. Infect. Dis. 3, 15\u201321 (2016).","journal-title":"Ther. Adv. Infect. Dis."},{"key":"492_CR23","doi-asserted-by":"publisher","first-page":"894","DOI":"10.1038\/nrmicro2693","volume":"9","author":"K Bush","year":"2011","unstructured":"Bush, K. et al. Tackling antibiotic resistance. Nat. Rev. Microbiol. 9, 894\u2013896 (2011).","journal-title":"Nat. Rev. Microbiol."},{"key":"492_CR24","doi-asserted-by":"publisher","first-page":"e00969-18","DOI":"10.1128\/mBio.00969-18","volume":"9","author":"AK Murray","year":"2018","unstructured":"Murray, A. K. et al. Novel insights into selection for antibiotic resistance in complex microbial communities. mBio 9, e00969-18 (2018).","journal-title":"mBio"},{"key":"492_CR25","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1093\/cid\/cir025","volume":"52","author":"MJ Schwaber","year":"2011","unstructured":"Schwaber, M. J. et al. Containment of a country-wide outbreak of carbapenem-resistant Klebsiella pneumoniae in Israeli hospitals via a nationally implemented intervention. Clin. Infect. Dis. 52, 848\u2013855 (2011).","journal-title":"Clin. Infect. Dis."},{"key":"492_CR26","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1093\/jac\/dkm356","volume":"60","author":"ME Falagas","year":"2007","unstructured":"Falagas, M. E. et al. Risk factors of carbapenem-resistant Klebsiella pneumoniae infections: a matched case-control study. J. Antimicrob. Chemother. 60, 1124\u20131130 (2007).","journal-title":"J. Antimicrob. Chemother."},{"key":"492_CR27","doi-asserted-by":"publisher","first-page":"555","DOI":"10.4103\/ijmm.IJMM_17_144","volume":"35","author":"B Mohan","year":"2017","unstructured":"Mohan, B. et al. Fecal carriage of carbapenem-resistant Enterobacteriaceae and risk factor analysis in hospitalised patients: a single centre study from India. Indian J. Med. Microbiol. 35, 555\u2013562 (2017).","journal-title":"Indian J. Med. Microbiol."},{"key":"492_CR28","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/j.ijid.2017.04.007","volume":"59","author":"A Bartolini","year":"2017","unstructured":"Bartolini, A. et al. Prevalence, molecular epidemiology and intra-hospital acquisition of Klebsiella pneumoniae strains producing carbapenemases in an Italian teaching hospital from January 2015 to September 2016. Int. J. Infect. Dis. 59, 103\u2013109 (2017).","journal-title":"Int. J. Infect. Dis."},{"key":"492_CR29","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1089\/mdr.2015.0179","volume":"22","author":"E Yusuf","year":"2016","unstructured":"Yusuf, E. et al. OXA-48 producing Klebsiella pneumoniae in a household contact of a previously infected patient: person-to-person transmission or coincidental community acquisition? Microb. Drug Resist. 22, 134\u2013136 (2016).","journal-title":"Microb. Drug Resist."},{"key":"492_CR30","doi-asserted-by":"publisher","first-page":"898","DOI":"10.1038\/s41564-018-0192-9","volume":"3","author":"P Munk","year":"2018","unstructured":"Munk, P. et al. Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries. Nat. Microbiol. 3, 898\u2013908 (2018).","journal-title":"Nat. Microbiol."},{"key":"492_CR31","doi-asserted-by":"publisher","first-page":"e00444-16","DOI":"10.1128\/mBio.00444-16","volume":"7","author":"DM Aanensen","year":"2016","unstructured":"Aanensen, D. M. et al. Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive Staphylococcus aureus in Europe. mBio 7, e00444-16 (2016).","journal-title":"mBio"},{"key":"492_CR32","doi-asserted-by":"publisher","first-page":"4398","DOI":"10.1128\/AAC.00329-11","volume":"55","author":"C Pitart","year":"2011","unstructured":"Pitart, C. et al. First outbreak of a plasmid-mediated carbapenem-hydrolyzing OXA-48 \u03b2-lactamase in Klebsiella pneumoniae in Spain. Antimicrob. Agents Chemother. 55, 4398\u20134401 (2011).","journal-title":"Antimicrob. Agents Chemother."},{"key":"492_CR33","doi-asserted-by":"publisher","first-page":"148rr116","DOI":"10.1126\/scitranslmed.3004129","volume":"4","author":"ES Snitkin","year":"2012","unstructured":"Snitkin, E. S. et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci. Transl. Med. 4, 148rr116 (2012).","journal-title":"Sci. Transl. Med."},{"key":"492_CR34","doi-asserted-by":"publisher","DOI":"10.1038\/srep20840","volume":"6","author":"K Zhou","year":"2016","unstructured":"Zhou, K. et al. Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum \u03b2-lactamase producing ST15 Klebsiella pneumoniae. Sci. Rep. 6, 20840 (2016).","journal-title":"Sci. Rep."},{"key":"492_CR35","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/S1473-3099(17)30489-9","volume":"18","author":"D Gu","year":"2018","unstructured":"Gu, D. et al. A fatal outbreak of ST11 carbapenem-resistant hypervirulent Klebsiella pneumoniae in a Chinese hospital: a molecular epidemiological study. Lancet Infect. Dis. 18, 37\u201346 (2018).","journal-title":"Lancet Infect. Dis."},{"key":"492_CR36","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1128\/CMR.00116-14","volume":"28","author":"AJ Mathers","year":"2015","unstructured":"Mathers, A. J., Peirano, G. & Pitout, J. D. D. The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin. Microbiol. Rev. 28, 565\u2013591 (2015).","journal-title":"Clin. Microbiol. Rev."},{"key":"492_CR37","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1073\/pnas.1616248114","volume":"114","author":"GC Cerqueira","year":"2017","unstructured":"Cerqueira, G. C. et al. Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proc. Natl Acad. Sci. USA 114, 1135\u20131140 (2017).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"492_CR38","doi-asserted-by":"publisher","first-page":"e0133727","DOI":"10.1371\/journal.pone.0133727","volume":"10","author":"JR Bowers","year":"2015","unstructured":"Bowers, J. R. et al. Genomic analysis of the emergence and rapid global dissemination of the clonal group 258 Klebsiella pneumoniae pandemic. PLoS ONE 10, e0133727 (2015).","journal-title":"PLoS ONE"},{"key":"492_CR39","doi-asserted-by":"publisher","first-page":"4086","DOI":"10.1128\/AAC.02530-12","volume":"57","author":"P Rodriguez-Zuluet","year":"2013","unstructured":"Rodriguez-Zuluet, P. et al. First outbreak of KPC-3-producing Klebsiella pneumoniae (ST258) clinical isolates in a Mexican medical center. Antimicrob. Agents Chemother. 57, 4086\u20134088 (2013).","journal-title":"Antimicrob. Agents Chemother."},{"key":"492_CR40","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1016\/j.ijantimicag.2014.08.006","volume":"44","author":"L Lopez-Cerero","year":"2014","unstructured":"Lopez-Cerero, L. et al. Characterisation of the first ongoing outbreak due to KPC-3-producing Klebsiella pneumoniae (ST512) in Spain. Int. J. Antimicrob. Agents 44, 538\u2013540 (2014).","journal-title":"Int. J. Antimicrob. Agents"},{"key":"492_CR41","doi-asserted-by":"publisher","first-page":"9","DOI":"10.2807\/1560-7917.ES2013.18.28.20525","volume":"18","author":"C Glasner","year":"2013","unstructured":"Glasner, C. et al. Carbapenemase-producing Enterobacteriaceae in Europe: a survey among national experts from 39 countries, February 2013. Eurosurveillance 18, 9\u201315 (2013).","journal-title":"Eurosurveillance"},{"key":"492_CR42","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1016\/j.cmi.2018.04.004","volume":"24","author":"R Kock","year":"2018","unstructured":"Kock, R. et al. Carbapenem-resistant Enterobacteriaceae in wildlife, food-producing, and companion animals: a systematic review. Clin. Microbiol. Infect. 24, 1241\u20131250 (2018).","journal-title":"Clin. Microbiol. Infect."},{"key":"492_CR43","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"492_CR44","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":"492_CR45","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. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072\u20131075 (2013).","journal-title":"Bioinformatics"},{"key":"492_CR46","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":"492_CR47","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\u2212Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"492_CR48","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":"492_CR49","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":"492_CR50","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":"492_CR51","first-page":"e000093","volume":"2","author":"S Argim\u00f3n","year":"2016","unstructured":"Argim\u00f3n, S. et al. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb. Genom. 2, e000093 (2016).","journal-title":"Microb. Genom."},{"key":"492_CR52","first-page":"e000131","volume":"3","author":"M Hunt","year":"2017","unstructured":"Hunt, M. et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb. Genom. 3, e000131 (2017).","journal-title":"Microb. Genom."},{"key":"492_CR53","first-page":"e000102","volume":"2","author":"KL Wyres","year":"2016","unstructured":"Wyres, K. L. et al. Identification of Klebsiella capsule synthesis loci from whole genome data. Microb. Genom. 2, e000102 (2016).","journal-title":"Microb. Genom."},{"key":"492_CR54","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":"492_CR55","unstructured":"Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically 10th edn (CLSI, 2015)."},{"key":"492_CR56","doi-asserted-by":"publisher","first-page":"4988","DOI":"10.1073\/pnas.1321364111","volume":"111","author":"FR Deleo","year":"2014","unstructured":"Deleo, F. R. et al. Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae. Proc. Natl Acad. Sci. USA 111, 4988\u20134993 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"492_CR57","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","volume":"43","author":"NJ Croucher","year":"2015","unstructured":"Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15 (2015).","journal-title":"Nucleic Acids Res."},{"key":"492_CR58","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1093\/bioinformatics\/btx610","volume":"34","author":"J Hadfield","year":"2018","unstructured":"Hadfield, J. et al. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics 34, 292\u2013293 (2018).","journal-title":"Bioinformatics"}],"container-title":["Nature Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41564-019-0492-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-019-0492-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-019-0492-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T03:50:16Z","timestamp":1671249016000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41564-019-0492-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,7,29]]},"references-count":58,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2019,11]]}},"alternative-id":["492"],"URL":"https:\/\/doi.org\/10.1038\/s41564-019-0492-8","relation":{},"ISSN":["2058-5276"],"issn-type":[{"value":"2058-5276","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,7,29]]},"assertion":[{"value":"16 October 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 May 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 July 2019","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"}}]}}