Whole-Genome Sequencing Investigation of a Large Nosocomial Outbreak Caused by ST131 H30Rx KPC-Producing Escherichia coli in Italy
Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
PubMed
34203731
PubMed Central
PMC8232337
DOI
10.3390/antibiotics10060718
PII: antibiotics10060718
Knihovny.cz E-zdroje
- Klíčová slova
- Escherichia coli, H30Rx, KPC-producing, ST131, WGS, outbreak,
- Publikační typ
- časopisecké články MeSH
KPC-producing Escherichia coli (KPC-Ec) remains uncommon, being mainly reported as the cause of sporadic episodes of infection rather than outbreak events. Here we retrospectively describe the dynamics of a large hospital outbreak sustained by KPC-Ec, involving 106 patients and 25 hospital wards, during a six-month period. Twenty-nine representative KPC-Ec isolates (8/29 from rectal swabs; 21/29 from other clinical specimens) have been investigated by Whole-Genome Sequencing (WGS). Outbreak isolates showed a multidrug-resistant profile and harbored several resistance determinants, including blaCTX-M-27, aadA5, dfrA17, sulI, gyrA1AB and parC1aAB. Phylogenomic analysis identified the ST131 cluster 1 (23/29 isolates), H30Rx clade C, as responsible for the epidemic event. A further two KPC-Ec ST131 clusters were identified: cluster 2 (n = 2/29) and cluster 3 (n = 1/29). The remaining KPC-Ec resulted in ST978 (n = 2/29) and ST1193 (n = 1/29), and were blaKPC-3 associated. The KPC-Ec ST131 cluster 1, originated in a previous KPC-Kp endemic context probably by plasmid transfer, and showed a clonal dissemination strategy. Transmission of the blaKPC gene to the globally disseminated high-risk ST131 clone represents a serious cause of concern. Application of WGS in outbreak investigations could be useful to better understand the evolution of epidemic events in order to address infection control and contrast interventions, especially when high-risk epidemic clones are involved.
Biomedical Center Faculty of Medicine in Pilsen Charles University 323 00 Pilsen Czech Republic
Clinical Pathology and Microbiology Unit S Giovanni di Dio Hospital 88900 Crotone Italy
Microbiology and Virology Unit A Manzoni Hospital 23900 Lecco Italy
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Brolund A., Lagerqvist N., Byfors S., Struelens M.J., Monnet D.L., Albiger B., Kohlenberg A., European Antimicrobial Resistance Genes Surveillance Network EURGen-Net Capacity Survey Group Worsening epidemiological situation of carbapenemase-producing Enterobacteriaceae in Europe, assessment by national experts from 37 countries, July 2018. Euro Surveill. 2019;24 doi: 10.2807/1560-7917.ES.2019.24.9.1900123. PubMed DOI PMC
Decraene V., Phan H.T.T., George R., Wyllie D.H., Akinremi O., Aiken Z., Cleary P., Dodgson A., Pankhurst L., Crook D.W., et al. A Large, Refractory Nosocomial Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Escherichia coli demonstrates carbapenemase gene outbreaks involving sink sites require novel approaches to infection control. Antimicrob. Agents Chemother. 2018;62:e01689-18. doi: 10.1128/AAC.01689-18. PubMed DOI PMC
Stoesser N., Sheppard A.E., Peirano G., Anson L.W., Pankhurst L., Sebra R., Phan H.T.T., Kasarskis A., Mathers A.J., Peto T.E.A., et al. Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli. Sci. Rep. 2017;7:5917. doi: 10.1038/s41598-017-06256-2. PubMed DOI PMC
Stoesser N., Sheppard A.E., Pankhurst L., De Maio N., Moore C.E., Sebra R., Turner P., Anson L.W., Kasarskis A., Batty E.M., et al. Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131. MBio. 2016;7:e02162. doi: 10.1128/mBio.02162-15. PubMed DOI PMC
Grundmann H., Glasner C., Albiger B., Aanensen D.M., Tomlinson C.T., Andrasević A.T., Cantón R., Carmeli Y., Friedrich A.W., Giske C.G., 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. 2017;17:153–163. doi: 10.1016/S1473-3099(16)30257-2. PubMed DOI
Petrella S., Ziental-Gelus N., Mayer C., Renard M., Jarlier V., Sougakoff W. Genetic and structural insights into the dissemination potential of the extremely broad-spectrum class A beta-lactamase KPC-2 identified in an Escherichia coli strain and an Enterobacter cloacae strain isolated from the same patient in France. Antimicrob. Agents Chemother. 2008;52:3725–3736. doi: 10.1128/AAC.00163-08. PubMed DOI PMC
Urban C., Bradford P.A., Tuckman M., Segal-Maurer S., Wehbeh W., Grenner L., Colon-Urban R., Mariano N., Rahal J.J. Carbapenem-resistant Escherichia coli harboring Klebsiella pneumoniae carbapenemase beta-lactamases associated with long-term care facilities. Clin Infect Dis. 2008;46:e127–e130. doi: 10.1086/588048. PubMed DOI
Goren M.G., Navon-Venezia S., Chmelnitsky I., Carmeli Y. Carbapenem-resistant KPC-2-producing Escherichia coli in a Tel Aviv Medical Center, 2005 to 2008. Antimicrob. Agents Chemother. 2010;54:2687–2691. doi: 10.1128/AAC.01359-09. PubMed DOI PMC
Naas T., Cuzon G., Gaillot O., Courcol R., Nordmann P. When carbapenem-hydrolyzing beta-lactamase KPC meets Escherichia coli ST131 in France. Antimicrob. Agents Chemother. 2011;55:4933–4934. doi: 10.1128/AAC.00719-11. PubMed DOI PMC
Morris D., Boyle F., Ludden C., Condon I., Hale J., O’Connell N., Power L., Boo T.W., Dhanji H., Lavallee C., et al. Production of KPC-2 carbapenemase by an Escherichia coli clinical isolate belonging to the international ST131 clone. Antimicrob. Agents Chemother. 2011;55:4935–4936. doi: 10.1128/AAC.05127-11. PubMed DOI PMC
Giani T., Antonelli A., Caltagirone M., Mauri C., Nicchi J., Arena F., Nucleo E., Bracco S., Pantosti A., Luzzaro F., et al. Evolving beta-lactamase epidemiology in Enterobacteriaceae from Italian nationwide surveillance, October 2013: KPC-carbapenemase spreading among outpatients. Euro Surveill. 2017;22:30583. doi: 10.2807/1560-7917.ES.2017.22.31.30583. PubMed DOI PMC
Iacchini S., Sabbatucci M., Gagliotti C., Rossolini G.M., Moro M.L., Iannazzo S., D’Ancona F., Pezzotti P., Pantosti A. Bloodstream infections due to carbapenemase-producing Enterobacteriaceae in Italy: Results from nationwide surveillance, 2014 to 2017. Euro Surveill. 2019;24 doi: 10.2807/1560-7917.ES.2019.24.5.1800159. PubMed DOI PMC
Piazza A., Caltagirone M., Bitar I., Nucleo E., Spalla M., Fogato E., D’Angelo R., Pagani L., Migliavacca R. Emergence of Escherichia coli Sequence Type 131 (ST131) and ST3948 with KPC-2, KPC-3 and KPC-8 carbapenemases from a Long-Term Care and Rehabilitation Facility (LTCRF) in Northern Italy. Adv. Exp. Med. Biol. 2016;901:77–89. doi: 10.1007/5584_2015_5017. PubMed DOI
Adler A., Miller-Roll T., Assous M.V., Geffen Y., Paikin S., Schwartz D., Weiner-Well Y., Hussein K., Cohen R., Carmeli Y. A multicenter study of the clonal structure and resistance mechanism of KPC-producing Escherichia coli isolates in Israel. Clin. Microbiol. Infect. 2015;21:230–235. doi: 10.1016/j.cmi.2014.10.008. PubMed DOI
Mavroidi A., Miriagou V., Malli E., Stefos A., Dalekos G.N., Tzouvelekis L.S., Petinaki E. Emergence of Escherichia coli sequence type 410 (ST410) with KPC-2 β-lactamase. Int. J. Antimicrob. Agents. 2012;39:247–250. doi: 10.1016/j.ijantimicag.2011.11.003. PubMed DOI
Landman D., Urban C., Bäcker M., Kelly P., Shah N., Babu E., Bratu S., Quale J. Susceptibility profiles, molecular epidemiology, and detection of KPC-producing Escherichia coli isolates from the New York City vicinity. J. Clin. Microbiol. 2010;48:4604–4607. doi: 10.1128/JCM.01143-10. PubMed DOI PMC
Leung V., Loo V.G., Frenette C., Domingo M.C., Bourgault A.M., Mulvey M.R., Robson H.G. First Canadian outbreak of Enterobacteriaceae-expressing Klebsiella pneumoniae carbapenemase type 3. Can. J. Infect. Dis. Med. Microbiol. 2012;23:117–120. doi: 10.1155/2012/725151. PubMed DOI PMC
Accogli M., Giani T., Monaco M., Giufrè M., García-Fernández A., Conte V., D’Ancona F., Pantosti A., Rossolini G.M., Cerquetti M. Emergence of Escherichia coli ST131 sub-clone H30 producing VIM-1 and KPC-3 carbapenemases, Italy. J. Antimicrob. Chemother. 2014;69:2293–2296. doi: 10.1093/jac/dku132. PubMed DOI
Chavda K.D., Chen L., Jacobs M.R., Bonomo R.A., Kreiswirth B.N. Molecular Diversity and Plasmid Analysis of KPC-Producing Escherichia coli. Antimicrob. Agents Chemother. 2016;60:4073–4081. doi: 10.1128/AAC.00452-16. PubMed DOI PMC
Petty N.K., Ben Zakour N.L., Stanton-Cook M., Skippington E., Totsika M., Forde B.M., Phan M.D., Gomes Moriel D., Peters K.M., Davies M., et al. Global dissemination of a multidrug resistant Escherichia coli clone. Proc. Natl. Acad. Sci. USA. 2014;111:5694–5699. doi: 10.1073/pnas.1322678111. PubMed DOI PMC
Ben Zakour N.L., Alsheikh-Hussain A.S., Ashcroft M.M., Khanh Nhu N.T., Roberts L.W., Stanton-Cook M., Schembri M.A., Beatson S.A. Erratum for Ben Zakour et al., Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131. MBio. 2016;7:e00958-16. doi: 10.1128/mBio.00958-16. PubMed DOI PMC
European Committee on Antimicrobial Susceptibility Testing . Breakpoint Tables for Interpretation of MICs and Zone Diameters, Version 6.0. EUCAST; Basel, Switzerland: 2016. [(accessed on 14 June 2021)]. Available online: http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/Breakpoint_table_v_6.0.pdf.
Perini M., Piazza A., Panelli S., Di Carlo D., Corbella M., Gona F., Vailati F., Marone P., Cirillo D.M., Farina C., et al. EasyPrimer: User-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typing. Sci. Rep. 2020;10:1307. doi: 10.1038/s41598-020-57742-z. PubMed DOI PMC
Perini M., Batisti Biffignandi G., Di Carlo D., Pasala A.R., Piazza A., Panelli S., Zuccotti G.V., Comandatore F. MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data. BMC Bioinform. 2021;22:76. doi: 10.1186/s12859-021-04020-y. PubMed DOI PMC
Bolger A.M., Lohse M., Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC
Nurk S., Bankevich A., Antipov D., Gurevich A.A., Korobeynikov A., Lapidus A., Prjibelski A.D., Pyshkin A., Sirotkin A., Sirotkin Y., et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J. Comput. Biol. 2013;20:714–737. doi: 10.1089/cmb.2013.0084. PubMed DOI PMC
Ondov B.D., Treangen T.J., Melsted P., Mallonee A.B., Bergman N.H., Koren S., Phillippy A.M. Mash: Fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016;17:132. doi: 10.1186/s13059-016-0997-x. PubMed DOI PMC
Wattam A.R., Davis J.J., Assaf R., Boisvert S., Brettin T., Bun C., Conrad N., Dietrich E.M., Disz T., Gabbard J.L., et al. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2017;45:D535–D542. doi: 10.1093/nar/gkw1017. PubMed DOI PMC
Gona F., Comandatore F., Battaglia S., Piazza A., Trovato A., Lorenzin G., Cichero P., Biancardi A., Nizzero P., Moro M., et al. Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis. Microb. Genom. 2020;6:e000347. doi: 10.1099/mgen.0.000347. PubMed DOI PMC
Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–1313. doi: 10.1093/bioinformatics/btu033. PubMed DOI PMC
Zankari E., Hasman H., Cosentino S., Vestergaard M., Rasmussen S., Lund O., Aarestrup F.M., Larsen M.V. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 2012;67:2640–2644. doi: 10.1093/jac/dks261. PubMed DOI PMC
Inouye M., Dashnow H., Raven L.A., Schultz M.B., Pope B.J., Tomita T., Zobel J., Holt K.E. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014;6:90. doi: 10.1186/s13073-014-0090-6. PubMed DOI PMC
Gupta S.K., Padmanabhan B.R., Diene S.M., Lopez-Rojas R., Kempf M., Landraud L., Rolain J.M. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob. Agents Chemother. 2014;58:212–220. doi: 10.1128/AAC.01310-13. PubMed DOI PMC
Joensen K.G., Scheutz F., Lund O., Hasman H., Kaas R.S., Nielsen E.M., Aarestrup F.M. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Micobiol. 2014;52:1501–1510. doi: 10.1128/JCM.03617-13. PubMed DOI PMC
Carattoli A., Zankari E., García-Fernández A., Voldby Larsen M., Lund O., Villa L., Møller Aarestrup F., Hasman H. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 2014;58:3895–3903. doi: 10.1128/AAC.02412-14. PubMed DOI PMC
Seemann T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–2069. doi: 10.1093/bioinformatics/btu153. PubMed DOI
Darling A.E., Mau B., Perna N.T. progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE. 2010;5:e11147. doi: 10.1371/journal.pone.0011147. PubMed DOI PMC
Sheppard A.E., Stoesser N., German-Mesner I., Vegesana K., Sarah Walker A., Crook D.W., Mathers A.J. TETyper: A bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data. Microb. Genom. 2018;4:e000232. doi: 10.1099/mgen.0.000232. PubMed DOI PMC
Guy L., Kultima J.R., Andersson Siv G.E. genoPlotR: Comparative gene and genome visualization in R. Bioinformatics. 2010;26:2334–2335. doi: 10.1093/bioinformatics/btq413. PubMed DOI PMC