Application of mini-MLST and whole genome sequencing in low diversity hospital extended-spectrum beta-lactamase producing Klebsiella pneumoniae population

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dc.contributor.authorBezdíček, Matějcs
dc.contributor.authorNykrýnová, Markétacs
dc.contributor.authorPlevová, Kristinacs
dc.contributor.authorBrhelová, Evacs
dc.contributor.authorKocmanová, Ivacs
dc.contributor.authorSedlář, Karelcs
dc.contributor.authorRáčil, Zdeněkcs
dc.contributor.authorMayer, Jiřícs
dc.contributor.authorLengerová, Martinacs
dc.coverage.issue8cs
dc.coverage.volume14cs
dc.date.accessioned2020-08-04T11:00:12Z
dc.date.available2020-08-04T11:00:12Z
dc.date.issued2019-08-13cs
dc.description.abstractStudying bacterial population diversity is important to understand healthcare associated infections’ epidemiology and has a significant impact on dealing with multidrug resistant bacterial outbreaks. We characterised the extended-spectrum beta-lactamase producing K. pneumoniae (ESBLp KPN) population in our hospital using mini-MLST. Then we used whole genome sequencing (WGS) to compare selected isolates belonging to the most prevalent melting types (MelTs) and the colonization/infection pair isolates collected from one patient to study the ESBLp KPN population’s genetic diversity. A total of 922 ESBLp KPN isolates collected between 7/2016 and 5/2018 were divided into 38 MelTs using mini-MLST with only 6 MelTs forming 82.8% of all isolates. For WGS, 14 isolates from the most prominent MelTs collected in the monitored period and 10 isolates belonging to the same MelTs collected in our hospital in 2014 were randomly selected. Resistome, virulome and ST were MelT specific and stable over time. A maximum of 23 SNV per core genome and 58 SNV per core and accessory genome were found. To determine the SNV relatedness cut-off values, 22 isolates representing colonization/infection pair samples obtained from 11 different patients were analysed by WGS with a maximum of 22 SNV in the core genome and 40 SNV in the core and accessory genome within pairs. The mini-MLST showed its potential for real-time epidemiology in clinical practice. However, for outbreak evaluation in a low diversity bacterial population, mini-MLST should be combined with more sensitive methods like WGS. Our findings showed there were only minimal differences within the core and accessory genome in the low diversity hospital population and gene based SNV analysis does not have enough discriminatory power to differentiate isolate relatedness. Thus, intergenic regions and mobile elements should be incorporated into the analysis scheme to increase discriminatory power.en
dc.formattextcs
dc.format.extent1-14cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationPLOS ONE. 2019, vol. 14, issue 8, p. 1-14.en
dc.identifier.doi10.1371/journal.pone.0221187cs
dc.identifier.issn1932-6203cs
dc.identifier.other158343cs
dc.identifier.urihttp://hdl.handle.net/11012/193228
dc.language.isoencs
dc.publisherPLOScs
dc.relation.ispartofPLOS ONEcs
dc.relation.urihttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221187cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/1932-6203/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectKlebsiella pneumoniaeen
dc.subjectmini-MLSTen
dc.titleApplication of mini-MLST and whole genome sequencing in low diversity hospital extended-spectrum beta-lactamase producing Klebsiella pneumoniae populationen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-158343en
sync.item.dbtypeVAVen
sync.item.insts2020.08.04 13:00:12en
sync.item.modts2020.08.04 12:24:28en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
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