Publication detail

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

BEZDÍČEK, M. NYKRÝNOVÁ, M. PLEVOVÁ, K. BRHELOVÁ, E. KOCMANOVÁ, I. SEDLÁŘ, K. RÁČIL, Z. MAYER, J. LENGEROVÁ, M.

Original Title

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

Type

journal article in Web of Science

Language

English

Original Abstract

Studying 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.

Keywords

Klebsiella pneumoniae; mini-MLST

Authors

BEZDÍČEK, M.; NYKRÝNOVÁ, M.; PLEVOVÁ, K.; BRHELOVÁ, E.; KOCMANOVÁ, I.; SEDLÁŘ, K.; RÁČIL, Z.; MAYER, J.; LENGEROVÁ, M.

Released

13. 8. 2019

Publisher

PLOS

ISBN

1932-6203

Periodical

PLOS ONE

Year of study

14

Number

8

State

United States of America

Pages from

1

Pages to

14

Pages count

14

URL

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221187

Full text in the Digital Library

http://hdl.handle.net/11012/193228

BibTex

@article{BUT158343,
  author="Matěj {Bezdíček} and Markéta {Nykrýnová} and Kristina {Plevová} and Eva {Brhelová} and Iva {Kocmanová} and Karel {Sedlář} and Zdeněk {Ráčil} and Jiří {Mayer} and Martina {Lengerová}",
  title="Application of mini-MLST and whole genome sequencing in low diversity hospital extended-spectrum beta-lactamase producing Klebsiella pneumoniae population",
  journal="PLOS ONE",
  year="2019",
  volume="14",
  number="8",
  pages="1--14",
  doi="10.1371/journal.pone.0221187",
  issn="1932-6203",
  url="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221187"
}