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

J 2019

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

BEZDÍČEK, Matěj, Marketa NYKRYNOVA, Kristina PLEVOVÁ, Eva BRHELOVÁ, Iva KOCMANOVA et. al.

Basic information

Original name

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

Authors

BEZDÍČEK, Matěj (203 Czech Republic, belonging to the institution), Marketa NYKRYNOVA (203 Czech Republic), Kristina PLEVOVÁ (203 Czech Republic), Eva BRHELOVÁ (203 Czech Republic, belonging to the institution), Iva KOCMANOVA (203 Czech Republic), Karel SEDLAR (203 Czech Republic), Zdeněk RÁČIL (203 Czech Republic, belonging to the institution), Jiří MAYER (203 Czech Republic, belonging to the institution) and Martina LENGEROVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

Plos one, San Francisco, Public Library of Science, 2019, 1932-6203

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

30302 Epidemiology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.740

RIV identification code

RIV/00216224:14110/19:00110968

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.1371/journal.pone.0221187

UT WoS

000485009500047

Keywords in English

genome sequencing; pneumoniae population; mini-MLST

Abstract

V originále

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.

Links

MUNI/A/1105/2018, interní kód MU

Name: Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit VI (Acronym: VýDiTeHeMA VI)

Investor: Masaryk University, Category A

Citovat

BEZDÍČEK, Matěj, Marketa NYKRYNOVA, Kristina PLEVOVÁ, Eva BRHELOVÁ, Iva KOCMANOVA, Karel SEDLAR, Zdeněk RÁČIL, Jiří MAYER and Martina LENGEROVÁ. Application of mini-MLST and whole genome sequencing in low diversity hospital extended-spectrum beta-lactamase producing Klebsiella pneumoniae population. Plos one. San Francisco: Public Library of Science, 2019, vol. 14, No 8, p. 1-14. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0221187.

@article{1569780,
   author = {Bezdíček, Matěj and Nykrynova, Marketa and Plevová, Kristina and Brhelová, Eva and Kocmanova, Iva and Sedlar, Karel and Ráčil, Zdeněk and Mayer, Jiří and Lengerová, Martina},
   article_location = {San Francisco},
   article_number = {8},
   doi = {http://dx.doi.org/10.1371/journal.pone.0221187},
   keywords = {genome sequencing; pneumoniae population; mini-MLST},
   language = {eng},
   issn = {1932-6203},
   journal = {Plos one},
   title = {Application of mini-MLST and whole genome sequencing in low diversity hospital extended-spectrum beta-lactamase producing Klebsiella pneumoniae population},
   url = {http://dx.doi.org/10.1371/journal.pone.0221187},
   volume = {14},
   year = {2019}
}

TY  - JOUR
ID  - 1569780
AU  - Bezdíček, Matěj - Nykrynova, Marketa - Plevová, Kristina - Brhelová, Eva - Kocmanova, Iva - Sedlar, Karel - Ráčil, Zdeněk - Mayer, Jiří - Lengerová, Martina
PY  - 2019
TI  - Application of mini-MLST and whole genome sequencing in low diversity hospital extended-spectrum beta-lactamase producing Klebsiella pneumoniae population
JF  - Plos one
VL  - 14
IS  - 8
SP  - 1-14
EP  - 1-14
PB  - Public Library of Science
SN  - 19326203
KW  - genome sequencing
KW  - pneumoniae population
KW  - mini-MLST
UR  - http://dx.doi.org/10.1371/journal.pone.0221187
L2  - http://dx.doi.org/10.1371/journal.pone.0221187
N2  - 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.
ER  -

BEZDÍČEK, Matěj, Marketa NYKRYNOVA, Kristina PLEVOVÁ, Eva BRHELOVÁ, Iva KOCMANOVA, Karel SEDLAR, Zdeněk RÁČIL, Jiří MAYER and Martina LENGEROVÁ. Application of mini-MLST and whole genome sequencing in low diversity hospital extended-spectrum beta-lactamase producing Klebsiella pneumoniae population. \textit{Plos one}. San Francisco: Public Library of Science, 2019, vol.~14, No~8, p.~1-14. ISSN~1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0221187.

Detailed Information on Publication Record