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.

Základní údaje

Originální název

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

Autoři

BEZDÍČEK, Matěj (203 Česká republika, domácí), Marketa NYKRYNOVA (203 Česká republika), Kristina PLEVOVÁ (203 Česká republika), Eva BRHELOVÁ (203 Česká republika, domácí), Iva KOCMANOVA (203 Česká republika), Karel SEDLAR (203 Česká republika), Zdeněk RÁČIL (203 Česká republika, domácí), Jiří MAYER (203 Česká republika, domácí) a Martina LENGEROVÁ (203 Česká republika, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30302 Epidemiology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.740

Kód RIV

RIV/00216224:14110/19:00110968

Organizační jednotka

Lékařská fakulta

DOI

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

UT WoS

000485009500047

Klíčová slova anglicky

genome sequencing; pneumoniae population; mini-MLST

Štítky

14110212, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 26. 11. 2019 13:40, Mgr. Tereza Miškechová

Anotace

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.

Návaznosti

MUNI/A/1105/2018, interní kód MU

Název: Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit VI (Akronym: VýDiTeHeMA VI)

Investor: Masarykova univerzita, Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit VI, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

BEZDÍČEK, Matěj, Marketa NYKRYNOVA, Kristina PLEVOVÁ, Eva BRHELOVÁ, Iva KOCMANOVA, Karel SEDLAR, Zdeněk RÁČIL, Jiří MAYER a 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, roč. 14, č. 8, s. 1-14. ISSN 1932-6203. Dostupné z: 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 a 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, roč.~14, č.~8, s.~1-14. ISSN~1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0221187.

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