New Multilocus Sequence Typing Scheme for Enterococcus faecium
Based on Whole Genome Sequencing Data

J 2023

New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data

BEZDÍČEK, Matěj, Jana HANSLIKOVA, Marketa NYKRYNOVA, Kristýna DUFKOVÁ, Iva KOCMANOVA et. al.

Basic information

Original name

New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data

Authors

BEZDÍČEK, Matěj (203 Czech Republic, guarantor, belonging to the institution), Jana HANSLIKOVA (203 Czech Republic), Marketa NYKRYNOVA (203 Czech Republic), Kristýna DUFKOVÁ (203 Czech Republic, belonging to the institution), Iva KOCMANOVA (203 Czech Republic), Petra KUBACKOVA (203 Czech Republic), Jiří MAYER (203 Czech Republic, belonging to the institution) and Martina LENGEROVÁ (203 Czech Republic, belonging to the institution)

Edition

Microbiology Spectrum, WASHINGTON, AMER SOC MICROBIOLOGY, 2023, 2165-0497

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10606 Microbiology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.700 in 2022

RIV identification code

RIV/00216224:14110/23:00131100

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.1128/spectrum.05107-22

UT WoS

001004310600001

Keywords in English

Enterococcus faesium; multilocus sequence typing; clonal complex; epidemiology; whole genome sequenging

Abstract

V originále

Enterococcus faecium is one of the most important pathogens causing health care associated infections. One of the main reasons for its clinical importance is a rapidly spreading resistance to vancomycin and linezolid, which significantly complicates antibiotic treatment of infections caused by such resistant strains. The MLST scheme currently used for Enterococcus faecium typing was designed in 2002 and is based on putative gene functions and Enterococcus faecalis gene sequences available at that time. As a result, the original MLST scheme does not correspond to the real genetic relatedness of E. faecium strains and often clusters genetically distant strains to the same sequence types (ST). Nevertheless, typing has a significant impact on the subsequent epidemiological conclusions and introduction of appropriate epidemiological measures, thus it is crucial to use a more accurate MLST scheme. Based on the genome analysis of 1,843 E. faecium isolates, a new scheme, consisting of 8 highly discriminative loci, was created in this study. These strains were divided into 421 STs using the new MLST scheme, as opposed to 223 STs assigned by the original MLST scheme. The proposed MLST has a discriminatory power of D = 0.983 (CI95% 0.981 to 0.984), compared to the original scheme's D = 0.919 (CI95% 0.911 to 0.927). Moreover, we identified new clonal complexes with our newly designed MLST scheme. The scheme proposed here is available within the PubMLST database. Although whole genome sequencing availability has increased rapidly, MLST remains an integral part of clinical epidemiology, mainly due to its high standardization and excellent robustness. In this study, we proposed and validated a new MLST scheme for E. faecium, which is based on genome-wide data and thus reflects the tested isolates' more accurate genetic similarity.IMPORTANCE Enterococcus faecium is one of the most important pathogens causing health care associated infections. One of the main reasons for its clinical importance is a rapidly spreading resistance to vancomycin and linezolid, which significantly complicates antibiotic treatment of infections caused by such resistant strains. Monitoring the spread and relationships between resistant strains causing severe conditions represents an important tool for implementing appropriate preventive measures. Therefore, there is an urgent need to establish a robust method enabling strain monitoring and comparison at the local, national, and global level. Unfortunately, the current, extensively used MLST scheme does not reflect the real genetic relatedness between individual strains and thus does not provide sufficient discriminatory power. This can lead directly to incorrect epidemiological measures due to insufficient accuracy and biased results.

Citovat

BEZDÍČEK, Matěj, Jana HANSLIKOVA, Marketa NYKRYNOVA, Kristýna DUFKOVÁ, Iva KOCMANOVA, Petra KUBACKOVA, Jiří MAYER and Martina LENGEROVÁ. New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data. Microbiology Spectrum. WASHINGTON: AMER SOC MICROBIOLOGY, 2023, vol. 11, No 4, p. 1-9. ISSN 2165-0497. Available from: https://dx.doi.org/10.1128/spectrum.05107-22.

@article{2294397,
   author = {Bezdíček, Matěj and Hanslikova, Jana and Nykrynova, Marketa and Dufková, Kristýna and Kocmanova, Iva and Kubackova, Petra and Mayer, Jiří and Lengerová, Martina},
   article_location = {WASHINGTON},
   article_number = {4},
   doi = {http://dx.doi.org/10.1128/spectrum.05107-22},
   keywords = {Enterococcus faesium; multilocus sequence typing; clonal complex; epidemiology; whole genome sequenging},
   language = {eng},
   issn = {2165-0497},
   journal = {Microbiology Spectrum},
   title = {New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data},
   url = {https://journals.asm.org/doi/10.1128/spectrum.05107-22},
   volume = {11},
   year = {2023}
}

TY  - JOUR
ID  - 2294397
AU  - Bezdíček, Matěj - Hanslikova, Jana - Nykrynova, Marketa - Dufková, Kristýna - Kocmanova, Iva - Kubackova, Petra - Mayer, Jiří - Lengerová, Martina
PY  - 2023
TI  - New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data
JF  - Microbiology Spectrum
VL  - 11
IS  - 4
SP  - 1-9
EP  - 1-9
PB  - AMER SOC MICROBIOLOGY
SN  - 21650497
KW  - Enterococcus faesium
KW  - multilocus sequence typing
KW  - clonal complex
KW  - epidemiology
KW  - whole genome sequenging
UR  - https://journals.asm.org/doi/10.1128/spectrum.05107-22
N2  - Enterococcus faecium is one of the most important pathogens causing health care associated infections. One of the main reasons for its clinical importance is a rapidly spreading resistance to vancomycin and linezolid, which significantly complicates antibiotic treatment of infections caused by such resistant strains. The MLST scheme currently used for Enterococcus faecium typing was designed in 2002 and is based on putative gene functions and Enterococcus faecalis gene sequences available at that time. As a result, the original MLST scheme does not correspond to the real genetic relatedness of E. faecium strains and often clusters genetically distant strains to the same sequence types (ST). Nevertheless, typing has a significant impact on the subsequent epidemiological conclusions and introduction of appropriate epidemiological measures, thus it is crucial to use a more accurate MLST scheme. Based on the genome analysis of 1,843 E. faecium isolates, a new scheme, consisting of 8 highly discriminative loci, was created in this study. These strains were divided into 421 STs using the new MLST scheme, as opposed to 223 STs assigned by the original MLST scheme. The proposed MLST has a discriminatory power of D = 0.983 (CI95% 0.981 to 0.984), compared to the original scheme's D = 0.919 (CI95% 0.911 to 0.927). Moreover, we identified new clonal complexes with our newly designed MLST scheme. The scheme proposed here is available within the PubMLST database. Although whole genome sequencing availability has increased rapidly, MLST remains an integral part of clinical epidemiology, mainly due to its high standardization and excellent robustness. In this study, we proposed and validated a new MLST scheme for E. faecium, which is based on genome-wide data and thus reflects the tested isolates' more accurate genetic similarity.IMPORTANCE Enterococcus faecium is one of the most important pathogens causing health care associated infections. One of the main reasons for its clinical importance is a rapidly spreading resistance to vancomycin and linezolid, which significantly complicates antibiotic treatment of infections caused by such resistant strains. Monitoring the spread and relationships between resistant strains causing severe conditions represents an important tool for implementing appropriate preventive measures. Therefore, there is an urgent need to establish a robust method enabling strain monitoring and comparison at the local, national, and global level. Unfortunately, the current, extensively used MLST scheme does not reflect the real genetic relatedness between individual strains and thus does not provide sufficient discriminatory power. This can lead directly to incorrect epidemiological measures due to insufficient accuracy and biased results.
ER  -

BEZDÍČEK, Matěj, Jana HANSLIKOVA, Marketa NYKRYNOVA, Kristýna DUFKOVÁ, Iva KOCMANOVA, Petra KUBACKOVA, Jiří MAYER and Martina LENGEROVÁ. New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data. \textit{Microbiology Spectrum}. WASHINGTON: AMER SOC MICROBIOLOGY, 2023, vol.~11, No~4, p.~1-9. ISSN~2165-0497. Available from: https://dx.doi.org/10.1128/spectrum.05107-22.

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