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One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods

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Harvard

Rebelo, AR, Ibfelt, T, Bortolaia, V, Leekitcharoenphon, P, Hansen, DS, Nielsen, HL, Ellermann-Eriksen, S, Kemp, M, Røder, BL, Frimodt-Møller, N, Søndergaard, TS, Coia, JE, Østergaard, C, Pedersen, M, Westh, H & Aarestrup, FM 2022, 'One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods', PLoS One, bind 17, nr. 2, e0261999, s. 1-17. https://doi.org/10.1371/journal.pone.0261999

APA

Rebelo, A. R., Ibfelt, T., Bortolaia, V., Leekitcharoenphon, P., Hansen, D. S., Nielsen, H. L., Ellermann-Eriksen, S., Kemp, M., Røder, B. L., Frimodt-Møller, N., Søndergaard, T. S., Coia, J. E., Østergaard, C., Pedersen, M., Westh, H., & Aarestrup, F. M. (2022). One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods. PLoS One, 17(2), 1-17. [e0261999]. https://doi.org/10.1371/journal.pone.0261999

CBE

Rebelo AR, Ibfelt T, Bortolaia V, Leekitcharoenphon P, Hansen DS, Nielsen HL, Ellermann-Eriksen S, Kemp M, Røder BL, Frimodt-Møller N, Søndergaard TS, Coia JE, Østergaard C, Pedersen M, Westh H, Aarestrup FM. 2022. One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods. PLoS One. 17(2):1-17. https://doi.org/10.1371/journal.pone.0261999

MLA

Vancouver

Author

Rebelo, Ana Rita ; Ibfelt, Tobias ; Bortolaia, Valeria ; Leekitcharoenphon, Pimlapas ; Hansen, Dennis Schrøder ; Nielsen, Hans Linde ; Ellermann-Eriksen, Svend ; Kemp, Michael ; Røder, Bent Løwe ; Frimodt-Møller, Niels ; Søndergaard, Turid Snekloth ; Coia, John Eugenio ; Østergaard, Claus ; Pedersen, Michael ; Westh, Henrik ; Aarestrup, Frank Møller. / One Day in Denmark : Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods. I: PLoS One. 2022 ; Bind 17, Nr. 2. s. 1-17.

Bibtex

@article{689551ffaf844e67bc89dc78924e399d,
title = "One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods",
abstract = "OBJECTIVES: Implementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark.METHODS: We performed a point-prevalence study of all bacterial isolates (n = 2,009) processed and reported in the Clinical Microbiology Laboratories in Denmark in one day in January 2018. We compared species identification as performed by classical methods (MALDI-TOF) and by bioinformatics analysis (KmerFinder and rMLST) of WGS (Illumina NextSeq) data. We compared the national point-prevalence of bacterial isolates observed in clinical settings with the research attention given to those same genera in scientific literature.RESULTS: The most prevalent bacterium was Escherichia coli isolated from urine (n = 646), followed by Staphylococcus spp. from skin or soft tissues (n = 197). The distribution of bacterial species throughout the country was not homogeneous. We observed concordance of species identification for all methods in 95.7% (n = 1,919) of isolates, furthermore obtaining concordance for 99.7% (n = 1,999) at genus level. The number of scientific publications in the country did not correlate with the number of bacterial isolates of each genera analysed in this study.CONCLUSIONS: WGS technologies have the potential to be applied in clinical settings for routine diagnostics purposes. This study also showed that bioinformatics databases should be continuously improved and results from local point-prevalence surveys should not be applied at national levels without previously determining possible regional variations.",
author = "Rebelo, {Ana Rita} and Tobias Ibfelt and Valeria Bortolaia and Pimlapas Leekitcharoenphon and Hansen, {Dennis Schr{\o}der} and Nielsen, {Hans Linde} and Svend Ellermann-Eriksen and Michael Kemp and R{\o}der, {Bent L{\o}we} and Niels Frimodt-M{\o}ller and S{\o}ndergaard, {Turid Snekloth} and Coia, {John Eugenio} and Claus {\O}stergaard and Michael Pedersen and Henrik Westh and Aarestrup, {Frank M{\o}ller}",
year = "2022",
month = feb,
day = "11",
doi = "10.1371/journal.pone.0261999",
language = "English",
volume = "17",
pages = "1--17",
journal = "PLOS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "2",

}

RIS

TY - JOUR

T1 - One Day in Denmark

T2 - Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods

AU - Rebelo, Ana Rita

AU - Ibfelt, Tobias

AU - Bortolaia, Valeria

AU - Leekitcharoenphon, Pimlapas

AU - Hansen, Dennis Schrøder

AU - Nielsen, Hans Linde

AU - Ellermann-Eriksen, Svend

AU - Kemp, Michael

AU - Røder, Bent Løwe

AU - Frimodt-Møller, Niels

AU - Søndergaard, Turid Snekloth

AU - Coia, John Eugenio

AU - Østergaard, Claus

AU - Pedersen, Michael

AU - Westh, Henrik

AU - Aarestrup, Frank Møller

PY - 2022/2/11

Y1 - 2022/2/11

N2 - OBJECTIVES: Implementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark.METHODS: We performed a point-prevalence study of all bacterial isolates (n = 2,009) processed and reported in the Clinical Microbiology Laboratories in Denmark in one day in January 2018. We compared species identification as performed by classical methods (MALDI-TOF) and by bioinformatics analysis (KmerFinder and rMLST) of WGS (Illumina NextSeq) data. We compared the national point-prevalence of bacterial isolates observed in clinical settings with the research attention given to those same genera in scientific literature.RESULTS: The most prevalent bacterium was Escherichia coli isolated from urine (n = 646), followed by Staphylococcus spp. from skin or soft tissues (n = 197). The distribution of bacterial species throughout the country was not homogeneous. We observed concordance of species identification for all methods in 95.7% (n = 1,919) of isolates, furthermore obtaining concordance for 99.7% (n = 1,999) at genus level. The number of scientific publications in the country did not correlate with the number of bacterial isolates of each genera analysed in this study.CONCLUSIONS: WGS technologies have the potential to be applied in clinical settings for routine diagnostics purposes. This study also showed that bioinformatics databases should be continuously improved and results from local point-prevalence surveys should not be applied at national levels without previously determining possible regional variations.

AB - OBJECTIVES: Implementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark.METHODS: We performed a point-prevalence study of all bacterial isolates (n = 2,009) processed and reported in the Clinical Microbiology Laboratories in Denmark in one day in January 2018. We compared species identification as performed by classical methods (MALDI-TOF) and by bioinformatics analysis (KmerFinder and rMLST) of WGS (Illumina NextSeq) data. We compared the national point-prevalence of bacterial isolates observed in clinical settings with the research attention given to those same genera in scientific literature.RESULTS: The most prevalent bacterium was Escherichia coli isolated from urine (n = 646), followed by Staphylococcus spp. from skin or soft tissues (n = 197). The distribution of bacterial species throughout the country was not homogeneous. We observed concordance of species identification for all methods in 95.7% (n = 1,919) of isolates, furthermore obtaining concordance for 99.7% (n = 1,999) at genus level. The number of scientific publications in the country did not correlate with the number of bacterial isolates of each genera analysed in this study.CONCLUSIONS: WGS technologies have the potential to be applied in clinical settings for routine diagnostics purposes. This study also showed that bioinformatics databases should be continuously improved and results from local point-prevalence surveys should not be applied at national levels without previously determining possible regional variations.

UR - http://www.scopus.com/inward/record.url?scp=85124500719&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0261999

DO - 10.1371/journal.pone.0261999

M3 - Journal article

C2 - 35148318

VL - 17

SP - 1

EP - 17

JO - PLOS ONE

JF - PLOS ONE

SN - 1932-6203

IS - 2

M1 - e0261999

ER -

ID: 74471031