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
SN - 1932-6203
VL - 17
JO - PLoS ONE
JF - PLoS ONE
IS - 2
M1 - e0261999
ER -