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Abstract
ObjectivesImplementing 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.MethodsWe 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.ResultsThe 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.ConclusionsWGS 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.
Highlights
Danish point-prevalence survey of bacterial isolates and comparison of species identification methods attributed to FMA
whole-genome sequencing (WGS) technologies have the potential to be applied in clinical settings for routine diagnostics purposes
In Denmark, large efforts go into tracking, reporting and controlling selected pathogens, namely methicillinresistant Staphylococcus aureus (MRSA), Shiga toxin-producing Escherichia coli (STEC), ESBL-producing invasive E. coli, carbapenemase-producing organisms (CPO), vancomycinresistant enterococci (VRE), Neisseria gonorrhoeae and Neisseria meningitidis isolates, amongst others
Summary
Of the 57 million yearly deaths worldwide, 8.5 million (approximately 15%) are the direct result of infectious diseases [1]. For Europe, the European Centre for Disease Prevention and Control (ECDC) has in place surveillance systems for many of the same pathogens, and the World Health Organization (WHO) includes several antimicrobial-resistant bacterial species of concern in their “WHO priority pathogens list for R&D of new antibiotics” [6] These systems are focused on bacteria causing infections considered most severe or those considered to have the highest potential to be transmitted or to be refractory to antimicrobial therapy. Very few studies have reported on the relative prevalence of all bacterial species observed nationally without pre-selection of settings or species One such example corresponds to a five-year analysis of clinical samples at one Ethiopian hospital [12]. The occurrence of all bacteria observed at the clinical microbiological laboratories in Denmark has not been yet elucidated,
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