ArticlePloS one2022
One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 14 citations in OpenAlex.
- Molecular analysis of Lancefield group C/G streptococci causing human infections in Sheffield, UK.Microbial genomics · 2026Article
- Genetic population structure of Haemophilus influenzae at local and global scales.Nature microbiology · 2025Article
- One day in Denmark: whole-genome sequence-based analysis of Escherichia coli isolates from clinical settings.The Journal of antimicrobial chemotherapy · 2025Article
- Genomic epidemiology of strains currently and formerly classified as Enterobacter spp. recovered from equine necropsy samples.PloS one · 2025Article
- Understanding bacterial diversity, infection dynamics, prevention of antibiotic resistance: an integrated study in an Algerian hospital context.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2024Article
- Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis.Microbiology spectrum · 2024Article
- Antimicrobial resistance patterns inFrontiers in microbiology · 2024Article
- Whole Genome Sequencing: Applications in Clinical Bacteriology.Medical principles and practice : international journal of the Kuwait University, Health Science Centre · 2024Review
- Predicting β-lactam susceptibility from the genome ofFrontiers in microbiology · 2023Article
- The Notable Achievements and the Prospects of Bacterial Pathogen Genomics.Microorganisms · 2022Article
- One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings.Frontiers in microbiology · 2022Article
- Haemophilus influenzae one day in Denmark: prevalence, circulating clones, and dismal resistance to aminopenicillins.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2021Article
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Authors and funding
16 authors at 12 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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