Michael Pedersen | PubMed Health

PubMed2026

Emerging trends in invasive Streptococcus dysgalactiae subsp. equisimilis infections in Denmark, 2014 to 2024: a nationwide genomic and registry-based study.

BACKGROUNDIncreasing incidence rates of invasive Streptococcus dysgalactiae subspecies equisimilis (iSDSE) have been detected worldwide.AIMWe aimed to investigate iSDSE infection incidence rates in Denmark during 2014-2024, and characterise the genomic population structure of a subset of iSDSE isolates and their antimicrobial resistance (AMR).METHODSUsing national register data, we estimated overall and sex-/age-stratified iSDSE incidences during 2014-2024, by retrospectively identifying cases of invasive infections with group C and G streptococci or S. dysgalactiae (including specified as subspecies equisimilis). From the voluntary national beta-haemolytic streptococci laboratory surveillance system, whole-genome-sequenced isolates from August 2020-September 2022 were used to investigate the iSDSE genomic population structure. Susceptibility to penicillin, erythromycin and clindamycin was determined and AMR genes identified.RESULTSDuring 2014-2024, iSDSE incidence rates increased significantly (linear trend analysis p < 0.001) with mean annual incidence ranging between 10.3 and 16.4 per 100,000, peaking in 2023. Incidence was higher in males, increasing with older age. Nearly 75% of the 1,223 iSDSE isolates belonged to four of 14 genetic clusters. Sequence types (STs) ST20 and ST17 were most prevalent, while emm-type stG62647, a variant associated internationally with higher virulence, dominated. All isolates were phenotypically susceptible to penicillin but approximately 10% were respectively erythromycin and clindamycin resistant. High erythromycin resistance prevalence (57%; 39/68), coinciding with gene ermA, occurred in one genetic cluster.CONCLUSIONThe findings illustrate the need for national registry-based surveillance to detect epidemiological changes and potential outbreaks. Further, continuous genomic surveillance can monitor the occurrence and expansion of genetic clades and AMR genes.

Denmark↗

PubMed2025

Comparison of whole-genome sequencing-based analysis methods for taxonomic classification of isolates unclassified by MALDI-TOF MS.

Taxonomic identification of clinical isolates is routinely achieved using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). If the species cannot be reliably identified, whole-genome sequencing can be applied. The aim of this study was to compare the results of approaches for taxonomic assignment for classification of isolates that are difficult to identify. Fifty-seven isolates were included in the study. The isolates were whole-genome sequenced and de novo assembled. Assembly-based classification was performed with the Genome Taxonomy Database Toolkit (GTDB-Tk), BLAST against 16S rRNA gene databases, the Type (Strain) Genome Server (TYGS), and ribosomal MLST (rMLST). Read-based classification was performed with MetaPhlAn4 and Kraken2. Thirty-two isolates were assigned to the same species with all four assembly-based classifiers, while the remaining 25 showed diverging assignments. When evaluating the results for the latter isolates, GTDB-Tk performed better than the other classifiers regarding which assignments were most likely correct. Of the read-based classifiers, MetaPhlAn4 performed better than Kraken2. Our evaluation identified GTDB-Tk to be the strongest tool for taxonomic assignment of isolates that are difficult to identify. Disagreements between classifiers are likely due to database limitations, wrongly assigned taxonomy, or unreliable 16S rRNA gene-based assignments.

Spectrometry, Mass, Matrix-Assisted Laser Desorpti↗