Whole genome sequencing characterization of Clostridioides difficile from Bulgaria during the COVID-19 pandemic

Increased incidence of Clostridioides difficile infections were documented in Bulgarian hospitals during COVID-19. WGS was performed on 39 isolates from seven hospitals during 2015-2022. Antimicrobial resistance and toxin genes were inferred from genomes. MLST profiles, cgMLST, and wgMLST phylogeny analyses were performed. Isolates were grouped into eight MLST types as predominant were ST3 (46.15%) and ST1/RT027 (33.33%). ST3 was detected in a single hospital (16/18) and characterized by two toxin variants: tcdA+/tcdB+ (14) and tcdA-/tcdB+ (4). Twelve ST3 strains belonged to the country-specific cgMLST HC2_6485 cluster and ten were identified as a putative outbreak in the infectious disease ward. All the ST1/RT027 isolates were distributed in six hospitals and clustered in an HC2_4711 with strains from neighbouring countries. All C. difficile were susceptible to vancomycin despite the Thr349Ile mutation in vanS in three isolates. We report the first insights into the C. difficile genotype hospital prevalence during the pandemic.