Co-occurrence of the cephalosporinase cepA and carbapenemase cfiA genes in a Bacteroides fragilis division II strain, an unexpected finding.

Background Bacteroides fragilis , an anaerobic gut bacterium and opportunistic pathogen, comprises two genetically divergent groups (or divisions) at the species level. Differences exist both in the core and accessory genomes and the beta-lactamase genes, with the cephalosporinase gene cep A represented only in division I and the carbapenemase gene cfi A only in division II. Methods Multidrug resistance in a clinical B. fragilis strain was examined by whole-genome sequencing. Results Strain CNM20200260 carried the antimicrobial resistance genes cep A, cfi A2, ant (6'), erm (F), mef (En2), est (T), tet (Q) and cat (A), along with 82-Phe mutation in gyr A (together with 47 amino acid changes in gyr A/B and par C/parE). bex A/B and other efflux pump genes were also observed. None of the detected insertion sequences was located upstream of cfi A2. The genome-based taxonomy coefficients (average nucleotide identity, DNA–DNA hybridization similarity and difference in genomic G + C%) with respect to genomes of the strains of B. fragilis division II and the novel species Bacteroides hominis (both cfi A-positive) met the criteria for CNM20200260 to belong to either species (>95%, >70% and <1%, respectively). No such similarity was seen with type strain NCTC 9343 or the representative genome FDAARGOS 1225 of B. fragilis (division I, cfi A-negative). Strain CNM20200260 harboured four out of nine Kyoto Encyclopedia of Genes and Genomes orthologues defined for division I and one of two defined for division II. Conclusions This is the first description of the co-occurrence of cep A and cfi A in a Bacteroides strain, confirming the complexity of the taxonomy of this species. [ABSTRACT FROM AUTHOR]