Genomic Background and Phylogeny of cfi A-Positive Bacteroides fragilis Strains Resistant to Meropenem-EDTA.

BACKGROUND: Bacteroides fragilis shows high antimicrobial resistance (AMR) rates and possesses numerous AMR mechanisms. Its carbapenem-resistant strains (metallo-β-lactamase cfi A-positive) appear as an emergent, evolving clade.

METHODS: This work examines the genomes, taxonomy, and phylogenetic relationships with respect to other B. fragilis genomes of two B. fragilis strains (CNM20180471 and CNM20200206) resistant to meropenem+EDTA and other antimicrobial agents.

RESULTS: Both strains possessed cfi A genes ( cfi A14b and the new cfi A28), along with other AMR mechanisms. The presence of other efflux-pump genes, mex AB/ mex JK/ mex XY- opr M, acr EF/ mdt EF- tol C, and especially cus R, which reduces the entry of carbapenem via the repression of porin OprD, may be related to meropenem-EDTA resistance. None of the detected insertion sequences were located upstream of cfi A. The genomes of these and other B. fragilis strains that clustered together in phylogenetic analyses did not meet the condition of >95% average nucleotide/amino acid identity, or >70% in silico genome-to-genome hybridization similarity, to be deemed members of the same species, although <1% difference in the genomic G+C content was seen with respect to the reference genome B. fragilis NCTC 9343T.

CONCLUSIONS: Carbapenem-resistant strains may be considered a distinct clonal entity, and their surveillance is recommended given the ease with which they appear to acquire AMR.