Genomic Background and Phylogeny of <i>cfi</i>A-Positive <i>Bacteroides fragilis</i> Strains Resistant to Meropenem-EDTA
Sylvia Valdezate,
Fernando Cobo,
Sara Monzón,
María J. Medina-Pascual,
Ángel Zaballos,
Isabel Cuesta,
Silvia Pino-Rosa,
Pilar Villalón
Affiliations
Sylvia Valdezate
National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain
Fernando Cobo
Department of Microbiology, Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain
Sara Monzón
Department of Microbiology, Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain
María J. Medina-Pascual
National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain
Ángel Zaballos
Bionformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain
Isabel Cuesta
Department of Microbiology, Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain
Silvia Pino-Rosa
National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain
Pilar Villalón
National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain
Background: Bacteroides fragilis shows high antimicrobial resistance (AMR) rates and possesses numerous AMR mechanisms. Its carbapenem-resistant strains (metallo-β-lactamase cfiA-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 cfiA genes (cfiA14b and the new cfiA28), along with other AMR mechanisms. The presence of other efflux-pump genes, mexAB/mexJK/mexXY-oprM, acrEF/mdtEF-tolC, and especially cusR, 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 cfiA. 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 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.
