Genomic characterization of multidrug-resistant Enterobacter asburiae clinical isolates co-harboring mcr-9 and...

Carbapenem-non-susceptible Enterobacter cloacae complex (ECC) strains represent an emerging clinical challenge in Taiwan. This study characterized the genomic context of plasmid-mediated multidrug-resistance genes, particularly the co-occurrence of bla_IMP-8 and mcr-9, in ECC isolates.

Three carbapenem-non-susceptible ECC isolates (YGH005, YGH008, and YGH009) recovered from sterile body sites in Taiwan in 2019 underwent whole-genome sequencing using the Oxford Nanopore PromethION platform. Species identification was confirmed using average nucleotide identity analysis. Resistance genes, sequence types (STs), and plasmid incompatibility groups were determined using bioinformatics tools. Phenotypic carbapenemase activity and colistin susceptibility were confirmed using mCIM/EDTA-mCIM and the colistin broth disk elution method, respectively. Resistance gene organization and plasmid structure characterization were performed using CAGECAT clinker.

Two isolates were identified as Enterobacter asburiae (ST25; YGH005 and YGH009) and one as Enterobacter intestinihominis (ST78; YGH008). All three isolates harbored chromosomal AmpC β-lactamases and the bla_IMP-8 and mcr-9 genes located on IncFIB-type plasmids. A conserved multidrug-resistance cassette characterized by a Class 1 integron containing bla_IMP-8 and an identical downstream cluster (IS26-wbuC-mcr-9-IS903B) were identified. This conserved architecture was shared by the historical reference plasmid pEC-IMPQ. Phenotypically, all isolates were susceptible to colistin and displayed inconsistent carbapenemase activity, indicating significant genotype-phenotype discordance.

The conserved multidrug-resistant genetic architectures across epidemiologically distinct ECC isolates suggest a potential for dissemination of last-resort antibiotic resistance genes. The possible inducibility of occult mcr-9 expression warrants further investigation, particularly under selective colistin pressure. Enhanced surveillance and antimicrobial stewardship are recommended.