Molecular epidemiology and β-lactam resistance mechanisms of Enterobacter cloacae complex isolates obtained from bloodstream infections, Kyoto, Japan

ABSTRACT The Enterobacter cloacae complex (ECC) comprises multiple species that require genomic analysis for precise identification. They produce inducible AmpC β-lactamase and may carry acquired β-lactamases, which are responsible for cefotaxime and cefepime resistance. To determine the molecular epidemiology, antimicrobial resistance, and β-lactam resistance mechanisms of the ECC, we conducted whole-genome sequencing analysis, antimicrobial susceptibility testing, and mutation analysis on bloodstream ECC isolates from patients in Kyoto, Japan. In 194 ECC isolates, 13 species and six unnamed taxa were identified, with Enterobacter xiangfangensis (36%) being the most common. A total of 38% of the isolates were nonsusceptible to cefotaxime and presented relatively high nonsusceptibility rates to all antimicrobial agents tested. Among the different species, Enterobacter hoffmannii presented the highest nonsusceptibility rates to both β-lactams and non-β-lactams. Among the cefotaxime-nonsusceptible isolates, 16% harbored genes encoding extended-spectrum β-lactamases (ESBLs), carbapenemase, and/or plasmid-mediated AmpC, and ampC derepression was the predominant resistance mechanism in the remaining isolates. The prevalent sequence types (STs) in cefotaxime-susceptible and cefotaxime-nonsusceptible isolates were different, although some STs were shared by both groups. Cefepime nonsusceptibility was detected in 7% of the isolates and was associated with E. hoffmannii ST78 and E. xiangfangensis ST93, which carry ESBLs. Sixty-four mutants, experimentally obtained from eight cefotaxime-susceptible isolates, had various ampD mutations, and 42% and 99% of the mutants were nonsusceptible to cefepime and piperacillin/tazobactam, respectively, indicating the risks associated with the use of these antimicrobials. Continuous surveillance via genomic and phenotypic analyses is needed to combat antimicrobial resistance in the ECC.IMPORTANCEThe Enterobacter cloacae complex (ECC) is a group of pathogenic bacteria that cause nosocomial infections. The ECC produces chromosomal inducible AmpC β-lactamases, which is associated with treatment failure despite initial susceptibility to third-generation cephalosporins in selected ampC-derepressed mutants. The complex antimicrobial resistance mechanisms of the ECC and challenges in species identification have complicated our understanding of the ECC and the selection of appropriate treatment. In this study, we performed phenotypic, whole-genome sequencing, and mutation analyses among ECC isolates from patients with bloodstream infections to determine the precise molecular-based epidemiology, resistance mechanisms to third-/fourth-generation cephalosporins, specific species and clones that contribute to antimicrobial resistance, and acquisition rates of fourth-generation cephalosporin resistance in ampC-derepressed mutants. These data will help elucidate the local epidemiology and complex β-lactam resistance mechanisms in the ECC and guide appropriate antimicrobial therapy and infection control strategies for ECC-related infections.