First identification and whole-genome characterization of human-associated Enterobacter roggenkampii and Enterobacter sichuanensis carrying blaIMI-4 carbapenemase in Costa Rica

ABSTRACT: Objective: All carbapenem-resistant Gram-negative bacterial isolates obtained in the Costa Rican National Network of Bacteriology Laboratories are routinely referred to the National Reference Center for Bacteriology for the national-laboratory for the surveillance and characterization of their carbapenem-related mechanism of resistance. As a result of this healthcare-associated infection surveillance, two bacterial isolates with unknown mechanisms for carbapenem resistance were investigated. Methods: The isolates were subjected to taxonomic identification, antimicrobial susceptibility testing, and whole-genome characterization, using Illumina and Oxford Nanopore technologies, and bioinformatic analyses. Results: The isolates were identified as Enterobacter roggenkampii and Enterobacter sichuanensis. Although the isolates presented different antimicrobial resistance profiles, both were resistant to carbapenems, positive for the modified carbapenem inactivation method (mCIM), and showed inhibition of carbapenem resistance with boronic acid. The full characterization of the isolates’ genomes, revealed the presence of the rare chromosomal blaIMI-4 gene inserted within 25-kb integrative mobile elements, closely related to EcloIMEX-2. Conclusions: The limited global distribution of the blaIMI-4 variant, along with its identification in two distinct bacterial species in Costa Rica within integrative mobile elements, underscores the critical need for regular antibiotic resistance surveillance using next-generation sequencing technologies. This study demonstrates that this practice allows the timely detection of novel or rare mechanisms of antibiotic resistance.