Identification of IMP-8-carrying Comamonas thiooxydans strains from a diarrheal sample: genomic insights into plasmid-borne carbapenemase in an environmental bacterium

The proliferation of carbapenem-resistant bacteria, facilitated by carbapenemase enzymes, constitutes a significant public health threat. Although the metallo-β-lactamase gene bla IMP-8 has been identified in various bacterial species, its occurrence in Comamonas thiooxydans within the human intestinal tract is not well understood. Three bacterial strains were isolated from an intestinal perforation patient's diarrheal samples using MacConkey agar with meropenem. Species identification was done via MALDI-TOF MS, and the IMP gene's presence was confirmed by PCR. Complete genome sequencing used Illumina and Nanopore platforms, while Southern blot confirmed the plasmid location of bla IMP-8 . Comparative genomic analysis, using Average Nucleotide Identity (ANI), was performed on 481 Comamonas genomes. Core-genome SNP analysis assessed the genetic relatedness of the three isolates. The three isolates were identified as Comamonas thiooxydans , carrying bla IMP-8 on plasmids. The earliest strain, L4020hy, also had a ~ 10 kb insertion for the NorR regulator. Among 481 Comamonas genomes, 93 were conspecific C. thiooxydans (≥ 95% ANI), including these isolates. Phylogenetically, they were closest to the environmental isolate Comamonas sp. A23. SNP analysis showed genetic distinctiveness among the clinical isolates, with 403, 322, and 251 core-genome SNPs between L4020 vs. L4037, L4020 vs. L4040, and L4037 vs. L4040, respectively. This study reports the identification of multiple strains of Comamonas thiooxydans harboring a bla IMP-8 -containing plasmid within the human intestinal tract. This finding highlights the potential for C. thiooxydans to serve as a reservoir and possible vector for carbapenem resistance genes within the human gut, warranting further surveillance.