Genomic insights into plasmid mediated carbapenem resistance in Citrobacter species from Czech surface and wastewater systems

Wastewater represents an important reservoir of antibiotic-resistant bacteria and resistance genes, facilitating their introduction into aquatic environments. In this study, we performed phenotypic and genomic characterisation of 75 Citrobacter isolates from hospital sewage, municipal wastewater, and surface water using whole-genome sequencing. The collection comprised seven species and exhibiting high genomic diversity (54 sequence types, including 17 novel) and a high prevalence of multidrug resistance. Carbapenemase genes were detected in 16 isolates, including six isolates from treated effluent, and were exclusively plasmid-borne. Notably, bla GES−5 was carried on ColE2-like plasmids closely related to those previously described in isolates from local healthcare settings. Furthermore, the co-occurrence of antibiotic resistance and metal tolerance genes on IncF plasmids suggests a potential for co-selection. These findings identify Citrobacter spp. as an overlooked reservoir of antibiotic resistance and demonstrate that wastewater systems represent critical points where high-risk determinants can bypass the treatment process.