Integrative Genomic and in silico Structural Analysis of Carbapenemase in Pseudomonas for Environmental Surveillance

The emergence of carbapenem-resistant bacteria in environmental reservoirs represents a growing public health concern, particularly in settings associated with healthcare waste. In this study, we reported the genomic and structural characterisation of a carbapenem-resistant Pseudomonas isolate (CW003PS) recovered from microwave-treated healthcare waste. Whole-genome sequencing and comparative genomic analyses revealed that CW003PS is closely related to Pseudomonas wenzhouensis but harbors a distinct antimicrobial resistance gene repertoire, including class D β-lactamase OXA-10 and metallo-β-lactamases VIM-2 and VIM-6, alongside multiple efflux systems and porin-associated alterations. VIM and OXA enzymes displayed significant binding affinity to ertapenems, an interaction not previously characterized in this species. To explore structural features associated with carbapenem resistance, protein structure modeling, molecular docking, and molecular dynamics simulations were applied to key β-lactamases identified in the genome. These analyses revealed differential structural conformations and binding behaviors with carbapenem antibiotics, revealing sequence-dependent structural and dynamic variability in enzyme–ligand interactions, providing testable hypotheses for future functional validation. While these computational analyses do not establish enzymatic activity, they provide structural hypotheses that complement genomic predictions and highlight features that may contribute to resistance phenotypes. Overall, this study integrates environmental genomics with in silico structural analysis to provide insights into the antimicrobial resistance architecture of a healthcare waste-associated Pseudomonas strain. The findings underscore the role of environmental reservoirs in disseminating carbapenemase-encoding bacteria and establish a framework for future experimental validation of resistance mechanisms.