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

Abstract

The emergence of carbapenem-resistant bacteria represents a growing public health concern, particularly in settings associated with healthcare waste. This study reported the genomic and structural characterisation of a carbapenem-resistant Pseudomonas isolate (CW003PS) recovered from microwave-treated healthcare waste. Whole-genome sequencing was performed for comprehensive genomic analysis, while protein structure modeling, molecular docking, and molecular dynamics (MD) simulations were applied to BlaVIM−2 to explore the expression mechanisms and structural features associated with carbapenem resistance. CW003PS is closely related to Pseudomonas wenzhouensis A20 but harbors a distinct antimicrobial resistance gene repertoire, including class D β-lactamase OXA-10 (BlaOXA−10) and metallo-β-lactamases VIM-2 and (BlaVIM−2) VIM-6(BlaVIM−6), alongside presence of insertion sequences and integrons. The molecular docking indicated strong binding affinity against CW003PS resistant antibiotics. Inhibitor CHEMBL3903047 demonstrated the highest binding affinity against BlaVIM−2 and its homolog VIM-2 enzyme (7AFX). MD simulations revealed potential inhibitor CHEMBL3903047-BlaVIM−2 had a stronger free ligand binding energy than ineffective inhibitor avibactam. Residual decomposition analysis indicated high energy interactions of CHEMBL3903047 with both active sites of the BlaVIM−2 dimer, suggest enhanced binding compared to avibactam. While these computational analyses do not establish enzymatic activity, they provide structural hypotheses that complement genomic predictions and contribute in designing and developing inhibitors. The role of mobile genetic elements in genotypic-phenotypic resistance, with in silico structural analysis to provide insights into the antimicrobial resistance architecture of Pseudomonas CW003PS 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.