Comprehensive genome analysis of MDR Klebsiella pneumoniae in influent and effluent of a selected wastewater treatment plant

This study investigates the antibiotic resistance profiles, virulence factors and genomic characteristics, of Klebsiella pneumoniae isolates obtained from influent and effluent samples of a wastewater treatment plant. Data generated sheds light on the dissemination and persistence of antibiotic resistance in compartments in a wastewater treatment plant (WWTP). Given the increasing concern regarding the role of wastewater in the dissemination of antibiotic-resistant bacteria, this research focused on K. pneumoniae populations using culture-based and genomics approaches. The culture-based approach showed that antibiotic resistance to β-lactam antibiotics was corroborated by PCR detection of the genes. Whole Genome Sequencing (WGS) analysis revealed a diverse array of Antibiotic-Resistant Genes (ARGs), including those encoding extended-spectrum β-lactamases (ESBLs) and resistance to other clinically relevant ˙antibiotics. Plasmid analysis unveiled various replicon types indicative of horizontal gene transfer mechanisms. Moreover, the identification of virulence genes implicated in adhesion, biofilm formation, and iron acquisition underscores the pathogenic potential of K. pneumoniae isolates in wastewater. In addition, the genomics comparison between K. pneumoniae strains from the influent and effluent of the WWTPs ecosystem reveal that "core" genome is shared. However, unique genomic clusters in the environmental strains suggests niche-specific adaptations, shedding light on the genomic plasticity of K. pneumoniae in response to environmental cues. This may have implications for antibiotic resistance dissemination and ecological interactions within wastewater ecosystems. Data presented here highlights the urgent need for enhanced surveillance and management strategies to mitigate the spread of antibiotic resistance through wastewater treatment plants ecosystems.