Genomic characterization of environmental Klebsiella pneumoniae through whole genome sequencing

Abstract

Klebsiella pneumoniae poses a significant public health threat due to its high antibiotic resistance and its role in severe infections, especially in healthcare settings. Investigating environmental K. pneumoniae is crucial for understanding reservoirs and transmission of resistance and virulence genes. However, environmental data on K. pneumoniae is scarce in Bangladesh and globally. This study aimed to characterize environmental K. pneumoniae using antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS). From seven thanas across Dhaka City, 140 wastewater samples were collected. Klebsiella spp. were detected using biochemical tests and morphological characteristics. AST was then performed to determine their phenotypic resistance profiles against seven antibiotics. Based on the AST results and morphological characteristics, 14 isolates were selected for Sanger sequencing using a novel primer targeting the rpoB gene, designed to detect K. pneumoniae. From these, three confirmed K. pneumoniae isolates were selected for WGS to enable genomic characterization. A phylogenetic tree was generated using the WGS data in comparison with nine clinical isolates of K. pneumoniae. The AST results for environmental Klebsiella spp. revealed high susceptibility to most antibiotics tested, unlike clinical isolates. However, whole genome sequencing identified resistance genes that were not consistent with the phenotypic AST results. The analysis also showed an absence of common virulence genes typically found in clinical isolates. The phylogenetic tree indicated that the three environmental K. pneumoniae isolates formed separate nodes compared to clinical isolates. These findings highlight the unique genomic features of environmental K. pneumoniae compared to their clinical counterparts, emphasizing the importance of environmental monitoring to understand the dynamics of antibiotic resistance and virulence in this pathogen.