Phylogenomics of novel clones of Aeromonas veronii recovered from a freshwater lake reveals unique biosynthetic gene clusters

Abstract

Aquatic ecosystems are important reservoirs for clinically relevant pathogens and antimicrobial resistance genes, thus present a significant risk to global health. Here, we assessed the phylogenomics of Aeromonas veronii (A. veronii) recovered from Lake Wilcox in Ontario using a combination of morphological, biochemical, and whole-genome sequencing (WGS) techniques. Eleven distinct bacterial colonies were isolated and identified as A. veronii (n=9), and two other Aeromonas species (A. caviae and A. allosaccharophila), with significant discrepancies noted between biochemical and WGS identification methods. Of note, 67% (n=6/9) of A. veronii isolates were human pathogens (Pathogenicity score [≥] 0.50). The genomic analysis revealed high genetic diversity among the A. veronii isolates, including the discovery of 41 novel alleles and seven new sequence types (ST) suggesting the lake as a reservoir for multiple human pathogenic clones of this bacterium. The comparison of the newly isolated and sequenced A. veronii with 214 A. veronii genomes revealed significant genetic diversity and suggests potential broad geographical dissemination of strains. Chromosomal genes (OXA-912 and cphA [cphA3, cphA4, cphA7]) genes encoding resistance to {beta}-lactamases were detected in all isolates. Human and non-human pathogenic strains of A. veronii differed in their virulence gene content, with type III secretion systems being associated with human pathogenic isolates. Mobilome analysis revealed the absence of plasmids in A. veronii isolates and the presence of 13 intact the great majority of which were P22-like (Peduoviridae) phages, and nine different insertion sequence families. Novel biosynthetic gene clusters were identified and characterized, indicating the potential for unique secondary metabolite production in A. veronii with different pathogenic potential. Overall, this study underscores the importance of continuous surveillance of aquatic ecosystems for the presence of pathogens, contributing to our understanding of their evolution, potential for human pathogenicity, and the ecological roles of their genetic elements.