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

• Published in: Microbiology spectrum 2024-11, Vol.12 (12), p.e0117124
• Main Authors: Lawal, Opeyemi U, Bryan, Noah, Parreira, Valeria R, Anderson, Rebecca, Chen, Yanhong, Precious, Melinda, Goodridge, Lawrence
• Format: Article
• Language: English
• Subjects: Aeromonas; antimicrobial resistance; biosynthetic gene cluster; Environmental Microbiology; genomics; global population structure; Research Article; water quality
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.01171-24

Aquatic ecosystems serve as crucial reservoirs for pathogens and antimicrobial resistance genes, thus presenting a significant global health risk. Here, we investigated the phylogenomics of from Lake Wilcox in Ontario. Among the 11 bacterial isolates, nine were identified as . Notably, 67% of isolates were potential human pathogens. Considerable genetic diversity was noted among the isolates, suggesting the lake as a reservoir for multiple human pathogenic strains. Comparison of the sequenced with global genomes highlighted significant genetic diversity and suggests widespread dissemination of strains. All the isolates carried chromosomal genes encoding resistance to β-lactams. Although virulence gene content differed between human and non-human pathogenic strains, type III secretion systems was associated with human pathogenic isolates. The assessment of AMR genes in global isolates showed that β-lactam and tetracycline resistance genes were predominant. Although the machine learning-based pangenome-wide association approach performed did not yield any source-based genes, some genes were enriched in a few isolates from different sources. The operon that mediates biofilm formation and genes encoding resistance to colistin, chloramphenicol, trimethoprim, and tetracycline were enriched in animal products, whereas macrolide resistance genes and Inc plasmid-types were linked to the aquatic environment. Novel biosynthetic gene clusters were identified, suggesting that with varying pathogenic potential could produce unique secondary metabolites. There is a need for continuous tracking of pathogens in aquatic ecosystems to contribute to our understanding of their evolutionary dynamics and the ecological roles of their genetic elements. Lakes and other aquatic ecosystems can harbor harmful bacteria that can make people sick and resist antibiotics, posing a significant global health risk. In this study, we investigated , a Gram-negative bacteria found in Lake Wilcox in Ontario. We used various techniques, including whole-genome sequencing (WGS), to analyze the bacteria and found that many of the isolates had the potential to cause human disease. We also discovered significant genetic diversity among the isolates, indicating that the lake may be a reservoir for multiple human pathogenic strains. All isolates carried genes that confer resistance to antibiotics, and some virulence genes were associated with human pathogenic isolates. This study highlights the importan