Phylogenomics of novel clones of
Aeromonas veronii
recovered from a freshwater lake reveals unique biosynthetic gene clusters
Authors: Lawal Opeyemi U. , Bryan Noah , Parreira Valeria R. , Anderson Rebecca , Chen Yanhong , Precious Melinda , Goodridge Lawrence 
Published: November 2024

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
Aeromonas veronii
from Lake Wilcox in Ontario. Among the 11 bacterial isolates, nine were identified as
A. veronii
. Notably, 67% of
A. veronii
isolates were potential human pathogens. Considerable genetic diversity was noted among the
A. veronii
isolates, suggesting the lake as a reservoir for multiple human pathogenic strains. Comparison of the
A. veronii
sequenced with global
A. veronii
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
mrkABCDF
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
A. veronii
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.

IMPORTANCE

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
Aeromonas veronii
, 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 importance of monitoring aquatic ecosystems for harmful bacteria to better understand their evolution, potential for human pathogenicity, and the ecological roles of their genetic elements. This knowledge can inform strategies for preventing the spread of antibiotic-resistant bacteria and protecting public health.