Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission.

species are ubiquitous in aquatic environments, colonize water systems in healthcare settings and are emerging opportunistic pathogens with reports surfacing in 25 countries across six continents infections are challenging to treat, and case fatality rates are high. Chromosomal and genes encoding carbapenemases and cephalosporinases are unique to . and reports of concomitant resistance to aminoglycosides, fluoroquinolones and sulfamethoxazole-trimethoprim are known. Here, we characterized whole-genome sequences of 94 isolates carrying multiple wide-spectrum metallo-β-lactamase ( ) and extended-spectrum serine‑β-lactamase ( ) genes from Australian aquatic environments and performed comparative phylogenomic analyses against national clinical and international strains. qPCR was performed to quantify the levels of species in the source environments. Antibiotic MIC testing revealed significant resistance to carbapenems and cephalosporins but susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole. Phylogenetics show that three environmental isolates are closely related to from Australian clinical isolates (∼36 SNPs), and a new species, sp. novel was discovered. Genomic signatures provide insight into potentially shared origins and a capacity to transfer mobile genetic elements with both national and international isolates.