Genomic analysis of environmentally sourced Stenotrophomonas species from Fiji and Australia

The World Health Organization identified Stenotrophomonas maltophilia as an underestimated, multi-drug-resistant and opportunistic nosocomial pathogen. It poses a threat to patients who are immunocompromised, suffering chronic disease, requiring indwelling catheters and undergoing mechanical ventilation, as well as victims of trauma and burns. Here, whole-genome sequences of 266 Stenotrophomonas spp. from diverse environmental sources in Fiji and Australia were generated and used to improve understanding of the phylogeny of the genus. Isolates were sourced from freshwater, soil, waste biosolids, wastewater and animal agriculture using selective differential growth media. Phylogenomic analysis identified eight species, plus a singular novel Australian isolate most closely related to Stenotrophomonas indicatrix and Stenotrophomonas lactitubi . The Fijian isolates were primarily S. maltophilia (Sm), with isolates belonging to 13 of the previously recognized 19 Sm subgroups, while most Australian isolates were notably non- maltophilia . A genotypic characterization of the collections was performed, with a focus on well-characterized antimicrobial resistance and virulence genes identified in S. maltophilia , highlighting the presence of these key genes within other Stenotrophomonas species, particularly S. indicatrix , S. lactitubi and Stenotrophomonas rhizophila . Allelic analysis of chromosomal β -lactamase bla L2 revealed its presence across the entire Stenotrophomonas genus, while carbapenemase gene bla L1 was restricted to S. maltophilia and its closest relatives. These data represent a significant contribution of non- maltophilia genome sequences to the public domain, and the first dataset representing Stenotrophomonas from Fiji.