Phylogenomics of an NDM-1-producing Providencia stuartii strain from Portugal reveals global clinical and environmental reservoirs

BACKGROUND: Recent reports indicate a significant rise in carbapenem-resistant Providencia stuartii (CRPS) infections across Europe. OBJECTIVES: This study characterizes a CRPS strain (Ps5822) isolated from a Ukrainian refugee, in a Portuguese hospital, and examine its phylogenetic placement within the global P. stuartii population. METHODS: The Ps5822 isolate was subjected to antimicrobial susceptibility testing (AST) along with whole-genome sequencing to detect antimicrobial resistance gene detection and replicon types. Additionally, all available P. stuartii genomes from the ENA and NCBI databases (N = 585) were downloaded to assess the phylogenetic positioning of Ps5822 within the global P. stuartii population. RESULTS: AST showed only cefiderocol and aztreonam as viable therapeutic options. Phylogenetic positioning of global P. stuartii genomes revealed that (1) Ps5822, NDM-1-producing, is clustered with 28 European CRPS strains linked to soldiers and refugees medically evacuated from the Ukrainian war and (2) that winged insect and wastewater treatment plants are important reservoirs of CRPS. CONCLUSIONS: These findings support that this extensive drug-resistant P. stuartii clone originated in Ukraine and spread by subsequent population movements. This study also emphasizes the widespread dissemination of CRPS isolates among clinical, environmental, and Conflict-Linked Reservoirs.