Identification of potential high-risk clones of Carbapenem-Resistant Pseudomonas aeuroginosa co-producing, KPC-2, VIM-2 and OXA-74 from tertiary hospitals in Metro Manila, Philippines

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is an opportunistic human pathogen and a global public health concern due to the limited treatment options available for infections by this pathogen. Identification of antimicrobial resistance (AMR) determinants at an early phase is crucial to administer the appropriate treatment in a timely manner, thereby alleviating the transmission and enhancing the outcomes of patients infected with these pathogens. This study investigated the whole genome sequence (WGS) of 35 CRPA isolates obtained from three hospitals in Metro Manila, Philippines, collected from August 2022 to January 2023. The investigation revealed that a high proportion of isolates obtained from Hospital B and C contained acquired AMR determinants. The traditional multilocus sequence type (MLST) analysis using Pasteur nomenclature in the PubMLST database revealed six different known sequence types (STs), namely ST111, ST175, ST1822, ST357, ST3753 and ST389 and the highest number of unknown STs (27 singletons). Moreover, to delineate the unknown STs identified, the Pasteur nomenclature in the Pathogenwatch database was used, which led to the identification of novel STs. Notably, a novel ST4b1c was found to co-produce the metallo-beta-lactamase (MBL) NDM-7, extended-spectrum beta-lactamases (ESBLs) CTX-M-15 and TEM-2, as well as class D OXA-395. Furthermore, potential high-risk clones represented by ST389 and novel STs (ST95c6, STf555, and STab6a) were identified, all of which co-produced carbapenemases KPC-2, VIM-2, and OXA-74. This study represents the first report in the Philippines on the co-production of ESBL KPC-2, MBL VIM-2 and Class D OXA-74 hosted by potential high-risk clones and novel STs. It underscores the need for continuous surveillance and monitoring of other problematic strains.