Successful management of a multi-species outbreak of carbapenem-resistant organisms in Fiji: a prospective genomics-enhanced investigation and response.

Abstract

Fiji is a Pacific Island nation grappling with the increasing threat of antimicrobial resistance (AMR). While genomic technologies are increasingly utilised to understand the emergence and spread of AMR globally, its application to inform outbreak responses in low- and middle-income settings has not been reported. Through an established capacity building program, suspected carbapenem-resistant organisms (CRO) identified at Colonial War Memorial Hospital in Fiji (Jan 2022-Oct 2023) underwent whole genome sequencing and analysis. Following a rapid increase in CROs, a joint outbreak investigation including detailed genomic epidemiology was undertaken. A multi-modal response was co-designed and implemented by hospital staff, and circulating strains monitored to assess impact. Six large genomic clusters accounted for 73% (n = 223/304) of all sequenced CRO isolates. Four genomic clusters (Acinetobacter baumannii NDM-1, A. baumannii OXA-23/OXA-58, Escherichia coli NDM-7, Pseudomonas aeruginosa NDM-1) were investigated in detail, with affected wards differing between species. Following outbreak interventions, E. coli and P. aeruginosa clusters decreased rapidly, however A. baumannii transmission persisted. Repeated international importation of CROs into Fiji were suspected. Carbapenem-resistant pathogens pose a major threat to the health system in Fiji. Genomics technologies are useful for understanding AMR and guiding successful response, in these settings. Strategies to ensure access to, and judicious use of the technology are justified. This work was funded by the Australian Government through the Department of Foreign Affairs and Trade Centre for Health Security, Medical Research Future Fund and National Health and Medical Research Council.