Genomic epidemiology of multidrug-resistant and ESBL-producing Proteus mirabilis in a military referral hospital in Ethiopia.

Abstract

Multidrug-resistant Proteus mirabilis has emerged as an important healthcare-associated pathogen; however, genomic epidemiological data from sub-Saharan Africa remain limited, particularly in military hospital settings. This study aimed to characterize the phenotypic and genomic resistance profiles of P. mirabilis isolates recovered from a military referral hospital in Ethiopia between May 2024 and May 2025. A total of 99 non-duplicate clinical isolates were analyzed using antimicrobial susceptibility testing according to Clinical and Laboratory Standards Institute (CLSI) guidelines, with phenotypic detection of extended-spectrum β-lactamase (ESBL) and carbapenemase production. Whole-genome sequencing was performed on a selected subset of 25 representative ESBL- and/or carbapenemase-associated P. mirabilis isolates to identify resistance genes, determine multilocus sequence types (MLST), analyze plasmid replicons, and reconstruct core-genome phylogeny. Using phenotypic detection, 96.0% of isolates were found to be resistant to at least one third- or fourth-generation cephalosporin, and 99.0% were classified as multidrug-resistant. ESBL production was confirmed in 60.6% (60/99) of isolates, while 6.1% (6/99) demonstrated carbapenemase activity. Genomic analysis revealed diverse ESBL determinants dominated by blaPER-13 (40.0%) and blaVEB-6 (28.0%), with additional detection of blaCTX-M-65. MLST analysis identified nine sequence types, with ST135 predominating (32.0%). Phylogenetic analysis demonstrated moderate genetic heterogeneity, with evidence of multiple lineages circulating within the hospital setting; however, transmission dynamics could not be definitively determined. Plasmid analysis showed a structured replicon distribution dominated by IncQ1 (36.0%) and several Col-type plasmids. These findings demonstrate extensive multidrug resistance associated with diverse ESBL determinants and multiple plasmid replicon types among P. mirabilis isolates in a military healthcare setting. The results highlight the need for strengthened antimicrobial stewardship, improved infection prevention strategies, and integration of genomic surveillance in comparable healthcare environments.