Molecular characterization of ESBL- and carbapenemase-producing Enterobacteriaceae isolated from cats in Lebanon

Antimicrobial resistance (AMR) represents a pressing global health challenge, influencing human, animal, and environmental health within the interconnected One Health framework. ESBL- and carbapenemase-producing Enterobacteriaceae constitute a major global public health threat. In Lebanon, their presence is particularly concerning, as they are detected across diverse environments, including hospitals, surface water, wastewater, poultry, and livestock. Despite close contact between pets and their owners, the role of companion animals, particularly cats, in spreading AMR determinants has been overlooked. Based on the One Health approach, the study addresses this gap by presenting the first Whole Genome Sequencing (WGS)-based report of multidrug-resistant (MDR) Enterobacteriaceae isolated from cats in Lebanon.

A total of 13 ESBL-producing Enterobacteriaceae, including 11 Escherichia coli and two Enterobacter hormaechei, were isolated from fecal samples of domestic and stray cats. The isolates were among those classified as World Health Organization (WHO) Critical Priority Pathogens, highlighting their public health importance. Whole-genome characterization and antimicrobial susceptibility testing revealed alarmingly high resistance rates to multiple antibiotics, including carbapenems and tigecycline. In silico resistome analysis identified over 37 diverse resistance determinants, including bla_CTX-M-15, bla_TEM-1B, bla_OXA-1, and bla_NDM-5. Plasmid analysis uncovered 17 distinct Inc groups, markedly IncU, IncFII, and IncFIB. Phylogenetic analysis demonstrated high genetic similarity among isolates of the same sequence type (ST), irrespective of their isolation source or geographical location. E. coli ST167, a high-risk clone, carried the bla_NDM-5 gene, associated with carbapenem resistance, on an IS26-flanked composite transposon. It's noteworthy that bla_CTX-M-15 was chromosomally encoded in one E. coli isolate within a rare genetic cassette, co-localized with qnrS1, Tn2, ISEcp1, and ISKpn19.

This study provides the first whole-genome sequencing-based evidence of multidrug-resistant ESBL- and carbapenemase-producing Enterobacteriaceae in cats in Lebanon, highlighting their overlooked role as reservoirs of antimicrobial resistance. The detection of high-risk clones, along with a diverse resistome and mobilome linked to multidrug resistance, reinforces the urgent need for integrated national AMR surveillance within a One Health framework.