Paws, Pathogens, and Public Health Risks: Molecular Characterization of ESBL- and Carbapenemase-Producing Bacteria Isolated from Cats in Lebanon

Abstract

Antimicrobial resistance (AMR) is a critical global health concern, impacting human, animal, and environmental health within the One Health Triad. ESBL- and carbapenemase-producing organisms are the biggest threat to global public health and have been found in several niches in Lebanon, including hospital settings, surface water, wastewater, poultry, and livestock. Despite the close contact between pets and their owners, companion animals, particularly cats, have not been adequately considered for their role in disseminating antimicrobial resistance genes. This study addresses the gap by presenting the first report of multidrug-resistant Enterobacteriaceae isolated from cats in Lebanon, marking the fifth report in the region. It is also the first attempt to genotype T. gondii DNA from oocysts in cat feces. Gram-negative pathogens were isolated from the fecal samples collected from seven different cats and 13 representative isolates were further characterized by whole-genome sequencing (WGS). Among the chosen isolates, nine (69.2%) were ESBL-producers, and four (30.7%) exhibited carbapenemase production. in silico analysis showed that Escherichia coli (11/13) belonged to diverse sequence types (STs) and phylogroups, showcasing variability in their resistome, plasmidome, and antimicrobial susceptibility testing patterns. The presence of resistance genes, including blaCTX-M-15 (n=10, 76.9%), blaTEM-1B (n=6; 46.1%), blaOXA-1 (n=6; 46.1%), and blaNDM-5 (n=4, 30.7%), was confirmed through in silico resistome analysis and antimicrobial susceptibility testing (AST) with ten different antibiotics. Over 27 distinct genes conferring resistance to eight antimicrobial agents beyond β-lactams and carbapenems, were identified. Plasmid incompatibility groups were determined in silico and through plasmid-based replicon typing, and IncU (n=9; 69.3%) was the most commonly detected type, followed by IncFII and IncFIB (n=8; 61.5%) with equal prevalence. The report marks the first detection of E. coli ST410 and ST90 harboring blaNDM-5 in Lebanon, the first detection of E. coli ST46 in extra-hospital settings, E. coli ST345, and the identification of two novel E. coli sequence types. Long-read Nanopore sequencing using the Oxford MinION platform of the high-risk E. coli clone ST167 unveiled a novel plasmid, pNDM-5_FII, harboring blaNDM-5, blaOXA-1, blaCTX-M-15, and other resistance determinants, revealing new insights into the dissemination of blaNDM-5 and characterizing IS26-mediated dissemination of blaCTX-M-15 in a pseudocompound transposon harboring blaOXA-1. This report underscores the imperative need to implement the ‘One Health’ approach by also including companion animals, especially cats, when studying AMR and the spread of pathogens in Lebanon.