Host-derived lactic acid bacteria inhibit multidrug-resistant uropathogenic Escherichia coli in dogs: a genomic and in vitro study

Abstract Background Uropathogenic Escherichia coli (UPEC) is the leading cause of bacterial cystitis in dogs, and these infections are commonly linked to intensive antimicrobial use, which promotes the selection of resistant strains. Materials and methods Seeking alternative strategies to reduce antimicrobial pressure in veterinary medicine, this study evaluated the in vitro inhibitory activity of lactic acid bacteria (LAB) isolated from the urogenital tract of six healthy dogs against five UPEC serotypes obtained from dogs with cystitis, using the spot-on-the-lawn (SOTL) assay. All isolates were further characterized by next-generation sequencing (NGS). Results LAB belonged to the genera Lacticaseibacillus and Enterococcus , comprising L. casei ( n = 2) and E. faecalis ( n = 4) isolated from both male and female dogs. The UPEC serotypes identified were O1:H28, O11:H25, O1:H6, O6:H31, and O25:H4, distributed among phylogroups B2 ( n = 2), F ( n = 2), and E ( n = 1). After functional classification of the AMRFinderPlus output, few acquired antimicrobial resistance genes were detected (six in O1:H28, one in O25:H4, and non in the remaining serotypes), most detected genes being virulence-metal/biocides-resistance, or efflux-associated. One L. casei strain and one E. faecalis strain demonstrated strong inhibitory activity against all tested serotypes. Pairwise comparisons revealed significant inhibition ( p < 0.001), and Pearson’s correlation analysis indicated moderate to strong positive associations among several LAB interactions. A significant LAB effect was observed in the linear mixed-effects model (F(5, 60) = 154.8, p < 0.001), with one L. casei strain exhibiting superior and consistent inhibitory capacity. Conclusion Overall, canine UPEC isolates displayed genetic heterogeneity, a predominantly virulence-associated gene repertoire with few acquired resistance genes, and potential zoonotic relevance, whereas host-derived LAB, particularly L. casei , showed promising antagonistic activity, supporting their potential as alternative or adjunct approaches for controlling bacterial cystitis pending further mechanistic and in vivo studies.