Monitoring antimicrobial resistance trends and emerging carbapenemases in Enterobacterales causing companion animal infections: a four-year study.

Abstract

This study assessed longitudinal trends in antimicrobial resistance (AMR) among Enterobacterales causing companion animal infections in Portugal between 2020 and 2023 and characterized carbapenemase-producing Enterobacterales (CPE). A collection of 4155 non-duplicate clinical Enterobacterales isolates underwent antimicrobial susceptibility testing mainly through disk diffusion, targeting &#x3b2;-lactams, fluoroquinolones, aminoglycosides and folate pathway inhibitors. Possible bacteria-AMR associations and temporal trends were statistically assessed. Potential CPE were selected on Brilliance&#x2122; CRE Agar, confirmed by multiplex PCR and characterized by whole-genome sequencing (Illumina NovaSeq). In silico MLST was performed and the clonality of the strains was evaluated through maximum likelihood phylogenetic trees and pairwise SNP matrixes. Klebsiella spp. and Enterobacter spp. exhibited a higher likelihood of AMR than Escherichia coli (P&#x202f;<&#x202f;0.001, ORs between 2.56 and 14.32). Most AMR phenotypes remained stable or declined over time, although fluoroquinolone resistance increased toward the end of the study period. Eighteen CPE mostly associated with high-risk global STs (E. coli ST410 and ST457, Klebsiella pneumoniae ST11, ST147 and ST307, respectively) were detected, carrying bla, bla, blaor bla. Genomic analysis showed four CPE strain pairs from epidemiologically unrelated sources had <&#x202f;10 SNPs differences, indicating possible recent clonal transmission of E. coli ST4981 and K. pneumoniae ST147 and ST273 strains. Overall, this study presents longitudinal AMR surveillance data from companion animal Enterobacterales infections and characterizes the genetic diversity of CPE, having detected international high-risk clones and possible transmission events. These findings reinforce the importance of integrating companion animals into One Health surveillance systems and antimicrobial stewardship strategies.