Antimicrobial Susceptibility in Chicken-Associated Commensal Bacteria and Assembly-Linked Resistance-Gene Profiling of Escherichia coli from Northern Hungary

Abstract

Background/Objectives: Regional antimicrobial-resistance surveillance can be strengthened by linking phenotypic susceptibility data with genomic evidence. We characterized chicken-associated commensal bacteria from Northern Hungary and examined resistance-gene evidence in available Escherichia coli assemblies. Methods: Broth-microdilution minimum inhibitory concentration (MIC) data were available for 166 bacterial isolates collected in 2022–2023. Among the 69 E. coli isolates in this collection, 24 had corresponding draft whole-genome assemblies, defined here as assembled contig sets that had not been resolved into closed genomes; these assemblies were linked to the MIC records of the same isolates. Analyses included MIC distributions, descriptive correlations, principal component analysis, assembly-quality assessment, resistance-gene profiling, and sequence-context analysis. Results: The collection comprised 26 Staphylococcus spp., 71 Enterococcus spp., and 69 E. coli isolates. In E. coli, ceftriaxone MIC50 and MIC90 values were 0.031 and 512 µg/mL, respectively. Five assemblies contained blaCTX-M-1-labelled intervals that were identical across 876 bp and corresponded to ceftriaxone MICs of 32–1024 µg/mL. In E. coli isolate 1316, seven resistance-gene calls co-occurred within a 12,933-bp region of one contig. Assembly quality varied substantially, and the draft assembly of E. coli isolate 832 was unsuitable for reliable gene-negative interpretation. Conclusions: The dataset showed heterogeneous susceptibility profiles and identifiable resistance-gene contexts. These findings support isolate-linked phenotypic and genomic surveillance while avoiding population-level, transmission, or clinical resistance classifications unsupported by the available data.