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

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.