Proteomic analysis and risk assessment of drug-resistant Escherichia coli isolated from silky fowl meat

Drug-resistant bacteria have increasingly become a significant environmental pollution issue, and the World Health Organization has recognized this as a major threat to global public health. This study aimed to investigate the occurrence and antibiotic resistance of Escherichia coli strains in silky chicken. A total of 26 E. coli strains were isolated from 60 commercial silky chicken, with an overall 43.3% occurrence, and antimicrobial susceptibility patterns were identified using seven classes of antibiotics, revealing high resistance levels in most isolates. Most isolates showed high resistance (>88%) to multiple antibiotics, including ampicillin, chloramphenicol, florfenicol, sulfamethoxazole trimethoprim, tetracycline, and streptomycin. Over half were resistant to six antibiotic classes, and 34.6% to five. Further risk assessment showed high additional risk for antibiotics such as ampicillin, nalidixic acid, ciprofloxacin, and streptomycin. LC–MS/MS analysis was conducted to investigate the effect of sub-MIC doses of ciprofloxacin on protein changes in isolates. Results revealed significant alterations in protein abundance and expression level. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that drug-resistant E. coli strains could have diverse expression strategies in response to ciprofloxacin treatment, thereby affecting various Biological Processes and Molecular Functions. • Prevalence of multidrug-resistant E. coli exceeds 88% in silky fowl meat samples. • All E. coli isolates demonstrate susceptibility to meropenem. • High additional risk observed for antibiotics AMP, CIP, NA, and STR. • Different E. coli isolates have diverse ciprofloxacin-induced protein changes.