Genetic characterization and transmission of the multidrug resistance gene cfr in fecal and environmental pathways on a chicken farm in China

• Published in: Poultry science Vol. 104; no. 6; p. 105079
• Main Authors: Feng, Yiming, Li, Tiantian, Zhao, Shiyun, Li, Xuexue, Zhai, Yajun, Yuan, Li, Liu, Jianhua, Hu, Gongzheng, He, Dandan, Pan, Yushan
• Format: Journal Article
• Language: English
• Published: England Elsevier Inc 01.06.2025; Elsevier
• Subjects: Animals; Anti-Bacterial Agents - pharmacology; antibiotic resistance; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; cfr; Chicken; Chickens; China; digestion; Drug Resistance, Multiple, Bacterial - genetics; Escherichia coli; Escherichia coli - drug effects; Escherichia coli - genetics; Farm environment; farms; Feces - microbiology; Gene Transfer, Horizontal; genetic variation; Klebsiella pneumoniae - drug effects; Klebsiella pneumoniae - genetics; MICROBIOLOGY AND FOOD SAFETY; multiple drug resistance; Phylogeny; Plasmid; Plasmids; Poultry Diseases - epidemiology; Poultry Diseases - microbiology; Poultry Diseases - transmission; public health; resistance genes; Transmission; China; Farm environment; Plasmid; Chicken; cfr; Transmission
• ISSN: 0032-5791; 1525-3171; 1525-3171
• DOI: 10.1016/j.psj.2025.105079

•Revealed the multidrug resistance and genetic diversity of cfr-positive strains.•The cfr gene was identified in five distinct genetic environments.•The cfr spreading through both clonal transmission and plasmid- and IS26-mediated horizontal gene transfer.•The selective pressure exerted by florfenicol likely plays a crucial role in driving the high prevalence of cfr. The emergence and spread of the multidrug-resistant gene cfr have raised significant public health concerns worldwide. To investigate its prevalence and dissemination dynamics, 18 cfr-positive strains were isolated in 2021 from fecal and environmental samples. Antimicrobial susceptibility testing showed that all strains were 100 % multidrug-resistant. Conjugation experiments demonstrated that a cfr- carrying IncFII(K)-IncR-IncFIB multi-replicon plasmid could transfer to E. coli J53. S1-nuclease digestion and Southern blotting identified cfr on plasmids of varying sizes, while whole-genome sequencing confirmed its presence on multiple plasmid types: IncX4, IncN, IncFII(K)-IncR-IncFIB, IncFIB-IncFII-IncR-IncHI2-IncHI2A multi-replicon plasmids, and two plasmids of unknown types. Genetic environment analysis revealed that cfr is categorized into five distinct structures (Types I-V). Reverse PCR results showed that Types I, II, and IV can form three circular intermediates of varying lengths (cfr-IS26). Network analysis further indicated strong association between cfr, tet(M), and dfrA14 mediated by IS26. Phylogenetic analysis revealed that the four ST1140 E. coli strains and all nine K. pneumoniae strains showed minimal genetic divergence. These findings suggest both clonal and horizontal transmission of cfr within the poultry farm. Continuous monitoring of cfr in animal-related environments is essential to mitigate its potential transfer to humans.