Microbiological risk assessment of Turkey and chicken meat for consumer: Significant differences regarding multidrug resistance, mcr or presence of hybrid aEPEC/ExPEC pathotypes of E. coli

To assess the microbiological risk for consumers, we propose a lab workflow based on six virulence/antimicrobial resistance (AMR) traits, and including a duplex PCR for the screening of extraintestinal pathogenic E. coli (ExPEC). This protocol was tested in 100 poultry meat products. The characterization of 323 isolates revealed that poultry meat is a rich phylogenetic source of E. coli phylogmups (A to G) and Escherichia Glade I. Non-susceptible E. coli isolates to monobactams, 3rd-generation cephalosporins and/or fluoroquinolones, were present in 71% of the samples. Besides, 47% carried >= 2 different E. coli positive for ESBL, pAmpC or mcr genes. Isolates from 78% of the poultry meat exhibited ExPEC status, and 53% were carriers of isolates positive for the uropathogenic (UPEC) status. The sequence types (STs) identified in 86% of the samples belonged to the so-called ExPEC high-risk lineages, being 73% carriers of clonal groups identified in human infections of the same Health Area. Moreover, different human-associated clones co-occurred in same meat sample: ST131-B2 (CH40-22), ST648-F (CH4-58), ST93-A (CH11-neg) or ST95-B2 (CH38-27), ST354-F (CH88-58), ST155-B1 (CH4-neg). Globally, 84% of the meat samples posed >= 3 risks, including resistance genes, successful clones and virulence traits. Turkey meat showed significant higher rates concerning mcr-carriage or multidrug resistance; while the ExPEC status rate, or the presence of hybrid pathotypes such as the aEPEC/ExPEC O153:H10-A-ST10 (CH11-54), were associated with chicken origin (P < 0.05). In a Farm to Fork Strategy, ExPEC should be clearly included in food surveillance.

Automated summary

A lab workflow was proposed to assess microbiological risks in poultry meat, revealing a rich diversity of E. coli strains. Notably, 71% of the samples contained E. coli isolates resistant to multiple antibiotics, with 47% carrying isolates positive for ESBL, pAmpC, or mcr genes.