Characteristics of antimicrobial resistance inEscherichia coliisolated from retail meat products in North Carolina
Authors: Aworh Mabel Kamweli , Thakur Siddhartha , Gensler Catherine , Harrell Erin , Harden Lyndy , Fedorka-Cray Paula J. , Jacob Megan 
Published: October 2023

Background

Escherichia coliis commonly used as an indicator for antimicrobial resistance (AMR) in food, animal, environment, and human surveillance systems. Our study aimed to characterize AMR inE. coliisolated from retail meat purchased from grocery stores in North Carolina, USA as part of the National Antimicrobial Resistance Monitoring System (NARMS).

Methods

Retail chicken (breast, n=96; giblets, n=24), turkey (n=96), and pork (n=96) products were purchased monthly from different counties in North Carolina during 2022. Label claims on packages regarding antibiotic use were recorded at collection.E. coliwas isolated from meat samples using culture-based methods and isolates were characterized for antimicrobial resistance using whole genome sequencing. Multi-locus sequence typing, phylogroups, and a single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenic tree were generated. Data were analyzed statistically to determine differences between antibiotic use claims and meat type.

Results

Of 312 retail meat samples, 138 (44.2%) were positive forE. coli, with turkey (78/138; 56.5%) demonstrating the highest prevalence. Prevalence was lower in chicken (41/138; 29.7%) and pork (19/138;13.8%). Quality sequence data was available from 84.8% (117/138) of theE. coliisolates, which included 72 (61.5%) from turkey, 27 (23.1%) from chicken breast, and 18 (15.4%) from pork. Genes associated with AMR were detected in 77.8% (91/117) of the isolates and 35.9% (42/117) were defined as MDR (≥3 distinct classes of antimicrobials). Commonly observed AMR genes includedtetB(35%),tetA(24.8%),aph(3’’)-lb(24.8%), andblaTEM-1 (20.5%), the majority of which originated from turkey isolates. Antibiotics use claims had no statistical effect on MDRE. coliisolates from the different meat types (X2=2.21, p =0.33). MDR was observed in isolates from meat products with labels indicating “no claims” (n=29; 69%), “no antibiotics ever” (n=9; 21.4%), and “organic” (n=4; 9.5%). Thirty-four different replicon types were observed. AMR genes were carried on plasmids in 17E. coliisolates, of which 15 (88.2%) were from turkey and two (11.8%) from chicken. Known sequence types (STs) were described for 81E. coliisolates, with ST117 (8.5%), ST297 (5.1%), and ST58 (3.4%) being the most prevalent across retail meat types. The most prevalent phylogroups were B1 (29.1%) and A (28.2%). Five clonal patterns were detected among isolates.

Conclusions

E. coliprevalence and the presence of AMR and MDR were highest in turkey retail meat. The lack of an association between MDRE. coliin retail meat and antibiotic use claim, including those with no indication of antimicrobial use, suggests that additional research is required to understand the origin of resistance. The presence of ST117, an emerging human pathogen, warrants further surveillance. The isolates were distinctly diverse suggesting an instability in population dynamics.