Escherichia coli resistant to the highest priority critically important fluoroquinolone or 3rd and 4th generation cephalosporin antibiotics persist in pigsties

Antimicrobial resistance threatens human and animal health, with antimicrobial usage being a key driver of selection, transmission, and spread of resistant bacteria. Livestock represents a potential reservoir for human transmission, leading authorities to restrict veterinary usage of fluoroquinolones and certain cephalosporins. However, growing evidence indicates that the corresponding resistance determinants can be retained even in the drugs’ absence. To obtain data on the magnitude and dynamics of this phenomenon in pig farming, we quantitatively and qualitatively assessed fluoroquinolone- and cephalosporin-resistant Escherichia coli in Thuringian pigsties practicing a closed management system to minimize the impact of externally introduced strains. Pooled fecal samples from consecutive fattening runs at one conventional and two organic farms and from 25 piglet groups from another conventional farm were collected over 16 months and screened for E. coli on plates containing enrofloxacin, ceftiofur, or cefquinome. Resistant bacteria were isolated on all farms; their counts varied strongly but were generally higher in piglets and declined with increasing animal age. Phylogenetic comparison of 393 isolates was performed via multiple-locus variable number tandem repeat analysis (MLVA) to follow strain dynamics and persistence. The isolates displayed large phylogenetic heterogeneity, featuring 52 different MLVA patterns. Still, conserved MLVA patterns indicated long-term persistence of specific strains in each farm's environment. This suggests that resistant strains appear well-adapted to the particular farm and its management practices, implying that, beyond restricting usage, further measures, including, e.g., consideration of the type of resistance as well as its persistence and transmission dynamics, will be indispensable to reduce the antimicrobial resistance load in pork production.