Resistance Determinants and Their Genetic Context in Enterobacteria from a Longitudinal Study of Pigs Reared under Various Husbandry Conditions

Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. Samples were collected from sows during lactation and from their piglets at five time points spanning the production cycle. Cefotaxime-resistant bacteria were quantified and isolated from feed, feces, manures, and carcasses of pigs reared with penicillin-using or antibiotic-free husbandries. The isolates were characterized by antibiotic susceptibility testing, whole-genome sequencing, and conjugation assays. The extended-spectrum β-lactamase (ESBL) phenotype was more frequent in isolates originating from antibiotic-free animals, while the bacteria isolated from penicillin-using animals were on average resistant to a greater number of antibiotics. The ESBL-encoding genes identified were bla(CTX-M-1), bla(CTX-M-15), and bla(CMY-2), and they colocalized on plasmids with various genes encoding resistance to β-lactams, co-trimoxazole, phenicols, and tetracycline, all antibiotics used in pig production. Groups of genes conferring the observed resistance and the mobile elements disseminating multidrug resistance were determined. The observed resistance to β-lactams was mainly due to the complementary actions of penicillin-binding proteins, an efflux pump, and β-lactamases. Most resistance determinants were shared by animals raised with or without antimicrobials. This suggests a key contribution of indigenous enterobacteria maternally transmitted along the sow lineage regardless of antimicrobial use. It is unclear whether the antimicrobial resistance observed in the enterobacterial populations of the commercial pig herds studied was present before the use of antibiotics or the extent to which historical antimicrobial use exerted a selective pressure defining the resistant bacterial populations in farms using penicillin prophylaxis. IMPORTANCE Antimicrobial resistance is a global threat that needs to be fought on numerous fronts along the One Health continuum. Vast quantities of antimicrobials are used in agriculture to ensure animal welfare and productivity and are arguably a driving force for the persistence of environmental and foodborne resistant bacteria. This study evaluated the impact of conventional, organic, and other antibiotic-free husbandry practices on the frequency and nature of antimicrobial resistance genes and multidrug-resistant enterobacteria. It provides knowledge about the relative contribution of specific resistance determinants to observed antibiotic resistance. It also shows the clear coselection of genes coding for extended-spectrum beta-lactamases and genes coding for resistance to antibiotics commonly used for prophylaxis or in curative treatments in pig operations.