LAUSR

The use of florfenicol in farm animals may select enterococci that carry resistance genes which confer resistance to linezolid, a critically important oxazolidinone antibiotic used in human medicine.  This cross-sectional study aimed to assess the occurrence of oxazolidinone resistance genes in florfenicol resistant enterococci from fattening pigs in Switzerland, and to characterize a subset of the isolates using whole genome sequencing (WGS). A total of 31 florfenicol-resistant enterococcal isolates were obtained from 27 (5%) of 565 cecal samples of fattening pigs from seven (11%) of 62 farms. Screening by PCR revealed the presence of cfr/poxtA in 1/31, optrA in 15/31 and poxtA in 15/31 enterococcal isolates, respectively. One randomly selected isolate per PCR-positive Enterococcus species and positive farm was selected for further analysis (n=10). In nine of the ten isolates, the presence of oxazolidinone resistance genes did not result in phenotypic resistance. WGS analysis showed the presence of E. faecalis (n=1), E. faecium (n=1), and E. hirae (n=1), harboring optrA18, optrA7 and a new optrA allele, respectively. E. durans (n=1), E. faecium (n=4), and E. hirae (n=1), carried the wild-type poxtA , and E. faecalis (n=1) co-harbored cfr(D) and poxtA2 . Except for optrA7, all oxazolidinone resistance genes were found on plasmids. MLST analysis identified E. faecalis ST19 and ST376, E. faecium ST80 belonging to hospital-adapted clade A1, and  E. faecium ST21, ST55, ST269 and ST416, belonging to clade A2 which represents human commensals and animal strains. The occurrence of cfr(D, optrA and poxtA in various porcine Enterococcus spp. demonstrates the spread of oxazolidinone resistance genes among enterococci from fattening pigs in Switzerland. The presence in one sample of poxtA-carrying E. faecium  ST80 emphasizes the potential risk to human health through dissemination of strains carrying oxazolidinone resistance genes into the food chain.