Comparative evaluation of the antimicrobial resistance (AMR) of commensal E. coli from different animal production systems in Germany

Commensal bacteria are recognized as a reservoir of resistance determinants and mirror of antimicrobial usage in livestock production. The European Food Safety Authority recommends monitoring of antimicrobial resistance (AMR) in commensal Escherichia coli. In Germany, monitoring of AMR in commensal E. coli has been established within the national monitoring of zoonotic agents in the food chain. Within this framework commensal E. coli from different cattle production systems were collected at farm and at slaughter between 2009 and 2011 and tested for their resistance to 13 antimicrobials using broth microdilution according to CLSI guidelines. Minimum inhibitory concentrations (MIC) were evaluated using epidemiological cut off values (www.eucast.org). Altogether, 1730 E. coli isolates were tested. 188 from bulk tank milk, 909 from fattening steers, and 633 from veal calves. The proportion of isolates resistant to at least 1 or more than 1 antimicrobial class differed substantially between the three production systems, with isolates from veal calves at farm in 2010 displaying the highest resistance rates (91.9 % to 1 class, 89.3 % to >1 class) and those from bulk tank milk in 2009 the lowest (16.1 and 5.5 %, respectively), with beef cattle (2011) in between (24.0 and 17.5 %, respectively). Resistance to ampicillin, sulfamethoxazole, trimethoprim, tetracycline and streptomycin was highest in isolates of all sources albeit at different rates. Resistance to critically important antimicrobials (CIA) such as the 3rd generation cephalosporins cefotaxime and ceftazidime, and the fluoroquinolone ciprofloxacin was present at low proportions in isolates of most sources. However, it was substantially higher in veal calves, especially on farm (10.3 % for cefotaxime and 41.9 % for ciprofloxacin in 2010). Potential reasons for the difference include the age of the animals but more likely the extend of exposure to antimicrobials and the time lag between treatment and sampling. Large differences between veal calves and beef cattle can likely be attributed to the difference in exposure to antimicrobials that are well documented. Further investigations are needed to identify strategies to reduce antimicrobial usage especially in the veal calve industry. However, resistance to CIA in beef and dairy cattle needs to be closely monitored.