Resistance in indicator bacteria

Over the last 5-year monitoring period, there have been no statistically significant trends in the prevalence of fully sensitive indicator E. coli isolates from broilers, cattle or pigs. Nonetheless, in the last two monitoring years, there was a steady increase in fully sensitive E. coli from broilers and a steady decrease in fully sensitive E. coli from cattle.

As in previous years, no amikacin, colistin, meropenem or tigecycline resistance were detected in indicator E. coli. Resistance to ciprofloxacin continued to be low in cattle and pigs and increased in broilers, reaching the maximum prevalence of the last 10 years (18%). Similarly to 2021, in 2022 azithromycin resistance was detected in a small number of isolates from pigs (3%), while the occurrence of chloramphenicol resistance decreased (8%).

The relative occurrence of multidrug-resistant indicator E. coli compared to the previous year decreased in broilers and pigs, and increased in cattle. Combined resistance to ampicillin, sulfamethoxazole, and tetracycline (ASuT) continued to be the most common multidrug-resistance profile. However, the relative occurrence of other multidrug-resistance profiles has increased in isolates from broilers and cattle in the past 5 years.

Importantly, as in previous years, samples from broilers and from broiler meat examined for carbapenemase-producing (CP) E. coli (including OXA-48) were found negative. Similarly, CP-producing E. coli was not detected in turkey meat in 2022.

The occurrence of beta-lactamase-producing E. coli, obtained through selective procedures, continued the decreasing trend observed since 2018 in broilers and broiler meat. In 2022, imported turkey meat presented an occurrence of 52%. Antimicrobial susceptibility testing of ESBL/AmpC-producing E. coli from broilers showed an increase in resistance to fourth generation cephalosporins (cefepime), and a single isolate was found resistant to ertapenem. Resistance to ciprofloxacin was abundantly found in isolates from imported broiler meat (100%) and imported turkey meat (83%). Azithromycin resistance was also found in single isolates from those samples and isolates from imported turkey meat were also somewhat resistant to colistin (7%), ertapenem (2%) and gentamicin (10%).

Whole genome sequencing of beta-lactamase-producing E. coli revealed ESBL, AmpC and ESBL+AmpC genotypes. All AmpC genotypes encoded upregulated AmpC promotor C-42T mutations. The plasmid-mediated CMY-2 gene was observed in ESBL+AmpC genotypes. Among the ESBL genotypes, 14 different ESBL genes were detected, with most variation in isolates from imported turkey meat. The latter presented a high frequency of CTX-M-15 and 46% had more than one ESBL encoding gene.

In 2022, 39% of E. faecalis and 52% of E. faecium isolated from broilers were fully sensitive. None of the enterococci isolates showed resistance to ampicillin, chloramphenicol, daptomycin, gentamicin, linezolid, teicoplanin, tigecycline or vancomycin. Combined resistance to tetracycline and erythromycin continued to be among the most common resistance profiles.