Resistance in indicator bacteria

Over the last 5-year monitoring period, there has been no statistically significant increasing or decreasing trends in the prevalence of fully sensitive indicator E. coli isolates from broilers, cattle or pigs. Nonetheless, fluctuations were observed from 2020 to 2021, with an increase in fully sensitive E. coli from broilers (64% in 2021) and a decrease in fully sensitive E. coli from pigs and cattle (43% in pigs and 87% in cattle in 2021).

As in previous years, no colistin, meropenem or tigecycline resistance was detected in indicator E. coli. Resistance to ciprofloxacin continued to be low in E. coli from cattle and pigs and levelled out in E. coli from broilers at a prevalence similar to 2020 (16%). Azithromycin resistance was detected in few isolates from pigs (3%).

Compared to 2020, resistance to ampicillin, sulfamethoxazole and tetracycline decreased in E. coli isolates from broilers and increased in isolates from cattle and pigs. An increase was also observed in the prevalence of isolates from pigs resistant to chloramphenicol and trimethoprim. While the relative occurrence of multidrug-resistant indicator E. coli from broilers and cattle was similar to the previous year, it increased among isolates from pigs. Combined resistance to ampicillin, sulfamethoxazole and tetracycline (ASuT) continued to be overall the most common multidrug-resistance profile.

The observed occurrence of E. coli producing extended-spectrum cephalosporinases (ESC), obtained through selective procedures, decreased in Danish pigs and imported pork, but continued to increase in isolates from imported beef. Importantly, as in previous years, samples examined for carbapenemase-producing (CP) E. coli (including OXA-48) were found negative.

The phenotypic and genotypic resistance profiles of ESC-producing E. coli were mostly in agreement, however 17 isolates revealed both ESBL and AmpC enzymes encoding genes, even though susceptibility testing did not show combined ESBL and AmpC resistance.

Among the AmpC-producing isolates, resistance was mainly conferred by upregulated AmpC promotor C-42T mutations. T-32A AmpC mutation, and plasmid-mediated AmpC enzymes CMY-2 and DHA-1 were also sporadically observed. Among the ESBL-producing isolates, 25 different ESBL genes were detected, with most variation among isolates from pigs. Overall, the most commonly observed ESBL encoding genes were CTX-M-1 and TEM-1B.

In 2021, 21% of E. faecalis isolated from pigs were fully sensitive. No resistance to ampicillin, linezolid, teicoplanin, tigecycline, vancomycin, ciprofloxacin or daptomycin was detected in any of the isolates. Resistance to all other antibiotics in the test panel decreased in 2021 compared to 2019. Resistance to tetracycline, erythromycin and chloramphenicol continued to be the most common.