Research – EU Harmonised Surveillance of Antimicrobial Resistance (AMR) in E. coli from Retail Meats in UK (2020 -Year 6, chicken)

Gov UK

Lay person’s summary
This report presents results of the EU harmonised surveillance of antimicrobial resistance (AMR) in E. coliform retail chicken meats in the UK in 2020.
In accordance with European Directive 2003/99/E Con the monitoring of bacteria that can pass from animals to humans and causes disease (zoonoses and zoonotic agents), Member States (MS) are obliged to ensure that procedures are in place to monitor and report on the occurrence of antimicrobial resistance(AMR) in such bacteria.
The UK continued to be subject to EU rules during the transition period up to the end of December 2020.Further testing of retail beef, chicken and pork is being considered based on surveillance priorities. The requirements (with additional detailed guidance from the EU Reference Laboratory for Antimicrobial Resistance) state that 300 retail chicken meats should be tested by culture for the bacterium Escherichia coli. E. coli bacteria are a normal part of the gut flora of mammals and as such can be useful “indicators” of AMR in gut bacteria.
Whilst some strains of E. coli can cause disease, most strains of E. coli do not cause observable disease in healthy animals and humans. The EU requirements state that samples should be tested on an agar (growth medium) supplemented with a third generation cephalosporin. Third generation cephalosporins area group of antimicrobials which are important for treating infections in humans. E. coligrowth on this agar suggests antimicrobial resistance known as Extended Spectrum β-lactamase (ESBL) resistance and/or Amp C resistance.
ESBL resistance is also referred to as ESBL-phenotype, Amp C resistance is also referred to as Amp C-phenotype. The degrees of susceptibility/resistance of E. coli recovered from this agar must then be determined to a pre-defined panel of antimicrobials by Minimum Inhibitory Concentrations (MICs) tests. EU requirements also state that samples should be tested on two other supplemented agars which select bacteria which are resistant to carbapenems.
Carbapeems are another a group of antimicrobials which are very important in human medicine. Carbapenems are termed “last resort” antimicrobials because they are used to treat severe infections when all or almost all other treatment options have failed, because the infecting bacteria are resistant to most / all other relevant antimicrobials. Additionally, each meat sample is tested for counts of the number of background and AMR(Amp C and ESBL type resistance only) E. coli in each meat sample according to an EU protocol.
At the request of the FSA, other agar culture media used to test samples included an agar to specifically isolate E. coli with ESBL-only type resistance only (rather than for E. coli with both an AmpC and an ESBL type resistance as per one of the EU specified agars), and an agar to isolate colistin resistant E. coli. Colistin is another “last resort” antimicrobial, so it is important to monitor if resistance in E. coli to colistin is occurring in food samples.
Colistin resistance in E. coli isolates may involve a number of resistance genes such as mcr-1, mcr-2 andmcr-3. These mcr genes are considered particularly important as they are usually carried on genetic elements known as plasmids. As plasmids are “mobile” (can pass from one bacterium to another), the resistance genes located on them can potentially be shared with other bacteria within the gut. In total during 2020, 327 samples of fresh chicken were collected of which 315 were eligible for testing. The 315 eligible retail chicken meat samples were collected from England (n=274), Scotland (n=20), Wales (n=11), and Northern Ireland (n=10) from ten different supermarket chains. Sample collection was impacted by the coronavirus pandemic.
Monthly sampling was suspended for 3 months from April to June2020, resuming in July. Sample numbers were adjusted in subsequent months to reach the target of 300 samples. The types of chicken meat collected were whole chicken (n=127), chicken breast (n=113) and other cuts, including quarters, legs, thighs & drumsticks (n=75). Of the samples collected, 58.7% and 41.2% had skin on or off respectively.
Breast samples were the main sample type from which skin was removed. Of the 315 samples, 309 were stated as originating from the UK, five from Poland and one from Ireland. No growth was observed from any of the samples(meaning the test results were negative and the bacteria were therefore not resistant to carbapenem antimicrobials) on the two agars that selected for carbapenem-resistant E. coli.
Forty-one(13.0%) of the samples gave rise to E. coli on MacConkey agar + 1mg/L cefotaxime. These positive results imply the E. coli were resistant to cefotaxime. MIC analysis of these 41isolatesfound that39 of the total number of samples tested (12.4%) expressed an ESBL-phenotype resistance (including two isolates additionally expressed the Amp C phenotype resistance).
The remaining two of these 41 E. coli isolates(0.63%) expressed an Amp C-phenotype resistance but not ESBL-phenotype resistance. The observed frequencies of recovery of ESBL-phenotype E. coli from samples from individual supermarkets ranged from 0% to and 22.1% of the samples tested per supermarket, including those with an Amp C+ESBL-phenotype. A total of 54 of all the samples tested, representing 17.1%,gave rise to growth on the ESBL-only specific agar and a total of 3 (0.95%)of all the samples tested were positive for the mcr-1 transferable colistin resistance gene. These three samples all originated from Poland.
A further two samples were also originally positive for mcr-3 when multiple suspect colonies was tested. However, it was not possible to isolate individual mcr-3positive E. coli from the mix, so these results must be considered equivocal. Using MIC tests, the isolates from the Amp C/ESBL specific agar were tested for the degree of resistance to a total of 19 antimicrobials. Based on the MIC results, isolates were determined as resistant or sensitive to a particular antimicrobial using cut-offs known as ECOFFs (Epidemiological Cut Offs published by EUCAST). The ECOFF distinguishes between organisms without and with phenotypically expressed resistance mechanisms for a bacterial species to an antimicrobial. None of the 41 isolates from the Amp C/ESBL specific agar were microbiologically resistant to the ‘last resort’ carbapenem antimicrobials imipenem and meropenem or to colistin. The MIC of ertapenem against one Amp C+ESBL-phenotype isolate was just above the previous EUCAST ECOFF(currently there is only a tentative ECOFF for ertapenem), and as such was microbiologically resistant. This isolate was not clinically resistant though, using EUCAST clinical break point..None of the E. coli were resistant to the antibiotics temocillin or tigecycline.
Only one isolate was resistant to the antibiotic’s azithromycin or gentamicin, whilst about 60% of isolates were resistant to the quinolone antibiotics (ciprofloxacin or nalidixic acid)or to chloramphenicol. Isolates obtained from agar with 1 mg/L cefotaxime were all resistant to cefotaxime andto antibiotics of a similar type, such as ampicillin and ceftazidime and most were also resistant to cefepime. Most of the isolates were resistant to the older antibiotics’ sulfamethoxazole and tetracyclines, and approximately 50% were resistant to trimethoprim.
Genetic tests (whole genome sequencing) showed that most of the E. coli isolates from the ESBL agar carried the bla CTX-Mgene which confers resistance to third generation cephalosporin antimicrobials, and has been frequently detected in E. coli from chickens and chicken meat in previous studies, including the 2016 and 2018 surveys. None of the meat samples had bacterial counts of background E. coli (isolates obtained from agar without antibiotics) or presumptive Amp C/ESBL-producing E. coli above the detection limit (when using the EU method) of 3,000 E. coli colony forming units (cfu) per gram of meat. In summary, the results in 2020 showed that 12.4% and 1.6% of retail chicken meat samples were positive for ESBL or Amp C-phenotype E. coli, respectively (including the three isolates with the combined Amp C/ESBL-phenotype in both the ESBL or Amp C-phenotype groups) on the Amp C/ESBL specific agar. Whilst there was an increase in the percentage of isolates with an ESBL-phenotype there was a decrease in the percentage of isolates with an Amp C-phenotype between 2018 and 2020.
Overall, between 2018 and 2020, the percentages of samples positive on the Amp C/ESBL specific agar remained almost identical at 13.6% and 13.0%,respectively.None of the samples were positive for carbapenem-resistant E. coli on either of the two carbapenem selective agars. Between the 2016 and 2018 EUsurveys1there was a significant reduction in the proportion of chicken samples positive on the Amp C/ESBL specific agar and the ESBL agar.
Comparison with a paper on UK samples tested in 2013/142 also showed a significant reduction in samples positive for ESBL-producing E. coli between 2013/14 and the 2016 EU survey (65.4% to 29.7%), albeit sampling and isolation methods were similar, but not identical for the two studies.The2018 report for chicken meat samples1 suggests that these drops in the level of antimicrobial-resistant E. coli on retail chicken meat since 2013/14 may be linked to the restriction by the British Poultry Council to the use of third-and fourth-generation cephalosporins in flocks used for poultry meat production in the UK in 2012 as part of antimicrobial stewardship.
The 2020 survey results suggest that the proportions of Amp C or ESBL-phenotype E. coli in retail chicken have not changed since 2018. There was a slight increase in the proportions of samples that were positive on the ESBL-specific agar compared to the 2018. This was the first year that retail chicken samples were found to be positive for mcr plasmid-mediated colistin resistant E. coli. It should be considered that 2020 was an unusual year due to the impact of the coronavirus pandemic, although there is no reason to suppose this affected the proportions of retail chicken meat positive for AMR E. coli.

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