Salmonella and Campylobacter are becoming increasingly resistant to ciprofloxacin, one of the antibiotics of choice for treating infections caused by these bacteria. The conclusion is part of the latest report on antimicrobial resistance in zoonoses released today by the European Centre for Disease Prevention and Control (ECDC) and the European Food Safety Authority (EFSA), which also presents some positive trends in the animal sector.

The latest data from humans, animals and food show that a large proportion of Salmonella bacteria are multidrug-resistant (resistant to three or more antimicrobials). In humans, resistance to ciprofloxacin is common, particularly in certain types of Salmonella, and resistance to high concentrations of ciprofloxacin increased overall from 1.7% (2016) to 4.6% (2018). For Campylobacter, 16 out of 19 countries report very high or extremely high percentages of ciprofloxacin resistance.

High proportions of resistance to ciprofloxacin are also reported in Salmonella and E. coli bacteria from poultry. Ciprofloxacin is a fluoroquinolone, a class of antimicrobials categorised as critically important for use in humans. If fluoroquinolones lose their effectiveness, the impact on human health could be significant. However, combined resistance – simultaneous resistance to two critically important antimicrobials – to fluoroquinolones and third generation cephalosporines in Salmonella and to fluoroquinolones and macrolides in Campylobacter remains low.

For 2018, the report lists sporadic cases of human Salmonella infection with resistance to carbapenems, a last-line antimicrobial.

Mike Catchpole, ECDC’s chief scientist, said: “Finding carbapenem resistance in foodborne bacteria in the EU is a concern. The most effective way to prevent the spread of carbapenem-resistant strains is to continue screening and respond promptly to positive detections. ECDC is working with EU Member States and with EFSA in a One Health approach to enhance the early detection and monitoring, in an effort to fight the persisting threat of antimicrobial-resistant zoonotic infections.”

The report also includes key outcome indicators that help EU Member States assess their progress in reducing the use of antimicrobials and combatting antimicrobial resistance.

In food-producing animals, the summary indicator of susceptibility to all antimicrobials has increased in E. coli in just under 25% of Member States (6) over the period 2014-2018. This is a positive development as it means that in these countries, in case of need, treatments with antimicrobials would have a higher chance to be successful. Decreasing trends in the occurrence of extended-spectrum β-lactamase (ESBL) or AmpC-producing E. coli have been observed in about 40% Member States (11) during 2015-2018. This is also important because ESBL-AmpC producing E. coli are responsible for serious infections in humans.

Regarding last-line antimicrobials, resistance to colistin was not common in Salmonella and E. coli, and carbapenemase-producing E. coli were not detected in broilers, turkeys and broiler meat.

“The positive findings in food-producing animals are encouraging because they are a sign of improvement. However, we need to further investigate the reasons behind this change. Antimicrobial resistance is a serious threat to global public and animal health – or One Health – that requires global action,” said Marta Hugas, EFSA’s chief scientist.

In humans, the decline in resistance to ampicillin and to tetracyclines in Salmonella Typhimurium in many countries is another encouraging trend observed in 2013-2018.

The EU Summary Report is an annual ECDC and EFSA publication which looks at the status of antimicrobial resistance in bacteria affecting humans, animals and food.

The welfare of adult rabbits kept in conventional cage systems is worse than that of those housed in other systems used in the EU, EFSA has concluded. The main welfare issue they experience is restricted movement. The findings are part of a comprehensive comparison of the different rabbit housing systems used in the EU.

EFSA’s scientific opinion is based on an extensive survey of rabbit experts in the EU. The opinion relies on expert judgement because there is little data available on the subject. In its recommendations, EFSA emphasises the need for data on welfare of farmed rabbits to be collected across the EU. EFSA also suggests that conventional cages should be enlarged and structurally enhanced to improve rabbit welfare.

The experts considered a number of welfare consequences related to health and behaviour, such as restricted movement, resting problems, prolonged thirst or hunger, thermal stress and skin disorders.

Most rabbit farming in the EU takes place in five Member States: France, Hungary, Italy, Portugal and Spain. Farming practices vary widely both between and within these countries.

To capture this variability, EFSA’s scientific opinion focuses on six examples of housing systems: conventional cages; structurally enriched cages; elevated pens; floor pens; outdoor/partially outdoor systems; and organic systems.

The main conclusions are that:

EFSA has published two other opinions on welfare issues associated with farming of rabbits: one looks at stunning methods and identifies welfare hazards and indicators of consciousness in the slaughter process. It proposes corrective measures. The other covers welfare issues associated with killing for reasons other than meat production (e.g. disease control).

Rabbits are the second most farmed species in the EU in terms of numbers. Although there are rules stipulating minimum standards for the protection of farmed animals, including rabbits, there is no species-specific legislation protecting the welfare of farmed rabbits in the EU.

In 2017, the European Parliament adopted a resolution on minimum standards for the protection of farmed rabbits, and asked EFSA to provide a scientific opinion that would help implement the resolution.

The parliament was acting in response to concerns raised by NGOs, stakeholders and consumer groups about the poor welfare, high stress levels and high mortality and morbidity rates of rabbits farmed in Europe. There is also concern that electrical stunning of rabbits does not always render them fully unconscious, causing pain, stress and suffering.