Technical specifications for a EU-wide baseline survey of antimicrobial resistance in bacteria from aquaculture animals.

The European Commission requested scientific and technical assistance in the preparation of a EU-wide baseline survey of antimicrobial resistance (AMR) in bacteria from aquaculture animals. It is recommended that the survey would aim at estimating the occurrence of AMR in spp. isolated from Atlantic Salmon (), European seabass () and trout () intended to consumption, at harvesting (at farm/slaughter), at the EU level and in addition, at estimating the occurrence and diversity of AMR of , , , and in blue mussel () and Mediterranean mussel () from production areas and at dispatch centres at the EU level.

Azithromycin resistance in Escherichia coli and Salmonella from food-producing animals and meat in Europe.

Objectives: To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014-18 and the Danish AMR surveillance programme in 2016-19.

Methods: WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV, 23S rRNA and acrB genes using ResFinder v4.

Technical specifications for a baseline survey on the prevalence of methicillin-resistant (MRSA) in pigs.

The European Commission requested scientific and technical assistance in the preparation of a EU-wide baseline survey protocol for a European Union (EU) coordinated monitoring programme on the prevalence of methicillin-resistant (MRSA) in pigs. The objective of the survey is to estimate the MRSA prevalence in batches of fattening pigs at slaughter at both European and national levels, with a 95% level of confidence and a level of precision of 10% considering an expected prevalence of 50%. The survey protocol defines the target population, the sample size for the survey, sample collection requirements, the analytical methods (for isolation, identification, phenotypic susceptibility testing and further genotypic testing of MRSA isolates), the data reporting requirements and the plan of analysis.

Technical specifications on harmonised monitoring of antimicrobial resistance in zoonotic and indicator bacteria from food-producing animals and food.

Proposals to update the harmonised monitoring and reporting of antimicrobial resistance (AMR) from a public health perspective in ,  , and methicillin-resistant (MRSA) from food-producing animals and derived meat in the EU are presented in this report, accounting for recent trends in AMR, data collection needs and new scientific developments. Phenotypic monitoring of AMR in bacterial isolates, using microdilution methods for testing susceptibility and interpreting resistance using epidemiological cut-off values is reinforced, including further characterisation of those isolates of and showing resistance to extended-spectrum cephalosporins and carbapenems, as well as the specific monitoring of ESBL/AmpC/carbapenemase-producing . Combinations of bacterial species, food-producing animals and meat, as well as antimicrobial panels have been reviewed and adapted, where deemed necessary.

Estimation of the wild-type minimum inhibitory concentration value distribution.

Antimicrobial resistance has become one of the main public health burdens of the last decades, and monitoring the development and spread of non-wild-type isolates has therefore gained increased interest. Monitoring is performed based on the minimum inhibitory concentration (MIC) values, which are collected through the application of dilution experiments. In order to account for the unobserved population heterogeneity of wild-type and non-wild-type isolates, mixture models are extremely useful.

Risk factors for Salmonella seroconversion of fattening pigs in farrow-to-finish herds.

We did a prospective observational 9-month long study to quantify risk factors of managerial and hygiene practices, and pig-health status for Salmonella seroconversion of fattening pigs reared in subclinically infected French farrow-to-finish farms. During the fattening phase, 2,649 pigs belonging to the same batch of contemporary pigs, from 89 conventional farrow-to-finish farms were individually followed and regularly blood sampled on a monthly basis. Farm recruitment was based on the farmer's willingness to cooperate.

A pharmaco-epidemiological analysis of factors associated with antimicrobial consumption level in turkey broiler flocks.

An on-farm pharmaco-epidemiological survey of 246 turkey broiler flocks from 131 farms was carried out to assess the homogeneity of antimicrobial use between flocks on the same farm and to explore the possible relationships between farm and farmer characteristics and the level of antimicrobial use. The antimicrobial use in each flock was quantified by an invoice study, expressed as the number of national animal daily doses (ADD)/turkey broiler and characterised as "high", "medium" or "low" according to the tertiles of the resulting distribution. Antimicrobial use was then correlated with variables collected from the farmer by means of an alternating logistic regression method which calculates the pairwise odds ratio (PWOR) for within-farm clustering.

Impact of the Salmonella status of market-age pigs and the pre-slaughter process on Salmonella caecal contamination at slaughter.

The aim of this study was to evaluate the impact of the pre-slaughter process on Salmonella caecal contamination of pigs at slaughter. An observational study was carried out in 2001 on 101 conventional farrow-to-finish pig farms. On each farm, one batch of contemporary pigs was followed from the end of the fattening period until slaughter.

Listeria monocytogenes contamination of finishing pigs: an exploratory epidemiological survey in France.

Listeria monocytogenes is a foodborne pathogen of major concern for public health in industrialised countries. Since L. monocytogenes carriage by pigs at the herd level could be a primary source for carcass contamination, control measures should be designed to reduce the L.

A survey of group-level antibiotic prescriptions in pig production in France.

There is world-wide concern that antimicrobial use in food-producing animals might contribute to antimicrobial resistance both in animals and in humans. The relationship between antimicrobial use and resistance is likely to be related to frequency of prescription of the compound, dose and duration of treatment. Routine collection of that information is not possible today in France.