SUMMARY: A Bayesian modelling approach comparing the occurrence ofSalmonellaserovars in animals and humans was used to attribute salmonellosis cases to broilers, turkeys, pigs, laying hens, travel and outbreaks in 24 European Union countries.Salmonelladata for animals and humans, covering the period from 2007 to 2009, were mainly obtained from studies and reports published by the European Food Safety Authority. Availability of food sources for consumption was derived from trade and production data from the European Statistical Office. Results showed layers as the most important reservoir of human salmonellosis in Europe, with 42·4% (7 903 000 cases, 95% credibility interval 4 181 000–14 510 000) of cases, 95·9% of which was caused byS. Enteritidis. In Finland and Sweden, most cases were travel-related, while in most other countries the main sources were related to the laying hen or pig reservoir, highlighting differences in the epidemiology ofSalmonella, surveillance focus and eating habits across the European Union.

Reliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring. We evaluated the ability of: (i) MIC determination for Escherichia coli; (ii) cfu counting of E. coli; (iii) cfu counting of aerobic bacteria; and (iv) metagenomic shotgun sequencing to predict expected tetracycline resistance based on known antimicrobial consumption in 10 Danish integrated slaughter pig herds. In addition, we evaluated whether fresh or manure floor samples constitute suitable proxies for intestinal sampling, using cfu counting, qPCR and metagenomic shotgun sequencing. Metagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on antimicrobial consumption. Our metagenomic approach had sufficient resolution to detect antimicrobial-induced changes to individual resistance gene abundances. Pen floor manure samples were found to represent rectal samples well when analysed using metagenomics, as they contain the same DNA with the exception of a few contaminating taxa that proliferate in the extraintestinal environment. We present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programmes and potentially of integrated One Health monitoring in all reservoirs.

This study aimed to identify risk factors affecting PBW, high CV_PBW and the occurrence of IUGR piglets in 12 commercial Danish herds with hyperprolific sows using free-access stalls, floor or electronic sow feeding systems in the gestation unit. The following factors were investigated: the duration of previous lactation, the length of the interval from weaning to insemination, the length of gestation, litter size, parity, sow backfat thickness in late gestation and the type of feeding system in the gestation unit. The study included newborn piglets from 452 litters with the following production indicator averages: 21.3 piglets/L, 1235 g PBW, 22.9% CV_PBW and 10.9% and 11.8% within-litter occurrence of severe and mild IUGR piglets, respectively. Increasing length of weaning-to-insemination interval decreased PBW by 25.8 g/day. For 2nd to 9th parity sows, each additional piglet in the litter increased CV_PBW by 0.38%, the occurrence of severe IUGR piglets by 0.68% and mild IUGR piglets by 0.50%. Sows of 5th parity and older had a 1.39% higher CV_PBW and 49.1 g lighter piglets compared with sows of 2nd to 4th parity. PBW was lower in one ESF herd, suggesting complex interactions that need to be further elucidated. The main critical risk factor observed was litter size.

It is often stated that vaccines may help reduce antimicrobial use in swine production. However, limited evidence is available outside clinical trials. We studied the change in amounts of antimicrobials prescribed for weaners and finishers in herds following initiation of vaccination against five common endemic infections: Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, porcine circovirus type II, porcine reproductive and respiratory syndrome virus, and Lawsonia intracellularis. Comparison was made to the change after a randomly selected date in herds not vaccinating against each of the infections. Danish sow herds initiating vaccination during 2007–2013 were included (69–334 herds, depending on the analysis). Danish sow herds with no use of the vaccine in question were included as non-exposed herds (130–570 herds, depending on the analysis). Antimicrobial prescriptions for weaners in sow herds and for finishers in receiving herds were extracted from the VetStat database for a period of 12 months before and 6–18 months after the first purchase of vaccine, or random date and quantified as average animal daily doses (ADDs) per 100 animals per day. The herd-level difference between ADD in the period after and before vaccination was the outcome in linear regression models for weaner pigs, and linear mixed-effects models for finishing pigs, taking into account sow herds delivering pigs to two or more finisher herds. Three plausible risk factors (Baseline ADD, purchase of specific vaccine, purchase of other vaccines) and five confounders (herd size, export and herd health status, year and season) were initially considered in all 10 models. The main significant effect in all models was the Baseline ADD; the higher the Baseline ADD was for weaner and finishing pigs, the larger the decrease in ADD was following vaccination (or random date for non-vaccinating herds). Regardless of vaccination status, almost equal proportions of herds experienced a decrease and an increase in ADD resulting in no overall Change in ADD. Furthermore, only minor effects were found, when vaccinations were used in combination. In conclusion, this study provided little support for the hypothesis that vaccination against five common endemic diseases provides a plausible general strategy to reduce antimicrobial use in Danish pig herds.