• The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries.

      Van Gompel, Liese; Luiken, Roosmarijn E C; Sarrazin, Steven; Munk, Patrick; Knudsen, Berith E; Hansen, Rasmus B; Bossers, Alex; Aarestrup, Frank M; Dewulf, Jeroen; Wagenaar, Jaap A; et al. (2019-04-01)
      Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe. A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM). Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models. Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.
    • Attitudes and perceptions of Dutch companion animal veterinarians towards antimicrobial use and antimicrobial resistance.

      Hopman, Nonke E M; Mughini-Gras, Lapo; Speksnijder, David C; Wagenaar, Jaap A; van Geijlswijk, Ingeborg M; Broens, Els M (2019-06-29)
    • Comparing four diagnostic tests for Giardia duodenalis in dogs using latent class analysis.

      Uiterwijk, Mathilde; Nijsse, Rolf; Kooyman, Frans N J; Wagenaar, Jaap A; Mughini-Gras, Lapo; Koop, Gerrit; Ploeger, Harm W (2018-07-31)
      To accurately diagnose giardiosis in dogs, knowledge of diagnostic test characteristics and expected prevalence are required. The aim of this work was to estimate test characteristics (sensitivity and specificity) of four commonly used diagnostic tests for detection of Giardia duodenalis in dogs.
    • Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the environment: a pooled analysis.

      Dorado-García, Alejandro; Smid, Joost H; van Pelt, Wilfrid; Bonten, Marc J M; Fluit, Ad C; van den Bunt, Gerrita; Wagenaar, Jaap A; Hordijk, Joost; Dierikx, Cindy M; Veldman, Kees T; et al. (2018-02-01)
      In recent years, ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.