• 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.
    • Host factors associated with Giardia duodenalis infection in dogs across multiple diagnostic tests.

      Uiterwijk, Mathilde; Nijsse, Rolf; Kooyman, Frans N J; Wagenaar, Jaap A; Mughini-Gras, Lapo; Ploeger, Harm W (2019-11-21)
      Fecal samples from 1291 dogs from four groups (household, shelter, hunting and clinical dogs) were tested with qPCR, rapid enzyme immunochromatographic assay (IDEXX SNAP® Giardia), and direct immunofluorescence (DFA, Merifluor) for presence of G. duodenalis. Moreover, fecal samples were tested with centrifugation sedimentation flotation (CSF) coproscopical analysis for presence of gastrointestinal parasites. Associations were expressed as odds ratios (ORs).
    • 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.
    • Successful Host Adaptation of IncK2 Plasmids.

      Rozwandowicz, Marta; Brouwer, Michael S M; Mughini-Gras, Lapo; Wagenaar, Jaap A; Gonzalez-Zorn, Bruno; Mevius, Dik J; Hordijk, Joost (2019-01-01)
      The IncK plasmid group can be divided into two separate lineages named IncK1 and IncK2. IncK2 is found predominantly in poultry while IncK1 was reported in various mammals, including animals and humans. The physiological basis of this distinction is not known. In this manuscript we examined fitness cost of IncK1 and IncK2 plasmids at 37 and 42°C, which resembles mammalian and chicken body temperatures, respectively. We analyzed conjugation frequency, plasmid copy number and plasmid fitness cost in direct competition. Additionally, we measured levels of σ-32 in Escherichia coli carrying either wild type or conjugation-deficient IncK plasmids. The results show that IncK2 plasmids have a higher conjugation frequency and lower copy number at 42°C compared to IncK1. While the overall fitness cost to the host bacterium of IncK2 plasmids was higher than that of IncK1, it was not affected by the temperature while the fitness cost of IncK1 was shown to increase at 42°C compared to 37°C. These differences correlate with an increased expression of σ-32, a regulator of heat-shock protein expression, in E. coli with IncK2 compared to cells containing IncK1. This effect was not seen in cells containing conjugation deficient plasmids. Therefore, it is hypothesized that the assembly of the functional T4S may lead to these increased levels of σ-32. Increased activation of CpxR at 42°C may explain why IncK2 plasmids, and not IncK1, are predominantly found in chicken isolates.