RESUMEN
This study evaluated the contribution of cattle, sheep, poultry and pigs to the contamination of surface water from rivers by Campylobacter jejuni and C. coli using MLST, cgMLST and considered MALDI-TOF MS as an alternative technique. The 263 strains isolated from cattle (n = 61), sheep (n = 42), poultry (n = 65), pigs (n = 60) and surface water (n = 35) were distributed across 115 sequence types (STs), 49 for C. jejuni and 66 for C. coli. Considering MLST data, 14.2%, 11.4% and 2.8% of the surface water strains could be attributed to cattle, poultry and sheep, respectively, none to pigs, and 85.7% were non-attributed. Analysis of cg-MLST data with STRUCTURE indicated that C. jejuni strains from water were predominantly attributed to poultry (93.5%), weakly to sheep (<1%) and 6.3% non-attributed, and that conversely, C. coli strains from water were predominantly non-attributed (94.3%) and 5.7% attributed to poultry. Considering the protein profiles with a threshold of 94% and 97% of similarity, respectively, strains from surface water could be attributed to poultry (31.4% and 17.1%), and to cattle (17.1% and 5.7%); 54.1% and 77.1% were non-attributed. This study confirmed these livestock animals might contribute to the contamination of surface water, with a level of contribution depending on the typing technique and the method of analysis. MALDI-TOF could potentially be an alternative approach for source attribution.
RESUMEN
Microbial contamination of aggregates collected near an Atlantic salmon farm, in the Cherbourg roadstead, was followed monthly over one year to study the dynamics of Vibrio spp. and explore their impact on farmed fish. Salmon state of health was followed through blood and histopathological analyses. Vibrio were systematically found in aggregates with particularly high concentration in August. The Splendidus clade was strongly dominant in aggregates as well as in gills, and an increase in Vibrio diversity was observed in summer and autumn. Results did not demonstrate that aggregates directly impact the bacterial community of gills, but they suggested an aggregates-gills interaction. Gill contamination was correlated with water temperature and probably impacted by amoebae. Vibrio renipiscarius and Vibrio toranzoniae were isolated in North Atlantic for the first time. A better understanding of the interaction between marine aggregates, Vibrio spp. and fish is essential to improve salmon cage farming.