2% of the SW collection); poultry strains predominate in PG #302 (N = 84 i.e. 63.1% of

the P collection), LY2835219 molecular weight while all quinolone-sensitive mammal strains were assigned to PG #301A (N = 33 i.e. 71.7% of the DM collection). The seven strains harboring a “C. jejuni-like allele” all originate from poultry (Table 2). Genotype diversity within the C. jejuni collection All the strains from this study were further characterized by MLST. For the C. jejuni isolates, a total of 170 different STs were identified. Combining MLST with gyrA yielded 191 distinct genotypes. The Simpson’s Index of Diversity (SID) was 0.911 (95% confidence intervals (CI) 0.899–0.923) for gyrA alleles only, 0.979 (95% CI 0.974–0.984) for MLST only and 0.984 (95% CI 0.979-0.988) for the combination of MLST and gyrA. The indexes of association IA calculated for each source using a single representative of each genotype,

appeared low and fairly similar, suggesting that each of these populations was highly diverse by recombining to some degree: 0.22 (SW), 0.28 (DM) and 0.19 (P). Population differentiation estimated by the F ST values was highest between SW and DM (0.07787, P <0.00001), followed by DM and P (0.04074, Poziotinib P <0.00001) and lowest for SW and P (0.03476, P <0.00001). Nearly half of the strains from the DM set (43.4%), 18.9% of the SW set and 23.2% of the P set had genotypes identified in all three sources (Figure 3A). In the same way, 60.2%, 22.2% and 52.8% of the strains had genotypes specific to SW, DM and P origins, respectively. Finally, 14.6% and 6.3% of the environmental (SW) collection had genotypes common to DM and P sets, respectively. Genotypes not recovered from SW and common to both animal sets represented 15.1% and 10.4% of the DM

and P collections, respectively. Figure 3 Distribution of genotypes (ST +  gyrA ) by source. (A) C. jejuni collection, (B) C. coli collection. SW = Surface waters, DM = Domesticated Mammals, P = Poultry. Genotype diversity within the C. coli collection Among the C. coli isolates, a total of 146 STs were identified and yielded 194 distinct genotypes when combined with the gyrA locus. The SID value for the combined methods was of 0.994 (0.992 – 0.996) versus 0.987 (0.984 – 0.991) for MLST alone or 0.945 (0.936 – 0.953) for the gyrA Farnesyltransferase data alone. The IA determined from the SW collection had a value similar to those previously calculated from the C. jejuni sets (0.26). In contrast, the IA values from each of the animal population displayed a trend closer to zero indicating a random association between alleles of the 8 loci (i.e. in proximity to linkage equilibrium) by freely recombining (IA for DM = 0.03 and IA for P = 0.05). The population pairwise F STs approach generated 3 similar values for each pair combination: SW/DM (0.16295, P <0.00001); SW/P (0.16455, P <0.00001) and DM/P (0.