Number tandem repeatThe VNTR gave complete outcomes for 79 isolates only (Table 1). Each of the loci were polymorphic, showing from 3 (CVN7 and CVN15) to 14 alleles (CVN14). There was reduce genetic variability inside the sample of resistant isolates as shown by the allelic richness (Rs = two.3 ?1.2) vs. other samples (susceptible isolates from yellow-legged gulls Rs = four.5 ?3.six; susceptible isolates from slender-billed gulls Rs = 3.0 ?2.2; susceptible isolates from humans Rs = 4.3 ?2.9). On the other hand, the distinction of Rs involving each and every pair of samples was not important (Wilcoxon test, p-values variety between .574 and .936). Elsewhere, the gene diversities per locus were similar in all samples except for locus CVN2 which showed a higher worth for resistant YLG strains (Hs = 0.69) when compared with the 3 other sample groups (susceptible strains from YLG: Hs = 0.22, SBG: Hs = 0.26, humans: Hs = 0.17). Nonetheless, the difference of Hs between each and every pair of samples was not significant (Wilcoxon test, p-values range among .261 and .936).A substantial linkage disequilibrium (p < .001) was underscored at 3 loci pairs: (CVN1 ?CVN2, CVN1 ?CVN14, CVN2 ?CVN14) in the resistant YLG sample group, whereas no significant linkage disequilibrium was detected in any loci combination in other samples, even in the susceptible E. coli isolated from YLG.3.6|Phylogenetic analysis based on MLST, SNP, and VNTRThe minimum spanning tree presented in Figure 2 is based on genetic sequence similarity according to MLST (7 fragments of gene sequences shortened and aligned to the reference sequences in the MLST Databases at the University of Warwick (freely available at: http://mlst.warwick.ac.uk/mlst/) (i.e., 3,423 nucleotides in total)), SNP and VNTR analyses. The phylogenetic structure highlighted is similar to that underlined in Figure 1. Isolates of the same phylogroup tend to cluster together. Carbapenem-resistant isolates do not form a distinct cluster. Conversely, they are grouped in PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/21098350 three clusters that alsoF I G U R E 2 Minimum spanning tree of 79 with the studied Escherichia coli strains determined by MLST, SNPs and VNTR. The 13 strains for which part of the VNTR data was missing have been excluded. The phylogroups are shown as ovals. Clonal complexes are indicated by symbols proportional in size to the quantity of strains within them. Black lines connecting strains indicate that they differ at (1) least by a single VNTR (bold thick lines) to two VNTR and (2) seven markers (5 MLST genes and two SNPs (the thinnest lines))|VITTECOQ ET al.include carbapenem-susceptible strains isolated from the different host species (YLG, SBG, and humans). Furthermore, only one resistant isolate presents a exclusive sequence, the other people are grouped in five clonal complexes which includes two? strains. So as to test for potential artifacts within the deep branches brought on by VNTR which are inclined to possess a very rapid dynamics, we led precisely the same evaluation with out VNTR, i.e., MLST + SNP. The results obtained show precisely the same network topography; the only minor distinction MedChemExpress BFH772 issues the B2 group position, but all strains of this group cluster with each other as observed in Figure 2 (see Supplementary Information–Figure S1).detected in hospitals (INVS 2014). Numerous of those episodes (481 out of 913) were linked to a previous stay from the patient inside a foreign country (Cr et et al., 2012, Cuzon, Naas, Lesenne, Benhamou, Nordmann, 2010; INVS 2014), which underscores the rarity of carbapenemresistant infection originating in France. Furthermore, the res.