8% of the C. jejuni collection). A second group of 39 alleles contained all but 7 C. coli isolates (97.7% Doramapimod price of the C. coli collection). Interestingly, the 39 alleles related to C. coli encode only two different

peptide sequences that differ in one single amino acid (Thr86Ile substitution giving rise to quinolone resistance). By contrast, the 41 alleles related to C. jejuni encode 8 different peptide sequences (numbered between #1 and #14). The d N/d S ratios were lower for the C. coli (0.0075) than the C. jejuni (0.0498) collections, reflecting a higher level of synonymous changes within the gyrA sequences of the C. coli than in those of C. jejuni. The phylogenic tree in Figure 1 further highlights two clades for C. jejuni and three clades for C. coli. Figure 1 Neighbour-joining radial distance phylogenetic tree constructed with the 80 nucleotide gyrA alleles identified. PG = peptide group. Bootstrap

support values (%) for each of the nodes leading to the gyrA sequence clusters are indicated. Key: surface waters, green; domesticated mammals, blue; poultry, yellow; multi-source, grey. Genetic diversity among the gyrA sequences within each species The nucleotide sequences were aligned to an arbitrarily chosen reference allele (allele #1 and #301 for C. jejuni and C. coli, respectively). Selleck PLX4720 A total of 36 and 46 polymorphic sites were found for C. jejuni and C. coli, GDC 973 respectively. Next, nucleotide alleles were classified in a two-step approach: first, according to the encoded peptide (i.e. non-synonymous mutations) and second, according to similarities in nucleotide sequences (i.e. synonymous mutations). Tables 1 and 2 display this classification and show a selection

of synonymous and non-synonymous changes in sequences that were common to several alleles and which determined different peptide groups (PG). The 430 isolates of the C. jejuni Methocarbamol collection were classified into 9 PGs: 8 corresponded to PGs #1, 2, 3, 4, 5, 6, 8 and 14 related to C. jejuni (41 nucleotide alleles) and one corresponded to PG #301 related to C. coli (encoded by the nucleotide allele #301, Table 1). For refining grouping among the 302 C. coli strains, PG #301 (originally composed of 39 nucleotide alleles) was subdivided in four parts named A, B, C and D according to similarities in synonymous mutations in their nucleotide sequences (Table 2). PG #302 included all strains with the quinolone resistance C257T mutation (10 nucleotide alleles). The remaining peptide groups were specific to the C. jejuni species (PGs #7, 8, 9 and 23). Table 1 Distribution of C. jejuni gyrA alleles by source and conserved nucleotide Peptide group Allele no.* Nucleotide position Distribution by source** No. of ST 64 111 210 257 276 324 408 438 486 SW DM P   1 A G C C G A G C A 26 27 22 26   4 . . . . . . . . . 2 14 6 6   5 . . . . . . . . . 3 12 10 11   7 . . . . . . . . . 45 8 16 11   11 . . . . . . A . . 26 10   22   12 . . . . . . . . .     1 1   13 . . . . . . . . . 3   4 5   16 . . .