One of the samples isolated in Norway was from a patient of Afric

One of the samples isolated in Norway was from a patient of African origin and clustered JNK inhibitor with the four African sequences. The vacA genotype of this sample was s1b,

the genotype that is most common among the African, Spanish, and South American populations [21]. This pldA tree was unrooted and consisted of two main clusters, the East Asian cluster and the smaller African groups, nested within the vast majority of European sequences. The two African pldA sequences from the J99 and SouthAfrica7 genomes were found among the European sequences, as observed in the reference tree. Only three of the African strains formed a clade with 75% bootstrap analysis (in M1 consensus tree; data not shown). Figure 2 Phylogenetic tree of Helicobacter pylori pldA sequences. The pldA sequences were biogeographically classified: blue represents European strains, orange indicates hpEastAsian isolates, and green denotes African strains (hpAfrica). The outliers are identified by black arrows (see Discussion for more information). Additional file 1: Table S2 contain label with corresponding GenBank Accession

ID. Shown are radial consensus trees of 246 pldA sequences based on 1000 maximum likelihood bootstrap replicates analyzed in PhyML and visualized in FigTree (see Methods for details). Trees were constructed using either the K80 + G + I model chosen by ModelTest (A) or the GTR + I + G model MK 1775 (B) as used to construct the reference tree (Figure 1). The two pldA trees constructed using different models were compared in TOPD/FMTS using split distances. The average split distance was 0.58, which indicated that the two trees were neither identical (split difference = 0) nor completely different (1). A random split distance was calculated to analyze whether the split distances were significantly different. Because the random split distance resulted in a value close to 1 (0.999885, to be exact), our observations were probably not due to chance. Horizontal gene Liothyronine Sodium transfer analysis of pldA and OMPLA sequences The average GC content of the 19 pldA gene sequences

was 40.18 ± 0.35%, while the average GC content of the corresponding 19 whole-genome sequences was 38.98 ± 0.21%, a significant difference (P ≈ 10-12). The pldA mean GC content was greater than 1.5 standard deviations from the GC genomic mean, suggesting horizontal transfer. We further assessed whether the codon bias found in the pldA gene sequences could be due to biological or random effects. The codon adaptation index (CAI) was estimated by CAIcal [22] to be 0.77, while the eCAI estimate was 0.75 (with p <0.01; 99% probability for 99% of the population). This yields a CAI/eCAI ratio of 1.03; a CAI value higher than the expected eCAI value indicates codon bias. We collected 958 OMPLA sequences (listed in the Additional file 2: Table S3), of which 170 different species had pairwise sequence identities to H.

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