Limited boundaries for extensive horizontal gene transfer among Salmonella pathogens

Abstract

Recombination is thought to be rare within Salmonella, as evidenced by absence of gene transfer among SARC strains that represent the broad genetic diversity of the eight primary subspecies of this common facultative intracellular pathogen. We adopted a phylogenetic approach to assess recombination within the mutS gene of 70 SARB strains, a genetically homogeneous population of Salmonella enterica subspecies I strains, which have in common the ability to infect warm-blooded animals. We report here that SARB strains show evidence for widespread recombinational exchange in contrast to results obtained with strains exhibiting species-level genetic variation. Besides extensive allele shuffling, SARB strains showed notably larger recombinagenic patch sizes for mutS (at least approximately 1.1 kb) than previously reported for S. enterica SARC strains. Explaining these experimental dichotomies provides important insight for understanding microbial evolution, because they suggest likely ecologic and genetic barriers that limit extensive gene transfer in the feral setting.

Fig. 1.

Most parsimonious phylogenetic relationships of S. enterica group I mutS alleles. The tree shown resulted from a mutS multiple sequence alignment [clustal x (20)] that was analyzed phylogenetically by using paup* (21, 22). Nine mutS clades (designated as A–I) that contained multiple strains were identified from the tree. Distributions of these same strains within mutS, mdh, and MLEE clades are designated to the right of the mutS tree such that strains originating from the same mutS, mdh, and MLEE clades are depicted with a common color. Nodal support values in the form of bootstraps (5,000 iterations) are symbolized on the tree as follows: *, 76–100%; +, 51–75%; O, 26–50%; no symbol, 0–25%. The eight mdh clades presented here were obtained from maximum parsimony analysis as well. The seven MLEE clades were defined in a previous analysis of SARB strains (9). mutS and mdh trees were rooted by using E. coli as the outgroup (ECOR strains 52 and 64). Color cells that remain white represent those strains that could not be assigned to a specific multistrain clade for that data set. Disjunct distributions of color cells within the mdh and MLEE columns serve to illustrate the phylogenetic incongruence between these two markers of Salmonella chromosome evolution and mutS.

Fig. 2.

Phylogenetic discordance between S. enterica group I mutS and mdh alleles. (A) Histogram displaying the ILD test (24) results for 100 sixteen-strain SARB submatrices that compared mutS and mdh for congruence to each other. The score for rejection of the null hypothesis of congruence (P = 0.050) is denoted by a red line across the graph. (B) Comparison of 16-strain mutS phylogenies for the S. enterica SARC and SARB collections (submatrix 95). mutS trees shown resulted from the partitioned analysis of (i) the reported 510-bp horizontally transferred patch, (ii) the combined 5′ and 3′ flanking sequences surrounding the patch, and (iii) the total 1.1-kb mutS segment (2). Branches on the mutS tree are color-coded according to clades identified in the corresponding mdh trees. A black branch indicates a strain that did not cluster with any other strain in the mdh trees. Trees were rooted with two strains of E. coli. Bootstrap values are reported beside each respective node on the mutS trees.

Fig. 3.

Phylogenetic evidence for structural mosaicism of the group I S. enterica mutS gene. (A) Column I, congruence array of the three intragenic segments composing the 1.1-kb mutS sequence for the total mutS matrix and the 100 sixteen-strain submatrices. Intragene comparisons are noted at the top of each column (P, patch; 5′, 5′ flanking sequence; and 3′, 3′ flanking sequence). ILD scores are represented as individual color cells and are organized into four distinct ranges: red, 0.001–0.010; yellow, 0.011–0.050; green, 0.051–0.100; and blue, 0.101–1.00. Column II, ILD comparisons of the three intragenic segments to mdh for the total mutS matrix and 100 submatrices. (B) Compatibility matrix of the total mutS matrix showing pairwise comparisons of informative binary sites within (colored triangles) and between (white) the intragene segments indicated. Labels on the diagonal denote the 1.1-kb segment and corresponding base pair coordinates being compared. The matrices shown were constructed in a program written in C++ by M.K.M. for determination and visualization of incompatible sites. The algorithm is similar to that described in the program reticulate (25).