Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae

Abstract

Bacterial populations are subject to complex processes of diversification that involve mutation and horizontal DNA transfer mediated by transformation, transduction, or conjugation. Tracing the evolutionary events leading to genetic changes allows us to infer the history of a microbe. Here, we combine experimental and in silico approaches to explore the forces that drive the genome dynamics of Streptococcus agalactiae, the leading cause of neonatal infections. We demonstrate that large DNA segments of up to 334 kb of the chromosome of S. agalactiae can be transferred through conjugation from multiple initiation sites. Consistently, a genome-wide map analysis of nucleotide polymorphisms among eight human isolates demonstrated that each chromosome is a mosaic of large chromosomal fragments from different ancestors suggesting that large DNA exchanges have contributed to the genome dynamics in the natural population. The analysis of the resulting genetic flux led us to propose a model for the evolutionary history of this species in which clonal complexes of clinical importance derived from a single clone that evolved by exchanging large chromosomal regions with more distantly related strains. The emergence of this clone could be linked to selective sweeps associated with the reduction of genetic diversity in three regions within a large panel of human isolates. Up to now sex in bacteria has been assumed to involve mainly small regions; our results define S. agalactiae as an alternative paradigm in the study of bacterial evolution.

Fig. 1.

Transfer frequency of the Erm^R marker. (A) Transfer frequency of the 30 insertions (I-1 to I-30) distributed throughout the chromosome independently of any predicted mobile genetic element. Strain BM110 was used as recipient. All mating assays were performed twice, and standard deviations are indicated. Dashes on the x axis indicate insertions for which no transconjugant was detected. Dashed lines and arrows indicate putative gradients of transfer frequencies observed for three regions. The three arrows under the x-axis indicate putative mobile genetic elements predicted in the genome of strain NEM316 (20). (B) Transfer frequency of four insertions (I-17 to I-20) in the vicinity of genomic island X. Strain A909RF was used as recipient. All mating assays were performed three times, and standard deviations are indicated. Thick dashes indicate transfer frequency for gbs1121⁺ donors. Circles indicate transfer frequency for gbs1121⁻ donors.

Fig. 2.

Distribution of SNPs along the genome sequences of eight S. agalactiae strains. The number of SNPs (y-axis) is plotted according to the position of the corresponding 500-bp fragment on the strain 2603 V/R chromosome (x-axis). For each coordinate, identical colors indicate regions highly conserved between the corresponding strains (<0.05% polymorphism); gray denotes a high percentage of polymorphism with the seven other chromosomes (>0.7%). Empty sites represent previously described genomic islands larger than 5 kb (16); the black lines R1, R2, and R3 indicate the three regions displaying a low level of polymorphism in the eight genomes. Right brackets indicate clonal complexes; black arrow indicates the locus encoding the capsular polysaccharide. ST, sequence type.

Fig. 3.

Central position of CC19 according to the extent of highly conserved regions between the different CCs. The numbers in bold type indicate the total length in kilobases of the highly conserved regions between two CCs. The numbers in lightface type indicate the number of these highly conserved regions.

Fig. 4.

Polymorphism levels of regions R1 to R3 in 22 strains from various origins. The sequence of 37 loci (representing 15,119 kb) was compared using strain 2603 V/R as a reference. Colors indicate the level of nucleotide divergence. Gray boxes indicate absence of the locus. The marks on the left vertical line indicate the limits of the 37 loci. Asterisks indicate strains isolated from animals. Strain designations (left to right): 2603 V/R, 18RS21, CJB111, Mad74, 553–08, H36B, A909, CCH268, NEM316, CCH350, 515, CCH263, COH1, NEM1575, Ban29, Dak30, 411–07, 304–36, 043–14, 501–18, 2–22, SS1218. SNPs are detailed in Tables S5 and S6.