Recombination and Population Structure in Salmonella enterica

Salmonella enterica is a bacterial pathogen that causes enteric fever and gastroenteritis in humans and animals. Although its population structure was long described as clonal, based on high linkage disequilibrium between loci typed by enzyme electrophoresis, recent examination of gene sequences has revealed that recombination plays an important evolutionary role. We sequenced around 10% of the core genome of 114 isolates of enterica using a resequencing microarray. Application of two different analysis methods (Structure and ClonalFrame) to our genomic data allowed us to define five clear lineages within S. enterica subspecies enterica, one of which is five times older than the other four and two thirds of the age of the whole subspecies. We show that some of these lineages display more evidence of recombination than others. We also demonstrate that some level of sexual isolation exists between the lineages, so that recombination has occurred predominantly between members of the same lineage. This pattern of recombination is compatible with expectations from the previously described ecological structuring of the enterica population as well as mechanistic barriers to recombination observed in laboratory experiments. In spite of their relatively low level of genetic differentiation, these lineages might therefore represent incipient species. Salmonella enterica is a species of bacteria that causes severe diseases in humans and animals. We sequenced about a tenth of the genome from a broadly sampled collection of S. enterica. By comparing these genetic sequences, we were able to partially reconstruct the ancestry of this sample. We identified five lineages within S. enterica, one of which is almost as old as the common ancestor of our sample. We also found evidence for frequent homologous recombination in the ancestry of S. enterica, where fragments of genes from one individual bacterium are acquired by a distinct individual. These recombination events make the ancestry harder to reconstruct in its entirety, but also contain interesting information. We found in particular that recombination had happened more often between strains belonging to the same lineage than across lineage boundaries. This observation is compatible with the lineages of S. enterica becoming progressively isolated from each other, which could lead to their gradual splintering into new species.