Inference of Bacterial Microevolution Using Multilocus Sequence Data

TLDR

The authors present a model-based method that uses multilocus sequence data to infer bacterial clonal relationships and recombination sites, enabling determination of shared ancestry, ancestor age, and linking genetic events to phenotypic changes. The method assumes recombination introduces a constant substitution rate over contiguous sequence regions and is applicable to both MLST data from few loci and alignments of multiple bacterial genomes. The model outperforms existing MLST-based methods for subdividing recombinogenic bacteria, as demonstrated on Salmonella and Bacillus, and the ClonalFrame software is available online.

Abstract

Abstract We describe a model-based method for using multilocus sequence data to infer the clonal relationships of bacteria and the chromosomal position of homologous recombination events that disrupt a clonal pattern of inheritance. The key assumption of our model is that recombination events introduce a constant rate of substitutions to a contiguous region of sequence. The method is applicable both to multilocus sequence typing (MLST) data from a few loci and to alignments of multiple bacterial genomes. It can be used to decide whether a subset of isolates share common ancestry, to estimate the age of the common ancestor, and hence to address a variety of epidemiological and ecological questions that hinge on the pattern of bacterial spread. It should also be useful in associating particular genetic events with the changes in phenotype that they cause. We show that the model outperforms existing methods of subdividing recombinogenic bacteria using MLST data and provide examples from Salmonella and Bacillus. The software used in this article, ClonalFrame, is available from http://bacteria.stats.ox.ac.uk/.