Chapter 10 - Multi-Locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population Variation

For nearly 30 years, 16S rRNA gene sequencing has been a fundamental tool for identification and cataloguing of bacterial diversity, but the diversity at this locus lacks the resolution to distinguish closely related bacteria. Multi-locus sequence typing (MLST) established the utility of a portable, gene-by-gene approach to population analyses, using both allelic and nucleotide sequence data that catalogue variation at seven housekeeping loci; however, it did not provide sufficient discrimination to define all variants of all bacteria. Recent advances in high-throughput next-generation sequencing technologies have permitted whole-genome sequencing of a wide variety of bacterial species and facilitated the development of genome-wide expanded MLST schemes. This chapter describes a flexible, scalable and hierarchical gene-by-gene approach to bacterial classification and population analyses, based on the concept …