3 - Population Structure of Pathogenic Bacteria

Abstract

This chapter discusses the processes at work in bacterial populations, the biases that can impact our inferences, methods for identifying and studying bacterial populations. There are many processes that give rise to an immense diversity in bacterial population. Population genetics provides knowledge about the dynamics of antimicrobial resistance, vaccine escape, the impact of natural selection on bacterial populations and other processes, such as drift or demographic factors. It attempts to understand how genetic variation arises. Bacteria reproduce asexually through binary fission but gene exchange and subsequent recombination between bacteria is enabled by conjugation, transduction, and transformation. Researchers have studied the spread of resistance and the role of recombination on bacterial population structure. Multilocus enzyme electrophoresis (MLEE) uses the electrophoretic mobility of expressed water-soluble enzymes to indirectly assess genetic variation. The index of association (Ia) makes use of the variance in the distribution of pairwise allelic mismatches among bacteria. Multilocus sequence typing (MLST) later succeeded MLEE as the tool of choice for bacterial population genetics. Apart from mutational and recombinational processes, there are other population-level processes that generate genetic variation such as neutral genetic drift and natural selection but there has been no progress in developing analysis tools that assess their relative roles in shaping bacterial genetic variation. STRUCTURE and BAPS are some of the programs that perform population analyses. It was noted that STRUCTURE as well as BAPS may be inappropriate for less-recombinant species. This chapter reveals that population analyses have great potential in the study of pathogenic bacteria. Population analyses have great potential in the study of pathogenic bacteria, especially those in which there is a high rate of homologous recombination rendering straightforward phylogenetic analysis inappropriate.