Clonally Evolving Pathogenic Bacteria

© Springer International Publishing AG, part of Springer Nature 2018. Unlike those of animals and plants, sexual processes in bacteria are not linked to reproduction per se and are a consequence of horizontal (sometimes called lateral) gene transfer (HGT). This is the acquisition of genetic material from a nonparental source and its incorporation into the genome, usually by recombination. The relative and absolute rates of HGT in different bacteria vary greatly, and this has a major influence on population diversity, structure and evolution. Rates of HGT are influenced by both mechanistic and ecological considerations, and when HGT is absent or very rare, bacterial populations become completely clonal. In such populations, evolution occurs solely by the accumulation of mutations, accompanied by diversity reduction events such as periodic selection and/or stochastic bottlenecks, which can result in hitchhiking events that fix mutations, whether beneficial, deleterious or neutral in their effect on fitness. The net effect is the establishment of distinct lineages within the population, which are characterized by low genetic diversity accompanied by the relaxation of purifying selection and an enhancement of the effects of genetic drift. The best examples of such bacteria are well-known obligate pathogens that affect humans, including Mycobacterium tuberculosis, Mycobacterium leprae, Yersinia pestis, Bacillus anthracis, Salmonella enterica serovar Typhi and Bordetella pertussis. Each of these pathogens has evolved from a more diverse parental population as a result of a shift in niche from a free-living organism to an obligate parasite. In some cases, this was caused or accompanied by a HGT event, but ultimately the process has led to reproductive isolation: the inhibition of further HGT with the parental population, the wider bacterial community, and even among members of the population itself. While this reproductive isolation may have promoted specialization and eventually speciation, it can also result in loss of fitness, as a consequence of the accumulation of deleterious or mildly deleterious mutations, a process known as Muller’s ratchet. Since their emergence, the evolution of these organisms has been further influenced by ecological factors resulting from changes in human behaviour, including increased population numbers and density and the use of antibiotics.