Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences

Abstract

The identification of clones within bacterial populations is often taken as evidence for a low rate of recombination, but the validity of this inference is rarely examined. We have used statistical tests of congruence between gene trees to examine the extent and significance of recombination in six bacterial pathogens. For Neisseria meningitidis , Streptococcus pneumoniae , Streptococcus pyogenes, and Staphylococcus aureus , the congruence between the maximum likelihood trees reconstructed using seven house-keeping genes was in most cases no better than that between each tree and trees of random topology. The lack of congruence between gene trees in these four species, which include both naturally transformable and nontransformable species, is in three cases supported by high ratios of recombination to point mutation during clonal diversification (estimates of this parameter were not possible for Strep. pyogenes ). In contrast, gene trees constructed for Hemophilus influenzae and pathogenic isolates of Escherichia coli showed a higher degree of congruence, suggesting lower rates of recombination. The impact of recombination therefore varies between bacterial species but in many species is sufficient to obliterate the phylogenetic signal in gene trees.

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

“…This could be due to variable selective pressures on the genome and/or temporal/geographical structuring generated by random genetic drift, which would not be surprising considering the wide distribution and temporal dispersion of the isolates analyzed. These data support previous conclusions for low rates of recombination for B. cereus (Vilas-Boas et al, 2002), S. pyogenes Feil et al, 2001) and S. agalactiae (Jones et al, 2003). Finally, B. pseudomallei (and closely related species), M. catarrhalis, Staphylococcus epidermidis, Vibrio vulnificus, Campylobacter jejuni, Enterococcus faecium, E. coli, and S. aureus showed consistently low mean levels of ρ( ≤15).…”

“…Population recombination rate (ρ)-H. pylori, N. gonorrhoeae, N. meningitidis, and S. pneumoniae showed high mean levels (ρ> 50) of intragenic recombination across loci, which supports prior conclusions (e.g., Maynard-Smith et al, 1993;Suerbaum et al, 1998;Feil et al, 1999Feil et al, ,2000aFeil et al, ,2001). B. cereus, H. influenzae, Streptococcus agalactiae, and Streptococcus pyogenes showed moderate levels of recombination (15 < ρ ≤ 50).…”

How Does the Horizontal Gene Transfer in Bacteria Occur and Than Is It Tied Up

“…показал, что основным источником аллельной изменчивости являются не му-тации, а рекомбинационные события [24,36]. Такие бактерии характеризуются малой степенью клональ-ности и способны к интенсивному ГПГ.…”

Pulmonary Tuberculosis and Mycobacterium Tuberculosis: Modern Molecular Epidemiology and Perspectives

“…This statement was based on the preponderance of certain genotypes and on the low level of genetic polymorphism and not on a rigorous population genetics analysis. Contrary to a widespread idea, the restricted gene sequence diversity and empirical observation of some predominant genotypes in various epidemiological studies provide no indication of its population structure, as they are compatible with distinct population structures with variable levels of recombination [58,59,167,176]. Furthermore, until the year 2000, no marker presented the necessary properties (i.e., a polymorphic marker based on several independent loci) to conduct population genetic studies (see above).…”

“…One important outgrowth of the phylogenetic revolution is the recognition that phylogenetic trees provide an important and appropriate context to address questions in a variety of disciplines such as molecular epidemiology and evolutionary biology. More and more, the phylogenetic approach is used to explore the population structure and to infer the system of reproduction of various organisms [58,83].These analyses contribute complementary information beyond population genetics studies, such as genetic structuring in a population, identification of a genetically individualized entity, for example, cryptic species and epidemics. Furthermore, the congruence or incongruence of different gene phylogenies also provides substantial insight into the population structure.…”