Infect Genet Evol. 2013 Jan;13:187-97.

Hierarchical clustering of genetic diversity associated to different levels of mutation and recombination in Escherichia coli: a study based on Mexican isolates.

González-González A, Sánchez-Reyes LL, Delgado Sapien G, Eguiarte LE, Souza V.

Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, México D.F., Mexico.


Escherichia coli occur as either free-living microorganisms, or within the colons of mammals and birds as pathogenic or commensal bacteria. Although the Mexican population of intestinal E. coli maintains high levels of genetic diversity, the exact mechanisms by which this occurs remain unknown. We therefore investigated the role of homologous recombination and point mutation in the genetic diversification and population structure of Mexican strains of E. coli. This was explored using a multi locus sequence typing (MLST) approach in a non-outbreak related, host-wide sample of 128 isolates. Overall, genetic diversification in this sample appears to be driven primarily by homologous recombination, and to a lesser extent, by point mutation. Since genetic diversity is hierarchically organized according to the MLST genealogy, we observed that there is not a homogeneous recombination rate, but that different rates emerge at different clustering levels such as phylogenetic group, lineage and clonal complex (CC). Moreover, we detected clear signature of substructure among the A+B1 phylogenetic group, where the majority of isolates were differentiated into 4 discrete lineages. Substructure pattern is revealed by the presence of several CCs associated to a particular life style and host as well as to different genetic diversification mechanisms. We propose these findings as an alternative explanation for the maintenance of the clear phylogenetic signal of this species despite the prevalence of homologous recombination. Finally, we corroborate using both phylogenetic and genetic population approaches as an effective mean to establish epidemiological surveillance tailored to the ecological specificities of each geographic region.

PMID: 22995280



How bacterial species originate and go extinct through the time is a fascinating puzzle that a lot of evolutionary biologists attempt using different model systems and approaches. This understanding has been specially focused in the study of pathogenic bacterial species due the menace they represent to the human beings. Since several years ago, our lab has been interested into the elucidation of how the genetic diversity of some bacterial populations is originated and maintained. Our first model system was Escherichia coli. However, unlike other research groups, the lab was the first lab to study the population genetics of non-outbreak related E. coli samples (1).

Study bacterial population genetics is vital for interpreting the response of bacterial populations to selection pressures such as antibiotic treatment or vaccines targeted at only a subset of strains. These issues require an extensive understanding of both the selective and neutral forces that shape non-outbreak related bacterial populations over the short-term, and in particular, the relative roles of genome adaptation through point mutation, homologous recombination, gene loss, gene acquisition and gene replacement (2).

Escherichia coli is one of the most studied bacterial species. Members of this species can be found inhabiting both water and sediment environments (3) in addition to the vertebrate gut, where it occurs as either a commensal or pathogenic bacteria (4). As pathogenic bacteria, this species has been the cause of epidemic outbreaks throughout the world. In México, high levels of genetic diversity couple to specific host taxonomic groups have been reported for wild E. coli (1, 5). However, the exact mechanisms that generate this diversity are still unknown. Furthermore, studies on human-associated clinical isolated in this country are limited to the description of virulence genes and do not consider an evolutionary framework.

In this work we found that the levels of genetic diversity of non-outbreak related E. coli isolates from Mexico are explained mainly by homologous recombination rather point mutation. In addition, we observed that there is not a homogeneous recombination rate, but that different rates emerge at different clustering levels such as phylogenetic group, lineage and clonal complex (CC) (Figure 1). Interestingly, we found that CCs associated to highly pathogenic strains are coupled with higher recombination rates in contrast to other CCs associated with less pathogenic E. coli strains, which are affiliated with intermediate and low rates of recombination. We also found strains isolated from environmental sources as well as the domestication status and diet of animals as ecological barriers that could be delineating evolutionary units in E. coli.

We also recovered in the Mexican sample, the main phylogenetic groups that compose the whole species. However we found two more subgroups within the phylogenetic group A+B1. Although there is not a geographic structure of the genetic diversity in E. coli, we propose each geographic region has a slightly different evolutionary dynamics associated to the specific immunological context of each place. This could explain the prevalence of endemic diarrheas in different geographic areas as in Mexico in contrast to the mortal diseases elicited by the same pathogenic strains that can be lethal in other countries.

Thus, our study strongly suggests the importance of carry out investigations that explore the microevolutionary processes at a local scale. Such studies can provide valuable information regarding the evolutionary scenario and genetic reservoirs underlying the emergence of clonal complexes with epidemiological relevance.

About our last results we found that the genome size of the Mexican sample ranges from 4.5 to 6.0 MB. Interestingly, not only strains with serotypes associated to virulent strains harbor big genomes, but also the environmental isolates contain a considerable gene reservoir.

Further work has to be done to depict the genomic plasticity associated to each ecological niche found in this study.


1. Souza, V., Rocha, M., Valera, A., Eguiarte, L.E., 1999. Genetic structure of natural populations of Escherichia coli in wild hosts on different continents. Appl. Environ. Microbiol. 65, 3373-3385.

2. Feil, E.J., 2004. Small change: Keeping pace with microevolution. Nat. Rev. Microbiol. 2, 483-495.

3. Savageau, M.A., 1983. Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am. Nat. 122, 732-744.

4. Kaper, J.B., Nataro, J.P., Mobley, H.L., 2004. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123-140.

5. Souza, V., Travisano, M., Turner, P., Eguiarte, L.E., 2002b. Does experimental evolution reflect patterns in natural populations? Comparison of E. coli strains from long-term studies to those from wild isolates. Antoine van Leeuwenhoek. 81: 143-153.

Contact information:

Valeria Souza Saldívar

Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, México D.F. 04510, México. Phone: +52 55 56 22 90 06. Fax +52 55 56 22 89 95
E-mail address:
Figure1Fig 2. Evolutionary dynamics of Escherichia coli. The population structure of this bacterial species is conformed by five main phylogenetic groups (A, B1, B2, D and E). Likewise, each phylogenetic group is composed by different clonal complexes each one of these, associated with a particular ecological niche (ecotypes). Our study indicates that the diversification of E. coli is associated with particular levels of recombination within each phylogenetic group and clonal complex. Also, different patterns and levels of intra and inter-lineage recombination could explain the significant values of genetic structure recovered in the Mexican sample.


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