FEATURE ARTICLE
The Evolutionary Ecology of Escherichia coli
Abundantly studied and much feared, E. coli has more genomic plasticity than once believed and may have followed various routes to become a pathogen
Valeria Souza, Amanda Castillo, Luis Eguiarte
A New Evolutionary Paradigm
The studies described above examined mostly strains associated with humans. Indeed, with E. coli implicated in a large portion of the more than 2 million annual deaths from diarrheal diseases, the human strains are understandably the focus of attention. However, this tight focus may have limited our understanding of evolutionary issues. For this reason our group initiated a long-term study of the evolutionary ecology of E. coli with a particular emphasis on populations in wild hosts. The first step was to organize a collection of strains from various continents (mainly from America, Australia and Antarctica) associated with wild mammals and birds, as well as environmental strains, including samples from the air, water and soil. This collection amounts to more than 5,000 strains. We call it IECOL, the Institute of Ecology Collection of E. coli.
In the first study we used 201 strains associated with mammals, in which we completed a population-genetics analysis using 12 polymorphic genes—genes whose alleles code for a number of different enzymes. In comparing these strains we studied the use of 12 sugars, resistance to five antibiotics, their serotypes, and the number and size of their plasmids. We found that the diversity is even higher than reported from human strains of E. coli (0.68 on the 0-to-1 variation scale). The genetic diversity is greater in Mexican than in Australian strains, and each group of host organisms displays a particular group of related strains. The Mexican mammalian strains are those that exhibit statistically the lowest linkage disequilibrium. Such a low level in a bacterial strain signals recombination and lateral transfer and suggests that the E. coli associated with mammals in general are not, on average, as clonal as was suggested by data from strains solely derived from humans.
It is interesting that in certain groups of strains, such as those associated with carnivores, rodents and primates, recombination is more frequent than it is in hosts with very specific diets. We have now estimated that the overall effective population size of E. coli is 5.3 x 109—that is, two orders of magnitude higher than that calculated for E. coli isolated from human hosts. Our estimate of the parameter of recombination is almost two orders of magnitude greater than the rate of mutation, again indicating that lateral transfer happens far more frequently than had been thought. Additionally, we found that the worldwide population of E. coli may not be homogeneous, but rather there may be isolated subpopulations. We draw this conclusion from the fact that the estimated global migration rate is less than the estimated migration within Mexico by roughly an order of magnitude. We have estimated the rate of recombination by comparing the congruence between the genealogies of different genes and those derived from analysis of various genetic loci, and we conclude that intragene and intergene recombination in E. coli is more important than mutation.
We have also conducted an analysis of the genetic sequences of four metabolic genes using 50 strains in the IECOL collection. These results were consistent with our emerging hypothesis: The genetic diversity from intergene and intragene recombination was greater in strains associated with animals than in those associated with humans. This difference is especially clear in the gene gapA, which appears to have suffered a reduction in its diversity after invading humanity.
Thus, our best sampling and the new, more detailed studies suggest that the basic biology of E. coli is far more complex and interesting than classical studies indicated. E. coli is endowed not only with a great genetic and ecological diversity, but also with a high level of genetic recombination and exchange. These phenomena permit the generation of a large quantity of genotypes, even though they may not occur in each generation. It is not only genes that move; there is considerable recombination of plasmids and fragments of genes. Some of these combinations turn out to be successful and invade many environmental niches and new hosts, and so continues the spread of new variants of E. coli able to become highly competitive—for example, O157:H7, first identified as a human pathogen in 1982. This generates a structure populated with ecotypes and at the same time produces strains that can live in a large number of environments that before were believed secondary or atypical for the species.
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