Population Genetics of Pathogenic<i>Escherichia coli</i>

Denamur, Erick; Tenaillon, Olivier

doi:10.1002/9780470600122.ch14

Cited by 10 publications

(10 citation statements)

References 108 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, metabolic distances between Shigella strains were comparable to metabolic distances between Shigella and non-Shigella strains, while the distance between Shigella strains from the same phylogenetic group (i.e., those of the S3 Shigella group) was equal to the intragroup E. coli metabolic distance. This suggests that their metabolic networks have quickly evolved by genetic drift (11) and that most metabolic differences were not common to all Shigella strains. Among the 176 pseudoreactions (linked only to pseudogenes) found in at least one Shigella strain, none were pseudoreactions in all 6 Shigella strains and 92 were pseudoreactions in only one Shigella strain.…”

Section: Resultsmentioning

confidence: 99%

“…Among the 176 pseudoreactions (linked only to pseudogenes) found in at least one Shigella strain, none were pseudoreactions in all 6 Shigella strains and 92 were pseudoreactions in only one Shigella strain. Nev- ertheless, convergent inactivation of a few metabolic characters has been reported, indicating adaptive evolution (1,11,34,42). This could be a consequence of its parasitic lifestyle, which removes requirements for some degradation/biosynthesis pathways, as mentioned above.…”

Section: Resultsmentioning

confidence: 99%

“…This set of strains comprises 23 E. coli strains covering all main phylogenetic groups (A, B1, B2, D, E, and F) (11) and various pathogenic or nonpathogenic behaviors (commensal, ExPEc, InPEc), as well as 6 Shigella strains, which are human obligate intraintestinal pathogens belonging to the E. coli species (15,44). To obtain metabolic networks suitable for comparative analyses, we first developed a high-quality automated reconstruction process which builds homogenized genome annotations and combines metabolic evidence from the EcoCyc and MetaCyc databases (7, 28a).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Core and Panmetabolism in Escherichia coli

et al. 2011

Self Cite

View full text Add to dashboard Cite

Escherichia coli exhibits a wide range of lifestyles encompassing commensalism and various pathogenic behaviors which its highly dynamic genome contributes to develop. How environmental and host factors shape the genetic structure of E. coli strains remains, however, largely unknown. Following a previous study of E. coli genomic diversity, we investigated its diversity at the metabolic level by building and analyzing the genomescale metabolic networks of 29 E. coli strains (8 commensal and 21 pathogenic strains, including 6 Shigella strains). Using a tailor-made reconstruction strategy, we significantly improved the completeness and accuracy of the metabolic networks over default automatic reconstruction processes. Among the 1,545 reactions forming E. coli panmetabolism, 885 reactions were common to all strains. This high proportion of core reactions (57%) was found to be in sharp contrast to the low proportion (13%) of core genes in the E. coli pangenome, suggesting less diversity of metabolic functions compared to that of all gene functions. Core reactions were significantly overrepresented among biosynthetic reactions compared to the more variable degradation processes. Differences between metabolic networks were found to follow E. coli phylogeny rather than pathogenic phenotypes, except for Shigella networks, which were significantly more distant from the others. This suggests that most metabolic changes in non-Shigella strains were not driven by their pathogenic phenotypes. Using a supervised method, we were yet able to identify small sets of reactions related to pathogenicity or commensalism. The quality of our reconstructed networks also makes them reliable bases for building metabolic models.Escherichia coli is a versatile species encompassing commensal organisms, as well as intraintestinal E. coli (InPEc) and extraintestinal E. coli (ExPEc) pathogens (27, 49). This variety of lifestyles has been seen as a consequence of the huge E. coli genome plasticity (51). However, linking genomic elements to phenotypic behaviors is not trivial because several layers of biological processes separate genes from their phenotypic effects, and in extreme cases, the evolutionary path can lead either to the functional convergence of distinct sets of genes or to the functional divergence of an initially common set of genes. Consequently, in order to establish links between genomes and phenotypes, one needs an integrative layer. A recent study on a set of 20 E. coli strains (51) has shown that a large fraction of the shared genomic elements with known function is related to metabolism. Because it is now feasible to reconstruct metabolic networks at the genome scale (7,13,16,26), these metabolic networks can, in principle, be used as functional bridges between genomic diversity and phenotypic differences. Currently, such reconstructions are performed automatically from the annotation of input genomes, using algorithms that match these annotations with the contents of reference metabolic databases (13,16).In this work, we stu...

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Core and Panmetabolism in Escherichia coli

et al. 2011

Self Cite

View full text Add to dashboard Cite

show abstract

“…This species counts among the most demonstrative cases of near-clading. The MLEE A, B1, B2, D groups identified in the historical ECOR collection of strains by pioneer studies (Ochman and Selander, 1984;Whittam et al, 1983) have been fully corroborated, and their permanency as well, by many studies relying on various genetic markers (Chaudhuri and Henderson, 2012;Clermont et al, 2011;Denamur et al, 2010;Walk et al, 2009;Wirth et al, 2006). The fact that the rate of recombination in E. coli almost equals that of mutation (Bobay et al, 2015) has not prevented the long-term stability of a strong structuring into typical near-clades.…”

Section: Bacteriamentioning

confidence: 97%

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

Tibayrenc

Ayala

2017

Advances in Parasitology

View full text Add to dashboard Cite

“…Escherichia coli is a commensal and versatile pathogen that can cause death (1). Given these characteristics, it is an ideal organism for studying the transition of commensalism to pathogenicity.…”

mentioning

confidence: 99%

Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages

Miskinyte

Gordo

2013

Antimicrob Agents Chemother

View full text Add to dashboard Cite

Mutations causing antibiotic resistance usually incur a fitness cost in the absence of antibiotics. The magnitude of such costs is known to vary with the environment. Little is known about the fitness effects of antibiotic resistance mutations when bacteria confront the host's immune system. Here, we study the fitness effects of mutations in the rpoB, rpsL, and gyrA genes, which confer resistance to rifampin, streptomycin, and nalidixic acid, respectively. These antibiotics are frequently used in the treatment of bacterial infections. We measured two important fitness traits-growth rate and survival ability-of 12 Escherichia coli K-12 strains, each carrying a single resistance mutation, in the presence of macrophages. Strikingly, we found that 67% of the mutants survived better than the susceptible bacteria in the intracellular niche of the phagocytic cells. In particular, all E. coli streptomycin-resistant mutants exhibited an intracellular advantage. On the other hand, 42% of the mutants incurred a high fitness cost when the bacteria were allowed to divide outside of macrophages. This study shows that single nonsynonymous changes affecting fundamental processes in the cell can contribute to prolonged survival of E. coli in the context of an infection.

show abstract

Population Genetics of PathogenicEscherichia coli

Cited by 10 publications

References 108 publications

Core and Panmetabolism in Escherichia coli

Core and Panmetabolism in Escherichia coli

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages

Contact Info

Product

Resources

About