Mutational convergence acts as a major player in adaptive parallel evolution of Shigella spp.

Thomas, Achsah K.; Preetha, S B Kavya; Omanakuttan, Anjana; Vidyullata, Lakkaraju; Ashokan, Anjaly; Rajachandran, Vyshakh; Chattopadhyay, Sujay

doi:10.1038/s41598-019-39810-1

Cited by 8 publications

(11 citation statements)

References 48 publications

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“…As the ecological distinctness of the clade II strains were preliminary at this stage, we guided the model with inclusion of other Escherichia genomes that has exhibited traits of adaptation to one of the habitats. Such genomes included S. dysenteriae from the Shigella genus, which is essentially a lineage of E. coli that had evolved from multiple E. coli lineages to become highly specialized human pathogens through convergent evolution involving independent horizontal gene transfers and gene losses [35].…”

Section: Discussionmentioning

confidence: 99%

“…To minimize the inclusion of genes that were phylogenetic markers rather than informative of phenotype, we included another three more distantly related genomes, i.e., Shigella dysenteriae Sd197, E. coli ECOR66 (both gastrointestinal), and Escherichia clade IV TW14182 (environmental). Previous studies on these genomes showed evidences of adaptations to either external environment or gastrointestinal habitats for the genomes [3,21,22,[31][32][33][34][35][36]. Functional importance of sequence variations were scored using the DBS metric by comparing the protein coding genes of each strain to the profile HMMs of Gammaproteobacterial proteins (gproNOG.hmm) from the eggNOG database (http://eggnogdb.embl.de/).…”

Section: Random Forest Classifier Constructing and Trainingmentioning

confidence: 99%

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Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia

Shen

Koh

et al. 2020

Microorganisms

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The evolution, habitat, and lifestyle of the cryptic clade II of Escherichia, which were first recovered at low frequency from non-human hosts and later from external environments, were poorly understood. Here, the genomes of selected strains were analyzed for preliminary indications of ecological differentiation within their population. We adopted the delta bitscore metrics to detect functional divergence of their orthologous genes and trained a random forest classifier to differentiate the genomes according to habitats (gastrointestinal vs external environment). Model was built with inclusion of other Escherichia genomes previously demonstrated to have exhibited genomic traits of adaptation to one of the habitats. Overall, gene degradation was more prominent in the gastrointestinal strains. The trained model correctly classified the genomes, identifying a set of predictor genes that were informative of habitat association. Functional divergence in many of these genes were reflective of ecological divergence. Accuracy of the trained model was confirmed by its correct prediction of the habitats of an independent set of strains with known habitat association. In summary, the cryptic clade II of Escherichia displayed genomic signatures that are consistent with divergent adaptation to gastrointestinal and external environments.

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Section: Discussionmentioning

confidence: 99%

Section: Random Forest Classifier Constructing and Trainingmentioning

confidence: 99%

Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia

Shen

Koh

et al. 2020

Microorganisms

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“…(Gluck‐Thaler et al, 2020 ) as well as in the emergence of multiple dysentery‐causing Shigella spp. (Thomas et al, 2019 ). For bacterial plant pathogens, one trait of major economic and scientific interest is host specificity.…”

Section: Introductionmentioning

confidence: 99%

Parallel host shifts in a bacterial plant pathogen suggest independent genetic solutions

Donegan

Coletta-Filho

Almeida

2023

Molecular Plant Pathology

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While there are documented host shifts in many bacterial plant pathogens, the genetic foundation of host shifts is largely unknown. Xylella fastidiosa is a bacterial pathogen found in over 600 host plant species. Two parallel host shifts occurred—in Brazil and Italy—in which X. fastidiosa adapted to infect olive trees, whereas related strains infected coffee. Using 10 novel whole‐genome sequences from an olive‐infecting population in Brazil, we investigated whether these olive‐infecting strains diverged from closely related coffee‐infecting strains. Several single‐nucleotide polymorphisms, many derived from recombination events, and gene gain and loss events separated olive‐infecting strains from coffee‐infecting strains in this clade. The olive‐specific variation suggests that this event was a host jump with genetic isolation between coffee‐ and olive‐infecting X. fastidiosa populations. Next, we investigated the hypothesis of genetic convergence in the host shift from coffee to olive in both populations (Brazil and Italy). Each clade had multiple mutations and gene gain and loss events unique to olive, yet no overlap between clades. Using a genome‐wide association study technique, we did not find any plausible candidates for convergence. Overall, this work suggests that the two populations adapted to infect olive trees through independent genetic solutions.

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“…In these cases, the excess of beneficial mutations produced by the mutator clones drives them to a high frequency within the population, and the presence of a mutator allele can therefore be considered a signature of sustained adaptation. (iii) Genomic studies of epidemic bacterial clones and experimentally evolved laboratory strains ( 11 ) have revealed convergence at a molecular level ( 12 , 13 ) that can be seen as a hallmark of adaptation. Among all the possible mutations that may occur, finding mutations with comparable effects reflects the filtering action of natural selection.…”

Section: Introductionmentioning

confidence: 99%

Escherichia coli Genomic Diversity within Extraintestinal Acute Infections Argues for Adaptive Evolution at Play

Bridier‐Nahmias

Launay

Bleibtreu

et al. 2021

mSphere

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Adaptive processes in chronic bacterial infections are well described, but much less is known about the processes at play during acute infections. Here, by sequencing seven randomly selected isolates per patient, we analyzed Escherichia coli populations from three acute extraintestinal infections in adults (meningitis, pyelonephritis, and peritonitis), in which a high-mutation-rate isolate or mutator isolate was found. The isolates of single patients displayed between a few dozen and more than 200 independent mutations, with up to half being specific to the mutator isolate. Multiple signs of positive selection were evidenced: a high ratio of nonsynonymous to synonymous mutations (Ka/Ks ratio) and strong mutational convergence within and between patients, some of them at loci well known for their adaptive potential, such as rpoS, rbsR, fimH, and fliC. For all patients, the mutator isolate was likely due to a large deletion of a methyl-directed mismatch repair gene, and in two instances, the deletion extended to genes involved in some genetic convergence, suggesting potential coselection. Intrinsic extraintestinal virulence assessed in a mouse model of sepsis showed variable patterns of virulence ranging from non-mouse killer to mouse killer for the isolates from single patients. However, genomic signature and gene inactivation experiments did not establish a link between a single gene and the capacity to kill mice, highlighting the complex and multifactorial nature of the virulence. Altogether, these data indicate that E. coli isolates are adapting under strong selective pressure when colonizing an extraintestinal site. IMPORTANCE Little is known about the dynamics of adaptation in acute bacterial infections. By sequencing multiple isolates from monoclonal extraintestinal Escherichia coli infections in several patients, we were able to uncover traces of selection taking place at short time scales compared to chronic infection. High genomic diversity was observed in the patient isolates, with an excess of nonsynonymous mutations, and the comparison within and between different infections showed patterns of convergence at the gene level, both constituting strong signs of adaptation. The genes targeted were coding mostly for proteins involved in global regulation, metabolism, and adhesion/motility. Moreover, virulence assessed in a mouse model of sepsis was variable among the isolates of single patients, but this difference was left unexplained at the molecular level. This work gives us clues about the E. coli lifestyle transition between commensalism and pathogenicity.

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Mutational convergence acts as a major player in adaptive parallel evolution of Shigella spp.

Cited by 8 publications

References 48 publications

Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia

Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia

Parallel host shifts in a bacterial plant pathogen suggest independent genetic solutions

Escherichia coli Genomic Diversity within Extraintestinal Acute Infections Argues for Adaptive Evolution at Play

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