Diversity and disease pathogenesis in Mycobacterium tuberculosis

Warner, Digby F.; Koch, Anastasia; Mizrahi, Valerie

doi:10.1016/j.tim.2014.10.005

Cited by 61 publications

(36 citation statements)

References 81 publications

(132 reference statements)

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“…An individual patient is likely to host an in situ diversification of ecologically divergent ecotypes (202), often facilitated by evolution of hypermutation (203). While specialized ecotypes of P. aeruginosa and M. tuberculosis may be transmitted from one host to another, it is unlikely that a suite of ecotypes will be transmitted, making possible in situ adaptive radiation from a single inoculating clone.…”

Section: Models Of Speciation: Rapidly Speciating Taxa the Speedy Spementioning

confidence: 99%

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Cohan

2017

Microbiol Spectr

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Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.

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Section: Models Of Speciation: Rapidly Speciating Taxa the Speedy Spementioning

confidence: 99%

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Cohan

2017

Microbiol Spectr

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“…This is a prevalent scenario in Staphylococcus aureus , E . coli , or Mycobacterium tuberculosis , for instance, in which multiple resistances pose a serious threat to human health [9,12–14]. Thus, disclosing the evolutionary factors governing the maintenance of multiple resistance is key for designing effective treatments.…”

Section: Introductionmentioning

confidence: 99%

Multidrug-resistant bacteria compensate for the epistasis between resistances

et al. 2017

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Mutations conferring resistance to antibiotics are typically costly in the absence of the drug, but bacteria can reduce this cost by acquiring compensatory mutations. Thus, the rate of acquisition of compensatory mutations and their effects are key for the maintenance and dissemination of antibiotic resistances. While compensation for single resistances has been extensively studied, compensatory evolution of multiresistant bacteria remains unexplored. Importantly, since resistance mutations often interact epistatically, compensation of multiresistant bacteria may significantly differ from that of single-resistant strains. We used experimental evolution, next-generation sequencing, in silico simulations, and genome editing to compare the compensatory process of a streptomycin and rifampicin double-resistant Escherichia coli with those of single-resistant clones. We demonstrate that low-fitness double-resistant bacteria compensate faster than single-resistant strains due to the acquisition of compensatory mutations with larger effects. Strikingly, we identified mutations that only compensate for double resistance, being neutral or deleterious in sensitive or single-resistant backgrounds. Moreover, we show that their beneficial effects strongly decrease or disappear in conditions where the epistatic interaction between resistance alleles is absent, demonstrating that these mutations compensate for the epistasis. In summary, our data indicate that epistatic interactions between antibiotic resistances, leading to large fitness costs, possibly open alternative paths for rapid compensatory evolution, thereby potentially stabilizing costly multiple resistances in bacterial populations.

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“…A key aim of our study was to determine if HIV-1 coinfection, which represents a relatively recent addition to the adaptive landscape upon which M. tuberculosis evolves (Warner et al 2015), has had a detectable influence on M. tuberculosis evolution. To do this, each SNP containing codon site was evaluated using the MEDS method to determine whether selection pressures acting on these codon sites could differ between HIV-1 coinfected and HIV-1 uninfected individuals (Murrell et al 2012).…”

Section: Discussionmentioning

confidence: 99%

The Influence of HIV on the Evolution of Mycobacterium tuberculosis

Koch

Brites

Stucki

et al. 2017

Molecular Biology and Evolution

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HIV significantly affects the immunological environment during tuberculosis coinfection, and therefore may influence the selective landscape upon which M. tuberculosis evolves. To test this hypothesis whole genome sequences were determined for 169 South African M. tuberculosis strains from HIV-1 coinfected and uninfected individuals and analyzed using two Bayesian codon-model based selection analysis approaches: FUBAR which was used to detect persistent positive and negative selection (selection respectively favoring and disfavoring nonsynonymous substitutions); and MEDS which was used to detect episodic directional selection specifically favoring nonsynonymous substitutions within HIV-1 infected individuals. Among the 25,251 polymorphic codon sites analyzed, FUBAR revealed that 189-fold more were detectably evolving under persistent negative selection than were evolving under persistent positive selection. Three specific codon sites within the genes celA2b, katG, and cyp138 were identified by MEDS as displaying significant evidence of evolving under directional selection influenced by HIV-1 coinfection. All three genes encode proteins that may indirectly interact with human proteins that, in turn, interact functionally with HIV proteins. Unexpectedly, epitope encoding regions were enriched for sites displaying weak evidence of directional selection influenced by HIV-1. Although the low degree of genetic diversity observed in our M. tuberculosis data set means that these results should be interpreted carefully, the effects of HIV-1 on epitope evolution in M. tuberculosis may have implications for the design of M. tuberculosis vaccines that are intended for use in populations with high HIV-1 infection rates.

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Diversity and disease pathogenesis in Mycobacterium tuberculosis

Cited by 61 publications

References 81 publications

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Multidrug-resistant bacteria compensate for the epistasis between resistances

The Influence of HIV on the Evolution of Mycobacterium tuberculosis

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