Featured Organism: Reductive evolution in bacteria: Buchnera sp., Rickettsia prowazekii and Mycobacterium leprae

Wixon, Jo

doi:10.1002/cfg.70

Cited by 36 publications

(29 citation statements)

References 15 publications

(13 reference statements)

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“…Our comparison of “bad bugs” and their respective controls confirmed the findings of previous studies [3]-[9], revealing a significant reduction in the genome size of “bad bugs”. This genome reduction was accompanied by a significant decrease in ORF content, which demonstrates that many genes are progressively disappearing from the genomes of “bad bugs”.…”

Section: Discussionsupporting

confidence: 89%

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Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules

2011

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BackgroundWe conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans (“bad bugs”) to their closest non-epidemic related species (“controls”).Methodology/Principal FindingsWe found several significantly different features in the “bad bugs”, one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG) functional categories revealed a significantly smaller number of genes in the “bad bugs”, which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five “bad bugs” showed a greater number of poly (A) tails compared to the controls, whereas an elevated number of poly (A) tails was found to be strongly correlated to a low GC% content. The “bad bugs” had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA) showed that the “bad bugs” had surprisingly more toxin-antitoxin modules than did the controls.Conclusions/SignificanceWe conclude that pathogenic capacity is not the result of “virulence factors” but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution.

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Section: Discussionsupporting

confidence: 89%

“…In contrast, comparative genomic studies have revealed that in some cases, the genomes of bacteria, such as Rickettsia or Mycobacteria spp. [3]–[5], are reduced [4], [6]–[10]. For example, the genomes of Mycobacterium leprae , Yersinia pestis and Salmonella Typhi contain hundreds of degraded genes.…”

Section: Introductionmentioning

confidence: 99%

Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules

2011

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“…Reductive evolution involves the loss of nonessential bacterial genes in the host environment, including analogous gene products manufactured by the host that can be exploited by the bacterium (37). Consistent with irreversible host adaption in P314, MSHR6686 has cumulatively lost 285 kb at four distinct loci.…”

Section: Resultsmentioning

confidence: 99%

Within-Host Evolution of Burkholderia pseudomallei over a Twelve-Year Chronic Carriage Infection

Price

Sarovich

Mayo

et al. 2013

mBio

102

136

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Burkholderia pseudomallei causes the potentially fatal disease melioidosis. It is generally accepted that B. pseudomallei is a noncommensal bacterium and that any culture-positive clinical specimen denotes disease requiring treatment. Over a 23-year study of melioidosis cases in Darwin, Australia, just one patient from 707 survivors has developed persistent asymptomatic B. pseudomallei carriage. To better understand the mechanisms behind this unique scenario, we performed whole-genome analysis of two strains isolated 139 months apart. During this period, B. pseudomallei underwent several adaptive changes. Of 23 point mutations, 78% were nonsynonymous and 43% were predicted to be deleterious to gene function, demonstrating a strong propensity for positive selection. Notably, a nonsense mutation inactivated the universal stress response sigma factor RpoS, with pleiotropic implications. The genome underwent substantial reduction, with four deletions in chromosome 2 resulting in the loss of 221 genes. The deleted loci included genes involved in secondary metabolism, environmental survival, and pathogenesis. Of 14 indels, 11 occurred in coding regions and 9 resulted in frameshift mutations that dramatically affected predicted gene products. Disproportionately, four indels affected lipopolysaccharide biosynthesis and modification. Finally, we identified a frameshift mutation in both P314 isolates within wcbR, an important component of the capsular polysaccharide I locus, suggesting virulence attenuation early in infection. Our study illustrates a unique clinical case that contrasts a high-consequence infectious agent with a long-term commensal infection and provides further insights into bacterial evolution within the human host.

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“…Evidence suggests that the virulence potential of pathogenic bacteria is inversely proportional to overall genome size and gene content (Georgiades and Raoult, 2011), an observation which has been broadly demonstrated for phylogenetically dissimilar intracellular (Moran, 2002; Wixon, 2001) and extracellular (Georgiades and Raoult, 2011) disease-causing agents. Genome size itself has been shown to be a better predictor of bacterial virulence than the absolute number of classical “virulence factor” genes in comparing pathogenic bacteria compared to non-virulent or less-virulent counterparts (Georgiades and Raoult, 2011; Merhej et al, 2013), likely reflecting the process of gene loss during host adaptation (Merhej et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

Whole genome sequencing indicates Corynebacterium jeikeium comprises 4 separate genomospecies and identifies a dominant genomospecies among clinical isolates

Salipante

SenGupta

Cummings

et al. 2014

International Journal of Medical Microbiology

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Corynebacterium jeikeium is an opportunistic pathogen which has been noted for significant genomic diversity. The population structure within this species remains poorly understood. Here we explore the relationships among fifteen clinical isolates of C. jeikeium (reference strains K411 and ATCC 43734, and 13 primary isolates collected over a period of 7 years) through genetic, genomic, and phenotypic studies. We report a high degree of divergence among strains based on 16S ribosomal RNA (rRNA) gene and rpoB gene sequence analysis, supporting the presence of genetically distinct subgroups. Whole genome sequencing indicates genomic-level dissimilarity among subgroups, which qualify as 4 separate and distinct Corynebacterium species based on an Average Nucleotide Identity (ANIb) threshold of < 95%. Functional distinctions in antibiotic susceptibilities and metabolic profiles characterize two of these genomospecies, allowing their differentiation from others through routine laboratory testing. The remaining genomospecies can be classified through a biphasic approach integrating phenotypic testing and rpoB gene sequencing. The genomospecies predominantly recovered from patient specimens does not include either of the existing C. jeikeium reference strains, implying that studies of this pathogen would benefit from examination of representatives from the primary disease-causing group. The clinically dominant genomospecies also has the smallest genome size and gene repertoire, suggesting the possibility of increased virulence relative to the other genomospecies. The ability to classify isolates to one of the four C. jeikeium genomospecies in a clinical context provides diagnostic information for tailoring antimicrobial therapy and may aid in identification of species-specific disease associations.

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Featured Organism: Reductive evolution in bacteria: Buchnera sp., Rickettsia prowazekii and Mycobacterium leprae

Cited by 36 publications

References 15 publications

Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules

Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules

Within-Host Evolution of Burkholderia pseudomallei over a Twelve-Year Chronic Carriage Infection

Whole genome sequencing indicates Corynebacterium jeikeium comprises 4 separate genomospecies and identifies a dominant genomospecies among clinical isolates

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