Insights from genomic comparisons of genetically monomorphic bacterial pathogens

Achtman, Mark

doi:10.1098/rstb.2011.0303

Cited by 116 publications

(92 citation statements)

References 74 publications

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“…The final set of 149 genomes, including the completed genomes of ATCC 9150 (20) and AKU 12601 (21), yielded a 4,073,403-bp core genome after removing repetitive DNA (henceforth core genome). Mapping of all polymorphic sites within the core genome to ATCC 9150 identified only 4,584 SNPs (Table 1), which is comparable to the diversity found in Y. pestis (3), serovar Typhi (25), and other genetically monomorphic bacterial pathogens (26). These SNPs yielded a single (unambiguous) maximum parsimony tree, except for several polytomies and a few homoplasies (repeated, independent, convergent mutations) (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 66%

Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever

Zhou

McCann

Weill

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Multiple epidemic diseases have been designated as emerging or reemerging because the numbers of clinical cases have increased. Emerging diseases are often suspected to be driven by increased virulence or fitness, possibly associated with the gain of novel genes or mutations. However, the time period over which humans have been afflicted by such diseases is only known for very few bacterial pathogens, and the evidence for recently increased virulence or fitness is scanty. Has Darwinian (diversifying) selection at the genomic level recently driven microevolution within bacterial pathogens of humans? Salmonella enterica serovar Paratyphi A is a major cause of enteric fever, with a microbiological history dating to 1898. We identified seven modern lineages among 149 genomes on the basis of 4,584 SNPs in the core genome and estimated that Paratyphi A originated 450 y ago. During that time period, the effective population size has undergone expansion, reduction, and recent expansion. Mutations, some of which inactivate genes, have occurred continuously over the history of Paratyphi A, as has the gain or loss of accessory genes. We also identified 273 mutations that were under Darwinian selection. However, most genetic changes are transient, continuously being removed by purifying selection, and the genome of Paratyphi A has not changed dramatically over centuries. We conclude that Darwinian selection is not responsible for increased frequency of enteric fever and suggest that environmental changes may be more important for the frequency of disease. pathogen evolution | historical reconstruction | phylogeography

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Section: Resultsmentioning

confidence: 66%

Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever

Zhou

McCann

Weill

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

120

127

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“…The results of these efforts have been discussed elsewhere and are beyond the scope of this minireview (2,3,5,21,22,39,43,49,58,60,62,114,145,146). Instead, we will focus on aspects that are of immediate relevance to the development of novel antibiotics and diagnostic tests to detect drug resistance.…”

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confidence: 99%

Importance of the Genetic Diversity within the Mycobacterium tuberculosis Complex for the Development of Novel Antibiotics and Diagnostic Tests of Drug Resistance

Köser

Feuerriegel

Summers

et al. 2012

Antimicrob Agents Chemother

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e Despite being genetically monomorphic, the limited genetic diversity within the Mycobacterium tuberculosis complex (MTBC) has practical consequences for molecular methods for drug susceptibility testing and for the use of current antibiotics and those in clinical trials. It renders some representatives of MTBC intrinsically resistant against one or multiple antibiotics and affects the spectrum and consequences of resistance mutations selected for during treatment. Moreover, neutral or silent changes within genes responsible for drug resistance can cause false-positive results with hybridization-based assays, which have been recently introduced to replace slower phenotypic methods. We discuss the consequences of these findings and propose concrete steps to rigorously assess the genetic diversity of MTBC to support ongoing clinical trials.

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“…Several bacterial lineages have previously been identified as monomorphic pathogens: Mycobacterium leprae, Burkholderia mallei, Bordetella pertussis, Yersinia pestis, Salmonella enterica serovar Typhi, Bacillus anthracis, and Mycobacterium tuberculosis (47). SNPs within the core genomes of each lineage were identified and ranged from 7 to 226 SNPs per 100 kb (47)(48)(49)(50)(51)(52)(53)(54). In comparison, across nine full genomes of B. animalis subsp.…”

Section: Discussionmentioning

confidence: 99%

Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

Loquasto

Barrangou

Dudley

et al. 2013

Appl Environ Microbiol

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cMany strains of Bifidobacterium animalis subsp. lactis are considered health-promoting probiotic microorganisms and are commonly formulated into fermented dairy foods. Analyses of previously sequenced genomes of B. animalis subsp. lactis have revealed little genetic diversity, suggesting that it is a monomorphic subspecies. However, during a multilocus sequence typing survey of Bifidobacterium, it was revealed that B. animalis subsp. lactis ATCC 27673 gave a profile distinct from that of the other strains of the subspecies. As part of an ongoing study designed to understand the genetic diversity of this subspecies, the genome of this strain was sequenced and compared to other sequenced genomes of B. animalis subsp. lactis and B. animalis subsp. animalis. The complete genome of ATCC 27673 was 1,963,012 bp, contained 1,616 genes and 4 rRNA operons, and had a G؉C content of 61.55%. Comparative analyses revealed that the genome of ATCC 27673 contained six distinct genomic islands encoding 83 open reading frames not found in other strains of the same subspecies. In four islands, either phage or mobile genetic elements were identified. In island 6, a novel clustered regularly interspaced short palindromic repeat (CRISPR) locus which contained 81 unique spacers was identified. This type I-E CRISPR-cas system differs from the type I-C systems previously identified in this subspecies, representing the first identification of a different system in B. animalis subsp. lactis. This study revealed that ATCC 27673 is a strain of B. animalis subsp. lactis with novel genetic content and suggests that the lack of genetic variability observed is likely due to the repeated sequencing of a limited number of widely distributed commercial strains.

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Insights from genomic comparisons of genetically monomorphic bacterial pathogens

Cited by 116 publications

References 74 publications

Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever

Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever

Importance of the Genetic Diversity within the Mycobacterium tuberculosis Complex for the Development of Novel Antibiotics and Diagnostic Tests of Drug Resistance

Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

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