Measurably evolving pathogens in the genomic era

被引：183

作者：

Biek, Roman ^{[1
,2
]}

Pybus, Oliver G. ^{[3
]}

Lloyd-Smith, James O. ^{[2
,4
]}

Didelot, Xavier ^{[5
]}

机构：

[1] Univ Glasgow, Boyd Orr Ctr Populat & Ecosyst Hlth, Inst Biodivers Anim Hlth & Comparat Med, Coll Med Vet & Life Sci, Glasgow, Lanark, Scotland

[2] NIH, Fogarty Int Ctr, Bethesda, MD 20892 USA

[3] Univ Oxford, Dept Zool, Oxford, England

[4] Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA

[5] Univ London Imperial Coll Sci Technol & Med, Dept Infect Dis Epidemiol, London, England

来源：

TRENDS IN ECOLOGY & EVOLUTION | 2015年 / 30卷 / 06期

基金：

美国国家卫生研究院; 欧洲研究理事会; 英国生物技术与生命科学研究理事会; 美国国家科学基金会;

关键词：

bacteria; DNA virus; epidemiological models; evolutionary rate; infectious disease; phylodynamics; MYCOBACTERIUM-TUBERCULOSIS; POPULATION GENOMICS; TRANSMISSION TREES; EVOLUTIONARY RATES; ESCHERICHIA-COLI; MOLECULAR CLOCKS; GLOBAL SPREAD; RECOMBINATION; INFERENCE; DYNAMICS;

D O I：

10.1016/j.tree.2015.03.009

中图分类号：

Q14 [生态学（生物生态学）];

学科分类号：

071012 ; 0713 ;

摘要：

Current sequencing technologies have created unprecedented opportunities for studying microbial populations. For pathogens with comparatively low per-site mutation rates, such as DNA viruses and bacteria, whole-genome sequencing can reveal the accumulation of novel genetic variation between population samples taken at different times. The concept of 'measurably evolving populations' and related analytical approaches have provided powerful insights for fast-evolving RNA viruses, but their application to other pathogens is still in its infancy. We argue that previous distinctions between slow- and fast-evolving pathogens become blurred once evolution is assessed at a genome-wide scale, and we highlight important analytical challenges to be overcome to infer pathogen population dynamics from genomic data.

引用

页码：306 / 313

页数：8

共 83 条

[1] Mugsy: fast multiple alignment of closely related whole genomes [J].

Angiuoli, Samuel V. ;

Salzberg, Steven L. .

BIOINFORMATICS, 2011, 27 (03) :334-342

[2] Inference of the Properties of the Recombination Process from Whole Bacterial Genomes [J].

Ansari, M. Azim ;

Didelot, Xavier .

GENETICS, 2014, 196 (01) :253-+

[3] Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations [J].

Biek, Roman ;

O'Hare, Anthony ;

Wright, David ;

Mallon, Tom ;

McCormick, Carl ;

Orton, Richard J. ;

McDowell, Stanley ;

Trewby, Hannah ;

Skuce, Robin A. ;

Kao, Rowland R. .

PLOS PATHOGENS, 2012, 8 (11)

[4] Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis [J].

Bos, Kirsten I. ;

Harkins, Kelly M. ;

Herbig, Alexander ;

Coscolla, Mireia ;

Weber, Nico ;

Comas, Inaki ;

Forrest, Stephen A. ;

Bryant, Josephine M. ;

Harris, Simon R. ;

Schuenemann, Verena J. ;

Campbell, Tessa J. ;

Majander, Kerttu ;

Wilbur, Alicia K. ;

Guichon, Ricardo A. ;

Steadman, Dawnie L. Wolfe ;

Cook, Della Collins ;

Niemann, Stefan ;

Behr, Marcel A. ;

Zumarraga, Martin ;

Bastida, Ricardo ;

Huson, Daniel ;

Nieselt, Kay ;

Young, Douglas ;

Parkhill, Julian ;

Buikstra, Jane E. ;

Gagneux, Sebastien ;

Stone, Anne C. ;

Krause, Johannes .

NATURE, 2014, 514 (7523) :494-+

[5]

Bourque G, 2002, GENOME RES, V12, P26

[6] Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study [J].

Bryant, Josephine M. ;

Harris, Simon R. ;

Parkhill, Julian ;

Dawson, Rodney ;

Diacon, Andreas H. ;

van Helden, Paul ;

Pym, Alex ;

Mahayiddin, Aziah A. ;

Chuchottaworn, Charoen ;

Sanne, Ian M. ;

Louw, Cheryl ;

Boeree, Martin J. ;

Hoelscher, Michael ;

McHugh, Timothy D. ;

Bateson, Anna L. C. ;

Hunt, Robert D. ;

Mwaigwisya, Solomon ;

Wright, Laura ;

Gillespie, Stephen H. ;

Bentley, Stephen D. .

LANCET RESPIRATORY MEDICINE, 2013, 1 (10) :786-792

[7] High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection [J].

Chattopadhyay, Sujay ;

Weissman, Scott J. ;

Minin, Vladimir N. ;

Russo, Thomas A. ;

Dykhuizen, Daniel E. ;

Sokurenko, Evgeni V. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (30) :12412-12417

[8] Dense genomic sampling identifies highways of pneumococcal recombination [J].

Chewapreecha, Claire ;

Harris, Simon R. ;

Croucher, Nicholas J. ;

Turner, Claudia ;

Marttinen, Pekka ;

Cheng, Lu ;

Pessia, Alberto ;

Aanensen, David M. ;

Mather, Alison E. ;

Page, Andrew J. ;

Salter, Susannah J. ;

Harris, David ;

Nosten, Francois ;

Goldblatt, David ;

Corander, Jukka ;

Parkhill, Julian ;

Turner, Paul ;

Bentley, Stephen D. .

NATURE GENETICS, 2014, 46 (03) :305-+

[9] Whole Genome Sequencing of Mycobacterium tuberculosis Reveals Slow Growth and Low Mutation Rates during Latent Infections in Humans [J].

Colangeli, Roberto ;

Arcus, Vic L. ;

Cursons, Ray T. ;

Ruthe, Ali ;

Karalus, Noel ;

Coley, Kathy ;

Manning, Shannon D. ;

Kim, Soyeon ;

Marchiano, Emily ;

Alland, David .

PLOS ONE, 2014, 9 (03)

[10] Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans [J].

Comas, Inaki ;

Coscolla, Mireia ;

Luo, Tao ;

Borrell, Sonia ;

Holt, Kathryn E. ;

Kato-Maeda, Midori ;

Parkhill, Julian ;

Malla, Bijaya ;

Berg, Stefan ;

Thwaites, Guy ;

Yeboah-Manu, Dorothy ;

Bothamley, Graham ;

Mei, Jian ;

Wei, Lanhai ;

Bentley, Stephen ;

Harris, Simon R. ;

Niemann, Stefan ;

Diel, Roland ;

Aseffa, Abraham ;

Gao, Qian ;

Young, Douglas ;

Gagneux, Sebastien .

NATURE GENETICS, 2013, 45 (10) :1176-U311

← 1 2 3 4 5 6 7 8 9 →