Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

被引:423
作者
Jolley, Keith A. [1 ]
Bliss, Carly M. [1 ]
Bennett, Julia S. [1 ]
Bratcher, Holly B. [1 ]
Brehony, Carina [1 ]
Colles, Frances M. [1 ]
Wimalarathna, Helen [1 ]
Harrison, Odile B. [1 ]
Sheppard, Samuel K. [1 ]
Cody, Alison J. [1 ]
Maiden, Martin C. J. [1 ]
机构
[1] Univ Oxford, Dept Zool, Oxford OX1 3PS, England
来源
MICROBIOLOGY-SGM | 2012年 / 158卷
基金
英国生物技术与生命科学研究理事会; 英国惠康基金; 英国医学研究理事会;
关键词
POPULATION-STRUCTURE; MOLECULAR EPIDEMIOLOGY; PHYLOGENY; EVOLUTION; GENOMES; TREE; IDENTIFICATION; RECOMBINATION; MICROBIOLOGY; ALIGNMENT;
D O I
10.1099/mic.0.055459-0
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
No single genealogical reconstruction or typing method currently encompasses all levels of bacterial diversity, from domain to strain. We propose ribosomal multilocus sequence typing (rMLST), an approach which indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes), as a means of integrating microbial genealogy and typing. As with multilocus sequence typing (MLST), rMLST employs curated reference sequences to identify gene variants efficiently and rapidly. The rps loci are ideal targets for a universal characterization scheme as they are: (i) present in all bacteria; (ii) distributed around the chromosome; and (iii) encode proteins which are under stabilizing selection for functional conservation. Collectively, the rps loci exhibit variation that resolves bacteria into groups at all taxonomic and most typing levels, providing significantly more resolution than 16S small subunit rRNA gene phylogenies. A web-accessible expandable database, comprising whole-genome data from more than 1900 bacterial isolates, including 28 draft genomes assembled de novo from the European Bioinformatics Institute (EBI) sequence read archive, has been assembled. The rps gene variation catalogued in this database permits rapid and computationally non-intensive identification of the phylogenetic position of any bacterial sequence at the domain, phylum, class, order, family, genus, species and strain levels. The groupings generated with rMLST data are consistent with current nomenclature schemes and independent of the clustering algorithm used. This approach is applicable to the other domains of life, potentially providing a rational and universal approach to the classification of life that is based on one of its fundamental features, the translation mechanism.
引用
收藏
页码:1005 / 1015
页数:11
相关论文
共 62 条
[11]   Rapid Pneumococcal Evolution in Response to Clinical Interventions [J].
Croucher, Nicholas J. ;
Harris, Simon R. ;
Fraser, Christophe ;
Quail, Michael A. ;
Burton, John ;
van der Linden, Mark ;
McGee, Lesley ;
von Gottberg, Anne ;
Song, Jae Hoon ;
Ko, Kwan Soo ;
Pichon, Bruno ;
Baker, Stephen ;
Parry, Christopher M. ;
Lambertsen, Lotte M. ;
Shahinas, Dea ;
Pillai, Dylan R. ;
Mitchell, Timothy J. ;
Dougan, Gordon ;
Tomasz, Alexander ;
Klugman, Keith P. ;
Parkhill, Julian ;
Hanage, William P. ;
Bentley, Stephen D. .
SCIENCE, 2011, 331 (6016) :430-434
[12]   progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement [J].
Darling, Aaron E. ;
Mau, Bob ;
Perna, Nicole T. .
PLOS ONE, 2010, 5 (06)
[13]   An ecological and evolutionary perspective on human-microbe mutualism and disease [J].
Dethlefsen, Les ;
McFall-Ngai, Margaret ;
Relman, David A. .
NATURE, 2007, 449 (7164) :811-818
[14]   Inference of bacterial microevolution using multilocus sequence data [J].
Didelot, Xavier ;
Falush, Daniel .
GENETICS, 2007, 175 (03) :1251-1266
[15]   Population structure of Streptococcus oralis [J].
Do, Thuy ;
Jolley, Keith A. ;
Maiden, Martin C. J. ;
Gilbert, Steven C. ;
Clark, Douglas ;
Wade, William G. ;
Beighton, David .
MICROBIOLOGY-SGM, 2009, 155 :2593-2602
[16]   On the origin of prokaryotic species [J].
Doolittle, W. Ford ;
Zhaxybayeva, Olga .
GENOME RESEARCH, 2009, 19 (05) :744-756
[17]   MUSCLE: multiple sequence alignment with high accuracy and high throughput [J].
Edgar, RC .
NUCLEIC ACIDS RESEARCH, 2004, 32 (05) :1792-1797
[18]   Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences [J].
Feil, EJ ;
Holmes, EC ;
Bessen, DE ;
Chan, MS ;
Day, NPJ ;
Enright, MC ;
Goldstein, R ;
Hood, DW ;
Kalla, A ;
Moore, CE ;
Zhou, JJ ;
Spratt, BG .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (01) :182-187
[19]   The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity [J].
Fraser, Christophe ;
Alm, Eric J. ;
Polz, Martin F. ;
Spratt, Brian G. ;
Hanage, William P. .
SCIENCE, 2009, 323 (5915) :741-746
[20]  
Fujita, 1998, Genome Inform Ser Workshop Genome Inform, V9, P3