MLSTar: automatic multilocus sequence typing of bacterial genomes in R

被引:14
作者
Ferres, Ignacio [1 ]
Iraola, Gregorio [1 ,2 ]
机构
[1] Inst Pasteur Montevideo, Bioinformat Unit, Montevideo, Uruguay
[2] Univ Mayor, Ctr Integrat Biol, Santiago, Chile
关键词
MLST; PubMLST; R package; Microbial genomics; Multilocus genotyping; Bacterial genomes;
D O I
10.7717/peerj.5098
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes. The PubMLST database is the most comprehensive resource of described schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows us to (i) connect with the PubMLST database to select a target scheme, (ii) screen a desired set of genomes to assign alleles and sequence types, and (iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze more than 2,500 bacterial genomes from different species, showing great accuracy, and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.
引用
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页数:10
相关论文
共 22 条
[1]   A genomic overview of the population structure of Salmonella [J].
Alikhan, Nabil-Fareed ;
Zhou, Zhemin ;
Sergeant, Martin J. ;
Achtman, Mark .
PLOS GENETICS, 2018, 14 (04)
[2]   Elucidating global epidemiology of Burkholderia multivorans in cases of cystic fibrosis by multilocus sequence typing [J].
Baldwin, Adam ;
Mahenthiralingam, Eshwar ;
Drevinek, Pavel ;
Pope, Chris ;
Waine, David J. ;
Henry, Deborah A. ;
Speert, David P. ;
Carter, Phil ;
Vandamme, Peter ;
LiPuma, John J. ;
Dowson, Chris G. .
JOURNAL OF CLINICAL MICROBIOLOGY, 2008, 46 (01) :290-295
[3]   BLAST plus : architecture and applications [J].
Camacho, Christiam ;
Coulouris, George ;
Avagyan, Vahram ;
Ma, Ning ;
Papadopoulos, Jason ;
Bealer, Kevin ;
Madden, Thomas L. .
BMC BIOINFORMATICS, 2009, 10
[4]   Early Dissemination of NDM-1-and OXA-181-Producing Enterobacteriaceae in Indian Hospitals: Report from the SENTRY Antimicrobial Surveillance Program, 2006-2007 [J].
Castanheira, Mariana ;
Deshpande, Lalitagauri M. ;
Mathai, Dilip ;
Bell, Jan M. ;
Jones, Ronald N. ;
Mendes, Rodrigo E. .
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2011, 55 (03) :1274-1278
[5]   Development of an extended multilocus sequence typing for genotyping of Brucella isolates [J].
Chen, Yanfen ;
Zhen, Qing ;
Wang, Yufei ;
Xu, Jie ;
Sun, Yingjie ;
Li, Tiefeng ;
Gao, Lina ;
Guo, Fei ;
Wang, Dali ;
Yuan, Xitong ;
Yuan, Jing ;
Huang, Liuyu ;
Chen, Zeliang ;
Yu, Yaqin .
JOURNAL OF MICROBIOLOGICAL METHODS, 2011, 86 (02) :252-254
[6]   An extended multi-locus molecular typing schema for Streptococcus pneumoniae demonstrates that a limited number of capsular switch events is responsible for serotype heterogeneity of closely related strains from different countries [J].
Crisafulli, Giovanni ;
Guidotti, Silvia ;
Muzzi, Alessandro ;
Torricelli, Giulia ;
Moschioni, Monica ;
Masignani, Vega ;
Censini, Stefano ;
Donati, Claudio .
INFECTION GENETICS AND EVOLUTION, 2013, 13 :151-161
[7]  
Csardi G, 2006, InterJournal Complex Syst., V1695, P1
[8]   Extended sequence typing of Campylobacter spp, united kingdom [J].
Dingle, Kate E. ;
McCarthy, Noel D. ;
Cody, Alison J. ;
Peto, Tim E. A. ;
Maiden, Martin C. J. .
EMERGING INFECTIOUS DISEASES, 2008, 14 (10) :1620-1622
[9]   Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota [J].
Iraola, Gregorio ;
Forster, Samuel C. ;
Kumar, Nitin ;
Lehours, Philippe ;
Bekal, Sadjia ;
Garcia-Pena, Francisco J. ;
Paolicchi, Fernando ;
Morsella, Claudia ;
Hotzel, Helmut ;
Hsueh, Po-Ren ;
Vidal, Ana ;
Levesque, Simon ;
Yamazaki, Wataru ;
Balzan, Claudia ;
Vargas, Agueda ;
Piccirillo, Alessandra ;
Chaban, Bonnie ;
Hill, Janet E. ;
Betancor, Laura ;
Collado, Luis ;
Truyers, Isabelle ;
Midwinter, Anne C. ;
Dagi, Hatice T. ;
Megraud, Francis ;
Calleros, Lucia ;
Perez, Ruben ;
Naya, Hugo ;
Lawley, Trevor D. .
NATURE COMMUNICATIONS, 2017, 8
[10]   Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain [J].
Jolley, Keith A. ;
Bliss, Carly M. ;
Bennett, Julia S. ;
Bratcher, Holly B. ;
Brehony, Carina ;
Colles, Frances M. ;
Wimalarathna, Helen ;
Harrison, Odile B. ;
Sheppard, Samuel K. ;
Cody, Alison J. ;
Maiden, Martin C. J. .
MICROBIOLOGY-SGM, 2012, 158 :1005-1015