ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

被引：474

作者：

Hunt, Martin ^{[1
]}

Mather, Alison E. ^{[1
,2
]}

Sanchez-Buso, Leonor ^{[1
]}

Page, Andrew J. ^{[1
]}

Parkhill, Julian ^{[1
]}

Keane, Jacqueline A. ^{[1
]}

Harris, Simon R. ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Infect Genom, Wellcome Genome Campus, Hinxton CB10 1SA, England

[2] Univ Cambridge, Dept Vet Med, Madingley Rd, Cambridge CB3 0ES, England

来源：

MICROBIAL GENOMICS | 2017年 / 3卷 / 10期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

antimicrobial resistance; whole genome sequencing; genotyping; bacteria; sequence typing; NEISSERIA-GONORRHOEAE; VANCOMYCIN RESISTANCE; GENOMIC EPIDEMIOLOGY; IDENTIFICATION; ALIGNMENT; MUTATION; DATABASE; PLASMID; CANADA; GENES;

D O I：

10.1099/mgen.0.000131

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customizable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods.

引用

页数：11

共 44 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2] Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis [J].

Bradley, Phelim ;

Gordon, N. Claire ;

Walker, Timothy M. ;

Dunn, Laura ;

Heys, Simon ;

Huang, Bill ;

Earle, Sarah ;

Pankhurst, Louise J. ;

Anson, Luke ;

de Cesare, Mariateresa ;

Piazza, Paolo ;

Votintseva, Antonina A. ;

Golubchik, Tanya ;

Wilson, Daniel J. ;

Wyllie, David H. ;

Diel, Roland ;

Niemann, Stefan ;

Feuerriegel, Silke ;

Kohl, Thomas A. ;

Ismail, Nazir ;

Omar, Shaheed V. ;

Smith, E. Grace ;

Buck, David ;

McVean, Gil ;

Walker, A. Sarah ;

Peto, Tim E. A. ;

Crook, Derrick W. ;

Iqbal, Zamin .

NATURE COMMUNICATIONS, 2015, 6

[3] In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing [J].

Carattoli, Alessandra ;

Zankari, Ea ;

Garcia-Fernandez, Aurora ;

Larsen, Mette Voldby ;

Lund, Ole ;

Villa, Laura ;

Aarestrup, Frank Moller ;

Hasman, Henrik .

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2014, 58 (07) :3895-3903

[4] VFDB: a reference database for bacterial virulence factors [J].

Chen, LH ;

Yang, J ;

Yu, J ;

Ya, ZJ ;

Sun, LL ;

Shen, Y ;

Jin, Q .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D325-D328

[5] An outbreak of high-level azithromycin resistant Neisseria gonorrhoeae in England [J].

Chisholm, Stephanie A. ;

Wilson, Janet ;

Alexander, Sarah ;

Tripodo, Francesco ;

Al-Shahib, Ali ;

Schaefer, Ulf ;

Lythgow, Kieren ;

Fifer, Helen .

SEXUALLY TRANSMITTED INFECTIONS, 2016, 92 (05) :365-367

[6] High-Level Azithromycin Resistance Occurs in Neisseria gonorrhoeae as a Result of a Single Point Mutation in the 23S rRNA Genes [J].

Chisholm, Stephanie A. ;

Dave, Jayshree ;

Ison, Catherine A. .

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2010, 54 (09) :3812-3816

[7] Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data [J].

Clausen, Philip T. L. C. ;

Zankari, Ea ;

Aarestrup, Frank M. ;

Lund, Ole .

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 2016, 71 (09) :2484-2488

[8] CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community [J].

Connor, Thomas R. ;

Loman, Nicholas J. ;

Thompson, Simon ;

Smith, Andy ;

Southgate, Joel ;

Poplawski, Radoslaw ;

Bull, Matthew J. ;

Richardson, Emily ;

Ismail, Matthew ;

Elwood-Thompson, Simon ;

Kitchen, Christine ;

Guest, Martyn ;

Bakke, Marius ;

Sheppard, Samuel K. ;

Pallen, Mark J. .

MICROBIAL GENOMICS, 2016, 2 (09) :e000086

[9] Vancomycin resistance in gram-positive cocci [J].

Courvalin, P .

CLINICAL INFECTIOUS DISEASES, 2006, 42 :S25-S34

[10] Antimicrobial Resistance Prediction in PATRIC and RAST [J].

Davis, James J. ;

Boisvert, Sebastien ;

Brettin, Thomas ;

Kenyon, Ronald W. ;

Mao, Chunhong ;

Olson, Robert ;

Overbeek, Ross ;

Santerre, John ;

Shukla, Maulik ;

Wattam, Alice R. ;

Will, Rebecca ;

Xia, Fangfang ;

Stevens, Rick .

SCIENTIFIC REPORTS, 2016, 6

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