CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

被引：2257

作者：

Alcock, Brian P. ^{[1
,2
,3
]}

Raphenya, Amogelang R. ^{[1
,2
,3
]}

Lau, Tammy T. Y. ^{[2
,3
,15
]}

Tsang, Kara K. ^{[1
,2
,3
]}

Bouchard, Megane ^{[2
,4
]}

Edalatmand, Arman ^{[2
,3
]}

Huynh, William ^{[2
,3
]}

Nguyen, Anna-Lisa, V ^{[2
,4
]}

Cheng, Annie A. ^{[2
,3
,16
]}

Liu, Sihan ^{[2
,3
,17
]}

Min, Sally Y. ^{[2
,3
]}

Miroshnichenko, Anatoly ^{[2
,3
]}

Tran, Hiu-Ki ^{[2
,3
]}

Werfalli, Rafik E. ^{[2
,3
]}

Nasir, Jalees A. ^{[2
,3
]}

Oloni, Martins ^{[2
,3
]}

Speicher, David J. ^{[2
,3
]}

Florescu, Alexandra ^{[2
,4
,20
]}

Singh, Bhavya ^{[5
,21
]}

Faltyn, Mateusz ^{[2
,6
]}

Hernandez-Koutoucheva, Anastasia ^{[7
,18
]}

Sharma, Arjun N. ^{[2
,3
,19
]}

Bordeleau, Emily ^{[1
,2
,3
]}

Pawlowski, Andrew C. ^{[8
,22
]}

Zubyk, Haley L. ^{[1
,2
,3
]}

Dooley, Damion ^{[9
]}

Griffiths, Emma ^{[10
]}

Maguire, Finlay ^{[11
]}

Winsor, Geoff L. ^{[10
]}

Beiko, Robert G. ^{[11
]}

Brinkman, Fiona S. L. ^{[10
]}

Hsiao, William W. L. ^{[9
,10
,12
]}

Domselaar, Gary, V ^{[13
,14
]}

McArthur, Andrew G. ^{[1
,2
,3
]}

机构：

[1] McMaster Univ, David Braley Ctr Antibiot Discovery, Hamilton, ON L8S 4K1, Canada

[2] McMaster Univ, MG DeGroote Inst Infect Dis Res, Hamilton, ON L8S 4K1, Canada

[3] McMaster Univ, Dept Biochem & Biomed Sci, Hamilton, ON L8S 4K1, Canada

[4] McMaster Univ, Hlth Sci Program, Hamilton, ON L8S 4K1, Canada

[5] McMaster Univ, Honours Biol Program, Hamilton, ON L8S 4K1, Canada

[6] McMaster Univ, Arts & Sci Program, Hamilton, ON L8S 4K1, Canada

[7] Univ Nacl Autonoma Mexico, Ctr Genome Sci, Cuernavaca 62210, Morelos, Mexico

[8] Harvard Med Sch, Harvard Univ, Dept Genet, Boston, MA 02115 USA

[9] Univ British Columbia, Dept Pathol & Lab Med, Vancouver, BC V6T 2B5, Canada

[10] Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC V5A 1S6, Canada

[11] Dalhousie Univ, Fac Comp Sci, Halifax, NS B3H 1W5, Canada

[12] British Columbia Ctr Dis Control, Publ Hlth Lab, Vancouver, BC V5Z 4R4, Canada

[13] Publ Hlth Agcy Canada, Natl Microbiol Lab, Winnipeg, MB R3E 3R2, Canada

[14] Univ Manitoba, Max Rady Coll Med, Dept Med Microbiol & Infect Dis, Winnipeg, MB R3E 0J9, Canada

[15] British Columbia Canc Genome Sci Ctr, Vancouver, BC V5Z 1G1, Canada

[16] McMaster Univ, Stem Cell & Canc Res Inst, Hamilton, ON L8S 4K1, Canada

[17] Shift Hlth, Toronto, ON M5R 3N5, Canada

[18] Univ London, London Sch Hyg & Trop Med, London WC1E 7HT, England

[19] McMaster Univ, MG DeGroote Sch Med, Hamilton, ON L8S 4K1, Canada

[20] Univ Toronto, MD PhD Program, Toronto, ON M5S 1A8, Canada

[21] McMaster Univ, Chem Biol Grad Program, Hamilton, ON L8S 4K1, Canada

[22] Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA

来源：

NUCLEIC ACIDS RESEARCH | 2020年 / 48卷 / D1期

基金：

加拿大自然科学与工程研究理事会; 加拿大健康研究院; 加拿大创新基金会;

关键词：

ANTIMICROBIAL RESISTANCE; READ ALIGNMENT; DISCOVERY;

D O I：

10.1093/nar/gkz935

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD's Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.

引用

页码：D517 / D525

页数：9

共 44 条

[1] ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999
[2] A brief history of the antibiotic era: lessons learned and challenges for the future
Aminov, Rustam I.
[J]. FRONTIERS IN MICROBIOLOGY, 2010, 1
[3] [Anonymous], 2013, ANT RES THREATS US
[4] BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
Barrett, Tanya
Clark, Karen
Gevorgyan, Robert
Gorelenkov, Vyacheslav
Gribov, Eugene
Karsch-Mizrachi, Ilene
Kimelman, Michael
Pruitt, Kim D.
Resenchuk, Sergei
Tatusova, Tatiana
Yaschenko, Eugene
Ostell, James
[J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) : D57 - D63
[5] Alexander Fleming and the discovery of penicillin
Bennett, JW
Chung, KT
[J]. ADVANCES IN APPLIED MICROBIOLOGY, VOL 49, 2001, 49 : 163 - 184
[6] The Protein Data Bank
Berman, HM
Westbrook, J
Feng, Z
Gilliland, G
Bhat, TN
Weissig, H
Shindyalov, IN
Bourne, PE
[J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 235 - 242
[7] Sequencing-based methods and resources to study antimicrobial resistance
Boolchandani, Manish
D'Souza, Alaric W.
Dantas, Gautam
[J]. NATURE REVIEWS GENETICS, 2019, 20 (06) : 356 - 370
[8] Antibacterial drug discovery in the resistance era
Brown, Eric D.
Wright, Gerard D.
[J]. NATURE, 2016, 529 (7586) : 336 - 343
[9] Fast and sensitive protein alignment using DIAMOND
Buchfink, Benjamin
Xie, Chao
Huson, Daniel H.
[J]. NATURE METHODS, 2015, 12 (01) : 59 - 60
[10] BLAST plus : architecture and applications
Camacho, Christiam
Coulouris, George
Avagyan, Vahram
Ma, Ning
Papadopoulos, Jason
Bealer, Kevin
Madden, Thomas L.
[J]. BMC BIOINFORMATICS, 2009, 10

← 1 2 3 4 5 →