Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

Matthew Ezewudo; Amanda Borens; Alvaro Chiner-Oms; Paolo Miotto; Leonid Chindelevitch; Angela M. Starks; Debra Hanna; Richard Liwskil; Matteo Zignol; Christopher Gilpin; Stefan Niemann; Thomas Andreas Kohl; Robin M. Warren; Derrick Crook; Sebastien Gagneux; Sven Hoffner; Camilla Rodrigues; Inaki Comas; David M. Engelthaler; David Alland; Leen Rigouts; Christoph Lange; Keertan Dheda; Rumina Hasan; Ruth McNerney; Daniela M. Cirillo; Marco Schito; Timothy C. Rodwell; James Posey

doi:10.1038/s41598-018-33731-1

Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

Matthew Ezewudo
, Amanda Borens
, Alvaro Chiner-Oms
, Paolo Miotto
, Leonid Chindelevitch
, Angela M. Starks
, Debra Hanna
, Richard Liwskil
, Matteo Zignol
, Christopher Gilpin
, Stefan Niemann
, Thomas Andreas Kohl
, Robin M. Warren
, Derrick Crook
, Sebastien Gagneux
, Sven Hoffner
, Camilla Rodrigues
, Inaki Comas
, David M. Engelthaler
, David Alland

Leen Rigouts, Christoph Lange, Keertan Dheda, Rumina Hasan, Ruth McNerney, Daniela M. Cirillo, Marco Schito, Timothy C. Rodwell, James Posey

Mycobacteriology

Research output: Contribution to journal › A1: Peer-reviewed journal articles › peer-review

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Abstract

Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) (https://github.com/CPTR-ReSeqTB/UVP) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified

Original language	English
Article number	15382
Journal	Scientific Reports
Volume	8
Number of pages	10
ISSN	2045-2322
DOIs	https://doi.org/10.1038/s41598-018-33731-1
Publication status	Published - 2018

Keywords

SINGLE NUCLEOTIDE POLYMORPHISMS
DRUG-RESISTANCE
UNITED-STATES
EPIDEMIOLOGY
FRAMEWORK
TOOLS
PERFORMANCE
DISCOVERY
DATABASE
LINEAGE

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2018srep15382Final published version, 1.23 MBLicence: Unspecified

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Ezewudo, M., Borens, A., Chiner-Oms, A., Miotto, P., Chindelevitch, L., Starks, A. M., Hanna, D., Liwskil, R., Zignol, M., Gilpin, C., Niemann, S., Kohl, T. A., Warren, R. M., Crook, D., Gagneux, S., Hoffner, S., Rodrigues, C., Comas, I., Engelthaler, D. M., ... Posey, J. (2018). Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Scientific Reports, 8, Article 15382. https://doi.org/10.1038/s41598-018-33731-1

@article{68b96fc27e1546ff97fce73c78af798f,

title = "Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase",

abstract = "Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) (https://github.com/CPTR-ReSeqTB/UVP) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9\% agreement with the variants identified",

keywords = "SINGLE NUCLEOTIDE POLYMORPHISMS, DRUG-RESISTANCE, UNITED-STATES, EPIDEMIOLOGY, FRAMEWORK, TOOLS, PERFORMANCE, DISCOVERY, DATABASE, LINEAGE",

author = "Matthew Ezewudo and Amanda Borens and Alvaro Chiner-Oms and Paolo Miotto and Leonid Chindelevitch and Starks, \{Angela M.\} and Debra Hanna and Richard Liwskil and Matteo Zignol and Christopher Gilpin and Stefan Niemann and Kohl, \{Thomas Andreas\} and Warren, \{Robin M.\} and Derrick Crook and Sebastien Gagneux and Sven Hoffner and Camilla Rodrigues and Inaki Comas and Engelthaler, \{David M.\} and David Alland and Leen Rigouts and Christoph Lange and Keertan Dheda and Rumina Hasan and Ruth McNerney and Cirillo, \{Daniela M.\} and Marco Schito and Rodwell, \{Timothy C.\} and James Posey",

note = "FTX; DOAJ",

year = "2018",

doi = "10.1038/s41598-018-33731-1",

language = "English",

volume = "8",

journal = "Scientific Reports",

issn = "2045-2322",

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Ezewudo, M, Borens, A, Chiner-Oms, A, Miotto, P, Chindelevitch, L, Starks, AM, Hanna, D, Liwskil, R, Zignol, M, Gilpin, C, Niemann, S, Kohl, TA, Warren, RM, Crook, D, Gagneux, S, Hoffner, S, Rodrigues, C, Comas, I, Engelthaler, DM, Alland, D, Rigouts, L, Lange, C, Dheda, K, Hasan, R, McNerney, R, Cirillo, DM, Schito, M, Rodwell, TC & Posey, J 2018, 'Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase', Scientific Reports, vol. 8, 15382. https://doi.org/10.1038/s41598-018-33731-1

TY - JOUR

T1 - Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

AU - Ezewudo, Matthew

AU - Borens, Amanda

AU - Chiner-Oms, Alvaro

AU - Miotto, Paolo

AU - Chindelevitch, Leonid

AU - Starks, Angela M.

AU - Hanna, Debra

AU - Liwskil, Richard

AU - Zignol, Matteo

AU - Gilpin, Christopher

AU - Niemann, Stefan

AU - Kohl, Thomas Andreas

AU - Warren, Robin M.

AU - Crook, Derrick

AU - Gagneux, Sebastien

AU - Hoffner, Sven

AU - Rodrigues, Camilla

AU - Comas, Inaki

AU - Engelthaler, David M.

AU - Alland, David

AU - Rigouts, Leen

AU - Lange, Christoph

AU - Dheda, Keertan

AU - Hasan, Rumina

AU - McNerney, Ruth

AU - Cirillo, Daniela M.

AU - Schito, Marco

AU - Rodwell, Timothy C.

AU - Posey, James

N1 - FTX; DOAJ

PY - 2018

Y1 - 2018

N2 - Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) (https://github.com/CPTR-ReSeqTB/UVP) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified

AB - Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) (https://github.com/CPTR-ReSeqTB/UVP) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified

KW - SINGLE NUCLEOTIDE POLYMORPHISMS

KW - DRUG-RESISTANCE

KW - UNITED-STATES

KW - EPIDEMIOLOGY

KW - FRAMEWORK

KW - TOOLS

KW - PERFORMANCE

KW - DISCOVERY

KW - DATABASE

KW - LINEAGE

U2 - 10.1038/s41598-018-33731-1

DO - 10.1038/s41598-018-33731-1

M3 - A1: Peer-reviewed journal articles

SN - 2045-2322

VL - 8

JO - Scientific Reports

JF - Scientific Reports

M1 - 15382

ER -

Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

Abstract

Keywords

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