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 AllandLeen 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: Web of Science-article › 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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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",

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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: Web of Science-article

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

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Keywords

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