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

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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 languageEnglish
Article number15382
JournalScientific Reports
Volume8
Number of pages10
ISSN2045-2322
DOIs
Publication statusPublished - 2018

Keywords

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

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