Patterns of genomic interrelatedness of publicly available samples in the TB portals database

Kurt R Wollenberg; Brendan M Jeffrey; Michael A Harris; Andrei Gabrielian; Darrell E Hurt; Alex Rosenthal

doi:10.1016/j.tube.2022.102171

Patterns of genomic interrelatedness of publicly available samples in the TB portals database

Tuberculosis (Edinb). 2022 Mar:133:102171. doi: 10.1016/j.tube.2022.102171. Epub 2022 Jan 24.

Authors

Kurt R Wollenberg¹, Brendan M Jeffrey², Michael A Harris³, Andrei Gabrielian⁴, Darrell E Hurt⁵, Alex Rosenthal⁶

Affiliations

¹ Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA. Electronic address: kurt.wollenberg@nih.gov.
² Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA. Electronic address: brendan.jeffrey@nih.gov.
³ Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA. Electronic address: michael.harris2@nih.gov.
⁴ Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA. Electronic address: gabr@niaid.nih.gov.
⁵ Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA. Electronic address: darrellh@niaid.nih.gov.
⁶ Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA. Electronic address: alexr@niaid.nih.gov.

Abstract

The TB Portals program is an international collaboration for the collection and dissemination of tuberculosis data from patient cases focused on drug resistance. The central database is a patient-oriented resource containing both patient and pathogen clinical and genomic information. Herein we provide a summary of the pathogen genomic data available through the TB Portals and show one potential application by examining patterns of genomic pairwise distances. Distributions of pairwise distances highlight overall patterns of genome variability within and between Mycobacterium tuberculosis phylogenomic lineages. Closely related isolates (based on whole-genome pairwise distances and time between sample collection dates) from different countries were identified as potential evidence of international transmission of drug-resistant tuberculosis. These high-level views of genomic relatedness provide information that can stimulate hypotheses for further and more detailed research.

Keywords: Extensively-drug resistant; Multi-drug resistant; Mycobacterium tuberculosis.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Antitubercular Agents / therapeutic use
Databases, Factual
Drug Resistance, Multiple, Bacterial / genetics
Genomics
Humans
Microbial Sensitivity Tests
Mycobacterium tuberculosis* / genetics
Tuberculosis* / diagnosis
Tuberculosis* / drug therapy
Tuberculosis, Multidrug-Resistant* / diagnosis
Tuberculosis, Multidrug-Resistant* / drug therapy
Tuberculosis, Multidrug-Resistant* / genetics

Substances

Antitubercular Agents

Grants and funding

Z99 AI999999/ImNIH/Intramural NIH HHS/United States