At a glance
Whole-genome sequencing (WGS) generates DNA sequence data for the entire M. tuberculosis genome, which can be used for various applications in tuberculosis (TB) prevention and control activities.
Overview
Whole-genome sequencing (WGS) is a significant scientific advancement. Conventional genotyping methods, used prior to 2018, examine less than 1% of the genome. WGS can examine more than 90% of the genome.
CDC began performing retrospective WGS for isolates in select genotype-matched clusters in 2012. In 2018, the National TB Molecular Surveillance Center was established to perform WGS prospectively on all new M. tuberculosis isolates. The National TB Molecular Surveillance Center is part of the Antimicrobial Resistance Network.
CDC uses this WGS data for various types of analyses that serve different purposes:
- Whole-genome multilocus sequence typing (wgMLST)
- Whole-genome single nucleotide polymorphism comparison
- Detection of possible drug resistance
Whole-genome multilocus sequence typing (wgMLST)
wgMLST is a genotyping scheme that uses WGS data.
The wgMLST scheme for TB includes 2,672 different genetic loci, each of which is an individual gene in the genome. Each of these 2,672 loci is analyzed and assigned a number such that isolates that have the same sequence at a locus will have the same number assigned for that locus. Isolates that match at ≥99.7% of the loci will form a genotype cluster, designated with a wgMLSType name.
This new genotyping scheme has replaced GENType and PCRType for defining and alerting TB clusters.
Whole-genome single nucleotide polymorphism (wgSNP) comparison
wgSNP comparison is performed to identify single nucleotide polymorphisms (SNPs) that distinguish isolates in a genotype-matched cluster.
SNPs result from mutations at a single position in the DNA sequence. Because SNPs gradually accumulate over time, the number of SNPs that differ between isolates (SNP distance) can provide information about whether the TB cases could be the result of recent transmission.
The identified SNPs can also be mapped on to a phylogenetic tree to diagram the genetic relationship among isolates and the direction of genetic change. This information can be used to further ascertain the genetic similarity of isolates in a genotype-matched cluster and, when combined with available epidemiologic data, to help identify chains of TB transmission.
Detection of possible drug resistance
CDC evaluates WGS data to detect mutations associated with drug resistance for surveillance purposes.
CDC offers a Clinical Laboratory Improvement Amendments (CLIA)-compliant service, the Molecular Detection of Drug Resistance (MDDR) Service for rapid testing that provides a laboratory report to aid clinical management.
Whole-genome sequencing for investigation of recent TB transmission in the United States training
In 2018, CDC began universal WGS. This means an M. tuberculosis isolate is sequenced for each U.S. case of culture-confirmed TB disease. These videos can help state and local TB programs are use results of WGS and phylogenetic analyses to help guide TB cluster and outbreak investigations. An accompanying slide set is available for download.