Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Abstract

BackgroundTuberculosis (TB) caused an estimated 1.4 million deaths and 10.4 million new cases globally in 2015. TB rates in the United States continue to steadily decline, yet rates in the State of Hawaii are perennially among the highest in the nation due to a continuous influx of immigrants from the Western Pacific and Asia. TB in Hawaii is composed of a unique distribution of genetic lineages, with the Beijing and Manila families of Mycobacterium tuberculosis (Mtb) comprising over two-thirds of TB cases. Standard fingerprinting methods (spoligotyping plus 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats [MIRU-VNTR] fingerprinting) perform poorly when used to identify actual transmission clusters composed of isolates from these two families. Those typing methods typically group isolates from these families into large clusters of non-linked isolates with identical fingerprints. Next-generation whole-genome sequencing (WGS) provides a new tool for molecular epidemiology that can resolve clusters of isolates with identical spoligotyping and MIRU-VNTR fingerprints.MethodsWe performed WGS and SNP analysis and evaluated epidemiological data to investigate 19 apparent TB transmission clusters in Hawaii from 2003 to 2017 in order to assess WGS’ ability to resolve putative Mtb clusters from the Beijing and Manila families. This project additionally investigated MIRU-VNTR allele prevalence to determine why standard Mtb fingerprinting fails to usefully distinguish actual transmission clusters from these two Mtb families.ResultsWGS excluded transmission events in seven of these putative clusters, confirmed transmission in eight, and identified both transmission-linked and non-linked isolates in four. For epidemiologically identified clusters, while the sensitivity of MIRU-VNTR fingerprinting for identifying actual transmission clusters was found to be 100%, its specificity was only 28.6% relative to WGS. We identified that the Beijing and Manila families’ significantly lower Shannon evenness of MIRU-VNTR allele distributions than lineage 4 was the cause of standard fingerprinting’s poor performance when identifying transmission in Beijing and Manila family clusters.ConclusionsThis study demonstrated that WGS is necessary for epidemiological investigation of TB in Hawaii and the Pacific.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3502-1) contains supplementary material, which is available to authorized users.

Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences

“…All variant-calling pipelines compared here have been applied, formed the basis of, or have been proposed for transmission inference (e.g. pipeline A: [28]; B: [29]; C: [30]; D: [18]) and varied in quality control, choice of reference genome, mapper, caller, variant filters and genomic regions excluded (Table S1, available in the online version of this article).…”

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

“…Two schema exist for this approach: 183 the core genome (termed cgMLST; 2891 genes covering 2.86 million bases 31 ) and an extended 184 pan-genome including 1141 accessory loci 11 (termed wgMLST). These WGS-based approaches have been shown to perform better than contact tracing and with higher resolution than classical approaches such as MIRU-VNTR 12,13,30,31,33 . This currently recommended data processing workflow (Fig.…”

“…Currently, two Mtbc-specific pipelines are available, which perform multiple core tasks in single install set-up to produce genetic variant calls from raw Illumina sequence data (MTBseq 34 and 196 UVP-ReSeqTB 35 ). Other pathogen-agnostic pipelines can be used with an Mtbc-specific 197 reference genome and drug resistance database to achieve similar results 33,[36][37][38] . Numerous 198 custom-built pipelines also exist 8,[39][40][41][42][43][44][45][46] , often incorporating similar tools for mapping and variant calling with additional accessory tools and in-house scripts to parse and refine outputs.…”

Pulmonary Tuberculosis Outbreak in a High School, China

“…MIRU-VNTR typing is widely used to determine relatedness and track transmission dynamics of specific isolates of M. tuberculosis [19]. Because MIRU-VNTR analysis examines only a small proportion of M. tuberculosis genome, this method may have limited resolution [20,21]. Molecular epidemiological study in English Midlands showed MIRU-VNTR typing and epidemiological risk factors are poorly predictive of close genomic relatedness when comparing to WGS, and MIRU-VNTR performance varies markedly by lineage of M. tuberculosis [19].…”

“…Molecular epidemiological study in English Midlands showed MIRU-VNTR typing and epidemiological risk factors are poorly predictive of close genomic relatedness when comparing to WGS, and MIRU-VNTR performance varies markedly by lineage of M. tuberculosis [19]. Another study from Hawaii reported 24-loci MIRU-VNTR typing has specificity of 28.6% for identifying actual transmission clusters, and this traditional typing has poor performance especially when identifying transmission in Beijing and Manila family clusters [21]. Contrary to traditional genotyping methods, WGS Provides detailed insights into transmission dynamics [22,23].…”