Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

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Summary

Background

Tuberculosis incidence in the UK has risen in the past decade. Disease control depends on epidemiological data, which can be difficult to obtain. Whole-genome sequencing can detect microevolution within Mycobacterium tuberculosis strains. We aimed to estimate the genetic diversity of related M tuberculosis strains in the UK Midlands and to investigate how this measurement might be used to investigate community outbreaks.

Methods

In a retrospective observational study, we used Illumina technology to sequence M tuberculosis genomes from an archive of frozen cultures. We characterised isolates into four groups: cross-sectional, longitudinal, household, and community. We measured pairwise nucleotide differences within hosts and between hosts in household outbreaks and estimated the rate of change in DNA sequences. We used the findings to interpret network diagrams constructed from 11 community clusters derived from mycobacterial interspersed repetitive-unit–variable-number tandem-repeat data.

Findings

We sequenced 390 separate isolates from 254 patients, including representatives from all five major lineages of M tuberculosis. The estimated rate of change in DNA sequences was 0·5 single nucleotide polymorphisms (SNPs) per genome per year (95% CI 0·3–0·7) in longitudinal isolates from 30 individuals and 25 families. Divergence is rarely higher than five SNPs in 3 years. 109 (96%) of 114 paired isolates from individuals and households differed by five or fewer SNPs. More than five SNPs separated isolates from none of 69 epidemiologically linked patients, two (15%) of 13 possibly linked patients, and 13 (17%) of 75 epidemiologically unlinked patients (three-way comparison exact p<0·0001). Genetic trees and clinical and epidemiological data suggest that super-spreaders were present in two community clusters.

Interpretation

Whole-genome sequencing can delineate outbreaks of tuberculosis and allows inference about direction of transmission between cases. The technique could identify super-spreaders and predict the existence of undiagnosed cases, potentially leading to early treatment of infectious patients and their contacts.

Funding

Medical Research Council, Wellcome Trust, National Institute for Health Research, and the Health Protection Agency.

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Most cited references 26

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Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.

Gerton Lunter, Martin Goodson (2011)

High-volume sequencing of DNA and RNA is now within reach of any research laboratory and is quickly becoming established as a key research tool. In many workflows, each of the short sequences ("reads") resulting from a sequencing run are first "mapped" (aligned) to a reference sequence to infer the read from which the genomic location derived, a challenging task because of the high data volumes and often large genomes. Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in both. In addition, performance often deteriorates in the presence of sequence variation, particularly so for short insertions and deletions (indels). Here, we present a read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. This results in a higher useable sequence yield and improved accuracy compared to that of existing software.

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Transforming clinical microbiology with bacterial genome sequencing.

Xavier Didelot, Rory Bowden, Daniel J Wilson … (2012)

Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.

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Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis.

D. Van Soolingen, P. Hermans, P. E. W. de Haas … (1991)

In this study we established the usefulness of DNA fingerprinting for the epidemiology of tuberculosis on the basis of the DNA polymorphism generated by the insertion sequence (IS) IS986. Although clinical isolates of Mycobacterium tuberculosis displayed a remarkably high degree of restriction fragment length polymorphism, we showed that transposition of this IS element is an extremely rare event in M. tuberculosis complex strains grown either in vitro or in vivo for long periods of time. The M. tuberculosis and Mycobacterium africanum strains tested in this study contained 6 to 17 IS copies. In the Mycobacterium bovis strains, the copy numbers ranged between 1 and 5, and all 27 M. bovis BCG strains investigated invariably contained a single IS copy. This copy was located at a unique chromosomal position, reinforcing the idea that the frequency of IS transposition is very low in M. tuberculosis complex strains. Various microepidemics are described in which each microepidemic corresponds to a particular fingerprint type. The extent of similarity between Dutch and African strains was quantitatively assessed by computer-assisted analysis of DNA fingerprints. The results indicate that M. tuberculosis strains from regions in central Africa, where tuberculosis is highly prevalent, are generally more related to each other than isolates from the Netherlands, where the transmission rate is low and where the majority of the tuberculosis cases are presumed to be the result of reactivation of previously contracted M. tuberculosis infections.

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Author and article information

Journal

Journal ID (nlm-ta): Lancet Infect Dis

Journal ID (iso-abbrev): Lancet Infect Dis

Title: The Lancet Infectious Diseases

Publisher: Elsevier Science, The Lancet Pub. Group

ISSN (Print): 1473-3099

ISSN (Electronic): 1474-4457

Publication date PMC-release: February 2013

Publication date (Print): February 2013

Volume: 13

Issue: 2

Pages: 137-146

Affiliations

[a ]Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK

[b ]Department of Statistics, University of Oxford, Oxford, UK

[c ]West Midlands Public Health Laboratory, Health Protection Agency, Heart of England NHS Foundation Trust, Birmingham, UK

[d ]Heartlands Hospital and Birmingham Chest Clinic, Heart of England NHS Foundation Trust, Birmingham, UK

[e ]Oxford National Institute of Health Research Biomedical Research Centre, John Radcliffe Hospital, Headington, Oxford, UK

[f ]School of Immunity and Infection, University of Birmingham, Birmingham, UK

[g ]Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK

[h ]Health Protection Agency, County Hall, Glenfield, Leicester, UK

Author notes

[* ]Correspondence to: Dr Timothy M Walker, Nuffield Department of Medicine, John Radcliffe Hospital, Headley Way, Headington, Oxford OX3 9DU, UK timothy.walker@ 123456ndm.ox.ac.uk

[*]

These authors contributed equally

[†]

These authors also contributed equally

Article

Publisher ID: LANINF70277

DOI: 10.1016/S1473-3099(12)70277-3

PMC ID: 3556524

PubMed ID: 23158499

SO-VID: 2c55d3d3-14c0-4e54-8786-701d1873502b

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Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

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Summary

Background

Methods

Findings

Interpretation

Funding

Related collections

Point-Of-Care Testing for Tuberculosis

Most cited references 26

Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.

Transforming clinical microbiology with bacterial genome sequencing.

Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis.

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Cited by 428

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