The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study
Open accessAbstract
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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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Tiemersma, E. W., van der Werf, M. J., Borgdorff, M. W., Williams, B. G., & Nagelkerke, N. J. D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017601 · Cited by 583
Ford, C. B., Lin, P. L., Chase, M. R., Shah, R. R., Iartchouk, O., Galagan, J., Mohaideen, N., Ioerger, T. R., Sacchettini, J. C., Lipsitch, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.811 · Cited by 437
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Shapiro, E., Biezuner, T., & Linnarsson, S. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3542 · Cited by 1,177
Furin, J., Cox, H., & Pai, M. (2019) · The Lancet · doi:10.1016/s0140-6736(19)30308-3 · Cited by 873
Ellington, M. J., Ekelund, O., Aarestrup, F. M., Canton, R., Doumith, M., Giske, C., Grundman, H., Hasman, H., Holden, M. T. G., Hopkins, K. L., et al. (2017) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2016.11.012 · Cited by 603
Self-citationFord, C. B., Shah, R. R., Maeda, M. K., Gagneux, S., Murray, M. B., Cohen, T., Johnston, J. C., Gardy, J., Lipsitch, M., & Fortune, S. M. (2013) · Nature Genetics · doi:10.1038/ng.2656 · Cited by 457
Evolution and transmission of drug-resistant tuberculosis in a Russian population
Casali, N., Nikolayevskyy, V., Balabanova, Y., Harris, S. R., Ignatyeva, O., Kontsevaya, I., Corander, J., Bryant, J., Parkhill, J., Nejentsev, S., et al. (2014) · Nature Genetics · doi:10.1038/ng.2878 · Cited by 473
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Metadata
- Authors
- Walker, T. M., Ip, C. L., Harrell, R. H., Evans, J. T., Kapatai, G., Dedicoat, M. J., Eyre, D. W., Wilson, D. J., Hawkey, P. M., Crook, D. W., Parkhill, J., Harris, D., Walker, A. S., Bowden, R., Monk, P., Smith, E. G., & Peto, T. E.
- Venue
- The Lancet Infectious Diseases
- Publisher
- Elsevier BV
- Published
- 2013-02
- Volume
- 13
- Issue
- 2
- Pages
- 137-146
- ISSN
- 1473-3099 (ISSN-L)
- OpenAlex
- W2168358002
- Cited by
- 918
- References
- 3
- FWCI
- 40.27
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Walker, T. M., Ip, C. L., Harrell, R. H., Evans, J. T., Kapatai, G., Dedicoat, M. J., Eyre, D. W., Wilson, D. J., Hawkey, P. M., Crook, D. W., Parkhill, J., Harris, D., Walker, A. S., Bowden, R., Monk, P., Smith, E. G., & Peto, T. E. (2013). Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. The Lancet Infectious Diseases. https://doi.org/10.1016/s1473-3099(12)70277-3
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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