Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis

Tao Luo, Chongguang Yang, Ying Peng, Liping Lu, Guomei Sun, Jie Wu, Xiaoping Jin, Jianjun Hong, Fabin Li, Jian Mei, Kathryn Deriemer, Qian Gao

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48 Scopus citations

Abstract

Whole genome sequencing (WGS) of Mycobacterium tuberculosis has been used to trace the transmission of M. tuberculosis, the causative agent of tuberculosis (TB). Previously published studies using WGS were conducted in developed countries with a low TB burden. We sought to evaluate the relative usefulness of traditional VNTR and SNP typing methods, WGS and epidemiological investigations to study the recent transmission of M. tuberculosis in a high TB burden country. We conducted epidemiological investigations of 42 TB patients whose M. tuberculosis isolates were classified into three clusters based on variable-number tandem repeat (VNTR) typing. We applied WGS to 32 (76.2%) of the 42 strains and calculated the pairwise genomic distances between strains within each cluster. Eighteen (56.3%) of the 32 strains had genomic differences 100 SNPs with every other strain, suggesting that direct transmission did not likely occurred. Ten strains were grouped into four WGS-based clusters with genomic distances ≤5 SNPs within each cluster, and confirmed epidemiological links were identified in two of these clusters. Our results indicate that WGS provides reliable resolution for tracing the transmission of M. tuberculosis in high TB burden settings. The high resolution of WGS is particularly useful to confirm or exclude the possibility of direct transmission events defined by traditional typing methods.

Original languageEnglish (US)
Pages (from-to)434-440
Number of pages7
JournalTuberculosis
Volume94
Issue number4
DOIs
StatePublished - 2014

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Keywords

  • Contact tracing
  • Genotyping
  • Transmission
  • Tuberculosis
  • Whole genome sequencing

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Infectious Diseases
  • Microbiology (medical)
  • Medicine(all)

Cite this

Luo, T., Yang, C., Peng, Y., Lu, L., Sun, G., Wu, J., Jin, X., Hong, J., Li, F., Mei, J., Deriemer, K., & Gao, Q. (2014). Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis. Tuberculosis, 94(4), 434-440. https://doi.org/10.1016/j.tube.2014.04.005