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PLoS One. 2013;8(3):e58235. doi: 10.1371/journal.pone.0058235. Epub 2013 Mar 5.

Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak.

Author information

1
Curry International Tuberculosis Center, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, USA. midori.kato-maeda@ucsf.edu

Abstract

RATIONALE:

Current tools available to study the molecular epidemiology of tuberculosis do not provide information about the directionality and sequence of transmission for tuberculosis cases occurring over a short period of time, such as during an outbreak. Recently, whole genome sequencing has been used to study molecular epidemiology of Mycobacterium tuberculosis over short time periods.

OBJECTIVE:

To describe the microevolution of M. tuberculosis during an outbreak caused by one drug-susceptible strain. METHOD AND MEASUREMENTS: We included 9 patients with tuberculosis diagnosed during a period of 22 months, from a population-based study of the molecular epidemiology in San Francisco. Whole genome sequencing was performed using Illumina's sequencing by synthesis technology. A custom program written in Python was used to determine single nucleotide polymorphisms which were confirmed by PCR product Sanger sequencing.

MAIN RESULTS:

We obtained an average of 95.7% (94.1-96.9%) coverage for each isolate and an average fold read depth of 73 (1 to 250). We found 7 single nucleotide polymorphisms among the 9 isolates. The single nucleotide polymorphisms data confirmed all except one known epidemiological link. The outbreak strain resulted in 5 bacterial variants originating from the index case A1 with 0-2 mutations per transmission event that resulted in a secondary case.

CONCLUSIONS:

Whole genome sequencing analysis from a recent outbreak of tuberculosis enabled us to identify microevolutionary events observable during transmission, to determine 0-2 single nucleotide polymorphisms per transmission event that resulted in a secondary case, and to identify new epidemiologic links in the chain of transmission.

PMID:
23472164
PMCID:
PMC3589338
DOI:
10.1371/journal.pone.0058235
[Indexed for MEDLINE]
Free PMC Article

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