The mutation rate of mycobacterial repetitive unit loci in strains of M. tuberculosisfrom cynomolgus macaque infection

BMC Genomics

Research Article

Mark N Ragheb¹  Christopher B Ford¹  Michael R Chase¹  Sarah M Fortune²  JoAnne L Flynn³  Philana Ling Lin⁴ 

[1] Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA;Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA;Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA;Broad Institute of MIT and Harvard, Cambridge, MA, USA;Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA;Department of Pediatrics, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, PA, USA;

关键词: Mycobacterium tuberculosis;    Mycobacterial interspersed repetitive units;    MIRU;    Molecular epidemiology;    Copy number variation;    Whole-genome sequencing;    Read depth;    Paired-end mapping;    Mutation rate;   

DOI  :  10.1186/1471-2164-14-145

 received in 2012-12-20, accepted in 2013-02-26,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundMycobacterial interspersed repetitive units (MIRUs) are minisatellites within the Mycobacterium tuberculosis (Mtb) genome. Copy number variation (CNV) in MIRU loci is used for epidemiological typing, making the rate of variation important for tracking the transmission of Mtb strains. In this study, we developed and assessed a whole-genome sequencing (WGS) approach to detect MIRU CNV in Mtb. We applied this methodology to a panel of Mtb strains isolated from the macaque model of tuberculosis (TB), the animal model that best mimics human disease. From these data, we have estimated the rate of MIRU variation in the host environment, providing a benchmark rate for future epidemiologic work.ResultsWe assessed variation at the 24 MIRU loci used for typing in a set of Mtb strains isolated from infected cynomolgus macaques. We previously performed WGS of these strains and here have applied both read depth (RD) and paired-end mapping (PEM) metrics to identify putative copy number variants. To assess the relative power of these approaches, all MIRU loci were resequenced using Sanger sequencing. We detected two insertion/deletion events both of which could be identified as candidates by PEM criteria. With these data, we estimate a MIRU mutation rate of 2.70 × 10-03 (95% CI: 3.30 × 10-04- 9.80 × 10-03) per locus, per year.ConclusionOur results represent the first experimental estimate of the MIRU mutation rate in Mtb. This rate is comparable to the highest previous estimates gathered from epidemiologic data and meta-analyses. Our findings allow for a more rigorous interpretation of data gathered from MIRU typing.

【 授权许可】

Unknown   
© Ragheb et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.