Genotype of a historic strain of Mycobacterium tuberculosis
- 28 September 2012
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 109 (45), 18511-18516
- https://doi.org/10.1073/pnas.1209444109
Abstract
The use of ancient DNA in paleopathological studies of tuberculosis has largely been restricted to confirmation of disease identifications made by skeletal analysis; few attempts at obtaining genotype data from archaeological samples have been made because of the need to perform different PCRs for each genetic locus being studied in an ancient DNA extract. We used a next generation sequencing approach involving hybridization capture directed at specific polymorphic regions of the Mycobacterium tuberculosis genome to identify a detailed genotype for a historic strain of M. tuberculosis from an individual buried in the 19th century St. George's Crypt, Leeds, West Yorkshire, England. We obtained 664,500 sequencing by oligonucleotide ligation and detection (SOLiD) reads that mapped to the targeted regions of the M. tuberculosis genome; the coverage included 218 of 247 SNPs, 10 of 11 insertion/deletion regions, and the repeat elements IS1081 and IS6110. The accuracy of the SOLiD data was checked by conventional PCRs directed at 11 SNPs and two insertion/deletions. The data placed the historic strain of M. tuberculosis in a group that is uncommon today, but it is known to have been present in North America in the early 20th century. Our results show the use of hybridization capture followed by next generation sequencing as a means of obtaining detailed genotypes of ancient varieties of M. tuberculosis, potentially enabling meaningful comparisons between strains from different geographic locations and different periods in the past.Keywords
This publication has 61 references indexed in Scilit:
- A draft genome of Yersinia pestis from victims of the Black DeathNature, 2011
- Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciencesGenome Biology, 2010
- Variation among Genome Sequences of H37Rv Strains of Mycobacterium tuberculosis from Multiple LaboratoriesJournal of Bacteriology, 2010
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Drivers of tuberculosis epidemics: The role of risk factors and social determinantsSocial Science & Medicine, 2009
- Antibiotic Resistance and Single-Nucleotide Polymorphism Cluster Grouping Type in a Multinational Sample of Resistant Mycobacterium tuberculosis IsolatesAntimicrobial Agents and Chemotherapy, 2007
- Detecting emerging strains of tuberculosis by using spoligotypesProceedings of the National Academy of Sciences of the United States of America, 2006
- Novel Genetic Polymorphisms That Further Delineate the Phylogeny of the Mycobacterium tuberculosis ComplexJournal of Bacteriology, 2006
- Pathogenic microbial ancient DNA: a problem or an opportunity?Proceedings Of The Royal Society B-Biological Sciences, 2005
- A Greedy Algorithm for Aligning DNA SequencesJournal of Computational Biology, 2000