Genotype of a historic strain of Mycobacterium tuberculosis

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 109; no. 45; pp. 18511 - 18516
• Main Authors: Bouwman, Abigail S, Kennedy, Sandra L, Müller, Romy, Stephens, Richard H, Holst, Malin, Caffell, Anwen C, Roberts, Charlotte A, Brown, Terence A
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 06.11.2012; National Acad Sciences
• Subjects: Archaeology; Bacteria; Bacterial Typing Techniques; Base Sequence; Biological Sciences; Bones; Crypts; Deoxyribonucleic acid; DNA; England; Female; genome; Genome, Bacterial - genetics; Genomes; Genotype; Genotype & phenotype; Genotypes; high-throughput nucleotide sequencing; Humans; Hybridization; loci; Molecular Sequence Data; Mycobacterium tuberculosis; Mycobacterium tuberculosis - genetics; North America; oligonucleotides; Oligonucleotides - genetics; Paleontology; Phylogeny; Polymerase Chain Reaction; Product category rules; Pulmonary tuberculosis; Sequence Alignment; Sequence Analysis, DNA; Sequencing; single nucleotide polymorphism; Skeleton; Tuberculosis; England; North America
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1209444109

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.