IS-seq: a Novel High Throughput Survey of in Vivo IS6110 Transposition in Multiple Mycobacterium Tuberculosis Genomes

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2012 Jun 19

PMID 22703188

Citations 22

Authors

Alejandro Reyes

Andrea Sandoval

Andres Cubillos-Ruiz

Katherine E Varley

Ivan Hernandez-Neuta

Sofia Samper

Carlos Martin

Maria Jesus Garcia

Viviana Ritacco

Lucelly Lopez

Jaime Robledo

Maria Mercedes Zambrano

Robi D Mitra

Patricia Del Portillo

Affiliations

Soon will be listed here.

Abstract

Background: The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemiological marker, the identification of the precise chromosomal insertion sites has been limited by technical challenges. Here, we present IS-seq, a novel method that combines high-throughput sequencing using Illumina technology with efficient combinatorial sample multiplexing to simultaneously probe 519 clinical isolates, identifying almost all the flanking regions of the element in a single experiment.

Results: We identified a total of 6,976 IS6110 flanking regions on the different isolates. When validated using reference strains, the method had 100% specificity and 98% positive predictive value. The insertions mapped to both coding and non-coding regions, and in some cases interrupted genes thought to be essential for virulence or in vitro growth. Strains were classified into families using insertion sites, and high agreement with previous studies was observed.

Conclusions: This high-throughput IS-seq method, which can also be used to map insertions in other organisms, extends previous surveys of in vivo interrupted loci and provides a baseline for probing the consequences of disruptions in M. tuberculosis strains.

Citing Articles

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Functional genetic variation in / genes contributes to diversity in lineages and potential interactions with the human host.

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Hurtado-Paez U, Alvarez Zuluaga N, Arango Isaza R, Contreras-Moreira B, Rouzaud F, Robledo J Front Microbiol. 2023; 13:1076797.

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Comin J, Cebollada A, Ibarz D, Vinuelas J, Sahagun J, Torres L Sci Rep. 2022; 12(1):18766.

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References

Snyder E, Kampanya N, Lu J, Nordberg E, Karur H, Shukla M . PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. 2006; 35(Database issue):D401-6. PMC: 1669763. DOI: 10.1093/nar/gkl858. View

Niemann S, Koser C, Gagneux S, Plinke C, Homolka S, Bignell H . Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS One. 2009; 4(10):e7407. PMC: 2756628. DOI: 10.1371/journal.pone.0007407. View

Yesilkaya H, Dale J, Strachan N, Forbes K . Natural transposon mutagenesis of clinical isolates of Mycobacterium tuberculosis: how many genes does a pathogen need?. J Bacteriol. 2005; 187(19):6726-32. PMC: 1251597. DOI: 10.1128/JB.187.19.6726-6732.2005. View

McEvoy C, Falmer A, Gey van Pittius N, Victor T, van Helden P, Warren R . The role of IS6110 in the evolution of Mycobacterium tuberculosis. Tuberculosis (Edinb). 2007; 87(5):393-404. DOI: 10.1016/j.tube.2007.05.010. View

Cole S, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D . Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998; 393(6685):537-44. DOI: 10.1038/31159. View

McEvoy C, Warren R, van Helden P, Gey van Pittius N . Multiple, independent, identical IS6110 insertions in Mycobacterium tuberculosis PPE genes. Tuberculosis (Edinb). 2009; 89(6):439-42. DOI: 10.1016/j.tube.2009.08.001. View

Bifani P, Mathema B, Liu Z, Moghazeh S, Shopsin B, Tempalski B . Identification of a W variant outbreak of Mycobacterium tuberculosis via population-based molecular epidemiology. JAMA. 1999; 282(24):2321-7. DOI: 10.1001/jama.282.24.2321. View

Kremer K, Glynn J, Lillebaek T, Niemann S, Kurepina N, Kreiswirth B . Definition of the Beijing/W lineage of Mycobacterium tuberculosis on the basis of genetic markers. J Clin Microbiol. 2004; 42(9):4040-9. PMC: 516354. DOI: 10.1128/JCM.42.9.4040-4049.2004. View

Gagneux S, DeRiemer K, Van T, Kato-Maeda M, de Jong B, Narayanan S . Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2006; 103(8):2869-73. PMC: 1413851. DOI: 10.1073/pnas.0511240103. View

10.

Comas I, Homolka S, Niemann S, Gagneux S . Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One. 2009; 4(11):e7815. PMC: 2772813. DOI: 10.1371/journal.pone.0007815. View

11.

Gutierrez M, Brisse S, Brosch R, Fabre M, Omais B, Marmiesse M . Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog. 2005; 1(1):e5. PMC: 1238740. DOI: 10.1371/journal.ppat.0010005. View

12.

Sassetti C, Boyd D, Rubin E . Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol. 2003; 48(1):77-84. DOI: 10.1046/j.1365-2958.2003.03425.x. View

13.

Ghanekar K, McBride A, Dellagostin O, Thorne S, Mooney R, McFadden J . Stimulation of transposition of the Mycobacterium tuberculosis insertion sequence IS6110 by exposure to a microaerobic environment. Mol Microbiol. 1999; 33(5):982-93. DOI: 10.1046/j.1365-2958.1999.01539.x. View

14.

Goodman A, McNulty N, Zhao Y, Leip D, Mitra R, Lozupone C . Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe. 2009; 6(3):279-89. PMC: 2895552. DOI: 10.1016/j.chom.2009.08.003. View

15.

Kaufmann S . How can immunology contribute to the control of tuberculosis?. Nat Rev Immunol. 2002; 1(1):20-30. DOI: 10.1038/35095558. View

16.

Lamichhane G, Tyagi S, Bishai W . Designer arrays for defined mutant analysis to detect genes essential for survival of Mycobacterium tuberculosis in mouse lungs. Infect Immun. 2005; 73(4):2533-40. PMC: 1087429. DOI: 10.1128/IAI.73.4.2533-2540.2005. View

17.

van Soolingen D, de Haas P, Hermans P, Groenen P, van Embden J . Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis. J Clin Microbiol. 1993; 31(8):1987-95. PMC: 265684. DOI: 10.1128/jcm.31.8.1987-1995.1993. View

18.

Abadia E, Zhang J, Dos Vultos T, Ritacco V, Kremer K, Aktas E . Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method. Infect Genet Evol. 2010; 10(7):1066-74. DOI: 10.1016/j.meegid.2010.07.006. View

19.

Warren R, Sampson S, Richardson M, Van der Spuy G, Lombard C, Victor T . Mapping of IS6110 flanking regions in clinical isolates of Mycobacterium tuberculosis demonstrates genome plasticity. Mol Microbiol. 2000; 37(6):1405-16. DOI: 10.1046/j.1365-2958.2000.02090.x. View

20.

Brudey K, Driscoll J, Rigouts L, Prodinger W, Gori A, Al-Hajoj S . Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 2006; 6:23. PMC: 1468417. DOI: 10.1186/1471-2180-6-23. View