Identifying likely transmission pathways within a 10-year community outbreak of tuberculosis by high-depth whole genome sequencing

PLoS ONE

Volumn 11, Issue 3, 2016, Pages

  Outhred, Alexander C ^a,b,c,d   Holmes, Nadine ^a,b   Sadsad, Rosemarie ^a,b   Martinez, Elena ^a,b   Jelfs, Peter ^a,b   Hill Cawthorne, Grant A ^c,e   Gilbert, Gwendolyn L ^b,c   Marais, Ben J ^c,d   Sintchenko, Vitali ^a,b,c  

^a NSW Mycobacterium Reference Laboratory   (Australia)

^b WESTMEAD HOSPITAL   (Australia)

^c University of Sydney   (Australia)

^d CHILDREN S HOSPITAL AT WESTMEAD   (Australia)

^e UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ETHAMBUTOL; ISONIAZID; PYRAZINAMIDE; RIFAMPICIN;

ANTIBIOTIC SENSITIVITY; ARTICLE; AUSTRALIA; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM ISOLATE; CLADISTICS; DISEASE TRANSMISSION; EPIDEMIC; GENE CLUSTER; GENE DELETION; GENE INSERTION; GENE MAPPING; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HUMAN; INTERSPERSED REPEAT; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TUBERCULOSIS; BACTERIAL GENOME; GENETICS; HIGH THROUGHPUT SEQUENCING; MICROBIOLOGY; MUTATION; PATHOGENICITY; TRANSMISSION;

AUSTRALIA; DISEASE OUTBREAKS; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; TUBERCULOSIS;

EID: 84961190913     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0150550     Document Type: Article

References (45)

1. World Health Organization. Global tuberculosis report 2014 [Internet]. Geneva, Switzerland: World Health Organization; 2014. Available: http://www.who.int/tb/publications/global-report/en/.
2. Marais BJ, Mlambo CK, Rastogi N, Zozio T, Duse AG, Victor TC, et al. Epidemic Spread of Multidrug- Resistant Tuberculosis in Johannesburg, South Africa. J Clin Microbiol. 2013; 51: 1818-1825. doi:10.1128/JCM.00200-13 PMID: 23554196.
3. Wilson DJ. Insights from Genomics into Bacterial Pathogen Populations. PLoS Pathog. 2012; 8: e1002874. doi:10.1371/journal.ppat.1002874 PMID: 22969423.
4. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. New Engl J Med. 2011; 364: 730-739. doi:10.1056/NEJMoa1003176 PMID: 21345102.
5. Kato-Maeda M, Ho C, Passarelli B, Banaei N, Grinsdale J, Flores L, et al. Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak. PLoS ONE. 2013; 8: e58235. doi:10.1371/journal.pone.0058235 PMID: 23472164.
6. Török ME, Reuter S, Bryant J, Köser CU, Stinchcombe SV, Nazareth B, et al. Rapid Whole-Genome Sequencing for Investigation of a Suspected Tuberculosis Outbreak. J Clin Microbiol. 2013; 51: 611- 614. doi:10.1128/JCM.02279-12 PMID: 23175259.
7. Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: A retrospective observational study. Lancet Infect Dis. 2013; 13: 137-146. doi:10.1016/S1473-3099(12)70277-3 PMID: 23158499.
8. Luo T, Yang C, Peng Y, Lu L, Sun G, Wu J, et al. Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis. Tuberculosis. 2014; 94: 434-440. doi:10.1016/j.tube.2014.04.005 PMID: 24888866.
9. Smit PW, Vasankari T, Aaltonen H, Haanperä M, Casali N, Marttila H, et al. Enhanced tuberculosis outbreak investigation using whole genome sequencing and IGRA. Eur Respir J. 2015; 45: 276-279. doi:10.1183/09031936.00125914 PMID: 25323236.
10. Bryant JM, Harris SR, Parkhill J, Dawson R, Diacon AH, van Helden P, et al. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: A retrospective observational study. Lancet Respir Med. 2013; 1: 786-792. doi:10.1016/S2213-2600(13)70231-5 PMID: 24461758.
11. Merker M, Kohl TA, Roetzer A, Truebe L, Richter E, Rüsch-Gerdes S, et al. Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients. PLoS ONE. 2013; 8: e82551. doi:10.1371/journal.pone.0082551 PMID: 24324807.
12. Pérez-Lago L, Comas I, Navarro Y, González-Candelas F, Herranz M, Bouza E, et al. Whole Genome Sequencing Analysis of Intrapatient Microevolution in Mycobacterium tuberculosis: Potential Impact on the Inference of Tuberculosis Transmission. J Infect Dis. 2014; 209: 98-108. doi:10.1093/infdis/jit439 PMID: 23945373.
13. Bareja C, Waring J, Stapledon R, Toms C, Douglas P, National Tuberculosis Advisory Committee. Tuberculosis notifications in Australia, 2011. Commun Dis Intell. 2014; 38: 356-368.
14. Lumb R, Bastian IB, Jelfs PJ, Keehner TJ, Pandey SK, Sievers A. Tuberculosis in Australia: bacteriologically- confirmed cases and drug resistance, 2011: A report of the Australian Mycobacterium Reference Laboratory Network. Commun Dis Intell. 2014; 38: 369-375.
15. Devlin S, Passmore E. Ongoing transmission of tuberculosis in Aboriginal communities in NSW. New South Wales Public Health Bull. 2013; 24: 38-42.
16. Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, et al. Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis. J Clin Microbiol. 2006; 44: 4498-4510. doi:10.1128/JCM.01392-06 PMID: 17005759.
17. Gurjav U, Jelfs P, McCallum N, Marais BJ, Sintchenko V. Temporal dynamics of Mycobacterium tuberculosis genotypes in New South Wales, Australia. BMC Infect Dis. 2014; 14: 455. doi:10.1186/1471-2334-14-455 PMID: 25149181.
18. van Soolingen D, Hermans PW, Haas PE de, Soll DR, van Embden JD. Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J Clin Microbiol. 1991; 29: 2578-2586. PMID: 1685494.
19. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements. Genome Res. 2004; 14: 1394-1403. doi:10.1101/gr.2289704 PMID: 15231754.
20. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998; 393: 537-544. doi:10.1038/31159 PMID: 9634230.
21. Wilm A, Aw PPK, Bertrand D, Yeo GHT, Ong SH, Wong CH, et al. LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012; 40: 11189-11201. doi:10.1093/nar/gks918 PMID: 23066108.
22. Nikolenko SI, Korobeynikov AI, Alekseyev MA. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics. 2013; 14: S7. doi:10.1186/1471-2164-14-S1-S7.
23. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv13033997 Q-Bio. 2013; Available: http://arxiv.org/abs/1303.3997.
24. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997; 35: 907-914. PMID: 9157152.
25. Coll F, Mallard K, Preston MD, Bentley S, Parkhill J, McNerney R, et al. SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics. 2012; 28: 2991-2993. doi:10.1093/bioinformatics/bts544 PMID: 23014632.
26. Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, Eiglmeier K, et al. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci. 2002; 99: 3684-3689. doi:10.1073/pnas.052548299 PMID: 11891304.
27. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. ArXiv12073907 Q-Bio. 2012; Available: http://arxiv.org/abs/1207.3907.
28. Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012; 28: i333-i339. doi:10.1093/bioinformatics/bts378 PMID: 22962449.
29. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J Comput Biol. 2012; 19: 455-477. doi:10.1089/cmb.2012.0021 PMID: 22506599.
30. Husemann P, Stoye J. r2cat: synteny plots and comparative assembly. Bioinformatics. 2010; 26: 570- 571. doi:10.1093/bioinformatics/btp690 PMID: 20015948.
31. Darling AE, Mau B, Perna NT. progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. PLoS ONE. 2010; 5: e11147. doi:10.1371/journal.pone.0011147 PMID: 20593022.
32. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol. 2013; 30: 2725-2729. doi:10.1093/molbev/mst197 PMID: 24132122 34.
33. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012; 29: 1969-1973. doi:10.1093/molbev/mss075 PMID: 22367748.
34. Reyes JF, Chan CHS, Tanaka MM. Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis. Infect Genet Evol. 2012; 12: 811-818. doi:10.1016/j.meegid.2011.05.018 PMID: 21683165.
35. Nakanishi N, Wada T, Arikawa K, Millet J, Rastogi N, Iwamoto T. Evolutionary robust SNPs reveal the misclassification of Mycobacterium tuberculosis Beijing family strains into sublineages. Infect Genet Evol. 2013; 16: 174-177. doi:10.1016/j.meegid.2013.02.007 PMID: 23438651.
36. Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, et al. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet. 2013; 45: 784-790. doi:10.1038/ng.2656 PMID: 23749189.
37. Sandegren L, Groenheit R, Koivula T, Ghebremichael S, Advani A, Castro E, et al. Genomic Stability over 9 Years of an Isoniazid Resistant Mycobacterium tuberculosis Outbreak Strain in Sweden. PLoS ONE. 2011; 6: e16647. doi:10.1371/journal.pone.0016647 PMID: 21304944.
38. Saunders NJ, Trivedi UH, Thomson ML, Doig C, Laurenson IF, Blaxter ML. Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background. J Infect. 2011; 62: 212-217. doi:10.1016/j.jinf.2011.01.003 PMID: 21237201.
39. Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads. Mol Biol Evol. 2014; 31: 1077-1088. doi:10.1093/molbev/msu088 PMID: 24600054.
40. Iqbal Z, Turner I, McVean G. High-throughput microbial population genomics using the Cortex variation assembler. Bioinformatics. 2013; 29: 275-276. doi:10.1093/bioinformatics/bts673 PMID: 23172865.
41. Peterlongo P, Schnel N, Pisanti N, Sagot M-F, Lacroix V. Identifying SNPs without a Reference Genome by Comparing Raw Reads. In: Chavez E, Lonardi S, editors. String Processing and Information Retrieval. Springer Berlin Heidelberg; 2010. pp. 147-158. Available: http://link.springer.com/chapter/10.1007/978-3-642-16321-0-14.
42. Lin PL, Ford CB, Coleman MT, Myers AJ, Gawande R, Ioerger T, et al. Sterilization of granulomas is common in active and latent tuberculosis despite within-host variability in bacterial killing. Nat Med. 2014; 20: 75-79. doi:10.1038/nm.3412 PMID: 24336248.
43. Cohen T, van Helden PD, Wilson D, Colijn C, McLaughlin MM, Abubakar I, et al. Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control. Clin Microbiol Rev. 2012; 25: 708-719. doi:10.1128/CMR.00021-12 PMID: 23034327.
44. Lew JM, Kapopoulou A, Jones LM, Cole ST. TubercuList- 10 years after. Tuberculosis. 2011; 91: 1-7. doi:10.1016/j.tube.2010.09.008 PMID: 20980199.