Control of artifactual variation in reported intersample relatedness during clinical use of a mycobacterium tuberculosis sequencing pipeline

Journal of Clinical Microbiology

Volumn 56, Issue 8, 2018, Pages

  Wyllie, David H ^a,b   Sanderson, Nicholas ^a   Myers, Richard ^c   Peto, Tim ^a,b   Robinson, Esther ^d   Crook, Derrick W ^a,b   Smith, E Grace ^d   Walker, A Sarah ^a,b  

^a JOHN RADCLIFFE HOSPITAL   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c PUBLIC HEALTH ENGLAND   (United Kingdom)

^d BIRMINGHAM HEARTLANDS HOSPITAL   (United Kingdom)

Author keywords

Artifact; Mycobacterium tuberculosis; Reference mapping; Relatedness; Single nucleotide variation

Indexed keywords

BACTERIAL DNA;

ARTICLE; ARTIFACT; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BIOINFORMATICS; BROTH DILUTION; CLINICAL PRACTICE; DECONTAMINATION; DNA SEQUENCE; HUMAN; INOCULATION; MYCOBACTERIUM TUBERCULOSIS; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; QUALITY CONTROL; QUANTITATIVE ANALYSIS; VALIDATION STUDY; CLASSIFICATION; GENETIC VARIATION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; MICROBIOLOGY; MOLECULAR EPIDEMIOLOGY; STANDARDS; TUBERCULOSIS;

DNA, BACTERIAL; GENETIC VARIATION; GENOME, BACTERIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR EPIDEMIOLOGY; MYCOBACTERIUM TUBERCULOSIS; SEQUENCE ANALYSIS, DNA; TUBERCULOSIS;

EID: 85050936833     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00104-18     Document Type: Article

References (30)

1. De Silva D, Peters J, Cole K, Cole MJ, Cresswell F, Dean G, Dave J, Thomas DR, Foster K, Waldram A, Wilson DJ, Didelot X, Grad YH, Crook DW, Peto TE, Walker AS, Paul J, Eyre DW. 2016. Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study. Lancet Infect Dis 16:1295–1303. https://doi.org/10.1016/S1473-3099(16)30157-8.
2. Gordon NC, Pichon B, Golubchik T, Wilson DJ, Paul J, Blanc DS, Cole K, Collins J, Cortes N, Cubbon M, Gould FK, Jenks PJ, Llewelyn M, Nash JQ, Orendi JM, Paranthaman K, Price JR, Senn L, Thomas HL, Wyllie S, Crook DW, Peto TEA, Walker AS, Kearns AM. 2017. Whole-genome sequencing reveals the contribution of long-term carriers in Staphylococcus aureus outbreak investigation. J Clin Microbiol 55:2188–2197. https://doi.org/10.1128/JCM.00363-17.
3. Walker TM, Lalor MK, Broda A, Ortega LS, Morgan M, Parker L, Churchill S, Bennett K, Golubchik T, Giess AP, Del Ojo Elias C, Jeffery KJ, Bowler I, Laurenson IF, Barrett A, Drobniewski F, McCarthy ND, Anderson LF, Abubakar I, Thomas HL, Monk P, Smith EG, Walker AS, Crook DW, Peto TEA, Conlon CP. 2014. Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study. Lancet Respir Med 2:285–292. https://doi.org/10.1016/S2213-2600(14)70027-X.
4. Pankhurst LJ, Del Ojo Elias C, Votintseva AA, Walker TM, Cole K, Davies J, Fermont JM, Gascoyne-Binzi DM, Kohl TA, Kong C, Lemaitre N, Niemann S, Paul J, Rogers TR, Roycroft E, Smith EG, Supply P, Tang P, Wilcox MH, Wordsworth S, Wyllie D, Xu L, Crook DW. 2016. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. Lancet Respir Med 4:49–58. https://doi.org/10.1016/S2213-2600(15)00466-X.
5. Bryant JM, Harris SR, Parkhill J, Dawson R, Diacon AH, van Helden P, Pym A, Mahayiddin AA, Chuchottaworn C, Sanne IM, Louw C, Boeree MJ, Hoelscher M, McHugh TD, Bateson AL, Hunt RD, Mwaigwisya S, Wright L, Gillespie SH, Bentley SD. 2013. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir Med 1:786–792. https://doi.org/10.1016/S2213-2600(13)70231-5.
6. Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O, Kontsevaya I, Corander J, Bryant J, Parkhill J, Nejentsev S, Horstmann RD, Brown T, Drobniewski F. 2014. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet 46:279–286. https://doi.org/10.1038/ng.2878.
7. Guerra-Assuncao JA, Crampin AC, Houben RM, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RP, McNerney R, Fine PE, Parkhill J, Clark TG, Glynn JR. 2015. Large-scale whole-genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. Elife 4:e05166. https://doi.org/10.7554/eLife.05166.
8. Guerra-Assunção JA, Houben RM, Crampin AC, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RP, McNerney R, Harris D, Parkhill J, Clark TG, Glynn JR. 2015. Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up. J Infect Dis 211:1154 –1163. https://doi.org/10.1093/infdis/jiu574.
9. Morgulis A, Gertz EM, Schaffer AA, Agarwala R. 2006. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biol 13:1028–1040. https://doi.org/10.1089/cmb.2006.13.1028.
10. Bedell JA, Korf I, Gish W. 2000. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 16:1040–1041. https://doi.org/10.1093/bioinformatics/16.11.1040.
11. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. https://doi.org/10.1186/gb-2009-10-3-r25.
12. Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851–1858. https://doi.org/10.1101/gr.078212.108.
13. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. https://doi .org/10.1093/bioinformatics/btp324.
14. Lunter G, Goodson M. 2011. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21:936–939. https://doi.org/10.1101/gr.111120.110.
15. World Health Organization. 2017. Global tuberculosis report 2017. World Health Organization, Geneva, Switzerland. http://apps.who.int/iris/bitstream/handle/10665/259366/9789241565516-eng.pdf.
16. Anonymous. 2017. SMI B 40: investigation of specimens for Mycobacterium species. Public Health England, London, United Kingdom.
17. Quan TP, Bawa Z, Foster D, Walker T, Del Ojo Elias C, Rathod P, Iqbal Z, Bradley P, Mowbray J, Walker AS, Crook DW, Wyllie DH, Peto TEA, Smith EG. 22 November 2017. Evaluation of whole-genome sequencing for mycobacterial species identification and drug susceptibility testing in a clinical setting: a large-scale prospective assessment of performance against line-probe assays and phenotyping. J Clin Microbiol https://doi.org/10.1128/JCM.01480-17.
18. Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris SR, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S. 2013. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet 45: 1176–1182. https://doi.org/10.1038/ng.2744.
19. Hatherell HA, Colijn C, Stagg HR, Jackson C, Winter JR, Abubakar I. 2016. Interpreting whole-genome sequencing for investigating tuberculosis transmission: a systematic review. BMC Med 14:21. https://doi.org/10.1186/s12916-016-0566-x.
20. Anonymous. 2012. ISO15189:2012. Medical laboratories—requirements for quality and competence. International Organization for Standardization, Geneva, Switzerland.
21. Nasidze I, Li J, Quinque D, Tang K, Stoneking M. 2009. Global diversity in the human salivary microbiome. Genome Res 19:636–643. https://doi.org/10.1101/gr.084616.108.
22. Bradley P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B, Earle S, Pankhurst LJ, Anson L, de Cesare M, Piazza P, Votintseva AA, Golubchik T, Wilson DJ, Wyllie DH, Diel R, Niemann S, Feuerriegel S, Kohl TA, Ismail N, Omar SV, Smith EG, Buck D, McVean G, Walker AS, Peto TE, Crook DW, Iqbal Z. 2015. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun 6:10063. https://doi.org/10.1038/ncomms10063.
23. Wood DE, Salzberg SL. 2014. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15:R46. https://doi.org/10.1186/gb-2014-15-3-r46.
24. Street TL, Sanderson ND, Atkins BL, Brent AJ, Cole K, Foster D, McNally MA, Oakley S, Peto L, Taylor A, Peto TEA, Crook DW, Eyre DW. 2017. Molecular diagnosis of orthopedic-device-related infection directly from sonication fluid by metagenomic sequencing. J Clin Microbiol 55: 2334–2347. https://doi.org/10.1128/JCM.00462-17.
25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352.
26. Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ, Clifton DA, Kapatai G, Ip CL, Bowden R, Drobniewski FA, Allix-Beguec C, Gaudin C, Parkhill J, Diel R, Supply P, Crook DW, Smith EG, Walker AS, Ismail N, Niemann S, Peto TE. 2015. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Lancet Infect Dis 15:1193–1202. https://doi.org/10.1016/S1473-3099(15)00062-6.
27. Mazariegos-Canellas O, Do T, Peto T, Eyre DW, Underwood A, Crook D, Wyllie DH. 2017. BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness. BMC Bioinformatics 18:477. https://doi.org/10.1186/s12859-017-1907-2.
28. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357. https://doi.org/10.1038/nmeth.1923.
29. Coll F, McNerney R, Guerra-Assuncao JA, Glynn JR, Perdigao J, Viveiros M, Portugal I, Pain A, Martin N, Clark TG. 2014. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat Commun 5:4812. https://doi.org/10.1038/ncomms5812.
30. Votintseva AA, Bradley P, Pankhurst L, Del Ojo Elias C, Loose M, Nilgiri-wala K, Chatterjee A, Smith EG, Sanderson N, Walker TM, Morgan MR, Wyllie DH, Walker AS, Peto TEA, Crook DW, Iqbal Z. 2017. Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples. J Clin Microbiol 55:1285–1298. https://doi.org/10.1128/JCM.02483-16.