Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

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The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources. This raises the need for stringent sequencing and analysis protocols for studies investigating sequence-based microbial signatures in clinical samples.

Vyšlo v časopise: Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples. PLoS Pathog 10(11): e32767. doi:10.1371/journal.ppat.1004437
Kategorie: Opinion
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004437

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1. FengH, ShudaM, ChangY, MoorePS (2008) Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma. Science 319: 1096–1100.

2. CastellarinM, WarrenRL, FreemanJD, DreoliniL, KrzywinskiM, et al. (2012) Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 22: 299–306.

3. KosticAD, GeversD, PedamalluCS, MichaudM, DukeF, et al. (2012) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 22: 292–298.

4. LinZ, PuetterA, CocoJ, XuG, StrongMJ, et al. (2012) Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES. J Virol 86: 2970–2977.

5. StrongMJ, O'GradyT, LinZ, XuG, BaddooM, et al. (2013) Epstein-Barr Virus and Human Herpesvirus 6 Detection in a non-Hodgkin's Diffuse Large B-Cell Lymphoma Cohort using RNA-Seq. J Virol 87: 13059–62.

6. StrongMJ, XuG, CocoJ, BaribaultC, VinayDS, et al. (2013) Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy. PLoS Pathog 9: e1003341.

7. BhattAS, FreemanSS, HerreraAF, PedamalluCS, GeversD, et al. (2013) Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome. N Engl J Med 369: 517–528.

8. LomanNJ, ConstantinidouC, ChristnerM, et al. (2013) A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of shiga-toxigenic escherichia coli o104:h4. JAMA 309: 1502–1510.

9. HasmanH, SaputraD, Sicheritz-PontenT, LundO, SvendsenCA, et al. (2013) Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol 52: 139–146.

10. WilsonMR, NaccacheSN, SamayoaE, BiagtanM, BashirH, et al. (2014) Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing. N Engl J Med 370: 2408–2417.

11. FrickeWF, RaskoDA (2014) Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat Rev Genet 15: 49–55.

12. KöserCU, EllingtonMJ, CartwrightEJP, GillespieSH, BrownNM, et al. (2012) Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology. PLoS Pathog 8: e1002824.

13. t HoenPAC, FriedlanderMR, AlmlofJ, SammethM, PulyakhinaI, et al. (2013) Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotech 31: 1015–1022.

14. NetworkTCGA (2012) Comprehensive molecular portraits of human breast tumours. Nature 490: 61–70.

15. NetworkTCGAR (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature 489: 519–525.

16. NetworkTCGA (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487: 330–337.

17. XuG, StrongMJ, LaceyMR, BaribaultC, FlemingtonEK, et al. (2014) RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets. PLoS ONE 9: e89445.

18. NixD, CourdyS, BoucherK (2008) Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9: 523.

19. AltschulSF, GishW, MillerW, MyersEW, LipmanDJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410.

20. PruittKD, TatusovaT, BrownGR, MaglottDR (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40: D130–D135.

21. HusonDH, MitraS, RuscheweyhH-J, WeberN, SchusterSC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21: 1552–1560.

22. NakazatoH, VenkatesanS, EdmondsM (1975) Polyadenylic acid sequences in E. coli messenger RNA. Nature 256: 144–146.

23. SrinivasanP, RamanarayananM, RabbaniE (1975) Presence of polyriboadenylate sequences in pulse-labeled RNA of Escherichia coli. Proc Natl Acad Sci U S A 72: 2910–2914.

24. OhtaN, SandersM, NewtonA (1975) Poly(adenylic acid) sequences in the RNA of Caulobacter crescenus. Proc Natl Acad Sci U S A 72: 2343–2346.

25. SarkarN (1996) Polyadenylation of mRNA in bacteria. Microbiology 142: 3125–3133.

26. LappalainenT, SammethM, FriedlanderMR, t HoenPAC, MonlongJ, et al. (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501: 506–511.

27. LaurenceM, HatzisC, BrashDE (2014) Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes. PLoS ONE 9: e97876.

28. PercudaniR (2013) A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences. Bioinform Biol Insights 7: 55–72.

29. XuB, ZhiN, HuG, WanZ, ZhengX, et al. (2013) Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing. Proc Natl Acad Sci U S A 110: 10264–10269.

30. SmutsH, KewM, KhanA, KorsmanS (2014) Novel Hybrid Parvovirus-Like Virus, NIH-CQV/PHV, Contaminants in Silica Column-Based Nucleic Acid Extraction Kits. J Virol 88: 1398.

31. NaccacheSN, GreningerAL, LeeD, CoffeyLL, PhanT, et al. (2013) The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns. J Virol 87: 11966–11977.

32. NaccacheSN, HackettJ, DelwartEL, ChiuCY (2014) Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis. Proc Natl Acad Sci U S A 111: E976.

33. ZhiN, HuG, WongS, ZhaoK, MaoQ, et al. (2014) Reply to Naccache et al: Viral sequences of NIH-CQV virus, a contamination of DNA extraction method. Proc Natl Acad Sci U S A 111: E977.