Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

Scientific Reports

Volumn 8, Issue 1, 2018, Pages

  Kirstahler, Philipp ^a   Bjerrum, Søren Solborg ^b   Friis Møller, Alice ^c   La Cour, Morten ^b   Aarestrup, Frank M ^a   Westh, Henrik ^c,d   Pamp, Sünje Johanna ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b Rigshospitalet   (Denmark)

^c HVIDOVRE HOSPITAL   (Denmark)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ADVERSE EVENT; AQUEOUS HUMOR; BACTERIUM; BACTERIUM IDENTIFICATION; CATARACT EXTRACTION; CLASSIFICATION; ENDOPHTHALMITIS; FEMALE; GENETICS; GENOMICS; HUMAN; INTRAVITREAL DRUG ADMINISTRATION; MALE; MICROBIOLOGY; MIDDLE AGED; POSTOPERATIVE COMPLICATION; PROCEDURES;

AQUEOUS HUMOR; BACTERIA; BACTERIAL TYPING TECHNIQUES; CATARACT EXTRACTION; DNA, BACTERIAL; ENDOPHTHALMITIS; FEMALE; GENOMICS; HUMANS; INTRAVITREAL INJECTIONS; MALE; MIDDLE AGED; POSTOPERATIVE COMPLICATIONS;

EID: 85048278788     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-018-22416-4     Document Type: Article

References (47)

1. Durand, M. L. Bacterial and Fungal Endophthalmitis. Clinical Microbiology Reviews 30, 597-613 (2017).
2. Bannerman, T. L., Rhoden, D. L., McAllister, S. K., Miller, J. M. & Wilson, L. A. The source of coagulase-negative staphylococci in the Endophthalmitis Vitrectomy Study. A comparison of eyelid and intraocular isolates using pulsed-field gel electrophoresis. Arch Ophthalmol 115, 357-361 (1997).
3. Buchta, V. et al. Outbreak of Fungal Endophthalmitis Due to Fusarium oxysporum Following Cataract Surgery. Mycopathologia 177, 115-121 (2014).
4. Foster, A. Cataract and 'Vision 2020-the right to sight' initiative. British Journal of Ophthalmology 85, 635-639 (2001).
5. Solborg Bjerrum, S., Kiilgaard, J. F., Mikkelsen, K. L. & la Cour, M. Outsourced cataract surgery and postoperative endophthalmitis. Acta Ophthalmol 91, 701-708 (2013).
6. Shorstein, N. H., Winthrop, K. L. & Herrinton, L. J. Decreased postoperative endophthalmitis rate after institution of intracameral antibiotics in a Northern California eye department. Journal of Cartaract & Refractive Surgery 39, 8-14 (2013).
7. Gower, E. W. et al. Characteristics of Endophthalmitis after Cataract Surgery in the United States Medicare Population. Ophthalmology 122, 1625-1632 (2015).
8. Avery, R. L. et al. Intravitreal injection technique and monitoring: updated guidelines of an expert panel. Retina 34(12), S1-S18 (2014).
9. McCannel, C. A. Meta-analysis of endophthalmitis after intravitreal injection of anti-vascular endothelial growth factor agents: causative organisms and possible prevention strategies. Retina 31, 654-661 (2011).
10. Endophthalmitis Vitrectomy Study Group. Results of the Endophthalmitis Vitrectomy Study. A randomized trial of immediate vitrectomy and of intravenous antibiotics for the treatment of postoperative bacterial endophthalmitis. Endophthalmitis Vitrectomy Study Group. Arch Ophthalmol 113, 1479-1496 (1995).
11. Yao, K. et al. The incidence of postoperative endophthalmitis after cataract surgery in China: a multicenter investigation of 2006-2011. British Journal of Ophthalmology 97, 1312-1317 (2013).
12. Seal, D. et al. Laboratory diagnosis of endophthalmitis: Comparison of microbiology and molecular methods in the European Society of Cataract & Refractive Surgeons multicenter study and susceptibility testing. Journal of Cataract & Refractive Surgery 34, 1439-1450 (2008).
13. Barry, P., Cordovés, L. & Gardner, S. ESCRS guidelines for prevention and treatment of endophthalmitis following cataract surgery: data, dilemmas and conclusions. (ESCRS, 2013).
14. Wilson, M. R. et al. Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing. New England Journal of Medicine 370, 2408-2417 (2014).
15. Oh, J. et al. Temporal Stability of the Human Skin Microbiome. Cell 165, 854-866 (2016).
16. Zankari, E. et al. Identification of acquired antimicrobial resistance genes. Journal of Antimicrobial Chemotherapy 67, 2640-2644 (2012).
17. Joensen, K. G. et al. Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance and Outbreak Detection of Verotoxigenic Escherichia coli. Journal of Clinical Microbiology 52, 1501-1510 (2014).
18. Breitwieser, F. P. & Salzberg, S. L. Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification. https://doi.org/10.1101/084715 (bioRxiv, 2016).
19. Doan, T. et al. Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Medicine 1-9 https://doi.org/10.1186/s13073-016-0344-6 (2016).
20. Mattos, F. B., Saraiva, F. P., Angotti-Neto, H. & Passos, A. F. Outbreak of Ochrobactrum anthropi endophthalmitis following cataract surgery. Journal of Hospital Infection 83, 337-340 (2013).
21. Venkateswaran, N., Wozniak, R. A. F. & Hindman, H. B. Ochrobactrum anthropi Keratitis with Focal Descemet's Membrane Detachment and Intracorneal Hypopyon. Case Reports in Ophthalmological Medicine 2016, 1-4 (2016).
22. Relman, D. A. Actionable Sequence Data on Infectious Diseases in the Clinical Workplace. Clinical Chemistry 61, 38-40 (2014).
23. Pallen, M. J. Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections. Parasitology 141, 1856-1862 (2014).
24. Didelot, X., Bowden, R., Wilson, D. J., Peto, T. E. A. & Crook, D. W. Transforming clinical microbiology with bacterial genome sequencing. Nature Reviews Genetics 13, 601-612 (2012).
25. Mollerup, S. et al. Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing. Journal of Clinical Microbiology 54, 980-987 (2016).
26. Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biology 1-12 https://doi.org/10.1186/s12915-014-0087-z (2014).
27. Glassing, A., Dowd, S. E., Galandiuk, S., Davis, B. & Chiodini, R. J. Inherent bacterial DNA contaminationof extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut Pathogens 1-12 https://doi.org/10.1186/s13099-016-0103-7 (2016).
28. Tanner, M. A., Goebel, B. M., Dojka, M. A. & Pace, N. R. Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Applied and Environmental Microbiology 64, 3110-3113 (1998).
29. Naccache, S. N. et al. The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns. Journal of Virology 87, 11966-11977 (2013).
30. Smuts, H., Kew, M., Khan, A. & Korsman, S. Novel hybrid parvovirus-like virus, NIH-CQV/PHV, contaminants in silica columnbased nucleic acid extraction kits. Journal of Virology 110, 10264-10269 (2014).
31. Lee, A. Y., Akileswaran, L., Tibbetts, M. D., Garg, S. J. & Van Gelder, R. N. Identification of Torque Teno Virus in Culture-Negative Endophthalmitis by Representational Deep DNA Sequencing. Ophthalmology 122, 524-530 (2015).
32. Merchant, S., Wood, D. E. & Salzberg, S. L. Unexpected cross-species contamination in genome sequencing projects. PeerJ 2, e675 (2014).
33. Kryukov, K. & Imanishi, T. Human Contamination in Public Genome Assemblies. PLoS ONE 11, e0162424 (2016).
34. Longo, M. S., O'Neill, M. J. & O'Neill, R. J. Abundant Human DNA Contamination Identified in Non-Primate Genome Databases. PLoS ONE 6, e16410 (2011).
35. Harper, D. R. A comparative study of the microbiological contamination of postmortem blood and vitreous humour samples taken for ethanol determination. Forensic Sci Int 43, 37-44 (1989).
36. Egger, S. F. et al. Bacterial growth in human vitreous humor. Exp Eye Res 65, 791-795 (1997).
37. Hasman, H. et al. Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples. Journal of Clinical Microbiology 52, 139-146 (2014).
38. Joensen, K. G. et al. Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease. European Journal of Clinical Microbiology & Infectious Diseases 36, 1325-1338 (2017).
39. Greninger, A. L. et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Medicine 1-13 https://doi.org/10.1186/s13073-015-0220-9 (2015).
40. Cao, M. D. et al. Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing. GigaScience 5, 32 (2016).
41. Quick, J. et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc 12, 1261-1276 (2017).
42. Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 15, 1-12 (2014).
43. Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L. Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science 3, (e104 (2017).
44. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J Mol Biol 215, 403-410 (1990).
45. Bartels, M. D. et al. Comparing Whole-Genome Sequencing with Sanger Sequencing for spa Typing of Methicillin-Resistant Staphylococcus aureus. Journal of Clinical Microbiology 52, 4305-4308 (2014).
46. Bankevich, A. et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology 19, 455-477 (2012).
47. Thomsen, M. C. F. et al. A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance. PLoS ONE 11, e0157718 (2016).