临床宏基因组学在呼吸感染性疾病精准诊疗中的疑问解析_Chinese Journal of Respiratory and Critical Care Medicine

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周永召 , 李亚伦 , 范红 ,  李为民

Corresponding author：

李为民, Email: weimin003@163.com

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DOI：

10.7507/1671-6205.201804048

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Citation： 周永召, 李亚伦, 范红, 李为民. 临床宏基因组学在呼吸感染性疾病精准诊疗中的疑问解析. Chinese Journal of Respiratory and Critical Care Medicine, 2018, 17(6): 539-543. doi: 10.7507/1671-6205.201804048 Copy

1.	Lozano R, Naghavi M, Foreman K, et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet, 2012, 380(9859): 2095-2128.
2.	Spellberg B, Guidos R, Gilbert D, et al. The epidemic of antibiotic-resistant infections: a call to action for the medical community from the Infectious Diseases Society of America. Clin Infect Dis, 2008, 46(2): 155-164.
3.	肖永红. 国家细菌耐药控制行动计划: 基于大健康理念的耐药控制宏图. 中华临床感染病杂志, 2016, 9(4): 289-293.
4.	Van Nimwegen KJ, Van Soest RA, Veltman JA, et al. Is the $1000 genome as near as we think? A cost analysis of next-generation sequencing. Clin Chem, 2016, 62(11): 1458-1464.
5.	中华医学会呼吸病学分会感染学组. 中国成人医院获得性肺炎与呼吸机相关性肺炎诊断和治疗指南(2018 年版). 中华结核和呼吸杂志, 2018, 41(4): 255-280.
6.	Ruppé E, Greub G, Schrenzel J. Messages from the first International Conference on Clinical Metagenomics (ICCMg). Microbes Infect, 2017, 19(4-5): 223-228.
7.	Kalil AC, Metersky ML, Klompas M, et al. Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society. Clin Infect Dis, 2016, 63(5): 61-111.
8.	Aguado JM, Vazquez L, Fernandez-Ruiz M, et al. Serum galactomannan versus a combination of galactomannan and polymerase chain reaction-based Aspergillus DNA detection for early therapy of invasive aspergillosis in high-risk hematological patients: a randomized controlled trial. Clin Infect Dis, 2015, 60(3): 405-414.
9.	Subramony A, Zachariah P, Krones A, et al. Impact of multiplex polymerase chain reaction testing for respiratory pathogens on healthcare resource utilization for pediatric inpatients. J Pediatr, 2016, 173: 196-201.
10.	Schlaberg R, Chiu CY, Miller S, et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch Pathol Lab Med, 2017, 141(6): 776-786.
11.	Franzosa EA, Hsu T, Sirota-Madi A, et al. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Microbiol, 2015, 13(6): 360-372.
12.	Parize P, Muth E, Richaud C, et al. Untargeted next-generation sequencing-based first-line diagnosis of infection in immunocompromised adults: a multicentre, blinded, prospective study. Clin Microbiol Infect, 2017, 23(8): 574. e1-574. e6.
13.	Quince C, Walker AW, Simpson JT, et al. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol, 2017, 35(9): 833-844.
14.	Van Dijk EL, Auger H, Jaszczyszyn Y, et al. Ten years of next-generation sequencing technology. Trends Genet, 2014, 30(9): 418-426.
15.	Zhernakova A, Kurilshikov A, Bonder MJ, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 2016, 352(6285): 565-569.
16.	Simner PJ, Miller S, Carroll KC. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clin Infect Dis, 2018, 66(5): 778-788.
17.	Moran Losada P, Chouvarine P, Dorda M, et al. The cystic fibrosis lower airways microbial metagenome. ERJ Open Res, 2016, 2(2): pii: 00096-2015.
18.	Langelier C, Zinter MS, Kalantar K, et al. Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients. Am J Respir Crit Care Med, 2018, 197(4): 524-528.
19.	Lewandowska DW, Schreiber PW, Schuurmans MM, et al. Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection. PloS One, 2017, 12(5): e0177340.
20.	Gerber JS, Ross RK, Bryan M, et al. Association of broad- vs narrow-spectrum antibiotics with treatment failure, adverse events, and quality of life in children with acute respiratory tract infections. JAMA, 2017, 318(23): 2325-2336.
21.	Pendleton KM, Erb-Downward JR, Bao Y, et al. Rapid pathogen identification in bacterial pneumonia using real-time metagenomics. Am J Respir Crit Care Med, 2017, 196(12): 1610-1612.
22.	Ruppé E, Cherkaoui A, Lazarevic V, et al. Establishing genotype-to-phenotype relationships in bacteria causing hospital-acquired pneumonia: a prelude to the application of clinical metagenomics. Antibiotics, 2017, 6(4): 30-45.
23.	Rogers GB, Wesselingh S. Precision respiratory medicine and the microbiome. Lancet Respir Med, 2016, 4(1): 73-82.
24.	中华医学会呼吸病学分会. 中国成人社区获得性肺炎诊断和治疗指南(2016 年版). 中华结核和呼吸杂志, 2016, 39(4): 241-242.
25.	Barbier F, Andremont A, Wolff M, et al. Hospital-acquired pneumonia and ventilator-associated pneumonia. Curr Opin Pulm Med, 2013, 19(3): 216-228.
26.	Grumaz S, Stevens P, Grumaz C, et al. Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med, 2016, 8(1): 73.
27.	Weterings V, Bosch T, Witteveen S, et al. Next-generation sequence analysis reveals transfer of methicillin resistance to a methicillin-susceptible Staphylococcus aureus strain that subsequently caused a methicillin-resistant Staphylococcus aureus outbreak: a descriptive study. J Clin Microbiol, 2017, 55(9): 2808-2816.
28.	Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother, 2012, 67(11): 2640-2644.
29.	McArthur AG, Waglechner N, Nizam F, et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother, 2013, 57(7): 3348-3357.
30.	Gupta SK, Padmanabhan BR, Diene SM, et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother, 2014, 58(1): 212-220.
31.	Stämmler F, Gläsner J, Hiergeist A, et al. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome, 2016, 4(1): 28.
32.	Lloyd CM, Marsland BJ. Lung homeostasis: influence of age, microbes, and the immune system. Immunity, 2017, 46(4): 549-561.
33.	Thoendel M, Jeraldo P, Greenwood-Quaintance KE, et al. A possible novel prosthetic joint infection pathogen, mycoplasma salivarium, identified by metagenomic shotgun sequencing. Clin Infect Dis, 2017, 65(2): 332-335.
34.	Goodwin S, Mcpherson JD, Mccombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet, 2016, 17(6): 333-351.
35.	Guan H, Shen A, Lv X, et al. Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing. J Neurovirol, 2016, 22(2): 240-245.
36.	Tsai YC, Conlan S, Deming C, et al. Resolving the complexity of human skin metagenomes using single-molecule sequencing. MBio, 2016, 7(1): e01948-15.
37.	Schmidt K, Mwaigwisya S, Crossman LC, et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother, 2017, 72(1): 104-114.
38.	Hasan MR, Rawat A, Tang P, et al. Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing. J Clin Microbiol, 2016, 54(4): 919-927.
39.	Noyes NR, Weinroth ME, Parker J, et al. Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. Microbiome, 2017, 5(1): 142.
40.	Thoendel M, Jeraldo P, Greenwood-Quaintance KE, et al. Impact of contaminating DNA in whole-genome amplification kits used for metagenomic shotgun sequencing for infection diagnosis. J Clin Microbiol, 2017, 55(6): 1789-1801.
41.	Kim D, Hofstaedter CE, Zhao C, et al. Optimizing methods and dodging pitfalls in microbiome research. Microbiome, 2017, 5(1): 52.

1. Lozano R, Naghavi M, Foreman K, et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet, 2012, 380(9859): 2095-2128.
2. Spellberg B, Guidos R, Gilbert D, et al. The epidemic of antibiotic-resistant infections: a call to action for the medical community from the Infectious Diseases Society of America. Clin Infect Dis, 2008, 46(2): 155-164.
3. 肖永红. 国家细菌耐药控制行动计划: 基于大健康理念的耐药控制宏图. 中华临床感染病杂志, 2016, 9(4): 289-293.
4. Van Nimwegen KJ, Van Soest RA, Veltman JA, et al. Is the $1000 genome as near as we think? A cost analysis of next-generation sequencing. Clin Chem, 2016, 62(11): 1458-1464.
5. 中华医学会呼吸病学分会感染学组. 中国成人医院获得性肺炎与呼吸机相关性肺炎诊断和治疗指南(2018 年版). 中华结核和呼吸杂志, 2018, 41(4): 255-280.
6. Ruppé E, Greub G, Schrenzel J. Messages from the first International Conference on Clinical Metagenomics (ICCMg). Microbes Infect, 2017, 19(4-5): 223-228.
7. Kalil AC, Metersky ML, Klompas M, et al. Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society. Clin Infect Dis, 2016, 63(5): 61-111.
8. Aguado JM, Vazquez L, Fernandez-Ruiz M, et al. Serum galactomannan versus a combination of galactomannan and polymerase chain reaction-based Aspergillus DNA detection for early therapy of invasive aspergillosis in high-risk hematological patients: a randomized controlled trial. Clin Infect Dis, 2015, 60(3): 405-414.
9. Subramony A, Zachariah P, Krones A, et al. Impact of multiplex polymerase chain reaction testing for respiratory pathogens on healthcare resource utilization for pediatric inpatients. J Pediatr, 2016, 173: 196-201.
10. Schlaberg R, Chiu CY, Miller S, et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch Pathol Lab Med, 2017, 141(6): 776-786.
11. Franzosa EA, Hsu T, Sirota-Madi A, et al. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Microbiol, 2015, 13(6): 360-372.
12. Parize P, Muth E, Richaud C, et al. Untargeted next-generation sequencing-based first-line diagnosis of infection in immunocompromised adults: a multicentre, blinded, prospective study. Clin Microbiol Infect, 2017, 23(8): 574. e1-574. e6.
13. Quince C, Walker AW, Simpson JT, et al. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol, 2017, 35(9): 833-844.
14. Van Dijk EL, Auger H, Jaszczyszyn Y, et al. Ten years of next-generation sequencing technology. Trends Genet, 2014, 30(9): 418-426.
15. Zhernakova A, Kurilshikov A, Bonder MJ, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 2016, 352(6285): 565-569.
16. Simner PJ, Miller S, Carroll KC. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clin Infect Dis, 2018, 66(5): 778-788.
17. Moran Losada P, Chouvarine P, Dorda M, et al. The cystic fibrosis lower airways microbial metagenome. ERJ Open Res, 2016, 2(2): pii: 00096-2015.
18. Langelier C, Zinter MS, Kalantar K, et al. Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients. Am J Respir Crit Care Med, 2018, 197(4): 524-528.
19. Lewandowska DW, Schreiber PW, Schuurmans MM, et al. Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection. PloS One, 2017, 12(5): e0177340.
20. Gerber JS, Ross RK, Bryan M, et al. Association of broad- vs narrow-spectrum antibiotics with treatment failure, adverse events, and quality of life in children with acute respiratory tract infections. JAMA, 2017, 318(23): 2325-2336.
21. Pendleton KM, Erb-Downward JR, Bao Y, et al. Rapid pathogen identification in bacterial pneumonia using real-time metagenomics. Am J Respir Crit Care Med, 2017, 196(12): 1610-1612.
22. Ruppé E, Cherkaoui A, Lazarevic V, et al. Establishing genotype-to-phenotype relationships in bacteria causing hospital-acquired pneumonia: a prelude to the application of clinical metagenomics. Antibiotics, 2017, 6(4): 30-45.
23. Rogers GB, Wesselingh S. Precision respiratory medicine and the microbiome. Lancet Respir Med, 2016, 4(1): 73-82.
24. 中华医学会呼吸病学分会. 中国成人社区获得性肺炎诊断和治疗指南(2016 年版). 中华结核和呼吸杂志, 2016, 39(4): 241-242.
25. Barbier F, Andremont A, Wolff M, et al. Hospital-acquired pneumonia and ventilator-associated pneumonia. Curr Opin Pulm Med, 2013, 19(3): 216-228.
26. Grumaz S, Stevens P, Grumaz C, et al. Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med, 2016, 8(1): 73.
27. Weterings V, Bosch T, Witteveen S, et al. Next-generation sequence analysis reveals transfer of methicillin resistance to a methicillin-susceptible Staphylococcus aureus strain that subsequently caused a methicillin-resistant Staphylococcus aureus outbreak: a descriptive study. J Clin Microbiol, 2017, 55(9): 2808-2816.
28. Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother, 2012, 67(11): 2640-2644.
29. McArthur AG, Waglechner N, Nizam F, et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother, 2013, 57(7): 3348-3357.
30. Gupta SK, Padmanabhan BR, Diene SM, et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother, 2014, 58(1): 212-220.
31. Stämmler F, Gläsner J, Hiergeist A, et al. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome, 2016, 4(1): 28.
32. Lloyd CM, Marsland BJ. Lung homeostasis: influence of age, microbes, and the immune system. Immunity, 2017, 46(4): 549-561.
33. Thoendel M, Jeraldo P, Greenwood-Quaintance KE, et al. A possible novel prosthetic joint infection pathogen, mycoplasma salivarium, identified by metagenomic shotgun sequencing. Clin Infect Dis, 2017, 65(2): 332-335.
34. Goodwin S, Mcpherson JD, Mccombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet, 2016, 17(6): 333-351.
35. Guan H, Shen A, Lv X, et al. Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing. J Neurovirol, 2016, 22(2): 240-245.
36. Tsai YC, Conlan S, Deming C, et al. Resolving the complexity of human skin metagenomes using single-molecule sequencing. MBio, 2016, 7(1): e01948-15.
37. Schmidt K, Mwaigwisya S, Crossman LC, et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother, 2017, 72(1): 104-114.
38. Hasan MR, Rawat A, Tang P, et al. Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing. J Clin Microbiol, 2016, 54(4): 919-927.
39. Noyes NR, Weinroth ME, Parker J, et al. Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. Microbiome, 2017, 5(1): 142.
40. Thoendel M, Jeraldo P, Greenwood-Quaintance KE, et al. Impact of contaminating DNA in whole-genome amplification kits used for metagenomic shotgun sequencing for infection diagnosis. J Clin Microbiol, 2017, 55(6): 1789-1801.
41. Kim D, Hofstaedter CE, Zhao C, et al. Optimizing methods and dodging pitfalls in microbiome research. Microbiome, 2017, 5(1): 52.

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临床宏基因组学在呼吸感染性疾病精准诊疗中的疑问解析

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