Pathogen detection in suspected spinal infection: metagenomic next-generation sequencing versus culture

Babic M, Simpfendorfer C (2017) Infections of the spine. Infect Dis Clin North Am 31:279–297. https://doi.org/10.1016/j.idc.2017.01.003

Article  PubMed  Google Scholar 

Luzzati R, Giacomazzi D, Danzi M, Tacconi L, Concia E, Vento S (2009) Diagnosis, management and outcome of clinically-suspected spinal infection. J Infect 58:259–265. https://doi.org/10.1016/j.jinf.2009.02.006

Article  PubMed  Google Scholar 

Duarte R, Vaccaro A (2013) Spinal infection: state of the art and management algorithm. Eur spine J 22:2787–2799. https://doi.org/10.1007/s00586-013-2850-1

Article  PubMed  PubMed Central  Google Scholar 

Go JL, Rothman S, Prosper A, Silbergleit R, Lerner A (2012) Spine infections. Neuroimaging Clin N Am. https://doi.org/10.1016/j.nic.2012.06.002

Article  PubMed  Google Scholar 

Herren C, Jung N, Pishnamaz M, Breuninger M, Siewe J, Sobottke R (2017) Spondylodiscitis: diagnosis and treatment options a systematic review. Dtsch Arztebl Int. https://doi.org/10.3238/arztebl.2017.0875

Article  PubMed  PubMed Central  Google Scholar 

Nagashima H, Tanishima S, Tanida A (2018) Diagnosis and management of spinal infections. J Orthop Sci 23:8–13. https://doi.org/10.1016/j.jos.2017.09.016

Article  PubMed  Google Scholar 

Avenel G, Guyader P, Fiaux E, Alcaix D, Zarnitsky C, Pouplin-Jardin S, Kozyreff-Meurice M, Lequerré T, Vittecoq O (2021) Microbiological diagnosis of suspected vertebral osteomyelitis with a focus on the yield of percutaneous needle biopsy: a 10 year cohort study. Eur J Clin Microbiol Infect Dis 40:297–302. https://doi.org/10.1007/s10096-020-04022-3

Article  CAS  PubMed  Google Scholar 

Chew FS, Kline MJ (2001) Diagnostic yield of CT-guided percutaneous aspiration procedures in suspected spontaneous infectious diskitis. Radiology 218:211–214. https://doi.org/10.1148/radiology.218.1.r01ja06211

Article  CAS  PubMed  Google Scholar 

de Lucas E, González Mandly A, Gutiérrez A, Pellón R, Martín-Cuesta L, Izquierdo J, Sánchez E, Ruiz E, Quintana F (2009) CT-guided fine-needle aspiration in vertebral osteomyelitis: true usefulness of a common practice. Clin Rheumatol 28:315–320. https://doi.org/10.1007/s10067-008-1051-5

Article  PubMed  Google Scholar 

Kim C, Song K, Park W, Kim E, Park S, Kim H, Oh M, Kim N (2012) Microbiologically and clinically diagnosed vertebral osteomyelitis: impact of prior antibiotic exposure. Antimicrob Agents Chemother 56:2122–2124. https://doi.org/10.1128/aac.05953-11

Article  CAS  PubMed  PubMed Central  Google Scholar 

Simner PJ, Miller S, Carroll KC (2018) As a diagnostic tool for infectious diseases. Clin Infect Dis 66:778–788. https://doi.org/10.1093/cid/cix881

Article  CAS  PubMed  Google Scholar 

Gu W, Miller S, Chiu CY (2019) Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol 14:319–338. https://doi.org/10.1146/annurev-pathmechdis-012418-012751

Article  CAS  PubMed  Google Scholar 

Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, Berger A, Douglas V, Josephson SA, Chow FC, Fulton BD, DeRisi JL, Gelfand JM, Naccache SN, Bender J, Dien Bard J, Murkey J, Carlson M, Vespa PM, Vijayan T, Allyn PR, Campeau S, Humphries RM, Klausner JD, Ganzon CD, Memar F, Ocampo NA, Zimmermann LL, Cohen SH, Polage CR, DeBiasi RL, Haller B, Dallas R, Maron G, Hayden R, Messacar K, Dominguez SR, Miller S, Chiu CY (2019) Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis. New Engl J Med 380:2327–2340. https://doi.org/10.1056/NEJMoa1803396

Article  CAS  PubMed  Google Scholar 

Huang ZD, Zhang ZJ, Yang B, Li WB, Zhang CJ, Fang XY, Zhang CF, Zhang WM, Lin JH (2020) Pathogenic detection by metagenomic next-generation sequencing in osteoarticular infections. Front Cell Infect Microbiol 10:471. https://doi.org/10.3389/fcimb.2020.00471

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tarabichi M, Shohat N, Goswami K, Alvand A, Silibovsky R, Belden K, Parvizi J (2018) Diagnosis of periprosthetic joint infection: the potential of next-generation sequencing. J Bone Joint Surg Am 100:147–154. https://doi.org/10.2106/JBJS.17.00434

Article  PubMed  Google Scholar 

Berbari E, Kanj S, Kowalski T (2015) 2015 Infectious diseases society of America (IDSA) clinical practice guidelines for the diagnosis and treatment of native vertebral osteomyelitis in adults. Clin infect dis 61:e26-46. https://doi.org/10.1093/cid/civ482

Article  PubMed  Google Scholar 

Levitt A, Shah LM, Parsons MS, Agarwal V, Baldwin K, Bhattacharyya S, Boulter DJ, Burns J, Fink KR, Hunt CH, Hutchins TA, Kao LS, Khan MA, Lo BM, Moritani T, Reitman C, Repplinger MD, Shah VN, Singh S, Timpone VM, Corey AS (2021) ACR appropriateness criteria® suspected spine infection. J Am Coll Radiol 18:S488-s501. https://doi.org/10.1016/j.jacr.2021.09.001

Article  PubMed  Google Scholar 

Horan T, Gaynes R, Martone W, Jarvis W, Emori T (1992) CDC definitions of nosocomial surgical site infections, 1992: a modification of CDC definitions of surgical wound infections. Infect Control Hosp Epidemiol 13:606–608. https://doi.org/10.1086/646436

Article  CAS  PubMed  Google Scholar 

Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, Yao Y, Su Y, Huang Y, Wang M, Li B, Li H, Zhou C, Li C, Ye M, Xu X, Li Y, Hu B (2018) Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis 67:S231-s240. https://doi.org/10.1093/cid/ciy693

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim B, Lee J, Kim S, Lee G, Kang H (2013) Diagnostic yield of fluoroscopy-guided biopsy for infectious spondylitis. AJNR Am J Neuroradiol 34:233–238. https://doi.org/10.3174/ajnr.A3120

Article  CAS  PubMed  PubMed Central  Google Scholar 

Woo P, Lau S, Teng J, Tse H, Yuen K (2008) Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin microbiol infect 14:908–934. https://doi.org/10.1111/j.1469-0691.2008.02070.x

Article  CAS  PubMed  Google Scholar 

Ma C, Wu H, Chen G, Liang C, Wu L, Xiao Y (2021) The potential of metagenomic next-generation sequencing in diagnosis of spinal infection: a retrospective study. Eur Spine J. https://doi.org/10.1007/s00586-021-07026-5

Article  PubMed  Google Scholar 

Grumaz S, Grumaz C, Vainshtein Y, Stevens P, Glanz K, Decker SO, Hofer S, Weigand MA, Brenner T, Sohn K (2019) Enhanced performance of next-generation sequencing diagnostics compared with standard of care microbiological diagnostics in patients suffering from septic shock. Crit Care Med 47:e394–e402. https://doi.org/10.1097/ccm.0000000000003658

Article  PubMed  PubMed Central  Google Scholar 

Salipante S, Hoogestraat D, Abbott A, SenGupta D, Cummings L, Butler-Wu S, Stephens K, Cookson B, Hoffman N (2014) Coinfection of fusobacterium nucleatum and actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing. J Clin Microbiol 52:1789–1792. https://doi.org/10.1128/jcm.03133-13

Article  CAS  PubMed  PubMed Central  Google Scholar 

McIntyre A, Ounit R, Afshinnekoo E, Prill R, Hénaff E, Alexander N, Minot S, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan N, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell R, Rosen G, Mason C (2017) Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. Genome Biol 18:182. https://doi.org/10.1186/s13059-017-1299-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jakobsen T, Eickhardt S, Gheorghe A, Stenqvist C, Sønderholm M, Stavnsberg C, Jensen P, Odgaard A, Whiteley M, Moser C, Hvolris J, Hougen H, Bjarnsholt T (2018) Implants induce a new niche for microbiomes. APMIS 126:685–692. https://doi.org/10.1111/apm.12862

Article  PubMed  Google Scholar 

Thoendel M, Jeraldo P, Greenwood-Quaintance K, Yao J, Chia N, Hanssen A, Abdel M, Patel R (2017) Impact of contaminating DNA in Whole-Genome amplification kits used for metagenomic Shotgun sequencing for infection diagnosis. J Clin Microbiol 55:1789–1801. https://doi.org/10.1128/jcm.02402-16

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hasan M, Rawat A, Tang P, Jithesh P, Thomas E, Tan R, Tilley P (2016) Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing. J Clin Microbiol 54:919–927. https://doi.org/10.1128/jcm.03050-15

Article  CAS  PubMed  PubMed Central  Google Scholar 

Salzberg S, Breitwieser F, Kumar A, Hao H, Burger P, Rodriguez F, Lim M, Quiñones-Hinojosa A, Gallia G, Tornheim J, Melia M, Sears C, Pardo C (2016) Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system. Neurol neuroimmunol neuroinflam 3:e251. https://doi.org/10.1212/nxi.0000000000000251

Article  Google Scholar 

留言 (0)

沒有登入
gif