Abstract
Abscesses are often clinically manifested as local necrotic tissues in various organs or systems of the human body, which is commonly caused by microbial infection. Rapid and accurate identification of pathogens from clinical abscetic samples would greatly guide a clinician to make the precise choices of the antimicrobial treatment. Here, this study aimed to investigate the application of metagenomic next-generation sequencing (mNGS) in the microbial detection of clinical samples of abscess fluids from various organs or systems. Nine patients with abscess from various organs or systems were enrolled in this study. The pathogenic bacteria in abscess fluid were detected and compared by the conventional bacterial culture and mNGS respectively. The dominant pathogens of abscess fluids in 8 cases can be found directly from mNGS, dominating over 80% of the total reads abundance of the microbiome. Although the pathogens from 6 cases detected by mNGS were consistent with that from the conventional bacteria culture method, the fastidious obligate anaerobic bacteria in 2 cases additionally detected by mNGS were not found by the conventional culture method. Moreover, complex polymicrobial infection containing Parvimonas micra in one case negatively with conventional bacterial culture were demonstrated by the mNGS method. And the mNGS method can directly reflect the diversity of microbial ecology in the abscess fluids from the different parts of the human body. Conclusively, mNGS can be used as a supplemental method for the pathogen detection of clinically abscess fluids.
Similar content being viewed by others
Data availability
Supplement Table 1 showed the reads number information of all the species detected by mNGS in this study. The microbiome reads from abscess samples in this study were depleted of human host sequences and have been submitted to the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject) (accession number: PRJNA660600).
References
Blauwkamp TA, Thair S, Rosen MJ, Blair L, Lindner MS, Vilfan ID, Kawli T, Christians FC, Venkatasubrahmanyam S, Wall GD, Cheung A, Rogers ZN, Meshulam-Simon G, Huijse L, Balakrishnan S, Quinn JV, Hollemon D, Hong DK, Vaughn ML, Kertesz M, Bercovici S, Wilber JC, Yang S (2019) Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol 4:663–674. https://doi.org/10.1038/s41564-018-0349-6
Chiu CY, Miller SA (2019) Clinical metagenomics. Nat Rev Genet 20:341–355. https://doi.org/10.1038/s41576-019-0113-7
Co M, Cheng VCC, Wei J, Wong SCY, Chan SMS, Shek T, Kwong A (2018) Idiopathic granulomatous mastitis: a 10-year study from a multicentre clinical database. Pathology 50:742–747. https://doi.org/10.1016/j.pathol.2018.08.010
Elgouhari H, Othman M, Gerstein WH (2007) Bacteroides fragilis vertebral osteomyelitis: case report and a review of the literature. South Med J 100:506–511. https://doi.org/10.1097/01.smj.0000262587.48592.56
Guo L-Y, Feng W-Y, Guo X, Liu B, Liu G, Dong J (2019) The advantages of next-generation sequencing technology in the detection of different sources of abscess. J Inf Secur 78:75–86. https://doi.org/10.1016/j.jinf.2018.08.002
Jousimies-Somer H, Savolainen S, Mäkitie A, Ylikoski J (1993) Bacteriologic findings in peritonsillar abscesses in young adults. Clin Infect Dis 16(Suppl 4):S292–S298. https://doi.org/10.1093/clinids/16.supplement_4.s292
Kozlov A, Bean L, Hill EV et al (2018) Molecular identification of bacteria in intra-abdominal abscesses using deep sequencing. Open Forum Infect Dis 5:ofy025. https://doi.org/10.1093/ofid/ofy025
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
Lin J, Wu Z, Gong L et al (2019) Complex microbiome in brain abscess revealed by whole-genome culture-independent and culture-based sequencing. J Clin Med:8. https://doi.org/10.3390/jcm8030351
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
Miksić NG, Kljaić Dujić M, Rejc Marko J, Voršič M, But I (2019) Bacteroides fragilis sacral spondylodiscitis and epidural abscess after sacrocolpopexy: a case report and literature review. J Int Med Res 47:4568–4574. https://doi.org/10.1177/0300060519866270
Sendi P, Bregenzer T, Zimmerli W (2008) Spinal epidural abscess in clinical practice. QJM 101:1–12. https://doi.org/10.1093/qjmed/hcm100
Sibley CD, Church DL, Surette MG, Dowd SE, Parkins MD (2012) Pyrosequencing reveals the complex polymicrobial nature of invasive pyogenic infections: microbial constituents of empyema, liver abscess, and intracerebral abscess. Eur J Clin Microbiol Infect Dis 31:2679–2691. https://doi.org/10.1007/s10096-012-1614-x
Siu LK, Yeh K-M, Lin J-C, Fung CP, Chang FY (2012) Klebsiella pneumoniae liver abscess: a new invasive syndrome. Lancet Infect Dis 12:881–887. https://doi.org/10.1016/S1473-3099(12)70205-0
Tauch A, Fernández-Natal I, Soriano F (2016) A microbiological and clinical review on Corynebacterium kroppenstedtii. Int J Infect Dis 48:33–39. https://doi.org/10.1016/j.ijid.2016.04.023
Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY (2014) Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 370:2408–2417. https://doi.org/10.1056/NEJMoa1401268
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. N Engl J Med 380:2327–2340. https://doi.org/10.1056/NEJMoa1803396
Yu H-J, Deng H, Ma J, Huang SJ, Yang JM, Huang YF, Mu XP, Zhang L, Wang Q (2016) Clinical metagenomic analysis of bacterial communities in breast abscesses of granulomatous mastitis. Int J Infect Dis 53:30–33. https://doi.org/10.1016/j.ijid.2016.10.015
Funding
This work was supported by grants from the Natural Science Fund of Guangdong Province (No. 2020A1515010979); Science, Technology and Innovation Commission of Shenzhen Municipality of key funds (JCYJ20170412143551332) and basic research funds (JCYJ20180302144721183; JCYJ20180302144340004; JCYJ20180302144345028; JCYJ20180302144431923); the Shenzhen Nanshan District Scientific Research Program of the People’s Republic of China (No. 2019001, 2019004, 2019005, 2019027); and provincial medical funds of Guangdong (No. A2018163); Sanmin Project of Medicine in Shenzhen and Shenzhen Key Medical Discipline Construction Fund (No. SZXK06162).
Author information
Authors and Affiliations
Contributions
Yuxi Zhao, Peiyu Li, Qiwen Deng, and Zhijian Yu made substantial contributions to the conception or design of the work. Yuxi Zhao, Jinlian Chen, Bing Bai, Yu Wang, and Jinxin Zheng made substantial contributions to the acquisition and analysis of data. Yuxi Zhao, Jinlian Chen, Bing Bai, Peiyu Li, and Zhijian Yu drafted the work or revised it critically for important intellectual content. Peiyu Li and Qiwen Deng approved the version to be published and agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethics approval
This study was approved by the system review committee of Nanshan District People’s Hospital of Shenzhen city according to relevant laws and system guidelines. All patients or their legal guardians provide written informed consent.
Consent to participate
Not applicable
Consent for publication
Not applicable
Code availability
Not applicable
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(XLSX 32.3 kb)
Rights and permissions
About this article
Cite this article
Zhao, Y., Chen, J., Bai, B. et al. Pathogen determination from clinical abscess fluids using metagenomic next-generation sequencing. Folia Microbiol 66, 197–202 (2021). https://doi.org/10.1007/s12223-020-00829-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12223-020-00829-x