Detecting Circulating Microbial Cell-free DNA by Next-generation Sequencing in Patients with Complex-lung Disease: A Pilot Study

Overview

Journal Tzu Chi Med J

Specialty General Medicine

Date 2024 Feb 26

PMID 38406566

Authors

Yen-Han Tseng

Sheng-Wei Pan

Jia-Yih Feng

Wei-Juin Su

Chi-Ying F Huang

Yuh-Min Chen

Affiliations

Soon will be listed here.

Abstract

Objectives: Determining a diagnosis for non- (NTM)-lung disease (LD) remains difficult. The value of circulating cell-free DNA (cfDNA) secreted from microbes has been established in the detection of pathogens in septic patients. However, it is unknown whether NTM-derived cfDNA is detectable in plasma from patients with NTM-LD and whether this is associated with the disease status of NTM-LD, especially in patients with complex (MAC)-LD.

Materials And Methods: In this pilot study, from 2018 to 2019, we enrolled adult patients with MAC-LD at Taipei Veterans General Hospital in Taiwan for the detection of circulating cfDNA. We performed cfDNA extraction from plasma, next-generation sequencing (NGS) for nonhuman cfDNA, and sequence matching to a microbial database and then assessed the association between pathogen cfDNA and MAC-LD.

Results: Two (40%) plasma samples from MAC-LD patients had detectable MAC-specific cfDNA, namely one instance of DNA polymerase III alpha subunit and one instance of ATP-binding cassette transporters permease. The plasma samples from the three other MAC-LD cases and the one tuberculosis control were negative for either NTM-derived cfDNA or tuberculosis-related cfDNA. In addition to MAC-specific cfDNA, , , and were the most observed bacteria in our patients. The two patients with MAC-cfDNA positivity yielded higher radiographic scores ( = 0.076) and presented a higher number of nonhuman reads than those without MAC-cfDNA positivity ( = 0.083).

Conclusion: Using NGS method, we demonstrated MAC-cfDNA was detectable in patients with MAC-LD. Further large-scale research is warranted to assess the clinical value of detecting MAC-specific cfDNA in MAC-LD patients.

References

Nikkari S, McLaughlin I, Bi W, Dodge D, Relman D . Does blood of healthy subjects contain bacterial ribosomal DNA?. J Clin Microbiol. 2001; 39(5):1956-9. PMC: 88056. DOI: 10.1128/JCM.39.5.1956-1959.2001. View

Zhou K, Li C, Chen D, Pan Y, Tao Y, Qu W . A review on nanosystems as an effective approach against infections of . Int J Nanomedicine. 2018; 13:7333-7347. PMC: 6233487. DOI: 10.2147/IJN.S169935. View

Roth A, Fischer M, Hamid M, Michalke S, Ludwig W, Mauch H . Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J Clin Microbiol. 1998; 36(1):139-47. PMC: 124824. DOI: 10.1128/JCM.36.1.139-147.1998. View

Oreskovic A, Panpradist N, Marangu D, Ngwane M, Magcaba Z, Ngcobo S . Diagnosing Pulmonary Tuberculosis by Using Sequence-Specific Purification of Urine Cell-Free DNA. J Clin Microbiol. 2021; 59(8):e0007421. PMC: 8373247. DOI: 10.1128/JCM.00074-21. View

Reyes-Lamothe R, Sherratt D, Leake M . Stoichiometry and architecture of active DNA replication machinery in Escherichia coli. Science. 2010; 328(5977):498-501. PMC: 2859602. DOI: 10.1126/science.1185757. View

Smith C, Halse T, Shea J, Modestil H, Fowler R, Musser K . Assessing Nanopore Sequencing for Clinical Diagnostics: a Comparison of Next-Generation Sequencing (NGS) Methods for Mycobacterium tuberculosis. J Clin Microbiol. 2020; 59(1). PMC: 7771457. DOI: 10.1128/JCM.00583-20. View

Prevots D, Marras T . Epidemiology of human pulmonary infection with nontuberculous mycobacteria: a review. Clin Chest Med. 2015; 36(1):13-34. PMC: 4332564. DOI: 10.1016/j.ccm.2014.10.002. View

Daley C, Winthrop K . Mycobacterium avium Complex: Addressing Gaps in Diagnosis and Management. J Infect Dis. 2020; 222(Suppl 4):S199-S211. PMC: 7566660. DOI: 10.1093/infdis/jiaa354. View

Jeong B, Jeon K, Park H, Kim S, Lee K, Huh H . Intermittent antibiotic therapy for nodular bronchiectatic Mycobacterium avium complex lung disease. Am J Respir Crit Care Med. 2014; 191(1):96-103. DOI: 10.1164/rccm.201408-1545OC. View

10.

Xue H, Lozano-Duran R, Macho A . Insights into the Root Invasion by the Plant Pathogenic Bacterium . Plants (Basel). 2020; 9(4). PMC: 7238422. DOI: 10.3390/plants9040516. View

11.

Huang Y, Chen Y, Fan T, Chang N, Chen Y, Midha M . Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females. BMC Med Genomics. 2018; 11(Suppl 1):16. PMC: 5836824. DOI: 10.1186/s12920-018-0329-y. View

12.

Field S, Fisher D, Cowie R . Mycobacterium avium complex pulmonary disease in patients without HIV infection. Chest. 2004; 126(2):566-81. DOI: 10.1378/chest.126.2.566. View

13.

Chiu K, Yu A . Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions. PeerJ. 2019; 7:e7426. PMC: 6688590. DOI: 10.7717/peerj.7426. View

14.

Harper M, Boyce J, Adler B . Pasteurella multocida pathogenesis: 125 years after Pasteur. FEMS Microbiol Lett. 2006; 265(1):1-10. DOI: 10.1111/j.1574-6968.2006.00442.x. View

15.

McLaughlin R, Vali H, Lau P, Palfree R, De Ciccio A, Sirois M . Are there naturally occurring pleomorphic bacteria in the blood of healthy humans?. J Clin Microbiol. 2002; 40(12):4771-5. PMC: 154583. DOI: 10.1128/JCM.40.12.4771-4775.2002. View

16.

Volik S, Alcaide M, Morin R, Collins C . Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies. Mol Cancer Res. 2016; 14(10):898-908. DOI: 10.1158/1541-7786.MCR-16-0044. View

17.

Ben Salah I, Adekambi T, Raoult D, Drancourt M . rpoB sequence-based identification of Mycobacterium avium complex species. Microbiology (Reading). 2008; 154(Pt 12):3715-3723. DOI: 10.1099/mic.0.2008/020164-0. View

18.

Waugh J, Granger W, Gaggar A . Incidence, relevance and response for Ralsfonia respiratory infections. Clin Lab Sci. 2010; 23(2):99-106. PMC: 4086841. View

19.

Snider G, Doctor L, Demas T, Shaw A . Obstructive airway disease in patients with treated pulmonary tuberculosis. Am Rev Respir Dis. 1971; 103(5):625-40. DOI: 10.1164/arrd.1971.103.5.625. View

20.

Griffith D, Aksamit T, Brown-Elliott B, Catanzaro A, Daley C, Gordin F . An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med. 2007; 175(4):367-416. DOI: 10.1164/rccm.200604-571ST. View