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ORIGINAL ARTICLE
Differentiation complex sputum microbiome in patients suspected TB pulmonary
1
Doctoral Degree Program, Faculty of Medicine, Universitas Airlangga, Surabaya, INDONESIA
2
Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, INDONESIA
3
Dr. Soetomo General Academic Hospital, Surabaya, INDONESIA
4
Tuberculosis Laboratory, Institute of Tropical Disease, Universitas Airlangga, Surabaya, INDONESIA
5
Department of Internal Medicine Sub Pulmonology, Faculty of Medicine, Universitas Hang Tuah, Surabaya, INDONESIA
6
Department of Biochemistry, Faculty of Mathematics and Natural Science, Institut Pertanian Bogor, Bogor, INDONESIA
Publication date: 2024-11-06
Electron J Gen Med 2024;21(6):em612
KEYWORDS
ABSTRACT
Purpose::
This is the first study to attempt microbiome diversity using metagenomic full-length 16S rRNA from respiratory specimens suspected of chronic pulmonary TB patients.
Materials and methods::
A 33 patients with suspected chronic pulmonary TB were included. Sputum specimens were cultured to detect mycobacterium sp. and extracted using QiAmp DNA mini kit modification and 16S rRNA metagenomic sequencing by nanopore grid ion sequencer. Microbiome analysis was performed using Pavian and Krona tools.
Results::
9 patients were diagnosed with TB based on GeneXpert MTB/RIF assay, and 3 patients were detected with NTM pulmonary infection.The common genera identified from TB culture positive patients were streptococcus sp., prevotella sp., and veilonella sp. However, less was detected in two NTM infection patients. Metagenomic analysis revealed community bacteria species, including mycobacterium tuberculosis and NTM species, with the lowest number of unique reads. The abundance of streptococcus sp. were less than 30% in 4 patient with comorbid diabetes mellitus.
Conclusions::
Metagenomic targeted 16SrRNA full-length sequencing in the clinical respiratory specimen can provide diagnostic insight beyond standard microbiologic cultures and detailed profiling of microbial communities at the species level.
This is the first study to attempt microbiome diversity using metagenomic full-length 16S rRNA from respiratory specimens suspected of chronic pulmonary TB patients.
Materials and methods::
A 33 patients with suspected chronic pulmonary TB were included. Sputum specimens were cultured to detect mycobacterium sp. and extracted using QiAmp DNA mini kit modification and 16S rRNA metagenomic sequencing by nanopore grid ion sequencer. Microbiome analysis was performed using Pavian and Krona tools.
Results::
9 patients were diagnosed with TB based on GeneXpert MTB/RIF assay, and 3 patients were detected with NTM pulmonary infection.The common genera identified from TB culture positive patients were streptococcus sp., prevotella sp., and veilonella sp. However, less was detected in two NTM infection patients. Metagenomic analysis revealed community bacteria species, including mycobacterium tuberculosis and NTM species, with the lowest number of unique reads. The abundance of streptococcus sp. were less than 30% in 4 patient with comorbid diabetes mellitus.
Conclusions::
Metagenomic targeted 16SrRNA full-length sequencing in the clinical respiratory specimen can provide diagnostic insight beyond standard microbiologic cultures and detailed profiling of microbial communities at the species level.
REFERENCES (36)
1.
MoH. Factsheet country profile Indonesia 2022. Ministry of Health Indonesia, 2022. Available at: https://tbindonesia. or.id/wp-content/uploads/2023/02/Factsheet-Country-Profile-Indonesia-2022.pdf (Accessed: 26 July 2024).
2.
CBS. East Java Central Bureau of Statistics. Available at: https://jatim.bps.go.id/id/sta... (Accessed: 26 July 2024).
3.
Gadoev J, Asadov D, Harries AD, et al. Recurrent tuberculosis and associated factors: A five-year countrywide study in Uzbekistan. PLoS One. 2017;12(5): e0176473. https://doi.org/10.1371/journa... PMid:28472053 PMCid:PMC5417503.
4.
Griffith DE, Aksamit TR. Nontuberculous mycobacterial disease therapy. Chest. 2016;150(6):1177-8. https://doi.org/10.1016/j.ches....
5.
Diel R, Lipman M, Hoefsloot W. High mortality in patients with mycobacterium avium complex lung disease: A systematic review. BMC Infect Dis. 2018;18(1):206. https://doi.org/10.1186/s12879... PMid:29724184 PMCid:PMC5934808.
6.
Dheda K, Gumbo T, Maartens G, et al. The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. Lancet Respir Med. 2017;5(4):291-360. https://doi.org/10.1016/S2213-... PMid:28344011.
7.
Krishna P, Jain A, Bisen PS. Microbiome diversity in the sputum of patients with pulmonary tuberculosis. Eur J Clin Microbiol Infect Dis. 2016;35(7):1205-10. https://doi.org/10.1007/s10096... PMid:27142586.
8.
Kang S-Y, Kim H, Jung S, Lee SM, Lee SP. The lung microbiota in Korean patients with non-tuberculous mycobacterial pulmonary disease. BMC Microbiol. 2021;21(1):84. https://doi.org/10.1186/s12866... PMid:33736609 PMCid:PMC7977250.
9.
Nelson MT, Pope CE, Marsh RL, et al. Human and extracellular DNA depletion for metagenomic analysis of complex clinical infection samples yields optimized viable microbiome profiles. Cell Rep. 2019;26(8):2227-40.e5. https://doi.org/10.1016/j.celr... PMid:30784601 PMCid:PMC6435281.
10.
Hu Y, Cheng M, Liu B, et al. Metagenomic analysis of the lung microbiome in pulmonary tuberculosis–A pilot study. Emeerg Microbes Infect. 2020;9(1):1444-52. https://doi.org/10.1080/222217... PMid:32552447 PMCid:PMC7473061.
11.
Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L. Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment. Environ Microbiol Rep. 2019;11(4):487-94. https://doi.org/10.1111/1758-2... PMid:30058291 PMCid:PMC6618113.
12.
Santos A, van Aerle R, Barrientos L, Martinez-Urtaza J. Computational methods for 16S metabarcoding studies using nanopore sequencing data. Comput Struct Biotechnol J. 2020;18:296-305. https://doi.org/10.1016/j.csbj... PMid:32071706 PMCid:PMC7013242.
13.
Mizrahi H, Peretz A, Lesnik R, et al. Comparison of sputum microbiome of legionellosis-associated patients and other pneumonia patients: Indications for polybacterial infections. Sci Rep. 2017;7:40114. https://doi.org/10.1038/srep40... PMid:28059171 PMCid:PMC5216348.
14.
Meehan CJ, Goig GA, Kohl TA, et al. Whole genome sequencing of mycobacterium tuberculosis: Current standards and open issues. Nat Rev Microbiol. 2019; 17(9):533-45. https://doi.org/10.1038/s41579... PMid:31209399.
15.
Huang Z-D, Zhang Z-J, Yang B, et al. Pathogenic detection by metagenomic next-generation sequencing in osteoarticular infections. Front Cell Infect Microbiol. 2020;10:471. https://doi.org/10.3389/fcimb.... PMid:33042860 PMCid:PMC7527540.
16.
Zhang Y, Feng S, Chen W, Zhang Q-C, Shi S-F, Chen X-Y. Advantages of 16S rRNA PCR for the diagnosis of prosthetic joint infection. Exp Ther Med. 2020;20(4):3104-113. https://doi.org/10.3892/etm.20... PMid:32855678 PMCid:PMC7444347.
17.
d’Humières C, Salmona M, Dellière S, et al. The potential role of clinical metagenomics in infectious diseases: Therapeutic perspectives. Drugs. 2021;81(13):1453-66. https://doi.org/10.1007/s40265... PMid:34328626 PMCid:PMC8323086.
18.
Chen P, Sun W, He Y. Comparison of metagenomic next-generation sequencing technology, culture and GeneXpert MTB/RIF assay in the diagnosis of tuberculosis. J Thorac Dis. 2020;12(8):4014-24. https://doi.org/10.21037/jtd-2... PMid:32944313 PMCid:PMC747557.
19.
Yang Z. Optimised protocol of QIAamp® DNA mini Kit for bacteria genomic DNA extraction from both pure and mixture sample. Protoc Exch. 2019. https://doi.org/10.21203/rs.2.....
20.
Wick RR, Judd LM, Holt KE. Performance of neural network basecalling tools for Oxford nanopore sequencing. Genome Biol. 2019;20(1):129. https://doi.org/10.1186/s13059... PMid:31234903 PMCid:PMC6591954.
21.
De Coster W, D’hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: Visualizing and processing long-read sequencing data. Bioinformatics. 2018;34(15): 2666-9. https://doi.org/10.1093/bioinf... PMid:29547981 PMCid:PMC6061794.
22.
Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: Rapid and sensitive classification of metagenomic sequences. Genome Res. 2016;26(12):1721-9. https://doi.org/10.1101/gr.210... PMid:27852649 PMCid:PMC5131823.
23.
Ciuffreda L, Rodríguez-Pérez H, Flores C. Nanopore sequencing and its application to the study of microbial communities. Comput Struct Biotechnol J. 2021;19:1497-511. https://doi.org/10.1016/J.CSBJ... PMid:33815688 PMCid:PMC7985215.
24.
Yang L, Haidar G, Zia H, et al. Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: A feasibility and clinical validity study. Respir Res. 2019;20(1):265. https://doi.org/10.1186/s12931... PMid:31775777 PMCid:PMC6882222.
25.
Febriyanti I, Djuminar A, Merdekawati F, Nur Indra AL. Comparison of purity and concentration values of mycobacterium tuberculosis DNA extraction result from the boiling and spin column method. Indones J Med Lab Sci Technol. 2023;5(2):133-45. https://doi.org/10.33086/ijmls....
26.
Matsuo Y, Komiya S, Yasumizu Y, et al. Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinIONTM nanopore sequencing confers species-level resolution. BMC Microbiol. 2021;21(1):35. https://doi.org/10.1186/s12866... PMid:33499799 PMCid:PMC7836573.
27.
Fabbrizzi A, Amedei A, Lavorini F, Renda T, Fontana G. The lung microbiome: Clinical and therapeutic implications. Intern Emerg Med. 2019;14(8):1241-50. https://doi.org/10.1007/s11739... PMid:31667699.
28.
Ticlla MR, Hella J, Hiza H, et al. The sputum microbiome in pulmonary tuberculosis and its association with disease manifestations: A cross-sectional study. Front Microbiol. 2021;12:633396. https://doi.org/10.3389/fmicb.... PMid:34489876 PMCid:PMC8417804.
29.
Moniem NA, Amin NM. Bacteria in sputum of patients with chronic chest lesions in chest department of Beni-Suef University Hospital. Egypt J Chest Dis Tuberc. 2016; 65(4):841-4. https://doi.org/10.1016/j.ejcd....
30.
Philley JV; Kannan A., Olusola P et al. Microbiome diversity in sputum of nontuberculous mycobacteria infected women with a history of breast cancer. Cell Physiol Biochem. 2019;52(2):263-79. https://doi.org/10.33594/00000... PMid:30816674.
31.
Kateete DP, Mbabazi MM, Nakazzi F, et al. Sputum microbiota profiles of treatment-naïve TB patients in Uganda before and during first-line therapy. Sci Rep. 2021; 11(1):24486. https://doi.org/10.1038/s41598... PMid:34966183 PMCid:PMC8716532.
32.
Nasrum M, Hasanuddin U, Kamaruddin M. Sputum microbiota in normal human, new TB patients, and recurrent tuberculosis patients as identified by 16SrRNA sequencing. OSF. 2020. https://doi.org/10.31219/osf.i....
33.
Wahyuningsih S, F. Dibha A, D. Kharisma V, et al. Screening of compounds in temu ireng (curcuma aeruginosa roxb.) as tuberculosis drug using bioinformatics design. Res J Pharm Technol. 2023;16(10):4875-80. https://doi.org/10.52711/0974-....
34.
Byun MK, Chang J, Kim HJ, Jeong SH. Differences of lung microbiome in patients with clinically stable and exacerbated bronchiectasis. PLoS One. 2017;12(8): e0183553. https://doi.org/10.1371/journa... PMid:28829833 PMCidD PMC5567645.
35.
Turvey SL, Tyrrell GJ, Hernandez C, Kabbani D, Doucette K, Cervera C. Mycobacterium branderi infection: Case report and literature review of an unusual and difficult-to-treat non-tuberculous mycobacterium. Int J Infect Dis. 2017;58:65-7. https://doi.org/10.1016/j.ijid... PMid:28268125.
36.
Mertaniasih NM, Kusumaningrum D, Koendhori EB, Soedarsono, Kusmiati T, Dewi DNSS. Nontuberculous mycobacterial species and mycobacterium tuberculosis complex coinfection in patients with pulmonary tuberculosis in Dr. Soetomo Hospital, Surabaya, Indonesia. Int J Mycobacteriol. 2017;6(1):9-13. https://doi.org/10.4103/2212-5... PMid:28317798.
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