Differentiation complex sputum microbiome in patients suspected TB pulmonary
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Deby Kusumaningrum 1 2 3 * , Ni Made Mertaniasih 2 3 4 , Soedarsono Soedarsono 3 4 5 , Rahadian Pratama 6
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1 Doctoral Degree Program, Faculty of Medicine, Universitas Airlangga, Surabaya, INDONESIA2 Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, INDONESIA3 Dr. Soetomo General Academic Hospital, Surabaya, INDONESIA4 Tuberculosis Laboratory, Institute of Tropical Disease, Universitas Airlangga, Surabaya, INDONESIA5 Department of Internal Medicine Sub Pulmonology, Faculty of Medicine, Universitas Hang Tuah, Surabaya, INDONESIA6 Department of Biochemistry, Faculty of Mathematics and Natural Science, Institut Pertanian Bogor, Bogor, INDONESIA* Corresponding Author

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.

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article Type: Original Article

ELECTRON J GEN MED, Volume 21, Issue 6, December 2024, Article No: em612

https://doi.org/10.29333/ejgm/15583

Publication date: 06 Nov 2024

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