Deepanshi Mishra, Gita Satpathya, Naveet Wig, Daizy Paliwal and Subrat Kumar Panda

Targeted Metagenomics using Next Generation Sequencing in Laboratory Diagnosis of Hospitalized Sepsis Patients
Int.J.Adv.Microbiol.Health.Res.2021; 5(2):1-13

Publisher: IJAMHR, Category: Current Issues

Abstract

Introduction: Early knowledge of the causative agent in sepsis can provide early and accurate treatment with significantly better prognosis. Aim and objectives: Metagenomics for sepsis diagnosis is in the threshold for wider use in routine patient care. We evaluated targeted metagenomics in 14 hospitalized sepsis patients for bacterial detection along with broad range PCR assay. Materials and Methods: Targeted metagenomics by next generation sequencing (NGS) using ION Personal Genome Machine was done for 7 variable regions of 16S rRNA gene was done for bacterial detection in 14 hospitalized sepsis patients. NGS data was analyzed with Ion-Reporter software using QIIME and NCBI-BLSATN tools and NCBI-Genbank and Greengenes databases. A broad-range PCR-assay for 762bp region of 16S rRNA gene with Sanger’s sequencing was also done. Results and Conclusion: Operating taxonomic units (OTU) of varying numbers for 2-6 bacterial species were detected in 12 of the 14 specimens by NGS, though OTUs of a single bacteria were in far excess numbers in each. Broad-range PCR for bacteria was positive in these 12 patients, identification was possible in 10. Bacteria in these 2 patients could be identified by NGS (Enhydrobacter aerosaccus). In all specimens maximum numbers of OTUs detected in NGS were for the same bacteria which was detected by broad-range PCR-assay. The culture positive specimen was positive in both molecular assays. Bacterial detection and identification up to species level was possible in 87.5% patients using matagenomics, though the method is currently expensive and needs careful interpretation.