DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing.

ABSTRACT: Identification of bacteria causing tissue infections can be comprehensive and, in the cases of non- or slow-growing bacteria, near impossible with conventional methods. Performing shotgun metagenomic sequencing on bacterial DNA extracted directly from the infected tissue may improve time to diagnosis and targeted treatment considerably. However, infected tissue consists mainly of human DNA (hDNA) which hampers bacterial identification. In this proof of concept study, we present a modified version of the Ultra-Deep Microbiome Prep kit for DNA extraction procedure, removing additional human DNA. Tissue biopsies from 3 patients with orthopedic implant-related infections containing varying degrees of Staphylococcus aureus were included. Subsequent DNA shotgun metagenomic sequencing using Oxfor

SUBMITTER: Helmersen K 

PROVIDER: S-EPMC7031281 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature