Optimized Protocol for Simple Extraction of High-Quality Genomic DNA from Clostridium difficile for Whole-Genome Sequencing

James Heng Chiak Sim; Victoria Anikst; Akshar Lohith; Nader Pourmand; Niaz Banaei

doi:10.1128/JCM.00956-15

Optimized Protocol for Simple Extraction of High-Quality Genomic DNA from Clostridium difficile for Whole-Genome Sequencing

J Clin Microbiol. 2015 Jul;53(7):2329-31. doi: 10.1128/JCM.00956-15. Epub 2015 Apr 15.

Authors

James Heng Chiak Sim¹, Victoria Anikst¹, Akshar Lohith², Nader Pourmand², Niaz Banaei³

Affiliations

¹ Department of Pathology, Stanford University, Stanford, California, USA.
² Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.
³ Department of Pathology, Stanford University, Stanford, California, USA Department of Medicine, Stanford University, Stanford, California, USA Clinical Microbiology Laboratory, Stanford Health Care, Palo Alto, California, USA nbanaei@stanford.edu.

Abstract

Successful sequencing of the Clostridium difficile genome requires high-quality genomic DNA (gDNA) as the starting material. gDNA extraction using conventional methods is laborious. We describe here an optimized method for the simple extraction of C. difficile gDNA using the QIAamp DNA minikit, which yielded high-quality sequence reads on the Illumina MiSeq platform.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Clostridioides difficile / genetics*
DNA, Bacterial / chemistry
DNA, Bacterial / genetics
DNA, Bacterial / isolation & purification*
Genome, Bacterial*
High-Throughput Nucleotide Sequencing / methods
Sequence Analysis, DNA / methods*

Substances

DNA, Bacterial