DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq

TY - JOUR

T1 - DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq

AU - Krych, Lukasz

AU - Castro-Mejía, Josué L.

AU - Forero-Junco, Laura M.

AU - Moesby, Daniel N.

AU - Mikkelsen, Morten B.

AU - Rasmussen, Morten A.

AU - Sykulski, Maciej

AU - Nielsen, Dennis S.

PY - 2019/12/1

Y1 - 2019/12/1

N2 - Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.

AB - Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.

U2 - 10.1038/s42003-019-0617-x

DO - 10.1038/s42003-019-0617-x

M3 - Journal article

C2 - 31633060

SN - 2399-3642

VL - 2

JO - Communications Biology

JF - Communications Biology

M1 - 369

ER -