Solving the problem of comparing whole bacterial genomes across different sequencing platforms

Rolf S Kaas; Pimlapas Leekitcharoenphon; Frank M Aarestrup; Ole Lund

doi:10.1371/journal.pone.0104984

Solving the problem of comparing whole bacterial genomes across different sequencing platforms

PLoS One. 2014 Aug 11;9(8):e104984. doi: 10.1371/journal.pone.0104984. eCollection 2014.

Authors

Rolf S Kaas¹, Pimlapas Leekitcharoenphon¹, Frank M Aarestrup¹, Ole Lund²

Affiliations

¹ National Food Institute, Technical University of Denmark, Lyngby, Denmark.
² Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark.

Abstract

Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.

Publication types

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

MeSH terms

Base Sequence
DNA, Bacterial / genetics
Genome, Bacterial / genetics*
High-Throughput Nucleotide Sequencing / methods*
Humans
Molecular Sequence Data
Phylogeny
Polymorphism, Single Nucleotide / genetics
Salmonella typhimurium / genetics*
Salmonella typhimurium / isolation & purification
Sequence Analysis, DNA / methods*
Staphylococcus aureus / genetics*
Staphylococcus aureus / isolation & purification

Substances

DNA, Bacterial

Grants and funding

This study was supported by the Center for Genomic Epidemiology (www.genomicepidemiology.org) grant 09-067103/DSF from the Danish Council for Strategic Research. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.