Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms

<div><p>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.</p></div

<i>Staphylococcus aureus</i> phylogeny.

<p>Labels are colored according to isolate. The sequencing platforms applied are appended to the end of each label. If repetitive sequencing has been performed then the label has also been appended either “1” or “2”. (<b>A</b>) Phylogeny inferred with snpTree; (<b>B</b>) Phylogeny inferred with the novel SNP procedure; (<b>C</b>) Phylogeny inferred with the Nucleotide Difference (ND) method.</p

<i>Salmonella</i> DT104 phylogeny.

<p>Labels are colored according to isolate. The sequencing platforms applied are appended to the end of each label. If repetitive sequencing has been performed then the label has also been appended either “1” or “2”. (<b>A</b>) Phylogeny inferred with snpTree; (<b>B</b>) Phylogeny inferred with the novel SNP procedure; (<b>C</b>) Phylogeny inferred with the Nucleotide Difference (ND) method.</p

Reference Genomes.

<p>Reference Genomes.</p

<i>Salmonella</i> Montevideo phylogeny (low quality sequences removed).

<p>Labels are colored according to isolate. The sequencing platforms applied are appended to the end of each label. (<b>A</b>) Phylogeny inferred with novel SNP procedure; (<b>B</b>) Phylogeny inferred with the Nucleotide Difference (ND) method.</p

Comparison of the novel SNP procedure, the Nucleotide Difference (ND) method and snpTree.

<p>Comparison of the novel SNP procedure, the Nucleotide Difference (ND) method and snpTree.</p

Epidemiological information for the 47 <i>Salmonella</i> genomes used in this study (source: human).

<p>Epidemiological information for the 47 <i>Salmonella</i> genomes used in this study (source: human).</p

Evaluation results.

<p>Evaluation results.</p

Percentage of concordance of k-mer tree on various size of k.

<p>This evaluation was conducted on the set of 34 <i>S</i>. Typhimurium.</p

Distribution of SNPs across <i>Salmonella</i> core genes.

<p>Black bars represent number of SNPs at each core gene. Red and green small circles are core genes in the form of DNA and protein sequences respectively. The seven black dots represent house-keeping genes for MLST analysis of <i>Salmonella</i>.</p