BioNumerics shines at ASM software challenge

The 1st ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens (Sept 24-27, Washington, USA) featured a software challenge in which commercial and open source software packages for whole genome sequencing (WGS) surveillance could compete. Two “real-life” whole-genome sequencing (WGS) data sets were made available for this challenge, consisting of raw sequence reads for respectively 18 Listeria monocytogenes isolates and 50 Salmonella Enteritidis isolates. The goal of the challenge was to elucidate the outbreaks and answer a number of targeted questions posed by the organizers. Dr. Hannes Pouseele, Chief Operations Officer at Applied Maths, participated with the BioNumerics software.

A dual strategy was used for analysis of the WGS surveillance data:

  1. Cluster detection, i.e. identifying the isolates that are part of an outbreak, based on species-wide sample comparison using whole genome Multi Locus Sequence Typing (wgMLST).
  2. Cluster resolving, i.e. looking in depth in the structure on an outbreak, using a whole genome Single Nucleotide Polymorphism (wgSNP) approach.

Using the above strategy, not only did BioNumerics provide a clear-cut answer to the epidemiological questions for both data sets, it was one of the few packages that correctly pointed out a contaminated sample and the absence of a 56 kbp plasmid in one of the Listeria strains. Turnaround times were very reasonable at 25 to 45 minutes per sample, with the bulk of the time used for the de novo assembly. The results of both approaches were very concordant, yet complimentary: wgMLST allows to drill down from a species-wide perspective to strain level without losing any of its discriminatory power, while the wgSNP approach complements this on cluster level with its additional resolution. An obvious advantage of BioNumerics in comparison to many of the open source pipelines is the user friendliness of this push-button application.

An important observation is that the assignments from this ASM software challenge were extracted directly from the daily practice of foodborne pathogen outbreak investigation. We can therefore conclude that the encouraging results obtained with BioNumerics software once more confirm its status as the preferred package for WGS surveillance.

A detailed report on this analysis will be published, but for the impatient a preliminary version is available on request.

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