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Benefits and limitations

You now have all the information regarding the outbreak and have seen results of serological typing, and output of an analysis of the whole genome data. When you are ready, try and write down at least three benefits and three limitations of the use of whole genome data.

Take some time to think through your answers before checking them.

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You now have all the information regarding the outbreak and have seen results of serological typing, and output of an analysis of the whole genome data - below are some of the benefits and limitations but you may be able to identify more

Benefits of WGS

  • A higher resolution is obtained

  • Additional data is elicited for the same or less cost, it is already more cost effective to obtain whole genome sequences on the Illumina platform than to perform other sequence-based typing methods (e.g. MLST using seven PCR reactions), at least at major genome centres

  • Data can be used to determine gene-based typing identity eg MLST for comparison with previously acquired data

  • Data can be linked to other epidemiological information in the form of a database and shared over the internet

  • The time taken to perform WGS is similar or quicker than most molecular typing techniques.

    Limitations of WGS

  • Requires a bacterial isolate (serogrouping in this case study was determined from direct PCR of clinical specimen in 2 cases, MLST can also sometimes be determined in this way)

  • Requires sequencing hardware

  • Requires computing infrastructure / capacity, difficulty in interpretation?

  • May require a specialist skill set

  • A bottleneck may occur at the analysis stage?

  • Lack of criteria on when to apply WGS in outbreak investigation

  • Investigators would need some knowledge of the level of variation among genomes to be able to interpret data from cases. For meningococci MLST has provided good data, but for other species this may not be the case.

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