Go back

14/15

Application to your own practice

Review all of the information carefully and think about the benefits and limitations of using genomic data to investigate this outbreak specifically and more widely in other types of outbreak investigation.

  • Do you think using genomic data in this type of analysis adds value to existing methods in anyway?

  • Do you think using genomic data in this type of conflicts with existing methods in anyway?

  • Would the increased level of resolution offered by genomics have changed the public health management of this outbreak if whole genome data had been available in real time – would you have offered prophylaxis to the wider student and university staff population?

  • If genomics was available, in what types of circumstance might you consider using it as a public health tool?

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

»Show answers
» Hide answers

Feedback for Exercise 5

Do you think using genomic data in this type of analysis adds value to existing methods in any way?

Gathering whole genome data for some or all isolates from an outbreak may add value to existing methods. In some situations the level of resolution provided by WGS may not be required from all isolates, however if it is cheaper and quicker to produce WGS data than to use other sequence based typing methods such as MLST then applying WGS to a larger number of isolates may add value.

Value can be added to the investigation as WGS and gene-based analyses would enable the presence or absence of antibiotic resistance genes and specific virulence genes to be determined.

Using a database to link epidemiological information to WGS data adds value by enabling information to be shared by others. This may mean that seemingly isolated cases could be quickly linked to existing cases in other geographical areas, enabling interventions at an earlier stage.

Do you think using genomic data in this type of conflicts with existing methods in any way?

In this case study, genomic data was analysed using a gene-based method which enables comparison with other gene sequence based typologies. WGS is not as easily comparable with gel-based typing methods such as PFGE.

The use of genomics for investigation of outbreaks means that the data produced do not catagorise isolates as “same” or “different” to other isolates, but instead the output is in the form of descriptive analyses of the relationships between genomes. This requires investigators to think in different ways and the “naming” of types and of types of relationship may be a key challenge in adopting a genomics-driven approach.

How might this level of resolution might have changed the PH management if WGS had been available in real time?

If used in real time, WGS would have discriminated between cases 1 and 3 in the days immediately following case 3. As no isolate was available for case 2, WGS would not have added any information on this case nor for cases 4 and 5.

WGS would have provided evidence that a number of different genomic types were circulating in the student population during the time of the outbreak and may have linked the remote cases to the outbreak strain more quickly thus providing leads to be followed up regarding other possible exposure events.

» Continue