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12/15

Interpreting the immigrant community cluster

Look at the cluster again, it has been coloured according to the town of residence. Patients with evidence of an epidemiological link are shown in text of the same colour. White text indicates cases where there was no epidemiological link found.

As before, pay attention to the number of SNPs that separate the isolates.

  • What is your interpretation of the situation now?
  • If this information was available in real time would this change your management / practice?

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Feedback for Exercise 7

What is your interpretation of the situation?

The diagram shows that several of the TB cases where there was no epidemiological link can be linked strongly to other linked cases using the genomic data – 12 of the 13 isolates from people in Town A (shown in purple) are related by 0 to 3 SNPs, good evidence of recent transmission. All of the isolates from people in Town B are also closely related, with genomes differing by 0-3 SNPs - demonstrating transmission. The fact that there are only a small number of SNPs separating isolates from 3 towns suggests that transmission has taken place between as well as within towns.

Genomic data has also identified that the TB isolates of the remaining five cases from Town C are very unlikely to have been transmitted to one another. This suggests that these individuals all acquired their TB elsewhere, possibly before entering the UK.

If this information was available in real time would this change your management / practice?

Being able to rule out transmission in the seemingly linked individuals in one community group would mean that resources which might be used for further contact tracing in this community could be used elsewhere.

In this investigation the majority of cases had recently arrived in the UK from a country where TB is a lot more prevalent. As more TB strains will be circulating in a high prevalence setting, there is a likelihood that people in this community may have acquired their TB from a number of different sources despite being part of the same community here in the UK, however recent contact between members of this group within the UK could also be an explanation for their TB.

Using genomics provides increased resolution over other methods and enabled identification of:

1. Evidence of a recent chain of transmission (cases linked by 0 to 3 SNPs)

AND

2. Evidence of unrelated TB cases (cases separated by >12 SNPs, including up to 76 SNPs)

If genomics had been used here in real time it may have enabled resources used to heavily investigate presumed links between the individuals with unrelated TB genomes to be re-directed.

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