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8/15

Using genomic information in an outbreak investigation

The same diagram is now labelled to show the individuals who were diagnosed with TB in the school outbreak – take a few minutes to familiarise yourself with this way of presenting information

Now look at the chart below showing distribution of SNPs from the research study -

  • Where do the isolates from the school outbreak fit on this distribution?

  • What does this tell us about transmission?

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

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    Where do the isolates from the school outbreak fit on this distribution?

    Six of the isolates do not differ by any SNPs at all the strains isolated from the teacher (MrsY), three of her students (students A, B and C), the coffee shop worker (Miss Z) and student B who attended the neighbouring school.

    The other three students each had TB strains whose genomes differed from these strains at only one nucleotide out of the 4.4 million in the whole TB genome. Each of the three strains in students D, E and F differed from this strain at a different nucleotide.

    From this we can see that all of the isolates in this outbreak are only separated from each other by one SNP so they fall at the extreme left of the distribution.

    What does this tell us about transmission?

    The genomic data strongly suggests that this outbreak was the result of direct transmission within the school. The data also strongly suggests that the cases in the coffee shop worker and the student in the neighbouring school are part of the same transmission chain.

    Using genomics in this school cluster confirmed that all the cases were highly likely to be part of the same chain of transmission. Having this information in real time could have prevented further investigations in the second school.

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