A Shigella cell, seen in orange against a blue human cell
A Shigella bacterium seem by scanning electron microscopy

Disease detective: scenario

Now it’s your chance to test your skills as a disease detective.

Over the past 9 months there have been six cases of a rare respiratory pathogen in a hospital. An outbreak is suspected and it’s your job as part of the infection control team to investigate. An isolate from each infected patient has been obtained and whole genome sequenced, and the location and duration of their stay on each hospital ward has been documented.

The diagram below shows the hospital stays of each affected patient, where the colour indicates the ward they were staying in, and the lightning bolt is used to indicate when they were first diagnosed with the infection. Think about what this information tells you about the likely transmission chain.

Ward and timeline information for infected patients Epidemiological data (Click image to expand)

The whole genome sequence data were mapped to the reference genome for the rare pathogen. SNPs were called and used to construct a phylogenetic tree. The scale bar indicates the total number of SNP changes across the genome. The pathogen evolves at a rate of roughly 1 SNP per month. Compare the tree to the above epidemiological data.

Phylogenetic relationships of isolates

Phylogeny of isolates (Click image to expand)

Now consider what this information tells you about the outbreak, and think about the following questions: 1. Which patients are part of the outbreak? 2. What wards are involved? 3. Who is patient zero (the source of the outbreak)? Assume that there were no infections before January.

You will have a chance to check your answers in the quiz section, which is next.

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This article is from the free online course:

Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

Wellcome Genome Campus Advanced Courses and Scientific Conferences