How investigators turn a pile of case reports into a picture they can act on
Step 5 (descriptive epidemiology) is where these tools get used. Each one displays the outbreak's data a different way, and a Disease Detective needs to be able to read all of them.
A histogram of case counts by date of onset: its shape hints at how the outbreak is spreading (see below).
A spreadsheet with one row per case and columns for key variables (symptoms, exposures, dates): the investigator's master worksheet.
A map with one mark per case, used to spot geographic clustering: the modern descendant of John Snow's cholera map.
A table breaking case counts down by category (age group, exposure, location) to compare rates between groups.
Lab techniques (Pulsed-Field Gel Electrophoresis and Whole Genome Sequencing) that create a genetic "fingerprint" of a pathogen sample.
PulseNet is a CDC network that compares the DNA of germs from sick people. It used to compare PFGE fingerprints; today it mainly uses whole-genome sequencing (WGS), which reads nearly all of a germ's DNA. Similar DNA can help investigators find cases that may be part of the same outbreak. SNP (Single Nucleotide Polymorphism) mapping compares tiny, single-letter DNA differences to show how closely related two samples are.
Tests sometimes show a picture of a PFGE gel. The lab cuts each germ's DNA into pieces and pulls them through a gel with electricity. Small pieces travel farther, so they end up near the bottom; big pieces stay near the top. Each lane is one sample, and its line of bands is that germ's DNA fingerprint.
Swipe sideways to see every lane.
The first lane holds DNA pieces of known sizes (in kb). It works like a ruler, so labs can measure bands and compare gels from different labs.
Lanes that match band for band (patients 1 and 2 and the food) are the same strain: those cases are probably linked.
A pattern that differs by just a few bands (2 or 3, like patient 3) is closely related: one small change in the germ's DNA usually moves 2 or 3 bands. Germs can change a little as they spread, so that case may still belong to the outbreak; whole genome sequencing can tell.
Several bands in different places (patient 4) means a different strain. That person probably got sick from another source, even if they fell ill the same week.
An epi curve's shape is a clue in itself. Before any lab result comes back, the silhouette alone tells you how the outbreak is probably spreading. Here are the four classic shapes to recognize:
One sharp peak, all within a single incubation period. Everyone exposed at once, from one shared source.
A broad, sustained plateau: the source keeps exposing new people until it's found and fixed or removed.
Several irregular, unevenly spaced peaks: exposure keeps turning on and off, like a well only used sometimes.
Multiple rolling waves, each about one incubation period apart: the disease is spreading person to person, wave feeding wave.
Quick check: click a shape, then click the description that matches it:
If you know the agent's incubation period, the curve tells you when things happened. Tests ask this a lot:
Point-source: when was everyone exposed? Count back one median incubation period from the peak. Norovirus (median about 33 hours) peaking Saturday at 9 PM means the exposure was around noon Friday. You can check it from the edges too: earliest case minus the shortest incubation, and latest case minus the longest, should both land near the same time.
Continuous common-source: when was the source fixed? Cases keep appearing after the source is shut off: most within about one usual incubation period, the last ones up to the longest incubation period. To find when it was fixed, count back one usual incubation period from where cases start to fall, or the longest incubation period from the last case.
Propagated: when will the next wave peak? Waves are about one incubation period apart, so add one incubation period to the latest peak.
Two more patterns to recognize: a single sharp peak followed by a smaller bump about one incubation period later means a point-source outbreak with secondary spread (the first sick people passed it on at home). And an ill person whose symptoms started before the event, like a volunteer cook, is a clue that they were the source, not a victim.
The simulator below lets you build the two most commonly tested shapes yourself, case by case:
Q1An epi curve shows one sharp peak, all within a single incubation period, then drops off. What pattern is this?
Q2An epi curve shows waves of cases, each about one incubation period after the last. What pattern is this?
Q3On a PFGE gel, which DNA pieces travel farthest from the wells: small or large?