Tracking the Pathogen: Foodborne Outbreaks

By Christopher Kendra

Little Susie went about her Saturday like a normal 14 year-old girl. She woke up, watched cartoons, contemplated dismantling the patriarchy and had her favorite sandwich for lunch. Later in the day, she did in fact dismantle the patriarchy, but that’s not the point of this article. By Tuesday, Susie felt nauseous with a fever and terrible stomach cramps. By Wednesday, Susie was in the emergency department with the same symptoms plus diarrhea, vomiting, and dehydration; but Susie wasn’t alone. People across the country were getting sick with a horrid stomach bug and there was seemingly no connection between any of the cases. Susie dismantled the patriarchy on her own, but she did watch the same cartoons as everyone else. And while they do say that TV rots your brain, it most definitely does not cause gastroenteritis. Fast forward two weeks; Susie and her parents see the news headline: “Outbreak of Salmonella Linked to Popular Peanut Butter.” As it turns out, the peanut butter in Susie’s sandwich was part of a large batch that had been contaminated with Salmonella and recalled. But how was this all figured out? The path to getting here was long, complicated, and required coordinated efforts from multiple state and federal agencies.

While not a daily occurrence, foodborne outbreaks are not uncommon in the United States and there are multiple mechanisms of detecting and managing these microbial threats. Sources of contamination can arise from anywhere in production, processing, distribution, and the final retail of a food product1. The inoculum of contamination often occurs when cleaning and sterilizing processes are not effective and fecal residue from the environment, human handling, or animals used in the food source get into the product. Past this point, improper storage of food can propagate or enable the contamination to spread in between products and even contaminate equipment used in other manufacturing processes1.

Federal agencies work in coordination with state and hospital laboratories to identity and mitigate outbreaks, reducing the risk of widespread infection and halting potential fatalities (Figure 1). When Susie showed up to the hospital, her care team took blood and stool samples to try and identify what was making her sick. Once collected, the samples were sent to a clinical microbiology laboratory where scientists isolated potential bacteria in her samples. If bacteria grow from patient cultures, the laboratory team works to identify the bacteria by phenotypic and genotypic methods that help to (1) guide patient treatment, (2) survey for antimicrobial resistance, and (3) monitor for common foodborne threats. When the tests confirmed that Susie’s cultures were positive for Salmonella, samples were sent to the state department of health2.

Figure 1: Steps in a Foodborne Outbreak Investigation. Foodborne outbreak investigations involve multiple ongoing phases to identify, track, trace and, control the spread of a disease. From the moment a public health pathogen is detected in a patient, federal agencies such as the CDC, FDA and USDA begin the process of identifying the source of contamination and work to control its spread through recalls and material pipeline improvement.

At a state department of health, the exact species of public health threats are identified through molecular assay and DNA sequencing2,3. Once processed, the findings are reported back to the hospital laboratory and uploaded to PulseNet USA. PulseNet is a network of 83 state and county health departments connected through the Centers for Disease Control (CDC) to facilitate the rapid and advanced identification of 8 common pathogens of public concern such as E. coli and Salmonella4,5. When an isolate is reported to PulseNet, a sample of the bacteria is collected and subjected to whole genome sequencing (WGS) to completely characterize the DNA fingerprint of the microbe5. As this additional data is uploaded to PulseNet and compared against all samples in the database, strains that share highly similar DNA fingerprints are flagged and program managers inside the CDC are alerted. If three or more cases coincide with the same causal agent, the CDC initiates an investigation in coordination with the Food and Drug Administration (FDA) and the US Department of Agriculture (USDA). The CDC’s Epidemic Intelligence Service6 is then deployed to begin an initial outbreak investigation, collecting as much data as possible on the rising threat.

When collecting information on a potential microbial outbreak, the CDC aims to answer the following core questions:

1) What is the timeline that individuals are getting sick?

2) Are these incidents geographically concentrated or widespread?

3) What is common about the individuals involved in connection to this outbreak?7

By connecting common events, foods ingested, and even travel, health agencies are able to form hypothesis to identify the compounds and food products potentially associated with the outbreak and trace these products back to supplies and food manufacturers. Due to highly regulated food laws, food must be labeled in such a way that an item can be traced and associated with its batch, date of production, and location of manufacturing. An item’s lot number encodes all of this information and allows public health agencies to pinpoint suspected contaminated food items and begin testing to confirm the presence of a pathogen8,9. Once confirmed, notifications and recalls can be generated to alert the public of the risk and specify exactly what batch of food is contaminated, as well as where it might have been sold.

Post-investigation monitoring health agencies observe the incidence of the disease outbreak and determine the appropriate time to consider the outbreak over10. However, in cases where reports of the same microbe continue to arise even after the recall, additional investigations are conducted to determine if other batches of food product are also contaminated, and if a recall needs to be re-issued or expanded to include other lots (Figure 2).  Upon seeing a return to a normal level of steady state infections in the population, federal agencies will conclude that the outbreak has ended and consider their investigation over9.

Figure 2: Tracking Outbreak Cases. In this histogram of infection cases by date, the frequency of a specific foodborne pathogen is monitored. With the use of multiple product recalls, the case frequency of an outbreak can be quickly suppressed to normal, steady-state levels of infection.

Susie had been part of a group of individuals that ate peanut butter contaminated with Salmonella enterica serovar Senftenberg, an invasive non-typhoid strain of Salmonella capable of causing severe gastroenteritis in healthy individuals. Luckily, she was able to be treated with a combination therapy of a third-generation cephalosporin (cefotaxime)11, and a second-generation fluoroquinolone, (ciprofloxacin)11. With this, she would be able to live out a healthy life, post-patriarchal dismantling, thankful for the fact that we have laboratories, agencies, and regulations in place to identify and control outbreaks like this one.


  • Foodborne outbreaks are identified and tracked through a coordinated state and federal effort
  • Active and ongoing monitoring of public health threats is essential for catching foodborne outbreaks early


  1. Centers for Disease Control and Prevention. (2017, September 5). How food gets contaminated – the food production chain. Retrieved July 12, 2022, from 
  2. PA Department of Health. (n.d.). Foodborne illness. Retrieved July 11, 2022, from
  3. Centers for Disease Control and Prevention. (2020, February 21). Serotypes and the importance of serotyping salmonella. Retrieved July 11, 2022, from
  4. Centers for Disease Control and Prevention. (2021, September 29). Pulsenet. Retrieved July 11, 2022, from
  5. Centers for Disease Control and Prevention. (2021, September 29). PulseNet Methods. Retrieved July 11, 2022, from
  6. Centers for Disease Control and Prevention. (2022, May 23). Epidemic Intelligence Service (EIS). Retrieved July 11, 2022, from
  7. Centers for Disease Control and Prevention. (2016, September 15). Principles of Epidemiology. Retrieved July 11, 2022, from 
  8. Center for Food Safety and Applied Nutrition. (n.d.). Food Safety Modernization Act (FSMA). Retrieved July 11, 2022, from
  9. Center for Food Safety and Applied Nutrition. (n.d.). Full text of the Food Safety Modernization Act (FSMA). Retrieved July 11, 2022, from
  10. Centers for Disease Control and Prevention. (2018, June 20). Decide an outbreak is over. Retrieved July 11, 2022, from
  11. World Health Organization. (2019). World Health Organization Model List of Essential Medicines. Retrieved July 11, 2022, from 

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