The supply and trade of poultry breeders is responsible for the global spread of Salmonella Enteritidis

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Researchers at the University of Georgia have provided multifaceted evidence to suggest the likely origins of the global spread of Salmonella Enteritidis, which has caused recurrent outbreaks of the poultry-related food-borne pandemic.

Using hypothesis-driven data mining, the research team, led by Xiangyu Dengof UGAsCenter for Food Safety, analyzed more than 30,000 genomes of Salmonella Enteritidis obtained from global sources and international trade. live poultry for five decades. The team concluded that the spread was probably from breeding poultry, or that the broodstock chose to produce future generations of chickens.

The study, titled Global spread of Salmonella Enteritidis via centralized sourcing and international trade in poultry farm stocks, is now published in the journal Nature Communications.

Salmonella Enteritidis is a bacterial disease of poultry and a foodborne pathogen that makes people sick when contaminated food is eaten, causing symptoms such as diarrhea, fever, and abdominal cramps. In poultry, the disease often goes unnoticed, but it can manifest clinically as depression, poor growth, weakness, diarrhea and dehydration.

In the 1980s, increases in Salmonella Enteritidis infections linked to poultry products occurred simultaneously in America and Europe. The pathogen quickly reached other continents on a pandemic scale. From 2015 to 2018, the largest salmonella outbreak on record in Europe occurred in 16 countries and was attributed to contaminated eggs. Yet the source, how the bacteria spread rapidly across continents decades ago and how it caused major epidemics in recent years has remained a historical enigma.

Deng said his team tried to connect the dots to solve the mystery of the Salmonella Enteritidis pandemic, which is how the pathogen has increased simultaneously in many parts of the world. To help solve this mystery, the team had to understand how the poultry production industry has changed over the past 80 years.

In 1948 and 1951, The Chicken of Tomorrow competitions were held in the United States to improve poultry breeders – that is, to raise bigger and better chickens. At that time, poultry was not a primary source of protein as the birds were quite small. Several breeders have emerged from competitions, and over time they have consolidated through mergers and acquisitions.

By the late 2000s, only a few significant breeding groups remained. This has resulted in a very centralized supply and massive international trade in breeding stocks. The researchers speculated that breeding poultry infected with Salmonella Enteritidis would be the simplest explanation for the synchronized and widespread spread of the disease.

To examine problems of this magnitude, the research team needed large amounts of data more than what individual labs could generate. Deng said they were using publicly available Salmonellagenomas obtained through sources such as GenomeTrak and EnteroBase. They also collected decades of international live poultry trade data from the Food and Agriculture Organization of the United Nations, the United States Department of Agriculture’s Foreign Agricultural Services, and the United States Department of Agriculture. the Observatory of economic complexity. This allowed them to gather the information they needed.

Our data mining is hypothesis-driven and integrative. I think that’s the key to how we’ve managed not to get lost in huge volumes of genomic data, Deng said.

After the researchers analyzed the data, they found recent isolates from domestic poultry raised in the United States and in the South American country of Suriname that were genetically nearly identical. This was important because the most likely overlap in poultry production systems between the two countries is the supply of breeding stock.

The team then extended genomic research to global populations of Salmonella Enteritidis. Through reconstructing the evolutionary history and population dynamics of the pathogen, they discovered that the global dispersal of poultry pathogens likely had centralized origins.

The researchers then integrated the genomic data with records of import and export of live poultry between countries. This allowed them to conclude that the centralized origins were breeders infected with Salmonella Enteritidis. The bacteria were then disseminated in subsequent generations of birds, which explains the appearance of similar genomes on different continents.

In addition to helping solve the historical conundrum of this food-borne pandemic, the study provides clues for prospective surveillance and response for emerging pathogens in poultry. Researchers at the College of Agronomic and Environmental Sciences plan to use these clues to research methods to limit the spread of salmonella internationally.

Poultry production is a notable location for the repeated emergence of other strains of Salmonella, Deng explained. Despite decades of significant progress in controlling salmonella in poultry, the evidence provided here calls for further investigation and potential intervention into the global spread of salmonella from centralized origins at the peak of poultry production.

This study was funded in part by a Hatch project of the USDA National Institute of Food and Agriculture. Its other authors include Shaoting Li, Yingshu He, and David Ames Mann. The entire article can be read in Nature Communications atnature.com.

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