Salmonella infections are a major public health issue in the United States, causing over 1.3 million illnesses annually. These infections are a leading cause of foodborne illness, often traced back to raw or undercooked poultry meat and eggs. Emerging antimicrobial resistance in Salmonella isolates found in retail chicken meat is a growing concern, the trends of which were recently explored in a new study by a group of researchers from the University of Illinois Urbana-Champaign.

Salmonella comprises thousands of strains, known as serovars, which vary in their prevalence, distribution, and antimicrobial resistance across different regions. Controlling Salmonella outbreaks can be challenging, as the pathogen is very diverse and some serovars are multi-drug resistant. Furthermore, infections in poultry often aren’t easy to detect.
“The problem in detection is that some Salmonella serovars don’t infect poultry, and in many cases, the chickens do not present as clinically ill,” said Csaba Varga (IGOH), an assistant professor of epidemiology specializing in the distribution and spread of diseases. “They can appear healthy while still harboring Salmonella, and then humans consume the meat and get infected.”

To monitor Salmonella's presence and antimicrobial resistance in retail chicken meat, the National Antimicrobial Resistance Monitoring System for Enteric Bacteria has been sampling chickens since 2002. Longitudinal datasets like these are invaluable for tracking changes in the bacteria over time, said Varga. In his recent study, he and his team utilized this extensive dataset to explore trends in the prevalence of the most common serovars of Salmonella and their antimicrobial resistance patterns over recent years.

The team includes Nasim Sohail, a visiting research scholar at the College of Veterinary Medicine, and Hamid Sodagari, a postdoctoral researcher in Varga’s lab, and first author on the study.

They examined publicly available data on nearly 40,000 samples taken from retail chicken meat between 2013 and 2020. Of these, approximately 3,000 samples (7.7%) tested positive for Salmonella. The four most common serovars identified were S. Kentucky, S. Typhimurium, S. Infantis, and S. Enteritidis. Notably, S. Kentucky was the most prevalent serovar in poultry, constituting about 35% of Salmonella-positive samples. However, Varga points out that it is of less concern because S. Kentucky rarely infects humans, unlike the other three serovars.

While the average prevalence of S. Kentucky and S. Enteritis has remained relatively stable over the years, the researchers observed a significant decline in S. Typhimurium and a dramatic increase in S. Infantis from 2013 to 2020.

“We were expecting to see a decrease in Typhimurium due to the live attenuated Typhimurium vaccine that the poultry industry has been using,” explained Varga. “But controlling for one serovar can open up the niche, allowing others to take over. We expected to see a potential increase in other serovars due to this, however, we didn’t expect such a dramatic increase from S. Infantis.”

Varga went on to explain that the prevalence of S. Infantis surged from around 3% of positive Salmonella samples in 2015 to nearly 40% in 2020. This is particularly concerning due to the high levels of antimicrobial resistance found among S. Infantis samples.

“S. Infantis has become increasingly prevalent and has recently emerged as multidrug-resistant due to a plasmid (pESI) within that serovar,” said Sohail. “This plasmid contains several antimicrobial resistance and virulence genes, that help with the pathogenesis of S. Infantis. This is likely why it is increasing in prevalence not only in the United States but also across the globe.”

The other serovars also demonstrated varying levels of antimicrobial resistance. Additionally, the four serovars varied in their spatial distribution across the United States, with high-proportion clusters of S. Typhimurium more commonly detected along the East Coast, and S. Kentucky along the West Coast and southern states.

Several factors could influence the distribution of Salmonella serovars, such as environmental differences or variations in chicken management practices. However, the researchers say more studies are needed to explore these factors in detail. 
The emergence of a multidrug-resistant S. Infantis serovar in the United States and worldwide is a significant public health concern. These findings underscore the need for further research and the implementation of serovar-specific mitigation strategies in the poultry production chain, said Varga.

“Our results show that the vaccination against S. Typhimurium is working, but that the industry will have a new challenge to control S. Infantis,” explained Varga. “They will likely need to figure out a different type of intervention since the current mitigation efforts are not working against it. This just shows we need to consider serovar-specific control measures for Salmonella in the future.”

The team plans to further investigate how management practices affect the development of antimicrobial resistance, and explore what can be done to reduce Salmonella prevalence and resistance to antimicrobials. Varga stresses that even with efforts to reduce Salmonella, it is unlikely to disappear anytime soon. Therefore, consumers should take safety precautions when handling and consuming poultry. 

“We can work to reduce Salmonella, but it won’t disappear,” said Varga. “Consumers need to be aware that they must take food safety precautions to cook poultry meat to temperature and not cross-contaminate food products in the kitchen.”
​
The study is published in Food Control, found at https://doi.org/10.1016/j.foodcont.2024.110701. More information on other projects in the lab can be found at https://vetmed.illinois.edu/varga-lab/

Advances in genomics research and technology are providing a more comprehensive understanding of how our genetic code interacts with our environment to influence our health, behavior, and overall well-being. This has far-reaching implications for various fields, including healthcare, insurance, policing, and even judicial sentencing. The legal system faces the challenge of protecting individuals from potential misuse of genetic data, such as unfair denial of health insurance, while also allowing for the leveraging of its benefits, like improving early interventions for disease. Addressing these issues requires the judiciary to have a good understanding of genomics, ensuring that they can make informed decisions in cases involving genetic information.

To meet this growing need, the Carl R. Woese Institute for Genomic Biology at the University of Illinois Urbana-Champaign, in partnership with the National Courts and Sciences Institute, recently hosted the third "Genomics for Judges" workshop, which was held from June 27-28th. This workshop aimed to equip judges with the knowledge necessary to navigate the legal landscape shaped by advances in DNA sequencing, analysis, and more recently, artificial intelligence. The workshop was funded by the State Justice Institute.

The two-day workshop offered a comprehensive curriculum that included expert seminars and panels, interactive discussions, and hands-on experiments. Judges explored the latest developments in genomics and AI, increasing their understanding of its applications, implications, and limitations. By examining the intersection of genomics with the legal system, the event sought to prepare judges for the challenges and opportunities these technologies present.

The workshop featured many notable seminars, including one by Derek Hoiem, a professor of computer science, who provided an overview of AI. Hoiem differentiated between traditional narrow machine learning models and emerging generative AI technologies, like ChatGPT. He emphasized the importance of understanding AI's training processes, potential biases, and the role of digital forensics in verifying the authenticity of AI-generated media, a growing concern in legal contexts.

Another notable seminar was led by Brian Allan (IGOH), a professor of entomology, who discussed genetic modification in mosquitoes as a strategy to combat disease spread. He detailed current genetic modification techniques for tackling this, which include creating sterile mosquitoes or those resistant to diseases. Allan then highlighted the regulatory ambiguities surrounding genetically modified organisms and the legal questions judges might face in the future concerning the environmental and ethical implications of GMOs.

Alta Charo, the Warren P. Knowles Professor Emerita of Law and Bioethics at the University of Wisconsin-Madison, delivered a compelling keynote address on equity and access to emerging genome editing therapies. She reviewed recent advancements in genome editing, explaining the underlying mechanisms and the significant hurdles in making these therapies broadly accessible. Charo highlighted challenges such as financial barriers, the complexity of treatments, and the disparities in technological capabilities across different regions. She emphasized the critical role of the judiciary in ensuring that legal decisions regarding these technologies compel companies to address and devise solutions to these equity issues.

Additional seminars covered topics like diagnostics and classifications by AI models, using machine learning to predict health risks based on genomic data, and the future of human genetics in light of technological advances in genetic editing. These sessions underscored the transformative potential of genomics and AI in healthcare and emphasized the need for judicial understanding of these fields.

A highlight of the workshop was a hands-on experiment led by Dan Urban, IGB's Senior Outreach Activities Coordinator. Judges pipetted DNA samples from various commercially available snack foods into gels and used electrophoresis to separate the DNA, testing whether the snacks labeled as GMO-free actually contained GMOs. This experiment offered a practical demonstration of genetic testing techniques and their applications, and it quickly became a favorite among the judicial participants.

Case studies formed another critical part of the workshop, allowing judges to apply their newfound knowledge to hypothetical legal scenarios. In one hypothetical criminal case study, judges considered the legal processes involved in using AI to generate a suspect’s face from DNA evidence at a crime scene. They discussed the potential biases of such AI tools, the types of expert testimony required, and the ethical and legal ramifications of admitting AI-generated evidence in court. Another civil case study explored the idea of a lawsuit involving a genome editing tool used to cure an embryo of a life-threatening disease. In the hypothetical scenario presented, the child later develops cancer, and the parents believe it is related to genome editing. Judges examined the legal procedures for such a lawsuit, the necessary evidence, and the expert testimonies required to resolve the case.

The workshop, titled “AI in Genomics and Genetic Engineering” is part of the IGB’s Genomics forTM program, a series of workshops designed to educate different professional groups on genomics research, and explore with them its potential impact on the job sector they work in. 

“The Genomics for program is a prominent element of our efforts in outreach, and a vivid demonstration of our commitment to engage all sectors of the public with clear and trusted information on genomics,” said IGB director Gene Robinson. “We’re pleased and honored to again collaborate with the National Courts and Sciences Institute, one of the premier judicial training organizations in the country.” 
​
The workshop underscored the critical role of education in bridging the gap between advancing technology and the judiciary. By equipping judges with a robust understanding of genomics and AI, the IGB aims to ensure that legal decisions involving these technologies are informed, fair, and just.