Hospital-based outbreak detection system saves lives

University of Pittsburgh

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An infectious diseases detection platform developed by University of Pittsburgh scientists working with UPMC infection preventionists proved over a two-year trial that it stops outbreaks, saves lives and cuts costs.

The results are published today in the journal Clinical Infectious Diseases, making the case for adoption in hospitals nationwide and the development of a national early outbreak detection database.

“We saved lives while saving money. This isn’t theoretical – this happened in a real hospital with real patients,” said lead author Alexander Sundermann, Dr.P.H., assistant professor of infectious diseases in Pitt’s School of Medicine. “And it could easily be scaled. The more hospitals implement this practice, the more everyone benefits, not just by stopping previously undetected outbreaks within the walls of the hospital, but by finding medical device or medication-linked outbreaks sweeping the nation.”

The Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT) takes advantage of increasingly affordable genomic sequencing to analyze infectious disease samples from patients. When the sequencing detects that any two or more patients have near-identical strains of an infection, it flags the results for the hospital’s infection prevention team to find the commonality and stop the transmission.

Without genomic sequencing, hospital infection preventionists have no way of knowing if two hospitalized patients coincidentally have the same infection or if one of them was infected by the other. Because of this, patients with the same type of infection who don’t have an obvious link – such as staying in the same inpatient unit – may unknowingly spread the infection, leading to an outbreak growing significantly before it is detected. Conversely, infection preventionists may spend time and resources trying to avert a nonexistent outbreak when patients happen to have the same type of infection, but the transmission was from unrelated sources.

The study ran from November 2021 through October 2023 at UPMC Presbyterian Hospital. During that time, the analysis showed that EDS-HAT prevented 62 infections and five deaths, compared to if the system had not been running. It netted a savings of nearly $700,000 in infection treatment costs – a 3.2-fold return on investment.

“These results are remarkable,” said co-author Graham Snyder, M.D., M.S., medical director of infection prevention and hospital epidemiology at UPMC. “This project clearly illustrates how UPMC’s academic partnership with Pitt is providing our patients with outstanding patient care while creating innovative solutions that pave the way for better patient care worldwide.”

If health care facilities across the U.S. adopt EDS-HAT, a nationwide outbreak system could be developed, similar to PulseNet, the U.S. Centers for Disease Control and Prevention’s network for detecting multistate outbreaks of foodborne illness. Sundermann and colleagues previously found that, had such a system existed, the 2023 outbreak of deadly bacteria linked to contaminated eye drops could have been stopped far earlier. 

“It is a no-brainer to implement EDS-HAT at every health care facility nationwide,” said senior author Lee Harrison, M.D., professor of infectious diseases at Pitt’s School of Medicine and of epidemiology at Pitt’s School of Public Health. “We hope these findings will contribute to ongoing conversations among U.S. health care leadership, payors and policymakers about the benefits of genomic surveillance as standard practice in health care.”

Additional authors of this research are Praveen Kumar, Ph.D., Marissa P. Griffith, Kady D. Waggle, M.S., Vatsala Rangachar Srinivasa, M.P.H., Nathan Raabe, M.P.H., Emma G. Mills, Hunter Coyle, Deena Ereifej, M.P.H., Hanna M. Creager, Ph.D., Ashley Ayres, M.B.A., Daria Van Tyne, Ph.D., Lora Lee Pless, Ph.D., and Mark Roberts, M.D., all of Pitt, UPMC or both.

This work was supported by National Institute of Allergy and Infectious Diseases grant R01AI127472.

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Journal

Clinical Infectious Diseases

DOI

10.1093/cid/ciaf216 

Article Title

Real-Time Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control: Clinical and Economic Impact

Article Publication Date

28-Apr-2025

 

Global study links consumption of ultraprocessed foods to preventable premature deaths

Findings published in the American Journal of Preventive Medicine support a call for revised dietary guidelines and public policies to lessen the disease burden across nations

Elsevier

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Premature deaths attributable to ultraprocessed food (UPF) consumption levels in 8 countries increase significantly according to its share in the total energy intake, varying from 4% of the premature deaths in lower consumption settings, such as Colombia, to up to approximately 14% of the premature deaths in countries with the highest UPFs intake, such as the USA and the UK.

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Credit: American Journal of Preventive Medicine / Nilson et al.

Ann Arbor, April 28, 2025 - A study analyzing data from nationally representative dietary surveys and mortality data from eight countries (Australia, Brazil, Canada, Chile, Colombia, Mexico, United Kingdom, and United States) shows that premature deaths attributable to consumption of ultraprocessed foods (UPFs) increase significantly according to their share in individuals’ total energy intake. The new study, appearing in the American Journal of Preventive Medicine, published by Elsevier, reinforces the call for global action to reduce UPF consumption, supported by regulatory and fiscal policies that foster healthier environments.

UPFs are ready-to-eat-or-heat industrial formulations that are made with ingredients extracted from foods or synthesized in laboratories, with little or no whole foods in their composition. These have gradually been replacing traditional foods and meals made from fresh and minimally processed ingredients.

Lead investigator of the study Eduardo Augusto Fernandes Nilson, DSc, Oswaldo Cruz Foundation (Fiocruz), Brazil, says, "UPFs affect health beyond the individual impact of high content of critical nutrients (sodium, trans fats, and sugar) because of the changes in the foods during industrial processing and the use of artificial ingredients, including colorants, artificial flavors and sweeteners, emulsifiers, and many other additives and processing aids, so assessing deaths from all-causes associated with UPF consumption allows an overall estimate of the effect of industrial food processing on health."

While previous studies focused on specific dietary risk factors instead of food patterns, the current study modeled data from nationally representative dietary surveys and mortality data from eight countries (Australia, Brazil, Canada, Chile, Colombia, Mexico, United Kingdom, and United States) to link dietary patterns, considering the extent and purpose of industrial food processing, to deaths from all causes.

Dr. Nilson explains, "We first estimated a linear association between the dietary share of UPFs and all-cause mortality, so that each 10% increase in the participation of UPFs in the diet increases the risk of death from all causes by 3%. Then, using the relative risks and the food consumption data for all countries (ranging from 15% of the total energy intake in Colombia, to over 50% of the calories in the United States), we built a model that estimated that the percentage of all-cause premature preventable deaths due to the consumption of UPFs can vary from 4% in countries with lower UPF consumption to almost 14% in countries with the highest UPF consumption. For example, in 2018, 124,000 premature deaths were attributable to the consumption of UPFs in the United States."

High consumption of UPFs has been associated with 32 different diseases, including cardiovascular disease, obesity, diabetes, some types of cancer, and depression. For the first time, this study has estimated the burden of UPF intake on premature deaths from all-causes in different countries, showing that the attributable mortality is significant in all settings and that addressing UPF consumption should be a global public nutrition priority.

Dr. Nilson notes, "It is concerning that, while in high-income countries UPF consumption is already high but relatively stable for over a decade, in low- and middle-income countries the consumption has continuously increased, meaning that while the attributable burden in high-income countries is currently higher, it is growing in the other countries. This shows that policies that disincentivize the consumption of UPFs are urgently needed globally, promoting traditional dietary patterns based on local fresh and minimally processed foods."

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Journal

American Journal of Preventive Medicine

DOI

10.1016/j.amepre.2025.02.018 

Method of Research

Data/statistical analysis

Subject of Research

People

Article Publication Date

28-Apr-2025

 

Every dose counts: Safeguarding the success of vaccination in Europe

Marking European Immunization Week 2025, ECDC highlights the risks of suboptimal vaccination coverage in Europe

European Centre for Disease Prevention and Control (ECDC)

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For the years 2019–2023, the overall distribution of cases by age group and vaccination status followed the same pattern, with the unvaccinated population of 0–9 years and >20 years of age counting for approximately 80% of the total number of cases.

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Credit: ECDC

Marking European Immunization Week (EIW) 2025, the European Centre for Disease Prevention and Control (ECDC) highlights the risks of suboptimal vaccination coverage in Europe and publishes a set of operational tools that public health authorities can use to improve vaccination acceptance and uptake. The tenfold surge of reported measles cases in the European Union and European Economic Area (EU/EEA) and the detection of vaccine-derived poliovirus in four EU/EEA countries in 2024 are two clear signals of the need to achieve and maintain high immunisation coverage to protect European populations.

Vaccines have saved millions of lives worldwide. Vaccination remains one of the most effective tools in public health, preventing diseases such as measles, polio, diphtheria and pertussis. Nevertheless, more than 35 000 people were diagnosed with measles in the EU/EEA in 2024 and 23 people – 14 of them children below five years of age – died following their measles infection.

“Thanks to vaccination we have eradicated smallpox and controlled serious diseases, such as polio, diphtheria and tetanus. The challenge for immunisation today is how to safeguard these gains. Accelerated efforts are needed to sustain high vaccination coverage. Every vaccine dose counts, and timing matters for optimal protection,” says Pamela Rendi-Wagner, Director of ECDC.

Today, ECDC releases new data [2] on the almost tenfold increase in measles infections recorded in the EU/EEA in 2024. The data demonstrate the long-term impact of declining vaccination uptake and immunity gaps: among people with known vaccination status who fell ill with measles in 2024, eight out of ten had not been immunised.

Measles can affect anyone who is unprotected – not only children, but adolescents and adults as well. More than a quarter (26%) of people diagnosed with measles in 2024 were over 14 years old.

To prevent measles outbreaks and protect populations vulnerable to the disease, at least 95% of the population eligible for vaccination should receive two doses of the measles, mumps and rubella (MMR) vaccine. However, vaccination levels in the EU/EEA still fall short of this target, with recent estimates showing that only four countries (Hungary, Malta, Portugal and Slovakia) report such coverage for both doses.

Europe needs to close existing immunisation gaps to stay healthy

ECDC estimates that around 600 000 children aged 12–23 months may have missed their full primary polio vaccination course between 2022 and 2023. Between September and December 2024, circulating vaccine-derived poliovirus type 2 was detected in sewage samples in Finland, Germany, Poland, Spain and the United Kingdom. To date, no human polio cases have been reported, and the EU/EEA continues to be polio free – but, to keep it that way, targeted catch-up campaigns and improved surveillance need to address existing vaccination gaps [3].

The evidence is clear: insufficient vaccination coverage leaves too many people vulnerable to the disease, including children who are too young to be vaccinated and people who cannot receive vaccines due to medical reasons. Protecting these groups depends on high vaccination uptake in the general population eligible for vaccination.

Successful vaccination programmes are built on understanding and responding to people’s beliefs, concerns, and expectations. Understanding the social and behavioural barriers and facilitators to vaccination is essential to design effective strategies and interventions to increase vaccination acceptance and uptake.

To support EU/EEA countries to take such action, ECDC has published the report ‘Tools and methods for promoting vaccination acceptance and uptake: a social and behavioural science approach’ [3]. The report compiles a set of operational tools in usable and adaptable formats that fit the real-life context that public health authorities work in and describe vaccination programmes that can help tailor their efforts to the specific needs and challenges of diverse communities.

In addition, the deployment of modern digitalised immunisation information systems to identify and reach people who are unvaccinated is critical and should form an integral part of national efforts to improve the performance and management of the overall national immunisation programme.

Continuous EU and national investment in high-quality surveillance and prompt outbreak investigations are key to closely monitoring the epidemiology of vaccine-preventable diseases in the EU/EEA and to identifying and addressing immunity gaps in the population.

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Notes to editors

[1] European Immunization Week is marked each year during the last week of April and is an important opportunity to highlight the vital role of vaccination in protecting health and well-being at every stage of life. ECDC continues to support and strengthen national immunisation programmes, with a strong focus on vaccine quality, safety, and effectiveness, while working to ensure timely and equitable access for everyone.

[2] Annual Epidemiological Report for 2024. Stockholm: ECDC; 2025. Available from 28 April 2025: https://www.ecdc.europa.eu/en/publications-data/measles-annual-epidemiological-report-2024

[3] Tools and methods for promoting vaccination acceptance and uptake: a social and behavioural science approach. Stockholm: ECDC; 2025. Available from 28 April 2025: https://www.ecdc.europa.eu/en/publications-data/tools-and-methods-promoting-vaccination-acceptance-and-uptake

[4] Join ECDC's digital EIW event bridging epidemiology and social sciences to identify, understand and find joint solutions to address barriers against vaccination, close immunity gaps and improve vaccination coverage across the EU/EEA: "Closing vaccination gaps, reaching every community, Monday, 28 April, 13:30-15:30 CEST. Register here: bit.ly/EIW2025Event  

Genetic secrets of rice pave way for future farming and conservation

Discovered genes provide strategies to protect rice crops against climate change and to domesticate wild relatives that can grow in currently unproductive habitats

King Abdullah University of Science & Technology (KAUST)

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A photo of one of the wild polyploid Oryza presented in this work (O. coarctata) described in the study.

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Credit: King Abdullah University of Science and Technology

A new study, seen in Nature Genetics and led by researchers at King Abdullah University of Science and Technology (KAUST; Saudi Arabia) and Wageningen University & Research (the Netherlands), provides new insights on rice evolution, showing how the DNA of this valuable crop has changed across species. The findings are expected to not only help with improving rice yields but also with the introduction of rice into regions where rice production is currently untenable.  

Rice is one of the first domesticated crops (approximately 10,000 years ago). The artificial selection farmers have made for nutrition and other traits that maximize profit have reduced its genetic diversity and thus its resilience to environmental stresses.  

On the other hand, the wild relatives of rice (i.e. Oryza) have experienced some 15 million years of evolution, which has given these relatives a remarkable array of genetic variation across their genomes (all the DNA in an organism) and thus an ability to adapt to all sorts of environmental conditions, like heat, drought, and salinity.  

"The genus Oryza has an incredibly rich collection of genomes. We were able to explain the consequences of the evolution on the collective genomes of rice and its wild relatives," explained KAUST Prof. Rod Wing, who led the study along with his postdoctoral research associate, Alice Fornasiero.  

Humans are diploid, meaning they inherit two sets of chromosomes—one from each parent. Anything more or less can be fatal. Plants can be polyploidy, meaning then can receive multiple sets of chromosomes from their parents. These extra sets result in a larger genome that can facilitate adaptation to new or stressful environments and the evolution of novel traits and even new species.   

The study examined nine tetraploid and two diploid wild relatives of rice. The researchers found that the species could be distinguished by subsets of the genomes. These differences were mostly due to transposable elements, also known as jumping genes because they are DNA sequences that move from one location in the genome to another and a common natural means for creating genetic diversity.  

Additionally, the existence of diploid and tetraploid species resulted in genomes that varied more than twice in size. In some of this massive DNA were genes that have strengthened the robustness of the plant against hotter temperatures, drier and saltier soil, and other environmental stresses common to the Middle East and increasing worldwide with climate change.  

The study was also able to determine the evolutionary tree of wild rice, showing when new species emerged. This history offers clues for when rice underwent significant stress that stimulated genomic changes for the plant to endure.  

"The genome analysis of this work provides a comprehensive understanding of how rice and its complex wild relatives have evolved. This work offers a comprehensive framework for future efforts for developing robust rice crops that can potentially withstand harsh environments," said Wageningen University Professor Eric Schranz, who also contributed to the study.  

With more than 3.5 billion people relying on it as the main staple of their diet, rice is one of the most important food crops in the world. 

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Journal

Nature Genetics

DOI

10.1038/s41588-025-02183-5 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Oryza genome evolution through a tetraploid lens

Article Publication Date

28-Apr-2025

Extreme monsoon changes threaten the Bay of Bengal's role as a critical food source

After examining 22,000 years of rainfall patterns, Rutgers researchers warn that climate conditions may reduce fish stock

Rutgers University

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Although the Bay of Bengal covers less than 1% of the global ocean, it supplies nearly 8% of the world’s fishery production. Scientists are looking to the past to predict the effect of monsoons on future marine life there.

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Credit: Kate Littler/International Ocean Discovery Program

New research involving Rutgers professors has revealed that expected, extreme changes in India’s summer monsoon could drastically hamper the Bay of Bengal’s ability to support a crucial element of the region’s food supply: marine life.

The study, published in Nature Geoscience, was conducted by scientists from Rutgers University, the University of Arizona and collaborators from India, China and Europe. To reach their conclusions, the scientists examined how the monsoon, which brings heavy rains to the Indian subcontinent, has influenced the Bay of Bengal’s marine productivity over the past 22,000 years.

Although the Bay of Bengal covers less than 1% of the global ocean, it supplies nearly 8% of the world’s fishery production. Its coastal waters support densely populated regions that rely heavily on marine resources for food and livelihoods. 

“Millions of people living along the Bay of Bengal rely on the sea for protein, particularly from fisheries,” said Yair Rosenthal, a Distinguished Professor in the Department of Marine and Coastal Sciences and the Department of Earth and Planetary Sciences at Rutgers University and an author of the study. “The productivity of these waters – the ability of the ocean to support plankton growth – is the foundation of the marine food web. If ocean productivity declines, it will powerfully affect the ecosystem, ultimately reducing fish stocks and threatening food security for coastal communities.”

The monsoon is essential for providing freshwater to the region, but the researchers found that both extremely strong and extremely weak monsoon periods over the centuries caused a significant disruption – a 50% reduction in food available for marine life at the surface. This occurred because these extreme conditions inhibited mixing between the deep and surface zones of the ocean, preventing nutrients from reaching the upper region where marine life thrives.

With climate change expected to make the monsoon more intense and variable, and those extremes provoking stratification of the ocean layers, the food supply produced by the Bay of Bengal may be threatened, researchers said.

To understand how the Indian summer monsoon and ocean productivity have changed over time, scientists studied the fossil shells of foraminifera – tiny single-celled plankton that live in the ocean and build calcium carbonate shells. The shells preserve information about the environment they grew in, acting like natural recorders of past ocean and climate conditions. 

“By analyzing their chemistry and tracking the abundance of certain types that thrive in productive waters, we reconstructed long-term changes in rainfall, ocean temperatures and marine life in the Bay of Bengal,” said geoscientist Kaustubh Thirumalai, an assistant professor at the University of Arizona and lead author of the study. “Together, these chemical signals helped us understand how the monsoon and ocean conditions responded to global climate changes over the past 22,000 years.”

The sediments analyzed were recovered from the seafloor by scientists aboard the National Science Foundation-funded research vessel JOIDES Resolution as part of the International Ocean Discovery Program.

The researchers found that productivity of the Bay of Bengal’s waters collapsed during periods of very weak monsoons, such as Heinrich Stadial 1, and very strong monsoons, such as those in the early Holocene. The period known as Heinrich Stadial 1, a significantly cold period, occurred between 17,500 and 15,500 years ago. The early Holocene, a time marked by rapid warming and sea level rise because of melting glaciers, occurred between about 10,500 and 9,500 years ago.

The amount of monsoon rainfall controls the volume of river discharge into the Bay of Bengal. The freshwater significantly changes oceanographic conditions and affects the feeding cycle of fish and plankton. When monsoon rains are too intense, a freshwater layer can cap the ocean surface, blocking nutrients from below. Without nutrients, plankton growth drops – and with it, the entire food chain, including fish. Weaker monsoons also suppress nutrient delivery by reducing ocean circulation and wind-driven mixing.

“Both extremes threaten marine resource availability,” Thirumalai said.

When researchers compared ancient patterns with modern ocean data and model projections, they found an unsettling parallel: Future scenarios project warmer surface waters and stronger freshwater runoff, conditions that match past intervals when marine productivity dropped sharply. Compounding the risk, future winds may not be strong enough to counteract the stratification that suppresses mixing.

Looking at past climate patterns helps scientists understand how the interconnected components and processes that compose the physical Earth, including its atmosphere and biosphere, affect the climate, environment and all organisms over long timescales.

“The relationship between monsoons and ocean biology we have uncovered in the Bay of Bengal gives us real-world evidence of how marine ecosystems have reacted to warming and monsoon shifts and may do so in the future,” Rosenthal said. “These insights can help refine projections and inform sustainable management of fisheries and coastal resources as the impacts of climate change accelerate.”

Kaixuan Bu, an assistant research professor with the Department of Marine and Coastal Sciences at Rutgers-New Brunswick, also contributed to this study.

Explore more of the ways Rutgers research is shaping the future.

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Journal

Nature Geoscience

DOI

10.1038/s41561-025-01684-6 

Method of Research

Observational study

Subject of Research

Not applicable

Article Title

Extreme Indian summer monsoon states stifled Bay of Bengal productivity across the last deglaciation

Article Publication Date

28-Apr-2025