Sunday, September 22, 2024

 

Wastewater monitoring can detect foodborne illness, researchers find



Results of a new study suggest sewage monitoring could provide early warning of foodborne disease outbreaks to public health authorities



Penn State

sewage treatment plant in central Pennsylvania 

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The researchers tested raw sewage samples collected twice a week from two treatment plants in central Pennsylvania for non-typhoidal Salmonella and characterized isolates using whole genome sequencing. They recovered 43 Salmonella isolates from wastewater samples. 

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Credit: Provided by Ed Dudley/Penn State





UNIVERSITY PARK, Pa. — First used in the 1940s to monitor for polio, wastewater surveillance proved such a powerful disease monitoring tool that the U.S. Centers for Disease Control and Prevention (CDC) established the National Wastewater Surveillance System to support SARS-CoV-2 monitoring in September of 2020. Now, a team of scientists from Penn State and the Pennsylvania Department of Health have shown that domestic sewage monitoring is useful for a foodborne pathogen as well. 

In findings published today (Sept. 19) in the Journal of Clinical Microbiology, the researchers report that the bacteria Salmonella enterica was detected in samples from two wastewater treatment plants in central Pennsylvania during June 2022.

“Non-typhoidal Salmonella is a common cause of gastroenteritis worldwide, but current surveillance for the disease is suboptimal, so in this research we evaluated the utility of wastewater monitoring to enhance surveillance for this foodborne pathogen,” said Nkuchia M’ikanatha, lead epidemiologist, Pennsylvania Department of Health and an affiliated researcher in Penn State’s Department of Food Science, in the College of Agricultural Sciences. "In this study, we explored wastewater monitoring as a tool to enhance surveillance for this foodborne pathogen. Wastewater testing can detect traces of infectious diseases circulating in a community, even in asymptomatic individuals, offering an early warning system for potential outbreaks."

While health care providers are required to report salmonellosis cases, many go undetected. Salmonella bacteria, inhabiting the intestines of animals and humans, are shed in feces. The CDC estimates Salmonella causes roughly 1.35 million infections, 26,500 hospitalizations and 420 deaths annually in the U.S., primarily through contaminated food.

In June 2022, the researchers tested raw sewage samples collected twice a week from two treatment plants in central Pennsylvania for non-typhoidal Salmonella and characterized isolates using whole genome sequencing. They recovered 43 Salmonella isolates from wastewater samples, differentiated by genomic analysis into seven serovars, which are groupings of microorganisms based on similarities. Eight of the isolates, or nearly 20%, were from a rare type of Salmonella called Baildon.

The researchers assessed genetic relatedness and epidemiologic links between non-typhoidal Salmonella isolates from wastewater and similar bacteria from patients with salmonellosis. The Salmonella Baildon serovars isolated from wastewater were genetically indistinguishable from a similar bacteria found in a patient associated with a salmonellosis outbreak in the same period in the area. Salmonella Baildon from wastewater and 42 outbreak-related isolates in the national outbreak detection database had the same genetic makeup. One of the 42 outbreak-related isolates was obtained from a patient residing in the wastewater study sample collection catchment area, which serves approximately 17,000 people. 

Salmonella Baildon is a rare serovar — reported in less than 1% of cases nationally over five years, noted M’ikanatha, the study’s first author. He pointed out that this research demonstrates the value of monitoring sewage from a defined population to supplement traditional surveillance methods for evidence of Salmonella infections and to determine the extent of outbreaks.

“Using whole genome sequencing, we showed that isolates of variant Salmonella Baildon clustered with those from an outbreak that occurred in a similar time frame,” he said. “Case reports were primarily from Pennsylvania, and one individual lived within the treatment plant catchment area. This study provides support for using domestic sewage surveillance in assisting public health agencies to identify communities impacted by infectious diseases.”

Ed Dudley, a professor of food science and the senior author on the study, said these findings highlight the potential of wastewater monitoring as an early warning system for foodborne disease outbreaks, potentially even before physicians and laboratories report cases. This proactive approach could enable health officials to swiftly trace the source of contaminated food, ultimately reducing the number of people affected, suggested Dudley, who also directs Penn State’s E. coli Reference Center.

“While it may not happen overnight, I foresee a future where many, if not most, domestic wastewater treatment plants contribute untreated sewage samples for monitoring evidence of various illnesses,” he said. “This would likely involve collaboration among public health agencies, academia and federal entities, much like our pilot study. I see this as yet another crucial lesson from the pandemic.”

Contributing to the research at Penn State were Jasna Kovac, associate professor of food science and Lester Earl and Veronica Casida Career Development Professor of Food Safety; Erin Nawrocki and Yezhi Fu, postdoctoral scholars in the Dudley Lab; Zoe Goldblum, undergraduate researcher in the Department of Food Science; and Nicholas Cesari, Division of Infectious Disease Epidemiology, Pennsylvania Department of Health.

The CDC, the U.S. Food and Drug Administration and the U.S. Department of Agriculture’s National Institute of Food and Agriculture provided funding for this research.

A researcher prepares samples to search for Salmonella in sewage 

 

New data science tool greatly speeds up molecular analysis of our environment


UC Riverside-led team developed the tool through an international virtual research group



University of California - Riverside

Daniel Petras 

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Photo shows Daniel Petras.

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Credit: Petras lab, UC Riverside.




RIVERSIDE, Calif. -- A research team led by scientists at the University of California, Riverside, has developed a computational workflow for analyzing large data sets in the field of metabolomics, the study of small molecules found within cells, biofluids, tissues, and entire ecosystems.

Most recently, the team applied this new computational tool to analyze pollutants in seawater in Southern California. The team swiftly captured the chemical profiles of coastal environments and highlighted potential sources of pollution.

“We are interested in understanding how such pollutants get introduced in the ecosystem,” said Daniel Petras, an assistant professor of biochemistry at UC Riverside, who led the research team. “Figuring out which molecules in the ocean are important for environmental health is not straightforward because of the ocean’s sheer chemical diversity. The protocol we developed greatly speeds up this process. More efficient sorting of the data means we can understand problems related to ocean pollution faster.”

Petras and his colleagues report in the journal Nature Protocols that their protocol is designed not only for experienced researchers but also for educational purposes, making it an ideal resource for students and early-career scientists. This computational workflow is accompanied by an accessible web application with a graphical user interface that makes metabolomics data analysis accessible for non-experts and enables them to gain statistical insights into their data within minutes. 

“This tool is accessible to a broad range of researchers, from absolute beginners to experts, and is tailored for use in conjunction with the molecular networking software my group is developing,” said coauthor Mingxun Wang, an assistant professor of computer science and engineering at UCR. “For beginners, the guidelines and code we provide make it easier to understand common data processing and analysis steps. For experts, it accelerates reproducible data analysis, enabling them to share their statistical data analysis workflows and results.”

Petras explained the research paper is unique, serving as a large educational resource organized through a virtual research group called Virtual Multiomics Lab, or VMOL. With more than 50 scientists participating from around the world, VMOL is a community-driven, open-access community. It aims to simplify and democratize the chemical analysis process, making it accessible to researchers worldwide, regardless of their background or resources.

“I’m incredibly proud to see how this project evolved into something impactful, involving experts and students from across the globe,” said Abzer Pakkir Shah, a doctoral student in Petras’ group and the first author of the paper. “By removing physical and economic barriers, VMOL provides training in computational mass spectrometry and data science and aims to launch virtual research projects as a new form of collaborative science.”

All software the team developed is free and publicly available. The software development was initiated during a summer school for non-targeted metabolomics in 2022 at the University of Tübingen, where the team also launched VMOL.

Petras expects the protocol will be especially useful to environmental researchers as well as scientists working in the biomedical field and researchers doing clinical studies in microbiome science.

“The versatility of our protocol extends to a wide range of fields and sample types, including combinatorial chemistry, doping analysis, and trace contamination of food, pharmaceuticals, and other industrial products,” he said.

Petras received his master’s degree in biotechnology from the University of Applied Science Darmstadt and his doctoral degree in biochemistry from the Technical University Berlin. He did postdoctoral research at UC San Diego, where he focused on the development of large-scale environmental metabolomics methods. In 2021, he launched the Functional Metabolomics Lab at the University of Tübingen. In January 2024 he joined UCR, where his lab focuses on the development and application of mass spectrometry-based methods to visualize and assess chemical exchange within microbial communities.

The title of the paper is “Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.” 

The University of California, Riverside is a doctoral research university, a living laboratory for groundbreaking exploration of issues critical to Inland Southern California, the state and communities around the world. Reflecting California's diverse culture, UCR's enrollment is more than 26,000 students. The campus opened a medical school in 2013 and has reached the heart of the Coachella Valley by way of the UCR Palm Desert Center. The campus has an annual impact of more than $2.7 billion on the U.S. economy. To learn more, visit www.ucr.edu.

 

Study reveals large ocean heat storage efficiency during the last deglaciation




Institute of Atmospheric Physics, Chinese Academy of Sciences
Melting ice in the Southern Ocean. 

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Melting ice in the Southern Ocean.

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Credit: Jiuxin Shi





As one of the largest heat reservoirs in the climate system, the global ocean absorbs more than 90% of the excess energy from ongoing anthropogenic warming. In the last century, the greatest warming in the ocean has occurred in the upper 500 m, with relatively weak warming in the deep ocean, corresponding to a small ocean heat storage efficiency of ~0.1.

 

Paleoceanographic observations, however, suggest that on long time scales, the deep ocean warming can be comparable to or larger than the surface ocean warming, with ocean heat storage efficiency during the last deglaciation about ten times of its modern value. This raises the following question: what mechanisms are responsible for ocean heat uptake/storage and how large can its efficiency be?

 

Recently published in Science Advances, a joint study by an international team of scientists from China and USA has shed light on this issue. By combining state-of-the-art deglacial simulations and proxy-based reconstructions, they resolved the three-dimensional deglacial ocean temperature change and found that the deglacial ocean heat storage efficiency is substantially enhanced to ≥1 by strong warming in intermediate-depth waters in response to deglacial forcing.

 

“Our simulations and proxy reconstructions demonstrate that the three-dimensional ocean warming during the last deglaciation was strongly nonuniform with strongest warming occurring at intermediate depths, in striking contrast to contemporary observations,” said Dr. Chenyu Zhu from Institute of Atmospheric Sciences at the Chinese Academy of Sciences, the study's co-first author.

 

Utilizing sensitivity experiments, the study revealed that the large warming of intermediate waters can be related to surface warming at mid-to-subpolar latitudes through ventilation in response to greenhouse gases and ice sheet forcing and substantially enhanced by oceanic circulation change associated with meltwater forcing. “The unique ocean warming structure facilitates a large ocean heat storage efficiency. In particular, this resolves the paradox suggested by the conventional view that warming occurred at sites of deep-water formation that remained covered by sea ice”, said Prof. Zhengyu Liu, one of the corresponding authors of the study from The Ohio State University.

 

“These results have valuable implications. For example, if strong surface warming and strong ventilation are collocated like in our simulations, then the ocean will absorb more heat from the atmosphere, potentially slowing the rate of atmospheric warming” said Prof. Peter U. Clark, another corresponding author of the study from Oregon State University.

 

The study underscores the important role of surface warming pattern and oceanic circulation change in long-term ocean heat storage change and suggests that “the ocean can serve as a far greater reservoir of energy in the climate system than implied by contemporary observations,” according to the study.

 

Scientists turn to human skeletons to explore origins of horseback riding




University of Colorado at Boulder





As anyone who’s spent time in the saddle knows, riding a horse can be hard on your body. But can it change the way your skeleton looks?

The answer, according to archaeologists from the University of Colorado Boulder: It’s complicated. In a new study, the team drew on a wide range of evidence—from medical studies of modern equestrians to records of human remains across thousands of years.

The researchers concluded that horseback riding can, in fact, leave a mark on human skeletons, such as by subtly altering the shape of the hip joint. But those sorts of changes on their own can’t definitively reveal whether people have ridden horses during their lives. Many other activities, even sitting for long periods of time, can also transform human bones.

“In archaeology, there are vanishingly few instances in which we can tie a particular activity unequivocally to skeletal changes,” said Lauren Hosek, lead author of the study and an assistant professor in the Department of Anthropology at CU Boulder.

She and her colleagues reported their findings Sept. 20 in the journal Science Advances.

The results may have implications for researchers who study the origins of when humans first domesticated horses—and also cast doubt on a long-standing theory in archaeology known as the Kurgan hypothesis.

The first equestrians

The research lies at the center of what is among the old debates in archaeology, said William Taylor, a co-author of the new study and curator of archaeology at the CU Museum of Natural History.

He explained that the earliest, incontrovertible evidence of humans using horses for transport comes from the region around the Ural Mountains of Russia. There, scientists have uncovered horses, bridles and chariots dating back to around 4,000 years ago.

But the Kurgan hypothesis, which emerged in the early 20th century, argues that the close relationship between humans and horses began much earlier. Proponents believe that around the fourth millennium B.C., ancient humans living near the Black Sea called the Yamnaya first began galloping on horseback across Eurasia. In the process, the story goes, they may have spread a primordial version of the languages that would later evolve into English, French and more.

“A lot of our understanding of both the ancient and modern worlds hinges on when people started using horses for transportation,” Taylor said. “For decades, there’s been this idea that the distribution of Indo-European languages is, in some way, related to the domestication of the horse.”

Recently, scientists have pointed to human remains from the Yamnaya culture dating back to about 3500 B.C. as a key piece of evidence supporting the Kurgan hypothesis. These ancient peoples, the group argued, showed evidence of wear and tear in their skeletons that likely came from riding horses.

Hips can lie

But, in the new study, Hosek and Taylor argue that the story isn’t so simple.

Hosek has spent a lot of time poring over human bones to learn lessons about the past. She explained that the skeleton isn’t static but can shift and change shape over an individual’s lifetime. If you pull a muscle, for example, a reaction can emerge at the site where the muscle attaches to the underlying bone. In some cases, the bone can become more porous or raised ridges may form.

Reading those sorts of clues, however, can be murky at best. The hip joint is one example.

Hosek noted that when you flex your legs at the hip for long periods of time, including during long horse rides, the ball and socket of the hip joint may rub together along one edge. Over time, that rubbing can cause the round socket of the hip bone to become more elongated, or oval in shape. But, she said, other activities can cause the same kind of elongation.

Archaeological evidence shows that humans used cattle, donkeys and even wild asses for transport in some areas of western Asia centuries before they first tamed horses. Ancient peoples likely yoked these beasts of burden to pull carts or even smaller, two-wheeled vehicles that looked something like a chariot.  

“Over time, this repetitive, intense pressure from that kind of jostling in a flexed position could cause skeletal changes,” Hosek said. 

She’s seen similar changes, for example, in the skeletons of Catholic nuns from the 20th century. They never rode horses, but did take long carriage rides across the American West.

Ultimately, Hosek and Taylor say that human remains on their own can’t be used to put a date on when people first started riding horses—at least not with currently available science.  

“Human skeletons alone are not going to be enough evidence,” Hosek said. “We need to couple that data with evidence coming out of genetics and archaeology and by looking at horse remains, too.”

Taylor added that the picture doesn’t look good for the Kurgan hypothesis:

"At least for now, none of these lines of evidence suggest that the Yamnaya people had domestic horses.”

 

Study finds family members are most common perpetrators of infant and child homicides in the U.S.



Analysis of 44 years of FBI data sheds light on possible prevention strategies for pediatric homicide



Texas A&M University





Homicide is a leading cause of death among people 19 and younger in the United States, and firearms are used in a large proportion of these crimes. Although the homicide rate for this population declined in the 1990s and 2000s, it has increased every year since 2013, with a large spike during the COVID-19 pandemic.

Now, new research by Hannah Rochford, PhD, an assistant professor with the Texas A&M University School of Public Health, and two colleagues from the University of Iowa, provides insight into the characteristics of those who committed these crimes and their use of firearms from 1976 to 2020.

“The more national-level information we have about these perpetrators, the better we can develop comprehensive, evidence-based public health policies and prevention strategies,” Rochford said. “Unfortunately, the data has lagged behind data that is known for most other public health challenges. For example, the National Violent Death Reporting System did not exist at all before 2003, did not include a majority of states until 2015, and still does not fully represent violent deaths in all states. This makes it difficult to learn from past trends, like the youth violence surge of the late 1980s and early 1990s.”

For their study, published in Injury Epidemiology, the researchers sought to fill these gaps by describing trends between 1976-2020 in perpetrator characteristics (sex, age and relationship to victim) and firearm presence by the age, sex, and race of U.S. homicide victims from birth to 19 years of age.

To do so, researchers applied the multiply-imputed version of the Federal Bureau of Investigation’s 1976–2020 Supplementary Homicide Reports (SHR).

“The unimputed SHR is limited by ‘unit missingness’ because not every law enforcement agency provides data for the reports every year, and ‘item missingness’ because some homicide incidents were missing case information,” Rochford said. “For example, more than one quarter of homicide incidents were missing information on the perpetrator’s age, sex and race.”

After stratifying the descriptive analyses by victim age group, sex, race and five-year time periods, the team found that family members were the most common perpetrator of infant and toddler (ages 0–4) and child (ages 5–12) homicides, and acquaintances accounted for the majority of adolescent (ages 13–19) homicides. One quarter of adolescent homicides with female victims were perpetrated by an intimate partner.

The team found there was a sustained increase in the proportion of homicides committed with a firearm. From 2016 to 2020, the proportion of homicides that involved firearms was an all-time high across the study period for three categories: infants and toddlers at 14.8 percent, children at 53.1 percent, and adolescents at 88.5 percent. Firearm homicide was particularly burdensome to Black pediatric victims, with Black infants and toddlers experiencing twice the burden as White infants and toddlers, for example.

“These differences appear to align with developmental changes in family dependency and interaction, peer and romantic relations, and age-related role independence,” Rochford said. “For example, adult female family members were responsible for more than a quarter of all infant and toddler homicides, but to less than 1 percent of adolescent homicides.”

Rochford said these findings indicate that policy interventions that improve family stability and well-being may be most effective at preventing infant, toddler and child homicides, and programs that target peer and community relationships, as well as policies that focus on firearm access, may be more crucial for preventing adolescent homicides.

By Ann Kellett, Texas A&M University School of Public Health

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OBAMACARE

Affordable care act may increase access to colon cancer care for underserved groups



American Association for Cancer Research




LOS ANGELES – The Affordable Care Act (ACA) has led to increased guideline-concordant care for colon cancer among non-white patients, patients from rural areas, and patients from the most deprived neighborhoods in Pennsylvania, according to results presented at the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved, held September 21-24, 2024.

“The ACA was the largest change to the health insurance system in the United States since the introduction of Medicare and Medicaid in the 1960s, but there is limited evidence on how it affected cancer treatment for different patient populations,” explained Sriya Kudaravalli, a third-year medical student at the University of Pittsburgh School of Medicine, who presented the study. “We were interested in examining changes in receipt of guideline-concordant cancer treatment across various racial and socioeconomic groups after ACA insurance expansions. Understanding these changes can inform future policies to address treatment disparities.”

Kudaravalli explained that receiving guideline-concordant care is associated with improved cancer outcomes, including survival, and that insurance access is an important determinant of receiving guideline-concordant care. In the study, Kudaravalli and colleagues defined guideline-concordant care for stage 3 colon cancer as the use of adjuvant chemotherapy and the resection of affected regional lymph nodes based on medical literature and the criteria established by the National Comprehensive Cancer Network. The retrospective study then examined data between 2010 and 2019 from the Pennsylvania Cancer Registry for 3,290 patients aged 26-64 who were diagnosed with stage 3 colon cancer. The year the main insurance expansions under the ACA were implemented, 2014, served as the cutoff between pre- and post-ACA.

They compared the receipt of guideline-concordant care over the two time periods across several socioeconomic factors including, age, sex, race/ethnicity, insurance status, community type, and area deprivation index (ADI, a measurement developed by researchers at the University of Wisconsin to rank neighborhoods by socioeconomic disadvantage based on variables related to income, education, employment, and housing quality). In their study, Kudaravalli and colleagues grouped ADI scores into quartiles, with ADI quartile 1 representing the least disadvantaged neighborhoods and ADI quartile 4 representing the most disadvantaged neighborhoods.

About two-thirds of patients in the sample had private insurance (63.7%), 10.5% were covered by Medicare, 11.9% by Medicaid, and 13.8% were either uninsured or had an insurance status that was unknown or from another source. The study population included mostly males (54.5%), non-Hispanic whites (79.8%), and people living in urban areas (87.9%). About 4% were non-Hispanic Blacks and 3.6% were Hispanics with 7.5% living in large towns, 2.5% in small towns, and 2.1% in rural areas. Each of these variables was balanced pre- and post-ACA based on standardized mean differences.

Across the entire study period, 82.8% of patients received guideline-concordant care. However, post-ACA, the receipt of guideline-concordant care increased on average per year for non-white patients (7.8%), those in rural areas (7.7%), and those in ADI quartile 4 neighborhoods (3.5%). 

“Implementation of the ACA is associated with an increase in the quality of colon cancer care for underserved groups,” Kudaravalli said. “Availability of insurance coverage is important for reducing disparities in cancer care and outcomes. States that haven’t yet expanded Medicaid are missing an opportunity to improve access to guideline-concordant treatment for cancer.”

Kudaravalli said they plan to also examine the effect of the ACA on receipt of guideline-concordant care for prostate cancer and lung cancer.

Limitations of this study include the fact that patients with missing variables who were excluded from the final results tended to be from underserved groups, which could have decreased the size of the effect. Additionally, the data comes from a single state.

The research was supported by the Agency for Healthcare Research and Quality. Kudaravalli reports no conflicts of interest.