Vancomycin resistant Enterococcus spp. from crows and their environment in metropolitan Washington State, USA: Is there a correlation between VRE positive crows and the environment?
This executive summary was written for the Advanced Technical Communication in Public Health course at the University of Washington.
Roberts et al., 2016 Vancomycin resistant Enterococcus spp. from crows and their environment in metropolitan Washington State, USA: Is there a correlation between VRE positive crows and the environment? Vet Microbiol 2016 Oct 15;194:48-54.
Enterococci are opportunistic pathogens that cause a variety of infections in humans. The danger they pose is increased by several factors: their ability to withstand a range of temperatures, pH, and salinity; their resistance to antibiotics such as vancomycin; and their persistence in the environment, including carriage by animal species. Because birds have been previously linked to environmental contamination and because crows interact extensively with urban areas, Roberts et al. chose crows as an animal model for studying the appearance of vancomycin resistant enterococci (VRE) in wildlife.
In order to identify the relationship between crow VRE and environmental VRE, the researchers collected fecal material from several crow feeding sites: a Seattle area waste water treatment plant (WWTP), four dairy farms, and a restored wetland habitat at UW Bothell. In addition, they collected WWTP treated waste, dairy cow fecal samples, and wetland soil and water. These samples were processed and cultured to identify any VRE isolates. PCR assays then confirmed the presence of vanA, vanB, and vanC1 in each isolate. Any isolate that tested positive for one or more van genes was then speciated using 16S PCR and sequencing and checked for multidrug resistance.
In all, they collected 245 samples, 156 from crows and 89 from the environment. From those, 130 VRE isolates were identified. PCR analysis revealed 38 crow and 49 environmental VRE positive samples. Speciation of 57 of those isolates identified four crow vanA E. faecium, representing 2.7% of the total crows sampled and 10.3% of the characterized crow enterococci; 30 environmental E. faecium, encompassing 78.9% of samples; and vanC1 E. gallinarum in all crows and environmental isolates. The ubiquity of E. gallinarum may indicate a role in normal crow gut microbiota. The four crow E. faecium and a significant portion of the E. gallinarum were also multidrug resistant. Scientists found that the concentration of crow VRE differed by site, likely because of behavioral differences required for inhabiting each. Surprisingly, the variable levels of vanA E. faecium found among crows from different sites did not correlate with environmental levels of those same bacteria at any of the locations.
The work presented here is the first to compare crow VRE to that of their environment and highlights the human health risk of bird-borne disease. One limitation of the study is that crows’ mobility over the course of days and seasons may cause the acquisition of bacteria from distant areas; this may explain the identification of crow VRE that did not match those found in the examined environments and points to a more complex network of contamination. Roberts et al. close by raising two troubling questions: what is the magnitude of the risk birds pose to human health? And conversely, what risk do humans pose to animals as the source of pathogenic bacterial contamination?
Workplace exposures linked to pancreatic cancer risk for female textile workers in Shanghai
This news article was written for the Advanced Technical Communication in Public Health Course at the University of Washington.
Long-term exposure to solvents increased the risk of pancreatic cancer in a large cohort of female textile works in Shanghai, according to a study published by an international group of researchers in the February 2016 issue of the Journal of Occupational and Environmental Medicine. Their work is an eight-year follow-up to a smaller 2006 study that found no associations between pancreatic cancer in textile workers and occupational exposures including solvents, metals, lubricants, inks, resins, and pesticides. Researchers utilized a large data set compiled from decades of factory work records and interviews with relatives. Additionally, the new study could not confirm the 2006 study’s findings of a protective effect from exposure to a bacterial contaminant called endotoxin, commonly found in organic materials like cotton, according to lead author Nicholas Reul, formerly of the University of Washington Department of Environmental and Occupational Health Sciences and currently of the Washington Department of Labor.
Although the study did not identify any new hazardous associations, their results were concordant with prior literature and knowledge of these exposures according to Reul. He noted that few Americans are faced with the medical consequences of workplace exposures as the number of manufacturing and factory jobs in the US dwindles. “It’s something we don’t notice until something goes wrong,” Reul remarked. He promotes awareness of the need for different protections for workers that are regularly exposed to hazardous substances. “The idea of doing occupational health research,” he explained, is to use the data collected “to drive effective public policy so that we can make informed decisions about how to deal with this as a society.” His sentiments were echoed by Dr. Harvey Checkoway, now a researcher at the University of California San Diego and senior author of the publication. “In factory settings the exposures are typically much, much higher because of the indoor, enclosed environment,” he stated. Checkoway emphasizes that there must be serious efforts to minimize exposures to workers.
While the results found by Reul and colleagues are consistent with previous assumptions about the effects of exposures to hazardous substances in the textile industry, there is work left to be done. “The results of a single study don’t add up to real risk,” cautions Dr. Noah Seixas, professor of Environmental and Occupational Health Sciences at the University of Washington and an author on the original 2006 study. Seixas urges that not only people should be more aware of health risks at work, but that studies should determine whether risks are distributed among the population or whether there is discrimination based on industry and type of job.
One area where risk prevention and assessment are still lacking is gender. There is often a disparity between actual exposures and the reported data due to both biological differences and unevenly distributed tasks based on gender. In the textile industry, for example, women are more likely to weave and cart fibers while men are more likely to deal with chemical processes and engineering tasks, meaning estimates of solvent exposure in this study may be problematic. When asked how exposures quantifications are adjusted for gender, Seixas replied, “They’re not. And that may or may not be okay.”
In a lot of cases, it’s not okay, insists Dr. Melissa Friesen, a researcher at the National Cancer Institute in Bethesda, Maryland, and an expert in strategies for minimizing inaccurate workplace exposure estimates. “We almost never have information with which to develop gender-specific estimates of exposure,” she explained. “Studies assume that the risks observed for men also pertain to women and provide no information on women-specific tasks,” Friesen added. Reul concluded that considerations will likely be made for these disparities in the future, noting, “Gender concerns have and will continue to come up in occupational health.”
Shanghai textile workers’ risk of pancreatic cancer linked to solvent exposure
This is a news brief written for the Advanced Technical Communication in Public Health course at the University of Washington.
Long-term exposure to solvents increases the risk of pancreatic cancer in a large cohort of female textile workers in Shanghai, according to a study published by an international group of researchers this week in the Journal of Occupational and Environmental Medicine. The results better define cancer risk for textile workers and may influence guidelines for workplace exposure. Pancreatic cancer is the 10th highest mortality causing cancer among women in less-developed nations. The work serves as a follow-up to a 2006 case-cohort study and confirms previous findings of an etiological relationship between solvent exposure and pancreatic cancer in these workers. Researchers were unable to find relationships to any other previously linked workplace exposures such as metals, lubricants, inks, resins, and pesticides. Their findings also failed to confirm any association between pancreatic cancer and a bacterial contaminant commonly found in organic materials like cotton, called endotoxin; the previous study had indicated a possible protective effect of endotoxin exposure against the disease.
Dangerous mutations hide in healthy skin
AAAS Mass Media Fellowship application piece. A news story about the article, “The genomic landscapes of individual melanocytes from human skin,” published in Nature (Oct 2020).
Healthy skin can harbor a multitude of gene mutations that are known drivers of the dangerous skin cancer melanoma, according to a study published this week in Nature. The findings help explain how melanomas can arise suddenly and without any warning signs.
Jessica Tang, a researcher at UC San Francisco, set out to identify mutations in a rare population of cells in the skin, known as melanocytes. Melanocytes contain the skin-colorizing, protective pigment melanin. They are also the cells that develop into melanoma. Tang and colleagues found that roughly a fifth of healthy melanocytes have melanoma-causing mutations. Learning how mutations arise in these cells is critical for understanding how this deadly disease develops.
There are billions of cells in the human body. Each cell contains a copy of the entire genetic sequence. Mutations can happen naturally by chance or due to damage like exposure to ultraviolet light. Mutations cropping up in the wrong genes, though, can be dangerous. The outermost layer of the skin is thinner than the average human hair. Exposure to the sun’s UV rays through this thin layer can trigger cancer-causing mutations. Finding harmful mutations in cells from melanoma is expected. Finding them in their normal-appearing neighbors—is not.
Most surprising to the researchers was finding that the number of mutations in each cell differed based on how often skin was exposed to sunlight. Cells from skin that is usually protected from UV radiation, like the sole of the foot, showed the lowest mutation number, as one might expect. But in occasionally exposed skin, such as the back or the arms and legs, pigment cells had a higher number of mutations than those in skin that is frequently exposed, such the face or neck. The findings are consistent with the fact that melanomas are most often found on intermittently exposed skin. Figuring out why that is will require further research. This team also report that the number of mutations in normal skin located next to a tumor was higher than skin from a someone who was cancer-free. Doctors and researchers may be able to use melanocyte mutations as an indicator of cumulative sun damage and increased cancer risk.
The researchers managed to overcome a technical hurdle that complicates a lot of gene sequencing research. The most accurate sequencing methods require a large number of cells. Melanocytes, however, are rare and spread out in the skin. It’s impossible to take a biopsy. To overcome this, the team took a small number of melanocytes from skin and grew them in the lab to let them multiply until there were enough to properly sequence.
Using this simple but elegant technique, Tang and her team were able to “offer an unprecedented view of…mutations in normal melanocytes,” Inigo Martincorena explained in Nature Briefing.
The study’s results accord with previous reports of cancer-driving mutations appearing in tissues free of cancer. In 2015, Martincorena’s team detected cancer-causing mutations in samples of healthy eyelid skin. They found that more than a quarter of normal cells carried harmful mutations1. The same year, a group based at the Dana-Farber Cancer Institute in Boston described the accumulation of mutations during the normal aging process in healthy people. The mutations they detected were similar to those found in people with blood cancers2. Conventional wisdom in cancer research assumed that these mutations would be limited to cancer cells.
It now seems clear that health professionals are going to need in-depth knowledge of what normal-appearing skin can hide to better detect and prevent melanoma in its earliest stages. Detection used to rely on finding noticeable changes to the skin, such as the growth of an irregular mole. Doctors and researchers are now finding that these tumors often appear without warning3. The work done by Tang and her colleagues hints at why this is. Melanocytes may become primed with early mutations that only give rise to melanoma after acquiring further mutations. For melanoma, and perhaps many other cancer types, underestimating the danger of tissues that look normal could have serious consequences.
1. Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DCFullam A, Alexandrov LB, Tubio JM, Stebbings L, Menzies A, Widaa S, Stratton MR, Jones PH, Campbell PJ. Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. Science. 2015 May 22;348(6237):880-6. doi: 10.1126/science.aaa6806. PMID: 25999502; PMCID: PMC4471149.
2. Steensma, D. P., Bejar, R., Jaiswal, S., Lindsley, R. C., Sekeres, M. A., Hasserjian, R. P., & Ebert, B. L. (2015). Clonal hematopoiesis of indeterminate potential and its distinction from myelodysplastic syndromes. Blood, 126(1), 9–16. https://doi.org/10.1182/blood-2015-03-631747
3. Shitara D, Nascimento MM, Puig S, Yamada S, Enokihara MM, Michalany N, Bagatin E. Nevus-associated melanomas: clinicopathologic features. Am J Clin Pathol. 2014 Oct;142(4):485-91. doi: 10.1309/AJCP4L5CJGKTJVDD. PMID: 25239415.
Graduate Mental Health and Me
AAAS Mass Media Fellowship application submission. An essay about my experiences with mental illness as a graduate student and beyond.
Ask any graduate student their thoughts on wide-spread mental health crises in higher education, and many of them won’t be surprised. Researchers have found that roughly one third of students are at risk of psychiatric disorders1 and experience generalized anxiety disorder and depression at rates six times higher than the general population2. More than half report tremendous amounts of stress per a University of Arizona survey3. Suicide is one of the leading causes of deaths in medical residents4. It’s not difficult to figure out why this is happening.
Trainees have been workhorses for academia for a long time. At my graduate institution, for instance, students taught over 50% of the credit hours offered by the university. The National Center for Education Statistics reports a 41% increase in postbaccalaureate enrollment between 2000 and 20185. Meanwhile, grant funding for institutions like the National Institutes of Health has decreased in the same period6. For students, this translates to fewer opportunities, more competition, and a constant struggle to make ends meet7. The prospect of becoming a professor is impossible for a larger and larger proportion of students. The average age at which a researcher receives their first major NIH grant has increased from 36 to 42 between 1980 and 20088, meaning trainees can expect to work an average 6 years longer than their own mentors to reach the same point professionally. Add on a global pandemic that has limited productivity, eliminated access to coping mechanisms, and increased uncertainty, and we have trouble on our hands9.
I was unable to escape this trend myself. Hints of generalized anxiety disorder appeared throughout my life, but it wasn’t until I went through the absolute ringer of Ph.D. training that my illness fully developed. Constant tension headaches, mood swings, and an ugly mix of imposter syndrome and paranoia became every day realities. I felt I had to grin and bear it, trying to deliver coherent presentations and quality data through thunderous racing thoughts. With the stress and immense pressure that graduate students already feel, I had no idea that my inner tumult was not normal.
It all finally came to a head in early 2018. I was hyperfixated on escalating tensions with North Korea, discussing the possibility of nuclear assault to anyone with ears. My sleep schedule was destroyed. I was forgetful despite my obsessive note-taking habit. Never one to shy away from volunteer opportunities within my program, I was trying to ease my mind by keeping myself too busy to think that if I died, everything would be easier. And I broke. I had my first major panic attack sitting at my desk in the lab. As waves of nausea and crying washed over me, my quick-thinking lab manager pulled me into a private room and hugged me until I calmed down. I felt a deep, burning embarrassment. Why was I struggling while my peers seemed to flourish?
I finally accepted that what I needed was professional help. I visited a therapist, and eventually a psychiatrist. Honestly, I should have thanked my medication, Lexapro, in the acknowledgements of my thesis. Maybe it’s the years of therapy talking, but these days I’m trying to weaponize my anxiety. Instead of thinking of it as a burden, I try to make it a tool. What is my anxiety trying to tell me? What can I do that’s constructive rather destructive?
· “I’m going to screw this up because I’m a failure.” I know this means “this procedure makes me nervous,” so I should prepare a clear work plan, take good notes, and work slowly.
· “I have no idea what I’m doing and everyone will find out that I’m stupid.” Being unsure how to proceed doesn’t mean I’m stupid. Who can I ask for help to make sure I’m on the right path?
· “If this doesn’t work, then I won’t be able to accomplish any of the things I have planned in the future.” This one is just a lie that my illness likes to peddle. Focus on the task at hand. It’s time to take a break and regroup when I’m able to present in the moment.
I was able to get better because I had resources. I was lucky to be at a university that offered a limited number of free counseling sessions and health insurance that covered my psychiatric care. Many of my peers had no idea what mental health resources were available to them, and I still get asked for advice post-graduation. My program director thanked me for my candidness in sharing my experiences and has now integrated wellness into the student training plan. It’s vital that moves like this become ubiquitous. In addition to a planned study by the Council of Graduate Schools, individual institutions must develop methods for supporting students’ emotional health. Studies suggest that these should include promotion of careers outside of academia, developing a healthy work-life balance, and establishing supportive mentor relationships. When I started my postdoctoral work, I made sure my mentor knew about my diagnosis and what warning signs he should look for. When he could tell that I was struggling he reminded me, “You can’t shut down! Tell me what you need to help get you back on track.” Feeling heard has made it possible to keep moving personally and professionally. Neither academia nor mental illness will ever be easy, but trainees’ suffering can be eased by remembering to treat us like people, and not research machines.
1. Katia Levecque, Frederik Anseel, Alain De Beuckelaer, Johan Van der Heyden, and Lydia Gisle, Work organization and mental health problems in PhD students, Research Policy, Volume 46, Issue 4, 2017, Pages 868-879, ISSN 0048-7333, https://doi.org/10.1016/j.respol.2017.02.008.
2. Evans, T., Bira, L., Gastelum, J. et al. Evidence for a mental health crisis in graduate education. Nat Biotechnol 36, 282–284 (2018). https://doi.org/10.1038/nbt.4089
5. https://nces.ed.gov/programs/coe/indicator_chb.asp
6. https://fas.org/sgp/crs/misc/R43341.pdf
8. Matthews KR, Calhoun KM, Lo N, Ho V. The aging of biomedical research in the United States. PLoS One. 2011;6(12):e29738. doi: 10.1371/journal.pone.0029738. Epub 2011 Dec 28. PMID: 22216352; PMCID: PMC3247288.
9. https://escholarship.org/uc/item/80k5d5hw
Researchers confirm crows as carriers of antibiotic resistant bacteria
It all begins with an idea.
This piece is a news release written as an assignment for the Advanced Technical Communication for Public Health and the University of Washington.
UW Office of News and Information
News Release
Media Contact: Kathryn Baker FOR IMMEDIATE RELEASE
(206) 555-1234 February 3, 2016
Researchers confirm crows as carriers of antibiotic resistant bacteria
SEATTLE, Wash. – Seattle area crows carry antibiotic resistant bacteria picked up as a result of environmental contamination caused by humans according to a University of Washington study published today in Veterinary Microbiology.
Researchers confirmed a previous study1 showing that North American crows are carriers of antibiotic enterococci, bacteria responsible for a variety of human infections. They are the first to recognize that strains found in birds differ from those found in their habitats. Crows are of particular interest to scientists not only because of their ubiquity in urban areas on nearly every continent, but because birds were previously known to carry viruses. Additionally, the group’s previous work pointed to a possible linkage between the presence of birds and antibiotic resistant bacteria in the environment. Roberts et al. analyzed crow feces and environmental samples from a waste water treatment plant, four local dairy farms, and a recreated wetland habitat on the University of Washington Bothell campus, located roughly 20 miles northeast of Seattle. Their results revealed the presence of drug resistant bacterial populations in the guts of the birds as well as in each environment tested. Surprisingly, the bird and environmental strains differed at each site, indicating that the birds picked them up in other locations, such as garbage dumps.
These discoveries have greater implications for human health and the possibility of infection. Resistance to vancomycin, an antibiotic used for serious, life-threatening infections, began to emerge in the U.S. in hospitals in the 1990s due to overuse and has since spread to the environment through human waste. The abuse of antibiotics in farming practices has further contributed to this spread. Today, resistant strains are commonly found in many wildlife habitats and populations. Marilyn Roberts, a professor from the UW Department of Environmental and Occupational Health Sciences and lead investigator on the study, says that these findings bolster the idea of “one health” which states that the health of humans, animals, and the environment are inextricably entwined. She cautions people to avoid both birds and their waste to protect themselves. “Birds can be vectors and people don’t believe that. That’s an issue,” said Roberts. “You don’t want to feed crows. You don’t want to feed wildlife, period, because they may carry pathogens.” She urges the public to be aware of their environment, whether they are in local parks, urban settings, or out in the wilderness, and to remember that “wildlife should be left alone.” While VRE can possibly infect humans, especially the immunocompromised, Roberts offered encouragement saying, “unless you’re living with a bird or person or an animal that is chronically shedding VRE,” or “unless you have a scrape on your extremity,” and you fall into fresh, VRE-infected feces, “it’s probably not going to be that big of a deal.”
Roberts and colleagues plan to continue their work by analyzing samples from the same environmental sites to identify other drug resistant bacteria such as E. coli, Campylobacter, and Salmonella. She encourages concerned parties to be aware of the overuse of antibiotics in medical treatment, to help push the U.S. farming industry to halt the unnecessary use of antibiotics by purchasing products made without them, and to avoid contact with animals and their waste.
Roberts is joined on this study by David B. No, also from the UW Department of Environmental and Occupational Health Sciences, John M. Marzluff and Jack H. Delap of the UW School of Environmental and Forest Sciences, and Robert Turner of the UW School of Interdisciplinary Arts and Sciences.
1 Oracova, V., Zurek, L., Townsend, A., Clark, A.B., Ellis, J.C., Cizek, A., Literak, I., 2014b. American crows as carriers of vancomycin-resistant enterococci with vanA gene. Environ. Microbiol. 16, 939-949
FAQ about Anencephaly Investigation in Central Washington
It all begins with an idea.
This fact sheet is a re-write of a Washington State Department of Health fact sheet about Anencephaly. The goal was to increase accessibility and clarity.
The Washington State Department of Health is investigating a spike in the number of Central Washington infants born with a serious birth defect that affects the development of a baby’s brain and spine, a condition known as anencephaly. Anencephaly causes the brain, skull, and scalp of affected infants to be severely underdeveloped. It occurs early in pregnancy, often before a woman realizes she’s pregnant. Many infants with anencephaly are stillborn; the rest die within hours or days after delivery.
Recently, a health care provider in the Yakima-Franklin-Benton three-county area reported an unusual number of infants born with anencephaly, roughly five times the national average. We have joined local public health authorities and partnered with the Centers for Disease Control and Prevention (CDC) to conduct an investigation.
Here we have answered some common questions and concerns raised by community members regarding the investigation.
What did you look at during the investigation? What did you find?
We compared information from the medical records of women who had a pregnancy affected by anencephaly to that of women who had healthy pregnancies during the same time period. We looked at several potential risk factors for anencephaly including folic acid use, pre-pregnancy weight, family history, and health risk behaviors of the mother during pregnancy . We also evaluated the source of home drinking water.
We were unable to find any significant differences between women who had pregnancies affected by anencephaly and those with healthy pregnancies. However, we found that all the women investigated had low early pregnancy folic acid use. In the Yakima-Benton-Franklin area, in particular, folic acid use appears to be slightly lower than the statewide average: for 2009-2011, about 61% of people surveyed in the three-county area did not take a multivitamin, prenatal vitamin, or folic acid vitamin at all in the month before they got pregnant. This was true for only about 50% of people surveyed from the rest of Washington.
Should women who are pregnant or considering pregnancy in the three-county area be concerned?
While the rate of anencephaly in the region is higher than the national rate, the risk of having a baby with anencephaly is still quite low: about one in every 1,000 live births in the area is affected by anencephaly. From our preliminary investigation results, there is no reason to believe that women who live in the three-county area should take special precautions. However, all women who are pregnant or considering pregnancy should talk to their doctor and be aware of how they can best promote a healthy pregnancy.
What caused these cases of anencephaly?
We have explored several possible causes of anencephaly during our investigation.
Folic acid - The development of anencephaly is clearly linked to low levels of folic acid consumption in women in the month before becoming pregnant.
Radiation - Radiation from the Hanford Nuclear Facility has not been ruled out, but is unlikely to the be the cause. Radiation from the Fukushima disaster is highly unlikely to be the cause because these cases were diagnosed before the event and continued to occur after.
Pesticides - Pesticides are difficult to rule out as a cause because of the large number of pesticide products available and a variety possible routes for exposure. However, we found few cases with parents who worked in agriculture, no clear seasonal associations, and no clusters near farms, so pesticides are probably not the cause
Nitrates and bacteria in drinking water - The link between anencephaly and water contamination is unclear because not all affected cases used the same water supply: some households used private wells while the majority used public water systems. These public water systems were monitored and tested regularly and both nitrate and bacterial levels well within safe limits.
Is anencephaly preventable?
The most important way to prevent these birth defects is taking vitamins containing folic acid and eating foods high in folic acid. Some foods, like leafy greens and citrus fruits, are naturally high in folic acid. It is also added to many breakfast cereals and other grain products labeled “enriched,” such as bread, pasta, and rice. Most experts recommend all women of reproductive age take a daily supplement containing 400 micrograms of folic acid. Women who are pregnant or planning to become pregnant should follow their health care provider’s advice regarding diet, medications, and other health issues including taking vitamins containing folic acid.
What happens next?
The investigation is still ongoing. Although we were unable to find a definite cause, we are still concerned about the high rate of anencephaly in the area. Our study mainly used medical records which may not provide all of the information we need. We are continuing to track cases in the area looking for reasons for the higher rate. In addition, we held meetings with the affected communities to share our results and learn about community concerns. We also created an Anencephaly Advisory Committee to help identify ways to prevent or reduce cases of anencephaly in the area, to improve reporting, and to determine if additional investigation is necessary to identify possible causes.
Where can I learn more?
If you would like to know more about the investigation or need information in another language, please call our helpline at 1-800-555-1234.
For all other inquiries please visit: http://www.doh.wa.gov/AboutUs/ContactUs