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Microbiology, News

ASM Statement in Response to COVID-19 Hearing

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ASM Statement in Response to COVID-19 Hearing

Statement from the American Society for Microbiology 
in response to the 
House Select Subcommittee on the Coronavirus Pandemic Hearing: 
“Investigating the Origins of COVID-19” 
 
March 8, 2023 

On behalf of our 30,000 members in the United States and around the world, the American Society for Microbiology (ASM) shares the following points in response to the House Select Subcommittee on the Coronavirus Pandemic’s hearing to discuss the origins of COVID-19, the disease caused by the SARS-CoV-2 virus.     

ASM supports a science-based, open and comprehensive inquiry into the origins of the pandemic. We are encouraged that government and intelligence agencies continue their due diligence in the investigation.  The conclusions we draw about the origins of COVID-19 will inform the future of high-consequence pathogen research around the world and pandemic preparedness here in the U.S., so it is crucial that we conduct a free, open and complete inquiry and do not draw premature conclusions. Because pathogens know no borders, we also urge international collaboration, to the extent possible, in the search for evidence and answers. 

Novel pathogens with the ability to infect humans have emerged at an increasing rate over the past twenty years. Many threaten global health, but none more so in recent memory than SARS-CoV-2. In addition to novel pathogens, we must address seasonal threats with pandemic potential such as influenza, and recurring epidemic threats such as Ebola. Whenever such threats emerge, questions arise as to how the event happened. Understanding how an epidemic or pandemic starts helps us better prepare for future pandemics. It is essential to lead with science in order to achieve the most complete and accurate understanding of how infectious diseases emerge and spread.  

As such, we offer the following points for consideration: 

  • The United States is the world leader in life sciences research, including basic, clinical and translational research focused on pathogens and infectious diseases. Congress must continue to support the U.S. research ecosystem through a strong federal funding commitment, coupled with policies that enable innovative public private partnerships. By doing so, we can continue promising research to understand how viruses emerge and are transmitted; how they can be prevented, detected, and monitored; and, when they cause disease, how they can be diagnosed and treated. Without continued research in these areas, we will not be able to prevent or even prepare for future pandemics.

 

  • When this work involves working with enhanced potential pandemic pathogens (ePPPs), it must be accompanied by safeguards and conducted under strict biosafety and biosecurity measures in laboratories at the appropriate biocontainment safety level (BSL).  The American public can have confidence that research conducted on ePPPs in the U.S. adheres to the highest standards that set the bar for countries around the world. We have an impeccable track record in this country and recognize the need to continually refine and update standards. But for this leadership to continue, Congress must invest in the network of high containment laboratories to ensure that the infrastructure is sound, laboratorians are appropriately trained, and the work is conducted with minimal risk to both those working in the lab and to the general population.

 

  • Research on disease-causing microbes is necessarily international. As we have seen all too clearly, viruses know no borders. Many of the viruses emerge at the animal-human interface outside of the U.S., so the health and security of the American public depends on transparent research collaborations and sharing of samples and genomic sequencing information with other countries. Work outside the U.S. needs to occur at a biosafety level comparable to that which is applied domestically to reduce risk of lab accidents. With diplomacy and American leadership, ASM believes it is possible to both protect national security and work with governments and researchers in other countries to ensure that this work is being conducted safely. We all want the work to protect people throughout the world, and we need the information to anticipate and detect threats. 

We thank the Subcommittee for consideration of our views. ASM is committed to assisting the Committee, its members, the Congress, and the Administration as the U.S. continues to recover from and consider lessons learned from the COVID-19 pandemic.  

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The American Society for Microbiology is one of the largest professional societies dedicated to the life sciences and is composed of 30,000 scientists and health practitioners. ASM’s mission is to promote and advance the microbial sciences.  

ASM advances the microbial sciences through conferences, publications, certifications and educational opportunities. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences. 

Microbiology, News

Study Shows New York City Rats Carry SARS-CoV-2

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Study Shows New York City Rats Carry SARS-CoV-2

Washington, DC – A new study has demonstrated that rats are susceptible to infection with Alpha, Delta and Omicron variants of SARS-CoV-2 and wild rats in the New York City municipal sewer systems and elsewhere in the city have been exposed to SARS-CoV-2. The study was published in mBio, an open-access journal of the American Society for Microbiology. 

“Our findings highlight the need for further monitoring of SARS-CoV-2 in rat populations for potential secondary zoonotic transmission to humans,” said study principal investigator Henry Wan, Ph.D., Professor and Director of the Center for Influenza and Emerging Infectious Diseases at the University of Missouri. “Overall, our work in this space shows that animals can play a role in pandemics that impact humans, and it’s important that we continue to increase our understanding so we can protect both human and animal health.” 

Rats are widely distributed in urban communities in the United States. For example, New York City alone has approximately eight million wild rats. These wild rats have ample opportunities to interact with humans. Two previous studies suggested that rats in Asia (Hong Kong) and Europe (Belgium) were exposed to SARS-CoV-2; however, it is unknown which SARS-CoV-2 variant these rats were exposed to in both studies.  

In the new study, the researchers set out to determine whether the SARS-CoV-2 virus in humans has been transmitted to the rat population in urban areas of the United States, specifically New York City, and if so, which SARS-CoV-2 variant caused those infections. The researchers also set out to determine whether (and which) SARS-CoV-2 variants in NYC can cause infections in rats. 

“In Fall of 2021, U.S. Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) sampled Norway rats (Rattus norvegicus) in New York City to look for evidence of SARS-CoV-2 infection,” said study coauthor Tom DeLiberto, D.V.M., Ph.D., SARS-CoV-2 Coordinator at USDA APHIS Wildlife Services. “Two trapping efforts were conducted during September and November with permission from the NYC Department of Parks and Recreation in and around locations surrounding wastewater systems. Most of the rats were trapped in city parks within Brooklyn, although some were captured near buildings outside of park boundaries.”  

Biologists collected and processed samples from 79 rats for virological studies and genomic sequencing. The researchers found that the rats were exposed to SARS-CoV-2 and showed a possible link to the viruses that were circulating in humans during the early stages of the COVID-19 pandemic. Specifically, 13 of 79 rats (16.5%) tested positive. “To the best of our knowledge, this is one of the first studies to show SARS-CoV-2 variants can cause infections in the wild rat populations in a major U.S. urban area,” Dr. Wan said.  

To further investigate rat susceptibility to SARS-CoV-2 variants, the researchers conducted a virus challenge study and showed that Alpha, Delta and Omicron variants (variants found in humans) can cause infections in rats (wild-type Sprague Dawley rats), including high replication levels in the upper and lower respiratory tracts and induction of both innate and adaptive immune responses. Susceptibility to infection varied by type of variant. 

“Our findings highlight the need for further monitoring of SARS-CoV-2 in rat populations to determine if the virus is circulating in the animals and evolving into new strains that could pose a risk to humans,” Dr. Wan said. “SARS-CoV-2 virus presents a typical one-health challenge which requires collaborative, multisectoral and transdisciplinary approaches to fully understand such challenges.” 
 

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The American Society for Microbiology is one of the largest professional societies dedicated to the life sciences and is composed of 30,000 scientists and health practitioners. ASM’s mission is to promote and advance the microbial sciences.  
 
ASM advances the microbial sciences through conferences, publications, certifications and educational opportunities. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.  
Microbiology, News

Virologists Call for Rational Discourse on Gain of Function Research

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Virologists Call for Rational Discourse on Gain of Function Research

Washington, DC – January 26, 2023 – The study of viruses is under renewed scrutiny, say more than 150 experts in a new commentary published today in mSphere, mBio and the Journal of Virology, journals of the American Society for Microbiology.

The commentary’s authors call on policymakers to recognize the need for more rational discourse around the future of virology. They implore a more nuanced, evidence-based discussion around gain of function research and provide evidence to support the benefits of this type of research for human health. These concerns are especially focused on enhanced potential pandemic pathogen (ePPP) research and dual use research of concern (DURC).

“To respond rapidly to emerging viral threats we must be able to apply modern biology tools to viruses which will ensure that we reduce the burden of future disease outbreaks,” said Felicia Goodrum, Ph.D., co-Editor-in-Chief of ASM’s Journal of Virology.  

The current debate regarding the origin of SARS-CoV-2 pandemic is partly due to a theory that suggests it may have been caused by an accidental or intentional lab leak. However, evidence strongly suggests that the virus originated from zoonotic transmission, through the transfer of the virus from wild animals to humans.
 
Despite this, a narrative against this valuable research tool has developed, putting the field of virology at risk, despite its critical role in preparing humanity to fight threats posed by viruses.
 
“Research on dangerous pathogens does require oversight, but we must be careful to not overly restrict the ability of scientists to generate the knowledge needed to protect ourselves from these pathogens, said Michael Imperiale,” Ph.D., a professor with the Department of Microbiology and Immunology at the University of Michigan Medical School and Editor-in-Chief of ASM’s journal mSphere.
 
As policymakers take a renewed look at policies surrounding gain-of-function research, the authors state, the abundance of existing oversight around virology research should be considered and a concerted effort to avoid redundant measures should be implemented.
 
Gain of function research and regulations around virus research is the subject of a meeting by the National Science Advisory Board for Biosecurity to be held on January 27, which has released draft findings and recommendations.  
 
“It is critical that policy makers, virologists, and biosafety experts work together to ensure that research is conducted safely, with the common goal of reducing the burden of disease caused by viruses,” said Seema Lakdawala, Ph.D., an associate professor with the Department of Microbiology and Immunology at Emory University.
 
Read the full commentary: “Virology Under the Microscope: A Call for Rational Discourse.”

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The American Society for Microbiology is one of the largest single life science societies, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.   

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences. 

Microbiology, News

ASM Commends NSABB’s Proposed Biosecurity Oversight Framework

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ASM Commends NSABB’s Proposed Biosecurity Oversight Framework

Washington, D.C. – January 20, 2023 – The American Society for Microbiology (ASM) supports and appreciates the work of the National Science Advisory Board for Biosecurity (NSABB) to review and revise policies governing enhanced potential pandemic pathogen (ePPP) research and dual use research of concern (DURC).

The NSABB was charged with reviewing and revising the policies governing ePPP research and DURC, and providing recommendations on a forward-thinking approach to the funding review process for such studies.   
 
The NSABB, which is comprised of members with significant expertise in science, research methodology, biosecurity and bioethics, has an indispensable role in guiding policies that govern these important issues. ASM recognizes the importance of cutting-edge research on human, animal, and plant microbes as well as our responsibility as scientists to minimize the likelihood that results of experiments with microbes of concern are misused or that these pathogens accidentally escape laboratory containment. We are pleased to see that ASM’s recommendations were incorporated into the report, and we urge swift implementation of the recommended changes by the federal agencies engaged in this work.
 
ASM maintains the position that international collaboration is essential in all of sciences, including research involving ePPPs.  The U.S. has a robust system of oversight at the institutional, state and national levels. We are glad to see the report recognizes the importance of and seeks to strengthen these efforts, and also recommends that the U.S. government engage the international community in a dialogue about the oversight and responsible conduct of ePPP research and DURC.
 
As the NSABB recognizes, we also have an obligation to provide leadership and coordination to those conducting this important research in other countries. Diplomacy is essential to success, and we are encouraged that one of the report’s recommendations acknowledges the importance of global collaboration to global health security. We support next steps in this area to ensure international ePPP research in partnership with U.S. funders and entities be coupled to the strict biosafety and security standards that govern domestic research in the U.S.
 
Additionally, scientific publishers play a critical role in ensuring that this work is carried out and communicated in a manner that should instill public confidence. As one of the largest publishers of microbial science research in the world and as an organization that has implemented a rigorous process for assessing publications involving ePPP and DURC, ASM supports the report’s recommendation to develop and adopt more uniform editorial policies, review processes and best practices for safe communication of sensitive research findings. ASM stands ready to assist the federal agencies in engaging stakeholder groups to move this recommendation forward.
 
The United States has a strong track record of safely conducting life-saving research and adhering to the most stringent biosafety and biosecurity standards. This has enabled us to lead the world in science and innovation, and we have saved countless lives through the development of diagnostics, vaccines and therapeutics to target infectious disease threats. Building on this strong scientific and experiential foundation ensures this life saving work can continue into the future in a way that balances benefits with risks. ASM believes that this report’s findings and recommendations can help us do just that, and we look forward to working with governing bodies and stakeholders to achieve our goals.  
 

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The American Society for Microbiology is one of the largest single life science societies, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.  

Microbiology, News

Antibiotics’ Effect on the Mycobiome Varies from Person to Person

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Antibiotics’ Effect on the Mycobiome Varies from Person to Person

Washington, DC – November 30, 2022 – Antibiotic treatment disrupts the balance of beneficial and harmful bacteria in a person’s gut. That disruption can lead to the overgrowth of fungal species in the gut mycobiota, including the common intestinal yeast Candida albicans. However, researchers only have a limited understanding of the underlying mechanisms. 

This week in mBio, an open-access journal of the American Society for Microbiology, in a first of its kind study on human subjects, researchers in Europe report on how treatment with a common beta-lactam antibiotic led to significant changes in C. albicans in patients. Notably, they found that not all patients responded in the same way, and the degree to which C. albicans populations increased depended in large part on the microbiota of the individual. That variation suggests that the risk for C. albicans overgrowth, in response to antibiotic treatment, is not the same for everyone. 

“This study shows that the situation is more complex than previously thought, and with certain antibiotics such as beta-lactam, this increase in C. albicans varies from one person to another,” said microbiologist and senior author Marie-Elisabeth Bougnoux, M.D., Ph.D., at the Institut Pasteur in Paris, France.

Researchers have long studied the effects of antibiotics on the gut microbiota, but less attention has been paid to the mycobiota, or collection of gut fungal species. The authors of the new study point to 2 reasons.

“First, the mycobiota is difficult to study with metagenomics techniques,” said Margot Delavy, a Ph.D. student at the institute and first author on the paper, “and second, the concentration of fungi is much lower than that of bacteria,” making them harder to measure. “Repeatable metagenomic techniques to study the fungi of the gut have become available only recently,” she said. 

For the new study, Bougnoux and her colleagues used fecal samples to track the changes in the gut mycobiota in 2 groups of 11 healthy patients before, during, and after they were treated with cefotaxime (in one group) or ceftriaxone (in the other). Both drugs are third-generation cephalosporin antibiotics.
The group first identified the fraction of the fecal DNA that was associated with fungal species. Then, they used high-throughput sequencing to identify which fungal species were present in the healthy gut of the volunteers, before antibiotic treatment. They found that both diversity and abundance of species varied not only from person to person, but also from one collection to another in the same individual. The team used specific qPCR to quantify levels of C. albicans and found the fungus present in 95% of the participants.

The researchers carried out similar analyses during and after antibiotic treatment. They found that across the board, the fungal load — the fraction of fecal DNA — increased in all patients following treatment with antibiotics. But at the species level, those responses varied considerably. Some individuals experienced a significant increase in abundance of C. albicans and other species, while others didn’t. (At least one participant even showed a decrease.) 

Further analyses of the samples revealed that the variations in fungal response to antibiotic treatment was connected to the activity of the enzyme beta-lactamase, which is produced by endogenous bacteria from the subject’s microbiota. People with lower levels of beta-lactamase experienced more growth of fungi, including C. albicans, than those with higher levels of the enzyme. 

Bougnoux, whose previous work has focused on how intestinal C. albicans colonization leads to infection, said the group wanted to focus on antibiotic use because it’s a major risk factor for colonization. The new study, she noted, is a promising first step toward understanding how the mycobiota responds to treatment—but it’s only the beginning. 

“Our study was done on human volunteers who received only one antibiotic, but actual patients often receive several,” Bougnoux said. And those who receive the most are most likely to develop fungal infections, she added. “It remains to be seen if the relation we found between beta-lactams and reduced intestinal C. albicans colonization is also true in these patients.”

 

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The American Society for Microbiology is one of the largest single life science societies, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences. 

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences. 

Microbiology, News

New Discoveries Could Improve Cheese Production and Lead to Novel Cheeses

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New Discoveries Could Improve Cheese Production and Lead to Novel Cheeses

Washington, D.C. – November 15, 2022 – New research shows that the flavoring of various soft cheeses is due in part to the bacteria that colonize them during the ripening process. The research is published in Microbiology Spectrum, a journal of the American Society for Microbiology.
 
As cheese ages, beneficial bacteria degrade proteins and lipids (from milk fat) and produce the molecules responsible for characteristic aromas of ripening cheeses. (1) The diversity of “non-starter” bacteria, which spontaneously develop during ripening and form flavor compounds, is the key factor for developing the characteristics of cheese.
 
The role of microorganisms in flavor formation had not been fully understood, “due to the diversity of cheese varieties and the complexity of cheese microbial consortia,” said corresponding author Morio Ishikawa, Ph.D., a professor at the Department of Fermentation Science, Faculty of Applied Bioscience at the Tokyo University of Agriculture in Japan.
 
In the study, the investigators presented an approach to identifying and examining certain bacteria known to be involved in cheese production, including 3 phyla of bacteria, Firmicutes, which are lactic acid bacteria, and Actinobacteria and Proteobacteria, which produce characteristic flavors in certain cheeses. By comparing bacteria from across the 3 phyla to other known flavor-producing bacteria in a cheese ripening test, the researchers showed a relationship between specific microbes and flavor.
 
Ishikawa and his collaborators had used statistical analysis to reveal relationships between bacterial types and the various volatile flavor-producing organic compounds that each produces in surface-mold ripened cheeses. To test that relationship of specific microbes to flavor, they then selected non-starter bacteria of taxa that were strongly correlated with specific volatile compounds and flavors, and performed cheese-ripening tests. These tests showed that the bacteria from the correlational research were in fact responsible for the flavors of the cheeses.
 
Additionally, this research could provide a scientific basis for improving the safety and quality of cheese. “By isolating and investigating microorganisms involved in flavor formation as targets, rather than blindly examining them, we will be able to scientifically evaluate the safety of these microorganisms. At the same time, it may be possible to construct a cheese production method that uses only those microorganisms that play a major role in flavor production,” said Ishikawa.
 
“The comprehensive insights into the complex associations between microbiota and flavor improve our systematic understanding of mechanism of cheese flavor production,” said Ishikawa. The new research will not only provide a scientific basis for the traditional method of cheese production, but might also enable the creation of novel cheeses.
 
1. per Ishikawa, little or no lactose remains in cheese during ripening.

 

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The American Society for Microbiology is the largest single life science society, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.  

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.  

Microbiology, News

Boosting Accuracy, Reducing False Positives of PCR COVID-19 Tests

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Boosting Accuracy, Reducing False Positives of PCR COVID-19 Tests

Highlights: 

  • PCR tests are the gold standard for COVID-19 diagnosis, but they’re not always accurate. 

  • False positives and false negatives both have negative repercussions and risks for patients. 

  • New research suggests adding a test for the genetic response of the infected individual (the host) could improve accuracy. 

  • Researchers have derived and tested a classifier, based on 2 host genes, that could readily be added to existing PCR assays. 

Washington, D.C. – Dec. 12, 2022 – PCR swab tests that look for viral RNA have become the gold standard for identifying infection with the SARS-CoV-2 virus, but their results aren’t 100% accurate. This week in  mSystems,  researchers report that testing for levels of certain immune-related genes in an infected individual, in addition to looking for genetic material of the virus itself, could increase diagnostic accuracy. 

Researchers compared gene expression data from people diagnosed with COVID-19 to those of people diagnosed with other viral respiratory illnesses and people with non-viral conditions. The analysis revealed that expression of a combination of 2 host genes is strongly associated with SARS-CoV-2 infection. Furthermore, a test for that genetic response could be readily incorporated into existing PCR assays and retain its accuracy for existing and future variants of the virus. 

“We envision this as an add-on to a PCR test that still looks for direct evidence of the virus and uses the host genes as a fallback to make sure we catch situations where there might be false positive or false negative results from the viral PCR,” said computational biologist Eran Mick, Ph.D., at the University of California, San Francisco. 

Mick was one of 3 lead authors on the paper. The other 2 were UCSF microbiologist Estella Sanchez-Guerrero, Ph.D., and Jack Albright, an undergraduate student at Stanford University, who began working on the project as a high school intern at the Chan Zuckerberg (CZ) Biohub. Infectious disease researcher Charles Langelier, M.D., Ph.D., also at UCSF and CZ Biohub, was senior author on the study. 

The U.S. Food and Drug Administration approved the first PCR test for COVID-19 in the spring of 2020. However, during widespread use the test is vulnerable to false negatives—especially as the virus evolves into new variants that might escape detection—and false positives as through contamination by other samples in a testing lab. A person who received a false negative result might get sick without treatment and continue to spread the virus. A false positive result could cause a person to endure unnecessary isolation or have planned medical procedures canceled. 

“There are a lot of repercussions,” said Langelier. 

In November 2020, Mick and Langelier led a study that demonstrated COVID-19 causes a unique gene expression pattern in infected individuals. The observation prompted them to investigate whether those genes might have some diagnostic utility. In previously published work, the team used RNA sequencing data from nasopharyngeal swabs to identify combinations of multiple genes that could serve as diagnostic classifiers for COVID-19. 

However, according to Langelier, testing for the response of a large number of genes isn’t feasible on a routine basis and is incompatible with existing clinical PCR tests. For the new work, the researchers tested a range of 2-gene combinations to find a pair that could accurately diagnose COVID-19. They found that the optimal signature included  IFI6, a gene stimulated by interferon and strongly induced in COVID-19 compared to non-viral conditions, and  GBP5,  which is strongly induced in other viral infections. 

“It’s really a combination of 1 gene that does a good job at separating those with no viral infections from those with [an infection], and another gene that separates out the COVID-19 cases from other respiratory viral infections,” said Albright. 

“So many different biological processes change in the setting of an infection,” said Langelier. “It was surprising that all of that complex biology could be distilled down to these 2 genes with predictive value.” 

Once they identified the gene pair, the team showed that the classifier could be included in a PCR assay, is unaffected by cross-contamination (because it measures the host response) and works for all common variants of the virus.  

“To bring it down to such a small number of genes is a game changer,” said Mick. 

Mick noted that this 2-gene host signature is designed to be used in combination with a viral PCR test to diagnose COVID-19 because there is still significant overlap between the response to SARS-CoV-2 and the response to other viral infections. However, a purely host-based classifier could be used as a broad-range surveillance tool to identify people infected with any respiratory virus. Even before the pandemic, Mick noted that viral infections were a major public health issue, and many went undetected. A diagnostic tool that flags viral infections could be useful for screening vulnerable populations in nursing homes or hospitals.  

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The American Society for Microbiology is one of the largest single life science societies, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.   

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences. 

Microbiology, News

Occupational Hazard: COVID-19 False Positives in Lab Workers

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Occupational Hazard: COVID-19 False Positives in Lab Workers

Highlights

  • A new study analyzed genes in nasal swabs from asymptomatic people who tested positive for SARS-CoV-2.
  • The study found a cluster of people who worked together in a lab that focuses on plasmids.
  • Plasmids are tiny bits of DNA commonly used to study the proteins produced by viruses.
  • The analysis attributed the positive tests to the plasmid DNA, not the virus RNA.
  • The new study shows the importance of considering occupation in diagnostic exams.

Washington, D.C. – For some laboratory workers a positive test for SARS-CoV-2 may more accurately indicate an occupational exposure than a viral infection. This week in Microbiology Spectrum, researchers in Seattle report on a small group of laboratory workers whose false positive tests for the virus came not through viral RNA, but instead from a usually harmless bit of DNA, called a plasmid, that’s commonly used to study the virus.

“Plasmids are small DNA structures commonly found in bacteria, and we use them all the time in the lab to make proteins,” said virologist and study leader Lisa Frenkel, M.D., at the University of Washington, who co-directs the Center for Global Infectious Disease Research at Seattle Children’s Research Institute. “And here, the plasmid seemed to take hold in the noses of people who worked with it.” The study also showed that plasmids can spread to other members of a person’s household.

The number of asymptomatic people who test positive and work with SARS-CoV-2 plasmids in labs, is unknown, since most are unlikely to be tested when asymptomatic.

More importantly, the new study revealed that plasmids can linger in the nose, probably within bacteria, for weeks. They can interfere with clinical diagnostic tests. Frenkel explained that when physicians interpret diagnostic results they should consider a patient’s occupational exposure, as well as their medical history.

Frenkel, whose work usually focuses on HIV, did not originally set out to study lab workers or plasmids. But in late March 2020, as COVID-19 case counts grew worldwide, her lab (and those of many colleagues at Seattle Children’s) pivoted to work on SARS-CoV-2. They began looking for biomarkers that could predict how a person would respond to infection. They launched a prospective observational trial that monitored, on a weekly basis, a group of people who had tested positive for SARS-CoV-2 by polymerase chain reaction (PCR) test but didn’t show symptoms.

As they analyzed the data, the researchers realized that 4 of the asymptomatic subjects in their study who tested positive for SARS-CoV-2 by PCR all worked together in the same lab.

“We knew the principal investigator of that lab, and we knew what they were working on,” Frenkel said. Researchers in that lab had been working with a plasmid that encoded a SARS-CoV-2 protein.

That connection raised a question: Could the diagnostic tests be picking up DNA in the plasmid, rather than the virus? After all, PCR tests detect genetic material from the virus. To find out, the researchers analyzed nucleic acids taken from the nasal swabs of the 4 co-workers and 1 additional participant, a partner of 1 of the lab workers who was also asymptomatic and testing positive.

Senior scientist Ingrid Beck, M.S., proved that in all cases tested, the detected material came from the plasmid, not the virus. Multiple PCR assays conducted on the specimens amplified DNA sequences unique to the plasmid used in the lab, but not regions of the SARS-CoV-2 RNA. “They had it in their noses for long periods of time, either in nasal tissues or in bacteria,” Frenkel said. The researchers were most likely exposed to the plasmid through their lab work.

The findings raise other questions that remain unanswered. “Now we’re curious, did [the plasmid] vaccinate those people?” Frenkel asked. “We don’t know if they got mucosal immunity to that part of the virus. Could it protect them?”

Since the end of the study, Frenkel has resumed her work on HIV. “SARS-CoV-2 is going to evolve, but luckily it doesn’t evolve as quickly as HIV,” she said. “It’s a virus that we’re able to deal with better than HIV.”

 

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The American Society for Microbiology is one of the largest single life science societies, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences. 

Microbiology, News

New Zika Vaccine Shows Promise in Animal Models

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New Zika Vaccine Shows Promise in Animal Models

Washington, D.C. – Researchers from the University of California, Los Angeles (UCLA) have developed a Zika vaccine technology that is highly effective and safe in preclinical mouse models. In a pregnant mouse model, the vaccine prevented both the pregnant mothers and the developing fetuses from developing systemic infection. The research is published in Microbiology Spectrum, a journal of the American Society for Microbiology.

“Engineering the vaccine involved deleting the part of the Zika genome that codes for the viral shell,” said Vaithilingaraja Arumugaswami, D.V.M., Ph.D., Associate Professor of Molecular and Medical Pharmacology at UCLA. “This modification both stimulates an immunogenic reaction and prevents the virus from replicating and spreading from cell to cell.”

Vaccinated mice showed elevated levels of cell-mediated immune response, in the form of increased effector T cell populations, as compared to mice that had not been vaccinated. The researchers also tested the vaccine in a variety of other mouse models, in which it proved safe and protective.

The impetus for the work was the 2016 outbreak of Zika virus, which spread rapidly in the Americas and affected millions of people, leading to severe socioeconomic hardships. Zika was the first mosquito-borne virus that showed the ability to affect human reproduction.

To date, no vaccines or other treatments have been approved for Zika virus. Nor have investigations into other ways of fighting the virus led to clearly effective countermeasures. “But given that RNA viruses—the category to which both Zika and the SARS family of viruses belong—are highly prone to evolving and mutating rapidly, there will likely be more outbreaks in the near future,” said Arumugaswami.

The average length of time between periods of extensive Zika viral spread is approximately 7 years. “It is only a matter of time before we start seeing the virus spread again,” said Kouki Morizono, M.D., Ph.D., Associate Professor of Medicine at UCLA and co-senior author of this study.

To make matters worse, climate change is expanding the permissible habitats of mosquitoes like Aedes aegypti, which transmits Zika virus to humans, increasing the at-risk population.

“The ongoing COVID-19 pandemic has shown us the power of a strong pandemic preparedness plan and clear communication about prevention methods – all culminating in the rapid rollout of safe and reliable vaccines,” said Arumugaswami. As such, it is essential to develop a strong pandemic preparedness plan. “Our research is a crucial first step in developing an effective vaccination program that could curb the spread of Zika virus and prevent large-scale spread from occurring,” said Arumugaswami.

ASM’s Laboratory Practices Subcommittee and the Pan American Society for Clinical Virology’s (PASCV) Clinical Practice Committee updated the guidance for Zika laboratory testing in Sep. 2022. 

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The American Society for Microbiology is the largest single life science society, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences. 

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences. 

Microbiology, News

Oil-based Systems Show Promise for Eradicating Salmonella on Food Production Machinery

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Oil-based Systems Show Promise for Eradicating Salmonella on Food Production Machinery

Washington, D.C. – Recent outbreaks of food-borne Salmonella have been associated with chocolate and peanut butter. Although Salmonella cannot grow in either of these low-water foods, the cells survive, becoming more resistant to heat treatment, which has contributed to recent outbreaks. New research published in Applied and Environmental Microbiology suggests that oil formulations with food-grade organic acids can kill dried Salmonella on stainless steel surfaces.  

“Cleaning and sanitation of manufacturing environments are critical for a safe food supply,” said lead author Lynne McLandsborough, Ph.D., a professor of food science at University of Massachusetts Amherst. However, water-based cleaning is rarely used in processing peanut butter, because it promotes microbial growth. “Also, as anyone who has baked peanut butter cookies can tell you, peanut butter and water do not mix, and cleanup with water is challenging,” said McLandsborough.  

Instead, manufacturers often remove residual peanut butter from manufacturing systems using heated oil, followed by overnight cooling and application of flammable alcohol-based sanitizing agents.  

In the study, McLandsborough and collaborators dried Salmonella on stainless steel surfaces at controlled relative humidity. They then covered the dried bacteria with various oils with organic acids, varying the acid type, concentration, contact time and treatment temperature to identify highly antimicrobial formulations. 

By using peanut oil mixed with acetic acid at a concentration about half that of household vinegar and applying heat, “killing was much greater than expected, indicating a synergistic effect,” said McLandsborough. “Our results show that acidified oils could be used as an effective means of sanitation in low-moisture food processing facilities, where water-based cleaning can be challenging.” 

“To our knowledge, using oils as a carrier of organic acids is a novel approach to delivering antimicrobial compounds against food-borne pathogens,” said McLandsborough. The research may thus lead to adaptation of oil-based systems for industrial cleaning, for example, of machinery for processing chocolate and peanut butter, said McLandsborough. “That would enable more frequent cleaning, boosting the safety of these products.”  
 

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The American Society for Microbiology is the largest single life science society, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.  

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.