Proteins are the key players for virtually all molecular processes within the cell. To fulfil their diverse functions, they have to interact with other proteins. Such protein-protein interactions are mediated by highly complementary surfaces, which typically involve many amino acids that are positioned precisely to produce a tight, specific fit between two proteins. However, comparatively little is known about how such interactions are created during evolution.
Classical evolutionary theory suggests that any new biological feature involving many components (like the amino acids that enable an interaction between proteins) evolves in a stepwise manner. According to this concept, each tiny functional improvement is driven by the power of natural selection because there is some benefit associated with the feature. However, whether protein-protein interactions also always follow this trajectory was not entirely known.
Using a highly interdisciplinary approach, an international team led by Max Planck researcher Georg Hochberg from the Terrestrial Microbiology in Marburg have now shed new light on this question. Their study provides definitive evidence that highly complementary and biologically relevant protein-protein interactions can evolve entirely by chance.
Proteins cooperate in a photoprotection system
The research team made their discovery in a biochemical system that microbes use to adapt to stressful light conditions. Cyanobacteria use sunlight to produce their own food through photosynthesis. Since much light damages the cell, cyanobacteria have evolved a mechanism known as photoprotection: if light intensities become dangerously high, a light intensity sensor named Orange Carotenoid Protein (OCP) changes its shape. In this activated form, OCP protects the cell by converting excess light energy into harmless heat. In order to return into its original state, some OCPs depend on a second protein: The Fluorescence Recovery Protein (FRP) binds to activated OCP1 and strongly accelerates its recovery.
‘Our question was: Is it possible that the surfaces that allow these two proteins to form a complex evolved entirely by accident, rather than through direct natural selection?’ says Georg Hochberg. ‘The difficulty is that the end result of both processes looks the same, so we usually cannot tell why the amino acids required for some interaction evolved – through natural selection for the interaction or by chance. To tell them apart, we would need a time machine to witness the exact moment in history these mutations occurred, ‘Georg Hochberg explains.
Luckily, recent breakthroughs in molecular and computational biology has equipped Georg Hochberg and his team with a laboratory kind of time machine: ancestral sequence reconstruction. In addition, the light protection system of cyanobacteria, which is under study in the group of Thomas Friedrich from Technische Universität Berlin since many years, is ideal for studying the evolutionary encounter of two protein components. Early cyanobacteria acquired the FRP proteins from a proteobacterium by horizontal gene transfer. The latter had no photosynthetic capacity itself and did not possess the OCP protein.
To work out how the interaction between OCP1 and FRP evolved, graduate student Niklas Steube inferred the sequences of ancient OCPs and FRPs that existed billions of years ago in the past, and then resurrected these in the laboratory. After translation of the amino acid sequences into DNA he produced them using E. coli bacterial cells in order to be able to study their molecular properties.
A fortunate coincidence
The Berlin team then tested whether ancient molecules could form an interaction. This way the scientists could retrace how both protein partners got to know each other. ‘Surprisingly, the FRP from the proteobacteria already matched the ancestral OCP of the cyanobacteria, before gene transfer had even taken place. The mutual compatibility of FRP and OCP has thus evolved completely independently of each other in different species, says Thomas Friedrich. This allowed the team to prove that their ability to interact must have been a happy accident: selection could not plausibly have shaped the two proteins’ surfaces to enable an interaction if they had never met each other. This finally proved that such interactions can evolve entirely without direct selective pressure.
‘This may seem like an extraordinary coincidence,’ Niklas Steube says. ‘Imagine an alien spaceship landed on earth and we found that it contained plug-shaped objects that perfectly fit into human-made sockets. But despite the perceived improbability, such coincidences could be relatively common. But in fact, proteins often encounter a large number of new potential interaction partners when localization or expression patterns change within the cell, or when new proteins enter the cell through horizontal gene transfer.’ Georg Hochberg adds, ‘Even if only a small fraction of such encounters ends up being productive, fortuitous compatibility may be the basis of a significant fraction of all interactions we see inside cells today. Thus, as in human partnerships, a good evolutionary match could be the result of a chance meeting of two already compatible partners.’
Steube, N., et al. (2023). Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection. Nature Ecology & Evolution. doi.org/10.1038/s41559-023-02018-8.
Global data shows nearly 10 per cent of severe COVID-19 cases involve a secondary bacterial co-infection – with Staphylococcus aureus, also known as Staph A., being the most common organism responsible for co-existing infections with SARS-CoV-2. Researchers at Western have found if you add a ‘superbug’ – methicillin-resistant Staphylococcus aureus (MRSA) – into the mix, the COVID-19 outcome could be even more deadly.
The mystery of how and why these two pathogens, when combined, contribute to the severity of the disease remains unsolved. However, a team of Western researchers has made significant progress toward solving this “whodunit”.
New research by Mariya Goncheva, Richard M. Gibson, Ainslie C. Shouldice, Jimmy D. Dikeakos and David E. Heinrichs, has revealed that IsdA, a protein found in all strains of Staph A., enhanced SARS-CoV-2 replication by 10- to 15-fold. The findings of this study are significant and could help inform the development of new therapeutic approaches for COVID-19 patients with bacterial co-infections.
Interestingly, the study, which was recently published in iScience, also showed that SARS-CoV-2 did not affect the bacteria’s growth. This was contrary to what the researchers had initially expected.
We started with an assumption that SARS-CoV-2 and hospitalization due to COVID-19 possibly caused patients to be more susceptible to bacterial infections which eventually resulted in worse outcomes.”
Mariya Goncheva
Goncheva is a former postdoctoral associate, previously with the department of microbiology and immunology at Schulich School of Medicine & Dentistry.
Goncheva said bacterial infections are most commonly acquired in hospital settings and hospitalization increases the risk of co-infection. “Bacterial infections are one of the most significant complications of respiratory viral infections such as COVID-19 and Influenza A. Despite the use of antibiotics, 25 per cent of patients co-infected with SARS-CoV-2 and bacteria, die as a result. This is especially true for patients who are hospitalized, and even more so for those in intensive care units. We were interested in finding why this happens,” said Goncheva, lead investigator of the study.
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Goncheva, currently Canada Research Chair in virology and professor of biochemistry and microbiology at the University of Victoria, studied the pathogenesis of multi-drug resistant bacteria (such as MRSA) supervised by Heinrichs, professor of microbiology and immunology at Schulich Medicine & Dentistry.
When the COVID-19 pandemic hit, she pivoted to study interactions between MRSA and SARS-CoV-2.
For this study, conducted at Western’s level 3 biocontainment lab, Imaging Pathogens for Knowledge Translation (ImPaKT), Goncheva’s work created an out-of-organism laboratory model to study the interactions between SARS-CoV-2 and MRSA, a difficult-to-treat multi-drug resistant bacteria.
“At the beginning of the pandemic, the then newly opened ImPaKT facility made it possible for us to study the interactions between live SARS-CoV-2 virus and MRSA. We were able to get these insights into molecular-level interactions due to the technology at ImPaKT,” said Heinrichs, whose lab focuses on MRSA and finding drugs to treat MRSA infections. “The next step would be to replicate this study in relevant animal models.”
Goncheva, M. I., et al. (2023). The Staphylococcus aureus protein IsdA increases SARS CoV-2 replication by modulating JAK-STAT signaling. IScience. doi.org/10.1016/j.isci.2023.105975.
New research from the University of Missouri School of Medicine has established a link between western diets high in fat and sugar and the development of non-alcoholic fatty liver disease, the leading cause of chronic liver disease.
The research, based in the Roy Blunt NextGen Precision Health Building at MU, has identified the western diet-induced microbial and metabolic contributors to liver disease, advancing our understanding of the gut-liver axis, and in turn the development of dietary and microbial interventions for this global health threat.
We’re just beginning to understand how food and gut microbiota interact to produce metabolites that contribute to the development of liver disease. However, the specific bacteria and metabolites, as well as the underlying mechanisms were not well understood until now. This research is unlocking the how and why.”
Guangfu Li, PhD, DVM, co-principal investigator, associate professor in the department of surgery and Department of Molecular Microbiology and Immunology
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Compilation of the top interviews, articles, and news in the last year.
The gut and liver have a close anatomical and functional connection via the portal vein. Unhealthy diets change the gut microbiota, resulting in the production of pathogenic factors that impact the liver. By feeding mice foods high in fat and sugar, the research team discovered that the mice developed a gut bacteria called Blautia producta and a lipid that caused liver inflammation and fibrosis. That, in turn, caused the mice to develop non-alcoholic steatohepatitis or fatty liver disease, with similar features to the human disease.
“Fatty liver disease is a global health epidemic,” said Kevin Staveley-O’Carroll, MD, PhD, professor in the department of surgery, one of the lead researchers. “Not only is it becoming the leading cause of liver cancer and cirrhosis, but many patients I see with other cancers have fatty liver disease and don’t even know it. Often, this makes it impossible for them to undergo potentially curative surgery for their other cancers.”
As part of this study, the researchers tested treating the mice with an antibiotic cocktail administered via drinking water. They found that the antibiotic treatment reduced liver inflammation and lipid accumulation, resulting in a reduction in fatty liver disease. These results suggest that antibiotic-induced changes in the gut microbiota can suppress inflammatory responses and liver fibrosis.
Li, Staveley-O’Carroll and fellow co-principal investigator R. Scott Rector, PhD, Director of NextGen Precision Health Building and Interim Senior Associate Dean for Research -; are part of NextGen Precision Health, an initiative to expand collaboration in personalized health care and the translation of interdisciplinary research for the benefit of society. The team recently received a $1.2 million grant from the National Institutes of Health to fund this ongoing research into the link between gut bacteria and liver disease.
Yang, M., et al. (2023). Western diet contributes to the pathogenesis of non-alcoholic steatohepatitis in male mice via remodeling gut microbiota and increasing production of 2-oleoylglycerol. Nature Communications. doi.org/10.1038/s41467-023-35861-1.
Thought LeadersDr. Javier Yugueros-MarcosHead of Department World Organisation for Animal Health (WOAH)
In this interview, News-Medical talks to Dr Javier Yugueros-Marcos, Head of the Antimicrobial Resistance and Veterinary Products Department at the World Organisation for Animal Health, about how the world can work together to promote the sustainable and responsible use of antimicrobials.
Please could you introduce yourself and tell us about your role within the World Organisation for Animal Health (WOAH)?
My name is Javier Yugueros-Marcos, and I joined the World Organisation for Animal Health (WOAH, founded as OIE) one year ago in November 2021. I am leading the department in charge of the quality of veterinary products, which encompasses diagnostics, vaccines and therapeutics, including antimicrobials. Because of the importance of antimicrobials and antimicrobial resistance, about 80% of our activity revolves around them.
We monitor antimicrobial use all over the world, develop standards on the responsible and prudent use of antimicrobials, and assess the quality of actions in the field so that we can increase capacity-building and change practices.
WOAH’s mission is to help create a future in which humans and animals benefit and support each other for a healthier, more sustainable world. Why is this mission so important given the current state of global health, and how is the health of humans and animals interlinked?
Our work began in 1924 after an animal disease had a big impact on food security: Rinderpest. Since then, we have been working on improving animal health worldwide, bringing about transparency in terms of the status of animal health, and ensuring safe international trade of animals and animal products. All of this leads to better health for humans.
Today, the situation is not much different because animal diseases still exist, and we still care about transparency and reporting animal disease outbreaks for safe international trade. However, human and animal health are interlinked in terms of more than just international trade. Let me give you two examples.
One is zoonoses. It is estimated that 60% of infectious diseases in humans originate from animals. This percentage is increasing to three out of four, when talking about emerging pathogens. Notable examples include Ebola virus, Middle East respiratory syndrome-related coronavirus (MERS-CoV) and the first generation of severe acute respiratory syndrome coronavirus (SARS-CoV). We suspect the same for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus behind COVID-19, although we have not identified the intermediate species yet, if ever.
It is not only food-producing animals that humans risk contracting disease from, but also wildlife. And vice versa, as diseases can also be transmitted from humans to animals. Human population expansion is displacing animals from their environment, and the new contact that humans have with these displaced wild animals increases the risk of zoonotic disease occurrence and transmission.
The second example is antimicrobial resistance (AMR), which is the main topic of this interview. Pathogens have no borders, and the overuse and misuse of antimicrobials in any sector will immediately impact the others. When tackling this problem, it does not make sense to monitor the responsible use of antimicrobials in humans if we do not collect the same information in animals, and vice versa. Everything is connected. As long as we do not work together in this interconnected world, we will not be able to solve its problems. It took us a while, but I think that many stakeholders are finally acknowledging that.
World Organisation for Animal Health (WOAH, founded as OIE) – It’s Everyone’s Health.
Improving global health and well-being can only be achieved by also considering animals and the environment. How will the improvement of animal health consequently improve the health of humans and the environment?
Consider the examples I have just given of infectious human diseases coming from animals. Improving animal health will prevent many of these events from happening and will eventually ensure that we have a healthier human sector. This includes not only food-producing animals and wildlife but also companion animals which are increasingly present in our lives.
The other aspect of all this is to consider how dependent we are on animals for our livelihoods. Today, one out of five people depend on production animals for their income and livelihoods. This is not so evident in high-income countries, but it is highly present in low and middle-income countries which represent a huge proportion of the global population.
Whenever we talk about animals, we tend to think about terrestrial animals, but we also have to think about aquatic animals. Over 20 million people depend on the aquaculture sector. This is the fastest growing sector of those supplying protein for the world.
Every year you and your partners at the WHO, the FAO and UNEP celebrate World Antimicrobial Awareness Week. The theme for 2022 is “Preventing Antimicrobial Resistance Together”. What does this theme mean to you?
There is no more effective way to avoid antimicrobial misuse than employing them only when other approaches do not work, only when they are necessary. Prevention is the first thing that we have to bear in mind. We have to maximise the technologies existing today to improve biosecurity and ensure best-in-class animal husbandry practices. One way this is well underway is through the use of vaccination across the sectors.
Before this, I was working in the human health sector, so I am accustomedto promoting the term ‘hygiene’. Hygiene is the best way to prevent infection. And we have seen this with the recent COVID-19 pandemic, where we employed social distancing, hand sanitizer use, and other measures. Thus, hygiene was enhanced. The same applies for animals. And it is not only our hands that pose a risk – for example, farm workers need to think about changing their boots when they go into the farm, and checking visitors when they come onto the property.
All these factors, as well as how animals are raised and live, affect their capacity to fight infections. Maximising their immunity prevents them from getting sick, preventing all of us from using more antimicrobials.
This is something that has been somehow forgotten, and we would like to emphasise this message. Simple and easy measures can save a lot of trouble down the road.
Image Credit: World Health Organization
With antimicrobial resistance being described by WHO as one of the top 10 threats to global health, what impact is it actually having on animals worldwide?
We would like to be as advanced as our colleagues from the human health sector in this regard. Unfortunately, there is currently no data available on the burden of antimicrobial resistance in animals at global level, but we are working on it.
There are several regional initiatives (i.e. Europe, Asia, Americas…) collecting data on the prevalence of antimicrobial resistance in the animal health sector. But as I said, we do not have any comprehensive global data yet. Our colleagues from FAO are working on this. This year they have started a pilot to collect data on antimicrobial resistance in animals. They are beginning in Asia, and their goal is to collect data globally by the end of next year.
The other initiative that I wanted to mention is one that we are leading in collaboration with the University of Liverpool, which is called the Global Burden of Animal Diseases (or GBADs). It follows the same methodology as something that was done for humans a few years ago. We have recently developed a component on the economic impact of AMR in animals, particularly the socioeconomic impact on livelihoods where antimicrobial resistance is present.
One key objective of World Antimicrobial Awareness Week is improving awareness of AMR. Despite continued awareness, many people still do not fully understand the wider implications it has not only for human health, but for animal health and environmental health. What more can people and policymakers do to continue educating about this global health threat?
There are a couple of basic things that we must keep doing. One is repeating. Education is the simple exercise of repeating things. Something that we are starting to work on is making the messages evolve and targeting populations where the message can trigger actions.
We were discussing this with our Quadripartite colleagues (the Quadripartite alliance for One Health: FAO, UNEP, WHO and WOAH) a few weeks ago. One of the populations that were identified as powerful drivers of communication is the youth and children in particular. They learn everything; they listen to everything; they repeat everything that we can teach them. They represent the future. If we succeed in educating them and making them understand that antimicrobials do not have to be overused or misused, then we will be achieving a level of understanding that has not been gained until now.
In this regard, we have already engaged with young people and students. For example, we will participate in the upcoming Global AMR Youth Summit, organised by the World Health Students Alliance and taking place during the World Antimicrobial Awareness Week.
In terms of targeting populations and adapting the messages, we are currently working on renewing our web content and making it more understandable for non-technical populations, for example, concerned citizens.
In terms of the policymakers, the two actions needed are 1) bringing them the data to showcase that there is a problem, and 2) providing alternatives. It is then our responsibility as an organisation to set standards on how antimicrobials can be used responsibly and prudently. These recommendations are then used to guide the development of national regulations or legislation.
We are working on expanding the breadth of actions from food-producing animals to all animals, companion animals and wildlife included. We are making the role and the responsibilities of every actor within the chain much clearer, from the veterinary authorities to the farmer and pet owners. We are providing these overarching principles that in the end can be translated into legislation or regulation, and therefore have an action in the field. It is also within our responsibility to highlight the priority research areas for research agencies and countries to fund so that in the end we can provide alternatives to antimicrobials.
It has been described that to work collaboratively between sectors to tackle AMR, we need to use a One Health approach. What is meant by the term One Health and what are its advantages for global health?
One Health, in very simple words, is about working together. We are all interconnected. What is happening in the animal health sector is eventually going to impact the human sector. And the behaviour of humans has an impact on the animal health sector, as well as in food systems and ecosystems.
Translated into the world of governments, One Health is not much more than making all the sectors work together. We are trying to promote dialogue across sectors. At global level, the Quadripartite organisations have learned to dialogue, work together, and undertake actions in collaboration.
How will this level of international collaboration, especially between animal and human health professionals, help to tackle other problems such as rabies?
AMR is a health challenge and it can be taken as a model on how collaboration could improve our response. The same model can be applied to zoonotic diseases, those that may transmit from animals to humans, or humans to animals. When working on a human disease, if there is an animal component, we need to pick up the phone, write emails, and work with the department in charge of animal health.
The Quadripartite organisations have been working together on AMR since 2014/15. Today, AMR is one action track of the One Health joint action plan, which has been recently launched to advance One Health at global, regional and national levels. Our experience can be an asset to other people working in similar areas. AMR is a model, and then the model can be applied to other shared health challenges.
Alongside your current work surrounding antimicrobial resistance, what are some other priorities you are currently addressing within WOAH?
Our AMR strategy has four pillars: awareness, surveillance and research, capacity-building, and standards implementation.
In terms of awareness, this conversation is a good example. The World Antimicrobial Awareness Week, a global campaign to raise awareness and understanding of AMR and promote best practices among One Health stakeholders.
In terms of surveillance, we have a number of fascinating things ongoing. One is our database of worldwide antimicrobial use in animals, launched in 2015. For seven years, we have been using paper-based and Excel forms to collect the information from countries. This year marks a turning point, as last September we launched a totally digitalised system to allow countries to report and use their data for their own actions. The platform will become accessible for the public in the upcoming year.
At the same time, we are initiating a similar system for the detection of falsified and sub-standard products. The keys to antimicrobial stewardship are having the right antimicrobial for the right individual, at the right time, with the right dose, and for the right period. But it is also important to have the right product, because if products are falsified or sub-standard, inoculations are not going to have any efficacy, leading eventually to resistance. We are starting a pilot experience for a global system for alerting sub-standard and falsified products.
The other initiative that we have is the estimation of the economic burden of AMR. In terms of research, we are working with our Quadripartite partners, developing a One Health research priority agenda in collaboration with many different stakeholders. The goal is to provide a roadmap of priorities that should be tackled in terms of research from the One Health perspective.
Then, in terms of capacity-building, we support the Multi-Partner Trust Fund initiative in collaboration with our Quadripartite partners and the donors, which is today funding 10 low- and middle-income countries to implement their national action plans on AMR using a One Health approach. We have learned to talk to each other at global level, and we are scaling up these efforts at local level so that the Minister of Agriculture, the Minister of Health, the Minister of Environment, and the Minister of Aquaculture in a given country can do the same to successfully implement national action plans on AMR across the sectors. Kenya, Zimbabwe, Tajikistan and Morocco are examples of countries supported through this fund.
Last but not least, a strong legal framework is necessary if countries are to take effective action in the face of health threats such as AMR In addition to providing Standards on the responsible use of antimicrobials, we also have a programme on Veterinary Legislation Support (VLSP) that helps Members recognise and address their needs for clear, comprehensive veterinary legislation.
Image Credit: Pressmaster/Shutterstock.com
Are you hopeful that with this continued awareness, education and funding surrounding AMR, we will one day see a world without AMR?
I wish I could imagine such a world, but all organisms on Earth share the same planet and we are all connected. We all adapt to our environment. Antimicrobial resistance is a natural phenomenon that microorganisms implement to evolve in a hostile, toxic environment. As soon as they see an antimicrobial agent preventing them from thriving, they are going to develop resistance. Alexander Fleming warned us all when he received his Nobel prize. With every new antimicrobial that we have developed, sooner rather than later, resistance has appeared.
A world without antimicrobial resistance is difficult to imagine. However, we can learn how to live in a world where we can use antimicrobials sustainably and reduce the burden of human, animal and plant diseases. This is what we are working on. We are working on making every actor in the animal health sector aware that we must use antimicrobials responsibly to ensure they remain available for future generations.
Sustainability can be achieved by developing new antimicrobials, but also, more importantly, by using the ones that we have today responsibly.
This is where action for prevention is really important. If we encourage hygiene, improve security at farms, and keep animals in good conditions so that they have a strong immune system, then we can fight this battle and maintain low levels of antimicrobial resistance. Antimicrobials must be used responsibly and sustainably.
With the COVID-19 pandemic reminding us that all sectors must work together to achieve scientific progress, we have seen significant advancements in recent years, especially within disease diagnostics. Are there any particular fields within animal health that you are excited to watch evolve over the coming years?
I think COVID-19 has also taught us about the power of vaccination. I hope that after the pandemic everyone will understand its importance in terms of prevention. Hopefully, it will help encourage trust and confidence in this practice.
Regarding diagnostics, I am a little biased, because I worked for 18 years in the field of diagnostics, and, as a former colleague used to say, “without diagnosis, medicine is blind”. This is true for the human health sector, but even more so for the animal health sector, which is severely impacted by the lack of diagnostic tools, particularly innovative ones. I hope that this area will be reinforced, thanks to development in human health being imparted into the animal health sector.
What is next for you and your work at WOAH? Are you involved in any exciting upcoming projects?
I have mentioned several already, but I will pick the three most exciting ones.
First, the launch of the global database on antimicrobial use in animals, called ANIMUSE.
The global burden of animal diseases is also an exciting project because it will give us an idea of the socioeconomic impact of animal diseases. I think it will help mobilise resources and ratify the importance of AMR in the animal health sector.
Finally, the revision of standards we are undertaking. We are expanding the content to other animals, not only food-producing animals, and clarifying the responsibilities of every actor to use antimicrobials responsibly. I am very confident that this will help in the field if people know who does what and how to do it properly.
About Javier Y. Marcos
Javier Y. Marcos has a solid history of working in antimicrobial resistance (AMR), with eighteen years of experience in the development and commercialisation of diagnostics tests for infectious diseases, both for human and animal health. Having graduated as a Doctor in Veterinary Medicine in 1997, he also holds a PhD in Microbiology & Molecular Biology from the Leon University, Spain.
At the end of 2021, he was appointed as Head of the AMR & Veterinary Products Department at the World Organisation for Animal Health (WOAH, founded as OIE), being accountable for the enhanced quality of veterinary medicinal products, and the coordination of actions supporting a responsible and prudent use of antimicrobials in animal health worldwide.
Gut bacteria have been linked to an ever-increasing number of diseases. Research is now going beyond establishing a link between a disorder and the community of gut microbes, and has begun to identify specific organisms that are responsible for certain conditions. Scientists have now shown that a strain of bacteria in the Subdoligranulum genus can lead to the production of autoantibodies, which appears to cause the development of rheumatoid arthritis. The findings have been reported in Science Translational Medicine.
Rheumatoid arthritis is an autoimmune disease in which the joints are erroneously attacked by the immune system, and the inflammation and damage that occurs in affected joints causes pain, the loss of mobility, and other serious problems. Disruption of mucosal immunity, in the gut, has been proposed to be one cause of rheumatoid arthritis.
In this work, the researchers obtained blood samples from people who are at risk of developing RA, and the autoantibodies were isolated from those samples.
The scientists found that the autoantibodies were causing a response in certain bacteria in the Lachnospiraceae/Ruminococcaceae families. Further work revealed that bacteria of the genus Subdoligranulum, a member of those families that was isolated from the feces of people ate risk for RA, could bind to the autoantibodies and cause the activation of CD4+ T cells. This was occurring in individuals with RA, but not in healthy people.
The Subdoligranulum bacteria was put in an animal model, and the animals began to develop the same RA risk markers found in the blood of people who are at risk for RA. Some of the animals also developed RA.
“Through studies in humans and animal models, we were able to identify these bacteria as being associated with the risk for developing RA. They trigger an RA-like disease in the animal models, and in humans, we can show that this bacterium seems to be triggering immune responses specific to RA,” said study leader Kristine Kuhn, MD, Ph.D., an associate professor at CU School of Medicine.
This microbe could be a good therapeutic target for RA treatment, noted Kuhn. Now, the scientists want to assess large populations of people who are at risk for RA to see if the Subdoligranulum microbes are also linked to other factors like genetics, mucosal immunity, and environmental conditions that can lead to RA. It may help scientists find prevention strategies or other ways to stop the microbes from causing disease, added Kuhn.
Sepsis accounts for 20% of all fatalities worldwide and 20% to 50% of hospital deaths in the United States. For timely and effective antibiotic therapy crucial for sepsis survival, initial detection and identification of microbial infections are required. However, no etiologic pathogens are identified in more than 30% of cases. Distinguishing sepsis from non-infectious systemic disorders is essential since they frequently appear clinically similar during hospitalization.
About the study
In the present study, researchers created a sepsis diagnostic tool that combined host transcriptional profiling along with broad-range pathogen identification.
At two tertiary care hospitals, the team conducted a prospective observational examination of critically ill adult patients admitted to the intensive care unit (ICU) from the emergency department (ED). Patients were divided into five subgroups based on the presence or absence of sepsis. These patients included those who had: (1) clinically adjudicated sepsis as well as confirmed bacterial bloodstream infection (SepsisBSI); (2) clinically adjudicated sepsis as well as a confirmed non-bloodstream infection (Sepsisnon-BSI); (3) suspected sepsis characterized with negative clinical microbiological testing (Sepsissuspected); (4) patients having no evidence of sepsis and an explanation for their critical disease (No-sepsis); or (5) patients with an indeterminate status (Indeterm).
By conducting ribonucleic acid (RNA) sequencing on whole blood samples, the team first examined transcriptional variations between patients having clinically and microbiologically proven sepsis and those without symptoms of infection. A technique called gene set enrichment analysis (GSEA) detects clusters of genes within a dataset with related biological functions.
A differential gene expression (DE) study across the SepsisBSI and Sepsisnon-BSI groups was conducted to identify further variations between sepsis patients with infections in the bloodstream versus peripheral sites. The team developed a universal sepsis diagnostic classifier based on whole-blood gene expression patterns in response to the practical requirement to diagnose sepsis in SepsisBSI as well as Sepsisnon-BSI patients. The team utilized a bagged support vector machine (bSVM) learning strategy to choose the genes that most successfully differentiated patients with sepsis (SepsisBSI and Sepsisnon-BSI) and those without sepsis (No-sepsis).
A median of 2.3 × 107 reads was acquired after sequencing the RNA from obtained patients whose plasma specimens were available. Furthermore, DE analysis was performed to determine if a biologically plausible signal could be used to differentiate patients who did and did not have sepsis.
Results
Heart failure exacerbation, overdose/poisoning, cardiac arrest, and pulmonary embolism were the most frequently diagnosed conditions in the No-sepsis group. Irrespective of the subgroup, most patients required vasopressor support and mechanical ventilation. Patients in the SepsisBSI and Sepsisnon-BSI who had proven sepsis did not show any difference from No-sepsis patients with respect to age, sex, race, ethnicity, APACHE III score, immunocompromise, intubation status, maximal white blood cell count, or 28-day mortality. In the group of patients without sepsis, all but one patient demonstrated two or more systemic inflammatory response syndrome (SIRS) criteria.
The study also revealed the downregulation of pathways linked to ribosomal RNA processing and translation along with the upregulation of genes involved in innate immune signaling and neutrophil degranulation in sepsis patients. Using DE analysis, the team found 5,227 genes. The Sepsisnon-BSI cohort displayed enrichment in genes associated with defensins, antimicrobial peptides, and G alpha signaling as well as other pathways. On the other hand, the SepsisBSI cohort showed enrichment in genes associated with immunoregulatory interactions between non-lymphoid and lymphoid cells and CD28 signaling, among other functions.
The bSVM model displayed a mean cross-validation area under the receiver operating characteristic (ROC) curve (AUC) of 0.81. Samples with transcript counts lower than the quality control (QC) threshold had a lower mean input mass than samples with sufficient counts.
Interestingly, a number of differentially expressed genes have been identified as sepsis biomarkers, including increased CD177, repressed human leukocyte antigen – DR isotype (HLA-DRA), indicating a biologically significant transcriptome signature from plasma RNA. In the Sepsisnon-BSI group, plasma deoxyribonucleic acid (DNA) metagenomic next-generation sequencing (mNGS) revealed three out of eight bacterial urinary tract infection (UTI) pathogens and two out of 25 bacterial lower respiratory tract infection (LRTI) pathogens. None of the three patients with severe colitis caused by C. difficile had this pathogen. In eight out of 73 patients with proven sepsis, additional potential bacterial pathogens not identified by culture were found.
Conclusion
Overall, the study findings showed that reliable sepsis diagnosis is facilitated by the combination of host gene expression profiling with metagenomic pathogen identification from plasma nucleic acid. Future research is required to verify and gauge the therapeutic utility of this culture-independent diagnostic strategy.
Journal reference:
Kalantar, K., Neyton, L., Abdelghany, M., Mick, E., Jauregui, A., & Caldera, S. et al. (2022). Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults. Nature Microbiology. doi: 10.1038/s41564-022-01237-2https://www.nature.com/articles/s41564-022-01237-2
Microbiome: From Research and Innovation to Market
