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Microbiology

Urethra of Healthy Men Is Teeming With Microbial Life – Vaginal Sex Results in Distinct Microbiome

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Contrary to common beliefs, your urine is not germ-free. In fact, a new study shows that the urethra of healthy men is teeming with microbial life and that a specific activity—vaginal sex—can shape its composition. The research, published on March 24 in the journal Cell Reports Medicine, provides a healthy baseline for clinicians and scientists to contrast between healthy and diseased states of the urethra, an entrance to the urinary and reproductive systems.

“We know where bugs in the gut come from; they primarily come from our surroundings through fecal-oral transfer,” says co-senior author David Nelson, a microbiologist at Indiana University. “But where does genital microbiology come from?”

To flush out the answer, the team of microbiologists, statisticians, and physicians sequenced the penile urethra swabs of 110 healthy adult men. These participants had no urethral symptoms or sexually transmitted infections (STIs) and no inflammation of the urethra. DNA sequencing results revealed that two types of bacterial communities call the penile urethra home—one native to the organ, the other from a foreign source.

“It is important to set this baseline,” says co-senior author Qunfeng Dong, a bioinformatician at Loyola University Chicago. “Only by understanding what health is can we define what diseases are.”

The researchers found that most of the healthy men had a simple, sparse community of oxygen-loving bacteria in the urethra. In addition, these bacteria probably live close to the urethral opening at the tip of the penis, where there is ample oxygen. The consistent findings of these bacteria suggest that they are the core community that supports penile urethra health.

But some of the men also had a more complex secondary group of bacteria that are often found in the vagina and can disturb the healthy bacterial ecosystem of the vagina. The team speculates that these bacteria reside deeper in the penile urethra because they thrive in oxygen-scarce settings. Only men who reported having vaginal sex carry these bacteria, hinting at the microbes’ origins.

Delving into the participant’s sexual history, the team found a close link between this second bacterial community and vaginal sex but not other sexual behaviors, such as oral sex and anal sex. They also found evidence that vaginal sex has lasting effects. Vagina-associated bacteria remained detectable in the participants for at least two months after vaginal sex, indicating that sexual exposure to the vagina can reshape the male urinary-tract microbiome.

“In our study, one behavior explains 10% of the overall bacterial variation,” says Nelson, when discussing the influence of vaginal sex. “The fact that a specific behavior is such a strong determinant is just profound.”

Although current findings from the study show that vaginal bacteria can spread to the penile urethra, the team’s next plan is to test whether the reverse is true. Using the newly established baseline, the researchers also hope to offer new insights into bacteria’s role in urinary- and reproductive-tract diseases, including unexplained urethral inflammation and STIs.

“STIs really impact people who are socioeconomically disadvantaged; they disproportionately impact women and minorities,” says Nelson. “It’s a part of health care that’s overlooked because of stigma. I think our study has a potential to dramatically change how we handle STI diagnosis and management in a positive way.”

Reference: “Sexual behavior shapes male genitourinary microbiome composition” by Evelyn Toh, Yue Xing, Xiang Gao, Stephen J. Jordan, Teresa A. Batteiger, Byron E. Batteiger, Barbara Van Der Pol, Christina A. Muzny, Netsanet Gebregziabher, James A. Williams, Lora J. Fortenberry, J. Dennis Fortenberry, Qunfeng Dong and David E. Nelson, Cell Reports Medicine.
DOI: 10.1016/j.xcrm.2023.100981

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

Cell Press

Microbiology

Nasal Vaccines: Stopping the COVID-19 Virus Before It Reaches the Lungs

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The Pfizer-BioNTech and Moderna mRNA vaccines have played a large role in preventing deaths and severe infections from COVID-19. But researchers are still in the process of developing alternative approaches to vaccines to improve their effectiveness, including how they’re administered. Immunologist and microbiologist Michael W. Russell of the University at Buffalo explains how nasal vaccines work, and where they are in the development pipeline.

The immune system has two distinct components: mucosal and circulatory.

The mucosal immune system provides protection at the mucosal surfaces of the body. These include the mouth, eyes, middle ear, the mammary and other glands, and the gastrointestinal, respiratory, and urogenital tracts. Antibodies and a variety of other anti-microbial proteins in the sticky secretions that cover these surfaces, as well as immune cells located in the lining of these surfaces, directly attack invading pathogens.

The circulatory part of the immune system generates antibodies and immune cells that are delivered through the bloodstream to the internal tissues and organs. These circulating antibodies do not usually reach the mucosal surfaces in large enough amounts to be effective. Thus mucosal and circulatory compartments of the immune system are largely separate and independent.

The immune components people may be most familiar with are proteins known as antibodies, or immunoglobulins. The immune system generates antibodies in response to invading agents that the body identifies as “non-self,” such as viruses and bacteria.

Antibodies bind to specific antigens: the part or product of a pathogen that induces an immune response. Binding to antigens allows antibodies to either inactivate them, as they do with toxins and viruses, or kill bacteria with the help of additional immune proteins or cells.

The mucosal immune system generates a specialized form of antibody called secretory IgA, or SIgA. Because SIgA is located in mucosal secretions, such as saliva, tears, nasal and intestinal secretions, and breast milk, it is resistant to digestive enzymes that readily destroy other forms of antibodies. It is also superior to most other immunoglobulins at neutralizing viruses and toxins, and at preventing bacteria from attaching to and invading the cells lining the surfaces of organs.

There are also many other key players in the mucosal immune system, including different types of anti-microbial proteins that kill pathogens, as well as immune cells that generate antibody responses.

Mucus is one of the central secretions of the mucosal immune system.

Almost all infectious diseases in people and other animals are acquired through mucosal surfaces, such as by eating or drinking, breathing or sexual contact. Major exceptions include infections from wounds, or pathogens delivered by insect or tick bites.

The virus that causes COVID-19, SARS-CoV-2, enters the body via droplets or aerosols that get into your nose, mouth, or eyes. It can cause severe disease if it descends deep into the lungs and causes an overactive, inflammatory immune response.

This means that the virus’s first contact with the immune system is probably through the surfaces of the nose, mouth, and throat. This is supported by the presence of SIgA antibodies against SARS-CoV-2 in the secretions of infected people, including their saliva, nasal fluid, and tears. These locations, especially the tonsils, have specialized areas that specifically trigger mucosal immune responses.

Some research suggests that if these SIgA antibody responses form as a result of vaccination or prior infection, or occur quickly enough in response to a new infection, they could prevent serious disease by confining the virus to the upper respiratory tract until it is eliminated.

Vaccines can be given through mucosal routes via the mouth or nose. This induces an immune response through areas that stimulate the mucosal immune system, leading mucosal secretions to produce SIgA antibodies.

There are several existing mucosal vaccines, most of them taken by mouth. Currently, only one, the flu vaccine, is delivered nasally.

In the case of nasal vaccines, the viral antigens intended to stimulate the immune system would be taken up by immune cells within the lining of the nose or tonsils. While the exact mechanisms by which nasal vaccines work in people have not been thoroughly studied, researchers believe they work analogously to oral mucosal vaccines. Antigens in the vaccine induce B cells in mucosal sites to mature into plasma cells that secrete a form of IgA. That IgA is then transported into mucosal secretions throughout the body, where it becomes SIgA.

If the SIgA antibodies in the nose, mouth or throat target SARS-CoV-2, they could neutralize the virus before it can drop down into the lungs and establish an infection.

Nasal vaccines could provide a more approachable alternative to injections for patients leery of needles.

I believe that arguably the best way to protect an individual against COVID-19 is to block the virus at its point of entry, or at least to confine it to the upper respiratory tract, where it might inflict relatively little damage.

Breaking chains of viral transmission is crucial to controlling epidemics. Researchers know that COVID-19 spreads during normal breathing and speech, and is exacerbated by sneezing, coughing, shouting, singing and other forms of exertion. Because these emissions mostly originate from saliva and nasal secretions, where the predominant form of antibody present is SIgA, it stands to reason that secretions with a sufficiently high level of SIgA antibodies against the virus could neutralize and thereby diminish its transmissibility.

Existing vaccines, however, do not induce SIgA antibody responses. Injected vaccines primarily induce circulating IgG antibodies, which are effective in preventing serious disease in the lungs. Nasal vaccines specifically induce SIgA antibodies in nasal and salivary secretions, where the virus is initially acquired, and can more effectively prevent transmission.

Nasal vaccines may be a useful supplement to injected vaccines in hot spots of infection. Since they don’t require needles, they might also help overcome vaccine hesitancy due to fear of injections.

There have been over 100 oral or nasal COVID-19 vaccines in development around the world.

Most of these have been or are currently being tested in animal models. Many have reported successfully inducing protective antibodies in the blood and secretions, and have prevented infection in these animals. However, few have been successfully tested in people. Many have been abandoned without fully reporting study details.

According to the World Health Organization, 14 nasal COVID-19 vaccines are in clinical trials as of late 2022. Reports from China and India indicate that nasal or inhaled vaccines have been approved in these countries. But little information is publicly available about the results of the studies supporting approval of these vaccines.

Written by Michael W. Russell, Professor Emeritus of Microbiology and Immunology, University at Buffalo.

This article was first published in The Conversation.The Conversation

Michael W. Russell, University at Buffalo

Microbiology

Scientists Warn of Spike in “Flesh-Eating” Infections in Parts of the U.S. Due to Climate Change

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Continued warming of the climate would see a rise in the number and spread of potentially fatal infections caused by bacteria found along parts of the coast of the United States.

Vibrio vulnificus bacteria grow in warm shallow coastal waters and can infect a cut or insect bite during contact with seawater. A new study led by the UK’s University of East Anglia (UEA) shows that the number of V. vulnificus infections along the East Coast of the US, a global hotspot for such infections, has gone up from 10 to 80 per year over a 30-year period.

In addition, every year cases occur further north. In the late 1980s, cases were found in the Gulf of Mexico and along the southern Atlantic coast but were rare north of Georgia. Today they can be found as far north as Philadelphia.

The researchers predict that by 2041–2060 infections may spread to encompass major population centers around New York. Combined with a growing and increasingly elderly population, who are more susceptible to infection, annual case numbers could double.

By 2081–2100, infections may be present in every Eastern US state under medium-to-high future emissions and warming scenarios.

The findings, published today (March 23, 2023) in the journal Scientific Reports, are important because although the number of cases in the US is not large, someone infected with V. vulnificus has a one-in-five chance of dying. It is also the most expensive marine pathogen in the US to treat.

The illness peaks in the summer and sees the bacteria spread rapidly and severely damage the person’s flesh. As a result, it is commonly called a ‘flesh-eating’ illness and many people who survive have had limbs amputated.

Lead author of the study Elizabeth Archer, a postgraduate researcher in UEA’s School of Environmental Sciences, said: “The projected expansion of infections highlights the need for increased individual and public health awareness in the areas affected. This is crucial as prompt action when symptoms occur is necessary to prevent major health consequences.

“Greenhouse gas emissions from human activity are changing our climate and the impacts may be especially acute on the world’s coastlines, which provide a major boundary between natural ecosystems and human populations and are an important source of human disease.

“We show that by the end of the 21st Century, V. vulnificus infections will extend further northwards but how far North will depend upon the degree of further warming and therefore on our future greenhouse gas emissions.

“If emissions are kept low, then cases may extend northwards only as far as Connecticut. If emissions are high, infections are predicted to occur in every US state on the East Coast. By the end of the 21st Century we predict that around 140-200 V. vulnificus infections may be reported each year.”

The research team suggests that individuals and health authorities could be warned in real time about particularly risky environmental conditions through marine or Vibrio specific early warning systems.

Active control measures could include greater awareness programmes for at risk groups, for example the elderly and individuals with underlying health conditions, and coastal signage during high-risk periods.

Co-author Prof Iain Lake from UEA said: “The observation that cases of V. vulnificus have expanded northwards along the East Coast of the US is an indication of the effect that climate change is already having on human health and the coastline. Knowing where cases are likely to occur in future should help health services plan for the future.”

The study is the first to map how the locations of V. vulnificus cases have changed along the eastern coastline of the US. It also the first to explore how climate change may influence the spread of cases in the future.

Information on where people caught V. vulnificus infection was obtained from the US Centers for Disease Control and Prevention. This allowed the team to map how cases of Vibrio vulnificus have extended northwards over 30 years from 1988-2018.

Temperature information based on observations and computer-based climate models were then used to predict where in the US cases might occur by the end of the 21st Century.

Co-author Prof James Oliver from the University of North Carolina Charlotte, in the US, said: “This is a landmark paper which not only ties global climate change to disease but provides strong evidence for the environmental spread of this extremely deadly bacterial pathogen.”

Reference: “Climate warming and increasing Vibrio vulnificus infections in North America” by Elizabeth Archer et al., 23 March 2023, Scientific Reports.
DOI: 10.1038/s41598-023-28247-2

University of East Anglia

Microbiology

“Glow-in-the-Dark” Proteins: The Future of Viral Disease Detection?

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Although there have been significant advancements in diagnostic tests for viral diseases, many highly sensitive tests still rely on complex sample preparation and result interpretation methods, rendering them unsuitable for point-of-care settings or resource-limited areas. However, researchers have now revealed in ACS Central Science a novel, sensitive technique that can analyze viral nucleic acids in just 20 minutes using a one-step process with “glow-in-the-dark” proteins.

Bioluminescence, the scientific phenomenon behind the firefly’s glow, the anglerfish’s radiant lure, and the ghostly blue of phytoplankton-laden shores, is powered by a chemical reaction involving the luciferase protein. This luminescent protein has been integrated into sensors that emit visible light when detecting their target, making them ideal for straightforward point-of-care testing. However, until now, these sensors have not achieved the exceptional sensitivity necessary for clinical diagnostic tests.

The gene-editing technique known as CRISPR could provide this ability, but it requires many steps and additional specialized equipment to detect what can be a low signal in a complex, noisy sample. So, Maarten Merkx and colleagues wanted to use CRISPR-related proteins, but combine them with a bioluminescence technique whose signal could be detected with just a digital camera.

To make sure there was enough sample RNA or DNA to analyze, the researchers performed recombinase polymerase amplification (RPA), a simple method that works at a constant temperature of about 100 F. With the new technique, called LUNAS (luminescent nucleic acid sensor), two CRISPR/Cas9 proteins specific for different neighboring parts of a viral genome each have a distinct fragment of luciferase attached to them.

If a specific viral genome that the researchers were testing for was present, the two CRISPR/Cas9 proteins would bind to the targeted nucleic acid sequences and come close to each other, allowing the complete luciferase protein to form and shine blue light in the presence of a chemical substrate. To account for this substrate being used up, the researchers used a control reaction that shined green. A tube that changed from green to blue indicated a positive result.

When tested on clinical samples collected from nasal swabs, RPA-LUNAS successfully detected SARS-CoV-2 RNA within 20 minutes, even at concentrations as low as 200 copies per microliter. The researchers say that the LUNAS assay has great potential for detecting many other viruses effectively and easily.

Reference: “Glow-in-the-Dark Infectious Disease Diagnostics Using CRISPR-Cas9-Based Split Luciferase Complementation” by Harmen J. van der Veer, Eva A. van Aalen, Claire M. S. Michielsen, Eva T. L. Hanckmann, Jeroen Deckers, Marcel M. G. J. van Borren, Jacky Flipse, Anne J. M. Loonen, Joost P. H. Schoeber and Maarten Merkx, 15 March 2023, ACS Central Science.
DOI: 10.1021/acscentsci.2c01467

The study was funded by the Dutch Research Council | Nationaal Regieorgaan Praktijkgericht Onderzoek SIA (NRPO-SIA) and the Eindhoven University Fund.

American Chemical Society

Microbiology

New, Better Models Show How Infectious Diseases Like COVID-19 Spread

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The COVID-19 pandemic has emphasized the significance of modeling in comprehending the spread of diseases and in providing crucial insights into disease prevention and control. A new model has utilized COVID-19 data and combined two classic methodologies to enhance predictions about disease spread.

A widely used modeling technique involves dividing the population into compartments, such as susceptible (S), infected (I), and recovered (R), in what is known as the SIR model. This approach models the rates of change that describe the movement of individuals from one compartment to another.

KAUST researchers, led by Paula Moraga, integrated SIR compartment modeling in time and a point process modeling approach in space–time, while also taking into account age-specific contact patterns. To do this, they used a two-step framework that allowed them to model data on infectious locations over time for different age groups.

“The model gives more accurate predictions than previous approaches when making short/mid-range predictions in space and time,” says lead researcher André Amaral.

“It also accounts for different age classes so we can treat these groups separately, resulting in finer control over the number of infectious cases.”

Their approach paid off. In a simulation study to assess the model’s performance, and in a case study of COVID-19 cases in Cali, Colombia, the model performed better when making predictions and provided similar results for past time points, compared with models commonly used in predictive modeling.

“The model’s features can help decision-makers to identify high-risk locations and vulnerable populations to develop better strategies for disease control,” says Amaral.

It also can be used with any infectious disease that fits the compartment model assumptions, such as influenza. Furthermore, the model can account for different age groups and their associated contact patterns, meaning it allows more detailed conclusions about where, when, and to which population group decision-makers should focus their resources if they want to control disease spread.

“In future work, we might extend such an approach and use different temporal models to replace the SIR model. This would allow us to account for different epidemic dynamics and expand the number of scenarios that the model can be used for,” says Amaral.

“Finally, to improve the model’s predictive capabilities, we might work on developing ensemble approaches that combine a number of predictions from a number of different models and also account for potential time delays in collecting data,” he adds.

Moraga says the model’s performance demonstrates the importance of quality and detailed data by location, time, and population group to understand infectious disease dynamics while highlighting the need to strengthen national surveillance systems to improve public health decision-making.

Reference: “Spatio-temporal modeling of infectious diseases by integrating compartment and point process models” by André Victor Ribeiro Amaral, Jonatan A. González and Paula Moraga, 13 December 2022, Stochastic Environmental Research and Risk Assessment.
DOI: 10.1007/s00477-022-02354-4

King Abdullah University of Science & Technology (KAUST)

Microbiology

Unexplained Digestive Problems? Lone Star Tick Bites May Be To Blame

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The American Gastroenterological Association (AGA) has released new clinical guidance to help physicians and patients identify if unexplained digestive symptoms are due to alpha-gal syndrome, a food allergy that is caused by lone star tick bites. The AGA Clinical Practice Update was published today (March 21, 2023) in the medical journal Gastroenterology.

Alpha-gal syndrome is an allergy that causes your body to react to eating meat from mammals and products made from mammals. Symptoms usually start 2-6 hours after eating the mammalian meat or food.

Clinicians should consider alpha-gal syndrome in patients with unexplained gastrointestinal symptoms of abdominal pain, diarrhea, nausea, and vomiting, particularly those who live or have lived in an alpha-gal–prevalent area (this includes the Southeast, mid-Atlantic, Midwest, and East Central U.S. regions). For patients with suspected alpha-gal, there is a blood test that looks for immunoglobulin E antibodies (IgE) to alpha-gal. Patients with these antibodies may have alpha-gal allergy. The main treatment for alpha-gal allergy is to not eat foods that contain alpha-gal. This includes mammalian meat, fat, and products made from them.

About Alpha-gal syndrome

Alpha-gal syndrome is an allergy that causes your body to respond badly to ingesting mammalian products; meat from mammals or products made from mammals such as cheese, butter, milk, cream, gelatin, etc. Mammals are animals that have hair, such as cows, pigs, and deer.  Symptoms usually start 2-6 hours after eating the mammalian meat or food. The alpha-gal allergy can cause symptoms of the gastrointestinal tract (digestive system) like stomach pain, diarrhea (loose stool), nausea or upset belly, and vomiting (throwing up). It can also cause hives (an itchy rash), flushing of the skin, swelling of the face, or fainting.

About lone star ticks

Lone star ticks (Amblyomma americanum) are a species of tick found predominantly in the southeastern and eastern United States. They are named for the distinctive white spot on the back of adult females, which resembles the shape of the state of Texas. Lone star ticks are known for their aggressive behavior, feeding on a variety of hosts, including humans, dogs, and deer. They are also known to carry diseases such as Rocky Mountain spotted fever, tularemia, and alpha-gal syndrome, a food allergy that causes the body to react to mammalian meat.

As the official journal of the AGA Institute, Gastroenterology is the leading publication in the field of gastrointestinal disease. It provides reliable and current coverage of both clinical and basic gastroenterology, with regular contributions from renowned experts and the latest information on disease treatments. Original research is categorized by clinical and basic-translational content, as well as by content related to the alimentary tract, liver, pancreas, and biliary system.

American Gastroenterological Association

Microbiology

CDC Warns of Deadly Fungus Spreading at Alarming Rate in U.S. Healthcare Facilities

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Candida auris (C. auris), an emerging fungus considered an urgent antimicrobial resistance (AR) threat, spread at an alarming rate in U.S. healthcare facilities in 2020-2021, according to data from the Centers for Disease Control and Prevention (CDC) published in the Annals of Internal Medicine. Equally concerning was a tripling in 2021 of the number of cases that were resistant to echinocandins, the antifungal medicine most recommended for treatment of C. auris infections. In general, C. auris is not a threat to healthy people. People who are very sick, have invasive medical devices, or have long or frequent stays in healthcare facilities are at increased risk for acquiring C. auris. CDC has deemed C. auris as an urgent AR threat, because it is often resistant to multiple antifungal drugs, spreads easily in healthcare facilities, and can cause severe infections with high death rates.

“The rapid rise and geographic spread of cases is concerning and emphasizes the need for continued surveillance, expanded lab capacity, quicker diagnostic tests, and adherence to proven infection prevention and control,” said CDC epidemiologist Dr. Meghan Lyman, lead author of the paper.

As further explained in the article, C. auris has spread in the United States since it was first reported in 2016, with a total of 3,270 clinical cases (in which infection is present) and 7,413 screening cases (in which the fungus is detected but not causing infection) reported through December 31, 2021. Clinical cases have increased each year since 2016, with the most rapid rise occurring during 2020-2021. CDC has continued to see an increase in case counts for 2022. During 2019-2021, 17 states identified their first C. auris case ever. Nationwide, clinical cases rose from 476 in 2019 to 1,471 in 2021. Screening cases tripled from 2020 to 2021, for a total of 4,041. Screening is important to prevent spread by identifying patients carrying the fungus so that infection prevention controls can be used.

C. auris case counts have increased for many reasons, including poor general infection prevention and control (IPC) practices in healthcare facilities. Case counts may also have increased because of enhanced efforts to detect cases, including increased colonization screening, a test to see if someone has the fungus somewhere on their body but does not have an infection or symptoms of infection. The timing of this increase and findings from public health investigations suggest C. auris spread may have worsened due to strain on healthcare and public health systems during the COVID-19 pandemic.

The CDC’s Antimicrobial Resistance Laboratory Network, which provides nationwide lab capacity to rapidly detect antimicrobial resistance and inform local responses to prevent spread and protect people, provided some of the data for this report. CDC worked to significantly strengthen laboratory capacity, including in state, territorial, and local health departments, through supplemental funding supported by the American Rescue Plan Act. These efforts include increasing susceptibility testing capacity for C. auris from seven Regional Labs to more than 26 labs nationwide.

CDC continues to work with state, local, and territorial health departments and other partners to address this emerging threat to public health. Review more information on C. auris, the Antimicrobial Resistance Threats Report that identified C. auris as an urgent threat in the United States, or the WHO fungal priority pathogen list that identifies C. auris as a priority globally.

Reference: “Worsening Spread of Candida auris in the United States, 2019 to 2021” by Meghan Lyman, MD, Kaitlin Forsberg, MPH, D. Joseph Sexton, PhD, Nancy A. Chow, PhD, MS, Shawn R. Lockhart, PhD, Brendan R. Jackson, MD, MPH and Tom Chiller, MD, MPHTM, 21 March 2023, Annals of Internal Medicine.
DOI: 10.7326/M22-3469

Centers for Disease Control and Prevention

Microbiology

Surviving the Extreme: Scientists Discover Life in the Smoke of Underwater Volcanoes

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In the depths of the ocean, along tectonic plate boundaries, hydrothermal vents emit hot fluids. These fluids lack oxygen and are rich in metals like iron, manganese, and copper, as well as potentially carrying sulfides, methane, and hydrogen. As the hot water interacts with the cold, oxygen-rich seawater nearby, it forms hydrothermal plumes composed of smoke-like metal sulfide particles.

Rising hundreds of meters from the seafloor and dispersing thousands of kilometers away from their origin, hydrothermal plumes might appear to be inhospitable environments. Yet, a study recently published in Nature Microbiology reveals that specific bacteria manage to thrive in these seemingly precarious locations.

“We took a detailed look at bacteria of the genus Sulfurimonas”, says first author Massimiliano Molari from the Max Planck Institute for Marine Microbiology in Bremen, Germany. These bacteria have so far only known to grow in low-oxygen environments, but gene sequences had occasionally also been detected in hydrothermal plumes. As their name suggests, they are known to use energy from sulfide.

“It was assumed that they were flushed there from seafloor vent-associated environments. But we wondered whether the plumes might actually be a suitable environment for some members of the Sulfurimonas group.”

Together with colleagues from the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research in Bremerhaven (AWI), and the MARUM Center for Marine Environmental Sciences of Bremen University, Molari thus took on a challenging sampling trip to hydrothermal plumes in the Central Arctic and South Atlantic Ocean.

“We sampled plumes in extremely remote areas of ultraslow spreading ridges that were never studied before. Collecting hydrothermal plume samples is very complicated, as they are not easy to locate. Sampling becomes even more difficult when the plume is located at depths of more than 2500 meters and below Arctic sea ice, or within the stormy zones of the Southern Ocean”, explains Antje Boetius, group leader at the Max Planck Institute for Marine Microbiology and director of the AWI, who was the Chief scientist on the Arctic missions.

Onboard of the research vessel Polarstern, the scientists managed to collect samples and within this water studied the composition and metabolism of bacteria.

Molari and his colleagues identified a new Sulfurimonas species called USulfurimonas pluma (the superscript “U” stands for uncultivated) inhabiting the cold, oxygen-saturated hydrothermal plumes. Surprisingly, this microorganism used hydrogen from the plume as an energy source, rather than sulfide. The scientists also investigated the microbes’ genome and found it to be strongly reduced, missing genes typical for their relatives, but being well-equipped with others to allow them to grow in this dynamic environment.

“We think that the hydrothermal plume does not only disperse microorganisms from hydrothermal vents, but it might also ecologically connect the open ocean with seafloor habitats. Our phylogenetic analysis suggests that USulfurimonas pluma could have derived from a hydrothermal vent-associated ancestor, which acquired higher oxygen tolerance and then spread across the oceans. However, that remains to be further investigated”, Molari says.

A look at genome data from other plumes revealed that USulfurimonas pluma grows in these environments all over the world. “Obviously, they have found an ecological niche in cold, oxygen-saturated, and hydrogen-rich hydrothermal plumes”, says Molari. “That means we have to rethink our ideas on the ecological role of Sulfurimonas in the deep ocean – they might be much more important than we previously thought.”

Reference: “A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes” by Massimiliano Molari, Christiane Hassenrueck, Rafael Laso-Pérez, Gunter Wegener, Pierre Offre, Stefano Scilipoti and Antje Boetius, 9 March 2023, Nature Microbiology.
DOI: 10.1038/s41564-023-01342-w

Max Planck Institute for Marine Microbiology

Microbiology

Humans Are Leaving Behind a Frozen Legacy of Microbes on Mount Everest

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Located nearly 5 miles above sea level in the Himalayas, the barren, wind-swept depression between Mount Everest and its neighboring summit, Lhotse, remains devoid of snow. At the South Col, hundreds of thrill-seekers set up their final camp annually, preparing to ascend the world’s highest mountain from the southeast flank.

New research led by the University of Colorado Boulder indicates that these adventurers are inadvertently leaving behind a frozen signature of resilient microbes. These microorganisms can endure extreme conditions at high altitudes and remain dormant in the soil for decades, or potentially even centuries.

The research not only highlights an invisible impact of tourism on the world’s highest mountain, but could also lead to a better understanding of environmental limits to life on Earth, as well as where life may exist on other planets or cold moons. The findings were published last month in Arctic, Antarctic, and Alpine Research, a journal published on behalf of the Institute of Arctic and Alpine Research (INSTAAR) at CU Boulder.

“There is a human signature frozen in the microbiome of Everest, even at that elevation,” said Steve Schmidt, senior author on the paper and professor of ecology and evolutionary biology.

In decades past, scientists have been unable to conclusively identify human-associated microbes in samples collected above 26,000 feet. This study marks the first time that next-generation gene sequencing technology has been used to analyze soil from such a high elevation on Mount Everest, enabling researchers to gain new insight into almost everything and anything that’s in them.

The researchers weren’t surprised to find microorganisms left by humans. Microbes are everywhere, even in the air, and can easily blow around and land some distance away from nearby camps or trails.

“If somebody even blew their nose or coughed, that’s the kind of thing that might show up,” said Schmidt.

What they were impressed by, however, was that certain microbes which have evolved to thrive in warm and wet environments like our noses and mouths were resilient enough to survive in a dormant state in such harsh conditions.

This team of CU Boulder researchers—including Schmidt, lead author Nicholas Dragone and Adam Solon, both graduate students in the Department of Ecology and Evolutionary Biology and the Cooperative Institute for Research in Environmental Science (CIRES)—study the cryobiosphere: Earth’s cold regions and the limits to life in them. They have sampled soils everywhere from Antarctica and the Andes to the Himalayas and the high Arctic. Usually, human-associated microbes don’t show up in these places to the extent they appeared in the recent Everest samples.

Schmidt’s work over the years connected him with researchers who were headed to Everest’s South Col in May of 2019 to set up the planet’s highest weather station, established by the National Geographic and Rolex Perpetual Planet Everest Expedition.

He asked his colleagues: Would you mind collecting some soil samples while you’re already there?

So Baker Perry, co-author, professor of geography at Appalachian State University, and a National Geographic Explorer, hiked as far away from the South Col camp as possible to scoop up some soil samples to send back to Schmidt.

Dragone and Solon then analyzed the soil in several labs at CU Boulder. Using next-generation gene sequencing technology and more traditional culturing techniques, they were able to identify the DNA of almost any living or dead microbes in the soils. They then carried out extensive bioinformatics analyses of the DNA sequences to determine the diversity of organisms, rather than their abundances.

Most of the microbial DNA sequences they found were similar to hardy, or “extremophilic” organisms previously detected in other high-elevation sites in the Andes and Antarctica. The most abundant organism they found using both old and new methods was a fungus in the genus Naganishia that can withstand extreme levels of cold and UV radiation.

But they also found microbial DNA for some organisms heavily associated with humans, including Staphylococcus, one of the most common skin and nose bacteria, and Streptococcus, a dominant genus in the human mouth.

At high elevations, microbes are often killed by ultraviolet light, cold temperatures, and low water availability. Only the hardiest critters survive. Most—like the microbes carried up great heights by humans—go dormant or die, but there is a chance that organisms like Naganishia may grow briefly when water and the perfect ray of sunlight provides enough heat to help them momentarily prosper. But even for the toughest of microbes, Mount Everest is a Hotel California: “You can check out any time you like/ But you can never leave.”

The researchers don’t expect this microscopic impact on Everest to significantly affect the broader environment. But this work does carry implications for the potential for life far beyond Earth, if one day humans step foot on Mars or beyond.

“We might find life on other planets and cold moons,” said Schmidt. “We’ll have to be careful to make sure we’re not contaminating them with our own.”

Reference: “Genetic analysis of the frozen microbiome at 7900 m a.s.l., on the South Col of Sagarmatha (Mount Everest)” by Nicholas B. Dragone, L. Baker Perry, Adam J. Solon, Anton Seimon, Tracie A. Seimon and Steven K. Schmidt, 16 February 2023, Arctic, Antarctic, and Alpine Research.
DOI: 10.1080/15230430.2023.2164999

The study was funded by the National Geographic and Rolex Perpetual Planet Everest Expedition, the Department of Ecology and Evolutionary Biology, and the University of Colorado Boulder Libraries Open Access Fund

University of Colorado at Boulder

Microbiology

Study Shows Healthy Dogs and Cats Can Transmit Dangerous Microbes to Humans – And Vice Versa

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Multi-drug-resistant organisms can be transmitted between healthy dogs and cats and their hospitalized owners.

Fortunately, only a small number of cases were found suggesting pets are not a major source of antibiotic-resistant infections in hospital patients.

Healthy dogs and cats could be passing on multidrug-resistant organisms (MDROs; bacteria that resist treatment with more than one antibiotic) to their hospitalized owners, and likewise, humans could be transmitting these dangerous microbes to their pets, according to new research being presented at this year’s European Congress of Clinical Microbiology & Infectious Diseases (ECCMID) in Copenhagen, Denmark (April 15-18).

The study of over 2,800 hospital patients and their companion animals is by Dr. Carolin Hackmann from Charité University Hospital Berlin, Germany, and colleagues.

“Our findings verify that the sharing of multidrug-resistant organisms between companion animals and their owners is possible,” says Dr. Hackmann. “However, we identified only a handful of cases suggesting that neither cat nor dog ownership is an important risk factor for multidrug-resistant organism colonization in hospital patients.”

The role of pets as potential reservoirs of MDROs is a growing concern worldwide. Antimicrobial resistance happens when infection-causing microbes (such as bacteria, viruses, or fungi) evolve to become resistant to the drug designed to kill them. Estimates suggest that antimicrobial-resistant infections caused almost 1.3 million deaths and were associated with nearly 5 million deaths around the world in 2019.[1]

In this case control study, researchers wanted to find out whether pets (ie, cats and dogs) play a role in the infection of hospital patients with MDROs.

They focused on the most common superbugs in hospital patients—methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), 3rd generation cephalosporin-resistant Enterobacterales (3GCRE) and carbapenem-resistant Enterobacterales (CRE), which are resistant to multiple antibiotics including penicillin and cephalosporins.

Between June 2019 and September 2022, nasal and rectal swabs were collected from 2,891 patients hospitalized in Charité University Hospital Berlin (1,184 patients with previous colonization or colonization on admission and 1,707 newly admitted patients as controls), and from any dogs and cats that lived in their households.

Genetic sequencing was used to identify both the species of bacteria in each sample, and the presence of drug-resistance genes. Whole genome sequencing was used to confirm the possible sharing of resistant bacteria.

Participants were also asked about well-known risk factors for MDROs (e.g., recent MDRO infections or use of antibiotics, recent hospital stays, presence of urinary or central venous catheters), as well as information about the number of pets in the household, the closeness of contact, and pet health.

Overall, 30% (871/2,891) of hospital patients tested positive for MDROs, and 70% (2,020/2,891) tested negative. The rate of dog ownership was 11% (93/871) and cat ownership 9% (80/871) in those who tested MDRO-positive, and 13% (267/2,020 and 253/2,020 respectively) in MDRO-negatives.

All 626 pet owners were asked to send throat and stool swab samples of their pets. Overall, 300 pet owners sent back samples from 400 pets. Of these samples, 15% (30/203) of dogs and 5% (9/197) of cats tested positive for at least one MDRO. In four cases, MDROs were phenotypically matching (MDROs were the same species and showed the same antibiotic resistance) between pets and their owners.

Whole genome sequencing confirmed that only one of the matching pairs was genetically identical in a dog and its owner. The matching pathogen was 3GCR Escherichia coli (common in the intestines of healthy people and animals).

“Although the level of sharing between hospital patients and their pets in our study is very low, carriers can shed bacteria into their environment for months, and they can be a source of infection for other more vulnerable people in the hospital such as those with a weak immune system and the very young or old,” says Dr. Hackmann.

This is an observational study and cannot prove that close contact with pets causes colonization with MDROs, but only suggest the possibility of co-carriage, while the direction of transfer is unclear. The authors point to several limitations, including a possible under-reporting of MDRO colonization in pets due to problems in taking swab samples, which was done by the pet owners themselves. Finally, the study results apply to the setting of hospital patients in an urban area and therefore may not be applicable to the general population or MDRO high-risk groups like livestock farmers.

Reference:

Meeting: European Society of Clinical Microbiology and Infectious Diseases (ECCMID) 2023

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