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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

Inhibition of cell wall formation arrests staphylococcal cell division

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Reviewed by Emily Henderson, B.Sc.Mar 23 2023

We still do not understand exactly how antibiotics kill bacteria. However, this understanding is necessary if we want to develop new antibiotics. And that is precisely what is urgently needed, because bacteria are currently showing more and more resistance to existing antibiotics. Therefore, researchers from the University Hospital Bonn (UKB) and the University of Bonn used high-performance microscopes to observe the effect of different antibiotics on the cell division of Staphylococcus aureus. They found that the biosynthesis of peptidoglycan, core component of the bacterial cell wall, is the driving force during the entire process of cell division. In addition, they clarified how exactly different antibiotics block cell division within a few minutes. The results have now been published in the journal Science Advances.

The bacterial cell wall maintains the shape and integrity of unicellular organisms. Cell wall synthesis plays a key role in bacterial growth: the cell division protein FtsZ forms the so-called Z-ring in the center of the cell, thus initiating the division process. A new cell wall is formed there, for which peptidoglycan is produced as the core component. This constriction thus gives rise to two identical daughter cells.

Fluorescent proteins in Staphylococcus aureus under the microscope

The UKB research team led by Fabian Grein and Tanja Schneider, together with the team led by Ulrich Kubitscheck, Professor of Biophysical Chemistry at the University of Bonn, selected the bacterium Staphylococcus aureus, one of the most dangerous human pathogenic bacteria, as the model organism for their study. The focus was on the influence of antibiotics that inhibit peptidoglycan synthesis on cell division.

We found a rapid and strong effect of oxacillin and the glycopeptide antibiotics vancomycin and telavacin on cell division. The cell division protein FtsZ served as a marker here and we monitored it.”

Jan-Samuel Puls, a PhD student at the Institute of Pharmaceutical Microbiology at UKB

For this purpose, FtsZ was fluorescently labeled alongside other proteins. Then the researchers analyzed the effects on individual living bacterial cells over time and also used super-resolution microscopy. They established an automated image analysis for microscopy images that allowed them to quickly analyze all cells in the sample under study. “Staphylococcus aureus is only about one micrometer, which is one-thousandth of a millimeter. This makes microscopy particularly challenging,” says Dr. Fabian Grein, junior research group leader at the UKB’s Institute of Pharmaceutical Microbiology and a scientist at the German Center for Infection Research (DZIF).

Antibiotic effect on cell wall biosynthesis machinery inhibits cell division immediately

The Bonn research team found that the formation of peptidoglycan is the driving force during the entire process of cell division. Previously, peptidoglycan synthesis was thought to be essential only during a specific part of this process. The team showed that inhibition of cell wall assembly by glycopeptide antibiotics in Staphylococcus aureus occurs rapidly and with a dramatic effect on cell division. In addition, they clarified in detail the specific role of essential penicillin-binding protein 2 (PBP2), which links cell wall components, in cell division. The β-lactam antibiotic oxacillin prevents the proper localization of this protein. “This means that PBP2 does not get to the place where it is needed. As a result, the cell can’t divide,” Grein says. “Importantly, this all happens immediately after the antibiotics are added. So the first cellular effects, which have not been studied very intensively so far, are crucial.” Therefore, in view of the alarming increase in antibiotic resistance worldwide, he hopes the study results will provide a better understanding of how exactly these agents work at the cellular level, and thus a key to the development of new antibiotics. Understanding cellular mechanisms of antibiotic action and production is the goal of the DFG Collaborative Research Center TRR 261 “Antibiotic CellMAP”, which conducted these studies.

Source:

University of Bonn

Journal reference:

Puls, J.-S., et al. (2023). Inhibition of peptidoglycan synthesis is sufficient for total arrest of staphylococcal cell division. Science Advances. doi.org/10.1126/sciadv.ade9023

Microbiology

High-resolution mass spectrometric rapid identification of Candida auris

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Dr. Priyom Bose, Ph.D.By Dr. Priyom Bose, Ph.D.Mar 23 2023Reviewed by Danielle Ellis, B.Sc.

A recent study published in the Journal of Fungi used a novel OrbitrapTM high-resolution mass spectrometric technology coupled with liquid chromatography to identify geographically different clades of Candida auris (C. auris) isolates. This proof-of-concept methodology could accurately detect C. auris in the microbiology laboratory.

Study: Fast and Accurate Identification of Candida auris by High Resolution Mass Spectrometry. Image Credit: Jens Goepfert / ShutterstockStudy: Fast and Accurate Identification of Candida auris by High Resolution Mass Spectrometry. Image Credit: Jens Goepfert / Shutterstock

Background

Over a decade ago, C. auris was first found in East Asia, causing bloodstream infections. Although this fungal infection was initially found in India, South America, South Africa, and the Middle East, it soon prevailed globally. 

C. auris soon became a common nosocomial fungal pathogen, particularly among intensive care unit (ICU) patients. As a result, the Centers for Disease Control and Prevention (CDC) has classified C. auris as an urgent threat pathogen.

An important factor that allows C. auris outbreaks worldwide is the improper identification of yeast pathogens in hospital laboratories. Hence, there is an urgent need for accurate and rapid identification of C. auris in hospital laboratories, which can reduce their transmission in healthcare facilities.

Genomic analysis of worldwide C. auris isolates has indicated that around five clades have emerged in the last 20 years, independently and simultaneously. These five distinct geographically restricted clades are clade I: South Asia, clade II: East Asia, clade III: Africa, clade IV: South America, and clade V: Iran. Each clade differs from the other by around ten thousand single-nucleotide polymorphisms. 

Each clade has differential resistance to antifungal agents; for example, clade I is more resistant to fluconazole, while clade II exhibits susceptibility. Currently, C. auris isolates belonging to these clades have been introduced to many countries worldwide. Scientists have highlighted the importance of quickly identifying and monitoring these clades to restrict further spread. 

C. auris possesses several structurally unique sphingolipids and mannoproteins, enabling it to adhere to medical devices and hospital environments persistently. These proteins also aid in biofilm formation and prevent elimination by common disinfectants.

Several studies have indicated that molecular techniques fail to identify C. auris, whereas matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) technology can accurately identify this fungus at the species level.

The Study and its Findings

102 clinical C. auris strains were selected, representing all five clades. These clades were determined based on a short tandem repeat (STR) typing assay, which was subsequently compared to whole-genome sequencing results.

The current study applied OrbitrapTM high-resolution mass spectrometric technology to identify C. auris based on protein analysis methods. This technique was combined with liquid chromatography (LC) for initial separation. In this method, electrospray ionization (ESI) transfers proteins into the gas phase for ionization and is subsequently introduced to the mass spectrometer (LC-MS).

Mass analysis is conducted by either fragment ions or intact mass (MS) through tandem mass spectrometry (MS/MS). Some of the key features of the OrbitrapTM mass analyzer are a high resolution of up to 200,000, a high mass-to-charge ratio of 6,000, high mass accuracy between 2 and 5 ppm, and a dynamic range greater than 104.

C. auris clade differentiation using monoisotopic mass measurements depicted as heat map. Color scale ranges from blue (max signal) to dark red (no signal), representing abundance of measured monoisotopic masses in each strain. Clade specific differential protein masses are visible from the rectangular vertical boxes indicating the geographic affiliation and clade assignment and its vertically associated dendrogram indicating observed protein masses (columns vs. rows). X-axis indicating clade assignment and y-axis indicating observed MS1 protein masses.

In addition, this method is highly sensitive and can measure the exact mass of a compound. It can also identify minor structural changes due to a translated single nucleotide polymorphism into an amino acid change.

Importantly, this newly developed technology could identify all C. auris isolates with high confidence. Furthermore, it could differentiate C. auris across clades. Even though a limited number of isolates were present from each clade, this spectrometric technology identified C. auris clades with 99.6% identification accuracy.

Based on a principal component analysis (PCA) and a subsequent affinity clustering study, the South Asian, East Asian, and Iranian C. auris clades were more proteomically closely related. Long branches in the affinity clustering analysis suggested that the C. auris strains were present as outliers that required more attention, regardless of the detection technique.

Proteomic typing results indicated the capacity to track strains of the same origin isolated from diverse geographical locations. In the future, more precise matching and alignment of typing schemes (based on next-generation sequencing) is required to build on these results. This would significantly reduce false identifications and classifications of unknown strains associated with new clades or lineage.

Conclusions

Although the workflow linked to mass spectrometry and next-generation sequencing are not directly comparable, their results are similar, i.e., identifying unknown clinical microbes. The standard next-generation sequencing method is a highly time-consuming process that requires many delicate time-intensive quality-control steps, particularly during multiplexed sample runs.

In contrast, the newly developed methodology can provide results within 60 minutes. Therefore, applying the high-resolution OrbitrapTM mass spectrometer to accurately and rapidly identify C. auris clades is an attractive alternative to conventional platforms.

Journal reference:
  • Jamalian, A. et al. (2023) “Fast and Accurate Identification of Candida auris by High Resolution Mass Spectrometry”, Journal of Fungi, 9(2), p. 267. doi: 10.3390/jof9020267, https://www.mdpi.com/2309-608X/9/2/267
Microbiology

Candida auris infection without epidemiologic links to a prior outbreak

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Dr. Priyom Bose, Ph.D.By Dr. Priyom Bose, Ph.D.Mar 23 2023Reviewed by Danielle Ellis, B.Sc.

The Centers for Disease Control and Prevention (CDC) has classified Candida auris (C. auris) as an urgent public threat due to its role in elevating mortality, its ability to persist in hospital environments, and the high possibility of developing pan-drug resistance.

Notably, a recent study published in the journal Open Forum Infectious Diseases has pointed out that surfaces near patients with C. auris quickly become re-contaminated after cleaning.

Existing research has not adequately elucidated the environmental reservoirs of C. auris. Further, few studies have reported epidemiologic links associated with C. auris infection. 

Study: The Emergence and Persistence of Candida auris in Western New York with no Epidemiologic Links: A Failure of Stewardship?. Image Credit: Kateryna Kon / ShutterstockStudy: The Emergence and Persistence of Candida auris in Western New York with no Epidemiologic Links: A Failure of Stewardship? Image Credit: Kateryna Kon / Shutterstock

Background

C. auris is a species of fungus that grows as yeast. It is one of the few species of the genus Candida which cause candidiasis in humans. In the past, C. auris infection was primarily found in cancer patients or those subjected to feeding tubes.

In the United States (US), the emergence of C. auris was traced to New York, and surveillance for this fungal infection was focused mainly on New York City to detect outbreaks. Recently, scientists investigated the association between genomic epidemiology and C. auris infection in Western New York.

A Case Study

The study describes the emergence of C. auris in a patient hospitalized at a small community hospital in Genesee County, New York (NY). In January 2022, C. auris was isolated from the urine culture of a 68-year-old male on the 51st day of hospitalization.

This patient had no known epidemiological connections outside his immediate community. Before his hospitalization, he was not exposed to other patients or family members associated with C. auris infection.

This patient had no history of organ transplantation, decubitus ulcers, hemodialysis, feeding tubes, or nursing home stays. He had an active lifestyle with a history of mild vascular dementia. He was hospitalized due to pneumonia and was prescribed azithromycin treatment.

Post hospitalization, he tested positive for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and was treated with dexamethasone (6 mg) daily for 10 days and remdesivir (200 mg) once, followed by 100 mg daily for five days.

Since the patient’s chest radiograph showed left lobar consolidation, he was further treated with empiric ceftriaxone and azithromycin. As the respiratory symptoms deteriorated, he received non-invasive positive pressure ventilation, with subsequent endotracheal intubation for eight days. He was successfully extubated. He developed a fever and received antimicrobial therapy for 73 days. The patient had a urinary catheter and a peripherally inserted central line in his arm for 35 days. 

Microbiology culture test and serum procalcitonin levels remained negative and within normal levels. On the 22nd day of hospitalization, Candida albicans were isolated from respiratory samples. On the 51st day, the urine culture revealed the presence of azole-resistant C. auris.

The isolated C. auris (MRSN101498) was forwarded to the Multidrug-resistant organism Repository and Surveillance Network (MRSN), where genomic sequencing was performed. After the patient was discharged, the hospital room was cleaned using hydrogen peroxide and peracetic acid, followed by ultraviolet-C light. Other patients who shared rooms with the patient with C. auris were tested for infection.

Study Outcomes

C. auris was not detected in the Western NY community hospital in the past year. Physicians stated that the patient received excessive antibiotic treatment for a prolonged period. Genomic studies revealed that the MRSN101498 genome sequence was closely related to the 2013 Indian strain with minor genomic differences. Interestingly, the K143R mutation in ERG11 was found in MRSN101498, which is associated with triazole resistance in Candida albicans.

Whole genome single nucleotide polymorphism (SNP) analysis also highlighted that MRSN101498 was strongly genetically related to four other isolates, with marginal differences.

These isolates were linked to an outbreak in March 2017 in a hospital 47 miles northeast of Rochester, NY. Based on the current findings, it is highly likely that isolates from Western NY share a recent common ancestor.

Study Importance

This case study is important for several reasons, including the absence of epidemiologic links to C.auris infection. Since reports from rural sectors are rare, this study addresses a vital surveillance ‘blind spot.’ 

However, the current study failed to identify the potential reservoirs of MRSN101498 in Western NY. Sporicidal disinfectants were inefficient for both Clostridioides difficile and C. auris. However, terminal cleaning protocols that included UV irradiation and sporicidal cleaning agents were able to eradicate C. auris effectively.

The current study highlights the role of excessive antibiotic exposure in the emergence of C. auris. It also indicates the challenges in eliminating fungi from hospital settings. The authors recommend proper antibiotic treatment and cleaning procedures for drug-resistant pathogens.

Journal reference:
Microbiology

Memory B cell marker predicts long-lived antibody response to flu vaccine

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Memory B cells play a critical role to provide long-term immunity after a vaccination or infection. In a study published in the journal Immunity, researchers describe a distinct and novel subset of memory B cells that predict long-lived antibody responses to influenza vaccination in humans.

These effector memory B cells appear to be poised for a rapid serum antibody response upon secondary challenge one year later, Anoma Nellore, M.D., Fran Lund, Ph.D., and colleagues at the University of Alabama at Birmingham and Emory University report. Evidence from transcriptional and epigenetic profiling shows that the cells in this subset differ from all previously described memory B cell subsets.

The UAB researchers identified the novel subset by the presence of FcRL5 receptor protein on the cell surface. In immunology, a profusion of different cell-surface markers is used to identify and separate immune-cell types. In the novel memory B cell subset, FcRL5 acts as a surrogate marker for positive expression of the T-bet transcription factor inside the cells. Various transcription factors act as master regulators to orchestrate the expression of many different gene sets as various cell types grow and differentiate.

Nellore, Lund and colleagues found that the FcRL5+ T-bet+ memory B cells can be detected seven days after immunization, and the presence of these cells correlates with vaccine antibody responses months later. Thus, these cells may represent an early, easily monitored cellular compartment that can predict the development of a long-lived antibody response to vaccines.

This could be a boon to the development of a more effective yearly influenza vaccine. “New annual influenza vaccines must be tested, and then manufactured, months in advance of the winter flu season,” Lund said. “This means we must make an educated guess as to which flu strain will be circulating the next winter.”

Why are vaccine candidates made so far in advance? Pharmaceutical companies, Lund says, need to wait many weeks after vaccinating volunteers to learn whether the new vaccine elicits a durable immune response that will last for months. “One potential outcome of the current study is we may have identified a new way to predict influenza vaccine durability that would give us an answer in days, rather than weeks or months,” Lund said. “If so, this type of early ‘biomarker’ could be used to test flu vaccines closer to flu season — and moving that timeline might give us a better shot at predicting the right flu strain for the new annual vaccine.”

Seasonal flu kills 290,000 to 650,000 people each year, according to World Health Organization estimates. The global flu vaccine market was more than $5 billion in 2020.

To understand the Immunity study, it is useful to remember what happens when a vaccinated person subsequently encounters a flu virus.

Following exposure to previously encountered antigens, such as the hemagglutinin on inactivated influenza in flu vaccines, the immune system launches a recall response dominated by pre-existing memory B cells that can either produce new daughter cells or cells that can rapidly proliferate and differentiate into short-lived plasmablasts that produce antibodies to decrease morbidity and mortality. These latter B cells are called “effector” memory B cells.

“The best vaccines induce the formation of long-lived plasma cells and memory B cells,” said Lund, the Charles H. McCauley Professor in the UAB Department of Microbiology and director of the Immunology Institute. “Plasma cells live in your bone marrow and make protective antibodies that can be found in your blood, while memory B cells live for many years in your lymph nodes and in tissues like your lungs.

“Although plasma cells can survive for decades after vaccines like the measles vaccine, other plasma cells wane much more quickly after vaccination, as is seen with COVID-19,” Lund said. “If that happens, memory B cells become very important because these long-lived cells can rapidly respond to infection and can quickly begin making antibody.”

In the study, the UAB researchers looked at B cells isolated from blood of human volunteers who received flu vaccines over a span of three years, as well as B cells from tonsil tissue obtained after tonsillectomies.

They compared naïve B cells, FcRL5+ T-bet+ hemagglutinin-specific memory B cells, FcRL5neg T-betneg hemagglutinin-specific memory B cells and antibody secreting B cells, using standard phenotype profiling and single-cell RNA sequencing. They found that the FcRL5+ T-bet+ hemagglutinin-specific memory B cells were transcriptionally similar to effector-like memory cells, while the FcRL5neg T-betneg hemagglutinin-specific memory B cells exhibited stem-like central memory properties.

Antibody-secreting B cells need to produce a lot of energy to churn out antibody production, and they also must turn on processes that protect the cells from some of the detrimental side effects of that intense metabolism, including controlling the dangerous reactive oxygen species and boosting the unfolded protein response.

The FcRL5+ T-bet+ hemagglutinin-specific memory B cells did not express the plasma cell commitment factor, but did express transcriptional, epigenetic and metabolic functional programs that poised these cells for antibody production. These included upregulated genes for energy-intensive metabolic processes and cellular stress responses.

Accordingly, FcRL5+ T-bet+ hemagglutinin-specific memory B cells at Day 7 post-vaccination expressed intracellular immunoglobulin, a sign of early transition to antibody-secreting cells. Furthermore, human tonsil-derived FcRL5+ T-bet+ memory B differentiated more rapidly into antibody-secreting cells in vitro than did FcRL5neg T-betneg hemagglutinin-specific memory B cells.

Lund and Nellore, an associate professor in the UAB Department of Medicine Division of Infectious Diseases, are co-corresponding authors of the study, “A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans.”

Co-authors with Lund and Nellore are Esther Zumaquero, R. Glenn King, Betty Mousseau, Fen Zhou and Alexander F. Rosenberg, UAB Department of Microbiology; Christopher D. Scharer, Tian Mi, Jeremy M. Boss, Christopher M. Tipton and Ignacio Sanz, Emory University School of Medicine, Atlanta, Georgia; Christopher F. Fucile, UAB Informatics Institute; John E. Bradley and Troy D. Randall, UAB Department of Medicine, Division of Clinical Immunology and Rheumatology; and Stuti Mutneja and Paul A. Goepfert, UAB Department of Medicine Division of Infectious Diseases.

Funding for the work came from National Institutes of Health grants AI125180, AI109962 and AI142737 and from the UAB Center for Clinical and Translational Science.

  • Anoma Nellore, Esther Zumaquero, Christopher D. Scharer, Christopher F. Fucile, Christopher M. Tipton, R. Glenn King, Tian Mi, Betty Mousseau, John E. Bradley, Fen Zhou, Stuti Mutneja, Paul A. Goepfert, Jeremy M. Boss, Troy D. Randall, Ignacio Sanz, Alexander F. Rosenberg, Frances E. Lund. A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans. Immunity, 2023; DOI: 10.1016/j.immuni.2023.03.001

    • University of Alabama at Birmingham
    Microbiology

    Novel subset of memory B cells predicts long-lived antibody responses to influenza vaccination

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    Reviewed by Emily Henderson, B.Sc.Mar 22 2023

    Memory B cells play a critical role to provide long-term immunity after a vaccination or infection. In a study published in the journal Immunity, researchers describe a distinct and novel subset of memory B cells that predict long-lived antibody responses to influenza vaccination in humans.

    These effector memory B cells appear to be poised for a rapid serum antibody response upon secondary challenge one year later, Anoma Nellore, M.D., Fran Lund, Ph.D., and colleagues at the University of Alabama at Birmingham and Emory University report. Evidence from transcriptional and epigenetic profiling shows that the cells in this subset differ from all previously described memory B cell subsets.

    The UAB researchers identified the novel subset by the presence of FcRL5 receptor protein on the cell surface. In immunology, a profusion of different cell-surface markers is used to identify and separate immune-cell types. In the novel memory B cell subset, FcRL5 acts as a surrogate marker for positive expression of the T-bet transcription factor inside the cells. Various transcription factors act as master regulators to orchestrate the expression of many different gene sets as various cell types grow and differentiate.

    Nellore, Lund and colleagues found that the FcRL5+ T-bet+ memory B cells can be detected seven days after immunization, and the presence of these cells correlates with vaccine antibody responses months later. Thus, these cells may represent an early, easily monitored cellular compartment that can predict the development of a long-lived antibody response to vaccines.

    This could be a boon to the development of a more effective yearly influenza vaccine. “New annual influenza vaccines must be tested, and then manufactured, months in advance of the winter flu season,” Lund said. “This means we must make an educated guess as to which flu strain will be circulating the next winter.”

    Why are vaccine candidates made so far in advance? Pharmaceutical companies, Lund says, need to wait many weeks after vaccinating volunteers to learn whether the new vaccine elicits a durable immune response that will last for months. “One potential outcome of the current study is we may have identified a new way to predict influenza vaccine durability that would give us an answer in days, rather than weeks or months,” Lund said. “If so, this type of early ‘biomarker’ could be used to test flu vaccines closer to flu season -; and moving that timeline might give us a better shot at predicting the right flu strain for the new annual vaccine.”

    Seasonal flu kills 290,000 to 650,000 people each year, according to World Health Organization estimates. The global flu vaccine market was more than $5 billion in 2020.

    To understand the Immunity study, it is useful to remember what happens when a vaccinated person subsequently encounters a flu virus.

    Following exposure to previously encountered antigens, such as the hemagglutinin on inactivated influenza in flu vaccines, the immune system launches a recall response dominated by pre-existing memory B cells that can either produce new daughter cells or cells that can rapidly proliferate and differentiate into short-lived plasmablasts that produce antibodies to decrease morbidity and mortality. These latter B cells are called “effector” memory B cells.

    “The best vaccines induce the formation of long-lived plasma cells and memory B cells,” said Lund, the Charles H. McCauley Professor in the UAB Department of Microbiology and director of the Immunology Institute. “Plasma cells live in your bone marrow and make protective antibodies that can be found in your blood, while memory B cells live for many years in your lymph nodes and in tissues like your lungs.

    “Although plasma cells can survive for decades after vaccines like the measles vaccine, other plasma cells wane much more quickly after vaccination, as is seen with COVID-19,” Lund said. “If that happens, memory B cells become very important because these long-lived cells can rapidly respond to infection and can quickly begin making antibody.”

    In the study, the UAB researchers looked at B cells isolated from blood of human volunteers who received flu vaccines over a span of three years, as well as B cells from tonsil tissue obtained after tonsillectomies.

    They compared naïve B cells, FcRL5+ T-bet+ hemagglutinin-specific memory B cells, FcRL5neg T-betneg hemagglutinin-specific memory B cells and antibody secreting B cells, using standard phenotype profiling and single-cell RNA sequencing. They found that the FcRL5+ T-bet+ hemagglutinin-specific memory B cells were transcriptionally similar to effector-like memory cells, while the FcRL5neg T-betneg hemagglutinin-specific memory B cells exhibited stem-like central memory properties.

    Antibody-secreting B cells need to produce a lot of energy to churn out antibody production, and they also must turn on processes that protect the cells from some of the detrimental side effects of that intense metabolism, including controlling the dangerous reactive oxygen species and boosting the unfolded protein response.

    The FcRL5+ T-bet+ hemagglutinin-specific memory B cells did not express the plasma cell commitment factor, but did express transcriptional, epigenetic and metabolic functional programs that poised these cells for antibody production. These included upregulated genes for energy-intensive metabolic processes and cellular stress responses.

    Accordingly, FcRL5+ T-bet+ hemagglutinin-specific memory B cells at Day 7 post-vaccination expressed intracellular immunoglobulin, a sign of early transition to antibody-secreting cells. Furthermore, human tonsil-derived FcRL5+ T-bet+ memory B differentiated more rapidly into antibody-secreting cells in vitro than did FcRL5neg T-betneg hemagglutinin-specific memory B cells.

    Lund and Nellore, an associate professor in the UAB Department of Medicine Division of Infectious Diseases, are co-corresponding authors of the study, “A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans.”

    Co-authors with Lund and Nellore are Esther Zumaquero, R. Glenn King, Betty Mousseau, Fen Zhou and Alexander F. Rosenberg, UAB Department of Microbiology; Christopher D. Scharer, Tian Mi, Jeremy M. Boss, Christopher M. Tipton and Ignacio Sanz, Emory University School of Medicine, Atlanta, Georgia; Christopher F. Fucile, UAB Informatics Institute; John E. Bradley and Troy D. Randall, UAB Department of Medicine, Division of Clinical Immunology and Rheumatology; and Stuti Mutneja and Paul A. Goepfert, UAB Department of Medicine Division of Infectious Diseases.

    Funding for the work came from National Institutes of Health grants AI125180, AI109962 and AI142737 and from the UAB Center for Clinical and Translational Science.

    Source:

    University of Alabama at Birmingham

    Journal reference:

    Nellore, A., et al. (2023). A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans. Immunity. doi.org/10.1016/j.immuni.2023.03.001.

    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, News

    ‘Diversity in Microbiology’ collection is open for submissions

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    ‘Diversity in Microbiology’ collection is open for submissions

    23 March 2023

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    The Microbiology Society is pleased to open the call for submissions to its new collection, ‘Diversity in Microbiology’.

    The Society President, Professor Gurdyal Besra, has commissioned a number of articles from under-represented groups, highlighting the talent we have within our Society, and where our members are producing cutting-edge research within microbiology. This collection is open for submissions across our journals portfolio from members of underrepresented ethnic and racial groups, people who are disabled, and of other marginalised backgrounds.

    Authors wishing to submit to the collection should do so via the online submission system and note in the cover letter that their submission is intended for the ‘Diversity in Microbiology’ collection. If you have any questions, please contact [email protected]. 

    Greater diversity within all that we do will widen the talent pool available for the field of microbiology and create networks of ideas and collaborations, potentially leading to greater development and innovation. Working to be inclusive helps us ensure we have a thriving community, which in turn will pave the way for us to support microbiology into the future.  

    The Microbiology Society is a not-for-profit publisher and supports and invests in the microbiology community. All surplus income is invested back into the Society, be it through providing grants, facilitating policy activities, conferences and other activities. All members receive a 30% discount on Open Access (OA) charges and all corresponding authors at Publish and Read institutions are entitled to fee-free Open Access. The Society also has an inclusive OA policy and any corresponding author from a country in Group A or B of the HINARI programme is automatically entitled to a 100% discount on OA charges. 

    Image: iStock/Angelina Bambina.

    Microbiology, News

    Neurodiversity Celebration Week: Darya Chernikhova

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    Neurodiversity Celebration Week: Darya Chernikhova

    Posted on March 23, 2023   by Microbiology Society


    Neurodiversity Celebration Week takes place 13–19 March 2023; it aims to transform how neurodivergent individuals are perceived and supported by organisations, while creating a more inclusive and equitable culture.

    We spoke with Society Champion, Darya Chernikhova, about their experiences of working in microbiology as a neurodivergent person.

    “You will contribute to the world. It might take longer, or it might not, but it’ll be awesome.”  Darya Chernikhova

    Darya Chernikhova
    © Darya Chernikhova

    Could you tell us about yourself?

    I’m a masters student and I am working towards cryopreserving biodiversity-related microbiomes. Just like humans have gut microbiomes, everything from wild animals to butterflies to plants and soils has microbiomes. Each microbial situation can have tens of thousands of individual species of bacteria, archaea, viruses, fungi, etc. We can’t protect or restore biodiversity without paying attention to the microbiomes that go with it. Right now, most microbiome work is limited to sequencing or to isolating select bacterial species.

    I’d like to create frozen living archives of whole microbiome samples. Currently, I’m on an internship in Hawaii, learning cryopreservation techniques.

     

     

    It’s Neurodiversity Celebration Week 13–19 March 2023; will you be doing anything to raise awareness?

    I feel like my very person creates awareness the moment I walk into a room!

    I’m an oddball and an acquired taste. I’ve started telling people I’m neurodivergent as early as reasonably possible in a professional relationship. It doesn’t help me succeed, but it does help me feel better about the process, and I do feel that announcing myself helps to normalise difference and makes the world a better place. I tend not to do special things for specific occasions, but I do appreciate those occasions refreshing awareness and strength in my person. 

    As a neurodivergent person studying science, are there any challenges you have faced?

    I was an undergraduate in the 1990s. Back then, you had to choose a path and walk it.  Maybe you became a cancer researcher, or maybe a field biologist, and you needed mentors to get you started. People grew and switched jobs, but it was difficult and not celebrated in society. I couldn’t find a mentor or a path. So I became a software developer, and now I’ve gone back to school.

    In some ways it’s easier. Career changes are normalised and, after two decades of trying, I finally got the right diagnosis and medication. In other ways it’s still hard and sometimes harder. How do you ask for mentorship, when people don’t see you as a mentee? You’ve spent a lifetime studying people and relationships, and having diverse hobbies and interests so you know how to help the people around you and how to contribute to multiple projects. However, you’re still prone to burnout, and your colleagues aren’t always excited about you trying to do too much. 

    There are pressures to ‘get it done’ within a shortened career span, whatever you decide ‘it’ is. You have the life experience to know where the right balances are and that helps, but you’re still human enough to not be able to reach them.   

    There are also special challenges: I can be on time and I can work in the morning, but it takes a toll. Over the long term, going against natural circadian rhythms has been shown to carry health and longevity consequences. I have good days when I’m a productivity superhero and bad days when executive dysfunction reigns. I’m very sensitive to others’ feelings, but I can’t always react appropriately in real-time, and I definitely can’t represent myself in ways that generally get people accepted and promoted. Every professional field has its own social relationships and politics and I don’t fit. You kind of just have to be strong and find your personal path, even when you know you’re not likely to hit expected milestones.

    The hardest part is knowing when to quit. I’ve internalised that walking away is shameful. However, when you clutch at something, giving it your all, you’re wasting your potential. Don’t be exhausted and dejected, life’s short, and you are enough. Find a place that makes you 5% happier and the next, and the next. You will contribute to the world. It might take longer, or it might not, but it’ll be awesome. 

    Do you think more needs to be done to support neurodivergent people working in (or hoping to work in) science?

    Gosh yes! There is so much intersectionality too; I try to build up understanding that accommodations aren’t handouts to ‘special’ people. Rather, they are things that you can do to make your own environment function better.

    Take the example of ageism: neurodivergent people; women; people of colour and those from working class backgrounds are all groups more likely to enter academia later in life. Many grants  and scholarships for early career microbiologists carry a maximum age requirement. Trust me, I’m just as broke and enthusiastic. When your group/department/university/company sees an announcement of funding that carries an age limit, please respond back to the granter and gently and kindly let them know that you understand they’re a programme manager and don’t set the rules, but could they pass it up the chain to eliminate age requirements. There are groups that define early career as ‘X number of years of work in this field or after graduation, excluding the years taken off for family or personal obligations’.  With enough supporting voices, things will change.

    Let’s talk advice. Try not to give unsolicited common sense advice. We’ve tried it. But it’s wonderful to offer mentorship. Give all accommodation requests that you’re able to give, and don’t compare individuals’ accommodations or disabilities. Ask community-run support groups for advice. They have the context to suggest productive solutions. Implement diversity consultants’ suggestions. When you step back and reassess how a person might work better in your environment, what you’re actually doing is figuring out how your environment could work better. Be flexible and innovative, and you’ll be getting the best from all of your colleagues.

    Communication: in a homogenous culture, people sometimes struggle to communicate with ‘outsiders’. This can lead to neurodivergent people, or those from other cultures or classes, being pushed away and the creation of ‘in’ groups. Neurodivergent people are used to code-switching; we adapt and translate. Trust us to show you how to share.

    Be uncomfortable. Every day. Get a calendar and put checkmarks on the days when you’ve made yourself uncomfortable on behalf of a minority. Don’t wait until you’re secure enough in your position to really make a difference, you’ll never get there. By the time you get to Principal Investigator level, you’ll have leapfrogged all of the people you didn’t speak up for. We don’t have that choice of distancing, or stopping to rest, available to us. We are fighting hard for our place in the world every single day. To be an ally, be active in deed, as well as words.

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    © Darya Chernikhova

    Do you have any role models, if so, who?

    I don’t have heroes, but I do admire aspects of certain people. If I see someone being inventive or kind, I’ll want to be like them in that regard. I met Glenn Seaborg once (a physicist who discovered many new elements and isotopes, and has element 106 named after him). He gave a talk to our student group, and he was so kind. It postponed my undergraduate burnout by a year. I also met Eartha Kitt after a concert (a brilliant performer and US Civil Rights activist). She was powerful and magnetic. Dr David Vaughan got me into corals and is a force of nature and can-do action. My friend Carrie Hawks makes animated short films that talk so well about difficult topics. My friend Sky develops software for good causes. People in citizen science; people who do wonderful things without institutional support – I’d like to be like them.

     

    Could you tell us why you decided to join the Society and become a Champion?

    I was looking for mentors, and I wanted to contribute to diversity initiatives. The Society accepts people from all over the world, and everyone is so kind in emails and chat; I’ve been made to feel welcome. I’m glad it exists, and I’m glad to be hanging out with the Champions.

    If you would like to get involved with Society activities, or become a Champion, you can find out more via our Get Involved webpage.

     

     

     

     

     

    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

    Microbiome: From Research and Innovation to Market