Tag Archives: Pathogen

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

Multiplex PCR panels associated with reduced administration of antibiotics to hospitalized GI patients

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Reviewed by Emily Henderson, B.Sc.Mar 16 2023

Acute gastroenteritis afflicts adults of all ages, causing significant suffering and inflicting significant costs on the American healthcare system. A new study encompassing nearly 40,000 hospital visits from a geographically diverse healthcare database shows that sampling a single stool, using multiple polymerase chain reaction (PCR) panels, can identify more pathogens, notably diarrhea-causing E. coli and enteric viruses, and do so more rapidly than a conventional workup. The research is published in Journal of Clinical Microbiology, a publication of the American Society for Microbiology.

Using multiple PCR panels, “Fewer patients received antibiotics, required additional visits or diagnostic tests, or were hospitalized for gastroenteritis within 30 days [of index visit],” said Rena C. Moon, M.D., M.P.H., Principal Research Scientist, PINC AI Applied Sciences, Charlotte, NC. Additionally, healthcare costs were lower than with a conventional workup. Conventional workups may include testing a stool culture for a single suspect species of pathogen, use of a single pathogen PCR test, or identifying a pathogen using microscopy, immunology or an ova and parasites test.

Earlier studies showed that large multiplex PCR panels improve the speed and accuracy of diagnostic testing in patients with acute gastroenteritis, but their impact on costs and clinical outcomes had been uncertain. Our study shows that the benefits of multiplex panels can be achieved without increasing overall healthcare costs, and also facilitates more appropriate use of antibiotics.”

Ferric C. Fang, M.D., Professor of Laboratory Medicine, Pathology, and Microbiology at the University of Washington School of Medicine, Seattle

“This study illustrates the power of big data to analyze the healthcare impacts of diagnostic testing, and help laboratories select testing approaches that improve meaningful clinical outcomes,” Fang said.

Using multiplex PCR, more patients could be discharged and did not require hospitalization during the following month. That resulted in similar healthcare costs to patients undergoing the traditional stool work-up plus follow-up visits over the following month. Furthermore, multiplex PCR (using 12 or more) panels were associated with reduced administration of antibiotics to hospitalized patients.

The overall result: improved care with lower costs.

Source:

American Society for Microbiology

Microbiology

Host immune system forms small lesions in the intestines in response to bacterial infection

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Reviewed by Emily Henderson, B.Sc.Mar 14 2023

Yersinia bacteria cause a variety of human and animal diseases, the most notorious being the plague, caused by Yersinia pestis. A relative, Yersinia pseudotuberculosis, causes gastrointestinal illness and is less deadly but naturally infects both mice and humans, making it a useful model for studying its interactions with the immune system.

These two pathogens, as well as a third close cousin, Y. enterocolitica, which affects swine and can cause food-borne illness if people consume infected meat, have many traits in common, particularly their knack for interfering with the immune system’s ability to respond to infection.

The plague pathogen is blood-borne and transmitted by infected fleas. Infection with the other two depends on ingestion. Yet the focus of much of the work in the field had been on interactions of Yersinia with lymphoid tissues, rather than the intestine. A new study of Y. pseudotuberculosis led by a team from Penn’s School of Veterinary Medicine and published in Nature Microbiology demonstrates that, in response to infection, the host immune system forms small, walled-off lesions in the intestines called granulomas. It’s the first time these organized collections of immune cells have been found in the intestines in response to Yersinia infections.

The team went on to show that monocytes, a type of immune cell, sustain these granulomas. Without them, the granulomas deteriorated, allowing the mice to be overtaken by Yersinia.

“Our data reveal a previously unappreciated site where Yersinia can colonize and the immune system is engaged,” says Igor Brodsky, senior author on the work and a professor and chair of pathobiology at Penn Vet. “These granulomas form in order to control the bacterial infection in the intestines. And we show that if they don’t form or fail to be maintained, the bacteria are able to overcome the control of the immune system and cause greater systemic infection.”

The findings have implications for developing new therapies that leverage the host immune system, Brodsky says. A drug that harnessed the power of immune cells to not only keep Yersinia in check but to overcome its defenses, they say, could potentially eliminate the pathogen altogether.

A novel battlefield

Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica share a keen ability to evade immune detection.

“In all three Yersinia infections, a hallmark is that they colonize lymphoid tissues and are able to escape immune control and replicate, cause disease, and spread,” Brodsky says.

Earlier studies had shown that Yersinia prompted the formation of granulomas in the lymph nodes and spleen but had never observed them in the intestines until Daniel Sorobetea, a research fellow in Brodsky’s group, took a closer look at the intestines of mice infected with Y. pseudotuberculosis.

“Because it’s an orally acquired pathogen, we were interested in how the bacteria behaved in the intestines,” Brodsky says. “Daniel made this initial observation that, following Yersinia pseudotuberculosis infection, there were macroscopically visible lesions all along the length of the gut that had never been described before.”

The research team, including Sorobetea and later Rina Matsuda, a doctoral student in the lab, saw that these same lesions were present when mice were infected with Y. enterocolitica, forming within five days after an infection.

A biopsy of the intestinal tissues confirmed that the lesions were a type of granuloma, known as a pyogranuloma, composed of a variety of immune cells, including monocytes and neutrophils, another type of white blood cell that is part of the body’s front line in fighting bacteria and viruses.

Granulomas form in other diseases that involve chronic infection, including tuberculosis, for which Y. pseudotuberculosis is named. Somewhat paradoxically, these granulomas-;while key in controlling infection by walling off the infectious agent-;also sustain a population of the pathogen within those walls.

The team wanted to understand how these granulomas were both formed and maintained, working with mice lacking monocytes as well as animals treated with an antibody that depletes monocytes. In the animals lacking monocytes “these granulomas, with their distinct architecture, wouldn’t form,” Brodsky says.

Instead, a more disorganized and necrotic abscess developed, neutrophils failed to be activated, and the mice were less able to control the invading bacteria. These animals experienced higher levels of bacteria in their intestines and succumbed to their infections.

Groundwork for the future

The researchers believe the monocytes are responsible for recruiting neutrophils to the site of infection and thus launching the formation of the granuloma, helping to control the bacteria. This leading role for monocytes may exist beyond the intestines, the researchers believe.

We hypothesize that it’s a general role for the monocytes in other tissues as well.”

Igor Brodsky, senior author

But the discoveries also point to the intestines as a key site of engagement between the immune system and Yersinia.

“Previous to this study we knew of Peyer’s patches to be the primary site where the body interacts with the outside environment through the mucosal tissue of the intestines,” says Brodsky. Peyer’s patches are small areas of lymphoid tissue present in the intestines that serve to regulate the microbiome and fend off infection.

In future work, Brodsky and colleagues hope to continue to piece together the mechanism by which monocytes and neutrophils contain the bacteria, an effort they’re pursing in collaboration with Sunny Shin’s lab in the Perelman School of Medicine’s microbiology department.

A deeper understanding of the molecular pathways that regulate this immune response could one day offer inroads into host-directed immune therapies, by which a drug could tip the scales in favor of the host immune system, unleashing its might to fully eradicate the bacteria rather than simply corralling them in granulomas.

“These therapies have caused an explosion of excitement in the cancer field,” Brodsky says, “the idea of reinvigorating the immune system. Conceptually we can also think about how to coax the immune system to be reinvigorated to attack pathogens in these settings of chronic infection as well.”

Source:

University of Pennsylvania

Journal reference:

Sorobetea, D., et al. (2023). Inflammatory monocytes promote granuloma control of Yersinia infection. Nature Microbiology. doi.org/10.1038/s41564-023-01338-6.

Microbiology

A quick new way to screen virus proteins for antibiotic properties

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As conventional antibiotics continue to lose effectiveness against evolving pathogens, scientists are keen to employ the bacteria-killing techniques perfected by bacteriophages, the viruses that infect bacteria.

One major challenge standing in their way is the difficulty of studying individual bacteriophage (phage) proteins and determining precisely how the virus wields these tools to kill their host bacteria. New research from Lawrence Berkeley National Laboratory (Berkeley Lab) could help speed things along.

“We developed a high-throughput genetic screening approach that can identify the part of the bacterial cell targeted by a potent type of phage weapon called ‘single-gene lysis proteins,'” said Vivek Mutalik, a staff scientist in Berkeley Lab’s Biosciences Area and co-author on a new study describing the work in Nature Chemical Biology. “With rising antibiotic resistance, we urgently need antibiotic alternatives. Some of the smallest phages that we know of code for single-gene lysis proteins (Sgls), also known as ‘protein antibiotics,’ to inhibit key components of bacterial cell wall production that, when disrupted, consistently kill the cell.”

There appears to be at least one type of phage for every known strain of bacteria, and they are thought to be the most abundant biological entities on Earth. In fact, there are an estimated 1031 phage particles on the planet right now, or the equivalent of one trillion phages for every grain of sand. Each of these phages evolve alongside their chosen host strain, allowing them to counter bacterial resistance traits, as they arise, with improved biological weaponry.

This massive abundance, specificity, and efficacy means that there are plenty around to study, and that we should theoretically be able to use phages to control any harmful microbe. Phages are also harmless to non-bacterial cells, another reason they are so appealing as medicines and biocontrol tools.

The problem arises when trying to isolate a single phage from the environment and determine which microbe it targets and how. Scientists are often unable to assess phage-bacteria battles based on genomic sequence alone or study them in action because many bacteria can’t be cultured in a lab — and even if they could, there’s an inherent catch-22 of needing to know ahead of time which bacteria to culture in order to study the phages that infect and kill them.

To sidestep these obstacles and identify the cellular targets of Sgls, Mutalik and his colleagues used a technology the team previously invented called Dual-Barcoded Shotgun Expression Library Sequencing (Dub-seq). Dub-seq allows scientists to employ a coded library of DNA fragments to investigate how unknown genes function, and can be applied to complicated environmental samples that contain the DNA of many organisms — no culturing needed. In this study, the authors used six Sgls from six phages that infect different bacteria and identified the part of the bacterial cell wall or supporting molecules that each Sgl attacks. In collaboration with scientists from Texas A&M University, they conducted a detailed characterization of the function of one Sgl.

This work showed that the Sgl proteins target pathways for cell wall building that arose very early in the evolutionary history of bacteria and are still used by nearly all bacteria (including pathogenic bacteria). Since the Sgl proteins attack such fundamental and ubiquitous targets, they can kill bacteria other than the phage’s target strain — confirming they have great potential as antibiotics.

“Phages are extraordinary innovators when it comes to destroying bacteria. We’re really excited to uncover novel bacterial pathogen-targeting mechanisms that could be leveraged into therapies,” said first author Benjamin Adler, a postdoctoral fellow in Jennifer Doudna’s lab at UC Berkeley.

Now that the team has evaluated the Dub-seq approach for tackling this question, they can apply it to the thousands of single-gene lysis producing phages awaiting characterization in environmental samples that the team has collected from the ocean, soils, and even the human gut. The inspiration for the next breakthrough medicine could be in there, waiting.

  • Benjamin A. Adler, Karthik Chamakura, Heloise Carion, Jonathan Krog, Adam M. Deutschbauer, Ry Young, Vivek K. Mutalik, Adam P. Arkin. Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins. Nature Chemical Biology, 2023; DOI: 10.1038/s41589-023-01269-7

    • DOE/Lawrence Berkeley National Laboratory
    Microbiology

    Pattern recognition system that monitors disease-causing bacteria in C. elegans

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    A study published in Immunity by physician-scientist Read Pukkila-Worley, MD, and MD/PhD students Nicholas D. Peterson and Samantha Y. Tse describes a new manner of detecting microbial infection that intercepts pathogen-derived signals of growth to assess the relative threat of virulent bacteria. A nuclear hormone receptor in the nematode C. elegans senses a toxic metabolite produced by the bacterial pathogen Pseudomonas aeruginosa to activate innate immunity. These data reveal an ancient strategy that informs the origins of pathogen detection and may be among the most primordial forms of immune sensing in animals.

    “Our research adds to our understanding of how hosts differentiate between beneficial and harmful bacteria, which teaches us something important about how our immune systems evolved,” said Dr. Pukkila-Worley, associate professor of medicine.

    Distinguishing potentially harmful pathogens from benign microorganisms is one of the primary functions of the innate immune system in all animals. This is particularly important for nematodes, such as C. elegans — the transparent microscopic worm often used as a model organism to study genetics and gene function — that consume bacteria as their food source.

    Working with Pseudomonas aeruginosa, a bacteria that commonly infects immune-compromised patients in the hospital and is increasingly resistant to standard antibiotic treatments, Pukkila-Worley and colleagues performed a series of genetic screens with mutant bacteria, one-by-one, to see if any impacted the innate immune system response in C. elegans.

    They found that bacteria that cannot produce a specific phenazine metabolite were able to avoid detection by the innate immune system, suggesting that the bacterial phenazine metabolite was sensed to activate innate immunity.

    “This result was intriguing because P. aeruginosa use phenazines for growth and virulence. Thus, the innate immune system can intercept signals produced by bacteria in order to identify bacteria that have grown to dangerous levels and are poised to cause disease,” said Pukkila-Worley.

    Researchers in the Pukkila-Worley lab designed a second experiment to identify the sensor in the host that detects these phenazine metabolites. They discovered that a specialized type of transcription factor, a nuclear hormone receptor, binds the phenazine metabolite and directly activates anti-pathogen defenses.

    “One of the striking things about our results is that C. elegans senses this bacterial metabolite to detect an individual bacterial pathogen in a remarkably specific manner from among its bacterial food,”said Peterson, an MD/PhD student in the Pukkila-Worley lab.

    In humans, pattern-recognition systems in the intestine involving Toll-like receptors scan the physical structure of different bacteria to sense the presence of infectious microorganisms. Nematodes lost pattern-recognition receptors in evolution. Pukkila-Worley and colleagues show that nematodes use nuclear hormone receptors to detect specific pathogen-derived metabolites to activate innate immunity, which represents a new type of pattern-recognition.

    Since C. elegans have 274 nuclear hormone receptors, it’s possible that the nematode genome contains dozens of these metabolite recognition systems. Nuclear hormone receptors are also found in most animals, including humans, suggesting that similar metabolite detection systems might exist in other organisms.

    “It’s remarkable that C. elegans evolved mechanisms to differentiate good and bad bacteria even without canonical receptors for pathogen detection. This further supports the importance of understanding how our immune system evolved over time to deepen our understanding of host-microbiome interactions,” said Tse, an MD/PhD student in the Pukkila-Worley lab.

  • Nicholas D. Peterson, Samantha Y. Tse, Qiuyu Judy Huang, Khursheed A. Wani, Celia A. Schiffer, Read Pukkila-Worley. Non-canonical pattern recognition of a pathogen-derived metabolite by a nuclear hormone receptor identifies virulent bacteria in C. elegans. Immunity, 2023; DOI: 10.1016/j.immuni.2023.01.027

    • UMass Chan Medical School
    Microbiology

    Antibiotics can destroy many types of bacteria, but increasingly, bacterial pathogens are gaining resistance to many commonly used …

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    Antibiotics can destroy many types of bacteria, but increasingly, bacterial pathogens are gaining resistance to many commonly used types. As the threat of antibiotic resistance looms large, researchers have sought to find new antibiotics and other ways to destroy dangerous bacteria. But new antibiotics can be extremely difficult to identify and test. Bacteriophages, which are viruses that only infect bacterial cells, might offer an alternative. Bacteriophages (phages) were studied many years ago, before the development of antibiotic drugs, and they could help us once again.

    Image credit: Pixabay

    If we are going to use bacteriophages in the clinic to treat humans, we should understand how they work, and how bacteria can also become resistant to them. Microbes are in an arms race with each other, so while phages can infect bacteria, some bacterial cells have found ways to thwart the effects of those phages. New research reported in Nature Microbiology has shown that when certain bacteria carry a specific genetic mutation, phages don’t work against them anymore.

    In this study, the researchers used a new technique so they could actually see a phage attacking bacteria. Mycobacteriophages infect Mycobacterial species, including the pathogens Mycobacterium tuberculosis and Mycobacterium abscessus, as well as the harmless Mycobacterium smegmatis, which was used in this research.

    The scientists determined that Mycobacterial gene called lsr2 is essential for many mycobacteriophages to successfully infect Mycobacteria. Mycobacteria that carry a mutation that renders the Lsr2 protein non-functional are resistant to these phages.

    Normally, Lsr2 aids in DNA replication in bacterial cells. Bacteriophages can harness this protein, however, and use it to reproduce the phage’s DNA. Thus, when Lsr2 stops working, the phage cannot replicate and it cannot manipulate bacterial cells.

    In the video above, by first study author Charles Dulberger, a genetically engineered mutant phage infects Mycobacterium smegmatis. First, one phage particle (red dot at 0.42 seconds) binds to a bacterium. The phage DNA (green fluorescence) is injected into the bacterial cell (2-second mark). The bright green dots at the cells’ ends are not relevant. For a few seconds, the DNA forms a zone of phage replication, and fills the cell. Finally, the cell explodes at 6:25 seconds. (About three hours have been compressed to make this video.)

    The approach used in this study can also be used to investigate other links between bacteriophages and the bacteria they infect.

    “This paper focuses on just one bacterial protein,” noted co-corresponding study author Graham Hatfull, a Professor at the University of Pittsburgh. But there are many more opportunities to use this technique. “There are lots of different phages and lots of other proteins.”

    Sources: University of Pittsburgh, Nature Microbiology


    Carmen Leitch

    Microbiology

    Infections with many different types of bacteria including Streptococcus pneumonia, Listeria monocytogens, and Neisseria mengitidis can cause bacterial …

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    Infections with many different types of bacteria including Streptococcus pneumonia, Listeria monocytogens, and Neisseria mengitidis can cause bacterial meningitis. It’s estimated that every year over 1.2 million cases of bacterial meningitis happen around the world, and without treatment, this deadly disease is fatal to seven of ten people who are sickened by it. Even with antibiotic treatments, three of ten patients die. Survivors are left with issues like chronic headaches, seizures, loss of vision or hearing, and other neurological consequences. New research reported in Nature has revealed how bacteria are able to penetrate the meninges that surround and protect the brain to cause bacterial meningitis. The findings have shown that bacteria use neurons to evade immunity and infect the brain, and the work may aid in the creation of new therapeutics.

    A digitally-colorized SEM image depicts of Streptococcus pneumoniae bacteria (lavender), as they were being attacked by a white blood cell (pink). / Credit: CDC/ Dr. Richard Facklam

    Right now, antibiotics can help eliminate the bacterial pathogens that cause this illness. But steroids are also needed to control the dangerous inflammation that can occur along with the infection. However, reducing inflammation also weakens the immune response, making it harder to get rid of the infection.

    In this research, the scientists used Streptococcus pneumoniae and Streptococcus agalactiae bacteria, which can both cause bacterial meningitis in humans. They determined that when these bacteria get to the meninges, they release a toxin, which activates neurons in the meninges that sense pain. This pain neuron activation could explain why bacterial meningitis patients get horrible headaches, noted the researchers.

    The activated pain neurons then release a signaling molecule called CGRP, which binds to a receptor called RAMP1 on the surface of immune cells called macrophages. Once CGRP binds to RAMP1 on macrophages, the immune cells are basically disabled, and they stop responding to bacterial infections like they normally would.

    The link between CGRP and RAMP1 on macrophages also stops them from signaling to other immune cells, which allows the bacterial infection to not only penetrate the meninges but to spread infection.

    This work was confirmed with the use of a mouse model that lacked the pain neurons that are activated by bacteria. Compared to mice with those neurons, the engineered mice had less severe brain infections when they were exposed to bacteria that cause meningitis. There were also lower levels of CGRP in the engineered mice compared to normal mice. The normal mice, however, had higher levels of bacteria in the meninges.

    Additional experiments also showed that when mice were treated with drugs that block RAMP1, the severity of the bacterial infection was reduced. Mice treated with RAMP1 blockers were able to clear their infections faster too.

    It may be possible to help the immune system clear cases of bacterial meningitis with medications that block either CGRP or RAMP1, potentially in conjunction with antibiotics. There are already drugs that can do this, and they are generally used to treat migraine.

    Sources: Harvard Medical School, Nature


    Carmen Leitch

    Microbiology

    The Centers for Disease Control and Prevention (CDC) has issued an alert about a rise in extensively drug-resistant …

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    The Centers for Disease Control and Prevention (CDC) has issued an alert about a rise in extensively drug-resistant (XDR) Shigella infections (shigellosis). There has been a concerning increase in drug resistance among Shigella infections in the United States; they rose from zero in 2015 to 5 percent in 2022. There are few treatment options for these infections, the bacteria are easy to transmit from one person to another, and few microbes need to be transmitted for illness to occur. The microbes generally spread through the fecal-oral route, which means contaminated food and water can also cause the illness. The bacteria are also transmitted during sexual contact. The XDR strains of Shigella can also share those resistance genes with other bacteria. Therefore, the CDC is especially concerned about these infections, and is calling on health professionals to watch for cases of XDR shigellosis.

    A medical illustration of drug-resistant, Shigella sp. bacteria / Credit: CDC/ Antibiotic Resistance Coordination and Strategy Unit / Medical Illustrator: Stephanie Rossow

    Shigella causes abdominal cramping and diarrhea that can be bloody; it may also cause fever or tenesmus, a feeling of flu bowels. Usually, these infections resolve on their own after a few days, and only supportive care, such as hydrating fluids, are needed. Antibiotics can shorten the duration of the illness, reduce the likelihood of transmission to others, and can also prevent complications.

    Strains of XDR Shigella are resistant to many popular antibiotics that are usually used to treat shigellosis, including azithromycin, ciprofloxacin, ceftriaxone, trimethoprim-sulfamethoxazole (TMP-SMX), and ampicillin. Right now, there is no consensus on the best way to eliminate XDR Shigella. Strains of resistant Shigella include Shigella sonnei and Shigella flexneri.

    Shigella infections tend to impact certain populations, including children between the ages of 1 and 4. International travelers, and men who have sex with men are other groups who tend to have higher than usual rates of shigellosis.

    There have been 232 confirmed cases that have occured in recent years that the CDC has information about, and of those cases, 82 percent were men, 13 percent were women and 5 percent were children. While only 41 of these individuals answered questions about sexual activity, 88 percent of them reported male-to-male sexual contact.

    The CDC has noted that clinicians should consider shigellosis when patients, particularly young children, international travelers, or men who have sex with men present with acute diarrhea.

    A diagnosis is usually confirmed with a stool sample, particularly for patients who will receive antibiotics. Tests can also be performed to determined whether Shigella strains are susceptible to antibiotics.

    Source: CDC


    Carmen Leitch

    Microbiology

    Scientists have found that a gene that has been previously identified in many animals and their associated microbes …

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    Scientists have found that a gene that has been previously identified in many animals and their associated microbes can enable resistance to antimicrobial drugs. The resistance gene encodes for an enzyme called EstT, which can deactivate antibiotic drugs known as macrolides. The enzyme can disrupt the chemical ring structure of these antibiotics through hydrolysis. When the ring is broken or opened with water, the antibiotic loses both its active shape, and its target affinity, explained study leader Dr. Tony Ruzzini PhD, an assistant professor at the Western College of Veterinary Medicine (WCVM) of the University of Saskatchewan. The findings have been reported in the Proceedings of the National Academy of Sciences.

    Image credit: Pixabay

    This gene can take macrolide antibiotics out of commission, and illnesses can no longer be treated effectively. Macrolides such as tylosin, tilmicosin and tildipirosin are often used to treat cattle with bovine respiratory disease or liver abscesses, and may also be used to treat other diseases in livestock and companion animals.

    In this study, the researchers analyzed genes that were found within microbes that were living in watering bowls at a beef cattle feedlot in western Canada. The investigators isolated the microbes that were in the water, and compared the genes in the microbes to databases of antimicrobial resistance genes.

    A bacterium called Sphingobacterium faecium WB1 was found to carry the EstT gene, which was contained within a cluster of three antibiotic resistance genes (ARGs). It was also near plasmids and retrotransposons, suggesting it can move easily from one microbe to another. EstT is commonly found in microbes in the human microbiome too.

    “This gene, even though we found it in an environmental organism, it is also present in pathogens that are responsible for causing bovine respiratory disease,” noted Ruzzini.

    “Our finding adds to the considerable database of ARGs, which can be crossmatched to a bacteria’s DNA to determine if the bacterium has the potential to be resistant to a particular antimicrobial,” said first study author Dr. Poonam Dhindwal PhD, a postdoctoral fellow at WCVM.

    The researchers are continuing to study EstT to learn more about how it works.

    “As [antimicrobial resistance] surveillance systems rely more on molecular tools for detection, our knowledge of this specific gene and its integration into those systems will help to better inform antimicrobial use,” said Ruzzini.

    Sources: University of Saskatchewan, Proceedings of the National Academy of Sciences (PNAS)


    Carmen Leitch

    Microbiology

    Fungi that causes pine ghost canker detected in southern California trees

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    Fungal pathogens that cause die-back in grape, avocado, citrus, nut and other crops has found a new host and is infecting conifer trees causing Pine Ghost Canker in urban forest areas of Southern California.

    The canker can be deadly to trees.

    Scientists from University of California, Davis, first spotted evidence that the pathogens had moved to pines during a routine examination of trees in Orange County in 2018. Over four years, they found that more than 30 mature pines had been infected in an area of nearly 100 acres, according to a report in the journal Plant Disease.

    Akif Eskalen, a professor of Cooperative Extension in the Department of Plant Pathology at UC Davis, suspects drought and other stress conditions brought on by climate change weakened the tree species, making it more susceptible to new threats.

    “We have been seeing this on pine trees for the last several years,” he said. “Our common crop pathogens are finding new hosts.”

    Pine Ghost Canker — caused by the fungal pathogens Neofusicoccum mediterraneum and Neofusicoccum parvum — usually infects the lower part of a tree’s canopy, killing branches before moving on to the trunks. This dieback in some cases can be deadly.

    Points of entry

    The pathogens infect a tree by entering through wounds caused by either insects, such as red-haired pine bark beetles, or pruning — meaning trees in managed or landscaped areas could be at risk. Another route is via tiny natural openings known as lenticels that fungi can make their way through, said Marcelo Bustamante, a Ph.D. candidate in Eskalen’s lab who is first author on the paper.

    Spores from the fungi can disperse and the higher the prevalence means an increased chance of transmission. Rain, irrigation water and humidity by fog can trigger the right circumstances for the spores to spread, he said.

    “The detection of these pathogens in urban forests raises concerns of potential spillover events to other forest and agricultural hosts in Southern California,” Bustamante and others wrote in the report.

    Dead branches can indicate a canker. Detecting the fungi is not an emergency but “people should keep an eye on their plants when they see abnormalities,” Eskalen said.

    Cankers are localized areas on stems, branches and tree trunks that are usually dead, discolored and sunken. On bark, the spores can look like strings of discolored dots.

    The lab has posted a brochure about how to best manage wood canker diseases. Tips include:

    Karina Elfar, Molly Arreguin, Carissa Chiang, Samuel Wells and Karen Alarcon from the Department of Plant Pathology contributed to the paper, as did experts from Disneyland Resort Horticulture Department, State University of New York’s College of Environmental Science and Forestry, UC Irvine and UC Los Angeles.

  • Marcelo I. Bustamante, Shannon Colleen Lynch, Karina Elfar, John N. Kabashima, Rhonda Wood, Heather F. Neault, Madeleine B. Rauhe, Jeffrey Crain, Jasmine A. Lopez, Amanda Penicks, Humberto Mojica, Mike D. Atkinson, Christopher Shogren, Molly Arreguin, Carissa Frency Chiang, Samuel I. Wells, Karen S. Alarcon, Akif Eskalen. First Report of Neofusicoccum mediterraneum and Neofusicoccum parvum Causing Pine Ghost Canker on Pinus spp. in Southern California. Plant Disease, 2023; DOI: 10.1094/PDIS-09-22-2076-PDN

    • University of California – Davis