Category Archives: C. diff. Research & Development

New Study Evaluated Rectal Swabs For Clostridium difficile Testing

Clostridium difficile (C. diff) is among one of the top 18-drug-resistant threats to the United States according to the Centers for Disease Control and Prevention, responsible for around 250,000 infections on an annual basis and 14,000 deaths.

When it comes to diagnosis, microbiological testing of stool samples is often used. However, a new study suggests that for simple PCR-based detection of C. diff, dry rectal swabs were an effective substitute for the use of stool samples.

To read this article in its entirely please click on the following link:

http://www.contagionlive.com/news/dry-rectal-swabs-prove-effective-alternative-to-stool-samples-for-c-diff-diagnosis

“With this study, we proved that rectal swabs for the diagnosis of C. diff infection by PCR can replace the actually used stool samples,” study author Nathalie Jazmati, MD, University Hospital of Cologne, told our sister publication MD Magazine. “That will be more convenient for both patients and health care workers. Nevertheless, this was only a small study and our results have to be confirmed in a bigger clinical trial.”

In an effort to examine methods other than the analysis of stool specimens for C. diff confirmation, a research team from Germany examined the way rectal swabs with liquid transport medium and nylon flocked dry swabs performed for the detection of C. diff; they also evaluated the impact of storage temperature on the swabs.

For their study, the researchers collected 60 clinical stool samples that tested positive for C. diff by PCR and used them to simulate rectal swabs. Then, researchers dipped both wet and dry swabs into the stool and tested by PCR 3 times.

The first test took place immediately after the simulation “swab,” then, after 1 month and 3 months storage at -80°C. When the researchers tested the frozen samples, they first thawed them at room temperature for 15 minutes and the liquid swabs were vortexed for 30 seconds.

Testing all of the dry swabs 100% successfully detected C. diff, an equal rate of the stool sample testing; this proved true for all 3 phases of testing, and the researchers learned that no significant differences were found on the samples after they were frozen and thawed.

The detection rate for the other 30 liquid swabs was lower, at 83.2% accuracy. However, the researchers determined the temperature and the freezing and thawing of these samples did not have any significant impact.

The authors added that their results fall in line with other studies that tested PCR from rectal swabs in the detection of C. diff. The idea of using rectal swabs instead of stool samples isn’t new—it dates back to 1987.

Liquid swabs are currently cleared by the US Food and Drug Administration (FDA) for transport and the culture of gastrointestinal pathogens, the study authors continued, but it is not FDA approved for use with any molecular gastrointestinal assays.

In the future, dry swabs would “be appropriate and can probably speed up and facilitate the diagnosis of C. diff infection,” the researchers wrote, but warned, “nevertheless, using single step PCR-based detection of C. diff may lead to overdiagnosis of C. diff infection due to the high sensitivity but lower specificity of PCR.”

That marks a heightened importance for the careful clinical evaluation of the patient: Are they an asymptomatic carrier? Is there another reason for the patient’s diarrhea? Do they truly have a C. diff infection? All important questions to continue to ask.

While liquid swabs cannot substitute for the two-step laboratory diagnosis of C. diff, the researchers believe that their study shows the dry swab is a suitable alternative to stool sample testing.

Dr. Peter Setlow, a Molecular Biology and Biophysics Professor at UConn Health Shares Bathroom Hand Dryers Study; the Spreading of Fecal Bacteria

Using those hot-air hand dryers in restrooms actually spread bacteria, including fecal bacteria on your hands, according to a new study conducted at UConn.

“In most institutions, toilets don’t have lids and when you flush them you get a little bit of an aerosol,” said Dr. Peter Setlow, a molecular biology and biophysics professor at UConn Health.

So, where does that toilet plume go?

“The hand dryers grab that air in the bathroom and accelerate it,” Setlow said.

During the study, plates were placed under hand dryers to collect the bacteria being blown out of the hand dryer.

“We’d get up to 150, 200 individual bacterial colonies and obviously different because they were different colors, different shapes, different smell,” Setlow said.

They tested 36 bathrooms multiple times and got similar results. The study was done in a research area in the academic building at UConn Health in Farmington not open to the public. However, Setlow said hand dryers in most public bathrooms work the same way.

“The bacteria that are blown from the hand dryers are coming from the bathroom air,” said Setlow.

Setlow has been studying molecular biology for 50 years. He said of the nearly 500 papers he’s helped author, this one, published in Applied and Environmental Microbiology, has gotten the most attention.

People who spoke with NBC Connecticut said news of the study may make them change their habits.

“It definitely makes me hesitate to use them,” Amy Anderson, of West Hartford, said.

“I’d just shake off your hands maybe. Just dry them on your sweatshirt,” said Sean Brierty, of Barkhamsted.

Setlow said adding HEPA filters to the hand dryers reduced the amount of bacteria four-fold when they were attached to the same dryers previously tested.

To read the article in its entirety, please click on the following link to be redirected:

https://www.nbcconnecticut.com/news/local/Bathroom-Hand-Dryers-Spread-Fecal-Bacteria-UConn-Study-479721513.html

Researchers at Boston-based Massachusetts General Hospital, Ann Arbor-based University of Michigan and Cambridge-based Massachusetts Institute of Technology Are Developing Institution-Specific Models That Predict Patient’s Risk Of Acquiring C.diff. Infections

Researchers at Boston-based Massachusetts General Hospital, Ann Arbor-based University of Michigan and Cambridge-based Massachusetts Institute of Technology are developing hospital-specific machine learning models that predict patients’ risk of Clostridium difficile infections much sooner than current diagnostic methods allow, according to a study published in Infection Control & Epidemiology.

“Despite substantial efforts to prevent C. diff infection and to institute early treatment upon diagnosis, rates of infection continue to increase,” co-senior study author Erica Shenoy, MD, PhD, said in a press release. “We need better tools to identify the highest risk patients so that we can target both prevention and treatment interventions to reduce further transmission and improve patient outcomes.”

The study authors noted most previous approaches to C. diff  infection risk were limited in usefulness since they were not hospital-specific and were developed as “one-size-fits-all” models that only included a few risk factors.

Therefore, to predict a patient’s C. diff risk throughout the course of their hospital stay, the researchers took a “big data” approach that analyzed the entire EHR. This method allows for institution-specific models that could be tailored to different patient populations, different EHR systems and factors specific to each facility. 

“When data are simply pooled into a one-size-fits-all model, institutional differences in patient populations, hospital layouts, testing and treatment protocols, or even in the way staff interact with the EHR can lead to differences in the underlying data distributions and ultimately to poor performance of such a model,” said co-senior study author Jenna Wiens, PhD. “To mitigate these issues, we take a hospital-specific approach, training a model tailored to each institution.”

With this machine learning-based model, the researchers looked at de-identified data, which included individual patient demographics and medical history, details on admissions and daily hospitalization, and the likelihood of C. diff exposure. The data was gathered from the EHRs of roughly 257,000 patients admitted to either MGH or to Michigan Medicine over two-year and six-year periods, respectively.

The models proved to be highly successful at predicting patients who would ultimately be diagnosed with C. diff. In half of these infected patients, accurate predictions could have been made at least five days before collecting diagnostic samples, which would allow hospitals to focus on antimicrobial interventions on the highest-risk patients.

The study’s risk prediction score could guide early screening for C. diff if validated in subsequent studies. For patients who receive an earlier diagnosis, treatment initiation could curb illness severity, and patients with confirmed C. diff could be isolated to prevent transmission to other patients.

The algorithm code is freely available here for hospital leaders to review and adapt for their institutions. However, Dr. Shenoy notes facilities looking to apply similar algorithms to their own institutions must assemble the appropriate local subject-matter experts and validate the performance of the models in their institutions.

To read article in its entirety please click on the following link to be redirected:

https://www.beckershospitalreview.com/quality/how-machine-learning-models-are-rapidly-predicting-c-diff-infections.html

Researchers From North Carolina State University Find That Antibiotics Give C.diff. Nutrient-Rich Environment

Using a mouse model, researchers from North Carolina State University have found that antibiotic use creates a “banquet” for Clostridium difficile (C. diff), by altering the native gut bacteria that would normally compete with C. diff for nutrients. The findings could lead to the development of probiotics and other strategies for preventing C. diff infection.

C. diff is a harmful bacterium that can cause severe, recurrent and sometimes fatal infections in the gut. Although the bacteria are commonly found throughout our environment, C. diff infections primarily occur in patients who are taking, or who have recently finished taking, antibiotics.

“We know that antibiotics are major risk factors for C. diff infection because they alter the gut microbiota, or composition of bacteria in the gut, by eliminating the bacteria that are normally there,” says Casey Theriot, assistant professor of infectious disease at NC State and corresponding author of a paper describing the research. “Our latest work suggests that the microbiota may provide natural resistance to C. diff colonization by competing with C. diff for nutrients in that environment; specifically, for an amino acid called proline.”

Theriot and postdoctoral fellow Joshua Fletcher introduced C. diff to antibiotic-treated mice and monitored their gut environment at four intervals: 0, 12, 24, and 30 hours after introduction. They conducted metabolomic and RNA sequencing analysis of the gut contents and the C. diff at these time points to find out which nutrients the bacteria were “eating.” Metabolomics allowed the team to trace the abundance of the nutrients in the gut, and RNA analysis indicated which genes in the C. diff were active in metabolizing nutrients.

The researchers found that the amount of proline in the gut decreased as the population of C. diff increased. Additionally, the amount of a proline byproduct called 5-aminovalerate also increased, indicating that C. diff was metabolizing the proline. The RNA analysis further confirmed C. diff‘s use of proline, as genes related to proline metabolism in C. diff increased during the early stages of colonization, when proline was abundant.

“We’ve been able to show that in the absence of competition C. diff is metabolizing proline and other amino acids in the mouse model, using it as fuel to survive and thrive,” Theriot says. “Hopefully this information could lead to the development of better probiotics, or ‘good’ bacteria that can outcompete C. diff for nutrients in the gut. The ultimate goal is to control these bacteria in ways that don’t rely solely on antibiotics.”

To review article in its entirety please click on the following link to be redirected:

https://www.sciencedaily.com/releases/2018/03/180328204122.htm

Rutgers University and International Scientists Have Determined the Molecular Target and Mechanism of the Antibacterial Drug fidaxomicin (Trade Name Dificid)

Fidaxomicin was approved in 2011 for treatment of the CDC “urgent threat” bacterial pathogen Clostridium difficile (C. diff) and currently is one of two front-line drugs for treatment of C. diff.

A team of Rutgers University and international scientists has determined the molecular target and mechanism of the antibacterial drug fidaxomicin (trade name Dificid).

Resource:  https://www.sciencedaily.com/releases/2018/03/180329141050.htm

Fidaxomicin also exhibits potent antibacterial activity against other CDC “serious threat” bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Staphylococcus aureus (VRSA), and the tuberculosis bacterium, Mycobacterium tuberculosis. However, the low solubility and low systemic bioavailability of fidaxomicin have precluded use of fidaxomicin for treatment of MRSA, VRSA, and tuberculosis.

To design next-generation fidaxomicin derivatives with improved clinical activity against C. diff and useful clinical activity against MRSA, VRSA, and tuberculosis, it is essential to know how the drug binds to and inhibits its molecular target, bacterial RNA polymerase, the enzyme responsible for bacterial RNA synthesis.

In a paper published in Molecular Cell today, the researchers report results of cryo-electron microscopy (cryo-EM) and single molecule spectroscopy analyses showing how fidaxomicin binds to and inhibits bacterial RNA polymerase.

The researchers report a cryo-EM structure of fidaxomicin bound to Mycobacterium tuberculosis RNA polymerase at 3.5 Å resolution. The structure shows that fidaxomicin binds at the base of the RNA polymerase “clamp,” a part of RNA polymerase that must swing open to allow RNA polymerase to bind to DNA and must swing closed to allow RNA polymerase to hold onto DNA. The structure further shows that fidaxomicin traps the RNA polymerase “clamp” in the open conformation.

The researchers also report results of single-molecule fluorescence spectroscopy experiments that confirm that fidaxomicin traps the RNA polymerase “clamp” in the open conformation and that define effects of fidaxomicin on the dynamics of clamp opening and closing.

The researchers show that fidaxomicin inhibits bacterial RNA polymerase through a binding site and mechanism that differ from those of rifamycins, another class of antibacterial drugs that target bacterial RNA polymerase. The finding that fidaxomicin inhibits bacterial RNA polymerase functions through a different, non-overlapping binding site and mechanism explains why fidaxomicin is able to kill bacterial pathogens resistant to rifamycins and why fidaxomicin is able to function additively when combined with rifamycins.

The new results enable rational, structure-based design of new, improved fidaxomicin derivatives with higher antibacterial potency, higher solubility, and higher systemic bioavailability. Based on the structure of fidaxomicin bound to its target, the researchers identified atoms of fidaxomicin that are not important for binding to the target and thus that can be modified without compromising the ability to bind to the target. The researchers then developed chemical procedures that allow selective attachment of new chemical groups at those atoms, including new chemical groups that can improve potency, solubility, or systemic bioavailability.

“The results set the stage for development of improved fidaxomicin derivatives, particularly improved fidaxomicin derivatives having the solubility and systemic bioavailability needed for treatment of systemic infections, such as MRSA and tuberculosis,” said Ebright, Board of Governors Professor of Chemistry and Chemical Biology and Laboratory Director at the Waksman Institute of Microbiology at Rutgers, who led the research.

In addition to Richard H. Ebright, the research team included Wei Lin, David Degen, Abhishek Mazumder, Dongye Wang, Yon W. Ebright, Richard Y. Ebright, Elena Sineva, Matthew Gigliotti, Aashish Srivastava, Sukhendu Mandal, Yi Jiang, Ruiheng Yin, and Dennis Thomas from Rutgers University; Kalyan Das from KU Leuven; Zhening Zhang and Edward Eng from the National Resource for Automated Molecular Microscopy and the Simons Electron Microscopy Center; Stefano Donadio from NAICONS Srl.; Haibo Zhang and Changsheng Zhang from the Chinese Academy of Sciences Guangzhou.

To review the article in its entirety please click on the following link to be redirected:

https://www.sciencedaily.com/releases/2018/03/180329141050.htm

Immuron Announced First Patients Enrolled In Phase 1/2 (first-in-human) Clinical Trials For Immuron’s IMM-529 For Treatment of C.difficile Infections

The Australian biopharmaceutical company Immuron announced that the first patients have enrolled in phase 1/2 (first-in-human) clinical trials for Immuron’s IMM-529, an oral immunotherapeutic medication for treatment of Clostridium difficile infections (CDI).

As published in MD Mag February 16, 2018

To review this publication in its entirety please click on the following link to be redirected:

http://www.mdmag.com/medical-news/a-powerful-new-weapon-in-the-fight-against-clostridium-difficile-infection

According to Dan Peres, MD, senior vice president and head of medical development at Immuron, IMM-529 “has shown promise in successfully treating Clostridium-difficile” through its “unique delivery of antibodies.”

If the trials are successful, IMM-529 may be a powerful new weapon in the global fight against CDI. Peres reports that IMM-529 that has been effective in preclinical studies for prophylactic use, treatment of disease, and the prevention of recurrence in relation to CDI, and that the company is excited to enroll the first patients.

The placebo-controlled study to test the safety, tolerability and efficacy of IMM-529 will take place at Hadassah Medical Center in Jerusalem and include 60 CDI diagnosed patients in the 28 day study.

Patients enrolled in the study, led by Yoseph Caraco, MD, head of the clinical pharmacology unit at Hadassah Medical Center, will receive IMM-529 or a placebo 3 times a day during the 28 -day trial period, and be monitored for 2 additional months, determining any recurrence of the disease.

In a statement, Caraco said that he was optimistic about IMM-529 based on pre-clinical trial results and that IMM-529 could “be the answer we’re all looking for” when it comes to treatment of CDI.

IMM-529 targets CDI in 2 ways: by neutralizing toxin B (TcdB), a cytotoxin responsible for inflammation and diarrhea that characterizes CDI, and by binding Clostridium difficile spores and vegetative cells preventing further colonization. Caraco reported that IMM-529 approaches CDI by “targeting the main virulence factors of the disease with only minor disturbance to the natural biome” which could be extremely valuable in treating CDI.

In the earlier pre-clinical proof-of-concept study by led by Dena Lyras, MD, PhD with Monash University in Melbourne, Australia, IMM-529 was shown to be 80% effective in both the treatment of and prevention of CDI without the use of antibiotics.

In a December 2015 statement from Immuron, Lyras stated that she was “excited by the potential of these therapeutics in treating patients with both the acute and the relapse phase, of the disease.”

According to data supplied by the American Gastroenterological Association, approximately 500,000 people in the US are diagnosed with CDI each year, and CDI-associated deaths range from 14,000 to 30,000 per year.

In the European Union, according to a 2016 study led by Alessandro Cassini, MD, with the European Centre for Disease Prevention and Control in Stockholm, Sweden, more than 150,000 cases of hospital-acquired CDI infections (134,053–173,089; 95% CI) occur each year.

According to Immuron, the cost of CDI globally (calculated by CIDRAP, the Center for Infectious Disease and Policy at the University of Minnesota) is an estimated annual economic burden of more than $10 billion and increases in hypervirulent and antibiotic-resistant strains have led to CDI becoming a major medical concern.

Caraco stated that CDI poses “a growing risk amongst a greater population of patients, including those recently treated with antibiotics, the elderly, institutionalized and hospitalized.”

If IMM-529 is found to be safe and effective in clinical trials, it could prove a significant boon to the global fight against CDI at all 3 stages of the disease.

Researchers Utilize Deep Metagenomic Sequencing to Profile FMT ‘s Retracting the Gut Microbiome Features That Coincided With Successful Fecal Transplant Engraftment

A team led by investigators at the Broad Institute have started untangling the bacterial strains that influence successful fecal microbiota transplantation (FMT) engraftment in individuals treated for recurrent Clostridium difficile infection.

As they reported in Cell Host & Microbe today, researchers from the Broad Institute, Massachusetts Institute of Technology, Massachusetts General Hospital, and elsewhere used deep metagenomic sequencing to profile FMT in four FMT donors and 19 recipients with C. difficile infections, retracing the gut microbiome features that coincided with successful fecal transplant engraftment.

The initial gut microbial communities in both the donors and the recipients seemed to influence this process, the team noted, particularly bacterial abundance and strain phylogeny. The final gut microbe composition differed between donors and post-FMT recipients, though, with specific strains that originated in the host either taking hold or falling by the wayside in recipients in an “all-or-nothing” manner.

“This paper provides a context for understanding how to make these live biological therapeutics as an alternative to transferring raw fecal matter,” co-senior author Eric Alm, co-director of MIT’s Center for Microbiome Informatics and Therapeutics, said in a statement.

“We describe a model focused on three elements, including bacterial engraftment, growth, and mechanism of action, that need to be considered when developing these live therapies targeting the gut microorganisms, or microbiome,” added Alm, who is also affiliated with the Broad Institute and Finch Therapeutics.

Along with its use for treating recurrent C. difficile infection, the team noted that FMT has been proposed in other conditions such as inflammatory bowel disease and metabolic syndrome. Even so, there is a ways to go in understanding the factors influencing bacterial engraftment and effectiveness in the recipient gut — information needed to move the approach from a shotgun approach using fecal donor material to microbe-based treatments based on purified collections of specific bacteria.

“Although the success of FMT requires donor bacteria to engraft in the patient’s gut, the forces governing engraftment in humans are unknown,” the authors wrote.

To follow this process, the researchers used the Illumina GAIIx instrument to do deep metagenomic sequencing on seven stool samples from four healthy donors and 67 samples collected over time from 19 individuals treated for C. difficile infection with FMT.

With the help of statistical modeling and a new computational method dubbed Strain Finder, the team looked at the bacterial species that successfully engrafted in FMT recipients and followed strain genotypes over time. It also mapped the metagenomes to Human Microbiome Project reference genomes to take a look at bacterial taxa abundance.

Prior to treatment, for example, FMT recipients had lower-than-usual gut microbiome diversity. And while gut microbial community patterns shifted in recipients after FMT, the resulting gut microbiomes continued to differ from the original donor microbiomes, the researchers reported.

Even so, their analytical methods made it possible predict post-FMR metagenomic operational taxa unit abundance and incidence.

With nearly 1,100 bacterial strains in the 79 samples considered, the team traced transmission of certain strains from FMT donors to recipients, noting that bacterial strains tended to engraft in an “all-or-nothing” manner, “whereby no strains or complete sets of strains colonize the patients.”

“We find that engraftment can be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient,” Alm and co-authors wrote. “Furthermore, donor strains within a species engraft in an all-or-nothing manner and previously undetected strains frequently colonize patients receiving FMT.”

Such patterns were supported by the researchers’ follow-up analyses on 16S ribosomal RNA sequence data for stool samples from 10 more FMT donors and 18 recipients, as well as an analysis of metagenomic sequence data for samples from five individuals treated with FMT for metabolic syndrome.

“Together,” they authors said, “these findings suggest that the principles of engraftment we discovered for recurrent C. difficile infection may generalize to other disease indications, including metabolic syndrome.”

 

To read article in its entirety please click on the following link to be redirected:

https://www.genomeweb.com/sequencing/donor-recipient-strain-analyses-offer-fecal-transplant-engraftment-clues