Tag Archives: dysbiosis

There Are Smart Antibiotics to treat C.difficile infections being developed by Researchers

Cationic amphiphilic bolaamphiphile-based delivery of antisense oligonucleotides provides a potentially microbiome sparing treatment

for C. difficile

The Journal of Antibiotics (2018) | Download Citation

Abstract

Conventional antibiotics for C. difficile infection (CDI) have mechanisms of action without organismal specificity, potentially perpetuating the dysbiosis contributing to CDI, making antisense approaches an attractive alternative. Here, three (APDE-8, CODE-9, and CYDE-21) novel cationic amphiphilic bolaamphiphiles (CABs) were synthesized and tested for their ability to form nano-sized vesicles or vesicle-like aggregates (CABVs), which were characterized based on their physiochemical properties, their antibacterial activities, and their toxicity toward colonocyte (Caco-2) cell cultures. The antibacterial activity of empty CABVs was tested against cultures of E. coli, B. fragilis, and E. faecalis, and against C. difficile by “loading” CABVs with 25-mer antisense oligonucleotides (ASO) targeting dnaE. Our results demonstrate that empty CABVs have minimal colonocyte toxicity until concentrations of 71 µM, with CODE-9 demonstrating the least toxicity. Empty CABVs had little effect on C. difficile growth in culture (MIC90 ≥ 160 µM). While APDE-8 and CODE-9 nanocomplexes demonstrated high MIC90 against C. difficile cultures (>300 µM), CYDE-21 nanocomplexes demonstrated MIC90 at CABV concentrations of 19 µM. Empty CABVs formed from APDE-8 and CODE-9 had virtually no effect on E. coli, B. fragilis, and E. faecalis across all tested concentrations, while empty CYDE-21 demonstrated MIC90 of >160 µM against E. coli and >40 µM against B. fragilisand E. faecalis. Empty CABVs have limited antibacterial activity and they can deliver an amount of ASO effective against C. difficile at CABV concentrations associated with limited colonocyte toxicity, while sparing other bacteria. With further refinement, antisense therapies for CDI may become a viable alternative to conventional antibiotic treatment.

Introduction

C. difficile infection (CDI) is the most frequently reported nosocomial bacterial infection [1] in the United States, accounting for more than 450,000 new cases annually and for more than four billion dollars in CDI-attributable annual health care costs [2]. CDI has a strong reliance on intestinal dysbiotic states, which, when combined with the presence of C. difficile in the human gut, represents the most common pathogenesis for CDI. The high prevalence of this infection is, in large part, due to formidable recurrence rates of 15–25% following first treatment [3] with conventional antibiotics (CAs). CAs have long been recognized as the most important risk factor for the development of CDI [4], due to their mechanisms of action lacking organismal specificity, leading to widespread changes in gut ecology [5], which can lead to CDI by disrupting the gut microbial community. Given the important role of intestinal dysbiosis in the development of CDI, there has also been recent interest in studying the effects of difficile-directed conventional antibiotics on the bacterial and fungal communities of human subjects being treated for CDI, as a way of potentially explaining the high persistence and recurrence rates of this disease. These more recent data [6] suggest that even difficile-directed conventional antibiotics could potentially contribute to the perpetuation of dysbiotic states, which in turn could perpetuate CDI, potentially leading to even primary treatment failures.

There has been previous [7, 8] interest in the development of antisense therapies to treat bacterial infections, in part due to concerns regarding antibiotic resistance to traditional drugs. Given the dependence of CDI on dysbiotic states, approaches using therapeutic antisense oligonucleotides (ASO) complimentary to specific C. difficile mRNAs could limit or prevent the expression of important bacterial genes leading to bacterial death, all while sparing other organisms. This approach would offer significant advantages over CAs, especially in terms of a more limited impact on gut microbial communities. Developing clinically effective antisense therapies targeting a Gram-positive organism requires several elements. Since antisense oligonucleotides will not be efficiently introduced into bacteria without assistance given the presence of both a cell membrane and a thick cell wall, a carrier molecule must be used to deliver the ASO. This carrier must complex with the ASO strongly enough to concentrate it, to protect it from degradation in the extracellular environment, and to focus its delivery on its target cell. In order to accomplish these activities, the carrier-ASO complex itself must be stable in the in vivo environment of the gut. Once at the cell, the carrier must be able to release its cargo. Simultaneously, the carrier must demonstrate both limited gut toxicity and limited antibacterial activity at the doses required to effectively treat the target bacteria.

Our group published the first [9] in vitro data for antisense therapies against CDI by complexing cyclohexyl dequalinium analogs to various ASO-targeting essential C. difficile genes. However, since dequalinium has both antibacterial activity as well as toxicity at higher doses, a better delivery compound for ASO is required if antisense approaches to CDI are to be further developed. Here, we report our data on vesicles formed from novel cationic amphiphilic bolaamphiphiles (CABs) as carriers for chimeric 25-mer 2′-O-methyl phosphorothioate ASO. CABs, characteristic of all bola-like compounds, have hydrophilic, positively charged end groups separated by a hydrophobic linker chain. This molecular structure enables CABs to form nano-sized vesicle-like aggregates (CABVs), which in turn allow them to complex with negatively charged oligonucleotides in addition to promoting electrostatic interactions with bacterial cell membranes for intracellular delivery of ASO. The synthesis, physiochemical properties, toxicity, and antibacterial properties of three novel CABs and their respective CABVs are described, and their specificity for C. difficile compared to several other organisms is also provided.

Please click on the following link to view graphs and read this article in its entirety:

https://www.nature.com/articles/s41429-018-0056-9

Study shows Microbiome Differences Between Intensive Care Unit Patients Hospitalized From Healthy Patients

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The microbiome of patients admitted to the intensive care unit (ICU) at a hospital differs dramatically from that of healthy patients, according to a new study published in mSphere.

 

Researchers analyzing microbial taxa in ICU patients’ guts, mouth and skin reported finding dysbiosis, or a bacterial imbalance, that worsened during a patient’s stay in the hospital. Compared to healthy people, ICU patients had depleted populations of commensal, health-promoting microbes and higher counts of bacterial taxa with pathogenic strains – leaving patients vulnerable to hospital-acquired infections that may lead to sepsis, organ failure and potentially death.

What is dysbiosis?  Pathogens, antibiotic use, diet, inflammation, and other forces can cause dysbiosis, a disruption in these microbial ecosystems that can lead to or perpetuate disease  (1)

What makes a gut microbiome healthy or not remains poorly defined in the field. Nonetheless, researchers suspect that critical illness requiring a stay in the ICU is associated with the the loss of bacteria that help keep a person healthy. The new study, which prospectively monitored and tracked changes in bacterial makeup, delivers evidence for that hypothesis.
“The results were what we feared them to be,” says study leader Paul Wischmeyer, an anesthesiologist at the University of Colorado School of Medicine. “We saw a massive depletion of normal, health-promoting species.”
Wischmeyer, who will move to Duke University in the fall, runs a lab that focuses on nutrition-related interventions to improve outcomes for critically ill patients.

He notes that treatments used in the ICU – including courses of powerful antibiotics, medicines to sustain blood pressure, and lack of nutrition – can reduce the population of known healthy bacteria. An understanding of how those changes affect patient outcomes could guide the development of targeted interventions to restore bacterial balance, which in turn could reduce the risk of infection by dangerous pathogens.
Previous studies have tracked microbiome changes in individual or small numbers of critically ill patients, but Wischmeyer and his collaborators analyzed skin, stool, and oral samples from 115 ICU patients across four hospitals in the United States and Canada. They analyzed bacterial populations in the samples twice – once 48 hours after admission, and again after 10 days in the ICU (or when the patient was discharged). They also recorded what the patients ate, what treatments patients received, and what infections patients incurred.
The researchers compared their data to data collected from a healthy subset of people who participated in the American Gut project dataset. (American Gut is a crowd-sourced project aimed at characterizing the human microbiome by the Rob Knight Lab at the University of California San Diego.) They reported that samples from ICU patients showed lower levels of Firmicutes and Bacteroidetes bacteria, two of the largest groups of microbes in the gut, and higher abundances of Proteobacteria, which include many pathogens.
Wischmeyer was surprised by how quickly the microbiome changed in the patients. “We saw the rapid rise of organisms clearly associated with disease,” he says. “In some cases, those organisms became 95 percent of the entire gut flora – all made up of one pathogenic taxa – within days of admission to the ICU. That was really striking.” Notably, the researchers reported that some of the patient microbiomes, even at the time of admission, resembled the microbiomes of corpses. “That happened in more people than we would like to have seen,” he says.
Wischmeyer suggests the microbiome could be tracked like other vital signs and could potentially be used to identify patient problems and risks before they become symptomatic. In addition, now that researchers have begun to understand how the microbiome changes in the ICU, Wischmeyer says the next step is to use the data to identify therapies – perhaps including probiotics – to restore a healthy bacterial balance to patients.
Everyone who collaborated on the project – including dietitians, pharmacists, statisticians, critical care physicians, and computer scientists – participated on a largely voluntary basis without significant funding to explore the role of the microbiome in ICU medicine, says Wischmeyer.

 

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

https://www.asm.org/index.php/journal-press-releases/94540-icu-patients-lose-helpful-gut-bacteria-within-days-of-hospital-admission?platform=hootsuite

Sources:

(1)  http://www.serestherapeutics.com

 

C. diff. Spores and More Global Broadcasting Network Welcome Guests; Dr. David Cook, Ph.D., and Dr. Michele Trucksis, Ph.D., M.D. Of Seres Therapeutics, Inc.

“Ecobiotics: A Novel Approach to Recurrent C. difficile infections”

Tuesday, February 23rd — Live Broadcast

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This episode introduces Seres Therapeutics, a leading microbiome therapeutics company, which recently published in the Journal of Infectious Diseases positive results from an open-label Phase 1b/2 study of SER-109 for the treatment of patients with recurrent
C. difficile infections (CDI).  Seres Therapeutics is creating a new class of medicines to treat diseases resulting from functional deficiencies in the microbiome, a condition known as dysbiosis.

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New insights into the human microbiome are fundamentally reshaping how we understand and treat a wide range of diseases, creating new possibilities for patients not served by current therapeutic approaches. Ecobiotics are ecological compositions of beneficial organisms that are designed to reestablish a healthy microbiome. The discovery efforts at Seres Therapeutics currently span metabolic, inflammatory, and infectious diseases.

Join Guests;  
Dr. David Cook, Ph.D., Executive Vice President of R&D and Chief Scientific Officer
And
Dr. Michele (Shelley) Trucksis, Ph.D., M.D., Executive Vice President and Chief Medical Officer

As we discuss the microbiome, CDI, clinical studies SER-109, Probiotics, ECOSPOR, and much more

 

C. diff. Spores and More™  Global Broadcasting Network –  producing educational programs dedicated to  C. difficile Infections and more —  brought to you by VoiceAmerica and sponsored by Clorox Healthcare

 

Seres Therapeutics Disclaimer:
“This interview will include forward-looking statements on Seres Therapeutics’ current expectations and projections about future events. These statements are based upon current beliefs, expectations and assumptions, and are subject to a number of important risks and uncertainties, including those set forth in Seres Therapeutics’ filings with the SEC, many of which are difficult to predict. Actual results may differ materially from such statements. The information included in this interview is provided only as of the date of this interview, and Seres Therapeutics undertakes no obligation to update any forward-looking statements stated in this interview on account of new information, future events, or otherwise, except as required by law. Seres Therapeutics has provided financial support to the C Diff Foundation.”