Similar Outcomes Identified in Comparison of C.Diff of Small Bowel and Colon - MD Magazine
In vivo commensal control of Clostridioides difficile virulence
Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile
FliW and CsrA govern flagellin (FliC) synthesis and play pleiotropic roles in virulence and physiology of Clostridioides difficile R20291
Structure and assembly of the S-layer determine virulence in C. difficile
Research Square is a preprint platform that makes research communication faster, fairer, and more useful.
Complete genome sequence of the newly discovered temperate Clostridioides difficile bacteriophage phiCDKH01 of the family Siphoviridae
A temperate siphovirus, phiCDKH01, was obtained from a clinical isolate of Clostridioides difficile. The phage genome is a 45,089-bp linear double-stranded DNA molecule with an average G+C content of 28.7%. It shows low similarity to known phage genomes, except for phiCD24-1. Genomic and phylogeneti …
Rethinking the Role of Constipation in Diabetes - Endocrinology Advisor
Constipation affects approximately 60% of patients with diabetes and 16% of adults overall. This story breaks down treatments and related conditions.
Antimicrobial resistance surveillance of Clostridioides difficile in Australia, 2015–18
AbstractBackground. Clostridioides difficile was listed as an urgent antimicrobial resistance (AMR) threat in a report by the CDC in 2019. AMR drives the evolut
K-mer based prediction of Clostridioides difficile relatedness and ribotypes
Comparative analysis of Clostridioides difficile whole-genome sequencing (WGS) data enables fine scaled investigation of transmission and is increasingly becoming part of routine surveillance. However, these analyses are constrained by the computational requirements of the large volumes of data involved. By decomposing WGS reads or assemblies into k-mers and using the dimensionality reduction technique MinHash, it is possible to rapidly approximate genomic distances without alignment. Here we assessed the performance of MinHash, as implemented by sourmash, in predicting single nucleotide differences between genomes (SNPs) and C. difficile ribotypes (RTs). For a set of 1,905 diverse C. difficile genomes (differing by 0-168,519 SNPs), using sourmash to screen for closely related genomes, at a sensitivity of 100% for pairs ≤10 SNPs, sourmash reduced the number of pairs from 1,813,560 overall to 161,934, i.e., by 91%, with a positive predictive value of 32% to correctly identify pairs ≤10 SNPs (maximum SNP distance 4,144). At a sensitivity of 95%, pairs were reduced by 94% to 108,266 and PPV increased to 45% (maximum SNP distance 1,009). Increasing the MinHash sketch size above 2000 produced minimal performance improvement. We also explored a MinHash similarity-based ribotype prediction method. Genomes with known ribotypes (n=3,937) were split into a training set (2,937) and test set (1,000) randomly. The training set was used to construct a sourmash index against which genomes from the test set were compared. If the closest 5 genomes in the index had the same ribotype this was taken to predict the searched genome’s ribotype. Using our MinHash ribotype index, predicted ribotypes were correct in 780/1000 (78%) genomes, incorrect in 20 (2%), and indeterminant in 200 (20%). Relaxing the classifier to 4/5 closest matches with the same RT improved the correct predictions to 87%. Using MinHash it is possible to subsample C. difficile genome k-mer hashes and use them to approximate small genomic differences within minutes, significantly reducing the search space for further analysis. Impact statement The genetic code, or DNA, of bacteria is increasingly used to track how infection spreads and to guide infection control interventions, as similar or identical DNA sequences are expected in samples from pair of individuals related by transmission. While obtaining the DNA sequence for bacteria is increasingly straightforward, comparing thousands or even millions of sequences requires substantial computing power and time using current approaches. Here we describe how a method for summarising sequencing data, MinHash, can be used to rapidly reduce the number of possible close sequence matches in Clostridioides difficile , an important healthcare-associated pathogen. It can also be used to approximate traditional schemes used to classify C. difficile into smaller subgroups in transmission analyses, such as ribotyping. Data summary The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ### Competing Interest Statement MHW has received consulting fees from Actelion, Astellas, MedImmune, Merck, Pfizer, Sanofi-Pasteur, Seres, Summit, and Synthetic Biologics; lecture fees from Alere, Astellas, Merck & Pfizer; and grant support from Actelion, Astellas, bioMerieux, Da Volterra, Merck and Summit. SDG has received consulting fees from Abbott, Aquarius Population Health, Astellas and MSD; lecture fees from Astellas, MSD and Orion Diagnostics; and grant support from Astellas. DWE declares lecture fees from Gilead outside the submitted work. No other author has a conflict of interest to declare.
Ser/Thr Kinase-Dependent Phosphorylation of the Peptidoglycan Hydrolase CwlA Controls Its Export and Modulates Cell Division in Clostridioides difficile
Cell growth and division require a balance between synthesis and hydrolysis of the peptidoglycan (PG). Inhibition of PG synthesis or uncontrolled PG hydrolysis can be lethal for the cells, making it imperative to control peptidoglycan hydrolase (PGH) activity. The synthesis or activity of several ke …
Immune response against Clostridioides difficile and translation to therapy
The pathogenesis of Clostridioides difficile infection (CDI) has largely been attributed to the action of two major toxins - A and B. An enhanced systemic humoral immune response against these toxins has been shown to be protective against recurrent CDI. Over the years, fully human monoclonal …
NAFLD and Infection, a Nuanced Relationship
In this narrative review, we synthetize current knowledge on several infections including urinary tract infection, pneumonia, Helicobacter pylori, coronavirus disease 2019, and Clostridioides difficile as they relate to NAFLD
The Elevated Risk of Recurrent Clostridioides Difficile Infection in Patients with Inflammatory Bowel Disease: a Systematic Review and Meta-analysis
Frequency of toxin genes and antibiotic resistance pattern of Clostridioides difficile isolates in diarrheal samples among hospitalized patients in Hamadan Iran
The results of this study showed toxigenic C. difficile with tcdA + /tcdB + profile is a major cause of nosocomial diarrhea in Hamadan, and clinical laboratories should routinely perform C. difficile diagnostic testing on diarrheal specimens of hospi …
Seres Therapeutics to Present Key Data on Investigational Microbiome Therapeutics for Recurrent C. difficile Infection and Ulcerative Colitis at the Digestive Disease Week (DDW) Annual Meeting - Yahoo Finance
Seres Therapeutics, Inc. (Nasdaq: MCRB), a leading microbiome therapeutics company, today announced that it will present recent research findings from its microbiome drug development portfolio at Digestive Disease Week® (DDW), which is taking place virtually from May 21-23, 2021. With two oral presentations and two posters of distinction, Seres will demonstrate the potential of microbiome-based therapies for patients with serious diseases like recurrent Clostridioides difficile infection (CDI) and ulcerative colitis (UC).
Molecular Characterization of, and Antimicrobial Resistance in, Clostridioides difficile from Thailand, 2017-2018
Clearance of Clostridioides difficile Colonization Is Associated with Antibiotic-Specific Bacterial Changes
The gut bacterial community prevents many pathogens from colonizing the intestine. Previous studies have associated specific bacteria with clearing Clostridioides difficile colonization across different community perturbations. However, those bacteria alone have been unable to clear C. dif …
Researchers Identify Clear Trends for C Diff Hospitalizations - MD Magazine
Females and older patients had higher rates of hospitalizations with CDI than males and younger patients.
Microbiota-mediated protection against antibiotic-resistant pathogens
Colonization by the microbiota provides one of our most effective barriers against infection by pathogenic microbes. The microbiota protects against infection by priming immune defenses, by metabolic exclusion of pathogens from their preferred niches, and through direct antimicrobial antagonism. Dis …
Metabolic Labeling of Clostridioides difficile Proteins
The introduction of stable isotopes in vivo via metabolic labeling approaches (SILAC or 15N-labeling) allows, after combination of differentially treated labeled and unlabeled cells or protein extracts, for correction of protein quantification errors implemented during elaborated sample p …
Molecular epidemiology and antimicrobial resistance of Clostridioides difficile in Germany 2014-2019
Clostridioides difficile is a Gram positive spore-forming rod and mainly responsible for nosocomial diarrhea in developed nations. Molecular and antimicrobial surveillance is important for monitoring the strain composition including genotypes of high epidemiological importance such as ribotype 027 ( …
Estimation of Risk of Death Attributable to Acute Gastroenteritis Not Caused by Clostridioides difficile Infection Among Hospitalized Adults in England
Approximately 5000 of the 276,000 deaths that occur annually among hospitalized adults in England can be attributed to AGE not caused by CDI, which is higher than previously estimated.
A cortex-specific penicillin-binding protein contributes to heat resistance in Clostridioides difficile spores
We have identified and characterised a cortex specific PBP in C. difficile. This is the first characterisation of a cortex-specific PBP in C. difficile and begins the process of unravelling cortex biogenesis in this important pathogen.
Jeffrey Aronson: When I Use a Word . . . A difficult infection - The BMJ - The BMJ
Surveying new biomedical words listed in the Oxford English Dictionary (OED) since 1970, I have found fewer examples each year. For example, the 1970 list contained 61 words and the [...]More...
News Ability of multi-drug resistant infection to evolve within cystic fibrosis patients highlights need for rapid treatment - SelectScience
Scientists have been able to track how a multi-drug resistant organism is able to evolve and spread widely among cystic fibrosis patients – showing that it can evolve rapidly within an individual during chronic infection.
Ability of multi-drug resistant infection to evolve within cystic fibrosis patients highlights need for rapid treatment - Mirage News
Scientists have been able to track how a multi-drug resistant organism is able to evolve and spread widely among cystic fibrosis patients - showing that...
Pediatric Appendicitis Patients More Likely to Suffer Additional C Diff Infection - Contagionlive.com
The proportion of cases with CDI in perforated appendicitis was found to be greater in comparison to the non-perforated cases.
S-layers: The Proteinaceous Multifunctional Armors of Gram-Positive Pathogens
S-layers are self-assembled crystalline 2D lattices enclosing the cell envelopes of several bacteria and archaea. Despite their abundance, the landscape of S-layer structure and function remains a land of wonder. By virtue of their location, bacterial S-layers have been hypothesized to add structura …
Cwl0971 a novel peptidoglycan hydrolase plays pleiotropic roles in Clostridioides difficile R20291
Clostridioides difficile is a Gram-positive, spore-forming, toxin-producing anaerobe that can cause nosocomial antibiotic-associated intestinal disease. Although the production of toxin A (TcdA) and toxin B (TcdB) contribute to the main pathogenesis of C. difficile, the mechanism of TcdA and TcdB re …
In situ analysis of antibiotic resistance genes in anaerobically digested dairy manure and its subsequent disposal facilities
The metagenomic and quantitative polymerase chain reaction approaches were combined to evaluate the profiles of ARGs and plasmids in anaerobically digested dairy manure in situ and reveal the persistence and elevation of typical ARGs and plasmids in its subsequent disposal facilities in CAFOs, respe …