Successful Treatment of Recurrent Clostridioides difficile Infection Using a Novel, Drinkable, Oral Formulation of Fecal Microbiota.

BACKGROUND: Fecal microbiota transplants can be administered orally in encapsulated form or require invasive procedures to administer liquid formulations. There is a need for an oral liquid formulation of fecal microbiota for patients who are unable to swallow capsules, especially if they require multiple, repeated administrations. AIMS: These studies were conducted to develop a protocol to manufacture an organoleptically acceptable powdered fecal microbiota formulation that can be suspended in a liquid carrier and used for fecal microbiota transplantation. METHODS: Several processing steps were investigated, including extra washes of microbiota prior to lyophilization and an addition of a flavoring agent. The viability of bacteria in the transplant formulation was tested using live/dead microscopy staining and engraftment into antibiotic-treated mice. After development of a clinical protocol for suspension of the powdered microbiota, the new formulation was tested in three elderly patients with recurrent Clostridioides difficile infections and who have difficulties in swallowing capsules. Changes in the microbial community structure in one of the patients were characterized using 16S rRNA gene profiling and engraftment analysis. RESULTS: The processing steps used to produce an organoleptically acceptable suspension of powdered fecal microbiota did not result in loss of its viability. The powder could be easily suspended in a liquid carrier. The use of the new formulation was associated with abrogation of the cycle of C. difficile infection recurrences in the three patients. CONCLUSION: We developed a novel organoleptically acceptable liquid formulation of fecal microbiota that is suitable for use in clinical trials for patients with difficulties in swallowing capsules.

Development of a Large-Scale Soil DNA Extraction Method for Molecular Quantification of Fusarium oxysporum f. sp. fragariae in Soil.

The most common soilborne diseases affecting the strawberry industry in California include Verticillium wilt due to Verticillium dahliae, charcoal root rot due to Macrophomina phaseolina, and Fusarium wilt due to Fusarium oxysporum f. sp. fragariae. Detection of these pathogens in soil is an important facet of disease management and fumigation recommendations. Whereas the soil populations of both M. phaseolina and V. dahliae can be readily quantified with quantitative PCR (qPCR) assays using DNA extractions with 500 mg of soil, the single-cell nature of the F. oxysporum chlamydospore does not provide enough pathogen DNA from 500-mg extractions to be reliably quantified. Here, we describe an improved DNA extraction protocol from 10 to 15 g of soil that allows for the quantification of F. oxysporum f. sp. fragariae populations below 10 CFU/g. The relationship between results from the TaqMan qPCR assay and pathogen population density in soil was determined by using this extraction method in pathogen-free soils artificially infested with a hygromycin-resistant strain of F. oxysporum f. sp. fragariae to facilitate accurate colony counts when plated on a selective medium. Although the protocol was developed for F. oxysporum f. sp. fragariae, it is applicable for detection and quantification of other soilborne pathogens.

Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly.

Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.

Boosting corrects a memory B cell defect in SARS-CoV-2 mRNA-vaccinated patients with inflammatory bowel disease.

Immunosuppressed patients with inflammatory bowel disease (IBD) generate lower amounts of SARS-CoV-2 spike antibodies after mRNA vaccination than healthy controls. We assessed SARS-CoV-2 spike S1 receptor binding domain-specific (S1-RBD-specific) B lymphocytes to identify the underlying cellular defects. Patients with IBD produced fewer anti-S1-RBD antibody-secreting B cells than controls after the first mRNA vaccination and lower amounts of total and neutralizing antibodies after the second. S1-RBD-specific memory B cells were generated to the same degree in IBD and control groups and were numerically stable for 5 months. However, the memory B cells in patients with IBD had a lower S1-RBD-binding capacity than those in controls, which is indicative of a defect in antibody affinity maturation. Administration of a third shot to patients with IBD elevated serum antibodies and generated memory B cells with a normal antigen-binding capacity. These results show that patients with IBD have defects in the formation of antibody-secreting B cells and affinity-matured memory B cells that are corrected by a third vaccination.

Differential hydrogen sulfide production by a human cohort in response to animal- and plant-based diet interventions.

BACKGROUND: Hydrogen sulfide (H2S) is a toxic end-product of microbial fermentation produced in the colon that may play a role in the pathogenesis of several diseases, including ulcerative colitis and colon cancer. However, the effect of diet interventions on intestinal burden of H2S gas exposure remains poorly understood. OBJECTIVE: Determine the effect of short-term (1-week) plant- and animal-based eating patterns on ex vivo fecal H2S production in healthy human volunteers. METHODS: The study design was an open-label, cross-over diet study and diets were self-administered. Each participant consumed two interventional diets: 1) an animal-based, low fiber (i.e. western) diet and 2) a plant-based, high fiber diet, separated by a two-week washout period. Participants collected full stool samples at the end of each week, which were processed within 2 h of collection to capture H2S production. Microfluidic qPCR (MFQPCR) was used to simultaneously quantify multiple taxonomic and functional groups involved in sulfate reduction and the fecal microbiota was characterized through high-throughput DNA sequencing. RESULTS: Median H2S production was higher following the animal-based diet compared to the plant-based diet (p = 0.02; median difference 29 ppm/g, 95% CI 16-97). However, there was substantial individual variability and 2 of 11 individuals (18%) produced more H2S on the plant-based diet. Using the top and bottom quartiles of H2S percent change between animal- and plant-based diet weeks to define responders and non-responders, significant taxonomic differences were observed between the responder and non-responder cohorts. CONCLUSIONS: Here we report that substrate changes associated with a 1-week plant-based diet intervention resulted in lower ex vivo H2S production compared to a 1-week animal-based diet intervention in most healthy individuals. However, H2S responsiveness to diet was not uniform across the entire cohort, and potential H2S production enterotypes were characterized that may predict individualized H2S responsiveness to diet.

High-affinity memory B cells induced by SARS-CoV-2 infection produce more plasmablasts and atypical memory B cells than those primed by mRNA vaccines.

Although both infections and vaccines induce memory B cell (MBC) populations that participate in secondary immune responses, the MBCs generated in each case can differ. Here, we compare SARS-CoV-2 spike receptor binding domain (S1-RBD)-specific primary MBCs that form in response to infection or a single mRNA vaccination. Both primary MBC populations have similar frequencies in the blood and respond to a second S1-RBD exposure by rapidly producing plasmablasts with an abundant immunoglobulin (Ig)A+ subset and secondary MBCs that are mostly IgG+ and cross-react with the B.1.351 variant. However, infection-induced primary MBCs have better antigen-binding capacity and generate more plasmablasts and secondary MBCs of the classical and atypical subsets than do vaccine-induced primary MBCs. Our results suggest that infection-induced primary MBCs have undergone more affinity maturation than vaccine-induced primary MBCs and produce more robust secondary responses.

A Cas12a-based gene editing system for Phytophthora infestans reveals monoallelic expression of an elicitor.

Phytophthora infestans is a destructive pathogen of potato and a model for investigations of oomycete biology. The successful application of a CRISPR gene editing system to P. infestans is so far unreported. We discovered that it is difficult to express CRISPR/Cas9 but not a catalytically inactive form in transformants, suggesting that the active nuclease is toxic. We were able to achieve editing with CRISPR/Cas12a using vectors in which the nuclease and its guide RNA were expressed from a single transcript. Using the elicitor gene Inf1 as a target, we observed editing of one or both alleles in up to 13% of transformants. Editing was more efficient when guide RNA processing relied on the Cas12a direct repeat instead of ribozyme sequences. INF1 protein was not made when both alleles were edited in the same transformant, but surprisingly also when only one allele was altered. We discovered that the isolate used for editing, 1306, exhibited monoallelic expression of Inf1 due to insertion of a copia-like element in the promoter of one allele. The element exhibits features of active retrotransposons, including a target site duplication, long terminal repeats, and an intact polyprotein reading frame. Editing occurred more often on the transcribed allele, presumably due to differences in chromatin structure. The Cas12a system not only provides a tool for modifying genes in P. infestans, but also for other members of the genus by expanding the number of editable sites. Our work also highlights a natural mechanism that remodels oomycete genomes.

Methanogen Abundance Thresholds Capable of Differentiating In Vitro Methane Production in Human Stool Samples.

BACKGROUND: Intestinal methane (CH4) gas production has been associated with a number of clinical conditions and may have important metabolic and physiological effects. AIMS: In this study, taxonomic and functional gene analyses and in vitro CH4 gas measurements were used to determine if molecular markers can potentially serve as clinical tests for colonic CH4 production. METHODS: We performed a cross-sectional study involving full stool samples collected from 33 healthy individuals. In vitro CH4 gas measurements were obtained after 2-h incubation of stool samples and used to characterize samples as CH4 positive (CH4+) and CH4 negative (CH4-; n = 10 and 23, respectively). Next, we characterized the fecal microbiota through high-throughput DNA sequencing with a particular emphasis on archaeal phylum Euryarchaeota. Finally, qPCR analyses, targeting the mcrA gene, were done to determine the ability to differentiate CH4+ versus CH4- samples and to delineate major methanogen species associated with CH4 production. RESULTS: Methanobrevibacter was found to be the most abundant methane producer and its relative abundance provides a clear distinction between CH4+ versus CH4- samples. Its sequencing-based relative abundance detection threshold for CH4 production was calculated to be 0.097%. The qPCR-based detection threshold separating CH4+ versus CH4- samples, based on mcrA gene copies, was 5.2 × 105 copies/g. CONCLUSION: Given the decreased time-burden placed on patients, a qPCR-based test on a fecal sample can become a valuable tool in clinical assessment of CH4 producing status.

Metalaxyl Resistance in Phytophthora infestans: Assessing Role of RPA190 Gene and Diversity Within Clonal Lineages.

Prior work has shown that the inheritance of resistance to metalaxyl, an oomycete-specific fungicide, is complex and may involve multiple genes. Recent research indicated that a single nucleotide polymorphism (SNP) in the gene encoding RPA190, the largest subunit of RNA polymerase I, confers resistance to metalaxyl (or mefenoxam) in some isolates of the potato late blight pathogen Phytophthora infestans. Using both DNA sequencing and high resolution melt assays for distinguishing RPA190 alleles, we show here that the SNP is absent from certain resistant isolates of P. infestans from North America, Europe, and Mexico. The SNP is present in some members of the US-23 and US-24 clonal lineages, but these tend to be fairly sensitive to the fungicide based on artificial media and field test data. Diversity in the level of sensitivity, RPA190 genotype, and RPA190 copy number was observed in these lineages but were uncorrelated. Controlled laboratory crosses demonstrated that RPA190 did not cosegregate with metalaxyl resistance from a Mexican and British isolate. We conclude that while metalaxyl may be used to control many contemporary strains of P. infestans, an assay based on RPA190 will not be sufficient to diagnose the sensitivity levels of isolates.

Encapsulation of α-Particle-Emitting 225Ac3+ Ions Within Carbon Nanotubes.

UNLABELLED: (225)Ac(3+) is a generator of α-particle-emitting radionuclides with 4 net α-particle decays that can be used therapeutically. Targeting (225)Ac(3+) by use of ligands conjugated to traditional bifunctional chelates limits the amount of (225)Ac(3+) that can be delivered. Ultrashort, single-walled carbon nanotubes (US-tubes), previously demonstrated as sequestering agents of trivalent lanthanide ions and small molecules, also successfully incorporate (225)Ac(3+). METHODS: Aqueous loading of both (225)Ac(3+) ions and Gd(3+) ions via bath sonication was used to construct (225)Ac@gadonanotubes ((225)Ac@GNTs). The (225)Ac@GNTs were subsequently challenged with heat, time, and human serum. RESULTS: US-tubes internally loaded with both (225)Ac(3+) ions and Gd(3+) ions show 2 distinct populations of (225)Ac(3+) ions: one rapidly lost in human serum and one that remains bound to the US-tubes despite additional challenge with heat, time, and serum. The presence of the latter population depended on cosequestration of Gd(3+) and (225)Ac(3+) ions. CONCLUSION: US-tubes successfully sequester (225)Ac(3+) ions in the presence of Gd(3+) ions and retain them after a human serum challenge, rendering (225)Ac@GNTs candidates for radioimmunotherapy for delivery of (225)Ac(3+) ions at higher concentrations than is currently possible for traditional ligand carriers.

Stable confinement of positron emission tomography and magnetic resonance agents within carbon nanotubes for bimodal imaging.

AIMS: Simultaneous positron emission tomography/MRI has recently been introduced to the clinic and dual positron emission tomography/MRI probes are rare and of growing interest. We have developed a strategy for producing multimodal probes based on a carbon nanotube platform without the use of chelating ligands. MATERIALS & METHODS: Gd(3+) and (64)Cu(2+) ions were loaded into ultra-short single-walled carbon nanotubes by sonication. Normal, tumor-free athymic nude mice were injected intravenously with the probe and imaged over 48 h. RESULTS & CONCLUSION: The probe was stable for up to 24 h when challenged with phosphate-buffered saline and mouse serum. Positron emission tomography imaging also confirmed the stability of the probe in vivo for up to 48 h. The probe was quickly cleared from circulation, with enhanced accumulation in the lungs. Stable encapsulation of contrast agents within ultra-short single-walled carbon nanotubes represents a new strategy for the design of advanced imaging probes with variable multimodal imaging capabilities.

Encapsulated gadolinium and dysprosium ions within ultra-short carbon nanotubes for MR microscopy at 11.75 and 21.1 T.

Single-walled carbon nanotubes (SWNTs) have gained interest for their biocompatibility and multifunctional properties. Ultra-short SWNTs (US-tubes) have demonstrated high proton relaxivity when encapsulating gadolinium ions (Gd(3+)) at clinical field strengths. At higher field strengths, however, Gd(3+) ions demonstrate decreased proton relaxation properties while chemically similar dysprosium ions (Dy(3+)) improve relaxation properties. This report investigates the first use of Gd(3+) and Dy(3+) ions within US-tubes (GNTs and DNTs, respectively) at ultra-high magnetic field (21.1 T). Both agents are compared in solution and as an intracellular contrast agent labeling a murine microglia cell line (Bv2) immobilized in a tissue-mimicking agarose phantom using two high magnetic fields: 21.1 and 11.75 T. In solution at 21.1 T, results show excellent transverse relaxation; DNTs outperformed GNTs as a T(2) agent with measured r(2)/r(1) ratios of 247 and 47, respectively. Additionally, intracellular DNTs were shown to be a better T(2) agent than GNTs with higher contrast percentages and contrast-to-noise ratios. As such, this study demonstrates the potential of DNTs at high magnetic fields for cellular labeling and future in vivo, MRI-based cell tracking.

Pica in persons with developmental disabilities: approaches to treatment.

Pica is a very serious problem in which an individual ingests substances without nutrition value, such as paper and paint. As this behavior is often life-threatening resulting in surgery, pica has received attention from researchers for several decades. During that time, a number of interventions have been devised, such as behavioral methods (e.g., aversive stimuli, overcorrection, time-out, reinforcement) and biological interventions (e.g., pharmacotherapy, nutritional supplements). This paper is a broad review of the research on treatment studies for this problem, with a focus on persons with autism and/or intellectual disability (ID), which constitutes almost all of the published treatment papers. In addition, strengths and weaknesses of different pica treatments are discussed. Upon review, applied behavior analysis (ABA) was found to have the most robust empirical support to treat this behavior. Most clinicians are drifting away from aversive techniques and relying on more positive procedures to guide their treatment plans. The implications of current status and future directions for research are also addressed.

Scaling methods to measure psychopathology in persons with intellectual disabilities.

Psychopathology prior to the last four decades was generally viewed as a set of problems and disorders that did not occur in persons with intellectual disabilities (ID). That notion now seems very antiquated. In no small part, a revolutionary development of scales worldwide has occurred for the assessment of emotional problems in persons with ID. The first standardized test to emerge was the Psychopathology Instrument for Mentally Retarded Adults (PIMRA) in 1984. Since that time, an impressive number of measures of general psychopathology have emerged for adults and children as well as for persons across the full range of levels of ID. The purpose of this review was to provide a description of available measures, to review papers published on these measures, and to discuss emerging trends in test development. The trends in this body of information for enhancing differential diagnosis of psychopathology in persons with ID are discussed.

Comorbidity of physical and motor problems in children with autism.

Autism and the related pervasive developmental disorders are a heavily researched group of neurodevelopmental conditions. In addition to core symptoms, there are a number of other physical and motor conditions that co-occur at high rates. This paper provides a review of factors and behaviors that correlate highly with disorders on the autism spectrum. Among these conditions are premature birth, birth defects, gross and fine motor skills, and obesity. Each of these topics is addressed, and what researchers have found are presented. These data have important implications for the types of collateral behaviors that should be assessed and treated, along with the core symptoms of autism.

Nanotechnology and MRI contrast enhancement.

Technical advances in nanotechnology are creating novel classes of MRI contrast-enhancing agents. These nanomaterials offer much higher relaxivities than most current clinical contrast agents, which translates into greater MRI contrast enhancement. These nanoscale agents also have the potential to revolutionize in vivo applications of contrast-enhanced MRI since they offer the multiple advantages of low toxicities, extremely high relaxivities and cell internalization capabilities. In this review, we discuss three types of such contrast agents currently in use or under development for medical imaging: small particles of iron oxide, fullerenes encapsulating Gd(3+) ions (gadofullerenes) and single-walled carbon nanotube nanocapsules encapsulating Gd(3+) ion clusters (gadonanotubes). The latest developments and projected future applications of these nanotechnology-inspired contrast agents in the field of medical imaging are also discussed.

Social-skills treatments for children with autism spectrum disorders: an overview.

Marked advances in the treatment of children with autism spectrum disorders (ASDs) has occurred in the past few decades, primarily using applied behavior analysis. However, reviews of trends in social skills treatment for children with ASDs have been scant, despite a robust and growing empirical literature on the topic. In this selective review of 79 treatment studies, the authors note that the research has been particularly marked by fragmented development, using a range of intervention approaches and definitions of the construct. Modeling and reinforcement treatments have been the most popular model from the outset, with most studies conducted in school settings by teachers or psychologists. Investigators have been particularly attentive to issues of generalization and follow-up. However, large-scale group studies and comparisons of different training strategies are almost nonexistent. These trends and their implications for future research aimed at filling gaps in the existing literature are discussed.

Regional techniques as an adjunct to general anesthesia for pediatric extremity and spine surgery.

The purpose of this review is to evaluate the safety of regional anesthesia techniques performed for postoperative analgesia in anesthetized children. Pediatric regional anesthesia techniques, such as nerve blocks and neuraxial injections of either local anesthetics or narcotics, can potentially reduce postoperative pain for all children undergoing surgery. However, children may react differently to anesthesia than adults, and they usually cannot tolerate the administration of regional anesthesia unless they are under general anesthesia. During a 5-year period (1999-2004) at the Shriners Hospitals for Children Northern California, 2236 regional anesthetic procedures were performed in 1809 patients. All of the regional procedures were performed with patients under general anesthesia. Ninety-one percent (1641) of patients were for orthopaedic extremity or spine surgeries. Patients ranged from 2 months to 20 years old, with 65% (1169) between the ages of 6 months and 12 years. One thousand eleven procedures were lower extremity blocks, 646 were upper extremity blocks, and 579 were neuraxial injections. Four hundred fifty-four peripheral nerve blocks were performed in patients aged 3 years or younger. Two self-limiting complications possibly related to peripheral nerve blocks were noted. No complications were noted in patients who received neuraxial injections. This retrospective review indicates that regional anesthesia techniques performed 'under general anesthesia have a low rate of complications in children. A prospective trial is recommended to establish the efficacy and safety of this practice.

Classifying mental retardation and specific strength and deficit areas in severe and profoundly mentally retarded persons with the MESSIER.

The MESSIER, a measure of social and communication skills and the Vineland Social Maturity Scale were administered to 618 severe and profoundly mentally retarded adults. The goal of the study was to establish the potential utility of the MESSIER for classifying level of intellectual disability in this group. Comparing MESSIER scores to previously established DSM-IV-TR diagnosis, 86% of the severe and 80% of the profoundly mentally retarded persons were correctly classified. The implications of these data in using the MESSIER for classification and treatment planning are discussed.