Negative interactions determine Clostridioides difficile growth in synthetic human gut communities.

Understanding the principles of colonization resistance of the gut microbiome to the pathogen Clostridioides difficile will enable the design of defined bacterial therapeutics. We investigate the ecological principles of community resistance to C. difficile using a synthetic human gut microbiome. Using a dynamic computational model, we demonstrate that C. difficile receives the largest number and magnitude of incoming negative interactions. Our results show that C. difficile is in a unique class of species that display a strong negative dependence between growth and species richness. We identify molecular mechanisms of inhibition including acidification of the environment and competition over resources. We demonstrate that Clostridium hiranonis strongly inhibits C. difficile partially via resource competition. Increasing the initial density of C. difficile can increase its abundance in the assembled community, but community context determines the maximum achievable C. difficile abundance. Our work suggests that the C. difficile inhibitory potential of defined bacterial therapeutics can be optimized by designing communities featuring a combination of mechanisms including species richness, environment acidification, and resource competition.

Environmental Contamination of Contact Precaution and Non-Contact Precaution Patient Rooms in Six Acute Care Facilities.

BACKGROUND: Environmental contamination is an important source of hospital multidrug-resistant organism (MDRO) transmission. Factors such as patient MDRO contact precautions (CP) status, patient proximity to surfaces, and unit type likely influence MDRO contamination and bacterial bioburden levels on patient room surfaces. Identifying factors associated with environmental contamination in patient rooms and on shared unit surfaces could help identify important environmental MDRO transmission routes. METHODS: Surfaces were sampled from MDRO CP and non-CP rooms, nursing stations, and mobile equipment in acute care, intensive care, and transplant units within 6 acute care hospitals using a convenience sampling approach blinded to cleaning events. Precaution rooms had patients with clinical or surveillance tests positive for methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, carbapenem-resistant Enterobacteriaceae or Acinetobacter within the previous 6 months, or Clostridioides difficile toxin within the past 30 days. Rooms not meeting this definition were considered non-CP rooms. Samples were cultured for the above MDROs and total bioburden. RESULTS: Overall, an estimated 13% of rooms were contaminated with at least 1 MDRO. MDROs were detected more frequently in CP rooms (32% of 209 room-sample events) than non-CP rooms (12% of 234 room-sample events). Surface bioburden did not differ significantly between CP and non-CP rooms or MDRO-positive and MDRO-negative rooms. CONCLUSIONS: CP room surfaces are contaminated more frequently than non-CP room surfaces; however, contamination of non-CP room surfaces is not uncommon and may be an important reservoir for ongoing MDRO transmission. MDRO contamination of non-CP rooms may indicate asymptomatic patient MDRO carriage, inadequate terminal cleaning, or cross-contamination of room surfaces via healthcare personnel hands.

Dominant Mutations in GRM1 Cause Spinocerebellar Ataxia Type 44.

The metabotropic glutamate receptor 1 (mGluR1) is abundantly expressed in the mammalian central nervous system, where it regulates intracellular calcium homeostasis in response to excitatory signaling. Here, we describe heterozygous dominant mutations in GRM1, which encodes mGluR1, that are associated with distinct disease phenotypes: gain-of-function missense mutations, linked in two different families to adult-onset cerebellar ataxia, and a de novo truncation mutation resulting in a dominant-negative effect that is associated with juvenile-onset ataxia and intellectual disability. Crucially, the gain-of-function mutations could be pharmacologically modulated in vitro using an existing FDA-approved drug, Nitazoxanide, suggesting a possible avenue for treatment, which is currently unavailable for ataxias.

Laboratory Analysis Techniques for the Perinatal Microbiome: Implications for Studies of Probiotic Interventions.

The microbiome is composed of many organisms and is impacted by an intricate exchange between genetics and environmental factors. The perinatal microbiome influences both the developing fetus and the pregnant person. The purpose of this article is to describe the tests that are currently available for laboratory analysis of the perinatal microbiome in relationship to probiotic interventions. This article focuses on the bacterial component of the microbiome. Although adverse outcomes associated with the perinatal microbiome have been studied, a comprehensive understanding of the physiologic perinatal microbiome is still emerging. Early efforts to influence the perinatal microbiome through probiotics are currently under investigation. Unique terminology is defined, and the microbial composition of perinatal microbiota is summarized. The outcomes of studies of antenatal probiotics are summarized. Microbiome testing and analysis are defined and compared. Implications for perinatal care and probiotics research are presented.

Increased sensitivity of the circadian system to light in delayed sleep-wake phase disorder.

KEY POINTS: This is the first study to demonstrate an altered circadian phase shifting response in a circadian rhythm sleep disorder. Patients with delayed sleep-wake phase disorder (DSWPD) demonstrate greater sensitivity of the circadian system to the phase-delaying effects of light. Increased circadian sensitivity to light is associated with later circadian timing within both control and DSWPD groups. DSWPD patients had a greater sustained pupil response after light exposure. Treatments for DSWPD should consider sensitivity of the circadian system to light as a potential underlying vulnerability, making patients susceptible to relapse. ABSTRACT: Patients with delayed sleep-wake phase disorder (DSWPD) exhibit delayed sleep-wake behaviour relative to desired bedtime, often leading to chronic sleep restriction and daytime dysfunction. The majority of DSWPD patients also display delayed circadian timing in the melatonin rhythm. Hypersensitivity of the circadian system to phase-delaying light is a plausible physiological basis for DSWPD vulnerability. We compared the phase shifting response to a 6.5 h light exposure (∼150 lux) between male patients with diagnosed DSWPD (n = 10; aged 20.8 ± 2.3 years) and male healthy controls (n = 11; aged 22.4 ± 3.3 years). Salivary dim light melatonin onset (DLMO) was measured under controlled conditions in dim light (<3 lux) before and after light exposure. Correcting for the circadian time of the light exposure, DSWPD patients exhibited 31.5% greater phase delay shifts than healthy controls. In both groups, a later initial melatonin phase was associated with a greater magnitude phase shift, indicating that increased circadian sensitivity to light may be a factor that contributes to delayed phase, even in non-clinical groups. DSWPD patients also had reduced pupil size following the light exposure, and showed a trend towards increased melatonin suppression during light exposure. These findings indicate that, for patients with DSWPD, assessment of light sensitivity may be an important factor that can inform behavioural therapy, including minimization of exposure to phase-delaying night-time light.

A Simplified Method for Generating Purkinje Cells from Human-Induced Pluripotent Stem Cells.

The establishment of a reliable model for the study of Purkinje cells in vitro is of particular importance, given their central role in cerebellar function and pathology. Recent advances in induced pluripotent stem cell (iPSC) technology offer the opportunity to generate multiple neuronal subtypes for study in vitro. However, to date, only a handful of studies have generated Purkinje cells from human pluripotent stem cells, with most of these protocols proving challenging to reproduce. Here, we describe a simplified method for the reproducible generation of Purkinje cells from human iPSCs. After 21 days of treatment with factors selected to mimic the self-inductive properties of the isthmic organiser-insulin, fibroblast growth factor 2 (FGF2), and the transforming growth factor ß (TGFß)-receptor blocker SB431542-hiPSCs could be induced to form En1-positive cerebellar progenitors at efficiencies of up to 90%. By day 35 of differentiation, subpopulations of cells representative of the two cerebellar germinal zones, the rhombic lip (Atoh1-positive) and ventricular zone (Ptf1a-positive), could be identified, with the latter giving rise to cells positive for Purkinje cell progenitor-specific markers, including Lhx5, Kirrel2, Olig2 and Skor2. Further maturation was observed following dissociation and co-culture of these cerebellar progenitors with mouse cerebellar cells, with 10% of human cells staining positive for the Purkinje cell marker calbindin by day 70 of differentiation. This protocol, which incorporates modifications designed to enhance cell survival and maturation and improve the ease of handling, should serve to make existing models more accessible, in order to enable future advances in the field.

Detecting early signs of deterioration and preventing hospitalizations in skilled nursing facilities using remote respiratory monitoring.

An increase in respiratory rate (RR) can be an early indicator of clinical deterioration, yet it remains an often-neglected vital sign. The most common way of measuring RR is by manually counting chest-wall movements, a time-consuming and error-prone process. Staffing and funding shortages, particularly in post-acute and long-term care, mean these RR measurements are often infrequent, potentially leading to missed diagnoses and preventable readmissions. Here we present a case series from skilled nursing facilities, highlighting how continuous respiratory monitoring using a contactless remote patient monitoring (RPM) system can support clinicians in initiating timely interventions, potentially reducing preventable hospitalizations, mortality, and associated financial implications.

Effectiveness and safety of manual therapy when compared with oral pain medications in patients with neck pain: a systematic review and meta-analysis.

BACKGROUND: This systematic review and meta-analysis seeks to investigate the effectiveness and safety of manual therapy (MT) interventions compared to oral pain medication in the management of neck pain. METHODS: We searched from inception to March 2023, in Cochrane Central Register of Controller Trials (CENTRAL), MEDLINE, EMBASE, Allied and Complementary Medicine (AMED) and Cumulative Index to Nursing and Allied Health Literature (CINAHL; EBSCO) for randomized controlled trials that examined the effect of manual therapy interventions for neck pain when compared to medication in adults with self-reported neck pain, irrespective of radicular findings, specific cause, and associated cervicogenic headaches. We used the Cochrane Risk of Bias 2 tool to assess the potential risk of bias in the included studies, and the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) approach to grade the quality of the evidence. RESULTS: Nine trials (779 participants) were included in the meta-analysis. We found low certainty of evidence that MT interventions may be more effective than oral pain medication in pain reduction in the short-term (Standardized Mean Difference: -0.39; 95% CI -0.66 to -0.11; 8 trials, 676 participants), and moderate certainty of evidence that MT interventions may be more effective than oral pain medication in pain reduction in the long-term (Standardized Mean Difference: - 0.36; 95% CI - 0.55 to - 0.17; 6 trials, 567 participants). We found low certainty evidence that the risk of adverse events may be lower for patients that received MT compared to the ones that received oral pain medication (Risk Ratio: 0.59; 95% CI 0.43 to 0.79; 5 trials, 426 participants). CONCLUSIONS: MT may be more effective for people with neck pain in both short and long-term with a better safety profile regarding adverse events when compared to patients receiving oral pain medications. However, we advise caution when interpreting our safety results due to the different level of reporting strategies in place for MT and medication-induced adverse events. Future MT trials should create and adhere to strict reporting strategies with regards to adverse events to help gain a better understanding on the nature of potential MT-induced adverse events and to ensure patient safety. TRIAL REGISTRATION: PROSPERO registration number: CRD42023421147.

Quality improvement study on the effectiveness of intranasal povidone-iodine decolonization on surgery patients.

Background: Surgical site infection prevention and treatment remains a challenge in healthcare settings globally. The routine use of intranasal mupirocin for decolonization has challenges and preoperative intranasal povidone-iodine decolonization is another option. The purpose of this quality improvement study was to assess if a one-time preoperative intranasal povidone-iodine application could reduce the risk of the likelihood of nasal carriage of Staphylococcus aureus after surgery. Methods: Ambulatory Surgery Center patients were enrolled in an intranasal povidone-iodine decolonization quality improvement study as they reported at the pre-operative holding area. Pre-decolonization intranasal samples were collected, followed by intranasal application of povidone-iodine. Patients waited for a minimum of 20 minutes after application before proceeding with surgery. Nasal samples were again collected after surgery. Each sample was tested for S. aureus colonization using the 16S rRNA-mecA-nuc triplex polymerase chain reaction, standard biochemical tests, and qualitative culturing. Findings: In the 98 patients enrolled, 36% of these patients had intranasal colonization with S. aureus by 16S rRNA-mecA-nuc triplex polymerase chain reaction before surgery. Using a qualitative culture technique, 28% of patients tested positive for S. aureus before surgery and 20% of patients tested positive for S. aureus after surgery (P = 0.039). Conclusion: Intranasal preoperative povidone-iodine is an effective strategy in the decolonization of S. aureus from the nares if properly implemented.

RNA therapy for polyglutamine neurodegenerative diseases.

Polyglutamine neurodegenerative diseases result from the expansion of a trinucleotide CAG repeat, encoding a polyglutamine tract in the disease-causing protein. The process by which each polyglutamine protein exerts its toxicity is complex, involving a variety of mechanisms including transcriptional dysregulation, proteasome impairment and mitochondrial dysfunction. Thus, the most effective and widely applicable therapies are likely to be those designed to eliminate production of the mutant protein upstream of these deleterious effects. RNA-based approaches represent promising therapeutic strategies for polyglutamine diseases, offering the potential to suppress gene expression in a sequence-specific manner at the transcriptional and post-transcriptional levels. In particular, gene silencing therapies capable of discrimination between mutant and wildtype alleles, based on disease-linked polymorphisms or CAG repeat length, might prove crucial in cases where a loss of wild type function is deleterious. Novel methods, such as gene knockdown and replacement, seek to eliminate the technical difficulties associated with allele-specific silencing by avoiding the need to target specific mutations. With a variety of RNA technologies currently being developed to target multiple facets of polyglutamine pathogenesis, the emergence of an effective therapy seems imminent. However, numerous technical obstacles associated with design, discrimination and delivery must be overcome before RNA therapy can be effectively applied in the clinical setting.

Probiotic interventions to reduce antepartum Group B streptococcus colonization: A systematic review and meta-analysis.

OBJECTIVE: To systematically review and meta-analyse studies of the efficacy of probiotics to reduce antenatal Group B Streptococcus (GBS) colonisation. PARTICIPANTS: Antenatal participants with known positive GBS colonisation or unknown GBS status. INTERVENTION: Probiotic interventions containing species of Lactobacillus or Streptococcus. DESIGN: Systematic review and meta-analysis. MEASUREMENTS AND FINDINGS: The systematic review included 10 studies. Five articles contained in vitro studies of probiotic interventions to determine antagonistic activity against GBS. Six clinical trials of probiotics to reduce antenatal GBS were systematically reviewed and meta-analysed. The meta-analysis revealed that the use of an antenatal probiotic decreased the probability of a positive GBS result by 44% (OR = 0.56, 95% CI = 8.7%, 194.1%, p = 0.02) (n = 709). However, only one clinical trial of 10 had a low risk of bias. KEY CONCLUSIONS: The probiotic interventions subjected to in vitro testing showed antagonistic activity against GBS through the mechanisms of acidification, immune modulation, and adhesion. The findings of the meta-analysis of the clinical trials revealed that probiotics are a moderately effective intervention to reduce antenatal GBS colonisation. More well-controlled trials with diverse participants and with better elucidation of variables influencing GBS colonisation rates are needed. IMPLICATIONS FOR PRACTICE: Probiotic interventions appear to be a safe and effective primary prevention strategy for antenatal GBS colonisation. Application of this low-risk intervention needs more study but may reduce the need for intrapartum antibiotic prophylaxis in countries or regions where antenatal GBS screening is used. Midwives can be instrumental in conducting and supporting larger well-controlled clinical trials.

A quality improvement study on the relationship between intranasal povidone-iodine and anesthesia and the nasal microbiota of surgery patients.

INTRODUCTION: The composition of the nasal microbiota in surgical patients in the context of general anesthesia and nasal povidone-iodine decolonization is unknown. The purpose of this quality improvement study was to determine: (i) if general anesthesia is associated with changes in the nasal microbiota of surgery patients and (ii) if preoperative intranasal povidone-iodine decolonization is associated with changes in the nasal microbiota of surgery patients. MATERIALS AND METHODS: One hundred and fifty-one ambulatory patients presenting for surgery were enrolled in a quality improvement study by convenience sampling. Pre- and post-surgery nasal samples were collected from patients in the no intranasal decolonization group (control group, n = 54). Pre-decolonization nasal samples were collected from the preoperative intranasal povidone-iodine decolonization group (povidone-iodine group, n = 97). Intranasal povidone-iodine was administered immediately prior to surgery and continued for 20 minutes before patients proceeded for surgery. Post-nasal samples were then collected. General anesthesia was administered to both groups. DNA from the samples was extracted for 16S rRNA sequencing on an Illumina MiSeq. RESULTS: In the control group, there was no evidence of change in bacterial diversity between pre- and post-surgery samples. In the povidone-iodine group, nasal bacterial diversity was greater in post-surgery, relative to pre-surgery (Shannon's Diversity Index (P = 0.038), Chao's richness estimate (P = 0.02) and Inverse Simpson index (P = 0.027). Among all the genera, only the relative abundance of the genus Staphylococcus trended towards a decrease in patients after application (FDR adjusted P = 0.06). Abundant genera common to both povidone-iodine and control groups included Staphylococcus, Bradyrhizobium, Corynebacterium, Dolosigranulum, Lactobacillus, and Moraxella. CONCLUSIONS: We found general anesthesia was not associated with changes in the nasal microbiota. Povidone-iodine treatment was associated with nasal microbial diversity and decreased abundance of Staphylococcus. Future studies should examine the nasal microbiota structure and function longitudinally in surgical patients receiving intranasal povidone-iodine.

Examining the association between the gastrointestinal microbiota and Gulf War illness: A prospective cohort study.

Gulf War Illness (GWI) affects 25-35% of the 1991 Gulf War Veteran (GWV) population. Patients with GWI experience pain, fatigue, cognitive impairments, gastrointestinal dysfunction, skin disorders, and respiratory issues. In longitudinal studies, many patients with GWI have shown little to no improvement in symptoms since diagnosis. The gut microbiome and diet play an important role in human health and disease, and preliminary studies suggest it may play a role in GWI. To examine the relationship between the gut microbiota, diet, and GWI, we conducted an eight-week prospective cohort study collecting stool samples, medications, health history, and dietary data. Sixty-nine participants were enrolled into the study, 36 of which met the case definition for GWI. The gut microbiota of participants, determined by 16S rRNA sequencing of stool samples, was stable over the duration of the study and showed no within person (alpha diversity) differences. Between group analyses (beta diversity) identified statistically significant different between those with and without GWI. Several taxonomic lineages were identified as differentially abundant between those with and without GWI (n = 9) including a greater abundance of Lachnospiraceae and Ruminococcaceae in those without GWI. Additionally, there were taxonomic differences between those with high and low healthy eating index (HEI) scores including a greater abundance of Ruminococcaceae in those with higher HEI scores. This longitudinal cohort study of GWVs found that participants with GWI had significantly different microbiomes from those without GWI. Further studies are needed to determine the role these differences may play in the development and treatment of GWI.

Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis.

INTRODUCTION: The recovery of other pathogens in patients with SARS-CoV-2 infection has been reported, either at the time of a SARS-CoV-2 infection diagnosis (co-infection) or subsequently (superinfection). However, data on the prevalence, microbiology, and outcomes of co-infection and superinfection are limited. The purpose of this study was to examine the occurrence of co-infections and superinfections and their outcomes among patients with SARS-CoV-2 infection. PATIENTS AND METHODS: We searched literature databases for studies published from October 1, 2019, through February 8, 2021. We included studies that reported clinical features and outcomes of co-infection or superinfection of SARS-CoV-2 and other pathogens in hospitalized and non-hospitalized patients. We followed PRISMA guidelines, and we registered the protocol with PROSPERO as: CRD42020189763. RESULTS: Of 6639 articles screened, 118 were included in the random effects meta-analysis. The pooled prevalence of co-infection was 19% (95% confidence interval [CI]: 14%-25%, I2 = 98%) and that of superinfection was 24% (95% CI: 19%-30%). Pooled prevalence of pathogen type stratified by co- or superinfection were: viral co-infections, 10% (95% CI: 6%-14%); viral superinfections, 4% (95% CI: 0%-10%); bacterial co-infections, 8% (95% CI: 5%-11%); bacterial superinfections, 20% (95% CI: 13%-28%); fungal co-infections, 4% (95% CI: 2%-7%); and fungal superinfections, 8% (95% CI: 4%-13%). Patients with a co-infection or superinfection had higher odds of dying than those who only had SARS-CoV-2 infection (odds ratio = 3.31, 95% CI: 1.82-5.99). Compared to those with co-infections, patients with superinfections had a higher prevalence of mechanical ventilation (45% [95% CI: 33%-58%] vs. 10% [95% CI: 5%-16%]), but patients with co-infections had a greater average length of hospital stay than those with superinfections (mean = 29.0 days, standard deviation [SD] = 6.7 vs. mean = 16 days, SD = 6.2, respectively). CONCLUSIONS: Our study showed that as many as 19% of patients with COVID-19 have co-infections and 24% have superinfections. The presence of either co-infection or superinfection was associated with poor outcomes, including increased mortality. Our findings support the need for diagnostic testing to identify and treat co-occurring respiratory infections among patients with SARS-CoV-2 infection.

Molecular and electrophysiological features of spinocerebellar ataxia type seven in induced pluripotent stem cells.

Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disease caused by a polyglutamine repeat expansion in the ATXN7 gene. Patients with this disease suffer from a degeneration of their cerebellar Purkinje neurons and retinal photoreceptors that result in a progressive ataxia and loss of vision. As with many neurodegenerative diseases, studies of pathogenesis have been hindered by a lack of disease-relevant models. To this end, we have generated induced pluripotent stem cells (iPSCs) from a cohort of SCA7 patients in South Africa. First, we differentiated the SCA7 affected iPSCs into neurons which showed evidence of a transcriptional phenotype affecting components of STAGA (ATXN7 and KAT2A) and the heat shock protein pathway (DNAJA1 and HSP70). We then performed electrophysiology on the SCA7 iPSC-derived neurons and found that these cells show features of functional aberrations. Lastly, we were able to differentiate the SCA7 iPSCs into retinal photoreceptors that also showed similar transcriptional aberrations to the SCA7 neurons. Our findings give technical insights on how iPSC-derived neurons and photoreceptors can be derived from SCA7 patients and demonstrate that these cells express molecular and electrophysiological differences that may be indicative of impaired neuronal health. We hope that these findings will contribute towards the ongoing efforts to establish the cell-derived models of neurodegenerative diseases that are needed to develop patient-specific treatments.

Sleep and circadian instability in delayed sleep-wake phase disorder.

STUDY OBJECTIVES: In patients with delayed sleep-wake phase disorder (DSWPD), the circadian clock may be more easily affected by light at night. This creates a potential vulnerability, whereby individuals with irregular schedules may have less stable circadian rhythms. We investigated the stability of circadian timing and regularity of sleep in patients with DSWPD and healthy controls. METHODS: Participants completed 2 dim-light melatonin onset (DLMO) assessments approximately 2 weeks apart while keeping their habitual sleep/wake schedule. After the second DLMO assessment, light sensitivity was assessed using the phase-resetting response to a 6.5-hour 150-lux stimulus. The change in DLMO timing (DLMO instability) was assessed and related to light sensitivity and the sleep regularity index. RESULTS: Relative to healthy controls, patients with DSWPD had later sleep rhythm timing relative to clock time, earlier sleep rhythm timing relative to DLMO, lower sleep regularity index, and greater DLMO instability. Greater DLMO instability was associated with increased light sensitivity across all participants, but not within groups. CONCLUSIONS: We find that circadian timing is less stable and sleep is less regular in patients with DSWPD, which could contribute to etiology of the disorder. Measures of light sensitivity may be informative in generating DSWPD treatment plans.

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota.

The human gut microbiome has a great deal of interpersonal variation due to both endogenous and exogenous factors, like household pet exposure. To examine the relationship between having a pet in the home and the composition and diversity of the adult gut microbiome, we conducted a case-control study nested in a larger, statewide study, the Survey of the Health of Wisconsin. Stool samples were collected from 332 participants from unique households and analyzed using 16S rRNA sequencing on the Illumina MiSeq. One hundred and seventy-eight participants had some type of pet in the home with dogs and cats being the most prevalent. We observed no difference in alpha and beta diversity between those with and without pets, though seven OTUs were significantly more abundant in those without pets compared to those with pets, and four were significantly more abundant in those with pets. When stratifying by age, seven of these remained significant. These results suggest that pet ownership is associated with differences in the human gut microbiota. Further research is needed to better characterize the effect of pet ownership on the human gut microbiome.