Genome sequences of Clostridium perfringens isolated from diseased dogs.

Two Clostridium perfringens isolates originating from two Norwegian dogs with acute hemorrhagic diarrhea were sequenced. Based on Illumina and Oxford Nanopore Technology sequencing, hybrid assemblies were generated, and one of the genomes was completed and closed. For both isolates, virulence genes and their genomic location have been identified.

Network-based integrative multi-omics approach reveals biosignatures specific to COVID-19 disease phases.

Background: COVID-19 disease is characterized by a spectrum of disease phases (mild, moderate, and severe). Each disease phase is marked by changes in omics profiles with corresponding changes in the expression of features (biosignatures). However, integrative analysis of multiple omics data from different experiments across studies to investigate biosignatures at various disease phases is limited. Exploring an integrative multi-omics profile analysis through a network approach could be used to determine biosignatures associated with specific disease phases and enable the examination of the relationships between the biosignatures. Aim: To identify and characterize biosignatures underlying various COVID-19 disease phases in an integrative multi-omics data analysis. Method: We leveraged a multi-omics network-based approach to integrate transcriptomics, metabolomics, proteomics, and lipidomics data. The World Health Organization Ordinal Scale WHO Ordinal Scale was used as a disease severity reference to harmonize COVID-19 patient metadata across two studies with independent data. A unified COVID-19 knowledge graph was constructed by assembling a disease-specific interactome from the literature and databases. Disease-state specific omics-graphs were constructed by integrating multi-omics data with the unified COVID-19 knowledge graph. We expanded on the network layers of multiXrank, a random walk with restart on multilayer network algorithm, to explore disease state omics-specific graphs and perform enrichment analysis. Results: Network analysis revealed the biosignatures involved in inducing chemokines and inflammatory responses as hubs in the severe and moderate disease phases. We observed distinct biosignatures between severe and moderate disease phases as compared to mild-moderate and mild-severe disease phases. Mild COVID-19 cases were characterized by a unique biosignature comprising C-C Motif Chemokine Ligand 4 (CCL4), and Interferon Regulatory Factor 1 (IRF1). Hepatocyte Growth Factor (HGF), Matrix Metallopeptidase 12 (MMP12), Interleukin 10 (IL10), Nuclear Factor Kappa B Subunit 1 (NFKB1), and suberoylcarnitine form hubs in the omics network that characterizes the moderate disease state. The severe cases were marked by biosignatures such as Signal Transducer and Activator of Transcription 1 (STAT1), Superoxide Dismutase 2 (SOD2), HGF, taurine, lysophosphatidylcholine, diacylglycerol, triglycerides, and sphingomyelin that characterize the disease state. Conclusion: This study identified both biosignatures of different omics types enriched in disease-related pathways and their associated interactions (such as protein-protein, protein-transcript, protein-metabolite, transcript-metabolite, and lipid-lipid interactions) that are unique to mild, moderate, and severe COVID-19 disease states. These biosignatures include molecular features that underlie the observed clinical heterogeneity of COVID-19 and emphasize the need for disease-phase-specific treatment strategies. The approach implemented here can be used to find associations between transcripts, proteins, lipids, and metabolites in other diseases.

Medicaid Policy Change and Immediate Postpartum Long-Acting Reversible Contraception.

Importance: Improving access to the choice of postpartum contraceptive methods is a national public health priority, and the need is particularly acute within the Medicaid population. One strategy to ensure individuals have access to the full range of contraceptive methods is the provision of a method prior to hospital discharge following a birth episode. Beginning in 2016, some states changed their Medicaid billing policy, allowing separate reimbursement for intrauterine devices and contraceptive implants to increase the provision of long-acting reversible contraceptive (LARC) methods immediately postpartum (IPP). Objective: To assess the association of a change in Medicaid billing policy with use of IPP LARC. Design, Setting, and Participants: The cohort study of postpartum Medicaid recipients in 9 treatment and 6 comparison states was conducted from January 2016 to October 2019. Data were analyzed from August 2023 to January 2024. Main Outcomes and Measures: The primary outcome was use of IPP LARC. Results: The final sample included 1 378 885 delivery encounters for 1 197 287 Medicaid enrollees occurring in 15 states. Mean age of beneficiaries at delivery was 27 years. The IPP LARC billing policy was associated with a mean increase of 0.74 percentage points (95% CI, 0.30-1.18 percentage points) in the immediate receipt of IPP LARC, with a prepolicy baseline rate of 0.54%. The IPP LARC billing policy was also associated with an overall increase of 1.48 percentage points (95% CI, 0.43-2.73 percentage points) in LARC use by 60 days post partum. Conclusions and Relevance: In this cohort study, changing Medicaid billing policy to allow for separate reimbursement of LARC devices from the global fee was associated with increased use of IPP LARC, suggesting that this may be a strategy to improve access to the full range of postpartum contraceptive methods.

Decomposition analysis of racial and ethnic differences in receipt of immediate postpartum, long-acting, reversible, and permanent contraception.

OBJECTIVES: This study aimed to determine the factors contributing to racial and ethnic disparities in the use of immediate postpartum, long-acting reversible contraception (IPP LARC) and permanent contraception among Medicaid recipients. STUDY DESIGN: We conducted a cross-sectional study using 3 years of national Medicaid claims data to examine the rates of IPP LARC use alone and a composite measure of postpartum permanent contraception and IPP LARC within 7 days of delivery by race and ethnicity. We used a Blinder-Oaxaca model to quantify the extent to which medical complexity, age, rurality, mode of delivery, and year explained differences in outcomes among different minoritized groups in comparison to non-Hispanic White women. RESULTS: Our study sample contained 1,729,663 deliveries occurring from 2016 through 2018 among 1,605,199 people living in 16 states. IPP LARC use rates were highest among Black (2.2%), followed by American Indian and Alaska Native at 2.1% and Hawaiian/Pacific Islander beneficiaries at 1.9%, Hispanic (all races) at 1.2%, and Asian at 1.0%. IPP LARC was lowest among White beneficiaries (0.8%). Medical complexity, age, rurality, year, and mode of delivery explained only 12.3% of the difference in IPP LARC rates between Black and White beneficiaries. Postpartum permanent contraception was highest among White (7.6%), Hispanic (7.2%), and American Indian and Alaska Native (6.8%), followed by Black (6.3%), Hawaiian/Pacific Islander (5.1%) and lowest among Asian women (4.1%). When we examined the use of IPP LARC or postpartum permanent contraception together, these same factors explained 94.4% of the differences between Black and White beneficiaries. CONCLUSIONS: While differences in the use of IPP LARC by race and ethnicity were identified, our findings suggest that overall use of inpatient highly effective contraception are similar across racial and ethnic groups. IMPLICATIONS: When IPP LARC and postpartum permanent contraception are examined jointly, their use is similar across racial and ethnic groups.

Defining a metagenomic threshold for detecting low abundances of Providencia alcalifaciens in canine faecal samples.

Introduction: Acute haemorrhagic diarrhoea syndrome (AHDS) in dogs is a condition of unknown aetiology. Providencia alcalifaciens is suspected to play a role in the disease as it was commonly found in dogs suffering from AHDS during a Norwegian outbreak in 2019. The role of this bacterium as a constituent of the canine gut microbiota is unknown, hence this study set out to investigate its occurrence in healthy dogs using metagenomics. Materials and methods: To decrease the likelihood of false detection, we established a metagenomic threshold for P. alcalifaciens by spiking culture-negative stool samples with a range of bacterial dilutions and analysing these by qPCR and shotgun metagenomics. The detection limit for P. alcalifaciens was determined and used to establish a metagenomic threshold. The threshold was validated on naturally contaminated faecal samples with known cultivation status for P. alcalifaciens. Finally, the metagenomic threshold was used to determine the occurrence of P. alcalifaciens in shotgun metagenomic datasets from canine faecal samples (n=362) collected in the HUNT One Health project. Results: The metagenomic assay and qPCR had a detection limit of 1.1x103 CFU P. alcalifaciens per faecal sample, which corresponded to a Cq value of 31.4 and 569 unique k-mer counts by shotgun metagenomics. Applying this metagenomic threshold to 362 faecal metagenomic datasets from healthy dogs, P. alcalifaciens was found in only 1.1% (95% CI [0.0, 6.8]) of the samples, and then in low relative abundances (median: 0.04%; range: 0.00 to 0.81%). The sensitivity of the qPCR and shotgun metagenomics assay was low, as only 40% of culture-positive samples were also positive by qPCR and metagenomics. Discussion: Using our detection limit, the occurrence of P. alcalifaciens in faecal samples from healthy dogs was low. Given the low sensitivity of the metagenomic assay, these results do not rule out a significantly higher occurrence of this bacterium at a lower abundance.

Detection of Klebsiella pneumoniae in healthy poultry: Insights and perspectives from culturing and metagenomics.

Previously, Klebsiella pneumoniae was found to occur more frequently in healthy turkey flocks than in healthy broiler flocks in Norway. This study aimed to investigate whether this higher occurrence could be attributed to a greater abundance of K. pneumoniae in turkey flocks. We compared culturing, qPCR, and shotgun metagenomic sequencing for the detection and quantification of K. pneumoniae. Using qPCR, we found that 20.7% of broiler flock samples and 63.9% of turkey flock samples were positive for K. pneumoniae. Culturing revealed a significantly higher abundance of K. pneumoniae in turkey flocks compared to broiler flocks. However, metagenomic analysis showed no difference in the relative abundance of Klebsiella spp. between broiler and turkey flocks, and no correlation between the results of culturing and metagenomic quantification. Interestingly, the differential abundance of K. quasipneumoniae was significantly different between the two hosts. Our results indicate that Klebsiella spp. are present in both turkey and broiler flocks at relatively low levels but with a higher abundance in turkey flocks. Our findings also suggest that shotgun metagenomic studies targeting low-abundance taxa such as Klebsiella have poor sensitivity when comparing groups, indicating that reliance on results from metagenomic analysis without experimental validation should be done with caution.

Effect of protective coating agents on microleakage and flexural strength of glass ionomer cement and zirconomer. an in vitro study.

PURPOSE: The objective of this study was to assess the microleakage and flexural strength of glass ionomer cement (GIC) and modified GIC (Zirconomer) when coated with protective coating agents such as COAT-IT and G-COAT plus. METHODS: Sixty tooth specimens were grouped into two groups based on the type of restorations (GIC (n = 30) and Zirconomer (n = 30)). The samples were further divided into three subgroups (n = 10) based on the protective coating agent (Petroleum jelly, G-COAT Plus, or COAT IT) applied. This study evaluated the microleakage at the occlusal and cervical margins of class V restoration after being subjected to dye penetration and sectioning. Each specimen was viewed under a 40 × microscope and was given scores based on the depth of dye penetration. They were statistically analyzed using the Kruskal-Wallis test and compared within the groups using the Mann- Whitney Test. In addition, flexural strength was assessed using standardized cuboid (25 × 2 × 2 mm) specimens of restorative materials with and without protective coating agents. The mean flexural strength data of all the subgroups were statistically evaluated using a one-way analysis of variance (ANOVA) and compared within the subgroups using the student t test. RESULTS: A statistically significant difference was found when occlusal margin microleakage scores were evaluated with G-COAT Plus demonstrating the lowest occlusal margin microleakage when applied over GIC restoration. The increasing order of occlusal margin microleakage scores is as follows: GIC with G-COAT Plus, Zirconomer with COAT-IT, GIC with COAT-IT, GIC, Zirconomer with G-COAT Plus, and Zirconomer. However, the cervical margin microleakage scores revealed no significant difference. While flexural strength was found to be highest for the GIC group coated with G-COAT Plus, it was observed that there was a significant improvement in the flexural strength of both GIC and Zirconomer when coated with either of the protective coating agents. CONCLUSION: Within the limitations of this in vitro study, it was observed that the application of protective coating agents can significantly reduce the potential microleakage and improve the flexural strength of the restorative material especially when zirconia-reinforced GIC is the restorative material.

The association of federal Medicaid abortion funding restrictions with adverse obstetric outcomes among United States Medicaid recipients.

OBJECTIVE: We examine the association of the Hyde Amendment with obstetrical outcomes in a national Medicaid population. STUDY DESIGN: We conducted a national study of Medicaid-funded abortions to determine the association of restrictions on adolescent, preterm, low-birth weight, and short interpregnancy interval births using administrative data. RESULTS: States that restricted coverage for abortion had a higher median rate of adolescent (10.2%; vs 7.4%; p-value < 0.001), preterm (11.4%; vs 10.1%; p < 0.001), short interpregnancy interval, (13.0% vs 9.6%; p < 0.001), and low birth weight births (10.2% vs 8.7%; p = 0.003) than states where Medicaid provided comprehensive coverage. CONCLUSIONS: Restricting federal funds for abortion is associated with adverse outcomes. IMPLICATIONS: When Medicaid does not provide comprehensive coverage for abortion care, few abortions are provided and higher rates of adverse obstetrical outcomes are noted.

The gut microbiota composition has no predictive value for the endotoxin-induced immune response or development of endotoxin tolerance in humans invivo.

BACKGROUND: It is largely unknown whether the gut microbiome regulates immune responses in humans. We determined relationships between the microbiota composition and immunological phenotypes in 108 healthy volunteers, using 16S sequencing, an ex vivo monocyte challenge model, and an in vivo challenge model of systemic inflammation induced by lipopolysaccharide (LPS). RESULTS: Significant associations were observed between the microbiota composition and ex vivo monocytic cytokine responses induced by several stimuli, most notably IL-10 production induced by Pam3Cys, Pseudomonas aeruginosa and Candida albicans, although the explained variance was rather low (0.3-4.8%). Furthermore, a number of pairwise correlations between Blautia, Bacteroides and Prevotella genera and cytokine production induced by these stimuli were identified. LPS administration induced a profound transient in vivo inflammatory response. A second LPS challenge one week after the first resulted in a severely blunted response, reflecting endotoxin tolerance. However, no significant relationships between microbiota composition and in vivo parameters of inflammation or tolerance were found (explained variance ranging from 0.4 to 1.5%, ns). CONCLUSIONS: The gut microbiota composition explains a limited degree of variance in ex vivo monocytic cytokine responses to several pathogenic stimuli, but no relationships with the LPS-induced in vivo immune response or tolerance was observed.

Metabolic effects of early life stress and pre-pregnancy obesity are long lasting and sex specific in mice.

Early life stress (ELS) is associated with metabolic, cognitive, and psychiatric diseases and has a very high prevalence, highlighting the urgent need for a better understanding of the versatile physiological changes and identification of predictive biomarkers. In addition to programming the hypothalamic-pituitary-adrenal (HPA) axis, ELS may also affect the gut microbiota and metabolome, opening up a promising research direction for identifying early biomarkers of ELS-induced (mal)adaptation. Other factors affecting these parameters include maternal metabolic status and diet, with maternal obesity shown to predispose offspring to later metabolic disease. The aim of the present study was to investigate the long-term effects of ELS and maternal obesity on the metabolic and stress phenotype of rodent offspring. To this end, offspring of both sexes were subjected to an adverse early-life experience, and their metabolic and stress phenotypes were examined. In addition, we assessed whether a prenatal maternal and an adult high-fat diet (HFD) stressor further shape observed ELS-induced phenotypes. We show that ELS has long-term effects on male body weight (BW) across the lifespan, whereas females more successfully counteract ELS-induced weight loss, possibly by adapting their microbiota, thereby stabilizing a balanced metabolome. Furthermore, the metabolic effects of a maternal HFD on BW are exclusively triggered by a dietary challenge in adult offspring and are more pronounced in males than in females. Overall, our study suggests that the female microbiota protects against an ELS challenge, rendering them more resilient to additional maternal- and adult nutritional stressors than males.

Gram-positive anaerobic cocci guard skin homeostasis by regulating host-defense mechanisms.

In atopic dermatitis (AD), chronic skin inflammation is associated with skin barrier defects and skin microbiome dysbiosis including a lower abundance of Gram-positive anaerobic cocci (GPACs). We here report that, through secreted soluble factors, GPAC rapidly and directly induced epidermal host-defense molecules in cultured human keratinocytes and indirectly via immune-cell activation and cytokines derived thereof. Host-derived antimicrobial peptides known to limit the growth of Staphylococcus aureus-a skin pathogen involved in AD pathology-were strongly upregulated by GPAC-induced signaling through aryl hydrocarbon receptor (AHR)-independent mechanisms, with a concomitant AHR-dependent induction of epidermal differentiation genes and control of pro-inflammatory gene expression in organotypic human epidermis. By these modes of operandi, GPAC may act as an "alarm signal" and protect the skin from pathogenic colonization and infection in the event of skin barrier disruption. Fostering growth or survival of GPAC may be starting point for microbiome-targeted therapeutics in AD.

Geographic Variation In Effective Contraceptive Use Among Medicaid Recipients In 2018.

Medicaid is the largest payer for publicly funded contraception, serving millions of women across the United States. However, relatively little is known about the extent to which effective contraceptive services vary geographically for Medicaid recipients. This study used national Medicaid claims to assess county-level variation in rates of provision of the most or moderately effective methods of contraception and provision of long-acting reversible contraception (LARC) across forty states and Washington, D.C., in 2018. County-level rates of most or moderately effective contraceptive use varied almost fourfold across states, from a low of 10.8 percent to a high of 44.4 percent. Rates of LARC provision varied almost tenfold, from a low of 1.0 percent to a high of 9.6 percent. Despite the fact that contraception is a core benefit within Medicaid, access and use vary substantially across and within states. Medicaid agencies have a variety of options to ensure that people have access to a choice of the full range of contraceptive methods, including removing or loosening utilization controls, incorporating quality metrics or value-based payments into contraceptive services, and adjusting reimbursement to remove barriers to the clinical provision of LARC.

CYSRT1: An Antimicrobial Epidermal Protein that Can Interact with Late Cornified Envelope Proteins.

Late cornified envelope (LCE) proteins are small cationic epidermal proteins with antimicrobial properties, and the combined deletion of LCE3B and LCE3C genes is a risk factor for psoriasis that affects skin microbiome composition. In a yeast two-hybrid screen, we identified CYSRT1 as an interacting partner of members of all LCE groups except LCE6. These interactions were confirmed in a mammalian cell system by coimmunoprecipitation. CYSRT1 is a protein of unknown function that is specifically expressed in cutaneous and oral epithelia and spatially colocalizes with LCE proteins in the upper layers of the suprabasal epidermis. Constitutive CYSRT1 expression is present in fully differentiated epidermis and can be further induced in vivo by disruption of the skin barrier upon stratum corneum removal. Transcriptional regulation correlates to keratinocyte terminal differentiation but not to skin bacteria exposure. Similar to LCEs, CYSRT1 was found to have antibacterial activity against Pseudomonas aeruginosa. Comparative gene sequence analysis and protein amino acid alignment indicate that CYSRT1 is highly conserved among vertebrates and has putative antimicrobial activity. To summarize, we identified CYSRT1 in the outer skin layer, where it colocalizes with LCE proteins and contributes to the constitutive epidermal antimicrobial host defense repertoire.

Computational approaches for network-based integrative multi-omics analysis.

Advances in omics technologies allow for holistic studies into biological systems. These studies rely on integrative data analysis techniques to obtain a comprehensive view of the dynamics of cellular processes, and molecular mechanisms. Network-based integrative approaches have revolutionized multi-omics analysis by providing the framework to represent interactions between multiple different omics-layers in a graph, which may faithfully reflect the molecular wiring in a cell. Here we review network-based multi-omics/multi-modal integrative analytical approaches. We classify these approaches according to the type of omics data supported, the methods and/or algorithms implemented, their node and/or edge weighting components, and their ability to identify key nodes and subnetworks. We show how these approaches can be used to identify biomarkers, disease subtypes, crosstalk, causality, and molecular drivers of physiological and pathological mechanisms. We provide insight into the most appropriate methods and tools for research questions as showcased around the aetiology and treatment of COVID-19 that can be informed by multi-omics data integration. We conclude with an overview of challenges associated with multi-omics network-based analysis, such as reproducibility, heterogeneity, (biological) interpretability of the results, and we highlight some future directions for network-based integration.

Hospital Characteristics Associated With Heterogeneity in Institutional Postacute Care Spending Reductions Under the Comprehensive Care for Joint Replacement Model.

Importance: Prior research concluded that institutional postacute care spending decreased under the Comprehensive Care for Joint Replacement (CJR) model. Less is known about how changes in institutional postacute care spending varied across different types of hospitals. Objective: To measure hospital-level heterogeneity in the association of the CJR model with changes in institutional postacute care spending and to identify hospital characteristics associated with this variation. Design Setting and Participants: Using 100% Medicare claims data, this cross-sectional study assessed institutional postacute care spending from 2016 to 2017 among US hospitals randomly selected to participate in the CJR model and control group hospitals that were eligible but not selected for the participation in the CJR model. A causal forest was used to estimate the treatment effect of the CJR model conditional on hospital characteristics. Analysis was conducted between October 2019 and October 2021. Main Outcomes and Measures: The unit of analysis was each hospital; the outcome was the average per-episode Medicare spending for institutional postacute care within 90 days after hospital discharge for hip or knee joint replacement. Results: This study included 531 CJR participating hospitals and 658 control group hospitals from 2016 to 2017. The CJR model was associated with a $761 reduction in institutional postacute care spending (95% CI, -$1172 to -$351). The reduction in spending under the CJR model did not vary across conditional on hospital characteristics. Limited evidence was found for greater savings among hospitals with higher pre-CJR spending. However, this finding did not hold for hospitals in the highest quintile of pre-CJR spending. Conclusions and Relevance: In this cross-sectional study of 1189 hospitals, findings did not show strong evidence for significant heterogeneity in how the CJR model was associated with reductions in institutional postacute care spending across a range of hospital characteristics. Savings were not concentrated in hospitals with specific characteristics, such as hospitals with high-volume joint replacement or hospitals serving less medically or socially complex patients. Findings suggest that the CJR model created opportunities for savings across a spectrum of different hospitals.

Association of Medicare bundled payment model with joint replacement care for people with dementia.

BACKGROUND: We examined whether the Comprehensive Care for Joint Replacement (CJR) model was associated with changes in the receipt of joint replacement among people with Alzheimer's disease and related dementias (ADRD) as well as spending, health service use, and postsurgical outcomes among people with ADRD who underwent a joint replacement surgery. METHODS: Retrospective cohort study using 2013-2017 Medicare claims and Minimum Data Set. We used a difference-in-differences analysis to compare people with ADRD residing in CJR-participating treatment areas versus nonparticipating control areas on the receipt of joint replacement, episode spending during the index hospitalization and subsequent 90-day post-discharge period, discharges to an institutional post-acute care setting, and readmissions within 90 days of hospital discharge. RESULTS: Our sample included 3,361,950 Medicare enrollees with ADRD (2,156,995 women [64%]; mean [SD] age, 83 [8.0] years; 2,646,405 white [78%], 344,478 black [10%], 224,010 Hispanic [7%]). The receipt of replacement among people with ADRD changed similarly between CJR-participating treatment and control areas after CJR model was implemented, suggesting no association of CJR model with the receipt of replacement. Among people with ADRD who received joint replacement, the CJR model was associated with a $1029 decrease in spending per episode (95% confidence interval [CI] -$1577, -$481, p < 0.001), a 1.62 percentage point decrease in discharges to an institutional post-acute care setting (95% CI -3.17, -0.07, p = 0.04), but no changes in 90-day readmission (95% CI -2.68, 0.00, p = 0.051). CONCLUSIONS: Despite concerns that the CJR model could hinder people with ADRD from receiving joint replacement, the receipt of joint replacement did not change among people with ADRD under CJR. The CJR model was associated with decreased spending for people with ADRD who received joint replacements, driven by reduced discharges to an institutional post-acute care setting, without any changes in 90-day readmission.