BrioBiotech (United States)

<title>Abstract</title> <bold>Objective: </bold>To investigate the impact of Nocardia infection on the airway microbiota composition in lung transplant recipients (LTRs) using mNGS and evaluate associations between microbial alterations and clinical parameters.. <bold>Methods</bold>: This single-center, retrospective cohort study analyzed 679 LTRs (2015–2024), including 20 Nocardia-infected patients (experimental group, EG), 40 matched controls, and 16 post-treatment group (TG) cases. Bronchoalveolar lavage fluid (BALF) was subjected to mNGS to characterize microbial composition. Multi-modal were applied to analyze integrated α/β-diversity metrics, LEfSe biomarker identification, SparCC co-occurrence networks, and clinical parameter correlations (NCT06594133). <bold>Results:</bold>Microbiome analysis demonstrated comparable alpha diversity but distinct beta diversity profiles (P=0.025) between groups. The EG exhibited significant enrichment of <italic>Nocardia</italic> species (predominantly <italic>N. farcinica</italic> and <italic>N. cyriacigeorgica</italic>), alongside decreased <italic>Rothia mucilaginosa</italic> and <italic>Burkholderia</italic>species versus controls. Therapeutic intervention substantially reduced <italic>Nocardia </italic>abundance in treated subjects. Network analysis revealed <italic>class_Caudoviricetes </italic>displayed inverse associations with <italic>Nocardia</italic>, <italic>Achromobacter</italic>, <italic>Mastadenovirus</italic>, and <italic>Yersinia</italic>. Nocardia-centered subnet showed positive correlations with <italic>Enterococcus</italic>, <italic>Mastadenovirus</italic>, and <italic>Yersinia</italic>, contrasting with negative correlations involving <italic>Capnocytophaga</italic>, <italic>Rothia</italic>, and <italic>class_Caudoviricetes. </italic>In EG, a robust positive correlation was found of CD4⁺ T-cell counts and the CD4/CD8 ratio with serum IgA, IgM, and IgG (each <italic>p</italic>&lt;0.05). Spearman analysis linked <italic>N. farcinica</italic> and <italic>N. cyriacigeorgica</italic> inversely to CD4⁺ count and albumin; <italic>N. farcinica </italic>also inversely correlated with IgG, IgA, total lymphocyte count, and hemoglobin; and <italic>N. cyriacigeorgica</italic>inversely correlated with the CD4/CD8 ratio and positively with CD8⁺ T cells. <bold>Conclusions:</bold> <italic>Nocardia</italic> infection induces significant alterations in the airway microbiota of LTRs, characterized by Nocardia enrichment and specific commensal depletion. These microbial shifts are strongly associated with host immune and nutritional status. Our findings highlight the critical role of airway microbial dysbiosis in <italic>Nocardia </italic>infection pathogenesis and suggest microbiota-targeted strategies that down-regulation the immunosuppressants might be a potential adjunct strategy in Nocardia infection in lung transplant recipients.

Abstract Background Gasdermin D (GSDMD)-mediated pyroptosis, a critical component of the innate immune response, is triggered by pathogenic microbial infections and plays a key role in host defense mechanisms. This process involves the cleavage of GSDMD by inflammatory caspases, releasing carboxy-terminal fragments (GSDMD-CT). Monitoring GSDMD-CT levels represents a promising approach for inflammatory diseases, including sepsis and systemic inflammatory response syndrome (SIRS). Methods We developed an immunoassay to measure plasma GSDMD-CT concentrations in 109 healthy individuals, 137 patients with SIRS, and 100 patients with sepsis. The diagnostic utility of GSDMD-CT in distinguishing sepsis from SIRS or healthy controls was assessed using receiver operating characteristic (ROC) analysis, alongside correlations with procalcitonin (PCT), and C-reactive protein (CRP). Results Plasma GSDMD-CT levels were significantly elevated in patients with sepsis compared to healthy control and SIRS groups. ROC analysis demonstrated an area under the curve (AUC) of 0.8701, with a sensitivity of 91.00% and specificity of 60.55% for differentiating sepsis from HC. Comparable performance was observed in distinguishing SIRS from HC. Diagnostic accuracy was further enhanced when GSDMD-CT was combined with PCT. Strikingly, GSDMD-CT mirrored the kinetic profile of PCT in antibiotic-treated patients with bacterial infections. Conclusion The GSDMD-CT assay demonstrates high sensitivity as a biomarker, offering potential for early and differential diagnosis of sepsis across diverse pathogens.

Abstract Post-weaning diarrhea can be costly for producers, especially in antibiotic free production flows (RWA), where the use of antimicrobials leads to a loss of valuable premiums on individual pigs. This field study examined the impact of an in-water essential oil blend on RWA pigs with post-weaning diarrhea using pen-level diarrhea scores, and percentages of diarrhea-related sick, fallback and removed pigs. A total of 3,598 pigs (~4 wk of age, mixed sex) in 73 pens from 2 RWA flows and 4 pig turns (2 turns per nursery barn) were enrolled. Sow sources were known to experiencing mild E. coli and/or rotavirus associated post-weaning diarrhea. In each barn, one-half of the pens were assigned to control (regular water) or treatment [AQUAGUTSWINE, at 250 mL/1000 L drinking water, a flavored liquid Vitamin C Supplement) designed by Probiotech International Inc. and supplying Star Anise, cinnamaldehyde oil blend and ascorbic acid (2,955 mg/kg)] for ~2 wk post weaning. Pen-level diarrhea was assessed every other day (scale from 0 to 4). Additionally, diarrhea-related sick pigs were assessed individually at the same time pen-level diarrhea was scored. In each pen, a pig was first identified as sick (sunken eyes, poor gut fill or lethargic/depressed) and then confirmed if it had diarrhea. Diarrhea-related fallbacks were assessed at the end of treatment (~2 wk post-weaning). A pig was considered fallback if it did not recover from its enteric problem (Previously marked as a diarrhea-related sick pig) by the end of the treatment. A diarrhea-related removal was a previously marked diarrhea-related sick pig that was removed from its pen. Mild post-weaning diarrhea related to E. coli and rotaviruses occurred in both flows. Overall, the VHP reduced pen-level diarrhea scores over time (1.2 vs 1.5, P &amp;lt; 0.01), and percentages of diarrhea-related sick (10.9 vs 14.3%, P = 0.36), fallback (3.5 vs 4.6%, P = 0.10) and removed pigs (0.17 vs 0.30%, P = 0.12) compared with the control group. These first results suggested that AQUAGUTSWINE could be an aid in reducing clinical impact of mild post-weaning diarrhea caused by E. coli and rotavirus in RWA pigs.

No abstract available.

Abstract Fear and anxiety in dogs can be elevated during transportation or visits to the veterinarian, groomer, and boarding or training kennels. The stress-related behaviors exhibited during these times can be a welfare concern to both pet, handler, and owner. In the case of training or grooming, the productivity of the session may be reduced due to unwanted stress related behaviors. Pet owners want to reduce stress during these events and are seeking natural botanical alternatives to medications. The botanical extracts in Cani-Calm (Probiotech International, Inc.) successfully decreased stress-related behaviors when fed to beagles for 11 days before a novel 1-hr car ride stress test. There has not been any investigation into the impact of these botanicals during a prolonged stress event similar to a boarding or training kennel. The objective was to evaluate Cani-Calm when offered during a 3-week training program at a boarding kennel. Fifty-one dogs of various ages, breed, and history were randomly assigned to either Control (no Cani-Calm; n = 26) or Cani-Calm (CC: 0.6 mL· kg BWT-1· day-1; n = 25). Cani-Calm was top-dressed on the morning meal daily. Trainers, blinded to treatment, assessed dog behavior and provided training timelines for each dog. Statistical analysis was performed using a Genmod analysis and Poisson distribution in SAS v9.3. Statistical significance was set at P &amp;lt; 0.05 and statistical trends were considered at 0.05 &amp;lt; P &amp;lt; 0.10. Length of the acclimation period before the onset of training due to stress-related behaviors was reduced (P = 0.001) in treated dogs compared with the control (Control: 1.57± 0.16 d; CC: 0.08 ± 0.71 d). There was no impact of treatment (P = 0.15) on percentage of dogs per group that required additional days of training beyond the planned program. However, there was an impact of treatment (P = 0.04; Control: 75%; CC: 96.3%) on the percentage of dogs that completed training earlier than the scheduled 3-week program. The results indicate a benefit of Cani-Calm during stressful events to decrease the display of behaviors that reduce training productivity and are a welfare concern for both animal and handler. Unlike the previous trial, during the current trial, there was no exposure to the botanicals before the stressful event; however, alterations in stress-related behaviors were demonstrated in both trials. Further research is warranted to evaluate time of exposure to the botanicals before the stress-event, and in larger populations.

Background: This study aims to preliminarily explore the impact of delayed influenza virus nucleic acid conversion (more than five days) to negative on treatment and length of hospital stay in children with severe influenza. Methods: This was a single-center retrospective study. General information, influenza virus nucleic acid test (per 3-5 days) results after receiving antiviral medication, antiviral drug usage, comorbid infections, invasive mechanical ventilation, and discharge prognosis of children with severe influenza were collected. Results: A total of 39 patients were included in the study. The patients were divided into four groups based on the time when the patient’s viral nucleic acid turned to negative after receiving antiviral medication: 3-5 days (35.8%, 14/39), 6-10 days (38.4%, 15/39), &gt;10 days (12.8%, 5/39), and maintaining as positive when discharge (12.8%, 5/39). More than half of pediatric patients with severe influenza exhibited delayed nucleic acid conversion (more than 5 days) after antiviral medication. The &gt;10 days group had a longer time from onset to PICU admission, PICU stay, and antiviral drug use duration, as well as a higher proportion of CBP use (P &lt; 0.05, respectively). Within the first 3 days of PICU admission, the proportion of patients with persistently reduced lymphocytes was lower in the 3-5 days group (28.6% (4/14)) than other two groups (P &gt; 0.05). Conclusions: Delayed nucleic acid conversion was associated with longer PICU length of stay. Persistent fever, co-infections, and impaired cellular immune function may contribute to the delay.

Abstract We present multiPrime, a novel approach that automatically designs minimal primer sets for large and diverse sequences. This tool enhances coverage by designing primers with mismatch tolerance, ensuring high compatibility and specificity. We compared multiPrime to existing tools using a dataset of 43,016 sequences. Our results demonstrate that multiPrime outperformed the existing tools and successfully amplified the target amplicons. We further expanded its application to include 30 viruses and validated the efficacy of multiPrime-designed primers in 80 clinical specimens, achieving a sensitivity of 94% and specificity of 89%.

Although the fast-growing metagenomic next-generation sequencing (mNGS) has been used in diagnosing infectious diseases, low detection rate of mNGS in detecting pathogens with low loads limits its extensive application. In this study, 130 patients with suspected pulmonary infections were enrolled, from whom bronchoalveolar lavage fluid (BALF) samples were collected. The conventional tests and mNGS of cell-free DNA (cfDNA) and whole-cell DNA (wcDNA) using BALF were simultaneously performed. mNGS of cfDNA showed higher detection rate (91.5%) and total coincidence rate (73.8%) than mNGS of wcDNA (83.1% and 63.9%) and conventional methods (26.9% and 30.8%). A total of 70 microbes were detected by mNGS of cfDNA, and most of them (60) were also identified by mNGS of wcDNA. The 31.8% (21/66) of fungi, 38.6% (27/70) of viruses, and 26.7% (8/30) of intracellular microbes can be only detected by mNGS of cfDNA, much higher than those [19.7% (13/66), 14.3% (10/70), and 6.7% (2/30)] only detected by mNGS of wcDNA. After in-depth analysis on these microbes with low loads set by reads per million (RPM), we found that more RPM and fungi/viruses/intracellular microbes were detected by mNGS of cfDNA than by mNGS of wcDNA. Besides, the abilities of mNGS using both cfDNA and wcDNA to detect microbes with high loads were similar. We highlighted the advantage of mNGS using cfDNA in detecting fungi, viruses, and intracellular microbes with low loads, and suggested that mNGS of cfDNA could be considered as the first choice for diagnosing pulmonary infections.

Since the first strain related to Thermicanaceae was reported in 1999, almost no literature on Thermicanaceae is available, particularly its genomics. We recently isolated a novel pathogenic bacterium, the △ strain DYY3, from the blood sample of a critically ill patient. The morphological, physiological, and biochemical characteristics of △ strain DYY3 were presented in this study, and the virulence factor genes and antibiotic resistance of DYY3 were also determined. Interestingly, the average nucleotide identity (ANI) and core-genes average amino acid identity (cAAI) analysis indicated that △ strain DYY3 was genus novel and species novel. Moreover, phylogenetic analysis based on both 16S rRNA gene and whole genomic core gene sequences suggested that △ strain DYY3 belonged to the family Thermicanaceae, and this novel taxon was thus named Haemobacillus shengwangii gen. nov., sp. nov. Besides, both the whole genome-based phylogenetic tree and amino acid identity analysis indicated that Thermicanus aegyptius, Hydrogenibacillus schlegelii, Brockia lithotrophica, and the newly discovered species H. shengwangii should belong to Thermicanaceae at the family level, and T. aegyptius was the closest species to H. shengwangii. We also constructed the first high-quality genome in the family Thermicanaceae using the next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing technologies, which certainly contributed to further genomics studies and metagenomic-based pathogenic detection in the future.

BackgroundTo evaluate the value of metagenomic next-generation sequencing (mNGS) for the early diagnosis of psittacosis, and to investigate its epidemiology by whole-genome capture.MethodsTwenty-one bronchoalveolar lavage fluid (BALF) and blood samples of 16 psittacosis patients from multiple centers during August 2019 to September 2021 were analyzed retrospectively. mNGS with normal datasets (10 M 75-bp single-end reads after sequencing) and larger datasets (30 M 150-bp paired-end reads after sequencing) as well as quantitative real-time polymerase chain reaction (qPCR) were used to detect the pathogen. Also, whole-genome capture of Chlamydophila psittaci was applied to draw the phylogenetic tree.ResultsmNGS successfully detected the pathogen in all 16 cases (100%), while qPCR was positive only in 5 out of 10 cases (50%), indicating a significantly higher sensitivity of mNGS than qPCR (p < 0.01). BALF-mNGS performed better than blood-mNGS (16/16 versus 3/5, p < 0.05). In addition, larger datasets (the read counts have tripled, and the base number was 12-fold larger compared to clinical mNGS with a normal dataset) of mNGS showed significantly increased contents of human DNA (p < 0.05) and decreased reads per million of the pathogen, suggesting no improvement. Whole-genome capture results of five samples (>60% coverage and >1 depth) were used to construct the phylogenetic tree.ConclusionSignificant advantages of mNGS with normal datasets were demonstrated in early diagnosing psittacosis. It is the first study to use whole-genome capture to analyze C. psittaci epidemiological information.