Biomarker Identification for Preterm Birth Susceptibility: Vaginal Microbiome Meta-Analysis Using Systems Biology and Machine Learning Approaches.

PROBLEM: The vaginal microbiome has a substantial role in the occurrence of preterm birth (PTB), which contributes substantially to neonatal mortality worldwide. However, current bioinformatics approaches mostly concentrate on the taxonomic classification and functional profiling of the microbiome, limiting their abilities to elucidate the complex factors that contribute to PTB. METHOD OF STUDY: A total of 3757 vaginal microbiome 16S rRNA samples were obtained from five publicly available datasets. The samples were divided into two categories based on pregnancy outcome: preterm birth (PTB) (N = 966) and term birth (N = 2791). Additionally, the samples were further categorized based on the participants' race and trimester. The 16S rRNA reads were subjected to taxonomic classification and functional profiling using the Parallel-META 3 software in Ubuntu environment. The obtained abundances were analyzed using an integrated systems biology and machine learning approach to determine the key microbes, pathways, and genes that contribute to PTB. The resulting features were further subjected to statistical analysis to identify the top nine features with the greatest effect sizes. RESULTS: We identified nine significant features, namely Shuttleworthia, Megasphaera, Sneathia, proximal tubule bicarbonate reclamation pathway, systemic lupus erythematosus pathway, transcription machinery pathway, lepA gene, pepX gene, and rpoD gene. Their abundance variations were observed through the trimesters. CONCLUSIONS: Vaginal infections caused by Shuttleworthia, Megasphaera, and Sneathia and altered small metabolite biosynthesis pathways such as lipopolysaccharide folate and retinal may increase the susceptibility to PTB. The identified organisms, genes, pathways, and their networks may be specifically targeted for the treatment of bacterial infections that increase PTB risk.

Enhanced B-cell differentiation and reduced proliferative capacity in chronic hepatitis C and chronic hepatitis B virus infections.

BACKGROUND & AIMS: Chronic microbial infections are frequently associated with B-cell activation and polyclonal proliferation, potentially leading to autoimmunity and lymphoproliferative disorders. We assessed B-cell phenotype and function in chronic hepatitis B (HBV) and chronic hepatitis C (HCV) virus infection. METHODS: We studied 70 patients with chronic HCV infection, 34 with chronic HBV infection and 54 healthy controls. B-cell phenotype was assessed by flow cytometry using monoclonal antibodies specific for CD27, the CD69, CD71, and CD86 activation markers and the chemokine receptor CXCR3. Differentiation into immunoglobulin-producing cells (IPC) was analysed by ELISpot upon stimulation and with CD40 ligand±IL-10 as surrogate bystander T-cell help or CpG oligodeoxynucleotide±IL-2, as innate immunity signal. Proliferation was examined by flow cytometry using carboxyfluorescein diacetate succinimidyl ester (CFSE) after stimulation with CpG. RESULTS: A significantly higher proportion of B cells from both HCV- and HBV-infected patients expressed activation markers compared with controls and a positive correlation was found between CXCR3(+) B cells and HCV RNA values. Memory B cells from patients with chronic HCV and HBV infections showed enhanced differentiation into IPC compared with controls, although this was restricted to IgG and at a lower level in HCV-compared with HBV-infected patients. Moreover, patients' activated B cells displayed significantly lower proliferative ability compared to healthy donors despite low expression of the FcRL4 exhaustion marker. CONCLUSIONS: B-cell activation, but not exhaustion, is common in chronic viral hepatitis. However, enhanced B-cell differentiation and deficient proliferative capacity were not associated with commitment to terminal differentiation.

Antibiotic Resistance in Microbes from Street Fruit Drinks and Hygiene Behavior of the Vendors in Delhi, India.

Microbial contamination of fruit juices has caused major outbreaks, leading to significant morbidity and mortality in developing countries. The inept hygiene and safety practices followed by the juice vendors are the leading risk factors of the microbial contamination of juices. In this pilot study, the five most crowded markets in urban Delhi, including Kamla Nagar, University of Delhi (north campus), Tilak Nagar, Chandni Chowk, and Rohini, were selected for a questionnaire survey on the fruit juice vendors and the sampling of water used for juice preparation as well as sugarcane, orange, and mix fruit juices collected from these markets for the enumeration of total bacterial count (TBC), Escherichia coli, Salmonella, and Vibrio. Antibiotic susceptibility tests were performed using ampicillin, cefotaxime, chloramphenicol, ciprofloxacin, and imipenem. The results indicated that the majority of the vendors were not following hygiene and safety practices when compared with the recommended standard safety practices. The use of municipal water by 95% of vendors with high TBC counts might have been the major source of microbial contamination in all types of fruit juices. E. coli and Salmonella contaminations were high in sugarcane (2 × 105 colony forming units (CFU)/mL) and mix fruit (2.2 × 105 CFU/mL) juice samples, respectively. On the other hand, Vibrio was found to be absent in almost all juice samples except for orange juice. All strains were found to be susceptible to chloramphenicol, but resistant to ampicillin and cefotaxime. Only a few strains were resistant to ciprofloxacin, and only E. coli strains were resistant to imipenem. Taken together, the overall microbiological standards of fruit juices served by street vendors were not within the acceptable limits, perhaps due to the poor quality of water used to prepare juices and poor hygiene and safety practices followed by the vendors. More importantly, the isolated microbes demonstrated resistance to ampicillin and cefotaxime, which may have pressing public health implications. Post hoc power analyses identified the minimum sample size required for 80% power.

Standardization of in vitro assays to evaluate the activity of polyherbal siddha formulations against Chikungunya virus infection.

Chikungunya, a viral fever caused by Aedes mosquito results in extreme morbidity in affected individuals and is a major public health concern in India. Currently, modern vaccines or formulations prescribed by physicians can only provide symptomatic relief for the pyretic and post pyretic phase of the disease. Siddha practitioners follows strict medical regimen based on traditional Indian knowledge/concepts to treat Chikungunya with considerable results. The current study was undertaken to standardize assays for the study of these siddha formulations and to check their efficacy and potential mode of action as antivirals for Chikungunya virus infection in in vitro system. Although, siddha practitioners follow a regime containing 4-6 formulations, of these Brahmanandha bairavam mathirai, a part of the regime for Chikungunya followed at National Institute of Siddha and Vishnu chakram along with Brahmanandha bairavam mathirai, a part of Thiruchergodu Regime were found of have antiviral activities. It was observed that both Vishnu chakram and Brahmanandha bairavam mathirai were equally effective in blocking Chikungunya virus from entering susceptible cells in the concentrations range of 0.0625 and 0.5 mg/ml. Additionally, it was also observed that Brahmanandha bairavam mathirai was more effective than Vishnu chakram against entry of Chikungunya in the cells. The assays used in this study provides insights to the possible mode of action of various formulations used by siddha practitioners for the treatment of Chikungunya infection.

In Vivo Evaluation of Withania somnifera-Based Indian Traditional Formulation ( Amukkara Choornam), Against Chikungunya Virus-Induced Morbidity and Arthralgia.

Chikungunya viral fever results in extreme morbidity and arthralgia in affected individuals. Currently, modern medicines providing symptomatic relief for the acute febrile phase and the chronic arthritic phase are only options available. Traditional Indian medical system, however, uses specific formulations for treatment of this infection; one such polyherbal formulation used to treat the postpyretic phase of chikungunya is amukkara choornam. The current study was undertaken to study the efficacy of amukkara choornam in the treatment of chikungunya in C57BL/6J mice. The formulation when administered to chikungunya-infected mice relieved morbidity and joint swelling. Analysis of virus clearance in brain and joint tissues on formulation treatment revealed a direct correlation of viral load in brain to morbidity during infection; likewise, joint swelling receded prior to complete viral clearance explaining possible immunomodulatory effect of amukkara choornam. This study provides insight into the possible mode of action of amukkara choornam during chikungunya.

In silico analysis of natural compounds targeting structural and nonstructural proteins of chikungunya virus.

Background: Chikungunya fever presents as a high-grade fever during its acute febrile phase and can be prolonged for months as chronic arthritis in affected individuals. Currently, there are no effective drugs or vaccines against this virus. The present study was undertaken to evaluate protein-ligand interactions of all chikungunya virus (CHIKV) proteins with natural compounds from a MolBase library in order to identify potential inhibitors of CHIKV. Methods: Virtual screening of the natural compound library against four non-structural and five structural proteins of CHIKV was performed. Homology models of the viral proteins with unknown structures were created and energy minimized by molecular dynamic simulations. Molecular docking was performed to identify the potential inhibitors for CHIKV. The absorption, distribution, metabolism and excretion (ADME) toxicity parameters for the potential inhibitors were predicted for further prioritization of the compounds. Results: Our analysis predicted three compounds, Catechin-5-O-gallate, Rosmarinic acid and Arjungenin, to interact with CHIKV proteins; two (Catechin-5-O-gallate and Rosmarinic acid) with capsid protein, and one (Arjungenin) with the E3. Conclusion: The compounds identified show promise as potential antivirals, but further in vitro studies are required to test their efficacy against CHIKV.