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.

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.