Microbial_drivers_of_pneumonia_in_adults_living_with_HIV_in_Ecuador

This is a longitudinal study focused on the effects of pathogens in microbial communities and their functional and resistance genes evaluation on the respiratory tract microbiome in forty adults living with HIV and having pneumonia. Sputum and oropharyngeal swabs are paired and serially collected on five different days plus a sample from bronchial lavage, a tongue swab, and a mouthwash. Also, we collect clinical information about HIV, immune status, pneumonia severity, antiretroviral therapy, antibiotics and antifungal treatments, and environmental factors. Our goals are to evaluate changes in the microbiome during treatment, and contrast microbiome taxonomic and resistance profiles in the different samples and times. Also, measure the changes and effects of resistance gene reservoirs and their association with clinical data. Patients came from four hospitals in Quito, Ecuador. From sputum and bronchial lavage samples, the host cells are separated from the microbes with a depleting procedure, subsequently, the microbial nucleic acids are extracted using a Zymo Research kit procedure. Human cells are counted using slide staining and microscopy and stored for future evaluations. DNA and RNA samples would be sent to the Wellcome Sanger Institute for NovaSeq deep sequencing, nanopore technology for long-read sequencing, and bioinformatics advice to analyze our samples.