The CHAIN Network Enterics Working Group led by Donna Denno, Judd Walson and Kirk Tickell, has identified three priority areas for investigation:
- Pathogen colonization/infection and antimicrobial susceptibility as predictors of mortality among children with and without diarrhea.
- The role of the enteric microbiome in hospital and post-discharge outcomes.
- Enteric dysfunction as a determinant of recovery.
The first area will be primarily addressed through CHAIN’s core nested case control analysis of rectal swabs collected at all sites. This analysis will utilize molecular methods, such as Taqman Card Array and 16s ribosomal sequencing, to detect pathogenic and commensal bacteria. The pathogen and antimicrobial analysis will be validated by a sub-study using traditional pathogen culture and antimicrobial testing at the Kilifi, Mbagathi, Migori, Karachi, Dhaka and Matlab hospital sites. This sub-study links to the microbiology sub-study and is culturing pathogens on selective and differential media to aid in isolation and identification of enteric pathogens such as Salmonella, Shigella and Campylobacter. Shigella, Salmonella and different E.coli isolates are being stored for future virulence testing and speciation. Extended Spectrum Beta Lactamase (ESBL) positive Enterobacteriaceae are being identified by direct culturing. ESBL positive pathogens are then identified using biochemical tests. The microbiology sub study has begun at the participating sites.
The second objective will also be addressed through the nested case control study of core CHAIN samples. The enterics working group has been coordinating with members of the Gordon Laboratory at Washington University (St. Louis) to ensure our SOPs are optimized for microbiome collection.
The third area of investigation, enteric dysfunction, will be explored in a core CHAIN analysis using whole stool samples collected at all CHAIN Network sites. These samples will be analysed for biomarkers of enteric dysfunction which broadly characterise enteric inflammation and damage, such as alpha-1-anti-trypsin, neopterin, myeloperoxidase and Reg-1-beta. Again, this core CHAIN analysis will be validated by a sub-study in which measures of enteric function will be conducted at hospital discharge and follow-up in a subset of children at Migori and Civil hospitals.