Metagenomics for Discovery of Novel Pathogens in Infectious Childhood Illnesses

Muhammad Imran Nisar, Furqan Kabir, Fyezah Jehan, and Syed Asad Ali of Aga Khan University in Pakistan will employ a metagenomic sequencing approach to better identify bacterial and viral infections, including those caused by novel pathogens, in newborns and infants in Pakistan. Pakistan has the highest neonatal mortality rate in the world. Almost one third of neonatal deaths are thought to be caused by an infectious disease, but accurate diagnosis is challenging in low-resource settings. In a recent study, despite using elaborate detection methods, only 28% of suspected infectious cases could be confirmed. In addition, novel pathogens escape detection because conventional microbiological methods are limited to detecting a predetermined selection. To overcome these limitations, they will establish a metagenomics approach for next generation sequencing with the cloud computing IDseq software to identify the infectious pathogens. They will sequence and analyze 150 archived blood and nasopharyngeal specimens from a previous study and additionally analyze blood and swab samples to be collected from sick newborns and infants with suspected infections over a six-month period at a primary healthcare center in a peri-urban community in Karachi, Pakistan.