Advanced Pathogen Detection in an Urban 'Hot Spot' for Global Emergence

Federico Costa of the Federal University of Bahia, Brazil, Mitermayer Galvão dos Reis of Fiocruz, Brazil, and Nathan Grubaugh and Albert I Ko of Yale University in the U.S. will establish metagenomic next generation sequencing in clinical settings in an urban region of Brazil classified as an infectious disease ‘hot spot’ to help develop new diagnostics and identify emerging pathogens. Rapid urbanization in Salvador, a metropolitan of 2.9 million inhabitants in Northeast Brazil, has produced a favorable environment for the emergence and spread of infectious diseases, and was the founding site for the recent Zika epidemic. Early detection is critical for preventing disease spread, particularly in Salvador, which is a transport hub and popular holiday destination. However, diagnosis can be challenging in low-resource settings, especially when the causative pathogen is unknown, the disease has diverse symptoms, or a known pathogen starts causing new symptoms. They will collect around 160 clinical samples from patients with suspected infections at a local infectious disease reference hospital and a maternity unit and apply a next generation sequencing approach together with the IDseq analysis platform to identify pathogens from the sequencing data.