Whole blood genome-wide transcriptome profiling and metagenomics next-generation sequencing in young infants with suspected sepsis in a low-and middle-income country: A study protocol

Author:

Popescu Constantin R.ORCID,Tembo Bentry,Chifisi Rhoda,Cavanagh Miranda M.M.,Lee Amy Huei-Yi,Chiluzi Blessings,Ciccone Emily J.,Tegha Gerald,Alonso-Prieto Esther,Claydon Jennifer,Dunsmuir Dustin,Irvine MikeORCID,Dumont GuyORCID,Ansermino J. MarkORCID,Wiens Matthew O.,Juliano Jonathan J.ORCID,Kissoon Niranjan,Mvalo TisunganeORCID,Lufesi Norman,Chiume-Kayuni Msandeni,Lavoie Pascal M.ORCID

Abstract

Conducting collaborative and comprehensive epidemiological research on neonatal sepsis in low- and middle-income countries (LMICs) is challenging due to a lack of diagnostic tests. This prospective study protocol aims to obtain epidemiological data on bacterial sepsis in newborns and young infants at Kamuzu Central Hospital in Lilongwe, Malawi. The main goal is to determine if the use of whole blood transcriptome host immune response signatures can help in the identification of infants who have sepsis of bacterial causes. The protocol includes a detailed clinical assessment with vital sign measurements, strict aseptic blood culture protocol with state-of-the-art microbial analyses and RNA-sequencing and metagenomics evaluations of host responses and pathogens, respectively. We also discuss the directions of a brief analysis plan for RNA sequencing data. This study will provide robust epidemiological data for sepsis in neonates and young infants in a setting where sepsis confers an inordinate burden of disease.

Funder

Grand Challenges Canada

Gates Foundation

Publisher

F1000 Research Ltd

Subject

Public Health, Environmental and Occupational Health,Health Policy,Immunology and Microbiology (miscellaneous),Biochemistry, Genetics and Molecular Biology (miscellaneous),Medicine (miscellaneous)

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