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 [version 2; peer review: 2 approved]
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 a...
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2020-11-01
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doaj-6cbc1364f8664cf6b4a279fab3ca59532021-01-12T18:06:35ZengF1000 Research LtdGates Open Research2572-47542020-11-01410.12688/gatesopenres.13172.214417Whole 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 [version 2; peer review: 2 approved]Constantin R. Popescu0Bentry Tembo1Rhoda Chifisi2Miranda M.M. Cavanagh3Amy Huei-Yi Lee4Blessings Chiluzi5Emily J. Ciccone6Gerald Tegha7Esther Alonso-Prieto8Jennifer Claydon9Dustin Dunsmuir10Mike Irvine11Guy Dumont12J. Mark Ansermino13Matthew O. Wiens14Jonathan J. Juliano15Niranjan Kissoon16Tisungane Mvalo17Norman Lufesi18Msandeni Chiume-Kayuni19Pascal M. Lavoie20BC Children’s Hospital Research Institute, Vancouver, BC, CanadaKamuzu Central Hospital, Lilongwe, MalawiKamuzu Central Hospital, Lilongwe, MalawiBC Children’s & Women’s Health Centre, Vancouver, BC, CanadaDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, CanadaKamuzu Central Hospital, Lilongwe, MalawiDepartment of Medicine, University of North Carolina, Chapel Hill, NC, USAUniversity of North Carolina Project Malawi, Lilongwe, MalawiBC Children’s & Women’s Health Centre, Vancouver, BC, CanadaBC Children’s Hospital Research Institute, Vancouver, BC, CanadaBC Children’s Hospital Research Institute, Vancouver, BC, CanadaBC Children’s Hospital Research Institute, Vancouver, BC, CanadaDepartment of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, CanadaBC Children’s Hospital Research Institute, Vancouver, BC, CanadaBC Children’s Hospital Research Institute, Vancouver, BC, CanadaDepartment of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USABC Children’s Hospital Research Institute, Vancouver, BC, CanadaUniversity of North Carolina Project Malawi, Lilongwe, MalawiClinical Services Directorate, Ministry of Health, Lilongwe, MalawiKamuzu Central Hospital, Lilongwe, MalawiBC Children’s Hospital Research Institute, Vancouver, BC, CanadaConducting 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.https://gatesopenresearch.org/articles/4-139/v2 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Constantin R. Popescu Bentry Tembo Rhoda Chifisi Miranda M.M. Cavanagh Amy Huei-Yi Lee Blessings Chiluzi Emily J. Ciccone Gerald Tegha Esther Alonso-Prieto Jennifer Claydon Dustin Dunsmuir Mike Irvine Guy Dumont J. Mark Ansermino Matthew O. Wiens Jonathan J. Juliano Niranjan Kissoon Tisungane Mvalo Norman Lufesi Msandeni Chiume-Kayuni Pascal M. Lavoie |
spellingShingle |
Constantin R. Popescu Bentry Tembo Rhoda Chifisi Miranda M.M. Cavanagh Amy Huei-Yi Lee Blessings Chiluzi Emily J. Ciccone Gerald Tegha Esther Alonso-Prieto Jennifer Claydon Dustin Dunsmuir Mike Irvine Guy Dumont J. Mark Ansermino Matthew O. Wiens Jonathan J. Juliano Niranjan Kissoon Tisungane Mvalo Norman Lufesi Msandeni Chiume-Kayuni Pascal M. Lavoie 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 [version 2; peer review: 2 approved] Gates Open Research |
author_facet |
Constantin R. Popescu Bentry Tembo Rhoda Chifisi Miranda M.M. Cavanagh Amy Huei-Yi Lee Blessings Chiluzi Emily J. Ciccone Gerald Tegha Esther Alonso-Prieto Jennifer Claydon Dustin Dunsmuir Mike Irvine Guy Dumont J. Mark Ansermino Matthew O. Wiens Jonathan J. Juliano Niranjan Kissoon Tisungane Mvalo Norman Lufesi Msandeni Chiume-Kayuni Pascal M. Lavoie |
author_sort |
Constantin R. Popescu |
title |
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 [version 2; peer review: 2 approved] |
title_short |
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 [version 2; peer review: 2 approved] |
title_full |
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 [version 2; peer review: 2 approved] |
title_fullStr |
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 [version 2; peer review: 2 approved] |
title_full_unstemmed |
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 [version 2; peer review: 2 approved] |
title_sort |
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 [version 2; peer review: 2 approved] |
publisher |
F1000 Research Ltd |
series |
Gates Open Research |
issn |
2572-4754 |
publishDate |
2020-11-01 |
description |
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. |
url |
https://gatesopenresearch.org/articles/4-139/v2 |
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