Deep sequencing of RNA from blood and oral swab samples reveals the presence of nucleic acid from a number of pathogens in patients with acute Ebola virus disease and is consistent with bacterial translocation across the gut

Miles Carroll, Sam Haldenby, Natasha Y. Rickett, Bernadett Pályi, Isabel Garcia-Dorival, Xuan Liu, Gary Barker, Joseph Akoi Bore, Fara Raymond Koundouno, E. Diane Williamson, Thomas R. Laws, Romy Kerber, Daouda Sissoko, Nóra Magyar, Antonino Di Caro, Mirella Biava, Tom E. Fletcher, Armand Sprecher, Lisa F.P. Ng, Laurent RéniaN'faly Magassouba, Stephan Günther, Roman Wölfel, Kilian Stoecker, David A. Matthews, Julian A. Hiscox*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)

Abstract

In this study, samples from the 2013-2016 West African Ebola virus outbreak from patients in Guinea with Ebola virus disease (EVD) were analyzed to discover and classify what other pathogens were present. Throat swabs were taken from deceased EVD patients, and peripheral blood samples were analyzed that had been taken from patients when they presented at the treatment center with acute illness. High-throughput RNA sequencing (RNA-seq) and bioinformatics were used to identify the potential microorganisms. This approach confirmed Ebola virus (EBOV) in all samples from patients diagnosed as acute positive for the virus by quantitative reverse transcription-PCR in deployed field laboratories. Nucleic acid mapping to Plasmodium was also used on the patient samples, confirming results obtained with an antigen-based rapid diagnostic test (RDT) conducted in the field laboratories. The data suggested that a high Plasmodium load, as determined by sequence read depth, was associated with mortality and influenced the host response, whereas a lower parasite load did not appear to affect outcome. The identifications of selected bacteria from throat swabs via RNA-seq were confirmed by culture. The data indicated that the potential pathogens identified in the blood samples were associated with translocation from the gut, suggesting the presence of bacteremia, which transcriptome data suggested may induce or aggravate the acute-phase response observed during EVD. Transcripts mapping to different viruses were also identified, including those indicative of lytic infections. The development of high-resolution analysis of samples from patients with EVD will help inform care pathways and the most appropriate general antimicrobial therapy to be used in a resource-poor setting.

Original languageEnglish
Article numbere00325-17
JournalmSphere
Volume2
Issue number4
DOIs
Publication statusPublished - 1 Jul 2017

Bibliographical note

Funding Information:
We acknowledge the help of Sophie Duraffour in the implementation of this study. This work was carried out in the context of the project EVIDENT (Ebola Virus Disease: Correlates of Protection, Determinants of Outcome, and Clinical Management), which received funding from the European Union's Horizon 2020 Research and Innovation Program under grant agreement 666100, and in the context of service contract IFS/2011/272-372 funded by the Directorate-General for International Cooperation and Development. The European Mobile Laboratory is a technical partner in the WHO Emerging and Dangerous Pathogens Laboratory Network (EDPLN) and the Global Outbreak Alert and Response Network (GOARN) and is headed by S.G. The work was funded by the Centre for Defence Enterprise (to D.A.M. and J.A.H.) and by the U.S. Food and Drug Administration (to J.A.H. and M.W.C.) program for Ebola Virus Disease: Correlates of Protection, Determinants of Outcome and Clinical Management, grant HHSF223201510104C. The research was also funded by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Emerging and Zoonotic Infections at the University of Liverpool in partnership with Public Health England (PHE) and the Liverpool School of Tropical Medicine (LSTM), which directly supported N.Y.R. and X.L. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England

Publisher Copyright:
© 2017 Carroll et al.

Keywords

  • Bioinformatics
  • Coinfection
  • Ebola
  • Ebola virus disease
  • Filovirus
  • Gene expression
  • Host-pathogen interactions
  • Informatics
  • Intracellular parasites
  • Malaria
  • Plasmodium falciparum
  • RNA-seq

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