title: Untargeted next-generation sequencing-based first-line diagnosis of infection in immunocompromised adults: a multicentre, blinded, prospective study.
abstract: OBJECTIVE
  Infections are the major cause of morbidity and mortality in immunocompromised patients. Improving microbiological diagnosis in these patients is of paramount clinical importance.
  
  
  METHODS
  We performed this multicentre, blinded, prospective, proof-of-concept study, to compare untargeted next-generation sequencing with conventional microbiological methods for first-line diagnosis of infection in 101 immunocompromised adults. Patients were followed for 30 days and their blood samples, and in some cases nasopharyngeal swabs and/or biological fluids, were analysed. At the end of the study, expert clinicians evaluated the results of both methods. The primary outcome measure was the detection rate of clinically relevant viruses and bacteria at inclusion.
  
  
  RESULTS
  Clinically relevant viruses and bacteria identified by untargeted next-generation sequencing and conventional methods were concordant for 72 of 101 patients in samples taken at inclusion (κ test=0.2, 95% CI 0.03-0.48). However, clinically relevant viruses and bacteria were detected in a significantly higher proportion of patients with untargeted next-generation sequencing than conventional methods at inclusion (36/101 (36%) vs. 11/101 (11%), respectively, p <0.001), and even when the latter were continued over 30 days (19/101 (19%), p 0.003). Untargeted next-generation sequencing had a high negative predictive value compared with conventional methods (64/65, 95% CI 0.95-1).
  
  
  CONCLUSIONS
  Untargeted next-generation sequencing has a high negative predictive value and detects more clinically relevant viruses and bacteria than conventional microbiological methods. Untargeted next-generation sequencing is therefore a promising method for microbiological diagnosis in immunocompromised adults.
authors.affiliation: Paris Descartes University, Sorbonne Paris Cité, Necker Pasteur Center for Infectious Diseases and Tropical Medicine, Necker Enfants Malades University Hospital, Institut Imagine, Paris, France.
authors.forename: P
authors.initials: P
authors.lastname: Parize
authors.affiliation: PathoQuest, Paris, France.
authors.forename: E
authors.initials: E
authors.lastname: Muth
authors.affiliation: Department of Microbiology, European Georges Pompidou Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Descartes, Paris, France.
authors.forename: C
authors.initials: C
authors.lastname: Richaud
authors.affiliation: PathoQuest, Paris, France.
authors.forename: M
authors.initials: M
authors.lastname: Gratigny
authors.affiliation: Paris Descartes University, Sorbonne Paris Cité, Necker Pasteur Center for Infectious Diseases and Tropical Medicine, Necker Enfants Malades University Hospital, Institut Imagine, Paris, France.
authors.forename: B
authors.initials: B
authors.lastname: Pilmis
authors.affiliation: PathoQuest, Paris, France.
authors.forename: A
authors.initials: A
authors.lastname: Lamamy
authors.affiliation: Department of Microbiology, European Georges Pompidou Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Descartes, Paris, France.
authors.forename: J-L
authors.initials: JL
authors.lastname: Mainardi
authors.affiliation: PathoQuest, Paris, France.
authors.forename: J
authors.initials: J
authors.lastname: Cheval
authors.affiliation: PathoQuest, Paris, France.
authors.forename: L
authors.initials: L
authors.lastname: de Visser
authors.affiliation: PathoQuest, Paris, France.
authors.forename: F
authors.initials: F
authors.lastname: Jagorel
authors.affiliation: PathoQuest, Paris, France.
authors.forename: L
authors.initials: L
authors.lastname: Ben Yahia
authors.affiliation: PathoQuest, Paris, France.
authors.forename: G
authors.initials: G
authors.lastname: Bamba
authors.affiliation: PathoQuest, Paris, France.
authors.forename: M
authors.initials: M
authors.lastname: Dubois
authors.affiliation: Paris Descartes University, Sorbonne Paris Cité, Laboratory of Microbiology, Necker Enfants Malades University Hospital, Paris, France.
authors.forename: O
authors.initials: O
authors.lastname: Join-Lambert
authors.affiliation: Paris Descartes University, Sorbonne Paris Cité, Laboratory of Microbiology, Necker Enfants Malades University Hospital, Paris, France.
authors.forename: M
authors.initials: M
authors.lastname: Leruez-Ville
authors.affiliation: Paris Descartes University, Sorbonne Paris Cité, Laboratory of Microbiology, Necker Enfants Malades University Hospital, Paris, France.
authors.forename: X
authors.initials: X
authors.lastname: Nassif
authors.affiliation: University Paris-Diderot, Hospital Beaujon, Clichy, France.
authors.forename: A
authors.initials: A
authors.lastname: Lefort
authors.affiliation: Paris Descartes University, Sorbonne Paris Cité, Necker Pasteur Center for Infectious Diseases and Tropical Medicine, Necker Enfants Malades University Hospital, Institut Imagine, Paris, France.
authors.forename: F
authors.initials: F
authors.lastname: Lanternier
authors.affiliation: Hematology Department, Necker Hospital, Paris Descartes - Sorbonne Paris Cité University, INSERM U1163 CNRS ERL8654, Imagine Institute, Paris, France.
authors.forename: F
authors.initials: F
authors.lastname: Suarez
authors.affiliation: Paris Descartes University, Sorbonne Paris Cité, Necker Pasteur Center for Infectious Diseases and Tropical Medicine, Necker Enfants Malades University Hospital, Institut Imagine, Paris, France.
authors.forename: O
authors.initials: O
authors.lastname: Lortholary
authors.affiliation: Paris Descartes University, Sorbonne Paris Cité, Necker Pasteur Center for Infectious Diseases and Tropical Medicine, Necker Enfants Malades University Hospital, Institut Imagine, Paris, France; Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, Paris, France. Electronic address: marc.lecuit@pasteur.fr.
authors.forename: M
authors.initials: M
authors.lastname: Lecuit
authors.affiliation: PathoQuest, Paris, France; Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, Paris, France. Electronic address: marc.eloit@pathoquest.com.
authors.forename: M
authors.initials: M
authors.lastname: Eloit
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D003141:Communicable Diseases / Q000175:diagnosis*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016867:Immunocompromised Host; D008297:Male; D008828:Microbiological Techniques; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D011237:Predictive Value of Tests; D000075082:Proof of Concept Study; D011446:Prospective Studies
keywords: Diagnostics; Immunodeficiency; Infection; Microorganisms; Next-generation sequencing