Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection

• Published in: PloS one Vol. 12; no. 5; p. e0177340
• Main Authors: Lewandowska, Dagmara W, Schreiber, Peter W, Schuurmans, Macé M, Ruehe, Bettina, Zagordi, Osvaldo, Bayard, Cornelia, Greiner, Michael, Geissberger, Fabienne D, Capaul, Riccarda, Zbinden, Andrea, Böni, Jürg, Benden, Christian, Mueller, Nicolas J, Trkola, Alexandra, Huber, Michael
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 23.05.2017; Public Library of Science (PLoS)
• Subjects: Adult; Analysis; Biology and Life Sciences; Cytomegalovirus; Diagnostic systems; Digestion; DNA Virus Infections - diagnosis; DNA Virus Infections - virology; Epidemiology; Etiology; Female; Genome, Viral; Health aspects; Herpesvirus 7, Human - genetics; Herpesvirus 7, Human - isolation & purification; High-Throughput Nucleotide Sequencing; Hospitals; Humans; Immunocompromised hosts; Immunosuppression; Immunotherapy; Infections; Infectious diseases; Lung Transplantation; Male; Medicine and Health Sciences; Metagenome; Metagenomics; Middle Aged; Multiplexing; Nuclease; Nucleic acids; Organ transplant recipients; Pathogens; Patients; Pediatrics; Pharynx; Picornaviridae Infections - virology; Polymerase chain reaction; Postoperative Complications - diagnosis; Postoperative Complications - virology; Research and Analysis Methods; Respiratory tract; Respiratory tract infection; Respiratory tract infections; Respiratory Tract Infections - diagnosis; Respiratory Tract Infections - virology; Rhinovirus; Rhinovirus - genetics; Rhinovirus - isolation & purification; Risk factors; RNA Virus Infections - diagnosis; RNA Virus Infections - virology; Roseolovirus Infections - diagnosis; Roseolovirus Infections - virology; Test procedures; Torque teno virus - genetics; Torque teno virus - isolation & purification; Transplant Recipients; Transplants & implants; Viral infections; Virology; Virus diseases; Viruses; Xenografts; Switzerland
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0177340

Lung transplant patients are a vulnerable group of immunosuppressed patients that are prone to frequent respiratory infections. We studied 60 episodes of respiratory symptoms in 71 lung transplant patients. Almost half of these episodes were of unknown infectious etiology despite extensive routine diagnostic testing. We re-analyzed respiratory samples of all episodes with undetermined etiology in order to detect potential viral pathogens missed/not accounted for in routine diagnostics. Respiratory samples were enriched for viruses by filtration and nuclease digestion, whole nucleic acids extracted and randomly amplified before high throughput metagenomic virus sequencing. Viruses were identified by a bioinformatic pipeline and confirmed and quantified using specific real-time PCR. In completion of routine diagnostics, we identified and confirmed a viral etiology of infection by our metagenomic approach in four patients (three Rhinovirus A, one Rhinovirus B infection) despite initial negative results in specific multiplex PCR. Notably, the majority of samples were also positive for Torque teno virus (TTV) and Human Herpesvirus 7 (HHV-7). While TTV viral loads increased with immunosuppression in both throat swabs and blood samples, HHV-7 remained at low levels throughout the observation period and was restricted to the respiratory tract. This study highlights the potential of metagenomic sequencing for virus diagnostics in cases with previously unknown etiology of infection and in complex diagnostic situations such as in immunocompromised hosts.