The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease.
INTRODUCTION:Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always foun...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0223952 |
| _version_ | 1819110885806833664 |
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| author | Anneloes L van Rijn Sander van Boheemen Igor Sidorov Ellen C Carbo Nikos Pappas Hailiang Mei Mariet Feltkamp Marianne Aanerud Per Bakke Eric C J Claas Tomas M Eagan Pieter S Hiemstra Aloys C M Kroes Jutte J C de Vries |
| author_facet | Anneloes L van Rijn Sander van Boheemen Igor Sidorov Ellen C Carbo Nikos Pappas Hailiang Mei Mariet Feltkamp Marianne Aanerud Per Bakke Eric C J Claas Tomas M Eagan Pieter S Hiemstra Aloys C M Kroes Jutte J C de Vries |
| author_sort | Anneloes L van Rijn |
| collection | DOAJ |
| description | INTRODUCTION:Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has not yet been applied in COPD exacerbations. OBJECTIVES:To study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS. STUDY DESIGN:88 nasopharyngeal swabs from 63 patients from the Bergen COPD Exacerbation Study (2006-2010) were analysed by mNGS and in-house qPCR for respiratory viruses. Both DNA and RNA were sequenced simultaneously using an Illumina library preparation protocol with in-house adaptations. RESULTS:By mNGS, 24/88 samples tested positive. Sensitivity and specificity, as compared with PCR, were 96% and 98% for diagnostic targets (23/24 and 1093/1120, respectively). Additional viral pathogens detected by mNGS were herpes simplex virus type 1 and coronavirus OC43. A positive correlation was found between Cq value and mNGS viral normalized species reads (log value) (p = 0.002). Patients with viral pathogens had lower percentages of bacteriophages (p<0.001). No correlation was found between viral reads and clinical markers. CONCLUSIONS:The mNGS protocol used was highly sensitive and specific for semi-quantitative detection of respiratory viruses. Excellent negative predictive value implicates the power of mNGS to exclude any pathogenic respiratory viral infectious cause in one test, with consequences for clinical decision making. Reduced abundance of bacteriophages in COPD patients with viral pathogens implicates skewing of the virome during infection, with potential consequences for the bacterial populations, during infection. |
| first_indexed | 2024-12-22T03:48:50Z |
| format | Article |
| id | doaj.art-74a773c530fe45e992dade27e7214948 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T03:48:50Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-74a773c530fe45e992dade27e72149482022-12-21T18:40:04ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-011410e022395210.1371/journal.pone.0223952The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease.Anneloes L van RijnSander van BoheemenIgor SidorovEllen C CarboNikos PappasHailiang MeiMariet FeltkampMarianne AanerudPer BakkeEric C J ClaasTomas M EaganPieter S HiemstraAloys C M KroesJutte J C de VriesINTRODUCTION:Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has not yet been applied in COPD exacerbations. OBJECTIVES:To study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS. STUDY DESIGN:88 nasopharyngeal swabs from 63 patients from the Bergen COPD Exacerbation Study (2006-2010) were analysed by mNGS and in-house qPCR for respiratory viruses. Both DNA and RNA were sequenced simultaneously using an Illumina library preparation protocol with in-house adaptations. RESULTS:By mNGS, 24/88 samples tested positive. Sensitivity and specificity, as compared with PCR, were 96% and 98% for diagnostic targets (23/24 and 1093/1120, respectively). Additional viral pathogens detected by mNGS were herpes simplex virus type 1 and coronavirus OC43. A positive correlation was found between Cq value and mNGS viral normalized species reads (log value) (p = 0.002). Patients with viral pathogens had lower percentages of bacteriophages (p<0.001). No correlation was found between viral reads and clinical markers. CONCLUSIONS:The mNGS protocol used was highly sensitive and specific for semi-quantitative detection of respiratory viruses. Excellent negative predictive value implicates the power of mNGS to exclude any pathogenic respiratory viral infectious cause in one test, with consequences for clinical decision making. Reduced abundance of bacteriophages in COPD patients with viral pathogens implicates skewing of the virome during infection, with potential consequences for the bacterial populations, during infection.https://doi.org/10.1371/journal.pone.0223952 |
| spellingShingle | Anneloes L van Rijn Sander van Boheemen Igor Sidorov Ellen C Carbo Nikos Pappas Hailiang Mei Mariet Feltkamp Marianne Aanerud Per Bakke Eric C J Claas Tomas M Eagan Pieter S Hiemstra Aloys C M Kroes Jutte J C de Vries The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. PLoS ONE |
| title | The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. |
| title_full | The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. |
| title_fullStr | The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. |
| title_full_unstemmed | The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. |
| title_short | The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. |
| title_sort | respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease |
| url | https://doi.org/10.1371/journal.pone.0223952 |
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