A case report demonstrating the utility of next generation sequencing in analyzing serial samples from the lung following an infection with influenza A (H7N9) virus
Section snippets
Background
Influenza and pneumonia remain the leading infectious causes of death worldwide [1], resulting in almost 3.5 million deaths yearly and are a persistent and pervasive public health issue [2]. Bacterial pneumonia and cytokine dysregulation in patients suffering from influenza are key factors that contribute to severe disease and mortality [3], [4], [5]. The microbes involved in lung infection are complex, with organisms ranging in virulence from commensal to highly pathogenic, and viral-bacterial
Objectives
We describe an initial attempt to explore the structure and dynamics of the microbiome correlated with lung infection by using NGS. Serial bronchoalveolar lavage fluid (BALF) samples were collected from a fatal H7N9-related case with severe pneumonia and acute respiratory distress syndrome (ARDS) and analyzed by NGS. The comprehensive pulmonary microbial community kinetics, and host inflammatory response during therapy were studied.
Patient
A 61-year-old female patient with severe pneumonia was admitted on 18 July 2013 [10], [11]. She had been healthy except for cholecystectomy 30 years prior. She started to experience fever and general malaise on 13 July (day 0 after illness onset) and sought medical attention on 14 July. A chest radiograph on 15 July revealed interstitial pneumonia in the left upper lung. Progressive dyspnea developed on 16 July and follow-up chest radiographs showed ground grass opacity and lower lung
Deep sequencing summary
In total eight BALF samples were collected at intervals of 2 days during the whole clinical course and processed and run on Ion Torrent PGM, retrospectively. The turnaround time of the whole process from each sample preparation to data back from the NGS was about 48 h.
To test for the presence of potential contaminants in the reagents used for nucleic acids extraction and sequencing library preparation, we prepared a control sample consisting of a defined template (Lambda gDNA, Life Technologies,
Discussion
We demonstrate an initial attempt to use unbiased NGS to explore the dynamics of lung microbiome with novel influenza A (H7N9) virus infection. The NGS method allowed us to perform metagenomic analyses of pulmonary infection within a reasonable timeframe. These findings strongly suggest that NGS methods can complement conventional diagnostics and also highlight their potential to aid clinical personnel and health agencies in making appropriate decisions. Our observations also indicate that
Funding
This work was supported by the National S&T Major Project, “China Mega-Project for Infectious Disease” (grant No. 2013ZX10004-001), the Nonprofit Industry Research Project of Chinese National Health and Family Planning Commission (grant No. 201402001), and National Science Fund for Distinguished Young Scholars (grant number 81425001/H0104) for Dr. Bin Cao, and the PUMC Youth FUND (grant No. 33320140031).
Competing interests
The authors have no competing interests to report.
Ethical approval
No ethical approval is required for this study.
References (22)
- et al.
Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome
Lancet
(2013) - et al.
High serum procalcitonin concentrations in patients with sepsis and infection
Lancet
(1993) - et al.
Interleukin 8 (IL-8) in the bronchoalveolar lavage fluid from patients with the adult respiratory distress syndrome (ARDS) and patients at risk for ARDSrleukin 8 (IL-8) in the bronchoalveolar lavage fluid from patients with the adult respiratory distress syndrome (ARDS) and patients at risk for ARDS
Cytokine
(1992) - et al.
Community-acquired pneumonia
N. Engl. J. Med.
(2014) - The top 10 causes of death Geneva: World Health Organization, 2013 In:...
- et al.
Fatal outcome of human influenza A (H5N1) is associated with high viral load and hypercytokinemial outcome of human influenza A (H5N1) is associated with high viral load and hypercytokinemia
Nat. Med.
(2006) - et al.
Bacterial coinfection in influenza: a grand rounds review
JAMA
(2013) Acute lower respiratory tract infection
N. Engl. J. Med.
(2008)- et al.
Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia?
Clin. Infect. Dis.
(2011) - et al.
Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis
J. Clin. Microbiol.
(2014)
Actionable diagnosis of neuroleptospirosis by next-generation sequencing
N. Engl. J. Med.
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