Detection of respiratory viruses and bacteria in children using a twenty-two target reverse-transcription real-time PCR (RT-qPCR) panel

Virus detection in critically ill children with acute respiratory disease: a new profile in view of new technology

AIM

To describe the epidemiology of critically ill children admitted to a paediatric intensive care unit (PICU) with acute respiratory disease. The association with intubation was analysed for the three most prevalent viruses and in those with and without viral co-infection.

METHODS

Patients admitted to the PICU (2004-2014) with acute respiratory disease were included. Analyses were performed utilising each respiratory viral infection or multiple viral infections as an exposure.

RESULTS

There were 1766 admissions with acute respiratory disease of which 1372 had respiratory virus testing and 748 had one or more viruses detected. The risk of intubation before or during the PICU stay was higher if parainfluenza virus was detected compared to respiratory syncytial virus (RSV) (OR: 2.20; 95% CI: 1.06-4.56). Sixty-three admissions had two or more viruses detected, and the combination of RSV and Rhinovirus/enterovirus was the most common. No significant difference was observed in the risk of intubation between patients with multiple and single viral infections.

CONCLUSION

Higher risk of intubation was found in patients with parainfluenza as compared to RSV. The risk of intubation comparing parainfluenza virus to other viruses and for patients with multiple versus single virus needs to be further studied.

The Impact of Multiple Viral Respiratory Infections on Outcomes for Critically Ill Children

OBJECTIVE

Advances in molecular diagnosis have led to increased testing for single and multiviral respiratory infection in routine clinical practice. This study compares outcomes between single and multiviral respiratory infections in children younger than 5 years old admitted to the PICU with respiratory failure.

DESIGN

Retrospective, single-center, cohort study.

SETTING

Tertiary-care, freestanding children's hospital.

PATIENTS

Children younger than 5 years old admitted to the PICU with respiratory failure and positive respiratory molecular panel. Children with comorbidity or history of similar infections were excluded. After exclusions, the children were divided into single or multiviral groups. Their demographics and PICU outcomes were compared and analyzed.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Four hundred seventy-seven children with respiratory failure tested positive on respiratory panel, out of which 432 had single and 45 had multiple viruses. Children with multiple viruses had a longer PICU stay (4.5 d) compared with the single viral group (3 d; p < 0.002). Multiviral infections were associated with higher utilization of central line (odds ratio, 2.4; 95% CI, 1.3-4.6; p = 0.008) but not with the need of invasive ventilation requirement or cardiovascular dysfunction. Further analysis among invasively ventilated patients showed multiviral infections resulted in higher association of prolonged ventilation (> 7 d) (odds ratio, 3.4; 95% CI, 1.2-9.4; p = 0.01) and bacterial lower respiratory tract infection confirmed by quantitative bronchoalveolar lavage (odds ratio, 2.1; 95% CI, 1.1-11.2; p = 0.03). Infections with human rhinovirus/Enterovirus, Adenovirus, parainfluenza, and influenza formed a significantly larger proportions of cases (p = 0.00089) as multiviral infections compared with individual infections.

CONCLUSIONS

Multiviral infections were associated with longer PICU stay, with prolonged mechanical ventilation, with bacterial lower respiratory infections, and with central line requirement. Certain common viruses resulted in higher percentages of PICU admission as multiviral infections.

Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

Background

Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illness. Using quantitative PCR (qPCR) for common respiratory viruses and for two genes known to be highly upregulated in viral infections (CCL8/CXCL11), we screened 92 asthmatic and 69 healthy children without illness for respiratory virus infections.

Results

We found 21 viral qPCR-positive and 2 suspected virus-infected subjects with high expression of CCL8/CXCL11. We applied a dual RNA-seq workflow to these subjects, together with 25 viral qPCR-negative subjects, to compare qPCR with sequencing-based virus detection and to generate the airway transcriptome for analysis. RNA-seq virus detection achieved 86% sensitivity when compared to qPCR-based screening. We detected additional respiratory viruses in the two CCL8/CXCL11-high subjects and in two of the qPCR-negative subjects. Viral read counts varied widely and were used to stratify subjects into Virus-High and Virus-Low groups. Examination of the host airway transcriptome found that the Virus-High group was characterized by immune cell airway infiltration, downregulation of cilia genes, and dampening of type 2 inflammation. Even the Virus-Low group was differentiated from the No-Virus group by 100 genes, some involved in eIF2 signaling.

Conclusions

Respiratory virus infection without illness is not innocuous but may determine the airway function of these subjects by driving immune cell airway infiltration, cellular remodeling, and alteration of asthmogenic gene expression.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1140-8) contains supplementary material, which is available to authorized users.

Human Parvoviruses

Parvovirus B19 (B19V) and human bocavirus 1 (HBoV1), members of the large Parvoviridae family, are human pathogens responsible for a variety of diseases. For B19V in particular, host features determine disease manifestations. These viruses are prevalent worldwide and are culturable in vitro, and serological and molecular assays are available but require careful interpretation of results. Additional human parvoviruses, including HBoV2 to -4, human parvovirus 4 (PARV4), and human bufavirus (BuV) are also reviewed. The full spectrum of parvovirus disease in humans has yet to be established. Candidate recombinant B19V vaccines have been developed but may not be commercially feasible. We review relevant features of the molecular and cellular biology of these viruses, and the human immune response that they elicit, which have allowed a deep understanding of pathophysiology.

Direct molecular detection of a broad range of bacterial and viral organisms and Streptococcus pneumoniae vaccine serotypes in children with otitis media with effusion

Background

Otitis media with effusion (OME) causes significant morbidity in children, but the causes of OME and methods for prevention are unclear. To look for potential infectious etiologies, we performed a pilot study using multiple-target real-time polymerase chain reaction (qPCR) for 27 infectious agents, including nine bacterial organisms and 18 respiratory viruses in middle ear fluids (MEFs) from children with OME. QPCR was also performed for the 13 Streptococcus pneumoniae serotypes contained in the current vaccine.

Results

Forty-eight MEF samples were obtained and qPCR detected bacterial nucleic acid (NA) in 39/48 (81 %) and viral NA in 7/48 (15 %). Alloiococcus otitidis and S. pneumoniae were both detected in 15/48 (31 %) MEFs, followed by M. catarrhalis in 14/48 (29 %), H. influenzae in 5/48 (10 %) and M. pneumoniae in 4/48 (8 %). Rhinoviruses were most common virus type detected, found in 4/48 (8 %) MEFs. Serotypes included in the current 13-serotype vaccine were detected in only 3/15 (20 %) S. pneumoniae qPCR-positive MEFs.

Conclusions

Bacteria may play an important role in OME, since over 80 % of MEFs contained bacterial NA. Further research into the role of A. otitidis in OME will be helpful. Serotypes of S. pneumoniae not included in the current 13-serotype vaccine may be involved in OME. Larger studies of OME S. pneumoniae serotypes are needed to help determine which additional serotypes should be included in future vaccine formulations in order to try to prevent OME.