Evaluation of Four Commercial Multiplex Molecular Tests for the Diagnosis of Acute Respiratory Infections

Approach to hematopoietic cell transplant candidates with respiratory viral detection

The management of respiratory viruses prior to hematopoietic cell transplant (HCT) can be controversial and requires special consideration of host factors, transplant parameters, and the specific respiratory virus (RV). In the setting of adenovirus (ADV), human metapneumovirus (HMPV), influenza, parainfluenza virus (PIV), and respiratory syncytial virus (RSV) detection prior to hematopoietic cell transplant (HCT), clinical practice guidelines recommend transplant delay when possible; however, there is much more ambiguity when other respiratory viruses, such as seasonal coronaviruses (CoVs), human rhinovirus (HRV), and SARS-CoV-2, are detected. Our aims for this review include detailing clinical practical guidelines and reviewing current literature on pre-transplant respiratory viral infections (RVIs), including antiviral therapies and prevention strategies, when available. We will center our discussion on three representative clinical scenarios, with the goal of providing practical guidance to clinicians.

Young Zambian infants with symptomatic RSV and pertussis infections are frequently prescribed inappropriate antibiotics: a retrospective analysis

Pediatric community-acquired pneumonia (CAP) remains a pressing global health concern, particularly in low-resource settings where diagnosis and treatment rely on empiric, symptoms-based guidelines such as the WHO's Integrated Management of Childhood Illness (IMCI). This study details the delivery of IMCI-based health care to 1,320 young infants and their mothers in a low-resource urban community in Lusaka, Zambia during 2015. Our Southern Africa Mother Infant Pertussis Study (SAMIPS) prospectively monitored a cohort of mother/infant pairs across infants' first four months of life, recording symptoms of respiratory infection and antibiotics prescriptions (predominantly penicillins), and tested nasopharyngeal (NP) samples for respiratory syncytial virus (RSV) and Bordetella pertussis. Our retrospective analysis of the SAMIPS cohort found that symptoms and antibiotics use were more common in infants (43% and 15.7%) than in mothers (16.6% and 8%), while RSV and B. pertussis were observed at similar rates in infants (2.7% and 32.5%) and mothers (2% and 35.5%), albeit frequently at very low levels. In infants, we observed strong associations between symptoms, pathogen detection, and antibiotics use. Critically, we demonstrate that non-macrolide antibiotics were commonly prescribed for pertussis infections, some of which persisted across many weeks. We speculate that improved diagnostic specificity and/or clinician education paired with timely, appropriate treatment of pertussis could substantially reduce the burden of this disease while reducing the off-target use of penicillins.

A Digital Microfluidic RT-qPCR Platform for Multiple Detections of Respiratory Pathogens

The coronavirus disease 2019 pandemic has spread worldwide and caused more than six million deaths globally. Therefore, a timely and accurate diagnosis method is of pivotal importance for controlling the dissemination and expansions. Nucleic acid detection by the reverse transcription-polymerase chain reaction (RT-PCR) method generally requires centralized diagnosis laboratories and skilled operators, significantly restricting its use in rural areas and field settings. The digital microfluidic (DMF) technique provides a better option for simultaneous detections of multiple pathogens with fewer specimens and easy operation. In this study, we developed a novel digital microfluidic RT-qPCR platform for multiple detections of respiratory pathogens. This method can simultaneously detect eleven respiratory pathogens, namely, mycoplasma pneumoniae (MP), chlamydophila pneumoniae (CP), streptococcus pneumoniae (SP), human respiratory syncytial virus A (RSVA), human adenovirus (ADV), human coronavirus (HKU1), human coronavirus 229E (HCoV-229E), human metapneumovirus (HMPV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus (FLUA) and influenza B virus (FLUB). The diagnostic performance was evaluated using positive plasmids samples and clinical specimens compared with off-chip individual RT-PCR testing. The results showed that the limit of detections was around 12 to 150 copies per test. The true positive rate, true negative rate, positive predictive value, negative predictive value, and accuracy of DMF on-chip method were 93.33%, 100%, 100%, 99.56%, and 99.85%, respectively, as validated by the off-chip RT-qPCR counterpart. Collectively, this study reported a cost-effective, high sensitivity and specificity on-chip DMF RT-qPCR system for detecting multiple respiratory pathogens, which will greatly contribute to timely and effective clinical management of respiratory infections in medical resource-limited settings.

Side-by-side comparison of parent vs. technician-collected respiratory swabs in low-income, multilingual, urban communities in the United States

Background

Home-based swabbing has not been widely used. The objective of this analysis was to compare respiratory swabs collected by mothers of 7–12-year-olds living in low-income, multilingual communities in the United States with technician collected swabs.

Methods

Retrospective data analysis of respiratory samples collected at home by mothers compared to technicians. Anterior nasal and throat specimens collected using flocked swabs were combined in dry tubes. Test was done using TaqMan array cards for viral and bacterial pathogens. Cycle threshold (Ct) values of ribonuclease P (RNP) gene were used to assess specimen quality. Ct < 40 was interpreted as a positive result. Concordance of pathogen yield from mother versus technician collected swabs were analyzed using Cohen’s Kappa coefficients. Correlation analysis, paired t-test, and Wilcoxon signed-rank test for paired samples were used for RNP Ct values.

Results

We enrolled 36 households in Cincinnati (African American) and 44 (predominately Chinese or Latino) in Boston. In Cincinnati, eight of 32 (25%) mothers did not finish high school, and 11 (34%) had finished high school only. In Boston, 13 of 44 (30%) mothers had less than a high school diploma, 23 (52%) had finished high school only. Mother versus technician paired swabs (n = 62) had similar pathogen yield (paired t-test and Wilcoxon signed rank test p-values = 0.62 and 0.63, respectively; 95% confidence interval of the difference between the two measurements = − 0.45–0.75). Median Ct value for RNP was 22.6 (interquartile range, IQR = 2.04) for mother-collected and 22.4 (IQR = 2.39) for technician-collected swabs (p = 0.62). Agreement on pathogen yield between samples collected by mothers vs. technicians was higher for viruses than for bacterial pathogens, with high concordance for rhinovirus/enterovirus, human metapneumovirus, and adenovirus (Cohen’s kappa coefficients ≥80%, p < 0.0001). For bacterial pathogens, concordance was lower to moderate, except for Chlamydia pneumoniae, for which kappa coefficient indicated perfect agreement.

Conclusion

Mothers with a range of education levels from low-income communities were able to swab their children equally well as technicians. Home-swabbing using dry tubes, and less invasive collection procedures, could enhance respiratory disease surveillance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-12523-3.

Meta-Analysis of the Diagnostic Efficacy of the Luminex xTAG Respiratory Viral Panel FAST v2 Assay for Respiratory Viral Infections

PURPOSE

Acute respiratory viral infections pose significant morbidity and mortality, making it essential to diagnose respiratory viral infections rapidly. In this study, the diagnostic efficacy of the Luminex xTAG Respiratory Virus Panel (RVP) FAST v2 test was evaluated on respiratory viral infections.

MATERIALS AND METHODS

Information was retrieved from electronic databases, including Embase, Web of Science, PubMed, and Cochrane Library, for systematic review. Studies that fulfilled predefined inclusion criteria were included. After the extraction of information, statistical software was utilized for quality evaluation, data analysis, and assessment of publication bias.

RESULTS

Eighty groups in fourfold tables from nine articles were included to perform statistical analyses. Therein, the mean specificity and mean sensitivity of Luminex xTAG RVP FAST v2 test for the detection of respiratory viral infections were 0.99 (0.98-0.99) and 0.88 (0.87-0.90), respectively. Additionally, the negative and positive likelihood ratios were 0.14 (0.11-0.19) and 87.42 (61.88-123.50), respectively. Moreover, the diagnostic odds ratio and area under the curve of summary receiver operating characteristic were 714.80 and 0.9886, respectively.

CONCLUSION

The Luminex xTAG RVP FAST v2 test could be a reliable and rapid diagnostic method for multiple respiratory viral infections.

Viral Respiratory Infections: New Tools for a Rapid Diagnosis

Respiratory tract infection is one of the most common diseases in human worldwide. Many viruses are implicated in these infections, including emerging viruses, such as the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Identification of the causative viral pathogens of respiratory tract infections is important to select a correct management of patients, choose an appropriate treatment, and avoid unnecessary antibiotics use. Different diagnostic approaches present variable performance in terms of accuracy, sensitivity, specificity, and time-to-result, that have to be acknowledged to be able to choose the right diagnostic test at the right time, in the right patient. This review describes currently available rapid diagnostic strategies and syndromic approaches for the detection of viruses commonly responsible for respiratory diseases.

Prognosis of Laboratory-Confirmed Influenza and Respiratory Syncytial Virus in Acute Heart Failure

Concomitant respiratory viral infections may influence clinical outcomes of acute decompensated heart failure (ADHF) but this association is based on indirect observation. The aim of this study was to evaluate the prevalence and impact of laboratory-confirmed influenza or respiratory syncytial virus (RSV) infection on outcomes in patients hospitalised for ADHF. Prospective cohort of patients hospitalised for ADHF with systematic influenza and RSV screening using real-time PCR on nasopharyngeal swabs. The primary outcome was all-cause mortality or readmission at 90 days. Among 803 patients with ADHF, 196 (24.5%) patients had concomitant flu-like symptoms of influenza. PCR was positive in 45 patients (27 for influenza, 19 for RSV). At 90 days, PCR positive patients had lower rates of all-cause mortality or readmission as compared to patients without flu-like symptoms (HR 0.40, 95% CI 0.18–0.91, p = 0.03), and non-significantly less all-cause mortality (HR 0.30, 95% CI 0.04–2.20, p = 0.24), or HF-related death or readmission (HR 0.36, 95% CI 0.13–0.99, p = 0.05). The prevalence of influenza or RSV infection in patients admitted for ADHF was low and associated with less all-cause mortality and readmission. Concomitant viral infection with ADHF may not in itself be a predictor of poor outcomes. (ClinicalTrials.gov NCT02444416).

Development and application of a method to detect 27 respiratory pathogens using multiplex RT-PCR combined with MassARRAY technology

Background

Respiratory tract infections are the most common infections that lead to morbidity and mortality worldwide. Early recognition and precise diagnosis of microbial etiology is important to treat LRTIs promptly, specifically and effectively.

Objectives

To establish a method based on multiplex reverse transcription (MRT)-PCR and MassARRAY technology for the simultaneous detection of 27 respiratory pathogens and explore its clinical application value.

Methods

Analytical sensitivity and specificity of the MRT-PCR-MassARRAY system were validated using inactivated bacterial and viral strains. Also we analyzed samples from 207 patients by MassARRAY methods and compared the results with consensus PCR/reverse transcription (RT)-PCR.

Results

The minimum detection limit of our MRT-PCR-MassARRAY method for pathogens was 10–100 copies/μl, with high specificity. Comparison test with consensus PCR/RT-PCR on 207 clinical samples, the positive, negative, and total correlation rates were 100, 98.68, and 99.03%, respectively. There was a high degree of agreement between the test results of the two methods (P < 0.01 by McNemar’s test).

Conclusion

Our detection system of 27 respiratory pathogens based on MassARRAY technology has high sensitivity and specificity, high throughput, and is simple to operate. It provides diagnostic value for the clinical diagnosis of respiratory pathogens and is of great significance in the screening of respiratory pathogens.

Etiology of Severe Acute Respiratory Infections, Bangladesh, 2017

In April 2017, surveillance detected a surge in severe acute respiratory infections (SARI) in Bangladesh. We collected specimens from SARI patients and asymptomatic controls for analysis with multipathogen diagnostic tests. Influenza A(H1N1)pdm09 was associated with the SARI epidemic, suggesting that introducing vaccines and empiric antiviral drugs could be beneficial.

Respiratory microbes detected in hospitalized adults with acute respiratory infections: associations between influenza A(H1N1)pdm09 virus and intensive care unit admission or fatal outcome in Vietnam (2015-2017)

Background

Acute respiratory tract infection (ARI) is a leading cause of hospitalization, morbidity, and mortality worldwide. Respiratory microbes that were simultaneously detected in the respiratory tracts of hospitalized adult ARI patients were investigated. Associations between influenza A(H1N1)pdm09 virus (H1N1pdm) detection and intensive care unit (ICU) admission or fatal outcome were determined.

Methods

This prospective observational study was conducted between September 2015 and June 2017 at Bach Mai Hospital, Hanoi, Vietnam. Inclusion criteria were hospitalized patients aged ≥15 years; one or more of symptoms including shortness of breath, sore throat, runny nose, headache, and muscle pain/arthralgia in addition to cough and fever > 37.5 °C; and ≤ 10 days from the onset of symptoms. Twenty-two viruses, 11 bacteria, and one fungus in airway specimens were examined using a commercial multiplex real-time PCR assay. Associations between H1N1pdm detection and ICU admission or fatal outcome were investigated by univariate and multivariate logistic regression analyses.

Results

The total of 269 patients (57.6% male; median age, 51 years) included 69 ICU patients. One or more microbes were detected in the airways of 214 patients (79.6%). Single and multiple microbes were detected in 41.3 and 38.3% of patients, respectively. Influenza A(H3N2) virus was the most frequently detected (35 cases; 13.0%), followed by H1N1pdm (29 cases; 10.8%). Hematological disease was associated with ICU admission (p < 0.001) and fatal outcomes (p < 0.001) using the corrected significance level (p = 0.0033). Sex, age, duration from onset to sampling, or number of detected microbes were not significantly associated with ICU admission or fatal outcomes. H1N1pdm detection was associated with ICU admission (odds ratio [OR] 3.911; 95% confidence interval [CI] 1.671–9.154) and fatal outcome (OR 5.496; 95% CI 1.814–16.653) after adjusting for the confounding factors of comorbidities, bacteria/Pneumocystis jirovecii co-detection, and age.

Conclusions

H1N1pdm was associated with severe morbidity and death in adult patients hospitalized with respiratory symptoms. The diagnosis of subtype of influenza virus may be epidemiologically important.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05988-x.

Nucleic acid amplification tests on respiratory samples for the diagnosis of coronavirus infections: a systematic review and meta-analysis

BACKGROUND

Management and control of coronavirus disease 2019 (COVID-19) relies on reliable diagnostic testing.

OBJECTIVES

To evaluate the diagnostic test accuracy (DTA) of nucleic acid amplification tests (NAATs) for the diagnosis of coronavirus infections.

DATA SOURCES

PubMed, Web of Science, the Cochrane Library, Embase, Open Grey and conference proceeding until May 2019. PubMed and medRxiv were updated for COVID-19 on 31st August 2020.

STUDY ELIGIBILITY

Studies were eligible if they reported on agreement rates between different NAATs using clinical samples.

PARTICIPANTS

Symptomatic patients with suspected upper or lower respiratory tract coronavirus infection.

METHODS

The new NAAT was defined as the index test and the existing NAAT as reference standard. Data were extracted independently in duplicate. Risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 tool. Confidence regions (CRs) surrounding summary sensitivity/specificity pooled by bivariate meta-analysis are reported. Heterogeneity was assessed using meta-regression.

RESULTS

Fifty-one studies were included, 22 of which included 10 181 persons before COVID-19 and 29 including 8742 persons diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The overall summary sensitivity was 89.1% (95%CR 84.0-92.7%) and specificity 98.9% (95%CR 98.0-99.4%). Nearly all the studies evaluated different PCRs as both index and reference standards. Real-time RT PCR assays resulted in significantly higher sensitivity than other tests. Reference standards at high risk of bias possibly exaggerated specificity. The pooled sensitivity and specificity of studies evaluating SARS-COV-2 were 90.4% (95%CR 83.7-94.5%) and 98.1% (95%CR 95.9-99.2), respectively. SARS-COV-2 studies using samples from the lower respiratory tract, real-time RT-PCR, and tests targeting the N or S gene or more than one gene showed higher sensitivity, and assays based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), especially when targeting only the RNA-dependent RNA polymerase (RdRp) gene, showed significantly lower sensitivity compared to other studies.

CONCLUSIONS

Pooling all studies to date shows that on average 10% of patients with coronavirus infections might be missed with PCR tests. Variables affecting sensitivity and specificity can be used for test selection and development.

Comparison of performance between Fast Track Diagnostics Respiratory Kit and the CDC global reference laboratory for influenza rRT-PCR panel for detection of influenza A and influenza B

Background

Reliable diagnostics are a key to identifying influenza infections.

Objectives

Our objectives were to describe the detection of influenza among severe acute respiratory infection (SARI) cases, to compare test results from the Fast Track Diagnostics (FTD) Kit for influenza detection to the Centers for Disease Control (CDC) human influenza virus detection and characterization panel, and to assess seasonality of influenza in Burkina Faso.

Methods

Nasopharyngeal and oropharyngeal specimens from SARI cases (hospitalized patients with fever, cough, and onset in the previous 10 days) were tested using the FTD‐33 Kit and the CDC rRT‐PCR influenza assays. We assessed sensitivity and specificity of the FTD‐33 Kit for detecting influenza A, influenza B, and the influenza A(H1N1)pdm09 strain using the CDC human influenza rRT‐PCR panel as the gold standard.

Results

From December 2016 to February 2019, 1706 SARI cases were identified, 1511 specimens were tested, and 211 were positive for influenza A (14.0%) and 100 for influenza B (6.6%) by either assay. Higher influenza circulation occurred between November and April with varying peaks of influenza A and influenza B. Sensitivity of the FTD‐33 assay was 91.9% for influenza A, 95.7% for influenza B, and 93.8% for A(H1N1)pdm09 subtype. Specificity was over 99% for all three tests.

Conclusions

Our study indicates that Burkina Faso has one peak of influenza each year which is similar to the Northern Hemisphere and differs from other countries in West Africa. We found high concordance of influenza results between the two assays indicating FTD‐33 can be used to reliably detect influenza among SARI cases.

[Virological diagnosis of lower respiratory tract infections]

INTRODUCTION

The etiological diagnosis of bronchopulmonary infections cannot be assessed with clinical, radiological and epidemiological data alone. Viruses have been demonstrated to cause a large proportion of these infections, both in children and adults.

BACKGROUND

The diagnosis of viral bronchopulmonary infections is based on the analysis of secretions, collected from the lower respiratory tract when possible, by techniques that detect either influenza and respiratory syncytial viruses, or a large panel of viruses that can be responsible for respiratory disease. The latter, called multiplex PCR assays, allow a syndromic approach to respiratory infection. Their high cost for the laboratory raises the question of their place in the management of patients in terms of antibiotic economy and isolation. In the absence of clear recommendations, the strategy and equipment are very unevenly distributed in France.

OUTLOOK

Medico-economic analyses need to be performed in France to evaluate the place of these tests in the management of patients. The evaluation of the role of the different viruses often detected in co-infection, especially in children, also deserves the attention of virologists and clinicians.

CONCLUSIONS

The availability of new diagnostic technologies, the recent emergence of SARS-CoV-2, together with the availability of new antiviral drugs are likely to impact future recommendations for the management of viral bronchopulmonary infections.

Identification of Viruses in Patients With Postviral Olfactory Dysfunction by Multiplex Reverse-Transcription Polymerase Chain Reaction

Objectives/Hypothesis

To investigate causative viruses in patients with postviral olfactory disorders (PVOD).

Study Design

Case‐control study.

Methods

One hundred fifty‐one consecutive patients diagnosed with PVOD were enrolled, and samples from 38 patients who visited the doctor within 3 months of symptom onset were collected and analyzed. Thirty‐two individuals who underwent surgery for nasal septal deviation during the same time period were collected as the control group. The Sniffin' Sticks psychophysical olfactory test was used to evaluate olfactory function. Olfactory cleft specimens were collected using nasopharyngeal flocked swabs (COPAN FLOQSwabs). Eighteen viruses were tested for with the Luminex xTAG RVP FAST v2 Assay Kit.

Results

Out of the 38 patients with PVOD, rhinoviruses were detected in 13 patients, and coronavirus OC43 was detected in one patient. The frequency of positive virus detection in the patients with anosmia was higher than in those with hyposmia (58.8% vs. 19.0%, P = 0.018). In control group, rhinovirus was identified in one patient (3.1%). Nasal obstruction was the most common symptom and was experienced by 71.0% of patients.

Conclusions

Rhinovirus and coronavirus are more commonly identified in PVOD. Our methods represent an approach to screen for viruses that may be involved in PVOD.

Level of Evidence

4 Laryngoscope, 131:158–164, 2021

Role of Human Bocavirus Respiratory Tract Infection in Hematopoietic Cell Transplant Recipients

BACKGROUND

Limited data exist regarding the impact of human bocavirus (BoV) in hematopoietic cell transplant (HCT) recipients.

METHODS

In a longitudinal surveillance study among allogeneic HCT recipients, pre-HCT and weekly post-HCT nasal washes and symptom surveys were collected through day 100, then at least every 3 months through 1 year post-HCT at the Fred Hutch (2005-2010). Samples were tested by multiplex semi-quantitative PCR for 12 viruses. Plasma samples from BoV+ subjects were analyzed by PCR. Separately, we conducted a retrospective review of HCT recipients with BoV detected in lower respiratory tract specimens.

RESULTS

Among 51 children and 420 adults in the prospective cohort, 21 distinct BoV respiratory tract infections (RTIs) were observed by 1 year post-HCT in 19 patients. Younger age and exposure to children were risk factors for BoV acquisition. Univariable models among patients with BoV RTI showed higher peak viral load in nasal samples (p=0.04) and presence of respiratory copathogens (p=0.03) were associated with presence of respiratory symptoms but BoV plasma detection was not. Only watery eyes and rhinorrhea were associated with BoV RTI in adjusted models. With additional chart review, we identified 6 HCT recipients with BoV detected in lower respiratory tract specimens [incidence rate of 0.4% (9/2509) per sample tested]. Although all cases presented with hypoxemia, 4 had respiratory copathogens or concomitant conditions that contributed to respiratory compromise.

CONCLUSIONS

BoV RTI is infrequent in transplant recipients and associated with mild symptoms. Our studies did not demonstrate convincing evidence that BoV is a serious respiratory pathogen.

Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

BACKGROUND

Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children.

METHODS

We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort.

RESULTS

We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001).

CONCLUSIONS

An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.

Prevalence of viral infection in acute exacerbation of interstitial lung diseases in Japan

Background

Fatal acute exacerbation of interstitial lung diseases is often accompanied by indicators of infection such as fever, cough, and sputum. Although viral infection can contribute to acute exacerbation of interstitial lung diseases, few studies have identified a relationship between acute exacerbations and viral infections. The present study aimed to prospectively clarify the role of viral infection in patients showing acute exacerbation of interstitial lung disease in Japan.

Methods

Nasopharyngeal swab specimens were collected from patients with acute exacerbation of interstitial lung disease between May 2017 and February 2019. Respiratory viruses were detected by the Luminex xTAG Respiratory Viral Panel FAST v2 RUO kit and the BioFire FilmArray Respiratory Panel assay.

Results

Three of 29 patients demonstrated respiratory viral infection during acute exacerbation of interstitial lung diseases. The infectious agents were identified as respiratory syncytial virus, respiratory syncytial virus and influenza A virus, and influenza A virus and rhino/enterovirus in the three patients, respectively.

Conclusions

These results suggest that viral infection did not frequently induce acute exacerbation of interstitial lung diseases in Japan.

The epidemiologic and clinical features of viral agents among hospitalized children with lower respiratory tract infections

Aim

Acute respiratory tract infections are among the most common infectious diseases worldwide. Respiratory viruses are the leading cause of respiratory infections in children. Herein, we aimed to determine the epidemiologic and clinical feautures of viral agents among hospitalized children with lower respiratory tract infections.

Material and Methods

Nasopharyngeal swab specimens were obtained from the 422 patients hospitalized with a diagnosis of lower respiratory tract infections between December 2012 and December 2016. Multiplex reverse-transcription polymerase chain reaction was performed for the detection of viruses.

Results

Viral respiratory pathogens were detected in 311 patients (73.7%). In regard to respiratory virus subtypes, 103 patients (33.1%) had respiratory syncytial virus, 102 (32.7%) had human rhinovirus, 49 (15.7%) had multiple viruses, 15 (4.8%) had parainfluenzavirus, 13 (4.1%) had adenovirus, nine (2.8%) had human metapneumovirus, eight (2.5%) had human coronaviruses, six (1.9%) had bocavirus, five (1.6%) had influenza virus, and one patient (0.3%) had enterovirus. The median age was lower in patients with multiple viruses (p<0.001). The respiratory syncytial virus was more commonly detected in patients with a history of prematurity (p<0.001). Stridor was more common in other viruses including parainfluenza viruses (p<0.001).

Conclusion

Respiratory viruses are the main causative agents of respiratory tract infections in children. Timely and accurate detection of viruses is necessary in terms of public health. The detection of respiratory viruses also contributes to epidemiologic results and vaccine studies.

Paramyxovirus infections in hematopoietic cell transplant recipients

PURPOSE OF REVIEW

In hematopoietic cell transplant (HCT) recipients, paramyxovirus infections are major viral respiratory tract infections that, if they progress to lower respiratory tract infections, are associated with reduced survival rates in this population. There are important knowledge gaps regarding treatment decisions for HCT recipients with these infections and in the identification of risk factors that predict infection severity. Here, we review recent data on paramyxovirus infections in HCT recipients focusing on risk factors, new diagnostic and prognostic tools, and management including new drugs and vaccines under development.

RECENT FINDINGS

Multiplexed molecular assays associated with immunodeficiency scoring index for respiratory syncytial virus (RSV) have improved our understanding of the epidemiology of RSV and other paramyxovirus infections and the risk factors for worse outcomes. Novel antiviral drugs, monoclonal antibodies, and vaccines are under evaluation with mixed preliminary results.

SUMMARY

Advances in our knowledge of paramyxovirus infections in HCT recipients in the last two decades contributed to better strategies for management and prevention of these infections. A widespread understanding of how to stratify HCT recipients with paramyxovirus infections who would benefit most from antiviral therapy remains to be ascertained. Vaccines and new drugs under development may mitigate the burden of paramyxovirus infections.

Combination of β-(1, 3)-D-glucan testing in serum and qPCR in nasopharyngeal aspirate for facilitated diagnosis of Pneumocystis jirovecii pneumonia

BACKGROUND

Currently, the biological diagnosis of Pneumocystis jirovecii pneumonia (PjP infection) usually relies on microbiological investigations in bronchial-alveolar lavage fluid (BALF) by conventional staining methods and/or molecular biology. However, bronchial-alveolar lavage is sometimes complicated to manage, especially in weakened patients. Therefore, alternative clinical samples-easier to collect-are warranted in such specific contexts.

OBJECTIVE

Over a four-year period, diagnostic performance of an original method based on combination of quantitative real-time polymerase chain reaction (qPCR) in nasopharyngeal aspirate (NPA) with measurement of β-(1, 3)-D-glucan antigen (BDG) in serum was prospectively assessed in a single centre.

PATIENTS/METHODS

Results were compared with those obtained in BALF through direct staining methods and qPCR. True positives were defined by an independent committee based on clinical, radiological and biological data. Overall, 48 individuals with a definitive diagnosis of PjP infection were included, and 48 controls were selected upon matching for age, sex and underlying disease(s).

RESULTS

qPCR results were strongly correlated between BALF and NPA (P < .0001). Altogether, greater diagnostic performance was achieved when establishing the positive cut-off of BDG antigen at 143 pg/mL. In such conditions, sensitivity of the testing based on either positive BDG measurement or positive qPCR in NPA was then calculated at 93.75%, _95% CI [82.37%-98.40%], and specificity at 97.87%, _95% CI [87.66%-100.00%].

CONCLUSIONS

Further validation through multicentre studies is now required, especially for establishing clear cut-offs. However, one could already state that combination of qPCR in the NPA with BDG measurement in serum may be a valuable substitute for BALF examination.

Epidemiology and Transmission of Respiratory Infections in Thai Army Recruits: A Prospective Cohort Study

Military recruits are at high risk of respiratory infections. However, limited data exist on military populations in tropical settings, where the epidemiology of respiratory infections differs substantially from temperate settings. We enrolled recruits undertaking a 10-week military training at two Royal Thai Army barracks between May 2014 and July 2015. We used a multiplex respiratory panel to analyze nose and throat swabs collected at the start and end of the training period, and from participants experiencing respiratory symptoms during follow-up. Paired sera were tested for influenza seroconversion using a hemagglutinin inhibition assay. Overall rates of upper respiratory illness and influenza-like illness were 3.1 and 2.0 episodes per 100 person-weeks, respectively. A pathogen was detected in 96% of samples. The most commonly detected microbes were Haemophilus influenzae type B (62.7%) or non–type B (58.2%) and rhinovirus (22.4%). At baseline, bacterial colonization was high and included H. influenzae type B (82.3%), H. influenzae non–type B (31.5%), Klebsiella pneumoniae (14.6%), Staphylococcus aureus (8.5%), and Streptococcus pneumoniae (8.5%). At the end of follow-up, colonization with H. influenzae non–type B had increased to 74.1%, and S. pneumoniae to 33.6%. In the serology subset, the rate of influenza infection was 3.4 per 100 person-months; 58% of influenza infections resulted in clinical disease. Our study provides key data on the epidemiology and transmission of respiratory pathogens in tropical settings. Our results emphasize the need for improved infection prevention and control in military environments, given the high burden of illness and potential for intense transmission of respiratory pathogens.

A prospective study on the epidemiology and clinical significance of viral respiratory infections among pediatric oncology patients

Respiratory infections in oncology are both common and potentially severe. However, there is still a gap in the literature, regarding the epidemiology of viral respiratory infections in children with cancer. We prospectively enrolled 224 patients, from September 2012 to August 2015. The cohort included children with hematologic or solid malignancies receiving chemotherapy, or undergoing hemopoietic stem cell transplantation, outpatients/inpatients exhibiting signs/symptoms of febrile/afebrile upper/lower respiratory infection. Viral infection was diagnosed by detection of ≥1 viruses from a sample at time of enrollment, using the CLART^® PneumoVir kit (GENOMICA, Spain). Α detailed questionnaire including demographics and medical history was also completed. Samples were processed in batches, results were communicated as soon as they became available. Children recruited in whom no virus was detected composed the no virus detected group. Viral prevalence was 38.4% in children presenting with respiratory illness. A single virus was found in 30.4%, with RSV being the most frequent. Viral coinfections were detected in 8%. Children with viral infection were more likely to be febrile upon enrollment and to present with lower respiratory signs/symptoms. They had longer duration of illness and they were more likely to receive antibiotics/antifungals. Only 22% of children with influenza received oseltamivir. Mortality was low (2.7%), however, pediatric intensive care unit (PICU) admission and death were correlated with virus detection. In our study mortality was low and PICU admission was related to virus identification. Further research is needed to clarify whether antibiotics in virus-proven infection are of value and underline the importance of oseltamivir's timely administration in influenza.

Use of TaqMan Array card for the detection of respiratory viral pathogens in children under 5 years old hospitalised with acute medical illness in Ballabgarh, Haryana, India

Historical specimens collected from hospitalized children were tested for the following 13 viruses: influenza A and B; respiratory syncytial virus (RSV); parainfluenza viruses 1-3; human metapneumovirus; rhinovirus; coronaviruses 229E, OC43, NL63 and HKU1 and Adenovirus using monoplex real-time reverse transcriptase polymerase chain reaction (rRT-PCR). They were retested using TaqMan Array Card (TAC), a micro-fluidic system, capable of simultaneous multi-pathogen testing, to evaluate its sensitivity and specificity against monoplex rRT-PCR. TAC showed high sensitivity (71%-100%) and specificity (98%-100%) for these viruses in comparison to monoplex rRT-PCR. Multi-specimen detection with high sensitivity and specificity makes TAC a potentially useful tool for both surveillance and outbreak investigations.

A novel real-time PCR assay panel for detection of common respiratory pathogens in a convenient, strip-tube array format

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Respanel is a laboratory-developed PCR test panel for common respiratory pathogens.

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Strip-tube array-based assay, designed for convenience and minimal hands-on time.

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Specificity and accuracy of Respanel is ≥95% against two commercial assays.

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Sensitivity of Respanel is 94% and 88% against two commercial assays.

Commercial multiplex assays, built on different chemistries and platforms are widely available for simultaneous detection of pathogens that cause respiratory infections. However, these tests are often difficult to implement in a resource limited setting because of high cost. In this study, we developed and validated a method for simultaneous testing of common respiratory pathogens (Respanel) by real-time PCR in a convenient, strip-tube array format. Primers and probes for sixteen PCR assays were selected from the literature or newly designed. Following optimization of individual PCR assays, strip-tube arrays were prepared by dispensing primer-probe mixes (PPM) into two sets of 8-tube strips. Nucleic acid extracts from specimens were mixed with PCR master mix, and dispensed column-wise into 2 × 8-wells of a 96-well plate. PPMs from strip-tubes were then added to the wells using a multichannel pipette for real-time PCR. Individual PCR assays were optimized using previously known specimens (n = 394) with 91%–100% concordance with culture, DFA or PCR results. Respanel was then tested in a routine manner at two different sites using specimens (n = 147) previously tested by Qiagen Resplex I&II or Fast-Track Diagnostics Respiratory Pathogens 21 assays. The sensitivity, specificity and accuracy of Respanel were 94%, 95% and 95%, respectively, against Resplex and 88%, 100% and 99%, respectively, against FTDRP21. Respanel detected more pathogens (p < 0.05) than Resplex but the rate of pathogen detection was not significantly different from FTDRP21. Respanel is a convenient and inexpensive assay that is more sensitive than Resplex and comparable to FTDRP21 for the detection of common respiratory pathogens.

Respiratory Viral Infections in Patients With Cancer or Undergoing Hematopoietic Cell Transplant

Survival rates for pediatric cancer have steadily improved over time but it remains a significant cause of morbidity and mortality among children. Infections are a major complication of cancer and its treatment. Community acquired respiratory viral infections (CRV) in these patients increase morbidity, mortality and can lead to delay in chemotherapy. These are the result of infections with a heterogeneous group of viruses including RNA viruses, such as respiratory syncytial virus (RSV), influenza virus (IV), parainfluenza virus (PIV), metapneumovirus (HMPV), rhinovirus (RhV), and coronavirus (CoV). These infections maintain a similar seasonal pattern to those of immunocompetent patients. Clinical manifestations vary significantly depending on the type of virus and the type and degree of immunosuppression, ranging from asymptomatic or mild disease to rapidly progressive fatal pneumonia Infections in this population are characterized by a high rate of progression from upper to lower respiratory tract infection and prolonged viral shedding. Use of corticosteroids and immunosuppressive therapy are risk factors for severe disease. The clinical course is often difficult to predict, and clinical signs are unreliable. Accurate prognostic viral and immune markers, which have become part of the standard of care for systemic viral infections, are currently lacking; and management of CRV infections remains controversial. Defining effective prophylactic and therapeutic strategies is challenging, especially considering, the spectrum of immunocompromised patients, the variety of respiratory viruses, and the presence of other opportunistic infections and medical problems. Prevention remains one of the most important strategies against these viruses. Early diagnosis, supportive care and antivirals at an early stage, when available and indicated, have proven beneficial. However, with the exception of neuraminidase inhibitors for influenza infection, there are no accepted treatments. In high-risk patients, pre-emptive treatment with antivirals for upper respiratory tract infection (URTI) to decrease progression to LRTI is a common strategy. In the future, viral load and immune markers may prove beneficial in predicting severe disease, supporting decision making and monitor treatment in this population.

Prevalence of Human Bocavirus in Africa and Other Developing Countries between 2005 and 2016: A Potential Emerging Viral Pathogen for Diarrhea

BACKGROUND

Human Bocavirus (HBoV) is an emerging virus discovered in 2005 from individuals suffering gastroenteritis and respiratory tract infections. Numerous studies related to the epidemiology and pathogenesis of HBoV have been conducted worldwide. This review reports on HBoV studies in individuals with acute gastroenteritis, with and without respiratory tract infections in Africa between 2005 and 2016.

MATERIAL AND METHOD

The search engines of PubMed, Google Scholar, and Embase database for published articles of HBoV were used to obtain data between 2005 and 2016. The search words included were as follows: studies performed in Africa or/other developing countries or/worldwide; studies for the detection of HBoV in patients with/without diarrhea and respiratory tract infection; studies using standardized laboratory techniques for detection.

RESULTS

The search yielded a total of 756 publications with 70 studies meeting the inclusion criteria. Studies included children and individuals of all age groups. HBoV prevalence in Africa was 13% in individuals suffering gastroenteritis with/without respiratory tract infection.

CONCLUSION

Reports suggest that HBoV infections are increasingly being recognized worldwide. Therefore, surveillance of individuals suffering from infections in Africa is required to monitor the prevalence of HBoV and help understand the role of HBoV in individuals suffering from gastroenteritis with/without respiratory tract infection.

Diagnostic accuracy of digital RNA quantification versus real-time PCR for the detection of respiratory syncytial virus in nasopharyngeal aspirates from children with acute respiratory infection

BACKGROUND

Virus-specific molecular assays such as real-time polymerase chain reaction (RT-PCR) are regularly used as the gold standard to diagnose viral respiratory tract infections, but simultaneous detection of multiple different pathogens is often challenging. A multiplex digital method of RNA quantification, nCounter (NanoString Technologies), can overcome this disadvantage and identify, in a single reaction, the presence of different respiratory viruses.

OBJECTIVES

To evaluate the accuracy of nCounter to identify and quantify RSV-A and RSV-B in nasopharyngeal aspirates (NPA) of children (6-23-months-old) with acute respiratory infection.

STUDY DESIGN

NPA was collected at enrolment in a prospective cross-sectional study conducted in Salvador, Brazil. A quantitative RT-PCR with a subgroup-specific primer and probeset for RSV-A and RSV-B was performed in parallel with a customized nCounter probeset containing viral targets in NPA.

RESULTS

Of 559 NPA tested, RSV was detected by RT-PCR in 139 (24.9%), by nCounter in 122 (21.8%) and by any method in 158 (28.3%) cases. Compared to the gold standard of qRT-PCR, sensitivity of nCounter was 74.3% (95%CI:63.3%-82.9% RSV-A) and 77.6% (95%CI:66.3%-85.9% RSV-B); specificity was 98.4% (95%CI:96.8%-99.2% RSV-A) and 97.8% (95%CI:96.0%-98.8% RSV-B); positive predictive value was 87.3% (95%CI:76.9%-93.4% RSV-A) and 82.5% (95%CI:71.4%-90.0% RSV-B) and negative predictive value was 96.1% (95%CI:94.1%-97.5% RSV-A), and 96.9% (95%CI:95.1%-98.2% RSV-B). Accuracy was 95.2% (95%CI:93.1%-96.7%) for RSV-A and 95.3% (95%CI:93.3%-96.9%) for RSV-B, while both methods significantly correlated for RSV-A (r = 0.44, p = 8 × 10^-5) and RSV-B (r = 0.73, p = 3 × 10^-12) quantification.

CONCLUSIONS

nCounter is highly accurate in detecting RSV-A/B in NPA. Robustness and high-throughput multiplexing indicate its use in large-scale epidemiological studies.

Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology

Background

Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy.

Objective

The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems.

Methods

We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States.

Results

The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present.

Conclusions

Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.

Severe infections in critically ill solid organ transplant recipients

BACKGROUND

Severe infections are among the most common causes of death in immunocompromised patients admitted to the intensive care unit. The epidemiology, diagnosis and treatment of these infections has evolved in the last decade.

AIMS

We aim to provide a comprehensive review of these severe infections in this population.

SOURCES

Review of the literature pertaining to severe infections in critically ill solid organ transplant recipients. PubMed and Embase databases were searched for documents published since database inception until November 2017.

CONTENT

The epidemiology of severe infections has changed in the immunocompromised patients. This population is presenting to the intensive care unit with specific transplantation procedure-related infections, device-associated infections, a multitude of opportunistic viral infections, an increasing number of nosocomial infections and bacterial diseases with a more limited therapeutic armamentarium. Both molecular diagnostics and imaging techniques have had substantial progress in the last decade, which will, we hope, translate into faster and more precise diagnoses, as well as more optimal empirical treatment de-escalation.

IMPLICATIONS

The key clinical elements to improve the outcome of critically ill solid organ transplant recipients depend on the knowledge of geographic epidemiology, specific surgical procedures, net state of immunosuppression, hospital microbial ecology, aggressive diagnostic strategy and search for source control, rapid initiation of antimicrobials and minimization of iatrogenic immunosuppression.

Non-culture based assays for the detection of fungal pathogens

Traditional, culture based methods for the diagnosis of fungal infections are still considered as gold standard, but they are time consuming and low sensitive. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. In this brief review, we highlighted the advantages and disadvantages of conventional diagnostic methods and possibility of non-culture based assays in diagnosis of superficial fungal infections and presented the overview on currently available immunochromatographic assays as well as availability of biomarkers detection by immunodiagnostic procedures in prompt and accurate diagnosis of invasive fungal infections. In addition, we presented diagnostic efficiency of currently available molecular panels and researches in this area.

Volatile fingerprinting of human respiratory viruses from cell culture

Volatile metabolites are currently under investigation as potential biomarkers for the detection and identification of pathogenic microorganisms, including bacteria, fungi, and viruses. Unlike bacteria and fungi, which produce distinct volatile metabolic signatures associated with innate differences in both primary and secondary metabolic processes, viruses are wholly reliant on the metabolic machinery of infected cells for replication and propagation. In the present study, the ability of volatile metabolites to discriminate between respiratory cells infected and uninfected with virus, in vitro, was investigated. Two important respiratory viruses, namely respiratory syncytial virus (RSV) and influenza A virus (IAV), were evaluated. Data were analyzed using three different machine learning algorithms (random forest (RF), linear support vector machines (linear SVM), and partial least squares-discriminant analysis (PLS-DA)), with volatile metabolites identified from a training set used to predict sample classifications in a validation set. The discriminatory performances of RF, linear SVM, and PLS-DA were comparable for the comparison of IAV-infected versus uninfected cells, with area under the receiver operating characteristic curves (AUROCs) between 0.78 and 0.82, while RF and linear SVM demonstrated superior performance in the classification of RSV-infected versus uninfected cells (AUROCs between 0.80 and 0.84) relative to PLS-DA (0.61). A subset of discriminatory features were assigned putative compound identifications, with an overabundance of hydrocarbons observed in both RSV- and IAV-infected cell cultures relative to uninfected controls. This finding is consistent with increased oxidative stress, a process associated with viral infection of respiratory cells.

Community-Acquired Pneumonia in Children: the Challenges of Microbiological Diagnosis

Community-acquired pneumonia (CAP) is the leading cause of mortality in children under 5 years of age globally. To improve the management of CAP, we must distinguish CAP from other common pediatric conditions and develop better diagnostic methods to detect the causative organism, so as to best direct appropriate resources in both industrialized and developing countries. Here, we review the diagnostic modalities available for identifying viruses and bacteria in the upper and lower respiratory tract of children, with a discussion of their utility and limitations in diagnosing CAP in children.

Epidemiology and seasonality of acute respiratory infections in hospitalized children over four consecutive years (2012-2016)

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The respiratory viral profile varied with age.

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The distribution of viruses is variable over the year depending on the species.

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Persistence of non-enveloped viruses throughout the year.

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Atmospheric temperature was rarely a limiting factor in the circulation of viruses.

Background

Acute respiratory infections are a principal cause of illness and mortality especially in young children worldwide.

Objectives

To study the epidemiology and seasonality of viral respiratory infections in hospitalized children (under the age of 16) between September 2012 and August 2016.

Study design

Nasopharyngeal swabs or aspirates were collected from 3199 symptomatic patients and then screened with a routine multiplex PCR assay.

Results

Respiratory viruses were detected for 1624 (50.8%) of the 3199 children in the study population. Of these, 210 (13.3%) were positive for two viruses, 28 (1.7%) were positive for three, and 3 (0.2%) were positive for four. The viral profile varied with age. Some viruses were significantly more frequent in children under the age of 1 month (such as human respiratory syncytial virus (p < 0.0001)), whereas others were significantly more frequent in children over that age (such as influenza viruses (p < 0.0001) and adenoviruses (p = .0006)). The distribution of viruses is variable over the year depending on the species. However, the atmospheric temperature was rarely found to be a limiting factor in the circulation of respiratory viruses.

Conclusions

our results constitute a detailed description of the distribution of respiratory viruses among hospitalized children over four consecutive years. Our data notably highlight the persistence of non-enveloped viruses and some enveloped viruses throughout the year–regardless of temperature variations.

Multiplex PCR for Detection and Identification of Microbial Pathogens

 Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests.

Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam

Background: Acute respiratory infections (ARI) are among the leading causes of hospitalization in children ≤5 years old. Rapid diagnostics of viral pathogens is essential to avoid unnecessary antibiotic treatment, thereby slowing down antibiotic-resistance. We evaluated the diagnostic performance of the Luminex xTAG Respiratory Viral Panel FAST v2 against viral specific PCR as reference assays for ARI in Vietnam.Methods: Four hundred and forty two nose and throat swabs were collected in viral transport medium, and were tested with Luminex xTAG Respiratory Viral Panel FAST v2. Multiplex RT-PCR and single RT-PCR were used as references.   Results: Overall, viral pathogens were detected in a total count of 270/294 (91.8%, 95% CI 88.1-94.7) by the Luminex among reference assays, whilst 112/6336 (1.8%, 95% CI, 1.4-2.1) of pathogens were detected by the Luminex, but not by reference assays. Frequency of pathogens detected by Luminex and reference assays was 379 and 292, respectively. The diagnostic yield was 66.7% (295/442, 95%CI 62.1-71.1%) for the Luminex assay and 54.1% (239/442, 95% CI, 49.3-58.8%) for reference assays. The Luminex kit had higher yields for all viruses except influenza B virus, respiratory syncytial virus, and human bocavirus. High agreements between both methods [mean (range): 0.91 (0.83-1.00)] were found for 10/15 viral agents.Conclusions: The Luminex assay is a high throughput multiplex platform for rapid detection of common viral pathogens causing ARI. Although the current high cost may prevent Luminex assays from being widely used, especially in limited resource settings where ARI are felt most, its introduction in clinical diagnostics may help reduce unnecessary use of antibiotic prescription.

Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam

BACKGROUND

Acute respiratory infections (ARI) are among the leading causes of hospitalization in children ≤5 years old. Rapid diagnostics of viral pathogens is essential to avoid unnecessary antibiotic treatment, thereby slowing down antibiotic-resistance. We evaluated the diagnostic performance of the Luminex xTAG Respiratory Viral Panel FAST v2 against viral specific PCR as reference assays for ARI in Vietnam.

METHODS

Four hundred and forty two nose and throat swabs were collected in viral transport medium, and were tested with Luminex xTAG Respiratory Viral Panel FAST v2. Multiplex RT-PCR and single RT-PCR were used as references.    Results: Overall, viral pathogens were detected in a total count of 270/294 (91.8%, 95% CI 88.1-94.7) by the Luminex among reference assays, whilst 112/6336 (1.8%, 95% CI, 1.4-2.1) of pathogens were detected by the Luminex, but not by reference assays. Frequency of pathogens detected by Luminex and reference assays was 379 and 292, respectively. The diagnostic yield was 66.7% (295/442, 95%CI 62.1-71.1%) for the Luminex assay and 54.1% (239/442, 95% CI, 49.3-58.8%) for reference assays. The Luminex kit had higher yields for all viruses except influenza B virus, respiratory syncytial virus, and human bocavirus. High agreements between both methods [mean (range): 0.91 (0.83-1.00)] were found for 10/15 viral agents.

CONCLUSIONS

The Luminex assay is a high throughput multiplex platform for rapid detection of common viral pathogens causing ARI. Although the current high cost may prevent Luminex assays from being widely used, especially in limited resource settings where ARI are felt most, its introduction in clinical diagnostics may help reduce unnecessary use of antibiotic prescription.

Sepsis and Challenging Infections in the Immunosuppressed Patient in the Intensive Care Unit

In 2017, most intensive care units (ICUs) worldwide are admitting a growing population of immunosuppressed patients. The most common causes of pre-ICU immunosuppression are solid organ transplantation, hematopoietic stem cell transplantation, and infection due to human immunodeficiency virus. In this article, the authors review the most frequent infections that cause critical care illness in each of these 3 immunosuppressed patient populations.

Respiratory RNA Viruses

Acute upper and lower respiratory infections are a major public health problem and a leading cause of morbidity and mortality worldwide. At greatest risk are young children, the elderly, the chronically ill, and those with suppressed or compromised immune systems. Viruses are the predominant cause of respiratory tract illnesses and include RNA viruses such as respiratory syncytial virus, influenza virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus. Laboratory testing is required for a reliable diagnosis of viral respiratory infections, as a clinical diagnosis can be difficult since signs and symptoms are often overlapping and not specific for any one virus. Recent advances in technology have resulted in the development of newer diagnostic assays that offer great promise for rapid and accurate detection of respiratory viral infections. This chapter emphasizes the fundamental characteristics and clinical importance of the various RNA viruses that cause upper and lower respiratory tract diseases in the immunocompromised host. It highlights the laboratory methods that can be used to make a rapid and definitive diagnosis for the greatest impact on the care and management of ill patients, and the prevention and control of hospital-acquired infections and community outbreaks.

Comparison of three multiplex PCR assays for detection of respiratory viruses: Anyplex II RV16, AdvanSure RV, and Real-Q RV

Background

Due to its great sensitivity, the nucleic acid amplification test (NAAT) is widely used for detection of respiratory viruses (RV). However, few reports have described a direct comparison between multiplex RT‐PCR assays for RV. The objective of this study was to perform a direct comparison of three multiplex RT‐PCR assays for the detection of respiratory viruses.

Methods

A total of 201 respiratory samples (161 nasopharyngeal swab samples and 40 sputum samples) were tested with three commercial RV assays: Seegene Anyplex II RV16 (AP), LG AdvanSure RV (AD), and Biosewoom Real‐Q RV (RQ). The additional tests for the discrepant results were conducted by repeat RV assay or monoplex PCR coupled direct sequencing. Data analysis using percent agreement, kappa, and prevalence‐adjusted and bias‐adjusted kappa (PABAK) values was performed for comparisons among the three RV assays.

Results

Of the 201 samples, AP, AD, and RQ detected 105 (52.2%), 99 (49.3%), and 95 (47.3%) positive cases respectively. The overall agreement, kappa, and PABAK values for the three assays ranged between 97%‐98%, 0.76‐0.86, and 0.93‐0.96 respectively. The performance of the three assays was very similar, with 94%‐100% agreement for all comparisons, each virus types. The additional testing of samples showed discrepant results demonstrating that AD assay had the highest rate of concordance with original results.

Conclusions

We suggest that all multiplex assay would be suitable for the detection of for respiratory viruses in clinical setting.

Convergence of Minds: For Better Patient Outcome in Intensive Care Unit Infections

BACKGROUND

There is emergence of resistance to the last-line antibiotics such as carbapenems in Intensive Care Units (ICUs), leaving little effective therapeutic options. Since there are no more newer antibiotics in the armamentarium in the near future, it has become imperative that we harness the interdisciplinary knowledge for the best clinical outcome of the patient.

AIMS

The aim of the conference was to utilize the synergies between the clinical microbiologists and critical care specialists for better patient care and clinical outcome.

MATERIALS AND METHODS

A combined continuing medical education program (CME) under the aegis of the Indian Association of Medical Microbiologists - Delhi Chapter and the Indian Society of Critical Care Medicine, Delhi and national capital region was organized to share their expertise on the various topics covering epidemiology, diagnosis, management, and prevention of hospital-acquired infections in ICUs.

RESULTS

It was agreed that synergy between the clinical microbiologists and critical care medicine is required in understanding the scope of laboratory tests, investigative pathway testing, hospital epidemiology, and optimum use of antibiotics. A consensus on the use of rapid diagnostics such as point-of-care tests, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and molecular tests for the early diagnosis of infectious disease was made. It was agreed that stewardship activities along with hospital infection control practices should be further strengthened for better utilization of the antibiotics. Through this CME, we identified the barriers and actionables for appropriate antimicrobial usage in Indian ICUs.

CONCLUSIONS

A close coordination between clinical microbiology and critical care medicine opens up avenues to improve antimicrobial prescription practices.

Prevalence and Seasonal Distribution of Respiratory Viruses During the 2014 - 2015 Season in Istanbul

Background

Acute respiratory tract infection (ARTI) is one of the most common infections worldwide, causing significant morbidity and mortality.

Objectives

This study was conducted to determine the prevalence and seasonal distribution of respiratory viruses in our region, in children and adults with a pre-diagnosis of ARTI.

Methods

A total of 845 nasopharyngeal swab specimens were analyzed with the RespiFinder Smart 22 kit (PathoFinder BV, Netherlands) and the Rotor-Gene 6000 real-time PCR system.

Results

At least one pathogen was detected in 612 (72.4%) of the specimens. Overall, 902 pathogens were detected; 821 (91%) were viruses and 81 (9%) were bacteria. The most commonly detected pathogens were influenza A virus (IFV-A) (n = 219), influenza B virus (IFV-B) (n=157), rhinovirus/enterovirus (n = 107), human bocavirus (HBoV) (n = 91), respiratory syncytial virus (RSV) A/B (n = 64), adenovirus (n = 56), human coronaviruses (n = 51), Mycoplasma pneumoniae (n = 49), parainfluenza viruses (n = 40), human metapneumovirus (n = 36), Bordetella pertussis (n = 15), Legionella pneumophila (n = 11), and Chlamydophila pneumoniae (n = 6), respectively. Among the 215 (25.4%) co-infected cases, IFV-A/HBoV and IFV-A/IFV-B were the most common co-infections. IFV-A was the most prevalent agent in all age groups except for children under 5 years of age, in whom RSV A/B was the most common pathogen. Approximately two thirds of the respiratory viruses were detected in early spring and winter, with peaks in January, March, and April.

Conclusions

With regard to the prevalence and seasonal distribution of respiratory viruses, our epidemiological data for the 2014 - 2015 season in Istanbul showed a predominance of IFV-A infections with a peak activity in early spring. Enhanced surveillance and early detection of respiratory viral pathogens can be useful in the diagnosis, treatment, and prevention of ARTIs, and for guiding the development of appropriate public health strategies.

Type-specific clinical characteristics of adenovirus-associated influenza-like illness at five US military medical centers, 2009-2014

Background

Adenovirus is a recognized cause of influenza‐like illness (ILI). The proportion of ILI attributable to adenovirus is not known. Moreover, knowledge gaps remain with respect to the epidemiologic, virologic, and clinical characteristics of adenovirus‐associated ILI among otherwise healthy individuals.

Methods

An observational, longitudinal study of <65‐year‐old patients with febrile ILI at five medical centers was conducted from 2009 to 2014. Nasopharyngeal specimens obtained at enrollment were first tested by single‐reaction PCR for adenovirus, then further evaluated by a multiplex PCR assay for other respiratory viral pathogens. Symptoms over a 28‐day period were collected.

Results

We enrolled 1536 individuals, among whom 43 (2·8%) were positive for adenovirus. The median age of cases was 3·4 years (range: 4 months to 41 years). Three were hospitalized. Species and serotype information was available for 33 (76·7%) cases. Species C (n = 21) was the most common, followed by B3 (n = 9) and one each of E4a, D46, and A. Species C infections were more frequent in children (P < 0·01). Half of the cases were positive for at least one other respiratory viral pathogen. Symptoms were generally mild and most commonly included cough (90%), fatigue (79%), rhinorrhea (74%), loss of appetite (71%), and sore throat (64%). Children with non‐C adenovirus infection were more likely to report sore throat (P = 0·05) and hoarseness (P = 0·06) than those with species C infection.

Conclusions

Adenovirus is frequently detected with other respiratory viruses. Persons with non‐C adenovirus infections reported more severe symptoms, suggesting there may be species‐specific differences in virulence and/or host response to infection.

Severe sensitivity loss in an influenza A molecular assay due to antigenic drift variants during the 2014/15 influenza season

The 2014-2015 influenza season in Belgium was dominated by the circulation of 2 influenza A(H3N2) subgroups: 3C.2a and 3C.3b. Analysis of 166 nasopharyngeal aspirates, collected in patients with respiratory illness at the start of the epidemic season, showed a decreased sensitivity for the detection of influenza A(H3N2)/3C.2a using a commercially available multiplex assay. Gene sequencing of the matrix protein showed a point mutation (C163T) leading to a mismatch with the assay probes.

Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing

Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspirate (NPA) specimens, spiked with control bacterial and viral pathogens, were processed using either a commercially available kit (MolYsis) or various detergents followed by DNase prior to the extraction of DNA. Relative quantities of human DNA and pathogen DNA were determined by real-time PCR. The MolYsis kit did not improve the pathogen-to-human DNA ratio, but significant reductions (>95%;P< 0.001) in human DNA with minimal effect on pathogen DNA were achieved in samples that were treated with 0.025% saponin, a nonionic surfactant. Specimen preprocessing significantly decreased NGS reads mapped to the human genome (P< 0.05) and improved the sensitivity of pathogen detection (P< 0.01), with a 20- to 650-fold increase in the ratio of microbial reads to human reads. Preprocessing also permitted the detection of pathogens that were undetectable in the unprocessed samples. Our results demonstrate a simple method for the reduction of background human DNA for metagenomic detection for a broad range of pathogens in clinical samples.