The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit

Duration of clinical symptoms in children with acute respiratory infection

AIM

To investigate duration of clinical symptoms associated with various respiratory viruses and with the co-detection of respiratory viral and bacterial pathogens.

METHODS

This prospective cohort study included 737 acutely ill children treated in a paediatric emergency department prior to the COVID-19 pandemic. Nasal swab samples were analysed with multiplex PCR panels for 16 viral and 7 bacterial respiratory pathogens. Parents filled in a questionnaire about the symptoms at the time of the visit and 14 days afterwards.

RESULTS

Persistent symptoms 2 weeks after the onset of acute illness were common: 32% of the patients with a coronavirus 229 E, NL63 or OC43 finding, 31% of those with human metapneumovirus and 25% of those with rhinovirus reported ongoing symptoms. At least one symptom lasting more than 4 weeks was observed in 3-4% of the children. Children with viral and bacterial co-detection had a longer duration of fever than those with only viral detection (3.3 days [SD 2.8] vs. 1.6 days [SD 2.4], p < 0.001).

CONCLUSION

Symptoms lasting for more than 2 to 4 weeks appear to be relatively frequent in all respiratory viral infections in children. Viral and bacterial co-detection may increase the duration of illness.

Viral Identification Using Multiplex Polymerase Chain Reaction Testing Does Not Reduce Antibiotic Prescribing in Paediatric Intensive Care Units

PCR tests for viral identification, performed on nasopharyngeal secretions, have experienced a major boom in the last few years. Their use is very frequent, but their indications are still not well defined, especially in Paediatric Intensive Care Units (PICU). These tests are used for the microbiological diagnosis of lower respiratory infections but can be used in other situations. The aim of the study was to investigate the effect of viral identification on antibiotic therapy management. We conducted a single-centre retrospective study from 1 October 2017 to 31 December 2019. This study included all consecutive FilmArray® Respiratory Panel tests performed in patients hospitalised in a PICU. Patients were identified using the microbiology laboratory prospective database and data were extracted from the medical record. 544 tests corresponding to 408 patients were included. The main reasons for testing were pneumonia (34%) and bronchiolitis (24%). In 70% of cases, at least one virus was identified, with Human Rhinovirus (56%) and Respiratory Syncytial Virus (28%) being the two predominant. Bacterial co-infection was present in 25% of cases. Viral identification was not associated with reduced antibiotic therapy. On multivariate analysis, antibiotic management was significantly associated with clinical gravity, CRP value or radiology findings regardless of virus identification. Viral identification has an epidemiological value, but antibiotic prescription relies on other factors.

Absence from day care or school and parental absence from work during children's respiratory infections

AIM

To investigate the social burden of nasopharyngeal detection of various respiratory viruses and the co-detection of viral and bacterial pathogens.

METHODS

This prospective cohort study included 737 children with a suspected respiratory tract infection or fever in a paediatric emergency department during one epidemiological year (2014-2015) in Finland. Nasopharyngeal swab samples were analysed with multiplex polymerase chain reaction for 16 viruses and 7 respiratory bacteria. Parents filled out a questionnaire regarding child's and parents' absence from day care, school, or work at the time of the visit and 14 days afterward.

RESULTS

The length of the children's absence from day care or school, or parental absence from work, did not significantly differ between the detected viral pathogens. Co-detection of any respiratory virus and Streptococcus pneumoniae or Haemophilus influenzae in the nasopharynx were associated with a 2.5-day (95% CI of the difference: 0.71 to 4.3) and 3.0-day (95% CI: 0.35 to 5.7) longer parental absence from work, respectively, compared with the detection of viruses alone when adjusted for age.

CONCLUSION

Nasopharyngeal detection of S. pneumoniae or H. influenzae was associated with an increase in the length of parental absence from work when compared with the detection of virus alone.

Antibiotic Prescribing Patterns for Outpatient Pediatrics at a Private Hospital in Abu Dhabi: A Clinical Audit Study

BACKGROUND

Antibiotics are commonly used in pediatrics. The aim and objectives were to evaluate the antibiotic prescribing patterns of pediatric outpatients at a private hospital in Abu Dhabi, UAE.

METHODS

A retrospective drug utilization review was conducted for pediatric patients aged 1-18 between June and December 2018. The prescriptions with inclusion criteria were reviewed and evaluated by using the WHO indicators.

RESULTS

419 encounters included were female (50.1%). Most pediatrics were aged 4-6 years (35.3%). The average number of drugs per prescription were 4.9 drugs. The percentage of parenteral medication prescriptions was 16.9%, and with antibiotic prescriptions was 43.0%, where cefaclor was the most prescribed antibiotic (31.1%). The average consultation time was 14 min, while the average dispensing time was 9.6 min. The most common diagnosis where antibiotics were prescribed was acute pharyngitis (33.4%). There were about 60.6% with lab investigation.

CONCLUSION

As per the WHO indicators, the pediatric outpatient department has a high rate of antibiotic use and polypharmacy, but adherence to the drug formulary and prescribing medicines using generic names was appropriate. The average time for consultation and dispensing were suitable. Irrational antibiotic use for inappropriate diagnoses such as acute otitis media and bronchiolitis were found.

Clinical and epidemiological characteristics of influenza virus infection in hospitalized children with acute respiratory infections in Sri Lanka

Influenza viruses (Inf-V) are an important cause of acute respiratory infection (ARI) in children. This study was undertaken to describe the clinical and epidemiological characteristics of Inf-V infections in a sample of hospitalized children with ARI. Nasopharyngeal aspirates (NPA) from 500 children between 1 month to 5 years old with symptoms of ARI were collected at the Teaching Hospital Kegalle Sri Lanka From May 2016 to June 2018, NPAs were tested for influenza A (Inf-A) and B (Inf-B) viruses, human respiratory syncytial virus (hRSV), human parainfluenza virus (hPIV) 1–3 using an immunofluorescence assay. The Inf-V were then subtyped using a multiplex RT-PCR. Inf-V were detected in 10.75% (54/502) of the hospitalized children with ARI and in that 5.57% (28/502) were positive for Inf-A and 5.17% (26/502) were positive for Inf-B. Of the 54 Inf-V positive children, 33 were aged between 6 and 20 months. Of the 28 children infected with Inf-A, 15 had uncharacterized lower respiratory infection, 7 had bronchopneumonia and 6 had bronchiolitis. Of the 26 children infected with Inf-B, 11 had uncharacterized lower respiratory infection, 10 had bronchiolitis, and 4 had bronchopneumonia. Inf-B circulated throughout the year with a few peaks, one in June and then in August followed by November to December in 2016 and one in April 2017 and January 2018. Inf-A circulated throughout the year with a major peak in March to April 2017 and July 2018. ARI was more common in boys compared to girls. Majority of the children infected with Inf-V were diagnosed with uncharacterized lower respiratory infection and mild to moderate bronchiolitis. Inf-V infections were prevalent throughout the year in the study area of Sri Lanka with variations in the type of the circulating virus.

Characteristics and etiology of infection in febrile infants aged ≤90 days

BACKGROUND

Infants ≤90 days old can exhibit non-specific signs of infection, even in cases of serious bacterial infection (SBI).

METHODS

This prospective study included infants aged ≤90 days hospitalized for fever from June 2017 to August 2019. Nasopharyngeal swabs were tested using multiplex real-time polymerase chain reaction (PCR) tests and 16S ribosomal RNA analysis of whole blood to determine causative microorganisms. Data pertaining to inflammatory markers, maximum body temperature (BT), and respiratory symptoms of infants and their cohabiting families were collected at admission.

RESULTS

A total of 110 infants were enrolled (age range, 9-90 days), 17 (15.5%) of whom presented with SBIs. White blood cell (WBC) count and absolute neutrophil count (ANC) were significantly higher in patients with SBIs than in those without, although maximum BT did not significantly differ between the SBI and non-SBI groups (n = 93). One or more viruses were detected in 82 infants (74.5%). Viruses were detected more frequently in infants with respiratory symptoms than in those without respiratory symptoms (P = 0.038), and patients with SBIs experienced significantly less respiratory symptoms than those without SBIs (P = 0.049). Moreover, viruses were more often detected in infants from cohabiting families with respiratory symptoms than in those whose family members did not exhibit respiratory symptoms (P = 0.0018).

CONCLUSION

White blood cell count, and ANC were significantly higher, and respiratory symptoms were less in infants ≤90 days old with SBIs than in those without SBIs. Microorganisms from nasopharyngeal by multiplex real-time PCR swabs could not be judged as SBI or non-SBI.

Epidemiologic and clinical characteristics of human bocavirus infection in infants and young children suffering with community acquired pneumonia in Ningxia, China

Background

Pneumonia has a high incidence rate and is a major cause of mortality in children, mostly community-acquired pneumonia (CAP). Human bocavirus (HBoV), since it first identified in 2005, has been repeatedly associated with respiratory tract infections. Nevertheless, the role and related information of HBoV as a pathogen of CAP has not been fulfilled. Here our study is to assess the epidemiological and clinical features in HBoV-positive children with CAP.

Methods

A total of 878 secretions of lower respiratory samples were obtained, multiplex PCR was used to detect HBoV and other respiratory viruses.

Results

Of all cases, HBoV was detected in 10.0%, with a peak incidence of infection among children < 2 year old, and predominantly noted in autumn and winter. Only 8 patients were HBoV single infection. Co-infection with other respiratory viruses was observed in 86.4%. Moreover, co-infection with bacteria occurred in 27.3% and with Mycoplasma pneumoniae (MP) in 33.0% of HBoV-positive patients. Among all HBoV-positive samples co-infected with bacteria, 87.5% are gram negative bacteria. Compared with HBoV-negative group, age (P = 0.048), wheezing (P = 0.015), tachypnea (P = 0.016), lactate dehydrogenase (P = 0.026) and severe pneumonia (P = 0.023) were statistically significant in HBoV-positive patients. Furthermore, HBoV-positive patients less than 1 year old were more likely to have co-infection with bacteria (P = 0.007).

Conclusions

HBoV can be detected alone in respiratory samples of children with CAP, maybe it is one of the causes of CAP in infants. The high incidence of severe pneumonia was found in HBoV-positive patients compared with HBoV-negative cases may indicate a relationship between severe pneumonia and HBoV.

Cytokine expression patterns in hospitalized children with Bordetella pertussis, Rhinovirus or co-infection

Mechanisms of interaction between Bordetella pertussis and other viral agents are yet to be fully explored. We studied the inflammatory cytokine expression patterns among children with both viral-bacterial infections. Nasopharyngeal aspirate (NPA) samples were taken from children, aged < 1 year, positive for Rhinovirus, Bordetella pertussis and for Rhinovirus and Bordetella pertussis. Forty cytokines were evaluated in NPA by using human cytokine protein arrays and a quantitative analysis was performed on significantly altered cytokines. Forty cytokines were evaluated in NPA by using human cytokine protein arrays and a quantitative analysis was performed on significantly altered cytokines. Our results show that co-infections display a different inflammatory pattern compared to single infections, suggesting that a chronic inflammation caused by one of the two pathogens could be the trigger for exacerbation in co-infections.

[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.

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.

Molecular Diagnosis of Pneumonia Using Multiplex Real-Time PCR Assay RespiFinder® SMART 22 FAST in a Group of Moroccan Infants

Background

In Morocco, pediatric pneumonia remains a serious public health problem, as it constitutes the first cause of mortality due to infectious diseases. The etiological diagnosis of acute respiratory tract infections is difficult. Therefore, it is necessary to use Multiplex real-time polymerase chain reaction assay tests in a routine setting for exact and fast identification.

Objectives

In this paper, we present the clinical results of pediatric pneumonia and describe their etiology by using molecular diagnosis. Study design: Tracheal secretion was collected from infants presenting respiratory distress isolated or associated with systemic signs, attending the unit of Neonatology between December 1, 2016, and Mai 31, 2018. Samples were tested with the multiplex RespiFinder® SMART 22 FAST which potentially detects 18 viruses and 4 bacteria.

Results

Of the 86 infants considered in this study (mean age 31 ± 19 days) suspected of acute respiratory tract infections, 71 (83%) were positive for one or multiple viruses or/and bacteria. The majority of acute respiratory tract infections had a viral origin (95%): respiratory syncytial viruses (A and B) (49%), rhinovirus (21%), coronaviruses 229E (11%), humain metapneumovirus (5%), influenza A (3%), influenza H1N1 (1%), adenovirus (2%), and parainfluenza virus type 4 (2%). Among our patients, 6% had Mycoplasma pneumoniae. Coinfections were not associated with severe respiratory symptoms.

Conclusion

The clinical spectrum of respiratory infections is complex and often nonspecific. Thus, the early and fast detection of related causative agents is crucial. The use of multiplex real time polymerase chain reaction may help choose an accurate treatment, reduce the overall use of unnecessary antibiotics, preserve intestinal flora, and decrease nosocomial infection by reducing the length of hospitalization.

Combining Procalcitonin and Rapid Multiplex Respiratory Virus Testing for Antibiotic Stewardship in Older Adult Patients With Severe Acute Respiratory Infection

OBJECTIVES

Virus infection is underevaluated in older adults with severe acute respiratory infections (SARIs). We aimed to evaluate the clinical impact of combining point-of-care molecular viral test and serum procalcitonin (PCT) level for antibiotic stewardship in the emergency department (ED).

DESIGN

A prospective twin-center cohort study was conducted between January 2017 and March 2018.

SETTING AND PARTICIPANTS

Older adult patients who presented to the ED with SARIs received a rapid molecular test for 17 respiratory viruses and a PCT test.

MEASURES

To evaluate the clinical impact, we compared the outcomes of SARI patients between the experimental cohort and a propensity score-matched historical cohort. The primary outcome was the proportion of antibiotics discontinuation or de-escalation in the ED. The secondary outcomes included duration of intravenous antibiotics, length of hospital stay, and mortality.

RESULTS

A total of 676 patients were included, of which 169 patients were in the experimental group and 507 patients were in the control group. More than one-fourth (27.9%) of the patients in the experimental group tested positive for virus. Compared with controls, the experimental group had a significantly higher proportion of antibiotics discontinuation or de-escalation in the ED (26.0% vs 16.1%, P = .007), neuraminidase inhibitor uses (8.9% vs 0.6%, P < .001), and shorter duration of intravenous antibiotics (10.0 vs 14.5 days, P < .001).

CONCLUSIONS AND IMPLICATIONS

Combining rapid viral surveillance and PCT test is a useful strategy for early detection of potential viral epidemics and antibiotic stewardship. Clustered viral respiratory infections in a nursing home is common. Patients transferred from nursing homes to ED may benefit from this approach.

Severe Sepsis in Pediatric Liver Transplant Patients: The Emergence of Multidrug-Resistant Organisms

OBJECTIVES

To describe characteristics of liver transplant patients with severe sepsis in the PICU.

DESIGN

Retrospective descriptive analysis.

SETTING

Tertiary children's hospital PICU.

PATIENTS

Liver transplant recipients admitted January 2010 to July 2016 for pediatric severe sepsis.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Between January 2010 and July 2016, 173 liver transplants were performed, and 36 of these patients (21%) were admitted with severe sepsis (54 episodes total). Median age at admission was 2 years (1-6.5 yr), 47.2% were male. Bacterial infections were the most common (77.8%), followed by culture negative (12.9%) and viral infections (7.4%). Fungal infections accounted for only 1.9%. Median time from transplant for viral and culture negative infections was 18 days (8.25-39.75 d) and 25 days (9-41 d), whereas 54.5 days (17-131.25 d) for bacterial infections. Bloodstream and intra-abdominal were the most common bacterial sites (45% and 22.5%, respectively). Multidrug-resistant organisms accounted for 47.6% of bacterial sepsis. Vancomycin-resistant Enterococcus and extended-spectrum beta-lactamase producers were the most frequently identified multidrug-resistant organisms. Patients with multidrug-resistant organism sepsis demonstrated higher admission Pediatric Logistic Organ Dysfunction scores (p = 0.043) and were noted to have an odds ratio of 3.8 and 3.6 for mechanical ventilation and multiple organ dysfunction syndrome, respectively (p = 0.047 and p = 0.044). Overall mortality was 5.5% (n = 2 patients), with both deaths occurring in multidrug-resistant organism episodes.

CONCLUSIONS

We report that multidrug-resistant organisms are increasingly being identified as causative pathogens for sepsis in pediatric liver transplant recipients and are associated with significantly higher odds for mechanical ventilation and higher organ failure. The emergence of multidrug-resistant organism infections in pediatric liver transplant patients has implications for patient outcomes, antibiotic stewardship, and infection prevention strategies.

Etiology and characteristics of community-acquired pneumonia in an influenza epidemic period

PURPOSE

The etiology of community-acquired pneumonia (CAP) in hospital patients is often ambiguous due to the limited pathogen detection. Lack of a microbiological diagnosis impairs precision treatment in CAP.

METHODS

Specimens collected from the lower respiratory tract of 195 CAP patients, viruses were measured by the Single-plex real-time PCR assay and the conventional culture method was exploited for bacteria.

RESULTS

Among the 195 patients, there were 46 (23.59%) pure bacterial infections, 20 (10.26%) yeast infections, 32 (16.41%) pure viral infections, 8 (4.10%) viral-yeast co-infections, and 17 (8.72%) viral-bacterial co-infections. The two most abundant bacteria were Acinetobacter baumannii and klebsiella pneumoniae, whereas the most common virus was influenza A.

CONCLUSIONS

Non-influenza respiratory microorganisms frequently co-circulated during the epidemic peaks of influenza, which easily being ignored in CAP therapy. In patients with bacterial and viral co-infections, identifying the etiologic agent is crucial for patient's therapy.

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

•

The respiratory viral profile varied with age.

•

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

•

Persistence of non-enveloped viruses throughout the year.

•

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.

Assessment of the multiplex PCR-based assay Unyvero pneumonia application for detection of bacterial pathogens and antibiotic resistance genes in children and neonates

BACKGROUND

Pneumonia is a major healthcare problem. Rapid pathogen identification is critical, but often delayed due to the duration of culturing. Early, broad antibacterial therapy might lead to false-negative culture findings and eventually to the development of antibiotic resistances. We aimed to assess the accuracy of the new application Unyvero P50 based on multiplex PCR to detect bacterial pathogens in respiratory specimens from children and neonates.

METHODS

In this prospective study, bronchoalveolar lavage fluids, tracheal aspirates, or pleural fluids from neonates and children were analyzed by both traditional culture methods and Unyvero multiplex PCR.

RESULTS

We analyzed specimens from 79 patients with a median age of 1.8 (range 0.01-20.1). Overall, Unyvero yielded a sensitivity of 73.1% and a specificity of 97.9% compared to culture methods. Best results were observed for non-fermenting bacteria, for which sensitivity of Unyvero was 90% and specificity 97.3%, while rates were lower for Gram-positive bacteria (46.2 and 93.9%, respectively). For resistance genes, we observed a concordance with antibiogram of 75% for those specimens in which there was a cultural correlate.

CONCLUSIONS

Unyvero is a fast and easy-to-use tool that might provide additional information for clinical decision making, especially in neonates and in the setting of nosocomial pneumonia. Sensitivity of the PCR for Gram-positive bacteria and important resistance genes must be improved before this application can be widely recommended.

Usefulness of multiplex PCR methods and respiratory viruses' distribution in children below 15 years old according to age, seasons and clinical units in France: A 3 years retrospective study

Background

To date, only influenza and RSV testing are recommended for respiratory viruses’ detection in paediatric units. In this study, we described, according to seasons, ages and clinical units, the results obtained in children (<15 years old) by multiplex-PCR (mPCR) tests allowing a quick and wide range detection of all respiratory viruses. These results were also compared with RSV specific detection.

Methods

All nasopharyngeal mPCR and RSV tests requested by clinicians in our French teaching hospitals group between 2011 and 2014 were retrospectively included. All repeated samples for the same children in the same month were discarded.

Results

Of the 381 mPCR tests (344 children) performed, 51.4% were positive. Positivity and viral co-infection rates were higher in the 6–36 months old strata (81% and 25%, p<0.0001 and p = 0.04, respectively). Viral distribution showed strong variations across ages. During specific influenza epidemic periods, only 1/39 (2.5%) mPCR tests were positive for influenza and 19/39 (48.7%) for other viruses. During specific RSV epidemic periods, only 8/46 (17.4%) mPCR tests were positive for RSV and 14/46 (30.4%) for other viruses. 477/1529 (31.2%) of RSV immunochromatography-tests were positive. Among the negatives immunochromatography-test also explored by mPCR, 28/62 (31%) were positive for other respiratory viruses.

Conclusion

This study provides a wide description of respiratory viruses’ distribution among children in hospital settings using mPCR over 3 years. It emphasizes the number of undiagnosed respiratory viruses according to the current diagnosis practice in France and gives a better picture of respiratory viruses identified in hospital settings by mPCR all over the year in France.

Assessment of the Usefulness of Multiplex Real-Time PCR Tests in the Diagnostic and Therapeutic Process of Pneumonia in Hospitalized Children: A Single-Center Experience

The aim of the study was assessment of the usefulness of multiplex real-time PCR tests in the diagnostic and therapeutic process in children hospitalized due to pneumonia and burdened with comorbidities. Methods. The study group included 97 children hospitalized due to pneumonia at the Karol Jonscher Teaching Hospital in Poznań, in whom multiplex real-time PCR tests (FTD respiratory pathogens 33; fast-track diagnostics) were used. Results. Positive test results of the test were achieved in 74 patients (76.3%). The average age in the group was 56 months. Viruses were detected in 61 samples (82% of all positive results); bacterial factors were found in 29 samples (39% of all positive results). The presence of comorbidities was established in 90 children (92.78%). On the basis of the obtained results, 5 groups of patients were established: viral etiology of infection, 34 patients; bacterial etiology, 7 patients; mixed etiology, 23 patients; pneumocystis, 9 patients; and no etiology diagnosed, 24 patients. Conclusions. Our analysis demonstrated that the participation of viruses in causing severe lung infections is significant in children with comorbidities. Multiplex real-time PCR tests proved to be more useful in establishing the etiology of pneumonia in hospitalized children than the traditional microbiological examinations.

Epidemiologic Analysis of Respiratory Viral Infections Mainly in Hospitalized Children and Adults in a Midwest University Medical Center After the Implementation of a 14-Virus Multiplex Nucleic Acid Amplification Test

OBJECTIVES

To investigate the etiology of viral respiratory tract infections mainly in hospitalized children and adults over a 12-month consecutive period after implementation of a 14-virus multiplex nucleic acid amplification test.

METHODS

From January 2014 to January 2015, a total of 2,237 respiratory samples were analyzed with the US Food and Drug Administration-cleared eSensor Respiratory Viral Panel (GenMark Diagnostics, Carlsbad, CA).

RESULTS

Of the 2,237 specimens tested, 788 specimens were positive for at least one virus, giving a positivity rate of 35.2%, and because of viral codetection, a total of 862 viral targets were identified. The age groups with the highest positivity rates were the 0- to 1-year (73.5%) and 2- to 6-year (78.4%) age groups. The overall viral codetection rate was 9.1%. Human rhinovirus (HRV) was the most prevalent respiratory virus found in children and adults. The peak of HRV seen in September 2014 represented a combination of HRV and enterovirus D68, 2014 epidemic respiratory infections.

CONCLUSION

The ability to detect a wider range of respiratory viruses gave us a better understanding of the etiology of respiratory infections in our population, particularly for HRV and enhanced our ability to detect viral coinfection.

[Methods of rapid diagnosis in clinical microbiology: Clinical needs]

The diagnostic methods of infectious diseases should be fast, accurate, simple and affordable. The speed of diagnosis can play a crucial role in healing the patient, allowing the administration of appropriate antibiotic treatment. One aspect that increasingly determines the need for rapid diagnostic techniques is the increased rates of serious infections caused by multidrug resistant bacteria, which cause a high probability of error in the empirical treatment. Some of the conventional methods such as Gram staining or antigen detection can generate results in less than 1 hour but lack sensitivity. Today we are witnessing a major change in clinical microbiology laboratories with the technological advances such as molecular diagnostics, digital microbiology and mass spectrometry. There are several studies showing that these changes in the microbiological diagnosis reduce the generation time of the test results, which has an obvious clinical impact. However, if we look into the future, other new technologies which will cover the needs required for a rapid microbiological diagnosis are on the horizon. This review provides an in depth analysis of the clinical impact that the implementation of rapid diagnostic techniques will have on unmet clinical needs.

Etiology, seasonality, and clinical characterization of viral respiratory infections among hospitalized children in Beirut, Lebanon

Acute respiratory tract viral infections occur worldwide and are one of the major global burdens of diseases in children. The aim of this study was to determine the viral etiology of respiratory infections in hospitalized children, to understand the viral seasonality in a major Lebanese hospital, and to correlate disease severity and the presence of virus. Over a 1‐year period, nasal and throat swabs were collected from 236 pediatric patients, aged 16‐year old or less and hospitalized for acute respiratory illness. Samples collected were tested for the presence of 17 respiratory viruses using multiplex real‐time RT‐PCR. Pathogens were identified in 165 children (70%) and were frequently observed during fall and winter seasons. Co‐infection was found in 37% of positive samples. The most frequently detected pathogens were human Rhinovirus (hRV, 23%), Respiratory Syncytial Virus (RSV, 19%), human Bocavirus (hBov, 15%), human Metapneumovirus (hMPV, 10%), and human Adenovirus (hAdV, 10%). A total of 48% of children were diagnosed with bronchiolitis and 25% with pneumonia. While bronchiolitis was often caused by RSV single virus infection and hAdV/hBoV coinfection, pneumonia was significantly associated with hBoV and HP1V1 infections. No significant correlation was observed between a single viral etiology infection and a specific clinical symptom. This study provides relevant facts on the circulatory pattern of respiratory viruses in Lebanon and the importance of using PCR as a useful tool for virus detection. Early diagnosis at the initial time of hospitalization may reduce the spread of the viruses in pediatric units. J. Med. Virol. 88:1874–1881, 2016. © 2016 Wiley Periodicals, Inc.

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.

Evaluation of epidemiological and clinical features of influenza and other respiratory viruses

AIM

In our study, we aimed to clinically and epidemiologically evaluate respiratory tract infections the viral agents of which were detected by molecular methods and to compare influenza and other respiratory tract viruses in this context.

MATERIAL AND METHODS

The records of 178 patients aged above 2 years who presented to pediatric emergency outpatient clinic with fever and respiratory tract infection findings between December 2013 and April 2014 were examined retrospectively.

RESULTS

At least one respiratory tract pathogen was detected by polymerase chain reaction in 78.6% (n=140) of the patients: influenza A 33.5%, influenza B 16.4%, respiratory syncytial virus 9.2%, adenovirus 7.8%, rhinovirus 7.1%, coronavirus 7.1%, human metapneumovirus 5.7%, human bocavirus 5.7%, parainfluenza virus 3.5%, coinfection 2.8%. The mean age of the patients was 6.3±3.6 years. Sixty-nine patients (49.2%) were aged between 2 and 5 years. Seventy-one patients (50.7%) were aged 5 years and above. Upper respiratory tract infection was found with a rate of 65.7% and lower respiratory tract infection was found with a rate of 34.2%. It was observed that the distribution of respiratory tract viruses showed variance by age groups. Influenza A infection was observed with the highest rate in both age groups. Influenza B was the second leading agent (p=0.008) above the age of 5 years and respiratory syncytial virus was the second leading agent in the 2-5 year age group (p=0.003). Influenza viruses were detected in 55.9% of 118 patients who were found to be compatible with the definition of "influenza-like illness" specified in the Center for Disease Control and Prevention guidelines and other viral agenst were detected in 44%. No difference could be found between the clinical pictures and radiological findings caused by influenza and other respiratory tract viruses.

CONCLUSIONS

In this study, it was concluded that influenza and other respiratory viruses can not be differentiated definitely by clinical and radiological findings, though there are some differences.

Comparative analytical evaluation of the respiratory TaqMan Array Card with real-time PCR and commercial multi-pathogen assays

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Viral and bacterial real-time PCR oligonucleotides were spotted on TaqMan Array Cards.

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Analytical sensitivity was compared with standalone laboratory PCR assays.

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TaqMan Array Card sensitivity was generally one log lower.

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Reproducibility across six independent testing sites was within one log.

In this study, a multicenter evaluation of the Life Technologies TaqMan^® Array Card (TAC) with 21 custom viral and bacterial respiratory assays was performed on the Applied Biosystems ViiA™ 7 Real-Time PCR System. The goal of the study was to demonstrate the analytical performance of this platform when compared to identical individual pathogen specific laboratory developed tests (LDTs) designed at the Centers for Disease Control and Prevention (CDC), equivalent LDTs provided by state public health laboratories, or to three different commercial multi-respiratory panels. CDC and Association of Public Health Laboratories (APHL) LDTs had similar analytical sensitivities for viral pathogens, while several of the bacterial pathogen APHL LDTs demonstrated sensitivities one log higher than the corresponding CDC LDT. When compared to CDC LDTs, TAC assays were generally one to two logs less sensitive depending on the site performing the analysis. Finally, TAC assays were generally more sensitive than their counterparts in three different commercial multi-respiratory panels. TAC technology allows users to spot customized assays and design TAC layout, simplify assay setup, conserve specimen, dramatically reduce contamination potential, and as demonstrated in this study, analyze multiple samples in parallel with good reproducibility between instruments and operators.

Aptasensors for viral diagnostics

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We discuss progress in aptamer-based detection of viruses.

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We consider the use of aptasensors for point-of-care diagnostics of viruses.

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Aptamers have distinct advantages over antibodies for virus recognition.

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There is strong demand for multiplexed diagnostic measurement of pathogens.

Novel viral diagnostic tools need to be affordable, fast, accurate and easy to use with sensitivity and specificity equivalent or superior to current standards. At present, viral diagnostics are based on direct detection of viral components or indirect detection by measuring antibodies generated in response to viral infection. While sensitivity of detection and quantification are still important challenges, we expect major advances from new assay formats and synthetic binding molecules, such as aptamers. Compared to traditional antibody-based detection, aptamers could provide faster adaptation to continuously evolving virus strains and higher discriminating capacity between specific virus serotypes. Aptamers are very stable and easily modifiable, so are ideal molecules for detection and chemical sensing applications. Here, we review the use of aptasensors for detection of viral pathogens and consider the feasibility of aptasensors to become standard devices for point-of-care diagnostics of viruses.

A comparison of human metapneumovirus and respiratory syncytial virus WHO-defined severe pneumonia in Moroccan children

Acute respiratory infections remain the principal cause of morbidity and mortality in Moroccan children. Besides bacterial infections, respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are prominent among other viruses due to their high prevalence and association with severe clinical episodes. We aimed to describe and compare RSV- and hMPV-associated cases of WHO-defined severe pneumonia in a paediatric population admitted to Morocco's reference hospital. Children aged 2-59 months admitted to the Hôpital d'Enfants de Rabat, Morocco meeting WHO-defined severe pneumonia criteria were recruited during 14 months and thoroughly investigated to ascertain a definitive diagnosis. Viral prevalence of RSV, hMPV and other viruses causing respiratory symptoms was investigated in nasopharyngeal aspirate samples through the use of molecular methods. Of the 683 children recruited and included in the final analysis, 61/683 (8·9%) and 124/683 (18·2%) were infected with hMPV and RSV, respectively. Besides a borderline significant tendency for higher age in hMPV cases, patients infected with either of the viruses behaved similarly in terms of demographics, patient history, past morbidity and comorbidity, vaccination history, socioeconomic background and family environment. Clinical presentation on arrival was also similar for both viruses, but hMPV cases were associated with more severity than RSV cases, had a higher risk of intensive care need, and received antibiotic treatment more frequently. RSV and hMPV are common and potentially life-threatening causes of WHO-defined pneumonia in Moroccan children. Both viruses show indistinctive clinical symptomatology, but in Moroccan children, hMPV was associated with a more severe evolution.

Viral infections in outpatients with medically attended acute respiratory illness during the 2012-2013 influenza season

BACKGROUND

While it is known that acute respiratory illness (ARI) is caused by an array of viruses, less is known about co-detections and the resultant comparative symptoms and illness burden. This study examined the co-detections, the distribution of viruses, symptoms, and illness burden associated with ARI between December 2012 and March 2013.

METHODS

Outpatients with ARI were assayed for presence of 18 viruses using multiplex reverse transcriptase polymerase chain reaction (MRT-PCR) to simultaneously detect multiple viruses.

RESULTS

Among 935 patients, 60% tested positive for a single virus, 9% tested positive for ≥1 virus and 287 (31%) tested negative. Among children (<18 years), the respective distributions were 63%, 14%, and 23%; whereas for younger adults (18-49 years), the distributions were 58%, 8%, and 34% and for older adults (≥50 years) the distributions were 61%, 5%, and 32% (P < 0.001). Co-detections were more common in children than older adults (P = 0.01), and less frequent in households without children (P = 0.003). Most frequently co-detected viruses were coronavirus, respiratory syncytial virus, and influenza A virus. Compared with single viral infections, those with co-detections less frequently reported sore throat (P = 0.01), missed fewer days of school (1.1 vs. 2 days; P = 0.04), or work (2 vs. 3 days; P = 0.03); other measures of illness severity did not vary.

CONCLUSIONS

Among outpatients with ARI, 69% of visits were associated with a viral etiology. Co-detections of specific clusters of viruses were observed in 9% of ARI cases particularly in children, were less frequent in households without children, and were less symptomatic (e.g., lower fever) than single infections.