Clinical impact of RT-PCR for pediatric acute respiratory infections: a controlled clinical trial

The Role of DNA Amplification and Cultural Growth in Complicated Acute Appendicitis

Bacterial growth of peritoneal fluid specimens obtained during surgical procedures for acute appendicitis may be useful to optimize further antibiotic therapy in complicated cases. DNA amplification represents a fast technique to detect microbial sequences. We aimed to compare the potential of DNA amplification versus traditional bacterial growth culture highlighting advantages and drawbacks in a surgical setting. Peritoneal fluid specimens were collected during surgery from 36 children who underwent appendectomy between May and December 2012. Real-time polymerase chain reaction (RT-PCR) and cultures were performed on each sample. RT-PCR showed an amplification of 16S in 18/36 samples, Escherichia coli (in 7 cases), Pseudomonas aeruginosa (3), Fusobacterium necrophorum (3), Adenovirus (2), E.coli (1), Klebsiella pneumoniae (1), Serratia marcescens/Enterobacter cloacae (1). Bacterial growth was instead observed only in four patients (3 E.coli and 1 P.aeruginosa and Bacteroides ovatus). Preoperative C-reactive protein and inflammation degree, the most reliable indicators of bacterial translocation, were elevated as expected. DNA amplification was a quick and useful method to detect pathogens and it was even more valuable in detecting aggressive pathogens such as anaerobes, difficult to preserve in biological cultures; its drawbacks were the lack of biological growths and of antibiograms. In our pilot study RT-PCR and cultures did not influence the way patients were treated.

Role of multiplex PCR analysis in children with febrile seizures

Background

The aim of this study was to assess multiplex PCR analysis in detecting causative viruses in children with febrile seizures.

Methods

The study was a retrospective analysis comparing data from a pre-multiplex era (2009) with a period after the introduction of routine respiratory multiplex analysis (2010–2013) in children with febrile seizures.

Results

We included 200 children with febrile seizures (mean age: 29.5 ± 1.4.months; 104 male) in the study. In 2009, in 10 out of 49 (20 %) children, microbiology testing (bacterial/fungal) was positive compared with a rate of 74 out of 151 (49 %) children during 2010–2013 (p < 0.01). The rate of positive virological studies increased from 10 (20 %) in 2009 to 73 (48.3 %) in the period 2010–2013 (p < 0.01). Multiplex PCR analysis confirmed viral infections in 52 of 73 cases (71.2 %).

Conclusion

Routine multiplex PCR analysis fosters the detection of respiratory viruses in children with febrile seizure. The precise role of multiplex analysis in the management of these children awaits further clarification.

Impact of Multiplex Polymerase Chain Reaction Testing for Respiratory Pathogens on Healthcare Resource Utilization for Pediatric Inpatients

OBJECTIVE

To assess whether multiplex polymerase chain reaction (mPCR) vs non-mPCR testing impacts the use of antibiotics, chest radiographs, and isolation precautions.

STUDY DESIGN

We retrospectively compared use of antibiotics, chest radiographs, and isolation precautions for patients <18 years old (excluding neonates) hospitalized at a tertiary referral center tested for respiratory pathogens in the emergency department or during the first 2 hospital days, during 2 periods: June 2010-June 2012 (non-mPCR group) vs October 2012-May 2014 (mPCR group).

RESULTS

Subjects (n = 2430) in the mPCR group were older, had more complex chronic conditions, and were admitted to the pediatric intensive care unit more often compared with the non-mPCR (n = 2349) group. Subjects in the mPCR group had more positive tests (42.4% vs 14.4%, P < .01), received fewer days of antibiotics (4 vs 5 median antibiotic days, P < .01), fewer chest radiographs performed, (59% vs 78%, P < .01), and were placed in isolation longer (20 vs 0 median isolation-hours, P < .01) compared with the non-mPCR group. In multivariable regression, patients tested with mPCR were less likely to receive antibiotics for ≥2 days (OR 0.5, 95% CI 0.5-0.6), chest radiographs at admission (OR 0.4, 95% CI 0.3-0.4), and more likely to be in isolation for ≥2 days (OR 2.4, 95% CI 2.1-2.8) compared with the non-mPCR group.

CONCLUSIONS

Use of mPCR testing for respiratory viruses among hospitalized patients was significantly associated with decreased healthcare resource utilization, including decreased use of antibiotics and chest radiographs, and increased use of isolation precautions.

Implementing an Antibiotic Stewardship Program: Guidelines by the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America

Evidence-based guidelines for implementation and measurement of antibiotic stewardship interventions in inpatient populations including long-term care were prepared by a multidisciplinary expert panel of the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America. The panel included clinicians and investigators representing internal medicine, emergency medicine, microbiology, critical care, surgery, epidemiology, pharmacy, and adult and pediatric infectious diseases specialties. These recommendations address the best approaches for antibiotic stewardship programs to influence the optimal use of antibiotics.

Paediatric apnoeas are not related to a specific respiratory virus, and parental reports predict hospitalisation

Aim

The aim of this study was to determine the frequency of apnoeas in previously healthy young infants with acute respiratory tract infection (ARI) and correlate their occurrence with isolated micro‐organisms, clinical findings, disease severity and outcome.

Methods

We performed reverse transcriptase real‐time polymerase chain reaction (RT‐PCR) on the nasal wash specimens of a prospective cohort study of 582 children with ARI. Clinical data on a subgroup of 241 infants under three months of age, with and without apnoeas, were compared.

Results

Our study found that 19 (7.9%) of the 241 infants under three months old had a history of apnoeas: eight had a respiratory syncytial virus (RSV), five had a different virus than RSV and seven RT‐PCR results were negative. Infants with apnoeas were more likely to have cyanosis, had longer hospital stays and required extra oxygen for a longer period. Most patients with parental reported apnoeas also experienced apnoeas during hospitalisation.

Conclusion

This study observed apnoeas irrespective of the isolated micro‐organism, and we hypothesise that they were related to the pathophysiology of the respiratory infection and not to the micro‐organism itself. Parental reported apnoeas were a major warning sign and predicted that apnoeas would occur in hospital.

Hospital Resource Utilization and Patient Outcomes Associated with Respiratory Viral Testing in Hospitalized Patients

Results suggest that health care providers do not use viral test results in making management decisions.

Testing patients for respiratory viruses should guide isolation precautions and provide a rationale for antimicrobial drug therapies, but few studies have evaluated these assumptions. To determine the association between viral testing, patient outcomes, and care processes, we identified adults hospitalized with respiratory symptoms from 2004 through 2012 at a large, academic, tertiary hospital in Canada. Viral testing was performed in 11% (2,722/24,567) of hospital admissions and was not associated with reduced odds for death (odds ratio 0.90, 95% CI 0.76–1.10) or longer length of stay (+1 day for those tested). Viral testing resulted in more resource utilization, including intensive care unit admission, but positive test results were not associated with less antibiotic use or shorter duration of isolation. Results suggest that health care providers do not use viral test results in making management decisions at this hospital. Further research is needed to evaluate the effectiveness of respiratory infection control policies.

Analytical performance of the automated multianalyte point-of-care mariPOC® for the detection of respiratory viruses

The analytical performance of mariPOC® respi test (ArcDia® Laboratories, Turku, Finland) was evaluated using nucleic acid amplification techniques (NAATs) as the gold standard. The mariPOC assay allows automated detection of antigens from 8 respiratory viruses: influenza A and B viruses, respiratory syncytial virus, adenovirus, human metapneumovirus, and parainfluenza viruses 1-3. Positive results from samples with high viral load are available in 20min. Nasopharyngeal aspirates (n=192) from patients with acute respiratory infection and from previously positive samples were analyzed by mariPOC and NAATs (Simplexa(TM) FluA/FluB & RSV kit [n=118] and Luminex® Respiratory virus panel xTAG® RVP FAST [n=74]). Sensitivity, specificity, positive predictive value, and negative predictive value of mariPOC were 85.4%, 99.2%, 95.9%, and 97%, respectively, and 84.6% of positive results were reported in 20min. The good analytical performance and extended portfolio of mariPOC show this rapid assay as a good alternative for the etiological diagnosis of acute respiratory infection in laboratories that are not equipped with molecular assays.

Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children

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Nasal aspirates were subjected to real-time PCR to detect 16 respiratory viruses.

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One or more viruses were detected in 83% of specimens.

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Rhinoviruses were the most frequently detected viruses.

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Seasonal distribution was seen for each virus.

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The clinical severity did not differ among main respiratory viral infections.

Background

Using the polymerase chain reaction (PCR) method it is possible to detect uncultivable viruses and discover multiple viral infections. However, the clinical importance of these findings in relation to symptoms is not known.

Objectives

The seasonal fluctuations of respiratory viruses and the clinical outcomes of single infections and dual infections were investigated.

Study design

Nasal aspirate samples were obtained from outpatients and inpatients of a children’s hospital and these samples were subjected to real-time PCR to detect 16 respiratory viruses. Seasonal variations of the 16 viruses and the clinical outcomes such as wheezing, the need for oxygenation and prolonged hospitalization of patients with single viral infections and multiple infections were determined for the 5 most often detected viruses.

Results

Among 512 specimens analyzed, one or more viruses were detected in 424 (83%) specimens. Two or more viruses were detected in 160 samples (31% of all samples). The epidemic peaks of the viruses did not coincide with each other. Rhinoviruses were the most frequently detected viruses and their coinfection rates were also higher. However, the disease severity in the lower respiratory tract did not differ in most respiratory viral infections regardless of whether there was single infection or dual infection with a rhinovirus and other respiratory virus.

Conclusions

Seasonal distribution was seen for each virus. There were no significant differences in clinical symptoms in the children studied. Because the infection of rhinoviruses is the common occurrence in children, it is hypothesized that the factors related to disease severity are mainly the underlying conditions of the children.

Clinical and laboratory characteristics of viral lower respiratory tract infections in preschool children

Background

Viral lower respiratory tract infections are the leading cause of hospitalizations in preschool children. Clinical pictures of different viral causes are not well characterized. The aim of this study was to establish the differences in clinical and laboratory characteristics between the different viral causes of lower respiratory tract infections in preschool children.

Methods

We included 278 preschool children hospitalized because of lower respiratory tract infection. White blood cell count and C-reactive protein values were determined and chest X-ray was performed in most patients. Polymerase chain reaction assay was used for the detection of viral pathogens from nasopharyngeal swab.

Results

Pneumonia was present in 71.4 % of all coronavirus infections, 35.1 % of all respiratory syncytial virus infections, and 13.0 % of all rhinovirus infections. Coronavirus (p = 0.03) and respiratory syncytial virus (p < 0.01) were retrospectively shown to be associated with the presence of pneumonia and rhinovirus (p < 0.01) with the absence of pneumonia. Wheezing was present in 81.5 % of all rhinovirus infections and in only 33.3 % of all adenovirus infections. Rhinovirus (p < 0.01) was associated with the presence of wheezing and adenovirus (p = 0.05) with the absence of wheezing. In adenovirus infections mean C-reactive protein value was 72.4 mg/L and white blood cell count 19.000/µl, both significantly higher than in other viruses (p < 0.01).

Conclusions

Clinical and laboratory characteristics of viral lower respiratory tract infections significantly differ. With the advance of viral detection methods and increase of knowledge it becomes possible to characterize different respiratory viral infections and to improve the differential diagnosis.

Association of respiratory viruses with outcomes of severe childhood pneumonia in Botswana

BACKGROUND

The highest incidence of childhood acute lower respiratory tract infection (ALRI) is in low- and middle-income countries. Few studies examined whether detection of respiratory viruses predicts ALRI outcomes in these settings.

METHODS

We conducted prospective cohort and case-control studies of children 1-23 months of age in Botswana. Cases met clinical criteria for pneumonia and were recruited within six hours of presentation to a referral hospital. Controls were children without pneumonia matched to cases by primary care clinic and date of enrollment. Nasopharyngeal specimens were tested for respiratory viruses using polymerase chain reaction. We compared detection rates of specific viruses in matched case-control pairs. We examined the effect of respiratory syncytial virus (RSV) and other respiratory viruses on pneumonia outcomes.

RESULTS

Between April 2012 and August 2014, we enrolled 310 cases, of which 133 had matched controls. Median ages of cases and controls were 6.1 and 6.4 months, respectively. One or more viruses were detected from 75% of cases and 34% of controls. RSV and human metapneumovirus were more frequent among cases than controls, but only enterovirus/rhinovirus was detected from asymptomatic controls. Compared with non-RSV viruses, RSV was associated with an increased risk of treatment failure at 48 hours [risk ratio (RR): 1.85; 95% confidence interval (CI): 1.20, 2.84], more days of respiratory support [mean difference (MD): 1.26 days; 95% CI: 0.30, 2.22 days], and longer duration of hospitalization [MD: 1.35 days; 95% CI: 0.20, 2.50 days], but lower in-hospital mortality [RR: 0.09; 95% CI: 0.01, 0.80] in children with pneumonia.

CONCLUSIONS

Respiratory viruses were detected from most children hospitalized with ALRI in Botswana, but only RSV and human metapneumovirus were more frequent than among children without ALRI. Detection of RSV from children with ALRI predicted a protracted illness course but lower mortality compared with non-RSV viruses.

Advancing rapid point-of-care viral diagnostics to a clinical setting

ABSTRACT 

We discuss here critical factors in ensuring the success of a viral diagnostic at the point of care. Molecular and immunoassay approaches are reviewed with a focus on their ability to meet the infrastructure and workflow limitations in clinical settings in both the developed and developing world. In addition to being low cost, easy-to-use, accurate and adapted for the intended laboratory and healthcare environment, viral diagnostics must also provide information that appropriately directs clinical treatment decisions. We discuss the challenges and implications of linking diagnostics to clinical decision-making at the point of care using three examples: respiratory viruses in the developed world, differential fever diagnosis in the developing world and HPV detection in resource-limited settings.

Detection of respiratory viruses in gargle specimens of healthy children

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Gargle samples were collected from children and tested respiratory viruses.

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In 45(45/200; 22.5%) episodes, some respiratory viruses detected without symptoms.

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Under asymptomatic conditions, detected viruses were mainly RVs and EV/RV untyped.

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PIVs, RSV and hCoV OC43 were detected only when clinical symptom was seen.

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Asymptomatic infections may play an important role in the viral circulation.

Background

Respiratory tract viral infection is one of the most common and important diseases in children. Polymerase chain reaction (PCR) tests are often used to detect viruses in samples, it is difficult to interpret the clinical significance of PCR positivity, which may reflect a past, imminent or active asymptomatic infection due to their high sensitivity. Although single respiratory viruses have been detected in samples from children with symptoms, other respiratory viruses can also be detected simultaneously. However, the clinical importance of these findings for the symptoms is not known.

Objectives

To investigate the prevalence of respiratory viruses among children without any symptoms such as acute respiratory illness and/or fever.

Study design

From week twenty-five 2013 to week twenty-six 2014, gargle samples were collected from children once a week and these samples were subjected to real-time PCR to detect respiratory viruses. On each sampling day, we asked the parents about their children’s health condition.

Results

Among the 286 samples collected, 200 were from asymptomatic children. In the asymptomatic condition, human parechovirus, adenovirus, enterovirus, rhinovirus, coronavirus 229E and HKU1 were observed in 45 episodes. In samples from symptomatic children, parainfluenza viruses, respiratory syncytial virus and coronavirus OC43 were detected in addition to those mentioned above.

Conclusions

Various viruses of different species were detected in the specimens from the children regardless of their health status. It might be speculated that host factors such as the function of the immune system influence the clinical outcome of the infection. However, this needs to be studied further.

PCR testing for paediatric acute respiratory tract infections

Acute respiratory tract infection (ARI) is a frequently occurring disease in children. It is a clinical diagnosis for which no internationally accepted diagnostic test is available. The majority of ARI is viral in origin, though diagnostic tests for viruses were rarely performed in the past. In the past 2 decades, new molecular techniques have been introduced in many hospitals. They are capable of generating a high yield of viral and bacterial diagnoses, but their impact upon clinical practices is still questionable. In this paper, we discuss the difficulties of diagnosing ARI in children, the indications for conventional and new diagnostics and their implications.

Clinical evaluation of viral acute respiratory tract infections in children presenting to the emergency department of a tertiary referral hospital in the Netherlands

Background

The relative incidence and clinical impact of individual respiratory viruses remains unclear among children presenting to the hospital emergency department with acute respiratory tract infection (ARTI).

Methods

During two winter periods, respiratory virus real-time multiplex PCR results were evaluated from children (< 18 years) presenting to the emergency department of a tertiary referral hospital with ARTI that had been sampled within 48 hours of hospital presentation. In an attempt to identify virus-specific distinguishing clinical features, single virus infections were correlated with presenting signs and symptoms, clinical findings and outcomes using multivariate logistic regression.

Results

In total, 274 children with ARTI were evaluated and most were aged < 3 years (236/274, 86%). PCR detected respiratory viruses in 224/274 (81.8%) children and included 162 (59%) single and 62 (23%) mixed virus infections. Respiratory syncytial virus (RSV) and human rhinovirus (HRV) single virus infections were common among children aged < 3 years, but proportional differences compared to older children were only significant for RSV (95% CI 1.3–15). Clinical differentiation between viral ARTIs was not possible due to common shared presenting signs and symptoms and the high frequency of mixed viral infections. We observed virus-associated outcome differences among children aged < 3 years. Oxygen treatment was associated with RSV (OR 3.6) and inversely correlated with FLU (OR 0.05). Treatment with steroids (OR 3.4) or bronchodilators (OR 3.4) was associated with HRV. Severe respiratory complications were associated with HRV (OR 3.5) and inversely correlated with RSV (OR 0.24).

Conclusions

Respiratory viruses are frequently detected in young children presenting to the hospital emergency department with ARTI and require PCR diagnosis since presenting signs and symptoms are not discriminant for a type of virus. RSV and HRV bear a high burden of morbidity in the pediatric clinical setting.

Utilization of viral molecular diagnostics among children hospitalized with community acquired pneumonia

OBJECTIVE

To examine whether results of a polymerase chain reaction-based respiratory viral panel (RVP) are associated with changes in antibiotic use or differential clinical outcomes among children hospitalized with pneumonia.

METHODS

We retrospectively identified otherwise healthy children hospitalized over a 3-year period at a single institution with community-acquired pneumonia who had an RVP performed within 24 hours of admission. We examined associations between RVP results and clinical outcomes as well as management decisions including initiation and duration of intravenous antibiotics.

RESULTS

Among 202 children, a positive RVP (n = 127, 63%) was associated with a more complicated clinical course, although this was due largely to more severe disease seen in younger children and those with respiratory syncytial virus (n = 38, 30% of positive detections). Detection of a virus did not influence antibiotic therapy. Included children were younger and had more severe illness than children hospitalized with pneumonia at the same institution without an RVP obtained.

CONCLUSIONS

In our study, only respiratory syncytial virus was associated with a more severe clinical course compared with RVP-negative children. Regardless of the virus detected, RVP positivity did not influence antibiotic usage. However, RVP use focused primarily on children with severe pneumonia. Whether similar testing influences management decisions among children with less severe illness deserves further study.

Screening for respiratory syncytial virus and isolation strategies in children hospitalized with acute respiratory tract infection

Nosocomial infection with respiratory syncytial virus (RSV) is an important health risk in pediatric care but is largely preventable by efficient infection control measures. Commonly applied rapid antigen detection tests (RADTs) miss a considerable number of RSV-infected patients. The objective of our analysis was to evaluate whether readily available host parameters are associated with false-negative RADT, and to assess how these parameters could be applied in an optimized RSV isolation strategy.We retrospectively analyzed a cohort of 242 children under the age of 2 years hospitalized with acute respiratory tract infection to identify host parameters associated with false-negative RADT test result. We subsequently simulated the outcome of different isolation strategies based on RADT result and host parameters in view of the overall isolation efficacy.Out of 242 hospitalized patients, 134 (55%) patients were found RSV-positive by RT-PCR, whereas 108 (45%) patients were tested negative. The performance of the RADT was compared with the result obtained by reverse transcription polymerase chain reaction on the identical nasopharyngeal wash. Overall, we found that 85 patients (35%) were tested true positive, 108 (45%) were tested true negative, whereas a false-negative test result was obtained in 49 patients (20%). Duration of respiratory symptoms for >3 days and a respiratory admission diagnosis are associated with false-negative RADT result. In comparison with RADT alone, consideration of these clinical parameters and RADT result can decrease the rate of nonisolated RSV-infected patients from approximately 24% to 8% (65% RSV pretest probability).Consideration of both RADT and clinical parameters associated with false-negative RADT can result in an optimized RSV infection control policy.

Bordetella pertussis: an underreported pathogen in pediatric respiratory infections, a prospective cohort study

Background

The incidence of pertussis has been increasing worldwide. In the Netherlands, the seroprevalence has risen higher than the reported cases, suggesting that laboratory tests for pertussis are considered infrequently and that even more pertussis cases are missed. The objective of our study was to determine the frequency of pertussis in clinically unsuspect cases compared to suspect cases with the intention of finding clinical predictors.

Methods

The present prospective cohort study was part of a controlled clinical trial evaluating the impact of molecular diagnostics on clinical decision making in pediatric respiratory infections, performed during 2 winter seasons. For this study, in the first season pertussis was only tested in case of clinical suspicion, in the second season, pertussis was also tested without clinical suspicion. Multivariate and univariate analysis were performed using SPSS 18 and Statistical software ‘R’.

Results

In the two seasons respectively 22/209 (10,5%) and 49/373 (13,1%) cases were clinically suspected of pertussis. Bordetella pertussis was detected by real time RT-PCR in respectively 2/22 (9,1%) and 7/49 (14,3%) cases. In the second season an additional 7 cases of pertussis were found in clinically unsuspected cases (7/257 = 2,7%). These additional cases didn’t differ in clinical presentation from children without a positive test for pertussis with respect to respiratory symptoms.

Conclusions

Pertussis in children sometimes mimics viral respiratory tract infections. If pertussis diagnostics are based on clinical suspicion alone, about 1 in 5 cases (19%) is missed. Despite widely accepted clinical criteria, paroxysmal cough is not a good predictor of pertussis. To prevent spreading, physicians should include B. pertussis in routine diagnostics in respiratory tract infections.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2334-14-526) contains supplementary material, which is available to authorized users.

The role of multiplex PCR in respiratory tract infections in children

BACKGROUND

Infants, toddlers, and children of primary-school age without any special risk factors generally have three to ten febrile respiratory infections per year. Most such infections are of viral origin and self-limiting, but viral infection is often hard to distinguish from bacterial infection. The use of a multiplex polymerase chain reaction (PCR) to detect viruses in respiratory secretions is potentially beneficial, as it might help physicians avoid giving antibiotics unnecessarily.

METHOD

This article is based on a selective review of the literature and on the findings of the authors' own investigations.

RESULTS

Multiplex PCR is a highly sensitive, highly specific test for the detection of viral nucleic acids in respiratory secretions. If PCR reveals the presence of RNA derived from respiratory syncytial virus, human metapneumovirus, parainfluenza virus, or influenza virus, then an acute infection caused by the corresponding pathogen is probably present, and further treatment can be given accordingly. On the other hand, the nucleic acids of adeno-, boca-, rhino- or coronaviruses can be found in relatively trivial infections as well as in asymptomatic persons, probably reflecting either a prior infection or a current subclinical one. For children in particular, upper respiratory infections are so common in the winter months that acute and prior infections with these pathogens cannot be distinguished by multiplex PCR. The use of multiplex PCR in children has not been shown to shorten hospital stays or to lessen antibiotic consumption or overall cost.

CONCLUSION

The detectability of viral nucleic acids is an important contribution to the diagnostic assessment of children with severe respiratory infection. For these highly sensitive diagnostic tests to be used optimally, primary viral infections must be distinguished from bacterial superinfections.

Three-year study of viral etiology and features of febrile respiratory tract infections in Japanese pediatric outpatients

BACKGROUND

For most febrile respiratory tract infections (RTIs) in children, the causative pathogen is never identified. We sought to identify the causative pathogen in individual cases of pediatric outpatient with RTIs and to determine whether particular clinical features of RTIs are associated with particular viruses.

METHODS

Over 3 years, we prospectively collected nasopharyngeal aspirate specimens from individual pediatric outpatients with an RTI accompanied by persistent fever (>3 days, ≥38.0°C) and peak temperature ≥39.0°C. Two methods-(1) viral culture for respiratory viruses and (2) real-time polymerase chain reaction (PCR) assays identifying 9 different respiratory viruses and 2 respiratory bacteria-were used to test specimens.

RESULTS

For 495 specimens, viral culture and real-time PCR assays together identified at least 1 pathogen in 83.0% and ≥1 viruses alone in 79.4%. These 2 methods identified 138 children with respiratory syncytial virus, 66 with human metapneumovirus, 73 with parainfluenza viruses, 124 with adenovirus, 23 with rhinovirus, 38 with enterovirus, 11 with influenza type C virus, 15 with Mycoplasma pneumoniae and 3 with Chlamydophila pneumoniae; the coinfection rate was 19.7% among all infections. Among the patients with single-pathogen infections, the rate of lower RTI was 37.6% for respiratory syncytial virus, 40.7% for human metapneumovirus, 18.2% for parainfluenza viruses and 2.2% for adenovirus (P < 0.01).

CONCLUSIONS

Viral culture and real-time PCR assays were used together to identify causative pathogens in 83% of febrile outpatient children with RTI; specific viruses were associated with particular clinical diagnoses.

Respiratory virus infections in febrile children presenting to a general practice out-of-hours service

BACKGROUND

Fever is common in young children and is assumed to be frequently caused by viral infections.

OBJECTIVES

To document respiratory viruses in children with fever presenting at a general practice out-of-hours service (OHS), evaluate presenting symptoms in febrile children with a virus infection, and examine the association between antibiotic prescription and the presence of a viral infection.

METHODS

Nasopharyngeal swabs were obtained to detect respiratory viruses in non-hospitalized children aged ≥ three months to six years presenting with fever at an OHS. Symptoms were assessed using physical examinations and questionnaires. Logistic regression analysis was used to reveal associations between symptoms or diagnoses, and the presence of at least one virus

RESULTS

In total 257 nasopharyngeal swabs were obtained in 306 eligible children; 53% of these children were infected by at least one virus. The most frequently detected viruses were adenovirus (10.9%), RSV type A (10.5%) and PIV type 1 (8.6%). Cough (OR 2.6; 95% CI: 1.4-4.6) and temperature ≥ 38.0°C (OR 2.1; 95% CI: 1.3-3.5) were independent predictors of the presence of a virus, but the discriminative ability was low (AUC 0.64; 95% CI: 0.58-0.71). Antibiotic prescription rate was 37.3%. In 57.4% of children with an antibiotic prescription, a virus was found.

CONCLUSION

In over 50% of all febrile children presenting at an OHS, a virus was found. Antibiotic prescription rate was high and not associated to the outcome of viral testing.

Integration of technology into clinical practice

It is an exciting time in clinical microbiology. New advances in technology are revolutionizing every aspect of the microbiology laboratory, from processing of specimens to bacterial identification; as a result, the microbiology laboratory is rapidly changing. With this change comes the challenge of selecting and implementing the technology that is most appropriate for each laboratory and clinical setting. This review focuses on issues surrounding implementation of new technology such that the improvements to clinical care are maximized.

The increasing application of multiplex nucleic acid detection tests to the diagnosis of syndromic infections

On 14 January 2013, the US Food and Drug Administration (FDA) announced permission for a multiplex nucleic acid test, the xTAG® Gastrointestinal Pathogen Panel (GPP) (Luminex Corporation, USA), which simultaneously detects 11 common viral, bacterial and parasitic causes of infectious gastroenteritis, to be marketed in the USA. This announcement reflects the current move towards the development and commercialization of detection technologies based on nucleic acid amplification techniques for diagnosis of syndromic infections. We discuss the limitations and advantages of nucleic acid amplification techniques and the recent advances in Conformité Européene - in-vitro diagnostic (CE-IVD)-approved multiplex real-time PCR kits for the simultaneous detection of multiple targets within the clinical diagnostics market.

Respiratory syncytial virus bronchiolitis in children

Respiratory syncytial virus is a highly infectious virus that commonly causes bronchiolitis and leads to high morbidity and a low, but important, incidence of mortality. Supportive therapy is the foundation of management. Hydration/nutrition and respiratory support are important evidence-based interventions. For children with severe disease, continuous positive airway pressure or mechanical ventilation may be necessary. Ribavirin may be used for treatment of patients with severe disease. Palivizumab provides important ongoing immunoprophylaxis during epidemic months for high-risk infants. Caregiver education and incorporating an explanation of all therapies and anticipatory guidance, including strategies for reducing the risk of infection, are vital.

Epidemiology and clinical presentation of parainfluenza type 4 in children: a 3-year comparative study to parainfluenza types 1-3

Background. Human parainfluenza viruses (HPIVs) are among the most common causes of respiratory tract infections in children. Little is known about the epidemiology and clinical presentation of HPIV type 4.

Methods. A retrospective chart review and comparison of patients positive for HPIV types 1–4 by multiplex polymerase chain reaction between 2009 and 2012 at Children's Hospital Colorado was performed. Patients who had only direct fluorescent antibody testing performed or concurrent viral infections were excluded.

Results. Of 11 533 samples, 752 (6.5%) were positive for HPIV. After exclusion criteria, 316 samples were included in the study. HPIV-4 had year-round prevalence with biennial peaks in odd-numbered years. HPIV-4 and HPIV-3 had similar clinical presentations. 50.8% and 51.5% of patients with HPIV-3–4 had hypoxia compared to 20.3% and 33.3% of patients with HPIV-1–2 (P < .01). HPIV-1 (23.6%) and HPIV-2 (24.2%) were more associated with stridor than HPIV-3 (6.6%) and HPIV-4 (0%) (P < .01). No patients with HPIV-4 had croup. Patients with HPIV-4 had similar lengths of stay and mortality as those with HPIV-1–3.

Conclusions. This is the first large-scale analysis of HPIV-4 clinical and epidemiologic features. HPIV-4 was most similar to HPIV-3 in clinical presentation. HPIV-4 had year-round prevalence with peaks in the autumn of odd-numbered years. HPIV-4 is a common respiratory pathogen capable of causing significant morbidity in children.

Laboratory testing trends for respiratory syncytial virus, 2007-2011

BACKGROUND

Antigen detection tests have been the most common diagnostic assay used to detect and diagnose respiratory syncytial virus (RSV). The utility and increased sensitivity of polymerase chain reaction (PCR) tests have been reported; however, their use in US hospital laboratories is not well characterized.

OBJECTIVE

To describe changes in RSV test types used by US hospital-affiliated laboratories, focusing on PCR testing prevalence.

STUDY DESIGN

Data were collected from 480 to 666 laboratories each RSV season (2007-2008 through 2010-2011) across 50 states, the District of Columbia, and Puerto Rico. A descriptive analysis was conducted using this convenience sample of RSV tests conducted from November to April each season. Total numbers and types of RSV tests performed were reported weekly and weekly proportions by test type were calculated. Kendall τ rank correlation was used to quantify associations between time and proportions of each test type.

RESULTS

PCR tests accounted for 2%, 3%, 16%, and 21% of weekly tests (total range, 381,068-481,654 over 4 seasons) conducted each season from 2007 to 2011, respectively. The proportion of laboratories reporting ≥1 PCR tests was 4%, 5%, 10%, and 16%, respectively. Decreases in antigen testing and viral culture were similarly observed.

CONCLUSIONS

Although antigen detection was the predominant test type reported in the sample of US hospital laboratories for RSV testing, PCR use increased to >20% of tests reported. These results demonstrate the increasing contribution of PCR to RSV surveillance. RSV surveillance systems relying solely on antigen detection results will not capture an increasing proportion of RSV test results.

Clinical and economical impact of multiplex respiratory virus assays

During the last decade, a variety of molecular assays targeting respiratory viruses have been developed and commercialized. Therefore, multiplex PCR are increasingly used in everyday clinical practice. This improves our understanding of respiratory virus epidemiology and enhances our concerns about their clinical impact in specific patient populations. However, questions remain regarding cost-effectiveness of performing these diagnostic tests in routine and their real impact on patient care. This article will review available data and highlight unresolved questions about cost-effectiveness, infection control, clinical utility and public health impact of multiplex respiratory virus assays.

The significance of rhinovirus detection in hospitalized children: clinical, epidemiological and virological features

Recent developments in molecular diagnostic tools have led to the easy and rapid detection of a large number of rhinovirus (HRV) strains. However, the lack of clinical and epidemiological data hampers the interpretation of these diagnostic findings. From October 2009 to January 2011, we conducted a prospective study in hospitalized children from whom samples were taken for the detection of respiratory viruses. Clinical, epidemiological and microbiological data from 644 patients with 904 disease episodes were collected. When HRV tested positive, strains were further characterized by sequencing the VP4/VP2 region of the HRV genome. HRV was the single respiratory virus detected in 254 disease episodes (28%). Overall, 99 different serotypes were detected (47% HRV‐A, 12% HRV‐B, 39% HRV‐C). Patients with HRV had more underlying pulmonary illness compared with patients with no virus (p 0.01), or patients with another respiratory virus besides HRV (p 0.007). Furthermore, cough, shortness of breath and a need for oxygen were significantly more present in patients with HRV infection. Particularly, patients with HRV‐B required extra oxygen. No respiratory symptom, except for oxygen need, was predictive of the presence of HRV. In 22% of HRV‐positive disease episodes, HRV infection was hospital acquired. Phylogenetic analysis revealed several clusters of HRV; in more than 25% of these clusters epidemiological information was suggestive of transmission within specific wards. In conclusion, the detection of HRV may help in explaining respiratory illness, particular in patients with pulmonary co‐morbidities. Identifying HRV provides opportunities for timely implementation of infection control measures to prevent intra‐hospital transmission.

Role of a respiratory viral panel in the clinical management of pediatric inpatients

BACKGROUND

Respiratory viral panels (RVPs) able to detect multiple pathogens are increasingly used in the management of pediatric inpatients. Despite this, few studies have examined whether the results of these tests are associated with clinically significant changes in medical management.

METHODS

In this retrospective cohort study, we identified pediatric inpatients between August 2009 and December 2010 for whom an RVP was ordered within 24 hours of admission to a large, tertiary-care children's hospital. We used linear regression to determine whether RVP was associated with length of stay (LOS), duration of antibiotics and the number of diagnostic microbiology tests ordered, adjusting for potential confounders.

RESULTS

We found that the association between results of the RVP and LOS was dependent on a patient's admission service, specifically admission to the hematology/oncology service. We also found that patients with a positive RVP had a shorter duration of intravenous antibiotic administration (P = 0.03; 42% reduction in the geometric mean), but that this was influenced by the primary admission service. We also found that positive results of the RVP were associated with decreased LOS and shorter duration of antibiotics in patients with some common respiratory diagnoses.

CONCLUSIONS

This study lacked sufficient evidence to claim an association between a positive RVP and LOS in pediatric patients, adjusting for their underlying diagnosis. However, we found that a positive RVP was associated with a shorter duration of intravenous antibiotic administration in certain groups of patients and those with some common respiratory diagnoses. These findings help clarify the utility of rapid viral testing in the management of hospitalized pediatric patients.

Interventions to improve antibiotic prescribing practices for hospital inpatients

BACKGROUND

The first publication of this review in Issue 3, 2005 included studies up to November 2003. This update adds studies to December 2006 and focuses on application of a new method for meta-analysis of interrupted time series studies and application of new Cochrane Effective Practice and Organisation of Care (EPOC) Risk of Bias criteria to all studies in the review, including those studies in the previously published version. The aim of the review is to evaluate the impact of interventions from the perspective of antibiotic stewardship. The two objectives of antibiotic stewardship are first to ensure effective treatment for patients with bacterial infection and second support professionals and patients to reduce unnecessary use and minimize collateral damage.

OBJECTIVES

To estimate the effectiveness of professional interventions that, alone or in combination, are effective in antibiotic stewardship for hospital inpatients, to evaluate the impact of these interventions on reducing the incidence of antimicrobial-resistant pathogens or Clostridium difficile infection and their impact on clinical outcome.

SEARCH METHODS

We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE from 1980 to December 2006 and the EPOC specialized register in July 2007 and February 2009 and bibliographies of retrieved articles. The main comparison is between interventions that had a restrictive element and those that were purely persuasive. Restrictive interventions were implemented through restriction of the freedom of prescribers to select some antibiotics. Persuasive interventions used one or more of the following methods for changing professional behaviour: dissemination of educational resources, reminders, audit and feedback, or educational outreach. Restrictive interventions could contain persuasive elements.

SELECTION CRITERIA

We included randomized clinical trials (RCTs), controlled clinical trials (CCT), controlled before-after (CBA) and interrupted time series studies (ITS). Interventions included any professional or structural interventions as defined by EPOC. The intervention had to include a component that aimed to improve antibiotic prescribing to hospital inpatients, either by increasing effective treatment or by reducing unnecessary treatment. The results had to include interpretable data about the effect of the intervention on antibiotic prescribing or microbial outcomes or relevant clinical outcomes.

DATA COLLECTION AND ANALYSIS

Two authors extracted data and assessed quality. We performed meta-regression of ITS studies to compare the results of persuasive and restrictive interventions. Persuasive interventions advised physicians about how to prescribe or gave them feedback about how they prescribed. Restrictive interventions put a limit on how they prescribed; for example, physicians had to have approval from an infection specialist in order to prescribe an antibiotic. We standardized the results of some ITS studies so that they are on the same scale (percent change in outcome), thereby facilitating comparisons of different interventions. To do this, we used the change in level and change in slope to estimate the effect size with increasing time after the intervention (one month, six months, one year, etc) as the percent change in level at each time point. We did not extrapolate beyond the end of data collection after the intervention. The meta-regression was performed using standard weighted linear regression with the standard errors of the coefficients adjusted where necessary.

MAIN RESULTS

For this update we included 89 studies that reported 95 interventions. Of the 89 studies, 56 were ITSs (of which 4 were controlled ITSs), 25 were RCT (of which 5 were cluster-RCTs), 5 were CBAs and 3 were CCTs (of which 1 was a cluster-CCT).Most (80/95, 84%) of the interventions targeted the antibiotic prescribed (choice of antibiotic, timing of first dose and route of administration). The remaining 15 interventions aimed to change exposure of patients to antibiotics by targeting the decision to treat or the duration of treatment. Reliable data about impact on antibiotic prescribing data were available for 76 interventions (44 persuasive, 24 restrictive and 8 structural). For the persuasive interventions, the median change in antibiotic prescribing was 42.3% for the ITSs, 31.6% for the controlled ITSs, 17.7% for the CBAs, 3.5% for the cluster-RCTs and 24.7% for the RCTs. The restrictive interventions had a median effect size of 34.7% for the ITSs, 17.1% for the CBAs and 40.5% for the RCTs. The structural interventions had a median effect of 13.3% for the RCTs and 23.6% for the cluster-RCTs. Data about impact on microbial outcomes were available for 21 interventions but only 6 of these also had reliable data about impact on antibiotic prescribing.Meta-analysis of 52 ITS studies was used to compare restrictive versus purely persuasive interventions. Restrictive interventions had significantly greater impact on prescribing outcomes at one month (32%, 95% confidence interval (CI) 2% to 61%, P = 0.03) and on microbial outcomes at 6 months (53%, 95% CI 31% to 75%, P = 0.001) but there were no significant differences at 12 or 24 months. Interventions intended to decrease excessive prescribing were associated with reduction in Clostridium difficile infections and colonization or infection with aminoglycoside- or cephalosporin-resistant gram-negative bacteria, methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. Meta-analysis of clinical outcomes showed that four interventions intended to increase effective prescribing for pneumonia were associated with significant reduction in mortality (risk ratio 0.89, 95% CI 0.82 to 0.97), whereas nine interventions intended to decrease excessive prescribing were not associated with significant increase in mortality (risk ratio 0.92, 95% CI 0.81 to 1.06).

AUTHORS' CONCLUSIONS

The results show that interventions to reduce excessive antibiotic prescribing to hospital inpatients can reduce antimicrobial resistance or hospital-acquired infections, and interventions to increase effective prescribing can improve clinical outcome. This update provides more evidence about unintended clinical consequences of interventions and about the effect of interventions to reduce exposure of patients to antibiotics. The meta-analysis supports the use of restrictive interventions when the need is urgent, but suggests that persuasive and restrictive interventions are equally effective after six months.

New molecular virus detection methods and their clinical value in lower respiratory tract infections in children

During the past decade, several new respiratory viruses and their subgroups have been discovered. All these new viruses, as well as previously known respiratory viruses, can be detected by sensitive PCR methods, which have become popular in the diagnostic workup of respiratory viral infections. Currently, respiratory viruses can be detected in up to 95% of children with lower respiratory tract illness. On the other hand, virus detection rates in asymptomatic children are also high (up to 68%), as are coinfection rates in symptomatic children (up to 43%) and justified concerns of causality have been raised. Imposing progress has been made in developing multiplex quantitative PCR assays; here, several primer sets are run within a single PCR mixture. These PCR assays give a better understanding of the dominant viral infection, of viral infections that may be incipient and of any waning infections than does a single-target PCR. Multiplex PCR assays are also gaining popularity due to their cost-effectiveness and short throughput time compared to multiple single-target PCRs. Our understanding of the indications of virus PCRs and our ability to interpret the results from a clinical point of view have improved. This paper reviews the progress in PCR assays and discusses their role in the diagnosis of lower respiratory tract infections in children.

RT-PCR detection of respiratory pathogens in newborn children admitted to a neonatal medium care unit

BACKGROUND

This study aimed to determine the prevalence of respiratory pathogens among newborns admitted to a neonatal medium care unit (NMCU) and to identify clinical predictors.

METHODS

A 1-y observational study was performed of neonates admitted to an NMCU in Amsterdam, The Netherlands. Nasopharyngeal samples were collected for the detection of respiratory viruses and bacteria by real-time PCR (RT-PCR). Cycle threshold (Ct) values were provided to estimate viral load. Predictors for the presence of study pathogens were identified.

RESULTS

From October 2010 through September 2011, 334 neonates (median age 1.3 d, 53.6% male) were included. Overall, 37 respiratory pathogens were detected in 34 children (10.2%): parainfluenza-1 (n = 9), human rhinovirus (n = 7), parainfluenza-3 (n = 6), respiratory syncytial virus (RSV, n = 6), Streptococcus pneumoniae (n = 3), adenovirus (n = 2), human coronavirus (n = 2), influenza A (n = 1), and bocavirus (n = 1). Neonates with higher viral loads (Ct <35; n = 11) were more often clinically ill than those with lower viral loads (Ct ≥35; n = 23). Two variables significantly contributed to the detection of study pathogens: age (odds ratio (OR) 1.21 for each day older; 95% confidence interval 1.12-1.30) and rhinorrhea (OR 6.71; 95% confidence interval 1.54-29.21).

CONCLUSION

Respiratory pathogens seem to play a role in neonates admitted to an NMCU. The influence of respiratory pathogen detection on clinical management remains to be determined.

Diagnostic value of respiratory virus detection in symptomatic children using real-time PCR

Background

Acute respiratory tract infections are an important public health problem. Sensitive and rapid diagnostic techniques have been developed and are used in daily clinical practice. Here we evaluate the clinical relevance of detecting 20 common respiratory pathogens by molecular methods in a general pediatric clinic.

Methods

Nasopharynx samples of children < 18 years of age with respiratory symptoms referred to a general pediatric clinic were tested for the presence of 19 viruses and Mycoplasma pneumoniae, using real-time polymerase chain reaction.

Results

Of 177 patients included in this retrospective study, 73% were positive for at least one virus. Respiratory syncytial virus (36.6%) and human rhinovirus (24%) were most frequently detected. Patients in whom a respiratory virus or Mycoplasma pneumoniae was detected, were younger (6 versus 24 months; p < 0.001) and more often hospitalized (116 versus 34; p = 0.001) than patients in whom no respiratory pathogen was detected. Also they were more likely to present with feeding problems, dyspnea, rhinorrhea and wheezing (all p < 0.05) than patients without a respiratory pathogen.

In the majority of cases, clinicians did not change their antibiotic management after detecting a viral respiratory pathogen. No difference in mean Ct value was found between patients with one respiratory pathogen and those with >1 respiratory pathogen (30.5 versus 31.2; p = 0.573).

Conclusion

Routine testing of common respiratory pathogens could lead to a better understanding of their role in disease in children with respiratory symptoms.

Molecular testing for infectious diseases should be done in the clinical microbiology laboratory

Over the past decade, there has been an explosion in the use of molecular tests to diagnose and manage infectious diseases. HIV is a prime example of an infectious agent whose diagnosis at least in the acute stage, susceptibility testing, and management are all dependent on molecular diagnostics. The ability to accurately diagnose a plethora of respiratory pathogens quickly, simply, and relatively inexpensively compared to traditional methods is becoming a reality. Direct sequencing and microarray analysis holds great promise for directly detecting a wide variety of organisms from clinical specimens. The question is where this testing should be done in the clinical laboratory. There are at least four models that have emerged: Molecular infectious disease testing as an arm of the clinical microbiology laboratory. Molecular infectious disease testing done in a central molecular pathology laboratory under the leadership of a clinical microbiologist. Molecular infectious disease testing done in a central molecular pathology laboratory under the leadership of an individual whose primary interest is in another area of molecular pathology. Molecular infectious disease testing sent to a reference laboratory and not done on site or within the institution's health care system. We have asked three individuals who have thought about this very complex issue to share their rationale for supporting one of these models. Frederick Nolte is the Director of Clinical Laboratories and Director of Molecular Pathology at the Medical University of South Carolina, is active in and held several positions of responsibility in AMP (Association of Molecular Pathology) and is Chair of the CLSI's Area Committee for Molecular Methods, Alex McAdam is the Director of the Infectious Diseases Diagnostic Division at Children's Hospital Boston and an editor of this journal, and his colleague, Nima Mosammaparast, is the Assistant Director of the Infectious Diseases Diagnostic Laboratory at Children's Hospital Boston.

Managing the morbidity associated with respiratory viral infections in children with congenital heart disease

Children with congenital heart disease (CHD) are at risk for increased morbidity from viral lower respiratory tract infections because of anatomical cardiac lesions than can worsen an already compromised respiratory status. Respiratory syncytial virus (RSV) remains an important pathogen in contributing toward the morbidity in this population. Although the acute treatment of RSV largely remains supportive, the development of monoclonal antibodies, such as palivuzumab, has reduced the RSV-related hospitalization rate in children with CHD. This review highlights the specific cardiac complications of RSV infection, the acute treatment of bronchiolitis in patients with CHD, and the search for new therapies against RSV, including an effective vaccine, because of the high cost associated with immunoprophylaxis and its lack of reducing RSV-related mortality.