Comprehensive detection of causative pathogens using real-time PCR to diagnose pediatric community-acquired pneumonia

Community-acquired pneumonia in children: updated perspectives on its etiology, diagnosis, and treatment

Pneumonia is a common pediatric infectious disease that is familiar to pediatricians and a major cause of hospitalization worldwide. Recent well-designed epidemiologic studies in developed countries indicated that respiratory viruses are detected in 30%-70%, atypical bacteria in 7%-17%, and pyogenic bacteria in 2%-8% of children hospitalized with community-acquired pneumonia (CAP). The etiological distribution of CAP varies widely by child age and the epidemiological season of the respiratory pathogen. Moreover, diagnostic tests, particularly for the detection of Streptococcus pneumoniae and Mycoplasma pneumoniae, the 2 major bacterial pathogens involved in pediatric CAP, have several limitations. Therefore, management and empirical antimicrobial therapy for children with CAP should be applied in a stepwise manner based on recent epidemiological, etiological, and microbiological evidence.

Establishment and Performance Evaluation of Multiplex PCR-Dipstick DNA Chromatography for Mycoplasma pneumoniae and Chlamydia pneumoniae Rapid Detection

Methods

Nasopharyngeal swab samples of 300 children with an acute respiratory tract infection were detected by a multiplex PCR-dipstick chromatography assay, and the results were compared with the DNA sequencing and serum IgM antibody assay.

Results

A multiplex PCR-dipstick DNA assay can specifically detect Mycoplasma pneumoniae and Chlamydia pneumoniae and shows a good specificity, with a minimum detection limit of 10 CFU/mL, respectively. Using DNA sequencing results as the gold standard, the sensitivity, specificity, positive predictive value, and negative predictive value of the multiplex PCR-dipstick DNA chromatography assay for the diagnosis of Mycoplasma pneumoniae were 96.61%, 100%, 100%, and 99.18% respectively, and those of Chlamydia pneumoniae were 95.24%, 100%, 100%, and 99.64% respectively. There was no statistical significance MP and CP diagnosis by the multiplex PCR-dipstick DNA assay and DNA sequencing (MP: P = 0.5; CP: P = 1.0), and the two assays had very high statistical consistency (MP: kappa = 0.979; CP: kappa = 0.974). The positive rate of the multiplex PCR-dipstick chromatography assay was significantly higher than that of the serum IgM antibody assay, with MP (17.7% vs. 13.3%), CP (5.7% vs. 3.3%), and mixed infection of MP and CP (1.3% vs. 0.67%).

Conclusions

A multiplex PCR-dipstick chromatography assay was successfully established for the joint detection of Mycoplasma pneumoniae and Chlamydia pneumoniae within 2 hours. It is simple, fast, sensitive, accurate, cost-effective with good diagnostic performance, which can be used for small laboratories and point-of-care diagnosis.

Antibiotic use and outcomes among children hospitalized with suspected pneumonia

BACKGROUND

Although viral etiologies predominate, antibiotics are frequently prescribed for community-acquired pneumonia (CAP).

OBJECTIVE

We evaluated the association between antibiotic use and outcomes among children hospitalized with suspected CAP.

DESIGNS, SETTINGS AND PARTICIPANTS

We performed a secondary analysis of a prospective cohort of children hospitalized with suspected CAP.

INTERVENTION

The exposure was the receipt of antibiotics in the emergency department (ED).

MAIN OUTCOME AND MEASURES

Clinical outcomes included length of stay (LOS), care escalation, postdischarge treatment failure, 30-day ED revisit, and quality-of-life (QoL) measures from a follow-up survey 7-15 days post discharge. To minimize confounding by indication (e.g., radiographic CAP), we performed inverse probability treatment weighting with propensity analyses.

RESULTS

Among 523 children, 66% were <5 years, 88% were febrile, 55% had radiographic CAP, and 55% received ED antibiotics. The median LOS was 41 h (IQR: 25, 54). After propensity analyses, there were no differences in LOS, escalated care, treatment failure, or revisits between children who received antibiotics and those who did not. Seventy-one percent of patients completed follow-up surveys after discharge. Among 16% of patients with fevers after discharge, the median fever duration was 2 days, and those who received antibiotics had a 37% decrease in the mean number of days with fever (95% confidence interval: 20% and 51%). We found no statistical differences in other QoL measures.

Clinical Characteristics and Etiology of Community-acquired Pneumonia in US Children, 2015-2018

BACKGROUND

Pneumonia has a major impact on childhood health and health care costs. This study was designed to obtain contemporary information on the clinical characteristics and etiology of community-acquired pneumonia (CAP) in children from both inpatient and outpatient settings in the USA.

METHODS

We conducted a prospective, multicenter, observational study of CAP among previously healthy children 2 months to 18 years of age in 6 children's hospitals in Ohio from 2015 to 2018. For pathogen detection, nasopharyngeal swabs were collected from all subjects. Blood and pleural fluid cultures were available per standard of care.

RESULTS

We enrolled a convenience sample of 441 patients: 380 hospitalized and 61 outpatients. Tachypnea and radiologic findings of consolidation and pleural effusion were more frequent among inpatients than outpatients. A pathogen was detected in 64.6% of patients: viruses in 55.6%, atypical bacteria in 8.8% and pyogenic bacteria in 4.3%. Eighteen (4.1%) patients had both viruses and bacteria detected. Rhinovirus/enterovirus (RV; 18.6%) and respiratory syncytial virus (RSV; 16.8%) were the viruses most frequently detected, and Mycoplasma pneumoniae (8.2%) and Streptococcus pneumoniae (2.3%) were the most common bacteria. Except for S. pneumoniae, which was identified more frequently in inpatients, there were no significant differences between inpatients and outpatients in the proportions of children with specific pathogens detected.

CONCLUSIONS

Rhinovirus/enterovirus and RSV among viruses and M. pneumoniae and S. pneumoniae among bacteria were the most common pathogens detected in children with CAP. Tachypnea and chest radiographs with consolidation and/or pleural effusion were associated with hospitalization.

Disparities in Outcomes During Lower Respiratory Tract Infection in American Indian Children: A 9-Year Retrospective Analysis in a Rural Population in South Dakota

BACKGROUND

American Indian (AI) children are at increased risk for severe disease during lower respiratory tract infection (LRTI). The reasons for this increased severity are poorly understood. The objective of this study was to define the clinical presentations of LRTI and highlight the differences between AI and non-AI previously healthy patients under the age of 24 months.

METHODS

We performed a retrospective chart review between October 2010 and December 2019. We reviewed 1245 patient charts and 691 children met inclusion criteria for this study. Data records included demographics, clinical, laboratory data, and illness outcomes.

RESULTS

Of 691 patients, 120 were AI and 571 were non-AI. There was a significant difference in breast-feeding history (10% of AI vs. 28% of non-AI, P < 0.0001) and in secondhand smoke exposure (37% of AI vs. 21% of non-AI, P < 0.0001). AI children had increased length of hospitalization compared with non-AI children (median of 3 vs. 2 days, P < 0.001). In addition, AI children had higher rates of pediatric intensive unit admission (30%, n = 37) compared with non-AI children (11%; n = 67, P < 0.01). AI children also had higher rates (62.5%, n = 75) and duration of oxygen supplementation (median 3 days) than non-AI children (48%, n = 274, P = 0.004; median 2 days, P = 0.0002). On a multivariate analysis, AI race was an independent predictor of severe disease during LRTI.

CONCLUSIONS

AI children have increased disease severity during LRTI with longer duration of hospitalization and oxygen supplementation, a higher rate of oxygen requirement and Powered by Editorial Manager and ProduXion Manager from Aries Systems Corporation pediatric intensive care unit admissions, and a greater need for mechanical ventilation. These results emphasize the need for improvement in health policies and access to health care in this vulnerable population.

Factors Associated With Antibiotic Prescribing and Outcomes for Pediatric Pneumonia in the Emergency Department

OBJECTIVES

Chest radiographs (CXRs) are often performed in children with respiratory illness to inform the decision to prescribe antibiotics. Our objective was to determine the factors associated with clinicians' plans to treat with antibiotics prior to knowledge of CXR results and the associations between preradiograph plans with antibiotic prescription and return to medical care.

METHODS

Previously healthy children aged 3 months to 18 years with a CXR for suspected pneumonia were enrolled in a prospective cohort study in the emergency department. Our primary outcomes were antibiotic prescription or administration in the emergency department and medical care sought within 7 to 15 days after discharge. Inverse probability treatment weighting was used to limit bias due to treatment selection. Inverse probability treatment weighting was included in a logistic regression model estimating the association between the intention to give antibiotics and outcomes.

RESULTS

Providers planned to prescribe antibiotics prior to CXR in 68 children (34.9%). There was no difference in the presence of radiographic pneumonia between those with and without a plan for antibiotics. Children who had a plan for antibiotics were more likely to receive antibiotics than those without (odds ratio [OR], 6.39; 95% confidence interval [CI], 3.7-11.0). This association was stronger than the association between radiographic pneumonia and antibiotic receipt (OR, 3.49; 95% CI, 1.98-6.14). Children prescribed antibiotics were more likely to seek care after discharge than children who were not (OR, 1.85; 95% CI, 1.13-3.05).

CONCLUSIONS

Intention to prescribe antibiotics based on clinical impression was the strongest predictor of antibiotic prescription in our study. Prescribing antibiotics may lead to subsequent medical care after controlling for radiographic pneumonia.

Risk factors of bacteremia in children hospitalized with community-acquired pneumonia: A nested case-control study

OBJECTIVE

To assess the risk factors of bacteremia in children hospitalized with community-acquired pneumonia (CAP).

STUDY DESIGN

The present, nested, case-control study enrolled a cohort of patients with CAP aged < 18 years who were hospitalized at Tokyo Metropolitan Children's Medical Center or Tama-Hokubu Medical Center between March 2010 and February 2018. Among the cohort with blood cultures (BCs), patients with bacteremia were identified and matched with five control patients based on their treatment facility, underlying disease, and age. Conditional logistic regression was used to calculate the odds ratios (ORs) of bacteremia for risk factor candidates.

RESULTS

BCs were obtained for 2,383 (84%) of the 2,853 patients in the CAP cohort. Of those with BCs, 34 (1.4%) had bacteremia. S. pneumoniae and H. influenzae accounted for 26 (76%) and four (12%) instances of the bacteremia pathogens, respectively. Bacteremia occurred more frequently among patients hospitalized in the spring than during other seasons (P = 0.022). On multivariate analysis, the severity of pneumonia was not associated with bacteremia incidence (OR: 0.92 [0.30-2.85]) while a white blood cell count > 16,000/μL (OR: 5.90 [2.14-16.3]) was shown to be a significant risk factor. The OR of the need for a ventilator on admission day was significantly high (28.4 [3.02-1374]) on univariate analysis, but the subject pool was too small to determine its significance on multivariate analysis.

CONCLUSIONS

The results of the present study supported BC collection in patients with leukocytosis and in those requiring ventilator use on admission.

Antibiotic Choice and Clinical Outcomes in Ambulatory Children with Community-Acquired Pneumonia

OBJECTIVES

To describe antibiotic prescribing patterns in ambulatory children with community-acquired pneumonia and to assess the relationship between antibiotic selection and clinical outcomes.

STUDY DESIGN

This was a retrospective cohort study of ambulatory Medicaid-enrolled children 0-18 years of age diagnosed with community-acquired pneumonia from 2010 to 2016. The exposure was antibiotic class: narrow-spectrum (aminopenicillins), broad-spectrum (amoxicillin/clavulanate and cephalosporins), macrolide monotherapy, macrolides with narrow-spectrum antibiotics, or macrolides with broad-spectrum antibiotics. The associations between antibiotic selection and the outcomes of subsequent hospitalization and development of severe pneumonia (chest drainage procedure, intensive care admission, mechanical ventilation) were assessed, controlling for measures of illness severity.

RESULTS

Among 252 177 outpatient pneumonia visits, macrolide monotherapy was used in 43.2%, narrow-spectrum antibiotics in 26.1%, and broad-spectrum antibiotics in 24.7%. A total of 1488 children (0.59%) were subsequently hospitalized and 117 (0.05%) developed severe pneumonia. Compared with children receiving narrow-spectrum antibiotics, the odds of subsequent hospitalization were higher in children receiving broad-spectrum antibiotics (aOR, 1.34; 95% CI, 1.17-1.52) and lower in children receiving macrolide monotherapy (aOR, 0.64; 95% CI, 0.55-0.73) and macrolides with narrow-spectrum antibiotics (aOR, 0.62; 95% CI, 0.39-0.97). Children receiving macrolide monotherapy had lower odds of developing severe pneumonia than children receiving narrow-spectrum antibiotics (aOR, 0.56; 95% CI, 0.33-0.93). However, the absolute risk difference was <0.5% for all analyses.

CONCLUSIONS

Macrolides are the most commonly prescribed antibiotic for ambulatory children with community-acquired pneumonia. Subsequent hospitalization and severe pneumonia are rare. Future efforts should focus on reducing broad-spectrum and macrolide antibiotic prescribing.

Clinical Characteristics of 204 Children With Human Adenovirus Type 7 Pneumonia Identified by Whole Genome Sequencing in Liuzhou, China

BACKGROUND

Clinical knowledge of human adenovirus type 7 (HAdV-7) pneumonia in children remains limited. Moreover, predictors for disease severity are largely unknown.

METHODS

This is a retrospective study of children hospitalized at Liuzhou Maternal and Child Health Hospital, China, with HAdV-7 pneumonia in 2018-2019. Demographics, clinical characteristics, laboratory results, and imaging data were collected. HAdV-7 was identified in plasma using whole genome sequencing, which yielded quantitative HAdV-7 sequence numbers.

RESULTS

There were 204 children; 145 (71%) were <2 years of age. There were 68 children with severe pneumonia (SP) and 136 with nonsevere pneumonia (NSP). Up to 43% in SP group with respiratory failure (SP-RF) were <12 months of age. Median duration of fever before hospitalization was shorter in NSP group than SP groups (P < 0.01). Fourteen (6.9%) underwent mechanical ventilation. There was a significant difference in mean plasma HAdV-7 sequence numbers among SP-RF, SP without respiratory failure (SP-NRF), and NSP groups (2485 ± 165, 2034 ± 124, and 286 ± 35, respectively) (P < 0.01). In a logistic regression analysis, we found that elevated plasma HAdV-7 sequence numbers significantly increased the risk of severe HAdV-7 pneumonia (OR 1.80, 95% confidence interval: 1.59-2.60, P < 0.01) after adjusting for age, fever duration, platelet counts, and serum lactate dehydrogenase levels.

CONCLUSIONS

Over two-thirds of children hospitalized with HAdV-7 pneumonia were <2 years of age. Approximately 40% of those with SP associated with respiratory failure were <12 months of age. Those with SP exhibited higher plasma HAdV-7 sequence numbers. Thus, plasma HAdV-7 sequence numbers have a potential in predicting severity of HAdV-7 pneumonia in children.

Antibiotics for hospitalized children with community-acquired pneumonia in Japan: Analysis based on Japanese national database

INTRODUCTION

Community-acquired pneumonia (CAP) is one of the most common causes of pediatric infection requiring hospitalization. Antimicrobial resistance due to the inappropriate use poses a threat worldwide. Our objective is to analyze and optimize the trends of antibiotics used for pediatric inpatients with CAP in a claims database provided by the Ministry of Health, Labour and Welfare.

METHODS

Our database randomly sampled 10% of the hospitalized patients every October from 2011 to 2014. Patients aged <15 years in whom antibiotic therapy was initiated within two days of admission were listed. Subsequently, we investigated the antibiotics administered on the first day of prescription.

RESULTS

A total of 4,831 antibiotics were prescribed for 3,909 patients. Many patients aged ≤ five years were treated with β-lactams alone whereas many patients aged ≥ six years were treated with a single antibiotic, such as a macrolide, tetracycline, and quinolone, which covers atypical bacteria. Combination therapy was primarily used in children aged ≥ six years (nearly 30%); the main combination was a β-lactam and non-β-lactam covering atypical bacteria. Ampicillin-sulbactam was the most frequently prescribed β-lactam in children of all ages other than infants. Ampicillin, however, was most often prescribed in infants, but its usage rate was low at other ages.

CONCLUSIONS

Antibiotics were appropriately prescribed and were similar to that recommended in the 2011 guidelines for pediatric inpatients with CAP. However, combination therapy was frequently prescribed in children aged ≥ six years. According to the revised guidelines in 2017, ampicillin should be used more frequently for patients hospitalized with CAP.

High concentration of Cas12a effector tolerates more mismatches on ssDNA

Rapid pathogen detection is critical for prompt treatment, interrupting transmission routes, and decreasing morbidity and mortality. The V-type CRISPR system had been used for rapid pathogen detection. However, whether single-stranded DNA in CRISPR system can cause false positives remains undetermined. Herein, we show that high molar concentration of Cas12a effector tolerated more mismatches on ssDNA and activated its trans-cleavage activity at six base matches. Reducing Cas12a and crRNA molar concentration increased the minimal base-match number required for Cas12a ssDNA activation to 11, which reducing nonspecific activation. We then established a Cas12a-based M tuberculosis detection system with a primer having an 8 bp overlap with crRNA. This system did not exhibit primer-induced false positives, and minimum detection copy reached 1 copy/uL (inputting 1-μL sample) in standard strains. The Cas12a-based M tuberculosis detection system showed 80.0% sensitivity and 100.0% specificity in verification using clinical specimens, compared with Xpert MTB/RIF, which showed 72.0% sensitivity and 90.9% specificity. All these results prove that appropriate concentration of cas12a effector can effectively perform nucleic acid detection.

Antibiotic Use and Outcomes in Children in the Emergency Department With Suspected Pneumonia

BACKGROUND AND OBJECTIVES

Antibiotic therapy is often prescribed for suspected community-acquired pneumonia (CAP) in children despite a lack of knowledge of causative pathogen. Our objective in this study was to investigate the association between antibiotic prescription and treatment failure in children with suspected CAP who are discharged from the hospital emergency department (ED).

METHODS

We performed a prospective cohort study of children (ages 3 months-18 years) who were discharged from the ED with suspected CAP. The primary exposure was antibiotic receipt or prescription. The primary outcome was treatment failure (ie, hospitalization after being discharged from the ED, return visit with antibiotic initiation or change, or antibiotic change within 7-15 days from the ED visit). The secondary outcomes included parent-reported quality-of-life measures. Propensity score matching was used to limit potential bias attributable to treatment selection between children who did and did not receive an antibiotic prescription.

RESULTS

Of 337 eligible children, 294 were matched on the basis of propensity score. There was no statistical difference in treatment failure between children who received antibiotics and those who did not (odds ratio 1.0; 95% confidence interval 0.45-2.2). There was no difference in the proportion of children with return visits with hospitalization (3.4% with antibiotics versus 3.4% without), initiation and/or change of antibiotics (4.8% vs 6.1%), or parent-reported quality-of-life measures.

CONCLUSIONS

Among children with suspected CAP, the outcomes were not statistically different between those who did and did not receive an antibiotic prescription.

Fatal Primary Human Bocavirus Pneumonia in an Immunocompetent Adult

A 70-year-old woman was admitted to our hospital for dyspnea and a fever of 2 weeks duration. Chest imaging showed bilateral infiltration, and a rapid diagnostic test for influenza virus, Mycoplasma pneumoniae, Streptococcus pneumoniae, and Legionella spp. was negative. She was intubated and mechanically ventilated and underwent bronchoalveolar lavage. Bronchoalveolar lavage fluid yielded no significant pathogens, and the multiplex polymerase chain reaction test was positive only for human bocavirus. Specific antibodies against significant pathogens were not increased in paired sera, so we diagnosed her with primary human bocavirus pneumonia.

Comprehensive Detection of Respiratory Bacterial and Viral Pathogens in the Middle Ear Fluid and Nasopharynx of Pediatric Patients With Acute Otitis Media

BACKGROUND

Acute otitis media (AOM) is a common ear infection caused by respiratory viruses and bacteria of the nasopharynx. The present study aimed to detect various respiratory viruses and bacteria in middle ear fluid (MEF) and nasopharyngeal aspirates (NPA) using polymerase chain reaction (PCR).

METHODS

We collected MEF and NPA samples from 122 pediatric patients with AOM. Real-time PCR detected 11 types of respiratory viruses (respiratory syncytial virus A/B, parainfluenza virus 1/2/3, human metapneumovirus, influenza virus A/B, adenovirus, human bocavirus and rhino virus) and 7 types of bacteria (Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Chlamydia pneumoniae, Streptococcus pyogenes, Legionella pneumophila and Moraxella catarrhalis). MEF specimens were also examined using bacterial culture.

RESULTS

At least 1 respiratory viral or bacterial pathogen was detected in MEF of 120 cases (98%) by viral and bacterial PCR and of 93 cases (76%) by viral PCR and bacterial culture. Respiratory viruses were detected in NPA of 84 cases (69%) and MEF of 67 cases (55%). The most common virus detected in MEF was respiratory syncytial virus (21%), followed by parainfluenza virus (15%). All the viruses present in MEF were also detected in NPA specimens. Bacteria were detected by PCR in MEF of 109 cases (89%); H. influenzae was the most frequently detected (65%).

CONCLUSIONS

In many cases, pediatric AOM was found to constitute a respiratory polymicrobial infection. Multiplex PCR was useful to detect multiple respiratory viruses and bacteria in AOM. To understand intractable AOM, further studies regarding the clinical features of each viral and bacterial coinfection are required.

Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure

Next-generation sequencing (NGS) has been applied in the field of infectious diseases. Bronchoalveolar lavage fluid (BALF) is considered a sterile type of specimen that is suitable for detecting pathogens of respiratory infections. The aim of this study was to comprehensively identify causative pathogens using NGS in BALF samples from immunocompetent pediatric patients with respiratory failure. Ten patients hospitalized with respiratory failure were included. BALF samples obtained in the acute phase were used to prepare DNA- and RNA-sequencing libraries. The libraries were sequenced on MiSeq, and the sequence data were analyzed using metagenome analysis tools. A mean of 2,041,216 total reads were sequenced for each library. Significant bacterial or viral sequencing reads were detected in eight of the 10 patients. Furthermore, candidate pathogens were detected in three patients in whom etiologic agents were not identified by conventional methods. The complete genome of enterovirus D68 was identified in two patients, and phylogenetic analysis suggested that both strains belong to subclade B3, which is an epidemic strain that has spread worldwide in recent years. Our results suggest that NGS can be applied for comprehensive molecular diagnostics as well as surveillance of pathogens in BALF from patients with respiratory infection.

Nosocomial infection by human bocavirus and human rhinovirus among paediatric patients with respiratory risks

BACKGROUND

Nosocomial infections by respiratory viruses undetected by rapid tests are not often diagnosed. For paediatric patients with background diseases, nosocomial infection could be fatal.

AIM

To determine the relationship between developing symptoms by respiratory viruses undetectable by rapid tests and respiratory risks and to improve the management of infection control.

METHODS

Two episodes of nosocomial infection by human bocavirus (HBoV) and human rhinovirus (HRV) were retrospectively investigated in a tertiary hospital paediatric ward in Japan. Viruses were identified by polymerase chain reaction to determine infection control management. When viruses of the same species were detected from different patients, the virus homology was investigated. The relationship between respiratory risks and developing symptoms was statistically investigated.

FINDINGS

Three and four patients with respiratory risks in the HBoV and HRV outbreaks, respectively, developed respiratory symptoms. The nucleotide sequences of two patients in the HBoV outbreak and all four patients in the HRV outbreak were phylogenetically close. In both outbreaks, the patients with respiratory risks developed significantly more symptoms than those without any risk (P = 0.035 and 0.018, respectively). After the patients with respiratory infection were separated from those with respiratory risks, no additional nosocomial infection occurred.

CONCLUSION

Patients with respiratory risks easily develop respiratory symptoms and acquire severe symptoms of nosocomial infection by those viruses. In a paediatric ward, we should adopt not only standard precautions but also isolation management of the patients with respiratory symptoms, even if they have negative results in rapid tests.

Genetic diversity of human respiratory syncytial virus in children with acute respiratory infections in Chennai, South India

Introduction

Human respiratory syncytial virus (HRSV) an RNA virus belonging to Pneumoviridae family, is an important cause of acute respiratory infections (ARIs) in young children. HRSV circulates as two subgroups A and B, which are further categorised into several genotypes. New genotypes may replace existing ones over successive epidemic seasons and multiple genotypes may cocirculate in the same community rendering it important to monitor them at the molecular level. The present study assessed the circulating genotypes of HRSV in Chennai.

Materials and Methods

Two hundred and sixty-seven children with ARI were recruited during the study from April 2016 to March 2018 for detecting HRSV A and B by real-time reverse transcription-polymerase chain reaction. Phylogeny and selection pressure analysis were done.

Results

Fifty-seven of the 267 samples (21.3%) were positive for HRSV, of which 7.1% and 14.2% were HRSV A and B, respectively, indicating that HRSV B was the major subgroup circulating in Chennai. Peak activity of HRSV was observed during the monsoon and winter months. Phylogenetic analysis of 2nd hypervariable region (HVR) of attachment glycoprotein gene (G gene) revealed that the HRSV A strains belonged to ON1 and HRSV B strains belonged to BA9 genotypes. Several unique amino acid substitutions were observed among the study strains. The Shannon entropy plot revealed that the HRSV A strains from our study have a high potential for amino acid substitutions in the 2nd HVR of G gene.

Conclusion

This study underlines the genetic diversity of HRSV and emphasises the need for continued molecular surveillance for infection management and prevention strategies.

Recommendations and guidelines for the treatment of pneumonia in Taiwan

Pneumonia is a leading cause of death worldwide, ranking third both globally and in Taiwan. This guideline was prepared by the 2017 Guidelines Recommendations for Evidence-based Antimicrobial agents use in Taiwan (GREAT) working group, formed under the auspices of the Infectious Diseases Society of Taiwan (IDST). A consensus meeting was held jointly by the IDST, Taiwan Society of Pulmonary and Critical Care Medicine (TSPCCM), the Medical Foundation in Memory of Dr. Deh-Lin Cheng, the Foundation of Professor Wei-Chuan Hsieh for Infectious Diseases Research and Education and CY Lee's Research Foundation for Pediatric Infectious Diseases and Vaccines. The final guideline was endorsed by the IDST and TSPCCM. The major differences between this guideline and the 2007 version include the following: the use of GRADE methodology for the evaluation of available evidence whenever applicable, the specific inclusion of healthcare-associated pneumonia as a category due to the unique medical system in Taiwan and inclusion of recommendations for treatment of pediatric pneumonia. This guideline includes the epidemiology and recommendations of antimicrobial treatment of community-acquired pneumonia, hospital-acquired pneumonia, ventilator-associated pneumonia, healthcare-associated pneumonia in adults and pediatric pneumonia.

Implementation of Point-of-Care Molecular Diagnostics for Mycoplasma pneumoniae Ensures the Correct Antimicrobial Prescription for Pediatric Pneumonia Patients

Mycoplasma pneumoniae is a leading causative pathogen of pneumonia among pediatric patients, and its accurate diagnosis may aid in the selection of appropriate antimicrobial agents. We established a rapid reporting system of a polymerase chain reaction (PCR) examination for M. pneumoniae that enables physicians to obtain test results approximately 90 minutes after ordering the test. In this study, we evaluated the impact of this system on antimicrobial prescriptions for pediatric pneumonia patients after its implementation from May 2016 to April 2017. In total, we identified 375 pediatric pneumonia patients, and the results of the rapid PCR examinations for Mycoplasma pneumoniae were reported immediately in 90.7% of patients (340/375), with physicians able to use these results to decide on patients' management before the prescription of antimicrobial agents. Of the 375 pediatric pneumoniae patients, M. pneumoniae was detected in 223 (59.5%). Among the 223 M. pneumoniae-positive pneumonia cases, antimicrobial agents for atypical pathogens (macrolides, tetracyclines or quinolones) were prescribed in 97.3% (217/223) at the initial evaluation, and their prescription rates increased to 99.1% (221/223) during management. In contrast, antimicrobial agents for atypical pathogens were prescribed only in 10.5% of 152 M. pneumoniae-negative pneumonia cases at the initial evaluations, and only 1 additional case was prescribed clarithromycin for persistent symptoms during management. In conclusion, we show that molecular technology could be applicable in the field of point-of-care testing in infectious disease, and its implementation will ensure the correct antimicrobial prescription for pediatric pneumonia patients.

A case report on parainfluenza virus type 4a infection in a 1-year-old boy with biphasic fever

A 1-year-old boy was infected with parainfluenza virus type 4a (PIV4a) during an influenza epidemic in January 2016. His body temperature was 38.2 °C on day 1 of the illness followed by an intermittent phase of 36.5 °C on days 2 and 3, and it rose again on day 3 and peaked at 39.6 °C on day 4, of which the fever pattern was reminiscent of an influenza case with biphasic fever. However, results of rapid influenza virus (IFV) antigen tests performed at the first clinical visit and during the second fever phase on day 4 were both negative. The PIV4a was isolated from all the nasal aspirate specimens on days 1, 4, and 7. Other common respiratory viruses were negative in all the specimens in the viral isolation trials using the multiplex cell culture system and RT-PCR tests. The fever disappeared within 5 days after the onset without any antibiotic treatment, which strongly suggested the PIV4a as the causative agent of the patient's illness. On the basis of the incubation period required for the appearance of the cytopathic effect (CPE) in the infected cells, from specimen inoculation to the cells, the viral load in the nasal cavity was speculated to be greatest on day 4. His cough started on day 1 and persisted until day 9, and the viral isolation indicated that the shedding of the active virus continued with the coughing even after the termination of fever.

Global distribution of NA1 genotype of respiratory syncytial virus and its evolutionary dynamics assessed from the past 11 years

Respiratory syncytial virus (RSV) is a potent pathogen having global distribution. The main purpose of this study was to gain an insight into distribution pattern of the NA1 genotype of group A RSV across the globe together with its evolutionary dynamics. We focused on the second hypervariable region of the G protein gene and used the same for Phylogenetic, Bayesian and Network analyses. Eighteen percent of the samples collected from 500 symptomatic pediatric patients with acute respiratory tract infection (ARI) were found to be positive for RSV during 2011-15 from New Delhi, India. Of these, group B RSV was predominant and clustered into two different genotypes (BA and SAB4). Similarly, group A viruses clustered into two genotypes (NA1 and ON1). The data set from the group A viruses included 543 sequences from 23 different countries including 67 strains from India. The local evolutionary dynamics suggested consistent virus population of NA1 genotype in India during 2009 to 2014. The molecular clock analysis suggested that most recent common ancestor of group A and NA1 genotype have emerged in during the years 1953 and 2000, respectively. The global evolutionary rates of group A viruses and NA1 genotype were estimated to be 3.49 × 10^-3 (95% HPD, 2.90-4.17 × 10^-3) and 3.56 × 10^-3 (95% HPD, 2.91 × 10^-3-4.18 × 10^-3) substitution/site/year, respectively. Analysis of the NA1 genotype of group A RSV reported during 11 years i.e. from 2004 to 2014 showed its dominance in 21 different countries across the globe reflecting its evolutionary dynamics. The Network analysis showed highly intricate but an inconsistent pattern of haplotypes of NA1 genotype circulating in the world. Present study seems to be first comprehensive attempt on global distribution and evolution of NA1 genotype augmenting the optimism towards the vaccine development.

Detection of pathogens by real-time PCR in adult patients with acute exacerbation of bronchial asthma

BACKGROUND

Respiratory tract infection is a major cause of acute exacerbation of bronchial asthma (AEBA). Although recent findings suggest that common bacteria are causally associated with AEBA, a comprehensive epidemiologic analysis of infectious pathogens including common/atypical bacteria and viruses in AEBA has not been performed. Accordingly, we attempted to detect pathogens during AEBA by using real-time polymerase chain reaction (PCR) in comparison to conventional methods.

METHODS

We prospectively enroled adult patients with AEBA from August 2012 to March 2014. Infectious pathogens collected in nasopharyngeal swab and sputum samples were examined in each patient by conventional methods and real-time PCR, which can detect 6 bacterial and 11 viral pathogens. The causal association of these pathogens with AEBA severity and their frequency of monthly distribution were also examined.

RESULTS

Among the 64 enroled patients, infectious pathogens were detected in 49 patients (76.6%) using real-time PCR and in 14 patients (21.9%) using conventional methods (p < 0.001). Real-time PCR detected bacteria in 29 patients (45.3%) and respiratory viruses in 28 patients (43.8%). Haemophilus influenzae was the most frequently detected microorganism (26.6%), followed by rhinovirus (15.6%). Influenza virus was the significant pathogen associated with severe AEBA. Moreover, AEBA occurred most frequently during November to January.

CONCLUSIONS

Real-time PCR was more useful than conventional methods to detect infectious pathogens in patients with AEBA. Accurate detection of pathogens with real-time PCR may enable the selection of appropriate anti-bacterial/viral agents as a part of the treatment for AEBA.

Missed opportunities for antimicrobial stewardship in pre-school children admitted to hospital with lower respiratory tract infection

AIM

To describe the usage of multiplex polymerase chain reaction on nasopharyngeal swab (NPS) samples in pre-school children presenting with lower respiratory tract infection (LRTI) at Christchurch Hospital, and its impact on the use of antibiotics empirically and at discharge.

METHODS

This retrospective cohort study included 237 children, ages 3 months to 5 years, admitted to hospital during the winter months of 2012-2015 with a diagnosis of community-acquired LRTI. Children were identified by discharge coding and their notes reviewed.

RESULTS

A significantly larger proportion of children who had a NPS sample taken (42/146, 36%) received no empiric antibiotics compared with children who did not have a sample taken (7/91, 7.7%, P < 0.001). Of those who did have a NPS sample taken 17 of 146 (11.6%) had their antibiotics discontinued prior to or at the time of discharge compared with only 3 of 91 (3.3%) of those who did not have a NPS sample (P < 0.025). Children with influenza detected were more likely to receive no antibiotics or have their antibiotics discontinued prior to or at discharge. Only a small proportion of children with other viruses identified had their antibiotics discontinued.

CONCLUSIONS

It appears that clinicians were generally reluctant to stop antibiotics prior to discharge in young children with LRTI in whom influenza or other viruses were identified. In our view, it makes sense to stop antibiotics when the clinical presentation and NPS testing is consistent with a viral aetiology. Not stopping antibiotics at or before discharge in these children represents a missed opportunity for antimicrobial stewardship.

Value of multiplex PCR to determine the bacterial and viral aetiology of pneumonia in school-age children

BACKGROUND

Conventional methods for the aetiological diagnosis of community-acquired pneumonia (CAP) are often insufficient owing to low sensitivity and the long wait for the results of culture and particularly serology, and it often these methods establish a diagnosis in only half of cases.

AIM

To evaluate the most common bacterial and viral agents in CAP using a fast responsive PCR method and investigate the relationship between clinical/laboratory features and aetiology, thereby contributing to empirical antibiotic selection and reduction of treatment failure.

METHODS

In children aged 4-15 years consecutively admitted with a diagnosis of CAP, the 10 most commonly detected bacterial and 12 most commonly detected viral agents were investigated by induced sputum using bacterial culture and multiplex PCR methods. Clinical and laboratory features were compared between bacterial and viral pneumonia.

RESULTS

In 78 patients, at least one virus was detected in 38 (48.7%) and at least one bacterium in 32 (41%). In addition, both bacteria and viruses were detected in 16 (20.5%) patients. Overall, the agent detection rate was 69.2%. The most common viruses were respiratory syncytial virus and influenza and the most frequently detected bacteria were S. pneumoniae and H. influenzae. PCR was superior to culture for bacterial isolation (41% vs 13%, respectively). Fever, wheezing and radiological features were not helpful in differentiating between bacterial and viral CAP. White blood cell count, CRP and ESR values were significantly higher in the bacterial/mixed aetiology group than in the viral aetiology group.

CONCLUSION

In CAP, multiplex PCR is highly reliable, superior in detecting multiple pathogens and rapidly identifies aetiological agents. Clinical features are poor for differentiation between bacterial and viral infections. The use of PCR methods allow physicians to provide more appropriate antimicrobial therapy, resulting in a better response to treatment, and it may be possible for use as a routine service if costs can be reduced.

Child pneumonia - focus on the Western Pacific Region

Worldwide, pneumonia is the leading cause of death in infants and young children (aged <5 years). We provide an overview of the global pneumonia disease burden, as well as the aetiology and management practices in different parts of the world, with a specific focus on the WHO Western Pacific Region. In 2011, the Western Pacific region had an estimated 0.11 pneumonia episodes per child-year with 61,900 pneumonia-related deaths in children less than 5 years of age. The majority (>75%) of pneumonia deaths occurred in six countries; Cambodia, China, Laos, Papua New Guinea, the Philippines and Viet Nam. Historically Streptococcus pneumoniae and Haemophilus influenzae were the commonest causes of severe pneumonia and pneumonia-related deaths in young children, but this is changing with the introduction of highly effective conjugate vaccines and socio-economic development. The relative contribution of viruses and atypical bacteria appear to be increasing and traditional case management approaches may require revision to accommodate increased uptake of conjugated vaccines in the Western Pacific region. Careful consideration should be given to risk reduction strategies, enhanced vaccination coverage, improved management of hypoxaemia and antibiotic stewardship.

Prevalence of Atypical Pathogens in Patients With Cough and Community-Acquired Pneumonia: A Meta-Analysis

PURPOSE

Community-acquired pneumonia (CAP), acute cough, bronchitis, and lower respiratory tract infections (LRTI) are often caused by infections with viruses or Streptococcus pneumoniae. The prevalence of atypical pathogens Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, and Bordetella pertussis among patients with these illnesses in the ambulatory setting has not been previously summarized. We set out to derive prevalence information from the existing literature.

METHODS

We performed a systematic review of MEDLINE for prospective, consecutive-series studies reporting the prevalence of M pneumoniae, C pneumoniae, L pneumophila and/or B pertussis in outpatients with cough, acute bronchitis, LRTI, or CAP. Articles were independently reviewed by 2 authors for inclusion and abstraction of data; discrepancies were resolved by consensus discussion. A meta-analysis was performed on each pathogen to calculate the pooled prevalence estimates using a random effects model of raw proportions.

RESULTS

Fifty studies met our inclusion criteria. While calculated heterogeneity was high, most studies reported prevalence for each pathogen within a fairly narrow range. In patients with CAP, the overall prevalences of M pneumoniae and C pneumoniae were 10.1% (95% CI, 7.1%-13.1%) and 3.5% (95% CI, 2.2%-4.9%), respectively. Consistent with previous reports, M pneumoniae prevalence peaked in roughly 6-year intervals. Overall prevalence of L pneumophila was 2.7% (95% CI, 2.0%-3.4%), but the organism was rare in children, with only 1 case in 1,765. In patients with prolonged cough in primary care, the prevalence of B pertussis was 12.4% (95% CI, 4.9%-19.8%), although it was higher in studies that included only children (17.6%; 95% CI, 3.4%-31.8%).

CONCLUSIONS

Atypical bacterial pathogens are relatively common causes of lower respiratory diseases, including cough, bronchitis, and CAP. Where surveillance data were available, we found higher prevalences in studies where all patients are tested for these pathogens. It is likely that these conditions are underreported, underdiagnosed, and undertreated in current clinical practice.

Human bocavirus: Current knowledge and future challenges

Human bocavirus (HBoV) is a parvovirus isolated about a decade ago and found worldwide in both respiratory samples, mainly from early life and children of 6-24 mo of age with acute respiratory infection, and in stool samples, from patients with gastroenteritis. Since then, other viruses related to the first HBoV isolate (HBoV1), namely HBoV2, HBoV3 and HBoV4, have been detected principally in human faeces. HBoVs are small non-enveloped single-stranded DNA viruses of about 5300 nucleotides, consisting of three open reading frames encoding the first two the non-structural protein 1 (NS1) and nuclear phosphoprotein (NP1) and the third the viral capsid proteins 1 and 2 (VP1 and VP2). HBoV pathogenicity remains to be fully clarified mainly due to the lack of animal models for the difficulties in replicating the virus in in vitro cell cultures, and the fact that HBoV infection is frequently accompanied by at least another viral and/or bacterial respiratory and/or gastroenteric pathogen infection. Current diagnostic methods to support HBoV detection include polymerase chain reaction, real-time PCR, enzyme-linked immunosorbent assay and enzyme immunoassay using recombinant VP2 or virus-like particle capsid proteins, although sequence-independent amplification techniques combined with next-generation sequencing platforms promise rapid and simultaneous detection of the pathogens in the future. This review presents the current knowledge on HBoV genotypes with emphasis on taxonomy, phylogenetic relationship and genomic analysis, biology, epidemiology, pathogenesis and diagnostic methods. The emerging discussion on HBoVs as true pathogen or innocent bystander is also emphasized.

Impact of Chest Radiography on Antibiotic Treatment for Children With Suspected Pneumonia

OBJECTIVE

National guidelines discourage routine chest radiographs (CXRs) to confirm suspected pneumonia in children managed as outpatients. However, limiting CXRs may lead to antibiotic overuse. We examined the impact of CXRs and clinical suspicion on antibiotic treatment for children with suspected pneumonia.

METHODS

Children aged 3 months to 18 years undergoing CXR for suspected pneumonia in a pediatric emergency department were prospectively enrolled. Before CXR, physicians indicated their initial plan for antibiotics (yes or no) and clinical suspicion for radiographic pneumonia (<5%, 5-10%, 11-20%, 21-50%, 51-75%, >75%). Subjects had radiographic pneumonia if their CXRs demonstrated definite or possible findings of pneumonia. We compared antibiotic treatment according to pre-CXR antibiotic plan and suspicion for pneumonia and CXR results.

RESULTS

Among the 107 children with a plan for antibiotics before CXR, 72% ultimately received antibiotics compared with 19% of the 1503 children without a pre-CXR plan for antibiotics (P < 0.001). Among those patients with a pre-CXR plan for antibiotics, 96% of children with radiographic pneumonia were ultimately treated compared with 54% without radiographic pneumonia (P < 0.001). If antibiotics were not initially planned, 37% with radiographic pneumonia were treated compared with 8% without radiographic pneumonia (P < 0.001). The use of CXR was more likely to influence antibiotic prescribing patterns when the clinical suspicion of pneumonia was low (<20%).

CONCLUSIONS

Among children with high suspicion for pneumonia, CXRs infrequently altered the initial plan for antibiotics. However, when clinical suspicion for pneumonia was low, the use of CXR may reduce unnecessary antibiotic use.

Identification of pathogens by comprehensive real-time PCR versus conventional methods in community-acquired pneumonia in Japanese adults

BACKGROUND

Community-acquired pneumonia (CAP) has high morbidity and mortality. Unfortunately, the pathogen detection rate using conventional culture methods is relatively low. We compared comprehensive real-time polymerase chain reaction (real-time PCR) analysis of nasopharyngeal swab specimens (NPS) and sputum samples against conventional methods for ability to detect causative pathogens of CAP.

METHODS

We prospectively enrolled adult CAP patients, including those with prior antibiotic use, from December 2012 to May 2014. For each patient, causative pathogens were investigated conventionally and by real-time PCR that can identify 6 bacterial and 11 viral pathogens.

RESULTS

Patients numbered 92 (mean age, 63 years; 59 male), including 30 (33%) with prior antibiotic use. Considering all patients, identification of causative pathogens by real-time PCR was significantly more frequent than by conventional methods in all patients (72% vs. 57%, p = 0.018). In patients with prior antibiotic use, identification rates also differed significantly (PCR, 77%; conventional, 50%; p = 0.027). Mixed infections were more frequent according to real-time PCR than conventional methods (26% vs. 4%, p < 0.001). By the real-time PCR, Streptococcus pneumoniae was most frequently identified (38%) as a causative pathogen, followed by Haemophilus influenzae (37%) and Mycoplasma pneumoniae (5%). PCR also identified viral pathogens (21%), with sensitivity enhanced by simultaneous examination of both NPS and sputum samples rather than only NPS samples.

CONCLUSIONS

Real-time PCR of NPS and sputum samples could better identify bacterial and viral pathogens in CAP than conventional methods, both overall and in patients with prior antibiotic treatment.

Beta-lactam versus beta- lactam/macrolide therapy in pediatric outpatient pneumonia

OBJECTIVE

The objective was to evaluate the comparative effectiveness of beta-lactam monotherapy and beta- lactam/macrolide combination therapy in the outpatient management of children with community-acquired pneumonia (CAP).

METHODS

This retrospective cohort study included children, ages 1-18 years, with CAP diagnosed between January 1, 2008 and January 31, 2010 during outpatient management in the Geisinger Health System. The primary exposure was receipt of beta-lactam monotherapy or beta-lactam/macrolide combination therapy. The primary outcome was treatment failure, defined as a follow-up visit within 14 days of diagnosis resulting in a change in antibiotic therapy. Logistic regression within a propensity score- restricted cohort was used to estimate the likelihood of treatment failure.

RESULTS

Of 717 children in the analytical cohort, 570 (79.4%) received beta-lactam monotherapy and 147 (20.1%) received combination therapy. Of those who received combination therapy 58.2% of children were under 6 years of age. Treatment failure occurred in 55 (7.7%) children, including in 8.1% of monotherapy recipients, and 6.1% of combination therapy recipients. Treatment failure rates were highest in children 6-18 years receiving monotherapy (12.9%) and lowest in children 6-18 years receiving combination therapy (4.0%). Children 6-18 years of age who received combination therapy were less likely to fail treatment than those who received beta-lactam monotherapy (propensity-adjusted odds ratio, 0.51; 95% confidence interval, 0.28, 0.95).

CONCLUSION

Children 6-18 years of age who received beta- lactam/macrolide combination therapy for CAP in the outpatient setting had lower odds of treatment failure compared with those who received beta-lactam monotherapy.

Etiology of Pneumonia in a Pediatric Population with High Pneumococcal Vaccine Coverage: A Prospective Study

BACKGROUND

Improved Childhood Immunizations Programs, especially the introduction of pneumococcal vaccination, better diagnostic methods and the importance of reduced antibiotic misuse, make this a critical time to increase knowledge on the etiology of pediatric pneumonia. Our main objective was to identify the contribution of various microbiological species that causes pneumonia in previously healthy children and adolescents in a population with high pneumococcal conjugate vaccine coverage.

METHODS

This prospective, observational study enrolled patients with clinical and radiological signs of pneumonia over a 2-year period. Both inpatients and outpatients were included. Paired sera, nasopharyngeal polymerase chain reaction and bacterial cultures from blood and pleura were analyzed to detect potential viral and bacterial causative pathogens.

RESULTS

TWO HUNDRED AND SIXTY-FIVE: cases of clinical and radiological verified pneumonia were identified. The pneumococcal vaccine coverage was 85%. We identified a causative pathogen in 84.2% of all cases; 63.4% with single viral etiology, 11.3% with pneumococcus and 7.5% with mycoplasma infection. Respiratory syncytial virus was the most common pathogen in children younger than 5 years, whereas mycoplasma was the most common in older children.

CONCLUSIONS

We identified the majority of 265 cases with radiology proven pneumonia as single viral infections, predominantly respiratory syncytial virus and a much lower proportion of bacterial causes. These findings may impact pneumonia management guidelines in areas where widespread pneumococcal vaccination is provided and contribute to reduced antibiotic overuse in pediatric pneumonia.

Uncomplicated pneumonia in healthy Canadian children and youth: Practice points for management

Although immunization has decreased the incidence of bacterial pneumonia in vaccinated children, pneumonia remains common in healthy children. Symptoms of bacterial pneumonia frequently overlap those present with viral infections or reactive airway disease. Optimally, the diagnosis of bacterial pneumonia should be supported by a chest radiograph before starting antimicrobials. Factors such as age, vital signs and other measures of illness severity are critical when deciding whether to admit a patient to hospital. Because Streptococcus pneumoniae continues to be the most common cause of bacterial pneumonia in children, prescribing amoxicillin or ampicillin for seven to 10 days remains the mainstay of empirical therapy for nonsevere pneumonia. If improvement does not occur, consideration should be given to searching for complications (empyema or lung abscess). Routine chest radiographs at the end of therapy are not recommended unless clinically indicated.

Impact of Human Rhinovirus Types and Viral Load on the Severity of Illness in Hospitalized Children With Lower Respiratory Tract Infections

BACKGROUND

Human rhinovirus (HRV) is not only responsible for at least one-half of all common colds but also associated with bronchitis, bronchiolitis, pneumonia and acute asthma exacerbation. However, the impact of different HRV types and viral load on disease severity has not been thoroughly elucidated.

METHODS

From January 2012 to September 2014, 1742 nasopharyngeal aspirate specimens from hospitalized children with lower respiratory tract infections were analyzed by quantitative HRV-specific real-time polymerase chain reaction.

RESULTS

Among these 1742 children, HRV (407/1742, 23%) was the second most common viral agent after respiratory syncytial virus. HRV-A, HRV-B, HRV-C and HRV untyped were detected in 229 (56%), 27 (7%), 100 (25%) and 51 (13%) specimens, respectively. Children except who experienced wheezing were more common in the HRV-C detection group than in the HRV-A detection group; there were no other significant differences between the 2 groups, including the percent of children diagnosed with severe diseases. Logistic regression models demonstrated that there was no difference in disease severity among HRV types. In HRV-A detection group, in children younger than 2 years, the viral load was higher in the severe group than in the nonsevere group; but in the HRV-C detection group, there was no difference.

CONCLUSIONS

HRV was frequently present in hospitalized children with lower respiratory tract infections in Chongqing, China. The disease severity for HRV-C and HRV-A was similar. A high load of HRV-A in the lower respiratory tract might be connected with disease severity in children younger than 2 years.

Molecular evolution of the hypervariable region of the attachment glycoprotein gene in human respiratory syncytial virus subgroup B genotypes BA9 and BA10

We studied the molecular evolution of the C-terminal 3rd hypervariable region in the attachment glycoprotein gene of human respiratory syncytial virus subgroup B (HRSV-B) genotypes BA9 and BA10. We performed time-scaled phylogenetic analyses using Bayesian Markov chain Monte Carlo methods. We also performed a genetic distance analysis (p-distance analysis), positive and negative selection analyses, and a Bayesian skyline plot (BSP) analysis. We found that genotype BA9 diverged from the common ancestor of genotypes BA7, BA8, and BA10, while genotype BA10 diverged from the ancestor of genotypes BA7 and BA8. Strains of both genotypes were distributed worldwide. BA9 and BA10 diverged between 1999 and 2001. Both BA9 and BA10 evolved rapidly (about 4.8×10(-3)substitutions/site/year) and formed three distinct lineages in a 10-year period. BA10 strains belonging to lineage 3 had large genetic distances (p-distance>0.07). Thus, it may be possible to classify these strains as a new genotype, BA11. No positive selection site was detected in either genotype. Phylodynamic analyses showed that the effective population size of BA10 decreased gradually since 2010 and BA9 slightly decreased since 2009. The results suggested that the recently prevalent HRSV-B genotypes BA9 and BA10 evolved uniquely, leading to epidemics of HRSV-B worldwide over a 15-year period.

Pathogens in COPD exacerbations identified by comprehensive real-time PCR plus older methods

Respiratory infection is a major cause of exacerbation in chronic obstructive pulmonary disease (COPD). Infectious contributions to exacerbations remain incompletely described. We therefore analyzed respiratory tract samples by comprehensive real-time polymerase chain reaction (PCR) in combination with conventional methods. We evaluated multiple risk factors for prolonged hospitalization to manage COPD exacerbations, including infectious agents. Over 19 months, we prospectively studied 46 patients with 50 COPD exacerbations, collecting nasopharyngeal swab and sputum samples from each. We carried out real-time PCR designed to detect six bacterial species and eleven viruses, together with conventional procedures, including sputum culture. Infectious etiologies of COPD exacerbations were identified in 44 of 50 exacerbations (88%). Infections were viral in 17 of 50 exacerbations (34%). COPD exacerbations caused by Gram-negative bacilli, including enteric and nonfermenting organisms, were significantly associated with prolonged hospitalization for COPD exacerbations. Our results support the use of a combination of real-time PCR and conventional methods for determining both infectious etiologies and risk of extended hospitalization.

Effects of bacterial and viral co-infections of mycoplasma pneumoniae pneumonia in children: analysis report from Beijing Children's Hospital between 2010 and 2014

The objective of this study was to describe the rates and impact of bacterial and viral co-infections of hospitalized children with Mycoplasma pneumoniae. The clinical characteristics, hospital expenses, and differences between single and co-infection MPP were explored. This study included 5,009 children from 2010 to 2014. Infections with various pathogens were identified by the following tests: positive specimens' culture, direct immunofluorescent antigen test for viruses, mycoplasma or chlamydia detection. The results indicated that 13.6% of them showed positive results, including bacterial pathogens in 2.5% of cases and viral pathogens in 9.8% of cases. The most commonly identified bacteria was Streptococcus pneumonia. Influenza and parainfluenza were the most commonly identified virus. Hospitalization expenses of patients with single infections were less than those who with co-infections. In conclusion, co-infections were more common in recent years. In severe MPP, rates of co-infection were higher than non-severe MPP. The longer the course of infection, the higher the co-infection rate.

Detection of respiratory viral and bacterial pathogens causing pediatric community-acquired pneumonia in Beijing using real-time PCR

OBJECTIVE

The aim of this study was to determine the etiology and prevalence of pediatric CAP in Beijing using a real-time polymerase chain reaction (PCR) technique.

METHODS

Between February 15, 2011 and January 18, 2012, 371 pediatric patients with CAP were enrolled at Beijing Children's Hospital. Sixteen respiratory viruses and two bacteria were detected from tracheal aspirate specimens using commercially available multiplex real-time reverse transcription PCR (RT-PCR) kits.

RESULTS

A single viral pathogen was detected in 35.3% of enrolled patients, multiple viruses in 11.6%, and virus/bacteria coinfection in 17.8%. In contrast, only 6.5% of patients had a single bacterial pathogen and 2.2% were infected with multiple bacteria. The etiological agent was unknown for 26.7% of patients. The most common viruses were respiratory syncytial virus (RSV) (43.9%), rhinovirus (14.8%), parainfluenza virus (9.4%), and adenovirus (8.6%). In patients under three years of age, RSV (44.6%), rhinovirus (12.8%), and Streptococcus pneumoniae (9.9%) were the most frequent pathogens. In children aged 3-7 years, S. pneumoniae (38.9%), RSV (30.6%), Haemophilus influenzae (19.4%), and adenovirus (19.4%) were most prevalent. Finally in children over seven years, RSV (47.3%), S. pneumoniae (41.9%), and rhinovirus (21.5%) infections were most frequent.

CONCLUSIONS

Viral pathogens, specifically RSV, were responsible for the majority of CAP in pediatric patients. However, both S. pneumoniae and H. influenzae contributed as major causes of disease. Commercially available multiplexing real-time PCR allowed for rapid detection of the etiological agent.

Children hospitalised with influenza-associated pneumonia during the 2009 pandemic displayed increased disease severity

AIM

The precise role of the influenza virus in the morbidity of hospitalised paediatric pneumonia cases is unknown. We identified how many cases hospitalised during the 2009 pandemic had influenza-associated pneumonia and assessed their severity.

METHODS

Children admitted to three Israeli medical centres during the 2009 influenza pandemic with radiologically confirmed pneumonia were prospectively screened for influenza. We compared the clinical, laboratory and radiologic findings for positive and negative cases.

RESULTS

The pandemic H1N1 virus was detected in 89 (30%) of the 297 patients hospitalised for pneumonia and 55% of the Paediatric Intensive Care Unit admissions for pneumonia. There were no significant differences in the rates of underlying disease between the two groups. Logistic regression analysis revealed that children with pandemic H1N1 virus-associated pneumonia had significantly increased disease severity than those without, with a higher incidence of hypoxemia (41.6% versus 24%) with a relative risk (RR) of 2.2, higher rate of paediatric intensive care unit admission (16.9% versus 5.8%, RR of 2.7) and higher rate of mechanical ventilation (10.1% versus 2.4%, RR:4.4).

CONCLUSION

During the 2009 influenza pandemic, 30% of children hospitalised for pneumonia had the influenza infection and these children displayed increased disease severity.

Incidence of viral infection detected by PCR and real-time PCR in childhood community-acquired pneumonia: a meta-analysis

Several studies examining the incidence of viral infection in childhood community‐acquired pneumonia (CAP) utilizing polymerase chain reaction (PCR) or real‐time PCR methods have been reported. We systematically searched Pubmed and Embase for studies reporting the incidence of respiratory viral infection in childhood CAP. The pooled incidences of viral infection were calculated with a random‐effects model. Sources of heterogeneity were explored by subgroup analysis and a univariant metaregression analysis. We included 21 eligible reports in our study. We found significant heterogeneity on the incidence of viral infection in childhood CAP. The random effects pooled incidence was 57.4% (95% confidence interval (CI): 50.8–64.1). The pooled incidence of mixed infection was 29.3% (95%CI: 23.0–35.6) with considerable heterogeneity. The pooled incidence of mixed infection was 29.3% (95%CI: 23.0–35.6). Rhinovirus, respiratory syncytial virus (RSV) and bocavirus were found to be the three most common viruses in childhood CAP. We also demonstrated that respiratory viruses were detected in 76.1% of patients aged ≤1 year, 63.1% of patients aged 2–5 years and 27.9% of patients aged ≥ 6 years. We conclude that respiratory viruses are widely detected in paediatric patients with CAP by PCR or real‐time PCR methods. More than half of viral infections are probably concurrent with bacterial infections. Rhinovirus, RSV and bocavirus are the three most frequent viruses identified in childhood CAP; the incidence of viral infection decreased with age.

Direct identification of Streptococcus agalactiae and capsular type by real-time PCR in vaginal swabs from pregnant women

Most group B streptococcus (GBS) infections in newborns are with capsular type Ia, Ib, or III. To prevent these infections more effectively, we developed a real-time PCR method to simultaneously detect GBS species and identify these 3 capsular types in vaginal swab samples from women at 36-39 weeks of gestation. DNA to be detected included those of the dltS gene (encoding a histidine kinase specific to GBS) and cps genes encoding capsular types. PCR sensitivity was 10 CFU/well for a 33-35 threshold cycle. Results were obtained within 2 h. Direct PCR results were compared with results obtained from cultures. Samples numbering 1226 underwent PCR between September 2008 and August 2012. GBS positivity rates by direct PCR and after routine culture were 15.7% (n = 192) and 12.6% (n = 154), respectively. Sensitivity and specificity of direct PCR relative to culture were 96.1% and 95.9%. Of GBS positive samples identified by PCR, capsular types determined directly by real-time PCR were Ia (n = 24), Ib (n = 32), and III (n = 26). Real-time PCR using our designed cycling probe is a practical, highly sensitive method for identification of GBS in pregnant carriers, allowing use of prophylactic intrapartum antibiotics in time to cover the possibility of unexpected premature birth.

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.

Epidemiology and microbiological investigations of community-acquired pneumonia in children admitted at the emergency department of a university hospital

•

Systematic antimicrobials are recommended in community-acquired pneumonia of child.

•

A large panel of bacteria and viruses was detected in 85 children exhibiting CAP.

•

More than 60% of children with CAP exhibited an exclusive viral infection.

•

A co-infection with at least 2 viruses was observed in >40% of the children.

•

Data suggest that the use of antimicrobials in child's CAP should be revisited.

Background

The management of children with community-acquired pneumonia (CAP) is largely influenced by the development of new molecular diagnostic tests that allow the simultaneous detection of a wide range of pathogens.

Objectives

Evaluation of a diagnostic approach including multiplex PCR assays for revisiting the epidemiology and etiology of CAP in children at hospital.

Study design

Children of all ages consulting at the Emergency Department of the University hospital of Saint-Etienne, France, during the 2012–2013 winter period were included. In addition to bacterial cultures, the following pathogens were detected using biplex commercially-available rt-PCR tests: adenovirus, respiratory syncytial virus, human metapneumovirus, bocavirus, rhinovirus/enterovirus, coronavirus, influenza viruses A and B, parainfluenza viruses, Mycoplasma pneumoniae and Chlamydophila pneumonia.

Results

From 85 patients with CAP, at least one pathogen was identified in 81 cases (95.3%), including 4 bacterial exclusive infections (4.7%), 53 viral exclusive infections (62.4%) and 24 mixed infections (28.2%). Coinfection by at least two viruses was observed in 37 cases (43.5%). Mean age was higher in the case of documented bacterial infection (P < 0.05). In the subgroup of viral exclusive infection, the mean age of severe cases was 2.0 years vs 3.8 years in mild and moderate cases (P < 0.05).

Conclusions

These findings highlight the huge proportion of CAP of viral origin, the high number of co-infection by multiple viruses and the low number of bacterial CAP, notably in children under 5 years, and address the need to re-evaluate the indications of empiric antimicrobial treatment in this age group.

Lessons learned and unlearned in periodontal microbiology

Periodontal diseases are initiated by bacterial species living in polymicrobial biofilms at or below the gingival margin and progress largely as a result of the inflammation elicited by specific subgingival species. In the past few decades, efforts to understand the periodontal microbiota have led to an exponential increase in information about biofilms associated with periodontal health and disease. In fact, the oral microbiota is one of the best-characterized microbiomes that colonize the human body. Despite this increased knowledge, one has to ask if our fundamental concepts of the etiology and pathogenesis of periodontal diseases have really changed. In this article we will review how our comprehension of the structure and function of the subgingival microbiota has evolved over the years in search of lessons learned and unlearned in periodontal microbiology. More specifically, this review focuses on: (i) how the data obtained through molecular techniques have impacted our knowledge of the etiology of periodontal infections; (ii) the potential role of viruses in the etiopathogenesis of periodontal diseases; (iii) how concepts of microbial ecology have expanded our understanding of host-microbe interactions that might lead to periodontal diseases; (iv) the role of inflammation in the pathogenesis of periodontal diseases; and (v) the impact of these evolving concepts on therapeutic and preventive strategies to periodontal infections. We will conclude by reviewing how novel systems-biology approaches promise to unravel new details of the pathogenesis of periodontal diseases and hopefully lead to a better understanding of their mechanisms.

Evaluation of new immunochromatographic assay kit for adenovirus detection in throat swab: comparison with culture and real-time PCR results

A new immunochromatographic (IC) assay kit, BD Veritor System Adeno was evaluated to comparing with commercial available kit, BD Adeno Examan, cell culture, and real-time PCR using throat swab samples. Specimens were collected from 146 pediatric patients between July 2011 and January 2012. Mean age of patients was 4 years (8 months-15 years old). Patients were diagnosed with pharyngitis (n = 67), tonsillitis (n = 45), pharyngoconjunctival fever (n = 26), upper respiratory tract infection (n = 6), conjunctivitis (n = 1), or bronchitis (n = 1). Thirty-one of the patients (21.2%) had more than one disease. Among all samples, 61 (41.8%) were positive for adenovirus with BD Veritor System Adeno; 68 (46.6%) with BD Adeno Examan; 63 (43.2%) with real-time PCR; and 65 (44.5%) with cell culture. Serotype 3 (n = 41; 63.1%) was predominant among the 65 adenovirus isolates, followed by serotype 2 (n = 12; 18.5%), 1 (n = 6; 9.2%), 5 (n = 4; 6.2%), and 4 (n = 2; 3.1%). Relative sensitivity and specificity of BD Veritor System Adeno, BD Adeno Examan, and real-time PCR were 93.8% and 98.7%, 96.9% and 93.8%, and 96.9% and 100%, respectively. Positive predictive and negative predictive values for these methods were 98.4% and 95.1%, 92.6% and 97.4%, and 100% and 97.6%, respectively. The sensitivity and specificity of real-time PCR was greater than that of IC assay kits. However, IC assay kits also showed high sensitivity and specificity appropriate for clinical use.