Pneumonia research to reduce childhood mortality in the developing world

Risk factors associated with wheezing in severe pediatric community-acquired pneumonia: a retrospective study

BACKGROUND

Wheezing is a common clinical manifestation in children with pneumonia. However, the risk factors associated with the development of wheezing pneumonia and its clinical features are not fully characterized, especially in children with severe pneumonia.

METHODS

We retrospectively recruited 1434 pediatric patients diagnosed with severe pneumonia between April 2012 and September 2019 in Fujian Maternity and Child Health Hospital. The medical records regarding demographic information, clinical manifestations, radiographic/laboratory findings, and complications were collected. Based on the presence or absence of wheezing symptoms and signs, subjects were divided into wheezing cohort (N.=684) and non-wheezing cohort (N.=750), and their clinical data were compared. Multivariate cox regression analysis was performed to identify independent risk factors of wheezing.

RESULTS

Demographic features including gender, weigh, onset season, birth weight, full-term birth or not, history of pneumonia were significantly associated with the occurrence of wheezing in severe CAP (P<0.05). Specifically, male gender, onset seasons in autumn/winter, and absence of a history of pneumonia were identified as independent risk factors of wheezing in multivariate analysis (P<0.05). As for clinical features, wheezing cohort differed from the non-wheezing one in terms of clinical manifestation (higher incidence of cough and breathless, but lower incidence of fever), laboratory finding (higher levels of red blood cells, hemoglobin, and albumin and lower levels of total or indirect bilirubin and creatine), pathogen detection (higher incidence of respiratory syncytial viral infection), and clinical complications (lesser risk of sepsis and hydrothorax) (P<0.05).

CONCLUSIONS

Severe CAP with wheezing is a special clinical entity of severe pneumonia in children, which has specific risk factors and differ from non-wheezing pneumonia in terms of clinical features and etiologic pathogens.

Pneumonia classification: A limited data approach for global understanding

As the human race has advanced, so too have the ailments that afflict it. Diseases such as pneumonia, once considered to be basic flu or allergies, have evolved into more severe forms, including SARs and COVID-19, presenting significant risks to people worldwide. In our study, we focused on categorizing pneumonia-related inflammation in chest X-rays (CXR) using a relatively small dataset. Our approach was to encompass a comprehensive view, addressing every potential area of inflammation in the CXR. We employed enhanced class activation maps (mCAM) to meet the clinical criteria for classification rationale. Our model incorporates capsule network clusters (CNsC), which aids in learning different aspects such as geometry, orientation, and position of the inflammation seen in the CXR. Our Capsule Network Clusters (CNsC) rapidly interpret various perspectives in a single CXR without needing image augmentation, a common necessity in existing detection models. This approach significantly cuts down on training and evaluation durations. We conducted thorough testing using the RSNA pneumonia dataset of CXR images, achieving accuracy and recall rates as high as 98.3% and 99.5% in our conclusive tests. Additionally, we observed encouraging outcomes when applying our trained model to standard X-ray images obtained from medical clinics.

Three-dimensional ultrashort echo time magnetic resonance imaging in pediatric patients with pneumonia: a comparative study

BACKGROUND

UTE has been used to depict lung parenchyma. However, the insufficient discussion of its performance in pediatric pneumonia compared with conventional sequences is a gap in the existing literature. The objective of this study was to compare the diagnostic value of 3D-UTE with that of 3D T1-GRE and T2-FSE sequences in young children diagnosed with pneumonia.

METHODS

Seventy-seven eligible pediatric patients diagnosed with pneumonia at our hospital, ranging in age from one day to thirty-five months, were enrolled in this study from March 2021 to August 2021. All patients underwent imaging using a 3 T pediatric MR scanner, which included three sequences: 3D-UTE, 3D-T1 GRE, and T2-FSE. Subjective analyses were performed by two experienced pediatric radiologists based on a 5-point scale according to six pathological findings (patchy shadows/ground-glass opacity (GGO), consolidation, nodule, bulla/cyst, linear opacity, and pleural effusion/thickening). Additionally, they assessed image quality, including the presence of artifacts, and evaluated the lung parenchyma. Interrater agreement was assessed using intraclass correlation coefficients (ICCs). Differences among the three sequences were evaluated using the Wilcoxon signed-rank test.

RESULTS

The visualization of pathologies in most parameters (patchy shadows/GGO, consolidation, nodule, and bulla/cyst) was superior with UTE compared to T2-FSE and T1 GRE. The visualization scores for linear opacity were similar between UTE and T2-FSE, and both were better than T1-GRE. In the case of pleural effusion/thickening, T2-FSE outperformed the other sequences. However, statistically significant differences between UTE and other sequences were only observed for patchy shadows/GGO and consolidation. The overall image quality was superior or at least comparable with UTE compared to T2-FSE and T1-GRE. Interobserver agreements for all visual assessments were significant and rated "substantial" or "excellent."

CONCLUSIONS

In conclusion, UTE MRI is a useful and promising method for evaluating pediatric pneumonia, as it provided better or similar visualization of most imaging findings compared with T2-FSE and T1-GRE. We suggest that the UTE MRI is well-suited for pediatric population, especially in younger children with pneumonia who require longitudinal and repeated imaging for clinical care or research and are susceptible to ionizing radiation.

RSV infection in children hospitalised with severe lower respiratory tract infection in a low-middle-income setting: A cross-sectional observational study

INTRODUCTION

Low- and middle-income countries carry the largest burden of Respiratory syncytial virus (RSV) disease, with most deaths occurring in these settings. This study aimed to investigate the burden of RSV disease in South African children hospitalised with lower respiratory tract infection (LRTI), with specific reference to incidence, risk factors, and co-infections.

METHODS

A database from a previous prospective study containing demographic, laboratory and clinical data on children hospitalised with LRTIs in Cape Town, South Africa, was used. A nasopharyngeal swab (NP) and induced sputum (IS) were tested for RSV PCR. Descriptive statistics were used to characterise the study population, and a multivariable analysis of risk factors and co-infections was done.

RESULTS

RSV was detected in 142 (30.9%; 95% CI 26.7-35.3) of the included 460 study children with LRTI. The median age of RSV-positive children was 4.6 (IQR 2.4-9.7) months compared to RSV-negative children of 10.5 (IQR 4.4-21.3) months, P = <0.001. Most cases occurred in autumn and winter with 126 (89%) cases over this period. IS demonstrated greater sensitivity for RSV diagnosis with 135 cases (95.1%) detected on IS and 57 cases (40.1%) identified on NP; P<0.001. The median length of hospital stay was 3.3 (SD 4.2) days in the RSV positive group and 2.7 (SD 3.3) days in the RSV negative group; P<0.001. The median number of detected viral pathogens was 1 (IQR 0-2) in RSV-positive children (when RSV was excluded from the count) compared to 2 (IQR 2-3) in RSV negative children; P<0.001. The presence of RSV was independently associated with a reduction in the frequency of most viruses tested for on PCR.

CONCLUSIONS

RSV is common in children hospitalised with LRTI and mainly affects younger children. There is an urgent need to find an effective vaccine to prevent RSV pneumonia in children worldwide, especially in LMICs that carry the greatest burden of disease.

Predictors for the duration of breastfeeding among ethiopia women of childbearing age with babies; application of accelerate failure time and parametric shared frailty models

Introduction

Duration of breastfeeding is the length of the time that infants who were initially breastfed continue to receive breast milk until weaning. The duration of breastfeeding is important for a child's health, growth, and development. However, the duration of breastfeeding decreases from time to time and further leads children to be exposed to malnutrition (stunting, wasting, and weight loss). Children who did not get enough breastfeeding are also exposed to different diseases. Previous studies used a simple survival model and didn’t see the shared frailty model on the variable of interest. Therefore, the current study aimed to investigate the factors affecting the duration of breastfeeding among Ethiopian women of reproductive age with babies.

Methods

A cross-sectional study design was conducted on 15,400 women of childbearing age with babies in nine regional states and two city administrations. The data source for the analysis was the 2016 EDHS data. The Cox-proportional hazard model, AFT, and parametric shared frailty models were conducted for the current investigation. Weibull-gamma shared frailty model was in favor of others for current data analysis.

Results

Among the covariates, women living in urban area (Φ = 0.96; 95% CI; (0.94,0.97); p-value = 0.001), non-educated women(Φ = 1.03; 95% CI; (1.00,1.06); p-value = 0.039), primary educated women (Φ = 1.13; 95% CI; (1.11,1.15); p-value < 0.001), age of a child (Φ = 0.99; 95% CI; (0.76.0.99); p-value < 0.001) and non-smoker mothers (Φ = 1.60; 95% CI; (1.57, 1.63); p-value < 0.001),birth interval between 2–3 years(Φ = 1.02; 95% CI;(1.09, 1.25, p-value = 0.027), birth interval, > 3 years(Φ = 1.28; 95% CI; (1.06, 1.43); p-value < 0.01 significantly affected the duration of breastfeeding. The median survival time of breastfeeding of women of reproductive age with babies considered under study was 23.4 months. Clustering had a significant effect on the variable of interest.

Conclusion

Residence area, level of education, age of the child, smoking status of women, and birth interval of successive birth significantly affected the duration of breastfeeding in the current investigation. Hence, the health staff should conduct health-related education for young women, educated women, urban women, smoker women, and women with a shorter interval of birth to increase the women's attitude and awareness towards the use of long-duration of breastfeeding.

Neural architecture search for pneumonia diagnosis from chest X-rays

Pneumonia is one of the diseases that causes the most fatalities worldwide, especially in children. Recently, pneumonia-caused deaths have increased dramatically due to the novel Coronavirus global pandemic. Chest X-ray (CXR) images are one of the most readily available and common imaging modality for the detection and identification of pneumonia. However, the detection of pneumonia from chest radiography is a difficult task even for experienced radiologists. Artificial Intelligence (AI) based systems have great potential in assisting in quick and accurate diagnosis of pneumonia from chest X-rays. The aim of this study is to develop a Neural Architecture Search (NAS) method to find the best convolutional architecture capable of detecting pneumonia from chest X-rays. We propose a Learning by Teaching framework inspired by the teaching-driven learning methodology from humans, and conduct experiments on a pneumonia chest X-ray dataset with over 5000 images. Our proposed method yields an area under ROC curve (AUC) of 97.6% for pneumonia detection, which improves upon previous NAS methods by 5.1% (absolute).

Classification of pneumonia using pre-trained convolutional networks on chest X-Ray images

Pneumonia is an infection that is caused to the people of all ages with mild to severe inflammation of the lung disease. The most common and best method for the diagnosis of pneumonia is chest radiography. But diagnosing pneumonia from chest radiographs is a difficult task, even for radiologists. To overcome, Pre-Trained Convolutional Neural Networks namely Inceptionv3 and Resnet50 are used as a feature extractor. The exacted features are fed into 1D CNN which is classifies into Normal, Bacterial Pneumonia and Viral Pneumonia. When comparing Inceptionv3 with 1D CNN and resnet50 with 1D CNN, it is analyzed that Inceptionv3 with 1D CNN gives the satisfactory results of 96.04%.

Paediatric pneumonia research priorities in the context of COVID-19: An eDelphi study

Background

Pneumonia remains the leading cause of infectious deaths in children under-five globally. We update the research priorities for childhood pneumonia in the context of the COVID-19 pandemic and explore whether previous priorities have been addressed.

Methods

We conducted an eDelphi study from November 2019 to June 2021. Experts were invited to take part, targeting balance by: gender, profession, and high (HIC) and low- and middle-income countries (LMIC). We followed a three-stage approach: 1. Collating questions, using a list published in 2011 and adding newly posed topics; 2. Narrowing down, through participant scoring on importance and whether they had been answered; 3. Ranking of retained topics. Topics were categorized into: prevent and protect, diagnosis, treatment and cross-cutting.

Results

Overall 379 experts were identified, and 108 took part. We started with 83 topics, and 81 further general and 40 COVID-19 specific topics were proposed. In the final ranking 101 topics were retained, and the highest ranked was to “explore interventions to prevent neonatal pneumonia”. Among the top 20 topics, epidemiological research and intervention evaluation was commonly prioritized, followed by the operational and implementation research. Two COVID-19 related questions were ranked within the top 20. There were clear differences in priorities between HIC and LMIC respondents, and academics vs non-academics.

Conclusions

Operational research on health system capacities, and evaluating optimized delivery of existing treatments, diagnostics and case management approaches are needed. This list should act as a catalyst for collaborative research, especially to meet the top priority in preventing neonatal pneumonia, and encourage multi-disciplinary partnerships.

Adjunctive everolimus therapy for tuberous sclerosis complex-associated refractory seizures: Results from the postextension phase of EXIST-3

OBJECTIVE

Epilepsy is highly prevalent in patients with tuberous sclerosis complex (TSC). Everolimus showed higher efficacy than placebo for seizures in the primary analysis of the EXIST-3 study. Here, we present the long-term outcomes of everolimus at the end of the postextension phase (PEP; data cutoff date: October 25, 2017).

METHODS

After completion of the extension phase, patients were invited to continue everolimus in the PEP with everolimus (targeted trough concentration = 5-15 ng/ml, investigator-judged). Efficacy assessments included changes in seizure status during the PEP collected at 12-week intervals as parent/caregiver-reported data through a structured questionnaire.

RESULTS

Among 361 patients, 343 entered the extension phase and 249 entered the PEP. After 12 weeks in the PEP, 18.9% (46/244) of patients were seizure-free since the last visit of the extension phase and 64.8% (158/244) had a stable/improved seizure status. At 24 weeks, the corresponding percentages were 18.2% (42/231) and 64.5% (149/231). Among 244 patients, the response rate was 32.8% (80/244) during the 12-week maintenance period of the core phase and 63.9% (156/244) at the end of the extension phase. Of the 149 responders at the end of the extension phase, 70.5% were seizure-free or had stable/improved seizure status. Long-term efficacy data showed persistent responses were observed in 183 of 361 patients (50.7%); 63.9% of these patients had a response that lasted at least 48 weeks. The most frequent Grade 3-4 adverse events (≥2% incidence) reported throughout the study were pneumonia, status epilepticus, seizure, stomatitis, neutropenia, and gastroenteritis. Four patients died during the study.

SIGNIFICANCE

The final analysis of EXIST-3 demonstrated the sustained efficacy of everolimus as adjunctive therapy in patients with TSC-associated treatment-refractory seizures, with a tolerable safety profile.

Real-world evaluation of costs of illness for pneumonia in adult patients in Dubai-A claims database study

Background

Pneumonia is a significant cause of morbidity and mortality among adults globally. This retrospective cohort analysis assessed the pneumonia burden and related healthcare resource utilization and costs in the at-risk (low, medium, and high-risk) adult patients in Dubai, United Arab Emirates (UAE).

Methods

The claims data from January 1, 2014 to June 30, 2019 were extracted from the Dubai Real-World Claims Database for patients, aged ≥18 year, having at least 1 pneumonia claim. Data for the inpatient, outpatient and emergency visits were assessed for 12-months, before (pre-index) and after (follow-up) a pneumonia episode. Healthcare costs were calculated based on dollar value of 2020.

Results

Total 48,562 records of eligible patients were analyzed (mean age = 39.9 years; low [62.1%], medium [36.2%] and high [1.7%] risk cohorts). Mean all-cause healthcare costs were approximately >45% higher in the follow-up period (1,947 USD/patient) versus pre-index period (1,327 USD/patient). During follow-up period, the mean annual pneumonia incidence rate was 1.3 episodes, with a similar pattern across all cohorts. Overall, mean claims and costs (USD) per patient (all-cause) were highest in the high-risk cohort in the follow-up period (claims: overall, 11.6; high-risk, 22.0; medium-risk, 13.9; low-risk, 9.9; costs: high-risk, 14,184; medium-risk, 2,240; low-risk, 1,388). Similarly, the mean pneumonia-related costs (USD) per patient were highest for the high-risk cohort (overall: 1,305; high-risk, 10,207; medium-risk, 1,283; low-risk, 882), however, the claims were similar across cohorts (claims/patient: overall: 2.0; high-risk, 1.9; medium-risk, 2.2; low-risk, 1.9). Most all-cause and pneumonia-related costs were due to inpatient visits (4,901 and 4,818 USD respectively), while outpatient (1,232 and 166 USD respectively) and emergency visits (347 and 206 USD respectively) contributed significantly lesser.

Conclusions

Pneumonia imposes a significant healthcare burden in the UAE, especially in the high-risk patients with severe comorbidities. These findings would guide clinicians and policy makers to make informed decisions.

The association between bacteria colonizing the upper respiratory tract and lower respiratory tract infection in young children: a systematic review and meta-analysis

BACKGROUND

Bacteria colonizing the upper respiratory tract (URT) of young children play a key role in the pathogenesis of lower respiratory tract infection (LRTI).

OBJECTIVES

To systematically review the literature on the association between bacteria colonizing the URT and LRTI among young children.

DATA SOURCES

MEDLINE, Academic Search Premier, Africa-Wide Information and CINAHL, Scopus and Web of Science.

STUDY ELIGIBILITY CRITERIA

Studies published between 1923 and 2020, investigating URT bacteria from LRTI cases and controls.

PARTICIPANTS

Children under 5 years with and without acute LRTI.

METHODS

Three reviewers independently screened titles, abstracts and full texts. Meta-analysis was done using Mantel-Haenszel fixed- or random-effects models.

RESULTS

Most eligible studies (41/50) tested nasopharyngeal specimens when investigating URT bacteria. Most studies were of cross-sectional design (44/50). Twenty-four studies were performed in children in lower- or lower-middle-income countries (LMICs). There was higher prevalence of Haemophilus influenzae (pooled OR 1.60; 95% CI 1.23-2.07) and Klebsiella spp. (pooled OR 2.04; 95% CI 1.17-3.55) from URT specimens of cases versus controls. We observed a positive association between the detection of Streptococcus pneumoniae from URT specimens and LRTI after excluding studies where there was more antibiotic treatment prior to sampling in cases vs. controls (pooled OR 1.41; 95% CI 1.04-1.90). High density colonization with S. pneumoniae (>6.9 log10 copies/mL) was associated with an increased risk for LRTI. The associations between both Streptococcus and Haemophilus URT detection and LRTI were supported, at genus level, by 16S rRNA sequencing. Evidence for the role of Moraxella catarrhalis and Staphylococcus aureus was inconclusive.

CONCLUSIONS

Detection of H. influenzae or Klebsiella spp. in the URT was associated with LRTI, while evidence for association with S. pneumoniae was less conclusive. Longitudinal studies assessing URT microbial communities, together with environmental and host factors are needed to better understand pathogenesis of childhood LRTI.

Etiology and Clinical Characteristics of Severe Pneumonia Among Young Children in Thailand: Pneumonia Etiology Research for Child Health (PERCH) Case-Control Study Findings, 2012-2013

BACKGROUND

Pneumonia remains the leading cause of death among children <5 years of age beyond the neonatal period in Thailand. Using data from the Pneumonia Etiology Research for Child Health (PERCH) Study, we provide a detailed description of pneumonia cases and etiology in Thailand to inform local treatment and prevention strategies in this age group.

METHODS

PERCH, a multi-country case-control study, evaluated the etiology of hospitalized cases of severe and very severe pneumonia among children 1-59 months of age. The Thailand site enrolled children for 24 consecutive months during January 2012-February 2014 with staggered start dates in 2 provinces. Cases were children hospitalized with pre-2013 WHO-defined severe or very severe pneumonia. Community controls were randomly selected from health services registries in each province. Analyses were restricted to HIV-negative cases and controls. We calculated adjusted odds ratios (ORs) and 95% CIs comparing organism prevalence detected by nasopharyngeal/oropharyngeal (NP/OP) polymerase chain reaction between cases and controls. The PERCH Integrated Analysis (PIA) used Bayesian latent variable analysis to estimate pathogen-specific etiologic fractions and 95% credible intervals.

RESULTS

Over 96% of both cases (n = 223) and controls (n = 659) had at least 1 organism detected; multiple organisms were detected in 86% of cases and 88% of controls. Among 98 chest Radiograph positive (CXR+) cases, respiratory syncytial virus (RSV) had the highest NP/OP prevalence (22.9%) and the strongest association with case status (OR 20.5; 95% CI: 10.2, 41.3) and accounted for 34.6% of the total etiologic fraction. Tuberculosis (TB) accounted for 10% (95% CrI: 1.6-26%) of the etiologic fraction among CXR+ cases.

DISCUSSION

More than one-third of hospitalized cases of severe and very severe CXR+ pneumonia among children 1-59 months of age in Thailand were attributable to RSV. TB accounted for 10% of cases, supporting evaluation for TB among children hospitalized with pneumonia in high-burden settings. Similarities in pneumonia etiology in Thailand and other PERCH sites suggest that global control strategies based on PERCH study findings are relevant to Thailand and similar settings.

Approach to Identifying Causative Pathogens of Community-Acquired Pneumonia in Children Using Culture, Molecular, and Serology Tests

Determining the causative pathogen(s) of community-acquired pneumonia (CAP) in children remains a challenge despite advances in diagnostic methods. Currently available guidelines generally recommend empiric antimicrobial therapy when the specific etiology is unknown. However, shifts in epidemiology, emergence of new pathogens, and increasing antimicrobial resistance underscore the importance of identifying causative pathogen(s). Although viral CAP among children is increasingly recognized, distinguishing viral from bacterial etiologies remains difficult. Obtaining high quality samples from infected lung tissue is typically the limiting factor. Additionally, interpretation of results from routinely collected specimens (blood, sputum, and nasopharyngeal swabs) is complicated by bacterial colonization and prolonged shedding of incidental respiratory viruses. Using current literature on assessment of CAP causes in children, we developed an approach for identifying the most likely causative pathogen(s) using blood and sputum culture, polymerase chain reaction (PCR), and paired serology. Our proposed rules do not rely on carriage prevalence data from controls. We herein share our perspective in order to help clinicians and researchers classify and manage childhood pneumonia.

Temperature-Controlled Adhesion to Carbohydrate Functionalized Microgel Films: An E. coli and Lectin Binding Study

The preparation of thermoresponsive mannose functionalized monolayers of poly(N-isopropylacrylamide) microgels and the analysis of the specific binding of concanavalin A (ConA) and E. coli above and below the lower critical solution temperature (LCST) are shown. Via inhibition and direct binding assays it is found that ConA binding is time-dependent, where at short incubation times binding is stronger above the LCST. Given larger incubation times, the interaction of ConA to the microgel network is increased below the LCST when compared to temperatures above the LCST, possibly due to increased ConA diffusion and multivalent binding in the more open microgel network below the LCST. For E. coli, which presents only monovalent lectins and is too large to diffuse into the network, binding is always enhanced above the LCST. This is due to the larger mannose density of the microgel layer above the LCST increasing the interaction to E. coli. Once bound to the microgel layer above the LCST, E. coli cannot be released by cooling down below the LCST. Overall, this suggests that the carbohydrate presenting microgel layers enable specific binding where the temperature-induced transition between swollen and collapsed microgels may increase or decrease binding depending on the receptor size.

Lectin and E. coli Binding to Carbohydrate-Functionalized Oligo(ethylene glycol)-Based Microgels: Effect of Elastic Modulus, Crosslinker and Carbohydrate Density

The synthesis of carbohydrate-functionalized biocompatible poly(oligo(ethylene glycol) methacrylate microgels and the analysis of the specific binding to concanavalin A (ConA) and Escherichia coli (E. coli) is shown. By using different crosslinkers, the microgels' size, density and elastic modulus were varied. Given similar mannose (Man) functionalization degrees, the softer microgels show increased ConA uptake, possibly due to increased ConA diffusion in the less dense microgel network. Furthermore, although the microgels did not form clusters with E. coli in solution, surfaces coated with mannose-functionalized microgels are shown to bind the bacteria whereas galactose (Gal) and unfunctionalized microgels show no binding. While ConA binding depends on the overall microgels' density and Man functionalization degree, E. coli binding to microgels' surfaces appears to be largely unresponsive to changes of these parameters, indicating a rather promiscuous surface recognition and sufficiently strong anchoring to few surface-exposed Man units. Overall, these results indicate that carbohydrate-functionalized biocompatible oligo(ethylene glycol)-based microgels are able to immobilize carbohydrate binding pathogens specifically and that the binding of free lectins can be controlled by the network density.

Early Prognosis Effect of Cellular Immune Paralysis on Brain Complications of Extracorporeal Membrane Oxygenation Children with Severe Sepsis

OBJECTIVE

The aim of the study was to explore the relationship between criticality, brain complications, and immune mechanisms in extracorporeal membrane oxygenation (ECMO) children with pneumonia and severe sepsis.

METHODS

Patients with simple pneumonia (group I), ECMO patients with pneumonia and severe sepsis accompanied by brain complications (group II), and those without brain complication (group III) admitted to our pediatric intensive care unit were selected to be investigated. The relationship among the peripheral blood subgroups of immune cells, immune factors, adaptive immune responses, endothelial factors, and criticality and brain complications was then studied.

RESULTS

Severe paralysis of normal immunity, excess abnormal immunity, and endothelial injury were consistent with the increase in the absolute value of base excess, lactic acid (Lac) content, and average hospitalization days and brain complications involved in group II (vs. group I). The ratio of CD63+ macrophage and CD63+ neutrophil subpopulation increased (p < 0.05); the expression levels of elastase+ neutrophil denatured subgroup (p < 0.05), the ratio of CCR2highCX3CR1low/CCR2lowCX3CR1high of macrophages and neutrophils (p < 0.0001), high-mobility group box 1 (HMGB1), YTHDF1, interleukin-17 protein and mRNA, and RAGE gene decreased to some extent (p < 0.05); the expression levels of Th1 cells chemokine CXCL9 protein and mRNA and sTIE2 protein increased to some extent (p < 0.05); the adaptive immune response of CD8+ CTL stimulated by lipopolysaccharide (LPS) was slightly enhanced (p < 0.05) in group III(vs. group II), which was consistent with the improvement of criticality, average hospitalization days, and the absence of brain complications in group III (vs. group II).

CONCLUSION

ECMO support with brain complication was related to the upregulation of HMGB1 and YTHDF1 protein; the decreased number of CD63+ macrophages and neutrophils; the increased denatured neutrophil subgroup, especially the upregulated ratio of CCR2highCX3CR1low/CCR2lowCX3CR1high of macrophages and neutrophils; the imbalance of Th17/Th1, LPS-specific CD8+ CTL adaptive immune response paralysis; and the reduced endothelial sTIE2 protein expression level which caused clinical deterioration and prolonged average hospitalization days.

Polyamines in the virulence of bacterial pathogens of respiratory tract

Polyamines are positively charged hydrocarbons that are essential for the growth and cellular maintenance in prokaryotes and eukaryotes. Polyamines have been demonstrated to play a role in bacterial pathogenicity and biofilm formation. However, the role of extracellular polyamines as a signaling molecule in the regulation of virulence is not investigated in detail. The bacterial pathogens residing in the respiratory tract remain asymptomatic for an extended period; however, the factors that lead to symptomatic behavior are poorly understood. Further investigation to understand the relation between the host-secreted factors and virulence of pathogenic bacteria in the respiratory tract may provide insights into the pathogenesis of respiratory tract infections. Polyamines produced within the bacterial cell are generally sequestered. Therefore, the pool of extracellular polyamines formed by secretion of the commensals and the host may be one of the signaling molecules that might contribute toward the alterations in the expression of virulence factors in bacterial pathogens. Besides, convergent mechanisms of polyamine biosynthesis do exist across the border of species and genus level. Also, several novel polyamine transporters in the host and bacteria remain yet to be identified. The review focuses on the role of polyamines in the expression of virulence phenotypes and biofilm formation of the respiratory tract pathogens.

Cascaded deep learning classifiers for computer-aided diagnosis of COVID-19 and pneumonia diseases in X-ray scans

Computer-aided diagnosis (CAD) systems are considered a powerful tool for physicians to support identification of the novel Coronavirus Disease 2019 (COVID-19) using medical imaging modalities. Therefore, this article proposes a new framework of cascaded deep learning classifiers to enhance the performance of these CAD systems for highly suspected COVID-19 and pneumonia diseases in X-ray images. Our proposed deep learning framework constitutes two major advancements as follows. First, complicated multi-label classification of X-ray images have been simplified using a series of binary classifiers for each tested case of the health status. That mimics the clinical situation to diagnose potential diseases for a patient. Second, the cascaded architecture of COVID-19 and pneumonia classifiers is flexible to use different fine-tuned deep learning models simultaneously, achieving the best performance of confirming infected cases. This study includes eleven pre-trained convolutional neural network models, such as Visual Geometry Group Network (VGG) and Residual Neural Network (ResNet). They have been successfully tested and evaluated on public X-ray image dataset for normal and three diseased cases. The results of proposed cascaded classifiers showed that VGG16, ResNet50V2, and Dense Neural Network (DenseNet169) models achieved the best detection accuracy of COVID-19, viral (Non-COVID-19) pneumonia, and bacterial pneumonia images, respectively. Furthermore, the performance of our cascaded deep learning classifiers is superior to other multi-label classification methods of COVID-19 and pneumonia diseases in previous studies. Therefore, the proposed deep learning framework presents a good option to be applied in the clinical routine to assist the diagnostic procedures of COVID-19 infection.

A Novel Transfer Learning Based Approach for Pneumonia Detection in Chest X-ray Images

Pneumonia is among the top diseases which cause most of the deaths all over the world. Virus, bacteria and fungi can all cause pneumonia. However, it is difficult to judge the pneumonia just by looking at chest X-rays. The aim of this study is to simplify the pneumonia detection process for experts as well as for novices. We suggest a novel deep learning framework for the detection of pneumonia using the concept of transfer learning. In this approach, features from images are extracted using different neural network models pretrained on ImageNet, which then are fed into a classifier for prediction. We prepared five different models and analyzed their performance. Thereafter, we proposed an ensemble model that combines outputs from all pretrained models, which outperformed individual models, reaching the state-of-the-art performance in pneumonia recognition. Our ensemble model reached an accuracy of 96.4% with a recall of 99.62% on unseen data from the Guangzhou Women and Children’s Medical Center dataset.

Recurrence of WHO-defined fast breathing pneumonia among infants, its occurrence and predictors in Pakistan: a nested case-control analysis

OBJECTIVES

Studies in low-income and middle-income countries have shown an adverse association between environmental exposures including poverty. There is little literature from South Asia. We aimed to test the associations between housing, indoor air pollution and children's respiratory health and recurrent fast breathing pneumonia in a poor urban setting in Pakistan.

SETTING

Primary health centres in a periurban slum in Karachi, Pakistan.

METHODS

Nested matched case-control study within a non-inferiority randomised controlled trial of fast breathing pneumonia (Randomised Trial of Amoxicillin vs Placebo for Pneumonia (RETAPP)) in periurban slums of Karachi, Pakistan. Cases were children aged 2-60 months enrolled in RETAPP with fast breathing pneumonia who presented again with fast breathing between 8 weeks and 12 months after full recovery. Controls, selected in a 2:1 ratio, were age-matched participants who did not represent. Multivariable conditional logistic regression analysis was undertaken to explore associations with potentially modifiable environmental predictors including housing type, indoor air quality, exposure to tobacco smoke, outdoor pollution, household crowding, water and sanitation quality, nutritional status, immunisation completeness, breast feeding and airways hyperactivity.

RESULTS

Fast breathing recurred in 151 (3.7%) of children out of the total (4003) enrolled in the trial. Poor-quality housing of either katcha or mixed type strongly predicted recurrence with adjusted matched ORs 2.43 (95% CI 1.02 to 5.80) and 2.44 (1.11 to 5.38), respectively. Poor air quality, cooking fuel, inadequate ventilation, nutritional status, water, sanitation and hygiene (WASH) index, wheeze at first presentation and group of initial trial assignment were not independently predictive of recurrence.

CONCLUSION

Poor-quality housing independently predicted recurrence of fast breathing pneumonia.

TRIAL REGISTRATION NUMBER

NCT02372461.

Immunization with proline rich region of pneumococcal surface protein A has no role in protection against Streptococcus pneumoniae serotype 19F

Pneumococcal surface protein A (PspA) is one of the major virulence factors expressed by almost all pneumococcal serotypes and was suggested to be a promising universal vaccine candidate for all pneumococcal sero-groups. Here, we expressed and purified the proline-rich region (PR) of PspA and tested it as a recombinant vaccine against infection caused by a clinical isolate (SP₁₉) of Streptococcus pneumoniae serotype 19F. Our results showed that BALB/c mice immunized with recombinant proline-rich (rPR) region showed a significant higher antibody titre against rPR region compared to control non-immunized group. However, immunized mice or mice recived polyclonal antibodies against rPR region challenged via the intra-peritoneal route with a lethal dose of SP₁₉ isolate showed no significant difference in survival compared to control non-immunized group. These results suggested that, immunization of BALB/c mice with rPR region of PspA is not protective against infection caused by serotype 19F in a mouse model.

Investigating Pneumonia Etiology Among Refugees and the Lebanese population (PEARL): A study protocol

Background: Community-acquired pneumonia (CAP), a leading cause of mortality, mainly affects children in developing countries. The harsh circumstances experienced by refugees include various factors associated with respiratory pathogen transmission, and clinical progression of CAP. Consequently, the etiology of CAP in humanitarian crisis situations may differ to that of settled populations, which would impact appropriate case management. Therefore, the Pneumonia Etiology Among Refugees and the Lebanese population (PEARL) study was initiated with the objective of identifying the causal pathogenic microorganisms in the respiratory tract of children and adults from both the refugee and host country population presenting with signs of CAP during a humanitarian crisis.

Methods: PEARL, a prospective, multicentric, case-control study, will be conducted at four primary healthcare facilities in Tripoli and the Bekaa valley over 15 months (including two high-transmission seasons/winters). Sociodemographic and medical data, and biological samples will be collected from at least 600 CAP cases and 600 controls. Nasopharyngeal swabs, sputum, urine and blood samples will be analyzed at five clinical pathology laboratories in Lebanon to identify the bacterial and viral etiological agents of CAP. Transcriptomic profiling of host leukocytes will be performed.

Conclusions: PEARL is an original observational study that will provide important new information on the etiology of pneumonia among refugees, which may improve case management, help design antimicrobial stewardship interventions, and reduce morbidity and mortality due to CAP in a humanitarian crisis.

Introducing a New Algorithm for Classification of Etiology in Studies on Pediatric Pneumonia: Protocol for the Trial of Respiratory Infections in Children for Enhanced Diagnostics Study

Background

There is a need to better distinguish viral infections from antibiotic-requiring bacterial infections in children presenting with clinical community-acquired pneumonia (CAP) to assist health care workers in decision making and to improve the rational use of antibiotics.

Objective

The overall aim of the Trial of Respiratory infections in children for ENhanced Diagnostics (TREND) study is to improve the differential diagnosis of bacterial and viral etiologies in children aged below 5 years with clinical CAP, by evaluating myxovirus resistance protein A (MxA) as a biomarker for viral CAP and by evaluating an existing (multianalyte point-of-care antigen detection test system [mariPOC respi] ArcDia International Oy Ltd.) and a potential future point-of-care test for respiratory pathogens.

Methods

Children aged 1 to 59 months with clinical CAP as well as healthy, hospital-based, asymptomatic controls will be included at a pediatric emergency hospital in Stockholm, Sweden. Blood (analyzed for MxA and C-reactive protein) and nasopharyngeal samples (analyzed with real-time polymerase chain reaction as the gold standard and antigen-based mariPOC respi test as well as saved for future analyses of a novel recombinase polymerase amplification–based point-of-care test for respiratory pathogens) will be collected. A newly developed algorithm for the classification of CAP etiology will be used as the reference standard.

Results

A pilot study was performed from June to August 2017. The enrollment of study subjects started in November 2017. Results are expected by the end of 2019.

Conclusions

The findings from the TREND study can be an important step to improve the management of children with clinical CAP.

International Registered Report Identifier (IRRID)

DERR1-10.2196/12705

Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in Streptococcus pneumoniae

Spr1654 from Streptococcus pneumoniae plays a key role in the production of unusual sugars, presumably functioning as a pyridoxal-5′-phosphate (PLP)-dependent aminotransferase. Spr1654 was predicted to catalyse the transferring of amino group to form the amino sugar 2-acetamido-4-amino-2, 4, 6-trideoxygalactose moiety (AATGal), representing a crucial step in biosynthesis of teichoic acids in S. pneumoniae. We have determined the crystal structures of the apo-, PLP- and PMP-bound forms of Spr1654. Spr1654 forms a homodimer, in which each monomer contains one active site. Using spectrophotometry and based on absorbance profiles of PLP- and PMP-formed enzymes, our results indicate that l-glutamate is most likely the preferred amino donor. Structural superposition of the crystal structures of Spr1654 on previously determined structures of other sugar aminotransferases in complex with glutamate and/or UDP-activated sugar allowed us to identify key Spr1654 residues for ligand binding and catalysis. The crystal structures of Spr1654 and in complex with PLP and PMP can direct the future rational design of novel therapeutic compounds against S. pneumoniae.

Who interacts with whom? Social mixing insights from a rural population in India

Acute lower respiratory infections (ALRI) are a leading cause of morbidity and mortality globally, with most ALRI deaths occurring in children in developing countries. Computational models can be used to test the efficacy of respiratory infection prevention interventions, but require data on social mixing patterns, which are sparse in developing countries. We describe social mixing patterns among a rural community in northern India. During October 2015-February 2016, trained field workers conducted cross-sectional face-to-face standardized surveys in a convenience sample of 330 households in Faridabad District, Haryana State, India. Respondents were asked about the number, duration, and setting of social interactions during the previous 24 hours. Responses were compared by age and gender. Among the 3083 residents who were approached, 2943 (96%) participated, of whom 51% were male and the median age was 22 years (interquartile range (IQR) 9–37). Respondents reported contact (defined as having had a face-to-face conversation within 3 feet, which may or may not have included physical contact) with a median of 17 (IQR 12–25) people during the preceding 24 hours. Median total contact time per person was 36 person-hours (IQR 26–52). Female older children and adults had significantly fewer contacts than males of similar age (Kruskal-Wallis χ2 = 226.59, p<0.001), but spent a longer duration in contact with young children (Kruskal-Wallis χ2 = 27.26, p<0.001), suggesting a potentially complex pattern of differential risk of infection between genders. After controlling for household size and day of the week, respondent age was significantly associated with number and duration of contacts. These findings can be used to model the impact of interventions to reduce lower respiratory tract infections in India.

Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory infections in 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016

BACKGROUND

Lower respiratory infections are a leading cause of morbidity and mortality around the world. The Global Burden of Diseases, Injuries, and Risk Factors (GBD) Study 2016, provides an up-to-date analysis of the burden of lower respiratory infections in 195 countries. This study assesses cases, deaths, and aetiologies spanning the past 26 years and shows how the burden of lower respiratory infection has changed in people of all ages.

METHODS

We used three separate modelling strategies for lower respiratory infections in GBD 2016: a Bayesian hierarchical ensemble modelling platform (Cause of Death Ensemble model), which uses vital registration, verbal autopsy data, and surveillance system data to predict mortality due to lower respiratory infections; a compartmental meta-regression tool (DisMod-MR), which uses scientific literature, population representative surveys, and health-care data to predict incidence, prevalence, and mortality; and modelling of counterfactual estimates of the population attributable fraction of lower respiratory infection episodes due to Streptococcus pneumoniae, Haemophilus influenzae type b, influenza, and respiratory syncytial virus. We calculated each modelled estimate for each age, sex, year, and location. We modelled the exposure level in a population for a given risk factor using DisMod-MR and a spatio-temporal Gaussian process regression, and assessed the effectiveness of targeted interventions for each risk factor in children younger than 5 years. We also did a decomposition analysis of the change in LRI deaths from 2000-16 using the risk factors associated with LRI in GBD 2016.

FINDINGS

In 2016, lower respiratory infections caused 652 572 deaths (95% uncertainty interval [UI] 586 475-720 612) in children younger than 5 years (under-5s), 1 080 958 deaths (943 749-1 170 638) in adults older than 70 years, and 2 377 697 deaths (2 145 584-2 512 809) in people of all ages, worldwide. Streptococcus pneumoniae was the leading cause of lower respiratory infection morbidity and mortality globally, contributing to more deaths than all other aetiologies combined in 2016 (1 189 937 deaths, 95% UI 690 445-1 770 660). Childhood wasting remains the leading risk factor for lower respiratory infection mortality among children younger than 5 years, responsible for 61·4% of lower respiratory infection deaths in 2016 (95% UI 45·7-69·6). Interventions to improve wasting, household air pollution, ambient particulate matter pollution, and expanded antibiotic use could avert one under-5 death due to lower respiratory infection for every 4000 children treated in the countries with the highest lower respiratory infection burden.

INTERPRETATION

Our findings show substantial progress in the reduction of lower respiratory infection burden, but this progress has not been equal across locations, has been driven by decreases in several primary risk factors, and might require more effort among elderly adults. By highlighting regions and populations with the highest burden, and the risk factors that could have the greatest effect, funders, policy makers, and programme implementers can more effectively reduce lower respiratory infections among the world's most susceptible populations.

FUNDING

Bill & Melinda Gates Foundation.

Everolimus for treatment-refractory seizures in TSC: Extension of a randomized controlled trial

Background

EXamining everolimus In a Study of Tuberous sclerosis 3 (EXIST-3) demonstrated significantly reduced seizure frequency (SF) with everolimus vs placebo. In this study, we evaluate the long-term efficacy and safety of everolimus for tuberous sclerosis complex (TSC)-associated treatment-refractory seizures.

Methods

After completion of the core phase, patients could enter an open-label extension phase and receive everolimus (target exposure, 3-15 ng/mL) for ≥48 weeks. Efficacy end points included change from baseline in average weekly SF expressed as response rate (RR, ≥50% reduction) and median percentage reduction (PR).

Results

Of 366 patients, 361 received everolimus in core/extension phases. The RR was 31% (95% CI, 26.2-36.1; N = 352) at week 18, 46.6% (95% CI, 40.9-52.5; N = 298) at 1 year, and 57.7% (95% CI, 49.7-65.4; N = 163) at 2 years. Median PR in SF was 31.7% (95% CI, 28.5-36.1) at week 18, 46.7% (95% CI, 40.2-54) at 1 year, and 56.9% (95% CI, 50-68.4) at 2 years. Ninety-five patients (26.3%) discontinued everolimus before 2 years; 103 (28.5%) had <2 years of follow-up at study cutoff, and 40% were exposed to everolimus for ≥2 years. An analysis classifying discontinued patients as nonresponders showed an RR of 30.2% (95% CI, 25.5-35.2; N = 361) at week 18, 38.8% (95% CI, 33.7-44.1; N = 358) at 1 year, and 41% (95% CI, 34.6-47.7; N = 229) at 2 years, suggesting sustained benefit over time. The incidence of grade 3/4 adverse events (AEs) (any cause) was 40.2%, and 13% discontinued because of AEs (pneumonia [1.7%] and stomatitis [1.4%]). Two deaths were suspected to be treatment-related (pneumonia and septic shock).

Conclusions

Sustained reductions in TSC-associated treatment-refractory seizures over time were achieved with adjunctive everolimus. The safety profile was consistent with the core phase with no new safety concerns.

Classification of evidence

This study provides Class IV evidence that long-term everolimus therapy reduces SF in patients with TSC-associated treatment-refractory seizures.

Pneumonia in Ghana-a need to raise the profile

Despite the high mortality, pneumonia retains a relatively low profile among researchers, funders and policymakers. Here we reflect on the problems and priorities of pneumonia in Ghana, briefly review the evidence base and reflect upon in-person discussions between Southampton-based authors MGH and JB and academic, clinical and policy colleagues in Ghana. The discussions took place in Accra in August 2017.

Impact of viral upper respiratory tract infection on the concentration of nasopharyngeal pneumococcal carriage among Kenyan children

Viral upper respiratory tract infection (URTI) predisposes to bacterial pneumonia possibly by facilitating growth of bacteria such as Streptococcus pneumoniae colonising the nasopharynx. We investigated whether viral URTI is temporally associated with an increase in nasopharyngeal pneumococcal concentration. Episodes of symptomatic RSV or rhinovirus URTI among children <5 years were identified from a longitudinal household study in rural Kenya. lytA and alu PCR were performed on nasopharyngeal samples collected twice-weekly, to measure the pneumococcal concentration adjusted for the concentration of human DNA present. Pneumococcal concentration increased with a fold-change of 3.80 (95%CI 1.95-7.40), with acquisition of RSV or rhinovirus, during 51 URTI episodes among 42 children. In repeated swabs from the baseline period, in the two weeks before URTI developed, within-episode variation was broad; within +/-112-fold range of the geometric mean. We observed only a small increase in nasopharyngeal pneumococcal concentration during RSV or rhinovirus URTI, relative to natural variation. Other factors, such as host response to viral infection, may be more important than nasopharyngeal pneumococcal concentration in determining risk of invasive disease.

Adjunctive everolimus for children and adolescents with treatment-refractory seizures associated with tuberous sclerosis complex: post-hoc analysis of the phase 3 EXIST-3 trial

BACKGROUND

Epilepsy occurs in 70-90% of patients with tuberous sclerosis complex. We aimed to assess the efficacy and safety of adjunctive everolimus for treatment-refractory seizures associated with tuberous sclerosis complex in paediatric patients enrolled in the EXIST-3 trial, a double-blind, placebo-controlled, randomised, phase 3 study.

METHODS

This post-hoc analysis focused on paediatric patients (age <18 years) in the EXIST-3 trial, which consisted of baseline (8 weeks), core (18 weeks), and extension phases (≥48 weeks) and was done at 99 centres in 25 countries worldwide. Briefly, patients with tuberous sclerosis complex-associated treatment-refractory seizures, who were receiving a stable dose of one to three antiepileptic drugs, were randomly assigned (1:1:1) to receive placebo, low-exposure everolimus (3-7 ng/mL), or high-exposure everolimus (9-15 ng/mL). Following the core phase, patients could enter the extension phase to receive everolimus at a targeted exposure range of 3-15 ng/mL up to 48 weeks after the last patient had completed the core phase. Efficacy endpoints were response rate (≥50% of reduction from baseline in average weekly seizure frequency) and median percentage reduction in seizure frequency during the 12-week maintenance period of the core phase, and at 12-week intervals throughout the extension phase. This study is registered with ClinicalTrials.gov, number NCT01713946.

FINDINGS

Between July 3, 2013, and May 29, 2015, 299 paediatric patients enrolled in the trial. In the younger subgroup (<6 years; n=104), 34 received placebo, 33 low-exposure everolimus, and 37 high-exposure everolimus; in the older subgroup (≥6 years to <18 years; n=195), 62 received placebo, 63 low-exposure everolimus, and 70 high-exposure everolimus. At the end of the core phase, response rate was higher in the treatment groups than placebo in both the younger subgroup (17·6% [6·8-34·5] for placebo vs 30·3% [95% CI 15·6-48·7; p=0·2245] for low-exposure everolimus vs 59·5% [42·1-75·2; p=0·0003] for high-exposure everolimus) and the older subgroup (12·9% [5·7-23·9] vs 27·0% [16·6-39·7; p=0·0491] vs 30·0% [19·6-42·1; p=0·0179]), as were median reduction in seizure frequency (12·3% [95% CI -10·1 to 24·8] vs 29·3% [95% CI 13·4 to 46·3; p=0·0474] vs 54·7% [43·5 to 73·1; p<0·0001] in younger patients; 13·5% [-3·0 to 26·8] vs 31·0% [16·1 to 42·9; p=0·0128] vs 34·8% [26·7 to 41·3; p=0·0006] in older patients). The efficacy persisted, with sustained seizure reduction after 1 year of treatment across both paediatric subgroups (response rate 48·9% [95% CI 38·1-59·8] for the younger subgroup vs 47·2% [39·3-55·2] for the older subgroup; median percentage reduction in seizure frequency 48·4% [95% CI 34·3-73·6] vs 48·0% [38·2-57·5]). At the cutoff date for the extension phase, grade 3 or 4 adverse events were reported in 45 (45%) younger patients (commonly pneumonia [n=16]) and 74 (38%) older patients (commonly pneumonia [n=8] and stomatitis [n=6]). Two deaths (pneumonia, which was suspected to be treatment-related, and sudden unexplained death due to epilepsy) were reported.

INTERPRETATION

Adjunctive everolimus resulted in sustained reductions in seizure frequency after 1 year and was well tolerated in paediatric patients with treatment-refractory seizures associated with tuberous sclerosis complex.

FUNDING

Novartis Pharmaceuticals Corporation.

Investigating Pneumonia Etiology Among Refugees and the Lebanese population (PEARL): A study protocol

Background: Community-acquired pneumonia (CAP), a leading cause of mortality, mainly affects children in developing countries. The harsh circumstances experienced by refugees include various factors associated with respiratory pathogen transmission, and clinical progression of CAP. Consequently, the etiology of CAP in humanitarian crisis situations may differ to that of settled populations, which would impact appropriate case management. Therefore, the Pneumonia Etiology Among Refugees and the Lebanese population (PEARL) study was initiated with the objective of identifying the causal pathogenic microorganisms in the respiratory tract of children and adults from both the refugee and host country population presenting with signs of CAP during a humanitarian crisis. Methods: PEARL, a prospective, multicentric, case-control study, will be conducted at four primary healthcare facilities in Tripoli and the Bekaa valley over 15 months (including two high-transmission seasons/winters). Sociodemographic and medical data, and biological samples will be collected from at least 600 CAP cases and 600 controls. Nasopharyngeal swabs, sputum, urine and blood samples will be analyzed at five clinical pathology laboratories in Lebanon to identify the bacterial and viral etiological agents of CAP. Transcriptomic profiling of host leukocytes will be performed. Conclusions: PEARL is an original observational study that will provide important new information on the etiology of pneumonia among refugees, which may improve case management, help design antimicrobial stewardship interventions, and reduce morbidity and mortality due to CAP in a humanitarian crisis.

Epidemiology, microbiology, and treatment patterns of pediatric patients hospitalized with pneumonia at two hospitals in China: a patient chart review study

Background

The etiology, epidemiology, treatment patterns, and clinical outcomes of neonatal and pediatric pneumonia patients in China are not well reported. This retrospective chart review study aimed to describe such information among neonatal (0 to 27 days) and pediatric (28 days to <18 years) pneumonia patients in two regions of China.

Methods

Electronic medical records of pneumonia hospitalizations (aged <18 years) admitted between 2008 and 2013 from four hospitals under Guangdong Provincial Hospital of Chinese Medicine (Southern China) and between 2010 and 2014 at Peking University People's Hospital (Beijing, Northern China) were reviewed.

Results

The average age of neonatal hospitalizations in Beijing (n=92) was 3.5 days. The mean length of hospital stay was 11.2 days, and no deaths occurred. Staphylococcus epidermidis was the most common bacteria found in Beijing patients, whereas Mycoplasma pneumoniae was the most common bacteria found in Guangdong patients. The average age of pediatric hospitalizations was 3.3 (±3.1) and 6.5 (±5.6) years in Guangdong (n=3,046) and Beijing (n=222), respectively. The mean length of hospital stay was 17.4 and 5.8 days, and overall mortality rates were 0.2% and 0.5%.

Conclusion

The findings revealed a low level of bacterial isolation and hence microbiological diagnoses. There was a low level of in-hospital mortality due to pneumonia, and the majority of hospitalizations were discharged from hospital, suggesting that current practice was generally effective. Neonatal hospitalizations were greater than pediatric hospitalizations in Beijing along with disparity in bacterial profile when compared with Guangdong, intending a need to improve neonatal pneumonia prophylaxis and selection of appropriate treatment.

Colonization Density of the Upper Respiratory Tract as a Predictor of Pneumonia-Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Pneumocystis jirovecii

Background.

There is limited information on the association between colonization density of upper respiratory tract colonizers and pathogen-specific pneumonia. We assessed this association for Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Pneumocystis jirovecii.

Methods.

In 7 low- and middle-income countries, nasopharyngeal/oropharyngeal swabs from children with severe pneumonia and age-frequency matched community controls were tested using quantitative polymerase chain reaction (PCR). Differences in median colonization density were evaluated using the Wilcoxon rank-sum test. Density cutoffs were determined using receiver operating characteristic curves. Cases with a pathogen identified from lung aspirate culture or PCR, pleural fluid culture or PCR, blood culture, and immunofluorescence for P. jirovecii defined microbiologically confirmed cases for the given pathogens.

Results.

Higher densities of H. influenzae were observed in both microbiologically confirmed cases and chest radiograph (CXR)–positive cases compared to controls. Staphylococcus aureus and P. jirovecii had higher densities in CXR-positive cases vs controls. A 5.9 log₁₀ copies/mL density cutoff for H. influenzae yielded 86% sensitivity and 77% specificity for detecting microbiologically confirmed cases; however, densities overlapped between cases and controls and positive predictive values were poor (<3%). Informative density cutoffs were not found for S. aureus and M. catarrhalis, and a lack of confirmed case data limited the cutoff identification for P. jirovecii.

Conclusions.

There is evidence for an association between H. influenzae colonization density and H. influenzae–confirmed pneumonia in children; the association may be particularly informative in epidemiologic studies. Colonization densities of M. catarrhalis, S. aureus, and P. jirovecii are unlikely to be of diagnostic value in clinical settings.

Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in 195 countries: a systematic analysis for the Global Burden of Disease Study 2015

BACKGROUND

The Global Burden of Diseases, Injuries, and Risk Factors (GBD) Study 2015 provides an up-to-date analysis of the burden of lower respiratory tract infections (LRIs) in 195 countries. This study assesses cases, deaths, and aetiologies spanning the past 25 years and shows how the burden of LRI has changed in people of all ages.

METHODS

We estimated LRI mortality by age, sex, geography, and year using a modelling platform shared across most causes of death in the GBD 2015 study called the Cause of Death Ensemble model. We modelled LRI morbidity, including incidence and prevalence, using a meta-regression platform called DisMod-MR. We estimated aetiologies for LRI using two different counterfactual approaches, the first for viral pathogens, which incorporates the aetiology-specific risk of LRI and the prevalence of the aetiology in LRI episodes, and the second for bacterial pathogens, which uses a vaccine-probe approach. We used the Socio-demographic Index, which is a summary indicator derived from measures of income per capita, educational attainment, and fertility, to assess trends in LRI-related mortality. The two leading risk factors for LRI disability-adjusted life-years (DALYs), childhood undernutrition and air pollution, were used in a decomposition analysis to establish the relative contribution of changes in LRI DALYs.

FINDINGS

In 2015, we estimated that LRIs caused 2·74 million deaths (95% uncertainty interval [UI] 2·50 million to 2·86 million) and 103·0 million DALYs (95% UI 96·1 million to 109·1 million). LRIs have a disproportionate effect on children younger than 5 years, responsible for 704 000 deaths (95% UI 651 000-763 000) and 60.6 million DALYs (95ÙI 56·0-65·6). Between 2005 and 2015, the number of deaths due to LRI decreased by 36·9% (95% UI 31·6 to 42·0) in children younger than 5 years, and by 3·2% (95% UI -0·4 to 6·9) in all ages. Pneumococcal pneumonia caused 55·4% of LRI deaths in all ages, totalling 1 517 388 deaths (95% UI 857 940-2 183 791). Between 2005 and 2015, improvements in air pollution exposure were responsible for a 4·3% reduction in LRI DALYs and improvements in childhood undernutrition were responsible for an 8·9% reduction.

INTERPRETATION

LRIs are the leading infectious cause of death and the fifth-leading cause of death overall; they are the second-leading cause of DALYs. At the global level, the burden of LRIs has decreased dramatically in the last 10 years in children younger than 5 years, although the burden in people older than 70 years has increased in many regions. LRI remains a largely preventable disease and cause of death, and continued efforts to decrease indoor and ambient air pollution, improve childhood nutrition, and scale up the use of the pneumococcal conjugate vaccine in children and adults will be essential in reducing the global burden of LRI.

FUNDING

Bill & Melinda Gates Foundation.

Utility of Assessing Cytokine Levels for the Differential Diagnosis of Pneumonia in a Pediatric Population

OBJECTIVES

Although pneumonia is easily diagnosed, determining the causative agent is difficult due to low pathogen detection rates. We performed a prospective observational study to evaluate the utility of measuring inflammatory cytokine levels to discriminate between pneumonia caused by typical bacteria, respiratory syncytial virus, or Mycoplasma pneumoniae in a pediatric population.

DESIGN

Serum inflammatory cytokine levels at early stages of the disease were evaluated for pneumonia caused by the three different pathogenic microorganisms.

SETTING

The Children's Hospital of Zhejiang University School of Medicine, China.

PATIENTS

One hundred sixty-six patients with bacterial pneumonia, 182 with M. pneumonia, and 167 with respiratory syncytial virus pneumonia.

MEASUREMENTS AND MAIN RESULTS

The levels of interleukin-6 for pneumonia were significantly higher with typical bacteria than with either Mycoplasma pneumoniae or respiratory syncytial virus (p < 0.001). The area under the curve for serum concentrations of interleukin-6 was 0.997. A serum interleukin-6 level of greater than or equal to 93.0 pg/mL had 100.0% sensitivity and 99.14% specificity in discriminating bacterial pneumonia from respiratory syncytial virus pneumonia and Mycoplasma pneumoniae pneumonia. The interleukin-6 levels were higher in patients with Mycoplasma pneumoniae pneumonia than in those with respiratory syncytial virus pneumonia (p < 0.001). They also simultaneously had lower interleukin-10 levels than patients with respiratory syncytial virus pneumonia who had interleukin-10 levels comparable to those of patients with bacterial pneumonia, indicating a significant difference in the interleukin-6/interleukin-10 ratio between patients with Mycoplasma pneumoniae pneumonia and respiratory syncytial virus pneumonia (median interleukin-6/interleukin-10 ratio, 2.5 vs 0.5; p < 0.001). At an optimal cut-off value of 0.8, the interleukin-6/interleukin-10 ratio showed 90.3% sensitivity and 88.0% specificity.

CONCLUSIONS

These results suggest that interleukin-6 is a good biomarker for identifying bacterial pneumonia and that the interleukin-6/interleukin-10 ratio is an effective biomarker for discriminating Mycoplasma pneumoniae pneumonia from respiratory syncytial virus pneumonia.

Etiology of severe pneumonia in Ecuadorian children

BACKGROUND

In Latin America, community-acquired pneumonia remains a major cause of morbidity and mortality among children. Few studies have examined the etiology of pneumonia in Ecuador.

METHODS

This observational study was part of a randomized, double blind, placebo-controlled clinical trial conducted among children aged 2-59 months with severe pneumonia in Quito, Ecuador. Nasopharyngeal and blood samples were tested for bacterial and viral etiology by polymerase chain reaction. Risk factors for specific respiratory pathogens were also evaluated.

RESULTS

Among 406 children tested, 159 (39.2%) had respiratory syncytial virus (RSV), 71 (17.5%) had human metapneumovirus (hMPV), and 62 (15.3%) had adenovirus. Streptococcus pneumoniae was identified in 37 (9.2%) samples and Mycoplasma pneumoniae in three (0.74%) samples. The yearly circulation pattern of RSV (P = 0.0003) overlapped with S. pneumoniae, (P = 0.03) with most cases occurring in the rainy season. In multivariable analysis, risk factors for RSV included younger age (adjusted odds ratio [aOR] = 1.9, P = 0.01) and being underweight (aOR = 1.8, P = 0.04). Maternal education (aOR = 0.82, P = 0.003), pulse oximetry (aOR = 0.93, P = 0.005), and rales (aOR = 0.25, P = 0.007) were associated with influenza A. Younger age (aOR = 3.5, P = 0.007) and elevated baseline respiratory rate were associated with HPIV-3 infection (aOR = 0.94, P = 0.03).

CONCLUSION

These results indicate the importance of RSV and influenza, and potentially modifiable risk factors including undernutrition and future use of a RSV vaccine, when an effective vaccine becomes available.

TRIAL REGISTRATION

ClinicalTrials.gov NCT 00513929.

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.

Decline in Child Hospitalization and Mortality After the Introduction of the 7-Valent Pneumococcal Conjugative Vaccine in Rwanda

Pneumonia is a public health problem in the tropics, and the 7-valent pneumococcal conjugative vaccine (PCV-7) has been introduced in an effort to prevent the disease and therefore reduce childhood mortality. In Rwanda, PCV-7 was introduced in 2009, and we aimed to determine its impact on the rate of child hospitalization/mortality due to pneumonia. A retrospective survey was conducted on hospitalization rates and pediatric deaths between two periods, that is, before the introduction of PCV-7 (2007-2009) and after the introduction of PCV-7 (2010-2013) in Kabutare District Hospital. There was a 53% reduction in hospitalization, with a significant decline in in-hospital deaths between the two periods. There was also a significant correlation between vaccination coverage and decline in hospitalization rates between 2009 and 2013. We conclude that PCV-7 vaccine is associated with significant reduction in the rate of child hospitalization and mortality but more mechanistic studies are warranted to determine the immunological impact, especially in the context of coinfections and malnutrition.

[Application of ultrasonic cardiac output monitor in evaluation of cardiac function in children with severe pneumonia]

OBJECTIVE

To study the clinical application of ultrasonic cardiac output monitor (USCOM) in evaluation of cardiac function in children with severe pneumonia.

METHODS

Twenty-nine children with severe pneumonia were enrolled in the observation group and forty-three children with common pneumonia were enrolled in the control group. The USCOM was used to measure the cardiac function indices in the two groups. The results were compared between the two groups. The changes in cardiac function indices after treatment were evaluated in the observation group.

ESULTS

The observation group had a significantly higher heart rate and significantly lower cardiac output, systolic volume, and aortic peak velocity than the control group (P<0.05). There were no significant differences in cardiac index or systemic vascular resistance between the two groups (P>0.05). In the observation group, the heart rate, cardiac output, systolic volume, aortic peak velocity, cardiac index, and systemic vascular resistance were significantly improved after treatment (P<0.05).

CONCLUSIONS

The USCOM is a fast, convenient, and accurate approach for dynamic measurement of cardiac function and overall circulation state in children with severe pneumonia. The USCOM can provide a basis for diagnosis, treatment, and evaluation of the disease, which is quite useful in clinical practice.

Tying malaria and microRNAs: from the biology to future diagnostic perspectives

Symptoms caused by bacterial, viral and malarial infections usually overlap and aetiologic diagnosis is difficult. Patient management in low-resource countries with limited laboratory services has been based predominantly on clinical evaluation and syndromic approaches. However, such clinical assessment has limited accuracy both for identifying the likely aetiological cause and for the early recognition of patients who will progress to serious or fatal disease. Plasma-detectable biomarkers that rapidly and accurately diagnose severe infectious diseases could reduce morbidity and decrease the unnecessary use of usually scarce therapeutic drugs. The discovery of microRNAs (miRNAs) has opened exciting new avenues to identify blood biomarkers of organ-specific injury. This review assesses current knowledge on the relationship between malaria disease and miRNAs, and evaluates how future research might lead to the use of these small molecules for identifying patients with severe malaria disease and facilitate treatment decisions.

Zinc as an adjunct to antibiotics for the treatment of severe pneumonia in children <5 years: a meta-analysis of randomised-controlled trials

The effect of Zn, as an adjunct to antibiotics, on the treatment of severe pneumonia in young children is still under debate; therefore, we performed a meta-analysis to evaluate the therapeutic role of Zn for severe pneumonia in children younger than 5 years. PubMed, Cochrane library and Embase databases were systematically searched from inception until October 2015 for randomised-controlled trials (RCT) that assessed the effect of Zn as an adjunct to antibiotics for severe pneumonia. Random-effects model was used for calculating the pooled estimates, and intention-to-treat principle was also applied. Nine RCT involving 2926 children were included. Overall, the pooled results showed that adjunct treatment with Zn failed to reduce the time to recovery from severe pneumonia (hazard ratios (HR)=1·04; 95% CI 0·90, 1·19; I(2)=39%; P=0·58), hospital length of stay (HR=1·04; 95% CI 0·83, 1·33; I(2)=57%; P=0·74), treatment failure (relative risk (RR)=0·95; 95% CI 0·79, 1·14; I(2)=20%; P=0·58) or change of antibiotics (RR=1·07; 95% CI 0·79, 1·45; I(2)=44%; P=0·67). In addition, continuous outcomes were consistent while meta-analysed with standard mean difference, and all outcomes remained stable in intention-to-treat analysis. No significant differences were observed in the two groups between death rate, adverse events or recovery times of severe pneumonia indicators. Our results suggested that adjunct treatment with Zn failed to benefit young children in the treatment of severe pneumonia. Considering the clinical heterogeneity, baseline characteristics of children, definition of severe pneumonia and Zn supplement way should be taken into consideration in future research. This study was registered at PRESPERO as CRD42015019798.

How Should Oxygen Supplementation Be Guided by Pulse Oximetry in Children: Do We Know the Level?

Supplemental oxygen is one of the most commonly prescribed therapies to children in hospital, but one of the least studied therapeutics. This review considers oxygen from a range of perspectives; discovery and early use; estimation of oxygenation in the human body-both clinically and by medical device; the effects of illness on oxygen utilization; the cellular consequences of low oxygen; and finally, how clinical studies currently inform our approach to targeting supplementing oxygen in those with lower than normal oxygen saturation.

Aetiological role of common respiratory viruses in acute lower respiratory infections in children under five years: A systematic review and meta-analysis

Background

Acute lower respiratory infection (ALRI) remains a major cause of childhood hospitalization and mortality in young children and the causal attribution of respiratory viruses in the aetiology of ALRI is unclear. We aimed to quantify the absolute effects of these viral exposures.

Methods

We conducted a systematic literature review (across 7 databases) of case–control studies published from 1990 to 2014 which investigated the viral profile of 18592 children under 5 years with and without ALRI. We then computed a pooled odds ratio and virus–specific attributable fraction among the exposed of 8 common viruses – respiratory syncytial virus (RSV), influenza (IFV), parainfluenza (PIV), human metapneumovirus (MPV), adenovirus (AdV), rhinovirus (RV), bocavirus (BoV), and coronavirus (CoV).

Findings

From the 23 studies included, there was strong evidence for causal attribution of RSV (OR 9.79; AFE 90%), IFV (OR 5.10; AFE 80%), PIV (OR 3.37; AFE 70%) and MPV (OR 3.76; AFE 73%), and less strong evidence for RV (OR 1.43; AFE 30%) in young children presenting with ALRI compared to those without respiratory symptoms (asymptomatic) or healthy children. However, there was no significant difference in the detection of AdV, BoV, or CoV in cases and controls.

Conclusions

This review supports RSV, IFV, PIV, MPV and RV as important causes of ALRI in young children, and provides quantitative estimates of the absolute proportion of virus–associated ALRI cases to which a viral cause can be attributed.

Distribution and transmission of Mycobacterium tuberculosis complex lineages among children in peri-urban Kampala, Uganda

Background

To gain insight into the transmission of tuberculosis (TB) in peri-urban Kampala-Uganda, we performed a household contact study using children as a surrogate for recent transmission of Mycobacterium tuberculosis (MTB). Using this approach, we sought to understand M. tuberculosis complex (MTBC) lineage diversity, distribution and how these relate to TB transmission to exposed children.

Method

MTBC isolates from children aged ≤ 15 years, collected from 2002 to 2010 in a household-contact study, were analyzed using a LightCycler RT-PCR SNP genotyping assay (LRPS). The resultant genotypic data was used to determine associations between MTBC lineage and the children’s clinical and epidemiological characteristics.

Results and discussion

Of the 761 children surveyed, 9 % (69/761) had culture-positive TB an estimate in the range of global childhood TB; of these 71 % (49/69) were infected with an MTBC strain of the “Uganda family”, 17 % (12/69) infected with MTBC lineage 4 strains other than MTBC Uganda family and 12 % (8/69) infected with MTBC lineage 3, thereby disproportionately causing TB in the study area. Overall the data showed no correlation between the MTBC lineages studied and transmission (OR = 0.304; P-value = 0.251; CI: 95 %; 0.039-2.326) using children a proxy for TB transmission.

Conclusions

Our findings indicate that MTBC Uganda family strains are the main cause of TB in children in peri-urban Kampala. Furthermore, MTBC lineages did not differ in their transmissibility to children.

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

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

Acute respiratory infection and bacteraemia as causes of non-malarial febrile illness in African children: a narrative review

The replacement of "presumptive treatment for malaria" by "test before treat" strategies for the management of febrile illness is raising awareness of the importance of knowing more about the causes of illness in children who are suspected to have malaria but return a negative parasitological test. The most common cause of non-malarial febrile illness (NMFI) in African children is respiratory tract infection. Whilst the bacterial causes of NMFI are well known, the increasing use of sensitive techniques such as polymerase chain reaction (PCR) tests is revealing large numbers of viruses that are potential respiratory pathogens. However, many of these organisms are commonly present in the respiratory tract of healthy children so causality and risk factors for pneumonia remain poorly understood. Infection with a combination of viral and bacterial pathogens is increasingly recognised as important in the pathogenesis of pneumonia. Similarly, blood stream infections with organisms typically grown by aerobic culture are well known but a growing number of organisms that can be identified only by PCR, viral culture, or serology are now recognised to be common pathogens in African children. The high mortality of hospitalised children on the first or second day of admission suggests that, unless results are rapidly available, diagnostic tests to identify specific causes of illness will still be of limited use in guiding the potentially life saving decisions relating to initial treatment of children admitted to district hospitals in Africa with severe febrile illness and a negative test for malaria. Malaria control and the introduction of vaccines against Haemophilus influenzae type b and pneumococcal disease are contributing to improved child survival in Africa. However, increased parasitological testing for malaria is associated with increased use of antibiotics to which resistance is already high.