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

A novel combined nomogram for predicting severe acute lower respiratory tract infection in children hospitalized for RSV infection during the post-COVID-19 period

Introduction

Off-season upsurge of respiratory syncytial virus (RSV) infection with changed characteristics and heightened clinical severity during the post-COVID-19 era are raising serious concerns. This study aimed to develop and validate a nomogram for predicting the risk of severe acute lower respiratory tract infection (SALRTI) in children hospitalized for RSV infection during the post-COVID-19 era using machine learning techniques.

Methods

A multicenter retrospective study was performed in nine tertiary hospitals in Yunnan, China, enrolling children hospitalized for RSV infection at seven of the nine participating hospitals during January-December 2023 into the development dataset. Thirty-nine variables covering demographic, clinical, and laboratory characteristics were collected. Primary screening and dimension reduction of data were performed using Least Absolute Shrinkage and Selection Operator (LASSO) regression, followed by identification of independent risk factors for RSV-associated SALRTI using Logistic regression, thus finally establishing a predictive nomogram model. Performance of the nomogram was internally evaluated by receiver operating characteristic (ROC) curve, calibration curve, and decision curve analysis (DCA) based on the development dataset. External validation of our model was conducted using same methods based on two independent RSV cohorts comprising pediatric RSV inpatients from another two participating hospitals between January-March 2024.

Results

The development dataset included 1102 patients, 239 (21.7%) of whom developed SALRTI; while the external validation dataset included 249 patients (142 in Lincang subset and 107 in Dali subset), 58 (23.3%) of whom were diagnosed as SALRTI. Nine variables, including age, preterm birth, underlying condition, seizures, neutrophil-lymphocyte ratio (NLR), interleukin-6 (IL-6), lactate dehydrogenase (LDH), D-dimer, and co-infection, were eventually confirmed as the independent risk factors of RSV-associated SALRTI. A predictive nomogram was established via integrating these nine predictors. In both internal and external validations, ROC curves indicated that the nomogram had satisfactory discrimination ability, calibration curves demonstrated good agreement between the nomogram-predicted and observed probabilities of outcome, and DCA showed that the nomogram possessed favorable clinical application potential.

Conclusion

A novel nomogram combining several common clinical and inflammatory indicators was successfully developed to predict RSV-associated SALRTI. Good performance and clinical effectiveness of this model were confirmed by internal and external validations.

High Prevalence of Non-typeable Haemophilus influenzae and Haemophilus haemolyticus Among Vaccinated Children with Community-Acquired Pneumonia in Vietnam

Among 467 children under five hospitalized with community-acquired pneumonia, the prevalence of Haemophilus influenzae or Haemophilus haemolyticus was 60.8%, all cases were non-typable H. influenzae (NTHi) or H. haemolyticus. NTHi/H. haemolyticus PCR detection was associated with about twice the risk for severe disease. The results highlight the need for increased awareness and research efforts to investigate the role of NTHi/H. haemolyticus in severe CAP among children.

The Impact of Artificial Intelligence on Microbial Diagnosis

Traditional microbial diagnostic methods face many obstacles such as sample handling, culture difficulties, misidentification, and delays in determining susceptibility. The advent of artificial intelligence (AI) has markedly transformed microbial diagnostics with rapid and precise analyses. Nonetheless, ethical considerations accompany AI adoption, necessitating measures to uphold patient privacy, mitigate biases, and ensure data integrity. This review examines conventional diagnostic hurdles, stressing the significance of standardized procedures in sample processing. It underscores AI's significant impact, particularly through machine learning (ML), in microbial diagnostics. Recent progressions in AI, particularly ML methodologies, are explored, showcasing their influence on microbial categorization, comprehension of microorganism interactions, and augmentation of microscopy capabilities. This review furnishes a comprehensive evaluation of AI's utility in microbial diagnostics, addressing both advantages and challenges. A few case studies including SARS-CoV-2, malaria, and mycobacteria serve to illustrate AI's potential for swift and precise diagnosis. Utilization of convolutional neural networks (CNNs) in digital pathology, automated bacterial classification, and colony counting further underscores AI's versatility. Additionally, AI improves antimicrobial susceptibility assessment and contributes to disease surveillance, outbreak forecasting, and real-time monitoring. Despite a few limitations, integration of AI in diagnostic microbiology presents robust solutions, user-friendly algorithms, and comprehensive training, promising paradigm-shifting advancements in healthcare.

Global, regional, and national incidence and mortality burden of non-COVID-19 lower respiratory infections and aetiologies, 1990-2021: a systematic analysis from the Global Burden of Disease Study 2021

BACKGROUND

Lower respiratory infections (LRIs) are a major global contributor to morbidity and mortality. In 2020-21, non-pharmaceutical interventions associated with the COVID-19 pandemic reduced not only the transmission of SARS-CoV-2, but also the transmission of other LRI pathogens. Tracking LRI incidence and mortality, as well as the pathogens responsible, can guide health-system responses and funding priorities to reduce future burden. We present estimates from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 of the burden of non-COVID-19 LRIs and corresponding aetiologies from 1990 to 2021, inclusive of pandemic effects on the incidence and mortality of select respiratory viruses, globally, regionally, and for 204 countries and territories.

METHODS

We estimated mortality, incidence, and aetiology attribution for LRI, defined by the GBD as pneumonia or bronchiolitis, not inclusive of COVID-19. We analysed 26 259 site-years of mortality data using the Cause of Death Ensemble model to estimate LRI mortality rates. We analysed all available age-specific and sex-specific data sources, including published literature identified by a systematic review, as well as household surveys, hospital admissions, health insurance claims, and LRI mortality estimates, to generate internally consistent estimates of incidence and prevalence using DisMod-MR 2.1. For aetiology estimation, we analysed multiple causes of death, vital registration, hospital discharge, microbial laboratory, and literature data using a network analysis model to produce the proportion of LRI deaths and episodes attributable to the following pathogens: Acinetobacter baumannii, Chlamydia spp, Enterobacter spp, Escherichia coli, fungi, group B streptococcus, Haemophilus influenzae, influenza viruses, Klebsiella pneumoniae, Legionella spp, Mycoplasma spp, polymicrobial infections, Pseudomonas aeruginosa, respiratory syncytial virus (RSV), Staphylococcus aureus, Streptococcus pneumoniae, and other viruses (ie, the aggregate of all viruses studied except influenza and RSV), as well as a residual category of other bacterial pathogens.

FINDINGS

Globally, in 2021, we estimated 344 million (95% uncertainty interval [UI] 325-364) incident episodes of LRI, or 4350 episodes (4120-4610) per 100 000 population, and 2·18 million deaths (1·98-2·36), or 27·7 deaths (25·1-29·9) per 100 000. 502 000 deaths (406 000-611 000) were in children younger than 5 years, among which 254 000 deaths (197 000-320 000) occurred in countries with a low Socio-demographic Index. Of the 18 modelled pathogen categories in 2021, S pneumoniae was responsible for the highest proportions of LRI episodes and deaths, with an estimated 97·9 million (92·1-104·0) episodes and 505 000 deaths (454 000-555 000) globally. The pathogens responsible for the second and third highest episode counts globally were other viral aetiologies (46·4 million [43·6-49·3] episodes) and Mycoplasma spp (25·3 million [23·5-27·2]), while those responsible for the second and third highest death counts were S aureus (424 000 [380 000-459 000]) and K pneumoniae (176 000 [158 000-194 000]). From 1990 to 2019, the global all-age non-COVID-19 LRI mortality rate declined by 41·7% (35·9-46·9), from 56·5 deaths (51·3-61·9) to 32·9 deaths (29·9-35·4) per 100 000. From 2019 to 2021, during the COVID-19 pandemic and implementation of associated non-pharmaceutical interventions, we estimated a 16·0% (13·1-18·6) decline in the global all-age non-COVID-19 LRI mortality rate, largely accounted for by a 71·8% (63·8-78·9) decline in the number of influenza deaths and a 66·7% (56·6-75·3) decline in the number of RSV deaths.

INTERPRETATION

Substantial progress has been made in reducing LRI mortality, but the burden remains high, especially in low-income and middle-income countries. During the COVID-19 pandemic, with its associated non-pharmaceutical interventions, global incident LRI cases and mortality attributable to influenza and RSV declined substantially. Expanding access to health-care services and vaccines, including S pneumoniae, H influenzae type B, and novel RSV vaccines, along with new low-cost interventions against S aureus, could mitigate the LRI burden and prevent transmission of LRI-causing pathogens.

FUNDING

Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care (UK).

Development and evaluation of a multiplex digital PCR method for sensitive and accurate detection of respiratory pathogens in children

The emergence of multiplex digital polymerase chain reaction (dPCR) and other detection technologies for respiratory pathogens in recent years has facilitated greater understanding of respiratory virus epidemics. In this study, a multiplex dPCR method was developed and evaluated as a means of detecting five respiratory pathogens in children with acute lower respiratory tract infection (ALRTI). With 139 nasopharyngeal swabs collected from children with ALRTI, pathogens were detected using dPCR and quantitative real-time PCR (qPCR) methods. Of those specimens, dPCR detected 86 positive cases, while qPCR identified 84. Moreover, dPCR exhibited higher sensitivity than qPCR, and displayed no cross-reactivity with common respiratory pathogens. These findings suggest that dPCR-based method could become one of the most promising options for acute respiratory pathogen detection.

Applications of Artificial Intelligence in Microbial Diagnosis

The diagnosis is an important factor in healthcare care, and it is essential to identify microorganisms that cause infections and diseases. The application of artificial intelligence (AI) systems can improve disease management, drug development, antibiotic resistance prediction, and epidemiological monitoring in the field of microbial diagnosis. AI systems can quickly and accurately detect infections, including new and drug-resistant strains, and enable early detection of antibiotic resistance and improved diagnostic techniques. The application of AI in bacterial diagnosis focuses on the speed, precision, and identification of pathogens and the ability to predict antibiotic resistance.

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

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

The Contribution of Viruses and Bacteria to Childhood Community-acquired Pneumonia: 11-Year Observational Study From Norway

BACKGROUND

Viruses are associated with pediatric community-acquired pneumonia (CAP) but are also common in the upper airways of healthy children. We have determined the contribution of respiratory viruses and bacteria by comparing children with CAP and hospital controls.

METHODS

Children less than 16 years old with radiologically confirmed CAP (n = 715) were enrolled over an 11-year period. Children admitted for elective surgery during the same period served as controls (n = 673). Nasopharyngeal aspirates were tested for 20 respiratory pathogens by semiquantitative polymerase chain reaction tests and cultivated for bacteria and viruses. We used logistic regression to calculate adjusted odds ratios [aOR; 95% confidence intervals (CIs)], and estimated population-attributable fractions (95% CI).

RESULTS

At least 1 virus was detected in 85% of cases and 76% of controls, and greater than or equal to 1 bacterium was detected in 70% of cases and controls. The presence of respiratory syncytial virus (RSV) (aOR, 16.6; 95% CI: 9.81-28.2), human metapneumovirus (HMPV) (13.0; 6.17-27.5) and Mycoplasma pneumonia e (27.7; 8.37-91.6) were most strongly associated with CAP. For RSV and HMPV, there were significant trends between lower cycle-threshold values indicating higher viral genomic loads, and higher aORs for CAP. The population-attributable fraction estimates of RSV, HMPV, human parainfluenza virus, influenza virus and M. pneumoniae were 33.3% (32.2-34.5), 11.2% (10.5-11.9), 3.7% (1.0-6.3), 2.3% (1.0-3.6) and 4.2% (4.1-4.4), respectively.

CONCLUSIONS

RSV, HMPV and M. pneumoniae were most strongly related to pediatric CAP and accounted for half of all cases. There were positive trends between increasing viral genomic loads of RSV and HMPV, and higher odds for CAP.

Proteomic profiling of urinary small extracellular vesicles in children with pneumonia: a pilot study

BACKGROUND

Small extracellular vesicles (sEV) play a crucial role in immune responses to viral infection. However, the composition of sEV derived from children with viral pneumonia remains ill defined.

METHODS

First, we performed mass spectrometry-based label-free proteomic analysis of urinary sEV in 7 children with viral pneumonia, 4 children with Mycoplasma pneumoniae pneumonia and 20 healthy children. Then a total of 33 proteins were selected to validate by multiple reaction monitoring analysis in an independent cohort of 20 healthy children and 29 children with pneumonia.

RESULTS

In the discovery phase, a total of 1621 proteins were identified, while 260 proteins have differential expression in children with viral pneumonia compared to healthy children. Biological pathways primarily associated with neutrophil degranulation, carbohydrate metabolism and endocytosis were enriched in children with viral pneumonia. Finally, the abundance of eight proteins was verified to be significantly higher in children with viral pneumonia than in healthy children.

CONCLUSIONS

This pilot study with proteomic profiles of urinary sEV provided insights to the host response to viral pathogen exposure and potential diagnostic biomarkers for children with viral pneumonia, and served as the basis for understanding the fundamental biology of infection.

IMPACT

There were significant differences in the proteomic features of urinary sEV between children with viral pneumonia and those with Mycoplasma pneumoniae pneumonia. Many viral infection-related proteins were identified in urinary sEV and overrepresented in children with viral pneumonia, which facilitates our understanding of the fundamental biology of viral infection. A total of eight proteins (ANPEP, ASAH1, COL11A1, EHD4, HEXB, LGALS3BP, SERPINA1 and SERPING1) were verified as potential biomarkers for the diagnosis of viral pneumonia in children.

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

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

Epidemiology and surveillance implications of community-acquired pneumonia in children

Community-acquired pneumonia (CAP) is the single largest infectious cause of hospitalization and death in children worldwide. With improved immunizations, the incidence of bacterial pneumonia and the number of colonized bacteria have decreased. However, respiratory viruses are still an important cause of CAP, especially as new infectious agents such severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerge. The SARS-CoV-2 virus emerged in 2019 and caused the current coronavirus disease 2019 pandemic. Therefore, it is necessary to elucidate the epidemiology and causative pathogens of CAP. Recently, the Pneumonia and Respiratory Disease Study Group, affiliated with the Korean Academy of Pediatric Allergy and Respiratory Disease, investigated the causative pathogens of respiratory infections in children hospitalized with CAP, the serotype of Streptococcus pneumoniae, and the prevalence of Mycoplasma pneumoniae with gene mutations. Antibiotic resistance and serotype test results can determine the use of empirical antibiotics. Moreover, it is possible to help develop future vaccines by comparing bacterial culture results with vaccine serotype and identifying the changes and prevalence of each serotype. Therefore, we will perform continuous national surveillance and monitor the epidemiology of respiratory pathogens in Korea and worldwide. The surveillance of these respiratory infections can play a role in monitoring the emergence of new infectious diseases such as SARS-CoV-2.

Value of sputum Gram stain, sputum culture, and bronchoalveolar lavage fluid Gram stain in predicting single bacterial pathogen among children with community-acquired pneumonia

Background

Currently, the microbial etiology of community-acquired pneumonia in children remains challenging. While Gram stain and sputum culture are commonly used to detect bacterial pathogens, it is unclear whether these approaches can predict single pathogen from bronchoalveolar lavage fluid (BALF) culture.

Methods

A retrospective study involving 287 children hospitalized for pneumonia was conducted. Sputum specimens were collected on admission; and BALF specimens were collected within 24 h after admission. Taking BALF culture as the reference standard, the sensitivity and specificity of Sputum Gram stain (SGS), sputum culture, and BALF Gram stain (BGS) were calculated. The agreement between these approaches and BALF culture was compared using kappa statistics.

Results

For SGS, the specificity was 23%. The overall sensitivity was 70%, including 87% for Gram-positive (G+) cocci, 56% for Gram-negative (G-) cocci, and 50% for G-bacilli. For sputum culture, the specificity was 70%. The overall sensitivity was 64%, including 71% for Streptococcus pneumoniae, 71% for Moraxella catarrhalis, and 64% for Haemophilus influenzae. For BGS, the specificity was 71%. The overall sensitivity was 60%, including 77% for G+cocci, 38% for G-cocci, and 44% for G-bacilli. While SGS had poor agreement with BALF culture, both sputum culture and BGS had moderate agreement with BALF culture.

Conclusions

Both sputum culture and BGS are helpful in predicting single bacterial pathogen from BALF culture among children with community-acquired pneumonia. Sputum cultures and BGS can provide early clues for BALF pathogen when BALF culture results are pending or bronchoscopy is not performed.

Molecular diagnostic of complicated pneumonia in the post-vaccine era

BACKGROUND

The etiological diagnosis of community-acquired pneumonia (CAP) is still a challenge. We compared the conventional culture method and real-time polymerase chain reaction (RT-PCR) for the identification of Streptococcus pneumoniae in severe pediatric CAP.

METHODS

A retrospective hospital-based study was conducted. From 2012 to 2018, we have selected patients who had peripheral blood and/or pleural fluid collected for etiological investigation by RT-PCR.

RESULTS

We included 113 children (median age: 3 years; interquartile range 1-6 years). RT-PCR increased the detection rate of S. pneumoniae by 6.5 times using blood samples and eight times using pleural fluid samples. Patients subjected to RT-PCR showed more prolonged hospitalization (p = 0.006), fewer comorbidities (p = 0.03), presence of pleural effusion (p = 0.001), presence of young forms of leukocytes (p = 0.001) and radiograph with characteristics of pneumonia (p = 0.002). The presence of pleural effusion [odds ratio (OR) = 14.7, 95% confidence interval (CI) 1.6-133.9; p = 0.01] and young forms of leukocytes (OR = 8.9, 95% CI 0.9-84.4; p = 0.05) were risk factors for positive RT-PCR pneumococcal when multivariate analysis was performed.

CONCLUSIONS

RT-PCR is a reliable method for diagnosing severe CAP using sterile materials and a potentially applicable method in patients with clinical, radiological and non-specific laboratory characteristics of lower respiratory tract infection, especially in complicated cases with pleural effusion.

Shionone-Targeted Pneumolysin to Ameliorate Acute Lung Injury Induced by Streptococcus pneumoniae In Vivo and In Vitro

Streptococcus pneumoniae (S. pneumoniae), as a Gram-positive bacterium, can cause severe bacterial pneumonia, and result in high morbidity and mortality in infected people. Meanwhile, isolated drug-resistant S. pneumoniae is growing, which raises concerns about strategies for combatting S. pneumoniae infection. To disturb S. pneumoniae pathogenicity and its drug-resistance, developing novel anti-infective strategies or compounds is urgent. In this study, the anti-infective effect of shionone was explored. A minimum inhibitory concentration (MIC) assay and growth curve determination were performed to evaluate the effect of the tetracyclic triterpenoid compound shionone against S. pneumoniae. Hemolysis tests, western blotting, oligomerization inhibition assays, and molecular docking were carried out to explore the anti-infective mechanism of shionone. Moreover, the protective effect of shionone was also confirmed in a mousepneumonia model. The results showed that the excellent hemolytic inhibitory activity of shionone was observed at less than 8 μg/mL. Meanwhile, shionone could disturb the oligomerization of pneumolysin (PLY) but did not interfere with PLY expression at less than 4 μg/mL. Molecular docking suggested that shionone targeted the ASP-59, ILE-60, THR-57, PHE-344, and ASN-346 amino acid sites to reduce S. pneumoniae pathogenicity. Furthermore, shionone alleviated lung histopathologic injury and decreased lung bacterial colonization in vivo. The above results showed that shionone could bind to the PLY active pocket under the concentrations of 8 μg/mL and neutralize PLY hemolysis activity to reduce S. pneumoniae pathogenicity in vitro and in vivo.

A retrospective observational study of biomarker levels and severity assessment in pediatric community-acquired pneumonia

METHODS

A retrospective chart review was conducted on children (aged 60 days to 18 years) diagnosed with CAP, and admitted to a regional, tertiary hospital (Charleston, WV, USA) for 3 years (2015-2018). Patients were stratified into 2 severity cohorts, mild (no ICU care), and moderate/severe (required ICU care). Biomarker values were then compared between the severity cohorts and area under the curve (AUC), and cut-off values and performance characteristics were calculated.

RESULTS

A total of 108 patients met inclusion criteria with 46% having moderate/severe CAP. Elevated levels of CRP (51.7 mg/L in mild vs. 104.8 mg/L in moderate/severe, P = .003, PCT (0.29 ng/ml in mild vs. 4.02 ng/mL in moderate/severe, P = .001) and band counts (8% in mild vs. 15% moderate/severe, P = .009) were associated with increased pneumonia severity. In predicting moderate/severe CAP, PCT had the highest AUC of 0.77 (P = .001) followed by bands AUC of 0.69 (P = .009) and CRP AUC of 0.67 (P = .003). Cut-off for PCT of 0.55 ng/mL had a sensitivity of 83% and a specificity of 65%. Cut-off level of 53.1 mg/L for CRP had a sensitivity of 79% and specificity of 52%. Cut off level of 12.5% bands had a sensitivity of 61% and specificity of 71%. In a multivariable model controlled for patient demographics and other biomarker levels, only PCT levels significantly predicted moderate/severe CAP (adjusted odds ratio: 1.40 [95% CI, 1.14-1.73], P = .002).

CONCLUSION

Biomarkers, in particular PCT, obtained early in hospitalization may perform as possible predictors for CAP severity in children and be beneficial in guiding CAP management. However, biomarkers in pneumonia should not drive severity assessment or patient management independent of clinical presentation.

The Accuracy of Lung Ultrasonography Diagnosis of Community-Acquired Pneumonia, in an Adult Cohort

Objective:

Community-acquired pneumonia (CAP) is a common respiratory infection, and diagnosis is frequently performed using a chest radiography (CXR). Sonography is an available method with less radiation exposure, but has not been confirmed for diagnosis of CAP. The objective was to compare the diagnostic accuracy of sonography.

Materials and Methods:

In this cross-sectional study, 90 adult patients (aged >18 years) were admitted to the emergency department of two university-affiliated hospitals in Southwest Iran, from July to December 2019, with a confirmed diagnosis of CAP. The patient symptoms and CXR results were included as part of this study. Within 24 hours after obtaining a CXR, a lung ultrasonogram (LUS) was performed. The diagnostic accuracy of semiquantitative LUS (SQLUS) was compared with CXR results using the Pearson chi-square test and Fisher’s exact test.

Results:

The mean age of participants was 52.98 ± 16.77 years. 51 were men (56.7%). 28 patients (31.1%), who had abnormal SQLUS results, were not associated with CXR findings ( P = .296). SQLUS showed poor diagnostic accuracy for LUS (31.11%).

Conclusion:

This study results could not confirm LUS as an accurate method for diagnosing CAP in adult patients; although due to the convenient sample of adults and clinical-based diagnosis of CAP, any generalization of the results should be made with caution.

Burden of pneumococcal disease due to serotypes covered by the 13-valent and new higher-valent pneumococcal conjugate vaccines in the United States

The addition of pneumococcal conjugate vaccines (PCVs) to the United States (US) national immunization program led to significant reductions in incidence, mortality, and associated sequelae caused by pneumococcal disease (PD) in children and adults through direct and indirect protection. However, there remains clinical and economic burden due to PD caused by serotypes not included in the current 13-valent PCV (PCV13) formulation. To address this unmet need, 15-valent PCV (PCV15) and 20-valent PCV (PCV20), containing additional serotypes to PCV13, were recently approved in the US for adults and are anticipated for pediatrics in the near future. The study objective was to estimate the annual number of cases, deaths, and economic burden of PD due to serotypes included in PCV13, PCV15, and PCV20 for both US pediatric and adult populations. An Excel-based model was developed to calculate clinical and economic outcomes using published age-group specific serotype coverage; incidence of invasive PD, community-acquired pneumonia, and acute otitis media; case fatality rates; and disease-related costs. The results showed that across all age groups, the estimated annual PD cases and associated deaths covered by PCV13 serotypes were 914,199 and 4320, respectively. Compared with PCV13 serotypes, the additional 2 and 7 serotypes covered by PCV15 and PCV20 were attributed with 550,475 and 991,220 annual PD cases, as well as 1425 and 3226 annual deaths, respectively. This clinical burden translates into considerable economic costs ranging from $903 to $1,928 million USD that could be potentially addressed by PCV15 and PCV20. The additional serotypes included in PCV20 contribute substantially to the clinical and economic PD burden in the US pediatric and adult populations. Despite the success of the PCV13 pediatric national immunization program and increased adult uptake of PCV13 and 23-valent polysaccharide vaccine, broader PCV serotype coverage is needed across all ages to further reduce pneumococcal disease burden.

Systematic review of clinical practice guidelines on the management of community acquired pneumonia in children

Childhood community acquired pneumonia (CAP) is the leading cause of mortality in children under 5 years worldwide. Clinical practice guidelines (CPGs) may be limited by method of development, scope of recommendations and the quality of supporting evidence. This study systematically identified, appraised and compared the recommendations of CPGs for the management of paediatric CAP using the AGREE II tool. The systematic review yielded 1409 non-duplicate results, of which 14 CPGs were appraised. Four of the fourteen CPGs were deemed high quality. Most CPGs were considered low-medium quality with 'rigour of development' and 'applicability' the weakest domains. These areas should be considered in deriving CPGs in the future. Recommendations were generally similar across all guidelines; however, there was notable heterogeneity in three areas. This suggests the need for further evidence to guide management decisions on oxygen saturation thresholds for admission, the utility of investigations such as acute phase reactants, and the duration of antibiotic therapy.

Analysis of severe human adenovirus infection outbreak in Guangdong Province, southern China in 2019

During 2018-2019, a severe human adenovirus (HAdV) infection outbreak occurred in southern China. Here, we screened 18 respiratory pathogens in 1704 children (≤ 14 years old) hospitalized with acute respiratory illness in Guangzhou, China, in 2019. In total, 151 patients had positive HAdV test results; 34.4% (52/151) of them exhibited severe illness. HAdV infection occurred throughout the year, with a peak in summer. The median patient age was 3.0 (interquartile range: 1.1-5.0) years. Patients with severe HAdV infection exhibited increases in 12 clinical indexes (P ​≤ ​0.019) and decreases in four indexes (P ​≤ ​0.007), compared with patients exhibiting non-severe infection. No significant differences were found in age or sex distribution according to HAdV infection severity (P ​> ​0.05); however, the distributions of comorbid disease and HAdV co-infection differed according to HAdV infection severity (P ​< ​0.05). The main epidemic types were HAdV-3 (47.0%, 71/151) and HAdV-7 (46.4%, 70/151). However, the severe illness rate was significantly higher in patients with HAdV-7 (51.4%) than in patients with HAdV-3 (19.7%) and other types of HAdV (20%) (P ​< ​0.001). Sequencing analysis of genomes/capsid genes of 13 HAdV-7 isolates revealed high similarity to previous Chinese isolates. A representative HAdV-7 isolate exhibited a similar proliferation curve to the curve described for the epidemic HAdV-3 strain Guangzhou01 (accession no. DQ099432) (P ​> ​0.05); the HAdV-7 isolate exhibited stronger virulence and infectivity, compared with HAdV-3 (P ​< ​0.001). Overall, comorbid disease, HAdV co-infection, and high virulence and infectivity of HAdV-7 were critical risk factors for severe HAdV infection; these data can facilitate treatment, control, and prevention of HAdV infection.

Chest Radiographs Using a Context-Fusion Convolution Neural Network (CNN): Can It Distinguish the Etiology of Community-Acquired Pneumonia (CAP) in Children?

Clinical symptoms and inflammatory markers cannot reliably distinguish the etiology of CAP, and chest radiographs have abundant information related with CAP. Hence, we developed a context-fusion convolution neural network (CNN) to explore the application of chest radiographs to distinguish the etiology of CAP in children. This retrospective study included 1769 cases of pediatric pneumonia (viral pneumonia, n = 487; bacterial pneumonia, n = 496; and mycoplasma pneumonia, n = 786). The chest radiographs of the first examination, C-reactive protein (CRP), and white blood cell (WBC) were collected for analysis. All patients were stochastically divided into training, validation, and test cohorts in a 7:1:2 ratio. Automatic lung segmentation and hand-crafted pneumonia lesion segmentation were performed, from which three image-based models including a full-lung model, a local-lesion model, and a context-fusion model were built; two clinical characteristics were used to build a clinical model, while a logistic regression model combined the best CNN model and two clinical characteristics. Our experiments showed that the context-fusion model which integrated the features of the full-lung and local-lesion had better performance than the full-lung model and local-lesion model. The context-fusion model had area under curves of 0.86, 0.88, and 0.93 in identifying viral, bacterial, and mycoplasma pneumonia on the test cohort respectively. The addition of clinical characteristics to the context-fusion model obtained slight improvement. Mycoplasma pneumonia was more easily identified compared with the other two types. Using chest radiographs, we developed a context-fusion CNN model with good performance for noninvasively diagnosing the etiology of community-acquired pneumonia in children, which would help improve early diagnosis and treatment.

Clinical manifestations and outcome of viral acute lower respiratory infection in hospitalised children in Myanmar

Background

Acute lower respiratory infection (ALRI) remains the leading cause of death in children worldwide, and viruses have been the major cause of ALRI. In Myanmar, ALRI is associated with high morbidity and mortality in children, and detailed information on ALRI is currently lacking.

Methods

This prospective study investigated the viral aetiologies, clinical manifestations, and outcomes of ALRI in hospitalised children aged 1 month to 12 years at the Yankin Children Hospital, Yangon, Myanmar from May 2017 to April 2019. The sample size was set to 300 patients for each year. Two nasopharyngeal swabs were obtained for the patients with suspected viral ALRI; one for rapid tests for influenza and respiratory syncytial virus (RSV), and the other for real-time PCR for the 16 ALRI-causing viruses. Pneumococcal colonization rates were also investigated using real-time PCR. Clinical information was extracted from the medical records, and enrolled patients were categorised by age and severity for comparison.

Results

Among the 5463 patients admitted with a diagnosis of ALRI, 570 (10.4%) were enrolled in this study. The median age of the patients was 8 months (interquartile range, 4–15 months). The most common symptoms were cough (93%) and difficulty in breathing (73%), while the most common signs of ALRI were tachypnoea (78%) and chest indrawing (67%). A total of 16 viruses were detected in 502 of 570 patients’ samples (88%), with RSV B (36%) and rhinovirus (28%) being the most commonly detected. Multiple viruses were detected in 221 of 570 samples (37%) collected from 570 patients. Severe ALRI was diagnosed in 107 of 570 patients (19%), and RSV B and human rhinovirus were commonly detected. The mortality rate was 5%; influenza virus A (29%) and RSV B (21%) were commonly detected, and stunting and lack of immunization were frequently observed in such cases. Additionally, 45% (259/570) of the patients had pneumococcal colonization.

Conclusions

Viral ALRI in hospitalised children with a median of 8 months has significant morbidity and mortality rates in Myanmar. RSV and rhinovirus were the most commonly detected from nasopharyngeal swabs, while influenza virus and RSV were the most frequently associated with fatal cases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07342-1.

Glycan Microarrays Containing Synthetic Streptococcus pneumoniae CPS Fragments and Their Application to Vaccine Development

Streptococcus pneumoniae is the leading source of life-endangering diseases like pneumonia, septicemia, and meningitis, as well as a major cause of death in children under 5 years old in developing countries. At least 98 serotypes of S. pneumoniae can be distinguished based on their structurally distinct capsular polysaccharides (CPS). Currently available CPS-based pneumococcal vaccines contain serotypes most frequently associated with invasive pneumococcal diseases. The polysaccharides used in commercial conjugate-vaccines are isolated from bacteria cultures comprising many laborious and operationally challenging steps followed by depolymerization of long polysaccharides into small fragments and their conjugation to the carrier protein. The medicinal chemistry approach for glycoconjugate vaccine development offers an exciting alternative to CPS isolation for a broad range of different glycan antigens. Glycan arrays containing well-defined synthetic glycans of CPS fragments and repeating units are used as a platform for the high-throughput screening of various serum samples and identification of protective glycotopes for vaccine candidates.

Bronchiolitis Management and Unnecessary Antibiotic Use Across 3 Canadian PICUs

OBJECTIVES

To describe the patient characteristics, clinical management, and infectious etiology in critically ill children with bronchiolitis. The secondary objective was to determine the association between antibiotic use and hospital length of stay among patients without concomitant bacterial infections.

METHODS

Retrospective cohort study including patients ≤2 years old with bronchiolitis admitted to 3 Canadian pediatric intensive care units between 2016 and 2018.

RESULTS

We included 372 patients with a median age of 2.1 months (interquartile range 1.2-6.6) and Pediatric Risk of Mortality III score 3.0 (interquartile range 0-3.0). Initial ventilatory management included high flow nasal cannula (28.2%) and noninvasive positive pressure ventilation (53.7%), of which 41.9% and 87.5%, respectively, did not require escalation of ventilatory support. Chest radiographs (81.7%) and respiratory virus testing (95.4%) were performed in most patients; 14.0% received systemic steroids. Respiratory syncytial virus was detected in 61.3% patients, and 7.5% had a culture-positive concomitant bacterial infection. Of 258 (69.4%) patients with a viral infection, only 45.3% received antibiotics. In this group, antibiotic use beyond 72 hours was not associated with hospital length of stay (ratio 1.14, 95% confidence interval 0.97-1.34).

CONCLUSIONS

High flow nasal canulae and noninvasive ventilation are commonly used in severe bronchiolitis. Despite contrary evidence, steroids and antibiotics were also frequently used. Evidence-based guidelines specific to children with severe bronchiolitis are needed to improve the care delivered to this patient population.

Etiology and the challenge of diagnostic testing of community-acquired pneumonia in children and adolescents

Background

Pneumonia is the leading cause of mortality in pediatric population. The etiology of pneumonia in this population is variable and changes according to age and disease severity and where the study is conducted. Our aim was to determine the etiology of community-acquired pneumonia (CAP) in children aged 1 month to 17 years admitted to 13 Colombian hospitals.

Methods

Prospective cohort study. Hospitalized children with radiologically confirmed CAP and ≤ 15 days of symptoms were included and followed together with a control group. Induced sputum (IS) was submitted for stains and cultures for pyogenic bacteria and Mycobacterium tuberculosis, and multiplex PCR (mPCR) for bacteria and viruses; urinary antigens for pneumococcus and Legionella pneumophila; nasopharyngeal swabs for viruses, and paired serology for atypical bacteria and viruses. Additional cultures were taken at the discretion of primary care pediatricians.

Results

Among 525 children with CAP, 71.6% had non-severe pneumonia; 24.8% severe and 3.6% very severe pneumonia, and no fatal cases. At least one microorganism was identified in 84% of children and 61% were of mixed etiology; 72% had at least one respiratory virus, 28% pyogenic bacteria and 21% atypical bacteria. Respiratory syncytial virus, Parainfluenza, Rhinovirus, Influenza, Mycoplasma pneumoniae, Adenovirus and Streptococcus pneumoniae were the most common etiologies of CAP. Respiratory syncytial virus was more frequent in children under 2 years and in severe pneumonia. Tuberculosis was diagnosed in 2.3% of children. IS was the most useful specimen to identify the etiology (33.6%), and blood cultures were positive in 3.6%. The concordance between all available diagnostic tests was low. A high percentage of healthy children were colonized by S. pneumoniae and Haemophilus influenzae, or were infected by Parainfluenza, Rhinovirus, Influenza and Adenovirus.

Conclusions

Respiratory viruses are the most frequent etiology of CAP in children and adolescents, in particular in those under 5 years. This study shows the challenges in making an etiologic diagnosis of CAP in pediatric population because of the poor concordance between tests and the high percentage of multiple microorganisms in healthy children. IS is useful for CAP diagnosis in pediatric population.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-022-03235-z.

Application of mNGS in the Etiological Analysis of Lower Respiratory Tract Infections and the Prediction of Drug Resistance

Lower respiratory tract infections (LRTIs) have high morbidity and mortality rates. However, traditional etiological detection methods have not been able to meet the needs for the clinical diagnosis and prognosis of LRTIs. The rapid development of metagenomic next-generation sequencing (mNGS) provides new insights for the diagnosis and treatment of LRTIs; however, little is known about how to interpret the application of mNGS results in LRTIs. In this study, lower respiratory tract specimens from 46 patients with suspected LRTIs were tested simultaneously using conventional microbiological detection methods and mNGS. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], genomic coverage, and relative abundance of the organism in predicting the true-positive pathogenic bacteria. True-positive viruses were identified according to the lg(RPKM) threshold of bacteria. We also evaluated the ability to predict drug resistance genes using mNGS. Compared to that using conventional detection methods, the false-positive detection rate of pathogenic bacteria was significantly higher using mNGS. It was concluded from the ROC curves that the lg(RPKM) and genomic coverage contributed to the identification of pathogenic bacteria, with the performance of lg(RPKM) being the best (area under the curve [AUC] = 0.99). The corresponding lg(RPKM) threshold for identifying the pathogenic bacteria was −1.35. Thirty-five strains of true-positive virus were identified based on the lg(RPKM) threshold of bacteria, with the detection of human gammaherpesvirus 4 being the highest and prone to coinfection with Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia. Antimicrobial susceptibility tests (AST) revealed the resistance of bacteria containing drug resistance genes (detected by mNGS). However, the drug resistance genes of some multidrug-resistant bacteria were not detected. As an emerging technology, mNGS has shown many advantages for the unbiased etiological detection and the prediction of antibiotic resistance. However, a correct understanding of mNGS results is a prerequisite for its clinical application, especially for LRTIs.

IMPORTANCE LRTIs are caused by hundreds of pathogens, and they have become a great threat to human health due to the limitations of traditional etiological detection methods. As an unbiased approach to detect pathogens, mNGS overcomes such etiological diagnostic challenges. However, there is no unified standard on how to use mNGS indicators (the sequencing reads, genomic coverage, and relative abundance of each organism) to distinguish between pathogens and colonizing microorganisms or contaminant microorganisms. Here, we selected the mNGS indicator with the best identification performance and established a cutoff value for the identification of pathogens in LRTIs using ROC curves. In addition, we also evaluated the accuracy of antibiotic resistance prediction using mNGS.

A semisynthetic glycoconjugate provides expanded cross-serotype protection against Streptococcus pneumoniae

Streptococcus pneumoniae (S. pneumoniae)infections are the leading cause of child mortality globally. Currentvaccines fail to induceaprotective immune response towards a conserved part of the pathogen,resulting in newserotypescausing disease. Therefore, new vaccinestrategies are urgently needed.Described is atwo-pronged approach combiningS. pneumoniaeproteins, pneumolysin (Ply) and pneumococcal surface protein A (PspA),with aprecisely defined synthetic oligosaccharide,wherebythe carrier protein actsas a serotype-independent antigen to provideadditional protection. Proof of concept in mice and swine modelsrevealed thatthe conjugatesinhibited colonization of the nasopharynx, decreased the bacterial load and reduced disease severity in the bacteria challenge model. Immunization of piglets provided the first evidence for the immunogenicity and protective potential of synthetic glycoconjugate vaccine in a large animal model.Acombination of synthetic oligosaccharides with proteins from the target pathogen opens the path to create broadly cross-protective ("universal") pneumococcal vaccines.

Pediatric Invasive Pneumococcal Disease (IPD) in Yogyakarta, Indonesia: A Case Series

Given the fact that invasive pneumococcal disease (IPD) has a high clinical burden, particularly among children in developing countries, data on its occurrence and clinical profile in Indonesia is still insufficient. We presented 3 cases of IPD in children who were admitted to Dr. Sardjito General Hospital, Yogyakarta, Indonesia between 2016 and 2019. While our first 2 patients had milder course of disease, our third patient who presented with meningoencephalitis had poor outcome. Risk factors shown in our cases were young age and malignancy history. Multiple antibiotic resistance was observed in our isolates. The fact that none of our patients have received pneumococcal vaccination marks the necessity of this vaccine especially for at-risk children.

Rapid Diagnostic Tests to Guide Case Management of and Improve Antibiotic Stewardship for Pediatric Acute Respiratory Illnesses in Resource-Constrained Settings: a Prospective Cohort Study in Southwestern Uganda

Pediatric acute respiratory illness (ARI) is one of the most common reasons for evaluation at peripheral health centers in sub-Saharan Africa and is frequently managed based on clinical syndrome alone. Although most ARI episodes are likely caused by self-limited viral infections, the majority are treated with antibiotics. This overuse contributes to the development of antimicrobial resistance. To evaluate the preliminary feasibility and potential impact of adding pathogen-specific and clinical biomarker diagnostic testing to existing clinical management algorithms, we conducted a prospective, observational cohort study of 225 children presenting with malaria-negative, febrile ARI to the outpatient department of a semi-urban peripheral health facility in southwestern Uganda from October 2019 to January 2020. In addition to routine clinical evaluation, we performed influenza and Streptococcus pneumoniae antigen testing and measured levels of C-reactive protein, procalcitonin, and lactate in the clinic's laboratory, and conducted a follow-up assessment by phone 7 days later. Almost one-fifth of participants (40/225) tested positive for influenza. Clinical biomarker measurements were low with C-reactive protein of >40 mg/L in only 11% (13/222) of participants and procalcitonin >0.25 ng/mL in only 13% (16/125). All but two children received antibiotic treatment; only 3% (7/225) were admitted. At follow-up, 59% (118/201) of caregivers reported at least one persistent symptom, but fever had resolved for all children. Positive influenza testing was associated with persistent symptoms. In summary, we demonstrate that simple, rapid pathogen-specific testing and biomarker measurement are possible in resource-limited settings and could improve syndromic management and, in turn, antibiotic stewardship. IMPORTANCE Globally, respiratory illness is one of the most common reasons that children seek care. It is often treated inappropriately with antibiotics, which can drive the development of antibiotic resistance. In resource-rich settings, testing for specific pathogens or measurement of clinical biomarkers, such as procalcitonin and C-reactive protein, is often employed to help determine which children should receive antibiotics. However, there are limited data on the use of these tests in resource-constrained, outpatient contexts in sub-Saharan Africa. We enrolled children with respiratory illness presenting to a clinic in southwestern Uganda and performed testing for influenza, Streptococcus pneumoniae, C-reactive protein, and procalcitonin on-site. Almost all children received antibiotics. We demonstrate that employing clinical algorithms that include influenza and clinical biomarker testing could significantly decrease antibiotic prescriptions. Our study therefore provides preliminary data to support the feasibility and potential utility of diagnostics to improve management of respiratory illness in resource-constrained settings.

Ceftaroline Fosamil for Treatment of Pediatric Complicated Skin and Soft Tissue Infections and Community-Acquired Pneumonia

Community-acquired pneumonia (CAP)/community-acquired bacterial pneumonia (CABP) and complicated skin and soft tissue infection (cSSTI)/acute bacterial skin and skin structure infection (ABSSSI) represent major causes of morbidity and mortality in children. β-Lactams are the cornerstone of antibiotic treatment for many serious bacterial infections in children; however, most of these agents have no activity against methicillin-resistant Staphylococcus aureus (MRSA). Ceftaroline fosamil, a β-lactam with broad-spectrum in vitro activity against Gram-positive pathogens (including MRSA and multidrug-resistant Streptococcus pneumoniae) and common Gram-negative organisms, is approved in the European Union and the United States for children with CAP/CABP or cSSTI/ABSSSI. Ceftaroline fosamil has completed a pediatric investigation plan including safety, efficacy, and pharmacokinetic evaluations in patients with ages ranging from birth to 17 years. It has demonstrated similar clinical and microbiological efficacy to best available existing treatments in phase III-IV trials in patients aged ≥ 2 months to < 18 years with CABP or ABSSSI, with a safety profile consistent with the cephalosporin class. It is also approved in the European Union for neonates with CAP or cSSTI, and in the US for neonates with ABSSSI. Ceftaroline fosamil dosing for children (including renal function adjustments) is supported by pharmacokinetic/pharmacodynamic modeling and simulations in appropriate age groups, and includes the option of 5- to 60-min intravenous infusions for standard doses, and a high dose for cSSTI patients with MRSA isolates, with a ceftaroline minimum inhibitory concentration of 2-4 mg/L. Considered together, these data suggest ceftaroline fosamil may be beneficial in the management of CAP/CABP and cSSTI/ABSSSI in children.

Viral and Atypical Bacterial Detection in Young Nepalese Children Hospitalized with Severe Pneumonia

Respiratory viruses cause a substantial proportion of respiratory tract infections in children but are underrecognized as a cause of severe pneumonia hospitalization in low-income settings. We employed 22 real-time PCR assays and retrospectively reanalyzed 610 nasopharyngeal aspirate specimens from children aged 2 to 35 months with severe pneumonia (WHO definition) admitted to Kanti Childrens' Hospital in Kathmandu, Nepal, from January 2006 through June 2008. Previously, ≥1 of 7 viruses had been detected by multiplex reverse transcription-PCR in 30% (188/627) of cases. Reanalyzing the stored specimens, we detected ≥1 pathogens, including 18 respiratory viruses and 3 atypical bacteria, in 98.7% (602/610) of cases. Rhinovirus (RV) and respiratory syncytial virus (RSV) were the most common, detected in 318 (52.1%) and 299 (49%) cases, respectively, followed by adenovirus (AdV) (10.6%), human metapneumovirus (hMPV) (9.7%), parainfluenza virus type 3 (8.4%), and enterovirus (7.7%). The remaining pathogens were each detected in less than 5%. Mycoplasma pneumoniae was most common among the atypical bacteria (3.7%). Codetections were observed in 53.3% of cases. Single-virus detection was more common for hMPV (46%) and RSV (41%) than for RV (22%) and AdV (6%). The mean cycle threshold value for detection of each pathogen tended to be lower in single-pathogen detections than in codetections. This finding was significant for RSV, RV, and AdV. RSV outbreaks occurred at the end of the monsoon or during winter. An expanded diagnostic PCR panel substantially increased the detection of respiratory viruses in young Nepalese children hospitalized with severe pneumonia. IMPORTANCE Respiratory viruses are an important cause of respiratory tract infections in children but are underrecognized as a cause of pneumonia hospitalization in low-income settings. Previously, we detected at least one of seven respiratory viruses by PCR in 30% of young Nepalese children hospitalized with severe pneumonia over a period of 36 months. Using updated PCR assays detecting 21 different viruses and atypical bacteria, we reanalyzed 610 stored upper-respiratory specimens from these children. Respiratory viruses were detected in nearly all children hospitalized for pneumonia. RSV and rhinovirus were the predominant pathogens detected. Detection of two or more pathogens was observed in more than 50% of the pneumonia cases. Single-virus detection was more common for human metapneumovirus and RSV than for rhinovirus and adenovirus. The concentration of virus was higher (low cycle threshold [CT] value) for single detected pathogens, hinting at a high viral load as a marker of clinical significance.

Differential nasopharyngeal microbiota composition in children according to respiratory health status

Acute respiratory infections (ARIs) constitute one of the leading causes of antibiotic administration, hospitalization and death among children <5 years old. The upper respiratory tract microbiota has been suggested to explain differential susceptibility to ARIs and modulate ARI severity. The aim of the present study was to investigate the relation of nasopharyngeal microbiota and other microbiological parameters with respiratory health and disease, and to assess nasopharyngeal microbiota diagnostic utility for discriminating between different respiratory health statuses. We conducted a prospective case-control study at Hospital Sant Joan de Deu (Barcelona, Spain) from 2014 to 2018. This study included three groups of children <18 years with gradual decrease of ARI severity: cases with invasive pneumococcal disease (IPD) (representative of lower respiratory tract infections and systemic infections), symptomatic controls with mild viral upper respiratory tract infections (URTI), and healthy/asymptomatic controls according to an approximate case-control ratio 1:2. Nasopharyngeal samples were collected from participants for detection, quantification and serotyping of pneumococcal DNA, viral DNA/RNA detection and 16S rRNA gene sequencing. Microbiological parameters were included on case-control classification models. A total of 140 subjects were recruited (IPD=27, URTI=48, healthy/asymptomatic control=65). Children's nasopharyngeal microbiota composition varied according to respiratory health status and infection severity. The IPD group was characterized by overrepresentation of Streptococcus pneumoniae, higher frequency of invasive pneumococcal serotypes, increased rate of viral infection and underrepresentation of potential protective bacterial species such as Dolosigranulum pigrum and Moraxella lincolnii. Microbiota-based classification models differentiated cases from controls with moderately high accuracy. These results demonstrate the close relationship existing between a child's nasopharyngeal microbiota and respiratory health, and provide initial evidence of the potential of microbiota-based diagnostics for differential diagnosis of severe ARIs using non-invasive samples.

Comprehensive Description of Pathogens and Antibiotic Treatment Guidance in Children With Community-Acquired Pneumonia Using Combined Mass Spectrometry Methods

The objective of this study was to evaluate the value of molecular methods in the management of community-acquired pneumonia (CAP) in children. Previously developed mass spectrometry (MS)-based methods combined with quantitative real-time PCR (combined-MS methods) were used to describe the aetiology and evaluate antibiotic therapy in the enrolled children. Sputum collected from 302 children hospitalized with CAP were analyzed using the combined-MS methods, which can detect 19 viruses and 12 bacteria related to CAP. Based on the results, appropriate antibiotics were determined using national guidelines and compared with the initial empirical therapies. Respiratory pathogens were identified in 84.4% of the patients (255/302). Co-infection was the predominant infection pattern (51.7%, 156/302) and was primarily a bacterial-viral mixed infection (36.8%, 111/302). Compared with that using culture-based methods, the identification rate for bacteria using the combined-MS methods (61.8%, 126/204) increased by 28.5% (p <0.001). Based on the results of the combined-MS methods, the initial antibiotic treatment of 235 patients was not optimal, which mostly required switching to β-lactam/β-lactamase inhibitor combinations or reducing unnecessary macrolide treatments. Moreover, using the combined-MS methods to guide antibiotic therapy showed potential to decrease the length of stay in children with severe CAP. For children with CAP, quantitative molecular testing on sputum can serve as an important complement to traditional culture methods. Early aetiology elucidated using molecular testing can help guide the antibiotic therapy.

Recommendations on off-label use of intravenous azithromycin in children

OBJECTIVE

Intravenous azithromycin (AZM) has been widely used in children worldwide, but there still remains much concern regarding its off-label use, which urgently needs to be regulated. Therefore, we developed a rapid advice guideline in China to give recommendations of rational use of intravenous AZM in children.

METHODS

This guideline focuses on antimicrobial therapy with intravenous AZM in children. The Delphi research method was used to select questions. A systematic literature review was also conducted. Data were pooled and ranked according to the GRADE system. Recommendations were developed based on expert clinical experience, patients' values and preferences, and evidence availability. After an external review, the recommendations were revised and approved.

RESULTS

This guideline included eighteen recommendations that covered four domains: (a) Indications: the treatment of pneumonia caused by atypical but common pathogens, such as Mycoplasma pneumoniae, Chlamydia trachomatis or Chlamydophila pneumoniae and Legionella pneumophila, more typical bacteria as well as the treatment of bronchitis of presumed bacterial aetiologies; (b) Usage and dosage: administration route, infusion concentrations, treatment duration, course of sequential treatment, and dosage stratified by age; (c) Adverse reactions and treatment: the management of gastrointestinal reactions, arrhythmias, pain or phlebitis at the infusion site, and anaphylaxis; and (d) Special population: children with renal or liver dysfunction, congenital heart disease, and obesity. This guideline will hopefully help promote a rational use of intravenous AZM in children worldwide.

CONCLUSION

This guideline has summarised the evidence and has developed recommendations on the use of intravenous AZM in children worldwide. Further attention and well-designed researches should be conducted on the off-label use of intravenous AZM in children.

Mycoplasma pneumoniae may cause dyspnoea and hospitalisations in young healthy adults

Polymerase chain reaction (PCR)-based diagnostics for Mycoplasma pneumoniae (M. pneumoniae) from the respiratory tract has become widely available, but the interpretation of the results remains unclear. M. pneumoniae has been suggested to cause mainly mild and self-limiting infections or asymptomatic carriage. However, systematic analyses of the association between PCR results and clinical findings are scarce. This study aimed to clarify the clinical features of PCR-positive M. pneumoniae infections in a hospital setting. We reviewed 103 PCR-positive patients cared for in a university hospital during a 3-year period. Data on age, sex, health condition, acute symptoms, other pathogens found, laboratory and X-ray results and treatments were collected. Over 85% of the patients had a triad of typical symptoms: fever, cough and shortness of breath. Symptoms in the upper respiratory tract were rare. In 91% of the cases, M. pneumoniae was the only pathogen found. The highest incidence was found in the age group of 30–40 years, and 68% of the patients did not have any underlying diseases. Most patients were initially empirically treated with beta-lactam antibiotics and needed 2–4 changes in their treatment. Only 6% were discharged without an antibiotic effective against M. pneumoniae. This study shows that M. pneumoniae often led to hospitalisation and that patients needed appropriate antimicrobial treatment to recover. Mixed infections were rare, and situations that could be interpreted as carriage did not occur.

[Virological diagnosis of lower respiratory tract infections]

INTRODUCTION

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

BACKGROUND

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

OUTLOOK

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

CONCLUSIONS

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

Diagnosis of Community-acquired Pneumonia in Hospitalized Children: A Multicenter Experience in Bolivia

BACKGROUND

Community-acquired pneumonia (CAP) represents a major cause of hospitalization, especially among young children. In the third world countries, information about CAP etiology is scarce. Therefore, rapid and highly sensitive diagnostic methods are crucial to determine etiologic agents.

METHODS

Between March 2016 and March 2017, we have prospectively studied the clinical, radiologic, laboratory, and molecular aspects of patients with CAP at 2 tertiary-level hospitals in Santa Cruz de la Sierra, using a multiplex real-time polymerase chain reaction (RT-PCR).

RESULTS

A total of 274 children were evaluated, with a median age of 13 months. An etiologic agent was identified in 187 patients (68.2%): 54% (n = 148) were viruses and 14.2% (n = 39) were bacteria. CAP prevalence was highest among children under 2 years (71%; 195/274); respiratory syncytial virus (RSV) was the most frequent cause in 22% (60/274), especially among infants, followed by influenza (14.5%; 40/274). Streptococcus pneumoniae accounted for 7% of the total (19/274), followed by Staphylococcus aureus (3%;8/274) and Haemophilus influenzae (1.4%;4/274). Together, these cases accounted for 79.5% (31/39) of all bacterial CAP. Pleural effusion (PE) complicated CAP in 13.8% (38/274), of which 29 were of bacterial etiology. RT-PCR increased the detection rate of pneumococcus by 47%. Coinfection occurred in 28 patients (10%); 26 (9.5%) required intensive care and 9 patients (3%) died.

CONCLUSIONS

RT-PCR provided additional diagnostic value to conventional, clinical, and laboratory methods. The higher prevalence of RSV, influenza, and Streptococcus pneumoniae reveals the need for preventive measures with better vaccine uptake and future research for RSV vaccines.

A New Phage Lysin Isolated from the Oral Microbiome Targeting Streptococcus pneumoniae

Streptococcus pneumoniae is highly pathogenic and causes several mucosal and invasive infections. Due to the rising number of multidrug-resistant (MDR) strains of S. pneumoniae, new antimicrobials with alternative mechanisms of action are urgently needed. In this study, we identified two new Streptococcal phages from the oral microbiome, 23TH and SA01. Their lysins, 23TH_48 and SA01_53, were recombinantly expressed, characterized and tested for their lethality. SA01_53 was found to only lyse its host strain of S. anginosus, while 23TH_48 was found to possess a broader lytic activity beyond its host strain of S. infantis, with several S. pneumoniae isolates sensitive to its lytic activity. 23TH_48 at a concentration of five activity units per mL (U/mL) was found to reduce cell counts of S. pneumoniae DSM 24048 by 4 log₁₀ colony forming units per mL (CFU/mL) within 1 h and effectively prevented and destroyed biofilms of S. pneumoniae R6 at concentrations of 228.8 ng/µL and 14.3 ng/µL, respectively. Given its high lytic activity, 23TH_48 could prove to be a promising candidate to help combat pneumococcal infections.

Antibiotic modification versus withhold in febrile patients without evidence of bacterial infection, unresponsive to initial empiric regimen: a multicentre retrospective study conducted in Israel

Prescribing antibiotics for febrile patients without proof of bacterial infection contributes to antimicrobial resistance. Lack of clinical response in these patients often leads to antibiotic escalation, although data supporting this strategy are scarce. This study compared outcomes of modifying, withholding, or continuing the same antibiotic regimen for such patients. Febrile or hypothermic stable patients with suspected infection, unresponsive to empiric antibiotic treatment, admitted to one of 15 internal medicine departments in three hospitals during a 5-year study period, were included. Patients with a definitive clinical or microbiological bacterial infection, malignancy, immunodeficiency, altered mental status, or need for mechanical ventilation were excluded. Participants were divided into groups based on treatment strategy determined 72 h after antibiotic initiation: antibiotic modified, withheld or continued. Outcomes measured included in-hospital and 30-day post-discharge-mortality rates, length of hospital stay (LOS) and days of antimicrobial therapy (DOT). A total of 486 patients met the inclusion criteria: 124 in the Antibiotic modified group, 67 in the Antibiotic withheld group and 295 in the Initial antibiotic continued group. Patient characteristics were similar among groups with no differences in mortality rates in-hospital (23% vs. 25% vs. 20%, p = 0.58) and within 30 days after discharge (5% vs. 3% vs. 4%, p = 0.83). Changing antibiotics led to longer LOS (9.0 ± 6.8 vs. 6.2 ± 5.6 days, p = 0.003) and more DOT (8.6 ± 6.0 vs. 3.2 ± 1.0 days, p < 0.001) compared to withholding treatment. Withholding as compared to modifying antibiotics, in febrile patients with no clear evidence of bacterial infection, is a safe strategy associated with decreased LOS and DOT.

Searching for Antipneumococcal Targets: Choline-Binding Modules as Phagocytosis Enhancers

Choline-binding proteins (CBPs) from Streptococcus pneumoniae comprise a family of modular polypeptides involved in essential events of this pathogen. They recognize the choline residues present in the teichoic and lipoteichoic acids of the cell wall using the so-called choline-binding modules (CBMs). The importance of CBPs in pneumococcal physiology points to them as novel targets to combat antimicrobial resistances shown by this organism. In this work we have tested the ability of exogenously added CBMs to act as CBP inhibitors by competing with the latter for the binding to the choline molecules in the bacterial surface. First, we carried out a thorough physicochemical characterization of three native CBMs, namely C-LytA, C-Cpl1, and C-CbpD, and assessed their affinity for choline and macromolecular, pneumococcal cell-wall mimics. The interaction with these substrates was evaluated by molecular modeling, analytical ultracentrifugation, surface plasmon resonance, and fluorescence and circular dichroism spectroscopies. Van't Hoff thermal analyses unveiled the existence of one noncanonical choline binding site in each of the C-Cpl1 and C-CbpD proteins, leading in total to 5 ligand-binding sites per dimer and 4 sites per monomer, respectively. Remarkably, the binding affinities of the CBMs do not directly correlate with their native oligomeric state or with the number of choline-binding sites, suggesting that choline recognition by these modules is a complex phenomenon. On the other hand, the exogenous addition of CBMs to pneumococcal planktonic cultures caused extensive cell-chaining probably as a consequence of the inhibition of CBP attachment to the cell wall. This was accompanied by bacterial aggregation and sedimentation, causing an enhancement of bacterial phagocytosis by peritoneal macrophages. In addition, the rational design of an oligomeric variant of a native CBM led to a substantial increase in its antibacterial activity by multivalency effects. These results suggest that CBMs might constitute promising nonlytic antimicrobial candidates based on the natural induction of the host defense system.

Bacterial pneumonia and its associated factors in children from a developing country: A prospective cohort study

Introduction

Pneumonia in children is a common disease yet determining its aetiology remains elusive.

Objectives

To determine the a) aetiology, b) factors associated with bacterial pneumonia and c) association between co-infections (bacteria + virus) and severity of disease, in children admitted with severe pneumonia.

Methods

A prospective cohort study involving children aged 1-month to 5-years admitted with very severe pneumonia, as per the WHO definition, over 2 years. Induced sputum and blood obtained within 24 hrs of admission were examined via PCR, immunofluorescence and culture to detect 17 bacteria/viruses. A designated radiologist read the chest radiographs.

Results

Three hundred patients with a mean (SD) age of 14 (±15) months old were recruited. Significant pathogens were detected in 62% of patients (n = 186). Viruses alone were detected in 23.7% (n = 71) with rhinovirus (31%), human metapneumovirus (HMP) [22.5%] and respiratory syncytial virus (RSV) [16.9%] being the commonest. Bacteria alone was detected in 25% (n = 75) with Haemophilus influenzae (29.3%), Staphylococcus aureus (24%) and Streptococcus pneumoniae (22.7%) being the commonest. Co-infections were seen in 13.3% (n = 40) of patients. Male gender (AdjOR 1.84 [95% CI 1.10, 3.05]) and presence of crepitations (AdjOR 2.27 [95% CI 1.12, 4.60]) were associated with bacterial infection. C-reactive protein (CRP) [p = 0.007]) was significantly higher in patients with co-infections but duration of hospitalization (p = 0.77) and requirement for supplemental respiratory support (p = 0.26) were not associated with co-infection.

Conclusions

Bacteria remain an important cause of very severe pneumonia in developing countries with one in four children admitted isolating bacteria alone. Male gender and presence of crepitations were significantly associated with bacterial aetiology. Co-infection was associated with a higher CRP but no other parameters of severe clinical illness.

Comparative Clinical Evaluation of NeoPlex RB-8 with Seeplex PneumoBacter ACE for Simultaneous Detection of Eight Respiratory Bacterial Pathogens

There are several convenient and accurate molecular assays to detect respiratory bacterial infection. The NeoPlex RB-8 detection kit (NeoPlex RB-8) is a new multiplex real-time PCR assay that simultaneously detects Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, Haemophilus influenzae, Bordetella pertussis, Bordetella parapertussis, and Moraxella catarrhalis in a single test. This study compared the clinical concordance of NeoPlex RB-8 with another method, Seeplex PneumoBacter ACE detection assay (Seeplex PB ACE), which simultaneously detects S. pneumoniae, M. pneumoniae, C. pneumoniae, L. pneumophila, H. influenzae, and B. pertussis We tested 2,137 nasopharyngeal swab and sputum specimens using both assays. For discordant Bordetella parapertussis and M. catarrhalis specimens, we also performed bidirectional sequencing. For S. pneumoniae, M. pneumoniae, C. pneumoniae, L. pneumophila, H. influenzae, and B. pertussis, which are detected by both NeoPlex RB-8 and Seeplex PB ACE, the positive and negative agreement between the two assays ranged from 91.7 to 100% (κ = 0.918 to 1). S. pneumoniae and H. influenzae were the most discordant targets and measured with higher sensitivity and specificity by NeoPlex RB-8 than Seeplex PB ACE. For Bordetella parapertussis and M. catarrhalis, which are not detected by Seeplex PB ACE, NeoPlex RB-8 sensitivity and specificity were >99%. Overall, NeoPlex RB-8 was highly comparable to Seeplex PB ACE, but NeoPlex RB-8 was more clinically accurate, with higher throughput and more convenience.

Blood biomarkers differentiating viral versus bacterial pneumonia aetiology: a literature review

Background and objectives

The goal of this literature review is to compare current studies regarding the accuracy of different serum markers in differentiating viral from bacterial pneumonia in the pediatric population with what is employed in the medical settings at present. Currently there is still a lack of significant research, that would give us evaluation on biomarkers benefits towards getting a definite diagnosis of pneumonia. Finding out the potential of biomarkers to differentiate between viral and bacterial pneumonia is also important because knowing the exact pathogen would prevent irrational use of antibiotics. At present, irrational, broad-spectrum antibiotic use and increasing antibiotic resistance in microorganisms are still one of the greatest challenges in clinical settings. The use of biomarkers in clinical practice would not only facilitate accurate diagnosis, but would also help to reduce the amount of antibiotics overuse.

Materials and methods

Literature search conducted on Medline and Google Scholar using a combination of terms. Articles that were in English and within ten years of the search date were manually sorted according to inclusion and exclusion criteria. Results: Initial search returned n = 13,408. After activating filters, n = 140 were identified of which n = 12 included for literature review.

Conclusions

Rise or drop in the concentration of a single marker is not accurate enough for predicting viral/bacterial community acquired pneumonia. This is because there is overlapping to a varying extent depending on the marker cut-off values, detection methods, analyses, the desired specificity, and sensitivity. Furthermore, the presence of mixed infection makes almost all markers suboptimal to be used universally. New markers such as MxA1 and HMGB1 gave promising results. However, to replicate a similar testing condition in a clinical environment may not be practical. Another approach is to make use of more than one marker and combine with clinical signs and symptoms. This may not be cost-effective in many clinical settings; nevertheless, in many studies, marker combination greatly improved the predictive power.

FebriDx®: A Rapid Diagnostic Test for Differentiating Bacterial and Viral Aetiologies in Acute Respiratory Infections

FebriDx® is a rapid, point-of-care diagnostic test that is designed to aid in the differentiation of bacterial and viral acute respiratory infections (ARIs), thus helping to guide decisions regarding the prescription of antibiotics in the outpatient setting. FebriDx carries a CE mark for use in the EU and is also approved in several other countries, including Canada, Saudi Arabia and Singapore. It is indicated for use in patients > 2 years old with symptoms consistent with a community-acquired ARI. The test involves the use of an immunoassay on a fingerstick blood sample to provide simultaneous, qualitative measurement of elevated levels of C-reactive protein (CRP) and myxovirus resistance protein A (MxA). In two prospective, multicentre studies in patients with acute upper respiratory tract infections, FebriDx was shown to be both sensitive and specific in identifying patients with a clinically significant infection and in differentiating between infections of bacterial and viral aetiology. The test is simple, requires no additional equipment and produces actionable results in ~ 10 min. As was demonstrated in a small, retrospective analysis, FebriDx results can help guide (improve) antibiotic prescribing decisions. Reducing the unnecessary or inappropriate prescription of antibiotics for ARIs of probable viral aetiology is important for antibiotic stewardship and can also reduce the unnecessary exposure of patients to the risk of antibiotic-related adverse events. FebriDx thus represents a useful diagnostic tool in the outpatient setting.

The Usefulness of Lung Ultrasound for the Aetiological Diagnosis of Community-Acquired Pneumonia in Children

The aetiology of community-acquired pneumonia (CAP) is not easy to establish. As lung ultrasound (LUS) has already proved to be an excellent diagnostic tool for CAP, we analysed its usefulness for discriminating between the aetiologically different types of CAP in children. We included 147 children hospitalized because of CAP. LUS was performed in all patients at admission, and follow-up LUS was performed in most patients. LUS-detected consolidations in viral CAP were significantly smaller, with a median diameter of 15 mm, compared to 20 mm in atypical bacterial CAP (p = 0.05) and 30 mm in bacterial CAP (p < 0.001). Multiple consolidations were detected in 65.4% of patients with viral CAP and in 17.3% of patients with bacterial CAP (p < 0.001). Bilateral consolidations were also more common in viral CAP than in bacterial CAP (51.9% vs. 8.0%, p < 0.001). At follow-up, a regression of consolidations was observed in 96.6% of patients with bacterial CAP and in 33.3% of patients with viral CAP (p < 0.001). We found LUS to be especially suitable for differentiating bacterial CAP from CAP due to other aetiologies. However, LUS must be interpreted in light of clinical and laboratory findings.

Synergy Between Two Chimeric Lysins to Kill Streptococcus pneumoniae

Phage lysins constitute a new generation of antimicrobials that are becoming a promising alternative and complementation to current antibiotic therapies, which are nowadays called into question by the increasing numbers of multiresistant bacteria. Streptococcus pneumoniae is a leading human pathogen causing serious infectious diseases in children and adults. Within the host-parasite interplay system of pneumococcus and its phages, several antipneumococcal lysins have been described and, among them, chimeric lysins Cpl-711 and PL3 stand out for their potent bactericidal activities. Here, evidence is presented on the synergistic cooperation of the catalytically diverse lysins Cpl-711 and PL3 in different assays, like purified cell wall enzymatic degradation, in vitro bacterial cell growth inhibition, and killing of both planktonic and biofilm grown cells. Synergy between Cpl-711 and PL3 has been shown to reduce the amount of enzyme necessary to inhibit growth in checkerboard assays with a sum of fractional inhibitory concentrations ≤0.5 for all pneumococcal strains tested, while also significatively increasing bactericidal effect by ≥2 logs with respect to the sum of activities of Cpl-711 and PL3 individual treatments. Moreover, the combination of these two lysins showed synergy in an adult zebrafish model of pneumococcal infection. This study consolidates the possibility of formulating highly efficient and synergistic antibacterial enzymes that could improve our ability to fight multiresistant bacterial infections.

Aetiology and risks factors associated with the fatal outcomes of childhood pneumonia among hospitalised children in the Philippines from 2008 to 2016: a case series study

OBJECTIVE

Pneumonia remains the leading cause of hospitalisations and deaths among children aged <5 years. Diverse respiratory pathogens cause acute respiratory infections, including pneumonia. Here, we analysed viral and bacterial pathogens and risk factors associated with death of hospitalised children.

DESIGN

A 9-year case series study.

SETTING

Two secondary-care hospitals, one tertiary-care hospital and one research centre in the Philippines.

PARTICIPANTS

5054 children aged <5 years hospitalised with severe pneumonia.

METHODS

Nasopharyngeal swabs for virus identification, and venous blood samples for bacterial culture were collected. Demographic, clinical data and laboratory findings were collected at admission time. Logistic regression analyses were performed to identify the factors associated with death.

RESULTS

Of the enrolled patients, 57% (2876/5054) were males. The case fatality rate was 4.7% (238/5054), showing a decreasing trend during the study period (p<0.001). 55.0% of the patients who died were either moderately or severely underweight. Viruses were detected in 61.0% of the patients, with respiratory syncytial virus (27.0%) and rhinovirus (23.0%) being the most commonly detected viruses. In children aged 2-59 months, the risk factors significantly associated with death included age of 2-5 months, sensorial changes, severe malnutrition, grunting, central cyanosis, decreased breath sounds, tachypnoea, fever (≥38.5°C), saturation of peripheral oxygen <90%, infiltration, consolidation and pleural effusion on chest radiograph.Among the pathogens, adenovirus type 7, seasonal influenza A (H1N1) and positive blood culture for bacteria were significantly associated with death. Similar patterns were observed between the death cases and the aforementioned factors in children aged <2 months.

CONCLUSION

Malnutrition was the most common factor associated with death and addressing this issue may decrease the case fatality rate. In addition, chest radiographic examination and oxygen saturation measurement should be promoted in all hospitalised patients with pneumonia as well as bacteria detection to identify patients who are at risk of death.

Improving vaccines against Streptococcus pneumoniae using synthetic glycans

Streptococcus pneumoniae remains a deadly disease in small children and the elderly even though conjugate and polysaccharide vaccines based on isolated capsular polysaccharides (CPS) are successful. The most common serotypes that cause infection are used in vaccines around the world, but differences in geographic and demographic serotype distribution compromises protection by leading vaccines. The medicinal chemistry approach to glycoconjugate vaccine development has helped to improve the stability and immunogenicity of synthetic vaccine candidates for several serotypes leading to the induction of higher levels of specific protective antibodies. Here, we show that marketed CPS-based glycoconjugate vaccines can be improved by adding synthetic glycoconjugates representing serotypes that are not covered by existing vaccines. Combination (coformulation) of synthetic glycoconjugates with the licensed vaccines Prevnar13 (13-valent) and Synflorix (10-valent) yields improved 15- and 13-valent conjugate vaccines, respectively, in rabbits. A pentavalent semisynthetic glycoconjugate vaccine containing five serotype antigens (sPCV5) elicits antibodies with strong in vitro opsonophagocytic activity. This study illustrates that synthetic oligosaccharides can be used in coformulation with both isolated polysaccharide glycoconjugates to expand protection from existing vaccines and each other to produce precisely defined multivalent conjugated vaccines.

Phage Lysins for Fighting Bacterial Respiratory Infections: A New Generation of Antimicrobials

Lower respiratory tract infections and tuberculosis are responsible for the death of about 4.5 million people each year and are the main causes of mortality in children under 5 years of age. Streptococcus pneumoniae is the most common bacterial pathogen associated with severe pneumonia, although other Gram-positive and Gram-negative bacteria are involved in respiratory infections as well. The ability of these pathogens to persist and produce infection under the appropriate conditions is also associated with their capacity to form biofilms in the respiratory mucous membranes. Adding to the difficulty of treating biofilm-forming bacteria with antibiotics, many of these strains are becoming multidrug resistant, and thus the alternative therapeutics available for combating this kind of infections are rapidly depleting. Given these concerns, it is urgent to consider other unconventional strategies and, in this regard, phage lysins represent an attractive resource to circumvent some of the current issues in infection treatment. When added exogenously, lysins break specific bonds of the peptidoglycan and have potent bactericidal effects against susceptible bacteria. These enzymes possess interesting features, including that they do not trigger an adverse immune response and raise of resistance is very unlikely. Although Gram-negative bacteria had been considered refractory to these compounds, strategies to overcome this drawback have been developed recently. In this review we describe the most relevant in vitro and in vivo results obtained to date with lysins against bacterial respiratory pathogens.