Etiology of severe childhood pneumonia in the Gambia, West Africa, determined by conventional and molecular microbiological analyses of lung and pleural aspirate samples

Diagnosis and Prognosis Evaluation of Severe Pneumonia by Lung Ultrasound Score Combined with Serum Inflammatory Markers

Introduction

To analyze the significance of lung ultrasound score (LUS) combined with serum inflammatory indexes in different severities of severe pneumonia and its clinical value on prognosis.

Methods

100 patients with severe pneumonia treated in the Gansu Provincial Hospital from June 2017 to June 2021 were selected as the research objects. According to the acute physiology and chronic health (APACHE II) score, they were divided into a low-risk group (28 cases), a medium-risk group (39 cases) and a high-risk group (33 cases). The general clinical data of the patients (age, gender, smoking history, and underlying diseases) were collected, the lung ultrasound score (LUS) of the patients was measured, and the serum inflammatory indicators (IL-6, IL-10, TNF-α, CRP and NLR) levels; Pearson correlation analysis to evaluate the correlation between LUS score, serum inflammatory index levels and disease severity; receiver operating characteristic (ROC) curve analysis to evaluate the prognostic value of the combined diagnosis of LUS score and serum inflammatory index for the severity of severe pneumonia.

Results

With the increase in the severity of severe pneumonia, the LUS score and the level of inflammation in the body continued to increase, and LUS combined with serum inflammatory indexes could distinguish the severity of low-risk, medium-risk and high-risk severe pneumonia and had high diagnostic value. In addition, the combined diagnosis of LUS and serum inflammatory markers is also closely related to the prognosis of patients with severe pneumonia, which can distinguish the prognosis.

Conclusion

LUS combined with serum inflammatory indicators (IL-6, IL-10, TNF-α, CRP and NLR) can differentiate the severity and prognosis of severe pneumonia, which may be a new direction for diagnosing severe pneumonia and guide early clinical intervention.

Preterm birth and detection of common respiratory pathogens among pediatric pneumonia

Pneumonia complicated by preterm birth is related to adverse clinical sequelae from the neonatal period to childhood. Children with pneumonia during 2009-2021 were enrolled at the Children's Hospital of Chongqing Medical University. Altogether 20 respiratory pathogens were detected and compared. Among 8,206 children, 779 were in the preterm group with 246 of early-preterm and 533 of late preterm. The positive rates for all viral pathogens were comparable between the preterm group and the full-term group. For bacterial pathogens, higher positive rates for Escherichia coli and Klebsiella pneumoniae were observed in the preterm group. Severe pneumonia developed in 16.52% of all, which was higher in the preterm group than in the full-term group. A significantly higher rate of severe pneumonia was observed in the early-preterm group compared to the late-preterm group. Preterm birth has an impact on the detection of bacterial pathogens in children and is a risk factor for severe pneumonia.

Prevalence of atypical pathogens in patients with severe pneumonia: a systematic review and meta-analysis

OBJECTIVES

We aimed to summarise the prevalence of atypical pathogens in patients with severe pneumonia to understand the prevalence of severe pneumonia caused by atypical pathogens, improve clinical decision-making and guide antibiotic use.

DESIGN

Systematic review and meta-analysis.

DATA SOURCES

PubMed, Embase, Web of Science and Cochrane Library were searched through November 2022.

ELIGIBILITY CRITERIA

English language studies enrolled consecutive cases of patients diagnosed with severe pneumonia, with complete aetiological analysis.

DATA EXTRACTION AND SYNTHESIS

We conducted literature retrieval on PubMed, Embase, Web of Science and The Cochrane Library to estimate the prevalence of Chlamydia, Mycoplasma and Legionella in patients with severe pneumonia. After double arcsine transformation of the data, a random-effects model was used for meta-analyses to calculate the pooled prevalence of each pathogen. Meta-regression analysis was also used to explore whether the region, different diagnostic method, study population, pneumonia categories or sample size were potential sources of heterogeneity.

RESULTS

We included 75 eligible studies with 18 379 cases of severe pneumonia. The overall prevalence of atypical pneumonia is 8.1% (95% CI 6.3% to 10.1%) In patients with severe pneumonia, the pooled estimated prevalence of Chlamydia, Mycoplasma and Legionella was 1.8% (95% CI 1.0% to 2.9%), 2.8% (95% CI 1.7% to 4.3%) and 4.0% (95% CI 2.8% to 5.3%), respectively. We noted significant heterogeneity in all pooled assessments. Meta-regression showed that the pneumonia category potentially influenced the prevalence rate of Chlamydia. The mean age and the diagnostic method of pathogens were likely moderators for the prevalence of Mycoplasma and Legionella, and contribute to the heterogeneity of their prevalence.

CONCLUSIONS

In severe pneumonia, atypical pathogens are notable causes, especially Legionella. The diagnostic method, regional difference, sample size and other factors contribute to the heterogeneity of prevalence. The estimated prevalence and relative heterogeneity factors can help with microbiological screening, clinical treatment and future research planning.

PROSPERO REGISTRATION NUMBER

CRD42022373950.

16S rRNA gene sequencing reveals an altered composition of gut microbiota in children with Mycoplasma pneumoniae pneumonia treated with azithromycin

Mycoplasma pneumoniae is one of the most important pathogens causing community acquired pneumonia in children, and the pathogenic mechanism of M. pneumoniae infection is complex. Azithromycin is an effective agent for treating the acquired lower respiratory tract infection and urogenital tract infection with slight adverse reactions. This study aimed to compare the intestinal microflora before (PP1) and after azithromycin intervention (PP2) in children with pneumonia caused by M. pneumoniae, combined with body fluid biochemical analysis to determine the intestinal flora affecting the progress of the disease. Fifteen children diagnosed with M. pneumoniae pneumonia were recruited. The fecal samples and clinical biochemical data were collected. 16S rRNA gene amplicon sequencing and bioinformatics analysis were conducted by the Beijing Genomics Institute. The operational taxonomic unit abundance analysis showed significant differences between the two groups. The species richness analysis showed differences in class, family, genus, order, species, and phylum. The abundance of Haemophilus, Pasteurellales, and Pasteurellaceae was found to be significantly higher in the PP1 group. The Pearson correlation analysis showed that the microbes strongly correlated with the clinical features. 16S rRNA gene sequencing data revealed altered composition of gut microbiota in children with M. pneumoniae pneumonia treated with azithromycin. The altered expression of microbes correlated with clinical features, which might help diagnose and treat the disease.

Human bocavirus-1 infections in Australian children aged < 2 years: a birth cohort study

To determine human bocavirus-1 (HBoV1) infection characteristics in young Australian children. Data were from the Observational Research in Childhood Infectious Diseases (ORChID) study, a Brisbane, Australia-based birth cohort of healthy, term, newborns followed prospectively for 2 years. Parents recorded daily symptoms, maintained an illness-burden diary, and collected weekly nasal swabs, which were tested for 17 respiratory viruses, including HBoV1, by real-time polymerase chain reaction (PCR) assays. Main outcomes measured were infection incidence, risk factors, symptoms, and healthcare use. One hundred fifty-eight children in the ORChID cohort provided 11,126 weekly swabs, of which 157 swabs were HBoV1 positive involving 107 incident episodes. Co-detections were observed in 65/157 (41.4%) HBoV1-positive swabs (or 41/107 [38.3%] infection episodes), principally with rhinovirus. Shedding duration was 1 week in 64.5% of episodes. The incidence of HBoV1 infections in the first 2 years of life was 0.58 episodes per child-year (95% confidence interval [CI] 0.47-0.71), including 0.38 episodes per child-year (95% CI 0.30-0.49) associated with respiratory symptoms. Recurrent episodes occurred in 18/87 (20.7%) children following their primary infection. In the first 2 years of life, incidence of HBoV1 episodes increased with age, during winter and with childcare attendance. Overall, 64.2% of HBoV1 episodes were symptomatic, with 26.4% having healthcare contact. Viral load estimates were higher when children were symptomatic than when asymptomatic (mean difference = 3.4; 95% CI 1.0-5.7 PCR cycle threshold units). After age 6 months, HBoV1 is detected frequently in the first 2 years of life, especially during winter. Symptoms are usually mild and associated with higher viral loads.

The dilemma of improving rational antibiotic use in pediatric community-acquired pneumonia

Pneumonia is the number one cause of disease and deaths in children under five years old, outside the neonatal period, with the greatest number of cases reported from resource-limited settings. The etiology is variable, with not much information on the local etiology drug resistance profile in many countries. Recent studies suggest an increasing contribution from respiratory viruses, also in children with severe pneumonia, with an increased relative contribution in settings that have good vaccine coverage against common bacterial pathogens. Respiratory virus circulation was greatly reduced during highly restrictive measures to contain the spread of COVID-19 but rebounded once COVID-19 restrictions were relaxed. We conducted a comprehensive literature review of the disease burden, pathogens, case management and current available prevention of community acquired childhood pneumonia, with a focus on rational antibiotic use, since the treatment of respiratory infections is the leading cause of antibiotic use in children. Consistent application of revised World Health Organisation (WHO) guidance that children presenting with coryzal symptoms or wheeze can be managed without antibiotics in the absence of fever, will help to reduce unnecessary antibiotic use, as will increased availability and use of bedside inflammatory marker tests, such as C-reactive protein (CRP) in children with respiratory symptoms and fever.

Systematic review and meta-analysis on the etiology of bacterial pneumonia in children in sub-Saharan Africa

Introduction

Before the introduction of vaccination to protect children from pneumonia, Streptococcus pneumoniae and Haemophilus influenzae type B (HiB) were the most frequent aetiological agents causing bacterial pneumonia in children under five years old. However, the etiology of childhood pneumonia appears to be changing and nonvaccine- type S. pneumoniae, non-typeable H. influenzae, and Staphylococcus aureus are becoming more relevant.

Objective

We conducted a systematic review aimed at identifying the common causes of bacterial pneumonia in children in sub-Saharan Africa.

Methods

We searched PubMed, Web of Science and African Index Medicus and included primary studies conducted since January 2010 that reported on the bacterial causes of pneumonia in children under five from sub-Saharan Africa. We extracted data items (about the study setting, pneumonia diagnosis, sampling, microbiological methods, and etiological agents) as well as study quality indicators.

Results

Streptococcus pneumoniae was the most common bacteria in blood cultures from children with pneumonia (8%, 95% CI: 4-14%), and H. influenzae was second (3%, 95% CI: 1-17%). Children’s nasopharynx commonly contained S. pneumoniae (66%), Moraxella catarrhalis (62%), and H. influenzae (44%).

Conclusion

S. pneumoniae and H. influenzae cause bacterial pneumonia in sub-Saharan African children. Our review also highlights the prevalence of potentially pathogenic bacteria in the nasopharynx of children under five and calls for more research into how nasopharyngeal colonization causes pneumonia.

Aetiology of childhood pneumonia in low- and middle-income countries in the era of vaccination: a systematic review

Background

This systematic review aimed to describe common aetiologies of severe and non-severe community acquired pneumonia among children aged 1 month to 9 years in low- and middle-income countries.

Methods

We searched the MEDLINE, EMBASE, and PubMed online databases for studies published from January 2010 to August 30, 2020. We included studies on acute community-acquired pneumonia or acute lower respiratory tract infection with ≥1 year of continuous data collection; clear consistent case definition for pneumonia; >1 specimen type (except empyema studies where only pleural fluid was required); testing for >1 pathogen including both viruses and bacteria. Two researchers reviewed the studies independently. Results were presented as a narrative summary. Quality of evidence was assessed with the Quality Assessment Tool for Quantitative Studies. The study was registered on PROSPERO [CRD42020206830].

Results

We screened 5184 records; 1305 duplicates were removed. The remaining 3879 titles and abstracts were screened. Of these, 557 articles were identified for full-text review, and 55 met the inclusion criteria - 10 case-control studies, three post-mortem studies, 11 surveillance studies, eight cohort studies, five cross-sectional studies, 12 studies with another design and six studies that included patients with pleural effusions or empyema. Studies which described disease by severity showed higher bacterial detection (Streptococcus pneumoniae, Staphylococcus aureus) in severe vs non-severe cases. The most common virus causing severe disease was respiratory syncytial virus (RSV). Pathogens varied by age, with RSV and adenovirus more common in younger children. Influenza and atypical bacteria were more common in children 5-14 years than younger children. Malnourished and HIV-infected children had higher rates of pneumonia due to bacteria or tuberculosis.

Conclusions

Several viral and bacterial pathogens were identified as important targets for prevention and treatment. Bacterial pathogens remain an important cause of moderate to severe disease, particularly in children with comorbidities despite widespread PCV and Hib vaccination.

Childhood Pneumonia Diagnostics in Sub-Saharan Africa: A Systematic Review

BACKGROUND

The prompt and accurate aetiological diagnosis of childhood pneumonia remains a challenge, especially in sub-Saharan Africa (SSA) because of limited resources for disease management.

OBJECTIVE

To review existing diagnostics for childhood pneumonia and potential modalities available to differentiate between bacterial and viral aetiologies in SSA.

METHODS

Online databases were searched for relevant articles published between January 2010 and December 2020 regarding childhood pneumonia diagnosis, conducted in SSA in children less than 18 years of age. The 2020 PRISMA checklist was utilized in appraising the selected studies and the QUADAS-2 tool was employed to assess the risk of bias in each of the studies selected.

RESULTS

A total of 1542 study titles and abstracts were screened following which 45 studies (39 on childhood pneumonia diagnostics and 6 on discriminating between bacterial and viral childhood pneumonia) were selected for review. Microbiological investigations (79.7%) constituted the most utilized index tests with blood-related specimen (32.8%) being the most utilized specimen. The most performed index diagnostic modality was polymerase chain reaction (PCR) (53.1%). The commonest reference gold standard technique was based on clinical diagnosis of the disease (46.2%). Only six studies in SSA attempted at using serum biomarkers, either singly or in combination to distinguish between aetiologies with use of combined biomarkers showing promise.

CONCLUSION

Microbiological investigations are the most employed diagnostic methods for childhood pneumonia in SSA. More studies are required to evaluate the potential use of serum biomarkers; either singly or in combination with the goal of discriminating bacterial and viral childhood pneumonia.

Aetiology of lobar pneumonia determined by multiplex molecular analyses of lung and pleural aspirate specimens in the Gambia: findings from population-based pneumonia surveillance

OBJECTIVES

To determine the causes of lobar pneumonia in rural Gambia.

DESIGN AND SETTING

Population-based pneumonia surveillance at seven peripheral health facilities and two regional hospitals in rural Gambia. 7-valent pneumococcal conjugate vaccine (PCV7) was introduced routinely in August 2009 and replaced by PCV13 from May 2011.

METHODS

Prospective pneumonia surveillance was undertaken among all ages with referral of suspected pneumonia cases to the regional hospitals. Blood culture and chest radiographs were performed routinely while lung or pleural aspirates were collected from selected, clinically stable patients with pleural effusion on radiograph and/or large, dense, peripheral consolidation. We used conventional microbiology, and from 8 April 2011 to 17 July 2012, used a multiplex PCR assay on lung and pleural aspirates. We calculated proportions with pathogens, associations between coinfecting pathogens and PCV effectiveness.

PARTICIPANTS

2550 patients were admitted with clinical pneumonia; 741 with lobar pneumonia or pleural effusion. We performed 181 lung or pleural aspirates and multiplex PCR on 156 lung and 4 pleural aspirates.

RESULTS

Pathogens were detected in 116/160 specimens, the most common being Streptococcus pneumoniae(n=68), Staphylococcus aureus (n=26) and Haemophilus influenzae type b (n=11). Bacteria (n=97) were more common than viruses (n=49). Common viruses were bocavirus (n=11) and influenza (n=11). Coinfections were frequent (n=55). Moraxella catarrhalis was detected in eight patients and in every case there was coinfection with S. pneumoniae. The odds ratio of vaccine-type pneumococcal pneumonia in patients with two or three compared with zero doses of PCV was 0.17 (95% CI 0.06 to 0.51).

CONCLUSIONS

Lobar pneumonia in rural Gambia was caused primarily by bacteria, particularly S. pneumoniae and S. aureus. Coinfection was common and M. catarrhalis always coinfected with S. pneumoniae. PCV was highly efficacious against vaccine-type pneumococcal pneumonia.

The global burden of hospitalisation due to pneumonia caused by Staphylococcus aureus in the under-5 years children: A systematic review and meta-analysis

BACKGROUND

Pneumonia is a leading cause of childhood morbidity and mortality. This study aimed to estimate the global hospitalisation due to Staphylococcus aureus pneumonia in under-5 children.

METHODS

We conducted a systematic review and meta-analysis of primary studies following the PRISMA-P guidelines. We searched Medline, Embase, Global Health, CINAHL, Global Index Medicus, Scopus, China National Knowledge Infrastructure, Wanfang, and CQvip. We included studies reporting data on Staphylococcus aureus pneumonia, confirmed by detection of the pathogen in sterile-site samples in under-5 hospitalised children, published in English or Chinese language and conducted between 1st January 1990 and 4th November 2021 and between 1st January 1990 and 30th September 2020, respectively. We excluded those testing upper respiratory tract samples and not reporting data on samples with other bacteria or absence of bacteria. We screened papers against pre-specified criteria, extracted data and assessed the bacteriological quality, and combined epidemiological and microbiological quality of studies using two self-designed checklists. Pooled proportions of hospitalisation episodes for Staphylococcus aureus pneumonia amongst all-cause pneumonia and the 95% confidence intervals were calculated using the random-effects model. The review protocol was registered on PROSPERO (CRD42021236606).

FINDINGS

Of 26,218 studies identified, thirty-five studies enroling 20,708 hospitalised pneumonia episodes were included. Out of the total hospitalised pneumonia cases in this population, the pooled proportion of Staphylococcal pneumonia cases was 3% (95% CI 2% to 4%; I²=96%). amongst 12 studies with higher microbiological quality, the pooled estimate was 6% (95% CI 2% to 10%; I²= 98%). Based on the recent global estimates of hospitalised pneumonia in this age group, the 3% and 6% estimates represent 738 thousand and 1.48 million hospitalisations in 2019, respectively. Based on the Grading of Recommendations Assessment, Development, and Evaluation (GRADE), the overall quality of evidence was considered to be moderate.

INTERPRETATION

Our findings are probably an underestimate because of the unknown and the likely limited sensitivity of current testing methods for Staphylococcal pneumonia diagnosis and widespread reported use of antibiotics before recruitment (in 46% of cases). Staphylococcus aureus is an important cause of hospitalisation for pneumonia in young children globally.

FUNDING

Bill and Melinda Gates Foundation (OPP 1,172,551) through a prime award to John Hopkins University.

The Etiology of Pneumonia From Analysis of Lung Aspirate and Pleural Fluid Samples: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study

BACKGROUND

An improved understanding of childhood pneumonia etiology is required to inform prevention and treatment strategies. Lung aspiration is the gold standard specimen for pneumonia diagnostics. We report findings from analyses of lung and pleural aspirates collected in the Pneumonia Etiology Research for Child Health (PERCH) study.

METHODS

The PERCH study enrolled children aged 1-59 months hospitalized with World Health Organization-defined severe or very severe pneumonia in 7 countries in Africa and Asia. Percutaneous transthoracic lung aspiration (LA) and pleural fluid (PF) aspiration was performed on a sample of pneumonia cases with radiological consolidation and/or PF in 4 countries. Venous blood and nasopharyngeal/oropharyngeal swabs were collected from all cases. Multiplex quantitative polymerase chain reaction (PCR) and routine microbiologic culture were applied to clinical specimens.

RESULTS

Of 44 LAs performed within 3 days of admission on 622 eligible cases, 13 (30%) had a pathogen identified by either culture (5/44) or by PCR (11/29). A pathogen was identified in 12/14 (86%) PF specimens tested by either culture (9/14) or PCR (9/11). Bacterial pathogens were identified more frequently than viruses. All but 1 of the cases with a virus identified were coinfected with bacterial pathogens. Streptococcus pneumoniae (9/44 [20%]) and Staphylococcus aureus (7/14 [50%]) were the predominant pathogens identified in LA and PF, respectively.

CONCLUSIONS

Bacterial pathogens predominated in this selected subgroup of PERCH participants drawn from those with radiological consolidation or PF, with S. pneumoniae and S. aureus the leading pathogens identified.

The Etiology of Childhood Pneumonia in The Gambia: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study

BACKGROUND

Pneumonia remains the leading cause of death in young children globally. The changing epidemiology of pneumonia requires up-to-date data to guide both case management and prevention programs. The Gambia study site contributed a high child mortality, high pneumonia incidence, low HIV prevalence, Haemophilus influenzae type b and pneumococcal conjugate vaccines-vaccinated rural West African setting to the Pneumonia Etiology Research for Child Health (PERCH) Study.

METHODS

The PERCH study was a 7-country case-control study of the etiology of hospitalized severe pneumonia in children 1-59 months of age in low and middle-income countries. Culture and nucleic acid detection methods were used to test nasopharyngeal/oropharyngeal swabs, blood, induced sputum and, in selected cases, lung or pleural fluid aspirates. Etiology was determined by integrating case and control data from multiple specimens using the PERCH integrated analysis based on Bayesian probabilistic methods.

RESULTS

At The Gambia study site, 638 cases of World Health Organization-defined severe and very severe pneumonia (286 of which were chest radiograph [CXR]-positive and HIV-negative) and 654 age-frequency matched controls were enrolled. Viral causes predominated overall (viral 58% vs. bacterial 28%), and of CXR-positive cases respiratory syncytial virus (RSV) accounted for 37%, Streptococcus pneumoniae 13% and parainfluenza was responsible for 9%. Nevertheless, among very severe cases bacterial causes dominated (77% bacterial vs. 11% viral), led by S. pneumoniae (41%); Mycobacterium tuberculosis, not included in "bacterial", accounted for 9%. 93% and 80% of controls ≥1 year of age were, respectively, fully vaccinated for age against Haemophilus influenzae and S. pneumoniae.

CONCLUSIONS

Viral causes, notably RSV, predominated in The Gambia overall, but bacterial causes dominated the severest cases. Efforts must continue to prevent disease by optimizing access to existing vaccines, and to develop new vaccines, notably against RSV. A continued emphasis on appropriate case management of severe pneumonia remains important.

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.

Invasive Haemophilus influenzae Infections after 3 Decades of Hib Protein Conjugate Vaccine Use

Haemophilus influenzae serotype b (Hib) was previously the most common cause of bacterial meningitis and an important etiologic agent of pneumonia in children aged <5 years. Its major virulence factor is the polyribosyl ribitol phosphate (PRP) polysaccharide capsule. In the 1980s, PRP-protein conjugate Hib vaccines were developed and are now included in almost all national immunization programs, achieving a sustained decline in invasive Hib infections. However, invasive Hib disease has not yet been eliminated in countries with low vaccine coverage, and sporadic outbreaks of Hib infection still occur occasionally in countries with high vaccine coverage. Over the past 2 decades, other capsulated serotypes have been recognized increasingly as causing invasive infections. H. influenzae serotype a (Hia) is now a major cause of invasive infection in Indigenous communities of North America, prompting a possible requirement for an Hia conjugate vaccine. H. influenzae serotypes e and f are now more common than serotype b in Europe. Significant year-to-year increases in nontypeable H. influenzae invasive infections have occurred in many regions of the world. Invasive H. influenzae infections are now seen predominantly in patients at the extremes of life and those with underlying comorbidities. This review provides a comprehensive and critical overview of the current global epidemiology of invasive H. influenzae infections in different geographic regions of the world. It discusses those now at risk of invasive Hib disease, describes the emergence of other severe invasive H. influenzae infections, and emphasizes the importance of long-term, comprehensive, clinical and microbiologic surveillance to monitor a vaccine's impact.

Nasopharyngeal Pneumococcal Colonization Density is Associated with Severe Pneumonia in Young Children in the Lao PDR

Background

No studies have explored the association between pneumococcal nasopharyngeal density and severe pneumonia using the World Health Organization (WHO) 2013 definition. In Lao People’s Democratic Republic (Lao PDR), we determine the association between nasopharyngeal pneumococcal density and severe pneumonia in children.

Methods

A prospective observational study was undertaken at Mahosot Hospital, Vientiane, from 2014 to mid-2018. Children <5 years admitted with acute respiratory infections (ARIs) were included. Clinical and demographic data were collected alongside nasopharyngeal swabs for pneumococcal quantification by lytA real-time quantitative polymerase chain reaction. Severe pneumonia was defined using the 2013 WHO definition. For pneumococcal carriers, a logistic regression model examined the association between pneumococcal density and severe pneumonia, after adjusting for potential confounders including demographic and household factors, 13-valent pneumococcal conjugate vaccine status, respiratory syncytial virus co-detection, and preadmission antibiotics.

Results

Of 1268 participants with ARI, 32.3% (n = 410) had severe pneumonia and 36.9% (n = 468) had pneumococcal carriage. For pneumococcal carriers, pneumococcal density was positively associated with severe pneumonia (adjusted odds ratio, 1.4 [95% confidence interval, 1.1–1.8]; P = .020).

Conclusions

Among children with ARIs and pneumococcal carriage, pneumococcal carriage density was positively associated with severe pneumonia in Lao PDR. Further studies may determine if pneumococcal density is a useful marker for pneumococcal conjugate vaccine impact on childhood pneumonia.

Study Protocol for Preventing Early-Onset Pneumonia in Young Children Through Maternal Immunisation: A Multi-Centre Randomised Controlled Trial (PneuMatters)

Background: Preventing and/or reducing acute lower respiratory infections (ALRIs) in young children will lead to substantial short and long-term clinical benefits. While immunisation with pneumococcal conjugate vaccines (PCV) reduces paediatric ALRIs, its efficacy for reducing infant ALRIs following maternal immunisation has not been studied. Compared to other PCVs, the 10-valent pneumococcal-Haemophilus influenzae Protein D conjugate vaccine (PHiD-CV) is unique as it includes target antigens from two common lower airway pathogens, pneumococcal capsular polysaccharides and protein D, which is a conserved H. influenzae outer membrane lipoprotein. Aims: The primary aim of this randomised controlled trial (RCT) is to determine whether vaccinating pregnant women with PHiD-CV (compared to controls) reduces ALRIs in their infants' first year of life. Our secondary aims are to evaluate the impact of maternal PHiD-CV vaccination on different ALRI definitions and, in a subgroup, the infants' nasopharyngeal carriage of pneumococci and H. influenzae, and their immune responses to pneumococcal vaccine type serotypes and protein D. Methods: We are undertaking a parallel, multicentre, superiority RCT (1:1 allocation) at four sites across two countries (Australia, Malaysia). Healthy pregnant Australian First Nation or Malaysian women aged 17-40 years with singleton pregnancies between 27⁺⁶ and 34⁺⁶ weeks gestation are randomly assigned to receive either a single dose of PHiD-CV or usual care. Treatment allocation is concealed. Study outcome assessors are blinded to treatment arms. Our primary outcome is the rate of medically attended ALRIs by 12-months of age. Blood and nasopharyngeal swabs are collected from infants at birth, and at ages 6- and 12-months (in a subset). Our planned sample size (n = 292) provides 88% power (includes 10% anticipated loss to follow-up). Discussion: Results from this RCT potentially leads to prevention of early and recurrent ALRIs and thus preservation of lung health during the infant's vulnerable period when lung growth is maximum. The multicentre nature of our study increases the generalisability of its future findings and is complemented by assessing the microbiological and immunological outcomes in a subset of infants. Clinical Trial Registration: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=374381, identifier: ACTRN12618000150246.

Detection of Streptococcus pneumoniae in Urine by Loop-Mediated Isothermal Amplification

Objective To assess the loop-mediated isothermal amplification (LAMP) to detect cell-free DNA from Streptococcus pneumoniae in urine samples from children with pneumococcal pneumonia.

Methods LAMP reactions using four primers (backward inner primer, forward inner primer, B3, and F3) targeting conserved regions of the S. pneumoniae ply gene and DNA from the recombinant plasmid pTrc99A-ply were optimized for temperature (65°C) and MgSO4 concentration (8 mM) conditions. Urine samples from 71 patients with symptoms of pneumonia and from 17 healthy children were tested side by side using the isothermal methodology LAMP and the commercial urinary antigen test, BinaxNOW S. pneumoniae assay. Percentages of sensitivity, specificity, positive predictive value (PPV), negative predictive value, and positive (LR) were calculated to compare both tests.

Results The specificity of the LAMP reaction was confirmed against several species of bacteria and yeast that can cause pneumonia or urine infections. The suitability of the LAMP assay was evaluated in urine samples from 71 patients and 17 healthy children. All patients (100%) with confirmed pneumococcal pneumonia were positive for the LAMP assay. Among patients with possible/probable pneumonia, 74.1% were identified as positive using the LAMP test. Notably, a higher specificity (95.4%), PPV (94.1%) and positive LR (21.7) were found compared with the urinary antigen test.

Conclusion The presence of S. pneumoniae cell-free DNA in urine samples of pediatric patients can be used as a specific diagnostic biomarker for community-acquired pneumonia by using the LAMP methodology.

Diarrhoeal children with concurrent severe wasting and stunting compared to severe wasting or severe stunting

OBJECTIVE

Children with both severe wasting and severe stunting (SWSS) represent an extreme form of malnutrition and are prone to develop severe infection. The study aims to demonstrate clinical features and aetiology of diarrhoea among children with SWSS compared to those with either severe wasting (SW) or severe stunting (SS), which may help in early identification of high-risk children.

METHODS

Data were extracted from the database of the diarrhoeal disease surveillance system (DDSS) of Dhaka Hospital, icddr,b from 2008 to 2017. Among 14 403 under-five diarrhoeal children, 149 had concurrent SWSS (WLZ/WHZ ˂-3 with LAZ/HAZ ˂-3), 795 had SW (WLZ/WHZ ˂-3 but LAZ/HAZ ≥-3) alone, and 1000 had only SS (LAZ/HAZ ˂-3 but WLZ/WHZ ≥-3).

RESULTS

In logistic regression analysis after adjusting for potential confounders, dehydrating diarrhoea and slum dwelling were independently associated with SWSS vs. SW (P < 0.05). When compared with SS, dehydration and maternal illiteracy were independently associated with SWSS (P < 0.05). In comparison with SW or SS, SWSS less often included infection with rotavirus (P < 0.05). Dehydration was independently associated with SW vs. SS after adjusting for potential confounders (P < 0.05).

CONCLUSION

Children with SWSS more often presented with dehydrating diarrhoea (69%) than children who had either SW (55%) or SS (43%). However, SWSS patients less frequently presented with rotavirus-associated diarrhoeal illnesses. This result underscores the importance of early detection and prompt management of dehydrating diarrhoea in children with concomitant severe wasting and severe stunting to reduce morbidity and mortality in these children, especially in poor settings.

Impact of the 10-valent pneumococcal conjugate vaccine on hospital admissions in children under three years of age in Iceland

INTRODUCTION

Pneumococcus is an important respiratory pathogen. The 10-valent pneumococcal vaccine (PHiD-CV) was introduced into the Icelandic vaccination programme in 2011. The aim was to estimate the impact of PHiD-CV on paediatric hospitalisations for respiratory tract infections and invasive disease.

METHODS

The 2005-2015 birth-cohorts were followed until three years of age and hospitalisations were recorded for invasive pneumococcal disease (IPD), meningitis, sepsis, pneumonia and otitis media. Hospitalisations for upper- and lower respiratory tract infections (URTI, LRTI) were used as comparators. The 2005-2010 birth-cohorts were defined as vaccine non-eligible cohorts (VNEC) and 2011-2015 birth-cohorts as vaccine eligible cohorts (VEC). Incidence rates (IR) were estimated for diagnoses, birth-cohorts and age groups, and incidence rate ratios (IRR) between VNEC and VEC were calculated assuming Poisson variance. Cox regression was used to estimate the hazard ratio (HR) of hospitalisation between VNEC and VEC.

RESULTS

51,264 children were followed for 142,315 person-years, accumulating 1,703 hospitalisations for the respective study diagnoses. Hospitalisations for pneumonia decreased by 20% (HR 0.80, 95%CI:0.67-0.95) despite a 32% increase in admissions for LRTI (HR 1.32, 95%CI:1.14-1.53). Hospital admissions for culture-confirmed IPD decreased by 93% (HR 0.07, 95%CI:0.01-0.50) and no hospitalisations for IPD with vaccine-type pneumococci were observed in the VEC. Hospitalisations for meningitis and sepsis did not change. A decrease in hospital admissions for otitis media was observed, but did not coincide with PHiD-CV introduction.

CONCLUSION

Following the introduction of PHiD-CV in Iceland, hospitalisations for pneumonia and culture confirmed IPD decreased. Admissions for other LRTIs and URTIs increased during this period.

Assessment of an Antibody-in-Lymphocyte Supernatant Assay for the Etiological Diagnosis of Pneumococcal Pneumonia in Children

New diagnostic tests for the etiology of childhood pneumonia are needed. We evaluated the antibody-in-lymphocyte supernatant (ALS) assay to detect immunoglobulin (Ig) G secretion from ex vivo peripheral blood mononuclear cell (PBMC) culture, as a potential diagnostic test for pneumococcal pneumonia. We enrolled 348 children with pneumonia admitted to Patan Hospital, Kathmandu, Nepal between December 2015 and September 2016. PBMCs sampled from participants were incubated for 48 h before harvesting of cell culture supernatant (ALS). We used a fluorescence-based multiplexed immunoassay to measure the concentration of IgG in ALS against five conserved pneumococcal protein antigens. Of children with pneumonia, 68 had a confirmed etiological diagnosis: 12 children had pneumococcal pneumonia (defined as blood or pleural fluid culture-confirmed; or plasma CRP concentration ≥60 mg/l and nasopharyngeal carriage of serotype 1 pneumococci), and 56 children had non-pneumococcal pneumonia. Children with non-pneumococcal pneumonia had either a bacterial pathogen isolated from blood (six children); or C-reactive protein <60 mg/l, absence of radiographic consolidation and detection of a pathogenic virus by multiplex PCR (respiratory syncytial virus, influenza viruses, or parainfluenza viruses; 23 children). Concentrations of ALS IgG to all five pneumococcal proteins were significantly higher in children with pneumococcal pneumonia than in children with non-pneumococcal pneumonia. The concentration of IgG in ALS to the best-performing antigen discriminated between children with pneumococcal and non-pneumococcal pneumonia with a sensitivity of 1.0 (95% CI 0.73-1.0), specificity of 0.66 (95% CI 0.52-0.78) and area under the receiver-operating characteristic curve (AUROCC) 0.85 (95% CI 0.75-0.94). Children with pneumococcal pneumonia were older than children with non-pneumococcal pneumonia (median 5.6 and 2.0 years, respectively, p < 0.001). When the analysis was limited to children ≥2 years of age, assay of IgG ALS to pneumococcal proteins was unable to discriminate between children with pneumococcal pneumonia and non-pneumococcal pneumonia (AUROCC 0.67, 95% CI 0.47-0.88). This method detected spontaneous secretion of IgG to pneumococcal protein antigens from cultured PBMCs. However, when stratified by age group, assay of IgG in ALS to pneumococcal proteins showed limited utility as a test to discriminate between pneumococcal and non-pneumococcal pneumonia in children.

Childhood pneumonia in low-and-middle-income countries: An update

OBJECTIVES

To review epidemiology, aetiology and management of childhood pneumonia in low-and-middle-income countries.

DESIGN

Review of published English literature between 2013 and 2019.

RESULTS

Pneumonia remains a major cause of morbidity and mortality. Risk factors include young age, malnutrition, immunosuppression, tobacco smoke or air pollution exposure. Better methods for specimen collection and molecular diagnostics have improved microbiological diagnosis, indicating that pneumonia results from several organisms interacting. Induced sputum increases microbiologic yield for Bordetella pertussis or Mycobacterium tuberculosis, which has been associated with pneumonia in high TB prevalence areas. The proportion of cases due to Streptococcus pneumoniae and Haemophilus influenzae b has declined with new conjugate vaccines; Staphylococcus aureus and H. influenzae non-type b are the commonest bacterial pathogens; viruses are the most common pathogens. Effective interventions comprise antibiotics, oxygen and non-invasive ventilation. New vaccines have reduced severity and incidence of disease, but disparities exist in uptake.

CONCLUSION

Morbidity and mortality from childhood pneumonia has decreased but a considerable preventable burden remains. Widespread implementation of available, effective interventions and development of novel strategies are needed.

Bacterial Aetiologies of Lower Respiratory Tract Infections among Adults in Yaoundé, Cameroon

Lower respiratory tract infections (LRTIs) remain a challenge in African healthcare settings and only few data are available on their aetiology in Cameroon. The purpose of this study was to access the bacterial cause of LRTIs in patients in Cameroon by two methods. Methods. Participants with LRTIs were enrolled in the referral centre for respiratory diseases in Yaoundé city and its surroundings. To detect bacteria, specimens were tested by conventional bacterial culture and a commercial reverse-transcriptase real-time polymerase chain reaction (RT-PCR) assay. One hundred forty-one adult patients with LRTIs were enrolled in the study. Among the participants, 46.8% were positive for at least one bacterium. Streptococcus pneumoniae and Haemophilus influenzae were the most detected bacteria with 14.2% (20/141) followed by Klebsiella pneumoniae, 9.2% (13/141), Staphylococcus aureus, 7.1% (10/141), and Moraxella catarrhalis, 4.3% (6/141). Bacterial coinfection accounted for 23% (14/61) with Haemophilus influenzae being implicated in 19.7% (12/61). The diagnostic performance of RT-PCR for bacteria detection (43.3%) was significantly different from that of culture (17.7%) (p< 0.001). Only Streptococcus pneumoniae detection was associated with empyema by RT-PCR (p<0.001). These findings enhance understanding of bacterial aetiologies in order to improve respiratory infection management and treatment. It also highlights the need to implement molecular tools as part of the diagnosis of LRTIs.

Vitamin D Deficiency is Associated with Increased Use of Antimicrobials among Preschool Girls in Ethiopia

Preschool children in Addis Ababa, Ethiopia, are highly exposed to influenza viruses. Factors related to infections, nutrition, and environmental conditions that might explain the burden of influenza among these children were investigated. Ninety-five preschool children, 48 girls and 47 boys, were followed clinically for 12 months. Illness and immune responses to influenza; three other respiratory viruses; five airway pathogenic bacteria; and levels of vitamins D, A, and B12 were assessed. Most of the children had antibodies to numerous respiratory viral and bacterial agents at study start, and many were infected during follow-up. Twenty-five girls and 25 boys fell ill during the study, and were treated with one or more courses of systemic antimicrobials. Ninety percent of both girls and boys had 25-hydroxyvitamin D [25(OH)D] levels below the recommended levels. While there was no overall difference in the levels of vitamins D, A, and B12 between girls and boys, treated girls had significantly lower 25(OH)D levels than non-treated girls and treated boys. There was a considerable number of short for age children, but only the short treated girls had significantly lower 25(OH)D levels than the non-treated children. Preschool girls with low 25(OH)D levels were more vulnerable to pathogenic microbes than boys.

Microbiological Diagnosis of Respiratory Illness

A wide variety of microorganisms are potential respiratory pathogens, and the spectrum of known pathogens for each respiratory infection syndrome has not changed markers over recent years. Detection of likely etiologic agents of respiratory infections can help direct management and can also play an important role in disease surveillance. For this purpose, we are still reliant on many traditional diagnostic tools that have been used for decades in order to determine the microbial etiology of respiratory infections. However, these tools have been increasingly supplemented by newer methods, particular molecular diagnostic techniques, which have enabled the more rapid detection of many pathogens that were previously difficult to detect. These advances have particularly lead to improvements in the ability to detect respiratory viruses and also other microorganisms that do not normally colonize the respiratory tract. Recognition of the existence of the lung microbiome has challenged the traditional views of pneumonia pathogenesis and may provide the opportunity for new diagnostic tools that are focused on more than just detection of specific known pathogens. Continued liaison between clinicians and laboratory staff is vital in order to facilitate the most cost-effective use of laboratory diagnostics.

Complicated pneumonia: current concepts and state of the art

PURPOSE OF REVIEW

This review aims to provide clinicians engaged in the care of infants and children an update on the current understanding of the epidemiology, etiology, diagnostic evaluation, and clinical management of complicated pneumonia. The review provides timely information surrounding areas of consensus and ongoing research.

RECENT FINDINGS

The epidemiology and etiologies of complicated pneumonia continue to evolve over the past several decades in context of the introduction of new vaccines. We review uncommon and emerging pathogens. Immunocompromised patients are particularly at risk for complications. The 2011 clinical practice guidelines for pediatric community-acquired pneumonia from The Pediatric Infectious Diseases Society/Infectious Diseases Society of America and the British Thoracic Society are changing approaches to evaluation and management. The efficacy of new diagnostic laboratory studies, and imaging techniques, continues to be studied. Antibiotics are the mainstay of treatment, with several new options to consider. Techniques for the drainage of parapneumonic effusions continue to optimize.

SUMMARY

Although much is known about complicated pneumonia, it remains a significant burden. New diagnostic and therapeutic interventions hold much promise. This review seeks to provide clinicians with evidence that motivates a reasoned approach to the evaluation and management of complicated pneumonia.

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

Community-acquired pneumonia (CAP) is the leading cause of mortality in children under 5 years of age globally. To improve the management of CAP, we must distinguish CAP from other common pediatric conditions and develop better diagnostic methods to detect the causative organism, so as to best direct appropriate resources in both industrialized and developing countries. Here, we review the diagnostic modalities available for identifying viruses and bacteria in the upper and lower respiratory tract of children, with a discussion of their utility and limitations in diagnosing CAP in children.

Short-course antimicrobial therapy for paediatric respiratory infections (SAFER): study protocol for a randomized controlled trial

Background

Community-acquired pneumonia (CAP) is commonly diagnosed in children. The Infectious Disease Society of America guidelines recommend 10 days of high-dose amoxicillin for the treatment of non-severe CAP but 5-day “short course” therapy may be just as effective. Randomized trials in adults have already demonstrated non-inferiority of 5-day short-course treatment for adults hospitalized with severe CAP and for adults with mild CAP treated as outpatients. Minimizing exposure to antimicrobials is desirable to avoid harms including diarrhoea, rashes, severe allergic reactions, increased circulating antimicrobial resistance, and microbiome disruption.

Methods

The objective of this multicentre, randomized, non-inferiority, controlled trial is to investigate whether 5 days of high-dose amoxicillin is associated with lower rates of clinical cure 14–21 days later as compared to 10 days of high-dose amoxicillin, the reference standard. Recruitment and enrolment will occur in the emergency departments of McMaster Children’s Hospital and the Children’s Hospital of Eastern Ontario. All children in the study will receive 5 days of amoxicillin after which point they will receive either 5 days of a different formulation of amoxicillin or a placebo. Assuming a clinical failure rate of 5% in the reference arm, a non-inferiority margin of 7.5%, one-sided alpha set at 0.025 and power of 0.80, 270 participants will be required. Participants from a previous feasibility study (n = 60) will be rolled over into the current study. We will be performing multiplex respiratory virus molecular testing, quantification of nasopharyngeal pneumococcal genomic loads, salivary inflammatory marker testing, and faecal microbiome profiling on participants.

Discussion

This is a pragmatic study seeking to provide high-quality evidence for front-line physicians evaluating children presenting with mild CAP in North American emergency departments in the post-13-valent pneumococcal, conjugate vaccine era. High-quality evidence supporting the non-inferiority of short-course therapy for non-severe paediatric CAP should be generated prior to making changes to established guidelines.

Trial registration

ClinicalTrials.gov, NCT02380352. Registered on 2 March 2015.

Electronic supplementary material

The online version of this article (10.1186/s13063-018-2457-2) contains supplementary material, which is available to authorized users.

Etiology of Childhood Pneumonia: What We Know, and What We Need to Know! : Based on 5th Dr. IC Verma Excellence Oration Award

Childhood community acquired pneumonia continues to be an important clinical problem at the individual, institutional and community levels. Determination of microbial etiology is critical to develop evidence-based management (therapeutic and prophylactic) decisions. For decades, the approach to this relied on culture of lung aspirate specimens obtained from children with radiographically confirmed pneumonia, before administering antibiotics. Such studies revealed the major bacteria associated with pneumonia, prompting the World Health Organization to develop a highly sensitive clinical definition of pneumonia and advocate empiric antibiotic therapy; in order to save lives (focusing on community settings lacking resources for diagnostic tests). However, it spawned research studies conducted in/from/by institutions enrolling children with the relatively non-specific WHO definition of pneumonia. Specificity got further compromised by abandoning lung aspiration and using naso/oro pharyngeal specimens; even in children who had received antibiotics. This led to the recovery of viruses more often than bacteria. The use of highly sensitive molecular based diagnostics (especially PCR) facilitated the detection of multiple organisms (bacteria, viruses, atypical organisms and even fungal species); making it difficult to attribute etiology in individual cases. This challenge was sought to be addressed through the multi-site PERCH Study (Pneumonia Etiology Research for Child Health), designed as a case-control study to conclusively determine the etiology of pneumonia. However, despite a slew of publications, the answer to the central question of etiology has not emerged so far. Since none of the PERCH Study sites was located in India, the Community Acquired Pneumonia Etiology Study (CAPES) was conducted at Chandigarh. This turned out to be the largest single-centre pneumonia etiology study, and generated a wealth of data. This article summarizes the current challenges in pneumonia etiology research; outlines the key observations from the PERCH and CAPES projects, as well as other important studies; and suggests a way forward for pneumonia etiology research in the current era.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past 25 years due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation in the clinical microbiology laboratory as well as user-friendly software and robust laboratory informatics systems have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting [3, 4]. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, has benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods continues to lag behind. The purpose of this chapter is to review, update, and discuss the interpretation and relevance of results produced by these advanced molecular techniques.

Impact of Childhood Nutritional Status on Pathogen Prevalence and Severity of Acute Diarrhea

Children with acute and chronic malnutrition are at increased risk of morbidity and mortality following a diarrheal episode. To compare diarrheal disease severity and pathogen prevalence among children with and without acute and chronic malnutrition, we conducted a cross-sectional study of human immunodeficiency virus-uninfected Kenyan children aged 6–59 months, who presented with acute diarrhea. Children underwent clinical and anthropometric assessments and provided stool for bacterial and protozoal pathogen detection. Clinical and microbiological features were compared using log binomial regression among children with and without wasting (mid-upper arm circumference ≤ 125 mm) or stunting (height-for-age z score ≤ −2). Among 1,363 children, 7.0% were wasted and 16.9% were stunted. After adjustment for potential confounders, children with wasting were more likely than nonwasted children to present with at least one Integrated Management of Childhood Illness danger sign (adjusted prevalence ratio [aPR]: 1.3, 95% confidence interval [CI]: 1.0 to 1.5, P = 0.05), severe dehydration (aPR: 2.4, 95% CI: 1.5 to 3.8, P < 0.01), and enteroaggregative Escherichia coli recovered from their stool (aPR: 1.8, 1.1–2.8, P = 0.02). There were no differences in the prevalence of other pathogens by wasting status after confounder adjustment. Stunting was not associated with clinical severity or the presence of specific pathogens. Wasted children with diarrhea presented with more severe disease than children without malnutrition which may be explained by a delay in care-seeking or diminished immune response to infection. Combating social determinants and host risk factors associated with severe disease, rather than specific pathogens, may reduce the disparities in poor diarrhea-associated outcomes experienced by malnourished children.

Microorganisms Associated With Pneumonia in Children <5 Years of Age in Developing and Emerging Countries: The GABRIEL Pneumonia Multicenter, Prospective, Case-Control Study

Background

Pneumonia, the leading infectious cause of child mortality globally, mainly afflicts developing countries. This prospective observational study aimed to assess the microorganisms associated with pneumonia in children aged <5 years in developing and emerging countries.

Methods

A multicenter, case-control study by the GABRIEL (Global Approach to Biological Research, Infectious diseases and Epidemics in Low-income countries) network was conducted between 2010 and 2014 in Cambodia, China, Haiti, India (2 sites), Madagascar, Mali, Mongolia, and Paraguay. Cases were hospitalized children with radiologically confirmed pneumonia; controls were children from the same setting without any features suggestive of pneumonia. Nasopharyngeal swabs were collected from all subjects; 19 viruses and 5 bacteria were identified by reverse-transcription polymerase chain reaction. Associations between microorganisms and pneumonia were quantified by calculating the adjusted population attributable fraction (aPAF) after multivariate logistic regression analysis adjusted for sex, age, time period, other pathogens, and site.

Results

Overall, 888 cases and 870 controls were analyzed; ≥1 microorganism was detected in respiratory samples in 93.0% of cases and 74.4% of controls (P < .001). Streptococcus pneumoniae, Mycoplasma pneumoniae, human metapneumovirus, rhinovirus, respiratory syncytial virus (RSV), parainfluenza virus 1, 3, and 4, and influenza virus A and B were independently associated with pneumonia; aPAF was 42.2% (95% confidence interval [CI], 35.5%-48.2%) for S. pneumoniae, 18.2% (95% CI, 17.4%-19.0%) for RSV, and 11.2% (95% CI, 7.5%-14.7%) for rhinovirus.

Conclusions

Streptococcus pneumoniae, RSV, and rhinovirus may be the major microorganisms associated with pneumonia infections in children <5 years of age from developing and emerging countries. Increasing S. pneumoniae vaccination coverage may substantially reduce the burden of pneumonia among children in developing countries.

The evidence for non-typeable Haemophilus influenzae as a causative agent of childhood pneumonia

Haemophilus influenzae type b (Hib) was a major cause of bacterial pneumonia in children prior to the introduction of Hib-conjugate vaccines. The widespread use of Hib-conjugate vaccines has resulted in a significant decline in the number of cases of invasive Hib disease, including bacteraemic pneumonia, in areas where the vaccine has been implemented. In many countries, non-typeable H. influenzae (NTHI) is now the most common cause of invasive haemophilus infection in all ages. NTHI are a recognized cause of bacteraemic and non-bacteraemic pneumonia in children and in adults. Less than 10% of cases of pediatric pneumonia are bacteraemic, and children generally do not expectorate lower respiratory tract secretions, so determining the microbial cause of a non-bacteraemic pneumonia is challenging. In this commentary the evidence that NTHI is a cause of pneumonia in children is briefly reviewed.

The Enduring Challenge of Determining Pneumonia Etiology in Children: Considerations for Future Research Priorities

Pneumonia kills more children each year worldwide than any other disease. Nonetheless, accurately determining the causes of childhood pneumonia has remained elusive. Over the past century, the focus of pneumonia etiology research has shifted from studies of lung aspirates and postmortem specimens intent on identifying pneumococcal disease to studies of multiple specimen types distant from the lung that are tested for multiple pathogens. Some major challenges facing modern pneumonia etiology studies include the use of nonspecific and variable case definitions, poor access to pathologic lung tissue and to specimens from fatal cases, poor diagnostic accuracy of assays (especially when testing nonpulmonary specimens), and the interpretation of results when multiple pathogens are detected in a given individual. The future of childhood pneumonia etiology research will likely require integrating data from complementary approaches, including applications of advanced molecular diagnostics and vaccine probe studies, as well as a renewed emphasis on lung aspirates from radiologically confirmed pneumonia and postmortem examinations.

Factors That Negatively Affect the Prognosis of Pediatric Community-Acquired Pneumonia in District Hospital in Tanzania

Community-acquired pneumonia (CAP) is still the most important cause of death in countries with scarce resources. All children (33 months ± 35 DS) discharged from the Pediatric Unit of Itigi Hospital, Tanzania, with a diagnosis of CAP from August 2014 to April 2015 were enrolled. Clinical data were gathered. Dried blood spot (DBS) samples for quantitative real-time polymerase chain reaction (PCR) for bacterial detection were collected in all 100 children included. Twenty-four percent of patients were identified with severe CAP and 11% died. Surprisingly, 54% of patients were admitted with a wrong diagnosis, which increased complications, the need for antibiotics and chest X-rays, and the length of hospitalization. Comorbidity, found in 32% of children, significantly increased severity, complications, deaths, need for chest X-rays, and oxygen therapy. Malnourished children (29%) required more antibiotics. Microbiologically, Streptococcus pneumonia (S. p.), Haemophilus influenza type b (Hib) and Staphylococcus aureus (S. a.) were the bacteria more frequently isolated. Seventy-five percent of patients had mono-infection. Etiology was not correlated with severity, complications, deaths, oxygen demand, or duration of hospitalization. Our study highlights that difficult diagnoses and comorbidities negatively affect clinical evolution. S. p. and Hib still play a large role; thus, implementation of current vaccine strategies is needed. DBS is a simple and efficient diagnostic method for bacterial identification in countries with scarce resources.

Childhood pneumococcal disease in Africa - A systematic review and meta-analysis of incidence, serotype distribution, and antimicrobial susceptibility

BACKGROUND

Determining the incidence, disease-associated serotypes and antimicrobial susceptibility of invasive pneumococcal disease (IPD) among children in Africa is essential in order to monitor the impact of these infections prior to widespread introduction of the pneumococcal conjugate vaccine (PCV).

METHODS

To provide updated estimates of the incidence, serotype distribution, and antimicrobial susceptibility profile of Streptococcus pneumoniae causing disease in Africa, we performed a systematic review of articles published from 2000 to 2015 using Ovid Medline and Embase. We included prospective and surveillance studies that applied predefined diagnostic criteria. Meta-analysis for all pooled analyses was based on random-effects models.

RESULTS

We included 38 studies consisting of 386,880 participants in 21 countries over a total of 350,613 person-years. The pooled incidence of IPD was 62.6 (95% CI 16.9, 226.5) per 100,000 person-years, including meningitis which had a pooled incidence of 24.7 (95% CI 11.9, 51.6) per 100,000 person-years. The pooled prevalence of penicillin susceptibility was 78.1% (95% CI 61.9, 89.2). Cumulatively, PCV10 and PCV13 included 66.9% (95% CI 55.9, 76.7) and 80.6% (95% CI 66.3, 90.5) of IPD serotypes, respectively.

CONCLUSIONS

Our study provides an integrated and robust summary of incidence data, serotype distribution and antimicrobial susceptibility for S. pneumoniae in children ≤5years of age in Africa prior to widespread introduction of PCV on the continent. The heterogeneity of studies and wide range of incidence rates across the continent indicate that surveillance efforts should be intensified in all regions of Africa to improve the integrity of epidemiologic data, vaccine impact and cost benefit. Although the incidence of IPD in young children in Africa is substantial, currently available conjugate vaccines are estimated to cover the majority of invasive disease-causing pneumococcal serotypes. These data provide a reliable baseline from which to monitor the impact of the broad introduction of PCV.

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.

Pneumonia

Pneumonia is an important cause of morbidity and mortality globally. It is the leading cause of death in infants and young children with the majority of these deaths occurring in low income countries. Risk factors affecting incidence and outcome include extremes of age, poor nutrition, immunosuppression, environmental exposures and socioeconomic determinants. Pneumonia can be caused by a wide range of pathogens including bacteria, viruses and fungi, and the etiology varies by epidemiological setting, comorbidities and whether the pneumonia is community-acquired or hospital-acquired. Streptococcus pneumoniae is the major cause of community-acquired bacterial pneumonia while Gram negative bacteria, often resistant to multiple antibiotics, are common causes of hospital-acquired pneumonia and pneumonia in immunosuppressed individuals. Diagnosis is generally clinical and management is based mainly on knowledge of likely causative pathogens as well as clinical severity and presence of known risk factors. Timely and effective antibiotic treatment and oxygen therapy if hypoxemic are critical to patient outcomes. Preventive measures range from improved nutrition and hygiene to specific vaccines that target common causes in children and adults such as the pneumococcal or influenza vaccines.

Valuable hematological indicators for the diagnosis and severity assessment of Chinese children with community-acquired pneumonia: Prealbumin

Chest X-ray is a "golden standard" for the diagnosis and severity assessment of community-acquired pneumonia (CAP). However, it cannot be used as routine examination of CAP in children. The present study aims to investigate the roles of prealbumin (PA) in CAP in children and further determine the usefulness of PA in diagnosis and severity assessment of CAP in children.This was a retrospective analysis of 174 cases of hospitalized children with CAP. The following indicators were recorded: vital sign, inflammatory indexes, PA, and respiratory pathogens immunoglobulin M antibody test results. A total of 33 healthy children were selected as the control group. The results of laboratory tests between CAP and control groups were compared. CAP group was further divided into mild CAP and severe CAP groups, and vital signs and laboratory examination results of 2 groups were compared.The total positive rate of Mycoplasma pneumoniae in this study was 27.4%, and there was no significant difference in different seasons (P = 0.356). Compared with controls, there was no significant difference between procalcitonin and C-reactive protein in CAP group (P = 0.355, 0.061). The white blood cell count, percentage of neutrophils, neutrophil count, and erythrocyte sedimentation rate in the CAP group were significantly higher than those in control group, and PA was significantly lower than that in the control group (all P < 0.05). In the traditional cutoff value (<170 mg/L), the sensitivity of PA for the diagnosis of CAP was 0.847, which was significant higher than traditional inflammatory indicators. Moreover, it was found that PA was an independent protective factor for CAP in children based on multivariate analysis (odds ratio: 0.974; 95% confidence interval: 0.956-0.993; P = 0.008). PA level in severe CAP group was significantly lower than in mild CAP group (P = 0.001). With a cutoff value of 125 mg/L, the sensitivity and specificity of PA for the severity assessment of CAP were 0.703 and 0.714, respectively.Combined with traditional inflammatory markers, PA may improve the diagnostic efficacy of CAP in children. PA can be used as a reference marker to complement the chest X-rays for severity assessment of children CAP.

Comparison of the frequency of bacterial and viral infections among children with community-acquired pneumonia hospitalized across distinct severity categories: a prospective cross-sectional study

Background

The comparison of the frequencies of bacterial and viral infections among children with community-acquired pneumonia (CAP) admitted in distinct severity categories, in an original study, is lacking in literature to-date. We aimed to achieve this goal.

Methods

Children aged 2-59-months-old hospitalized with CAP were included in this prospective study in Salvador, Brazil. Clinical data and biological samples were collected to investigate 11 viruses and 8 bacteria. Severity was assessed by using the World Health Organization criteria.

Results

One hundred eighty-one patients were classified as “non-severe” (n = 53; 29.3 %), “severe” (n = 111; 61.3 %), or “very severe” (n = 17; 9.4 %) CAP. Overall, aetiology was detected among 156 (86.2 %) cases; viral (n = 84; 46.4 %), bacterial (n = 26; 14.4 %) and viral-bacterial (n = 46; 25.4 %) infections were identified. Viral infection frequency was similar in severe/very severe and non-severe cases (46.1 % vs. 47.2 %; p = 0.9). Pneumococcal infection increased across “non-severe” (13.2 %), “severe” (23.4 %), and “very severe” (35.3 %) cases (qui-squared test for trend p = 0.04). Among patients with detected aetiology, after excluding cases with co-infection, the frequency of sole bacterial infection was different (p = 0.04) among the categories; non-severe (12.5 %), severe (29.3 %) or very severe (55.6 %). Among these patients, sole bacterial infection was independently associated with severity (OR = 4.4 [95 % CI:1.1–17.6]; p = 0.04) in a model controlled for age (OR = 0.7 [95 % CI:0.5–1.1]; p = 0.1).

Conclusions

A substantial proportion of cases in distinct severity subgroups had respiratory viral infections, which did not differ between severity categories. Bacterial infection, particularly pneumococcal infection, was more likely among severe/very severe cases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12887-016-0645-3) contains supplementary material, which is available to authorized users.

Prevention and Control of Childhood Pneumonia and Diarrhea

Pneumonia and diarrhea are the 2 leading infectious causes of death in children younger than 5 years worldwide, most of which occur in low- and middle-income countries (LMICs) in sub-Saharan Africa and Southern Asia. The past decade has seen large reductions in global childhood mortality, partly due to expansion of nonspecific public health interventions and vaccines against Streptococcus pneumoniae, Haemophilus influenzae, and rotavirus in LMICs. Further progress in this field depends on the international community's commitment to fund and implement programs using currently available vaccines and development of new vaccines against pathogens common to children in LMICs.

Etiology and Factors Associated with Pneumonia in Children under 5 Years of Age in Mali: A Prospective Case-Control Study

Background

There are very limited data on children with pneumonia in Mali. The objective was to assess the etiology and factors associated with community-acquired pneumonia in hospitalized children <5 years of age in Mali.

Methods

A prospective hospital-based case-control study was implemented in the Pediatric department of Gabriel Touré University Hospital at Bamako, Mali, between July 2011-December 2012. Cases were children with radiologically-confirmed pneumonia; Controls were hospitalized children without respiratory features, matched for age and period. Respiratory specimens, were collected to identify 19 viruses and 5 bacteria. Whole blood was collected from cases only. Factors associated with pneumonia were assessed by multivariate logistic regression.

Results

Overall, 118 cases and 98 controls were analyzed; 44.1% were female, median age was 11 months. Among pneumonia cases, 30.5% were hypoxemic at admission, mortality was 4.2%. Pneumonia cases differed from the controls regarding clinical signs and symptoms but not in terms of past medical history. Multivariate analysis of nasal swab findings disclosed that S. pneumoniae (adjusted odds ratio [aOR] = 3.4, 95% confidence interval [95% CI]: 1.6–7.0), human metapneumovirus (aOR = 17.2, 95% CI: 2.0–151.4), respiratory syncytial virus [RSV] (aOR = 7.4, 95% CI: 2.3–23.3), and influenza A virus (aOR = 10.7, 95% CI: 1.0–112.2) were associated with pneumonia, independently of patient age, gender, period, and other pathogens. Distribution of S. pneumoniae and RSV differed by season with higher rates of S. pneumoniae in January-June and of RSV in July-September. Pneumococcal serotypes 1 and 5 were more frequent in pneumonia cases than in the controls (P = 0.009, and P = 0.04, respectively).

Conclusions

In this non-PCV population from Mali, pneumonia in children was mainly attributed to S. pneumoniae, RSV, human metapneumovirus, and influenza A virus. Increased pneumococcal conjugate vaccine coverage in children could significantly reduce the burden of pneumonia in sub-Saharan African countries.

A review of the role of Haemophilus influenzae in community-acquired pneumonia

In an era when Haemophilus influenzae type b (Hib) conjugate vaccine is widely used, the incidence of Hib as a cause of community-acquired pneumonia (CAP) has dramatcally declined. Non-typeable H. influenzae (NTHi) strains and, occasionally, other encapsulated serotypes of H. influenzae are now the cause of the majority of invasive H. influenzae infectons, including bacteraemic CAP. NTHi have long been recognised as an important cause of lower respiratory tract infecton, including pneumonia, in adults, especially those with underlying diseases. The role of NTHi as a cause of non-bacteraemic CAP in children is less clear. In this review the evidence for the role of NTHi and capsulated strains of H. influenzae will be examined.

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.

Respiratory viruses associated with community-acquired pneumonia in children: matched case-control study

BACKGROUND

Community-acquired pneumonia (CAP) is the leading cause of death in children worldwide and a substantial proportion of childhood CAP is caused by viruses. A better understanding of the role of virus infections in this condition is needed to improve clinical management and preventive measures. The aim of the study was therefore to assess the association between specific respiratory viruses and childhood CAP.

METHODS

A case-control study was conducted during 3 years in Stockholm, Sweden. Cases were children aged ≤5 years with radiological CAP. Healthy controls were consecutively enrolled at child health units during routine visits and matched to cases on age and calendar time. Nasopharyngeal aspirates were obtained and analysed by real-time PCR for 15 viruses. Multivariate conditional logistic regression was used to account for coinfections with other viruses and baseline characteristics.

RESULTS

A total of 121 cases, of which 93 cases met the WHO criteria for radiological pneumonia, and 240 controls were included in the study. Viruses were detected in 81% of the cases (n=98) and 56% of the controls (n=134). Influenza virus, metapneumovirus and respiratory syncytial virus were detected in 60% of cases and were significantly associated with CAP with ORs >10. There was no association with parainfluenza virus, human enterovirus or rhinovirus and coronavirus and bocavirus were negatively associated with CAP.

CONCLUSIONS

Our study indicates viral CAP is an underestimated disease and points out hMPV as a new important target for the prevention of childhood CAP.

Vaccines for Nontypeable Haemophilus influenzae: the Future Is Now

Infections due to nontypeable Haemophilus influenzae result in enormous global morbidity in two clinical settings: otitis media in children and respiratory tract infections in adults with chronic obstructive pulmonary disease (COPD). Recurrent otitis media affects up to 20% of children and results in hearing loss, delays in speech and language development and, in developing countries, chronic suppurative otitis media. Infections in people with COPD result in clinic and emergency room visits, hospital admissions, and respiratory failure. An effective vaccine would prevent morbidity, help control health care costs, and reduce antibiotic use, a major contributor to the global crisis in bacterial antibiotic resistance. The widespread use of the pneumococcal conjugate vaccines is causing a relative increase in H. influenzae otitis media. The partial protection against H. influenzae otitis media induced by the pneumococcal H. influenzae protein D conjugate vaccine represents a proof of principle of the feasibility of a vaccine for nontypeable H. influenzae. An ideal vaccine antigen should be conserved among strains, have abundant epitopes on the bacterial surface, be immunogenic, and induce protective immune responses. Several surface proteins of H. influenzae have been identified as potential vaccine candidates and are in various stages of development. With continued research, progress toward a broadly effective vaccine to prevent infections caused by nontypeable H. influenzae is expected over the next several years.