Enhanced diagnosis of pneumococcal meningitis with use of the Binax NOW immunochromatographic test of Streptococcus pneumoniae antigen: a multisite study

Novel and Rapid Diagnostics for Common Infections in the Critically Ill Patient

There are several novel platforms that enhance detection of pathogens that cause common infections in the intensive care unit. These platforms have a sample to answer time of a few hours, are often higher yield than culture, and have the potential to improve antibiotic stewardship.

Estimating national, regional and provincial cost-effectiveness of introducing childhood 13-valent pneumococcal conjugate vaccination in China: a modelling analysis

Background

Although 13-valent pneumococcal conjugate vaccine (PCV13) is available in China's private market, it has yet to be introduced into the National Immunization Programme (NIP) and is therefore not available to large parts of the population. This study aimed to estimate the cost-effectiveness of including PCV13 in China's NIP at national and provincial levels.

Methods

We adopted a decision-tree Markov model to estimate the cost-effectiveness of adding 3-dose PCV13 in the NIP compared to the status quo in the private market from a societal perspective. The model hypothesized a birth cohort for five years after vaccine introduction. Treatment costs and vaccine program costs were calculated from Chinese Center for Disease Control and Prevention (CDC) and national insurance databases. Disease burden data, incidence rate ratios, and other parameters were derived from published and grey literature. Cases and deaths averted, quality-adjusted life years (QALYs) gained, and incremental cost-effectiveness ratios (ICERs) were estimated at the provincial, regional, and national levels. One-way, scenario and probabilistic sensitivity analyses were conducted to explore model uncertainty.

Findings

At the national level, introducing PCV13 in the NIP was predicted to prevent approximately 4807 pneumococcal deaths (66% reduction) and 1,057,650 pneumococcal cases (17% reduction) in the first five years of the 2019 birth cohort. Under the assumed base case price of US$ 25 per dose in the NIP, PCV13 in the NIP was cost-effective nationally with ICER of US$ 5.222 per QALY gained, and was cost-effective in 17 and cost-saving in 4 of the 31 provinces compared to the status quo. One-way and scenario sensitivity analyses indicated robust results when varying all model parameters, and probabilistic sensitivity analysis showed a 98% probability of cost-effectiveness nationally.

Interpretation

Our findings highlight the cost-effectiveness of introducing PCV13 in China's NIP. Provincial results supported subnational introduction of PCV13, and priority should be given to less socioeconomically developed provinces. Since vaccination cost is the most influential model parameter, efforts to improve PCV affordability after pooled procurement will benefit public health in a cost-effective manner.

Funding

The Bill & Melinda Gates Foundation.

Novel and Rapid Diagnostics for Common Infections in the Critically Ill Patient

There are several novel platforms that enhance detection of pathogens that cause common infections in the intensive care unit. These platforms have a sample to answer time of a few hours, are often higher yield than culture, and have the potential to improve antibiotic stewardship.

Pneumococcal meningitis in adults in 2014-2018 after introduction of pediatric 13-valent pneumococcal conjugate vaccine in Japan

We assessed the impact of the pediatric 13-valent pneumococcal conjugate vaccine (PCV13) on pneumococcal meningitis in adults in Japan in 2014–2018 by comparing epidemiological characteristics of adults with invasive pneumococcal disease with (n = 222) and without (n = 1258) meningitis. The annual incidence of pneumococcal meningitis in 2016–2018 was 0.20–0.26 cases/100,000 population. Age (p < 0.001) and case fatality rate (p = 0.003) were significantly lower in patients with meningitis than in those without meningitis. The odds of developing meningitis were higher in asplenic/hyposplenic or splenectomized patients (adjusted odds ratio [aOR] 2.29, 95% CI 1.27–4.14), for serotypes 10A (aOR 3.26, 95% CI 2.10–5.06) or 23A (aOR 3.91, 95% CI 2.47–6.19), but lower for those aged ≥ 65 years (aOR 0.59, 95% CI 0.44–0.81). PCV13 had an indirect effect on nonmeningitis, but its impact on meningitis was limited because of an increase in non-PCV13 serotypes. Of meningitis isolates, 78 (35.1%) and 3 (1.4%) were penicillin G- or ceftriaxone-resistant, respectively. We also confirmed an association of the pbp1bA641C mutation with meningitis (aOR 2.92, 95% CI 1.51–5.65).

Integration of Ni/NiO nanoparticles and a microfluidic ELISA chip to generate a sensing platform for Streptococcus pneumoniae detection

Enzyme-linked immunosorbent assays (ELISAs) are tests that uses antibody recognition and enzyme catalytic activity to identify a substance, and they have been widely used as a diagnostic tool in the clinic.

Management of Acute Bacterial Meningitis in Children

Acute community-acquired bacterial meningitis (ABM) in children continues to have high rates of neurological morbidity and mortality despite the overall declining rates of infection attributed to the use of vaccines and intrapartum Group B Streptococcus prophylaxis. Prompt diagnosis and early antibiotic therapy are crucial and should not be delayed to obtain cranial imaging. Differentiating bacterial from viral meningitis continues to be a clinical dilemma especially in patients with previous antibiotic exposure. Clinical models and inflammatory biomarkers can aid clinicians in their diagnostic approach. Multiplex polymerase chain reaction and metagenomic next-generation sequencing are promising tools that can help in early and accurate diagnosis. This review will present the epidemiology of ABM in children, indications of cranial imaging, role of different models and serum biomarkers in diagnosing ABM, and management including the use of adjunctive therapies and methods of prevention.

Performance of the ImmuView and BinaxNOW assays for the detection of urine and cerebrospinal fluid Streptococcus pneumoniae and Legionella pneumophila serogroup 1 antigen in patients with Legionnaires' disease or pneumococcal pneumonia and meningitis

The performances of the ImmuView Streptococcus pneumoniae (Sp) and Legionella pneumophila (Lp) urinary antigen test were compared to that of the BinaxNOW Sp and Lp assays, using frozen urine from 166 patients with Legionnaires' disease (LD) and 59 patients with pneumococcal pneumonia. Thirty Sp-positive or contrived cerebrospinal fluids (CSF) were also tested. Test specimens were collected and tested at different sites, with each site testing unique specimens by technologists blinded to expected results. No significant differences in test concordances were detected for the ImmuView and BinaxNOW assays for the Sp or Lp targets for urine from patients with pneumococcal pneumonia or LD when performance from both sites were combined. At one of two test sites the ImmuView Lp assay was more sensitive than the BinaxNOW assay, with no correlation between test performance and Lp serogroup 1 monoclonal type. Urines from six of seven patients with LD caused by Legionella spp. bacteria other than Lp serogroup 1 were negative in both assays. Both tests had equivalent performance for Sp-positive CSF. The clinical sensitivities for pneumococcal pneumonia were 88.1 and 94.4% for the ImmuView and Binax assays, and 87.6 and 84.2% for the Lp assays, respectively. Test specificities for pneumococcal pneumonia were 96.2 and 97.0% for the ImmuView and Binax assays, and 99.6 and 99.1% for the Lp assays. Both assays were highly specific for Sp in pediatric urines from children with nasopharyngeal colonization by the bacterium. ImmuView and BinaxNOW assay performance was equivalent in these studies.

National, regional, and state-level burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in India: modelled estimates for 2000-15

Background

India accounts for a disproportionate burden of global childhood illnesses. To inform policies and measure progress towards achieving child health targets, we estimated the annual national and state-specific childhood mortality and morbidity attributable to Streptococcus pneumoniae and Haemophilus influenzae type b (Hib) between 2000 and 2015.

Methods

In this modelling study, we used vaccine clinical trial data to estimate the proportion of pneumonia deaths attributable to pneumococcus and Hib. The proportion of meningitis deaths attributable to each pathogen was derived from pathogen-specific meningitis case fatality and bacterial meningitis case data from surveillance studies. We applied these proportions to modelled state-specific pneumonia and meningitis deaths from 2000 to 2015 prepared by the WHO Maternal and Child Epidemiology Estimation collaboration (WHO/MCEE) on the basis of verbal autopsy studies from India. The burden of clinical and severe pneumonia cases attributable to pneumococcus and Hib was ascertained with vaccine clinical trial data and state-specific all-cause pneumonia case estimates prepared by WHO/MCEE by use of risk factor prevalence data from India. Pathogen-specific meningitis cases were derived from state-level modelled pathogen-specific meningitis deaths and state-level meningitis case fatality estimates. Pneumococcal and Hib morbidity due to non-pneumonia, non-meningitis (NPNM) invasive syndromes were derived by applying the ratio of pathogen-specific NPNM cases to pathogen-specific meningitis cases to the state-level pathogen-specific meningitis cases. Mortality due to pathogen-specific NPNM was calculated with the ratio of pneumococcal and Hib meningitis case fatality to pneumococcal and Hib meningitis NPNM case fatality. Census data from India provided the population at risk.

Findings

Between 2000 and 2015, estimates of pneumococcal deaths in Indian children aged 1–59 months fell from 166 000 (uncertainty range [UR] 110 000–198 000) to 68 700 (44 600–86 000), while Hib deaths fell from 82 600 (52 300–112 000) to 15 600 (9800–21 500), representing a 58% (UR 22–78) decline in pneumococcal deaths and an 81% (59–91) decline in Hib deaths. In 2015, national mortality rates in children aged 1–59 months were 56 (UR 37–71) per 100 000 for pneumococcal infection and 13 (UR 8–18) per 100 000 for Hib. Uttar Pradesh (18 900 [UR 12 300–23 600]) and Bihar (8600 [5600–10 700]) had the highest numbers of pneumococcal deaths in 2015. Uttar Pradesh (9300 [UR 5900–12 700]) and Odisha (1100 [700–1500]) had the highest numbers of Hib deaths in 2015. Less conservative assumptions related to the proportion of pneumonia deaths attributable to pneumococcus indicate that as many as 118 000 (UR 69 000–140 000) total pneumococcal deaths could have occurred in 2015 in India.

Interpretation

Pneumococcal and Hib mortality have declined in children aged 1–59 months in India since 2000, even before nationwide implementation of conjugate vaccines. Introduction of the Hib vaccine in several states corresponded with a more rapid reduction in morbidity and mortality associated with Hib infection. Rapid scale-up and widespread use of the pneumococcal conjugate vaccine and sustained use of the Hib vaccine could help accelerate achievement of child survival targets in India.

Funding

Bill & Melinda Gates Foundation.

Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens

Globally, there are an estimated 10.6 million cases of meningitis and 288,000 deaths every year, with the vast majority occurring in low- and middle-income countries. In addition, many survivors suffer from long-term neurological sequelae. Most laboratories assay only for common bacterial etiologies using culture and directed PCR, and the majority of meningitis cases lack microbiological diagnoses, impeding institution of evidence-based treatment and prevention strategies. We report here the results of a validation and application study of using unbiased metagenomic sequencing to determine etiologies of idiopathic (of unknown cause) cases. This included CSF from patients with known neurologic infections, with idiopathic meningitis, and without infection admitted in the largest children’s hospital of Bangladesh and environmental samples. Using mNGS and machine learning, we identified and confirmed an etiology (viral or bacterial) in 40% of idiopathic cases. We detected three instances of Chikungunya virus (CHIKV) that were >99% identical to each other and to a strain previously recognized to cause systemic illness only in 2017. CHIKV qPCR of all remaining stored 472 CSF samples from children who presented with idiopathic meningitis in 2017 at the same hospital uncovered an unrecognized CHIKV meningitis outbreak. CSF mNGS can complement conventional diagnostic methods to identify etiologies of meningitis, and the improved patient- and population-level data can inform better policy decisions.

The burden of meningitis in low-and-middle-income countries remains significant, but the infectious causes remain largely unknown, impeding institution of evidence-based treatment and prevention decisions. We conducted a validation and application study of unbiased metagenomic next-generation sequencing (mNGS) to elucidate etiologies of meningitis in Bangladesh. This RNA mNGS study was performed on cerebrospinal fluid (CSF) specimens from patients admitted in the largest pediatric hospital, a World Health Organization sentinel site, with known neurologic infections (n = 36), with idiopathic meningitis (n = 25), and with no infection (n = 30), and six environmental samples, collected between 2012 and 2018. We used the IDseq bioinformatics pipeline and machine learning to identify potentially pathogenic microbes, which we then confirmed orthogonally and followed up through phone/home visits. In samples with known etiology and without infections, there was 83% concordance between mNGS and conventional testing. In idiopathic cases, mNGS identified a potential bacterial or viral etiology in 40%. There were three instances of neuroinvasive Chikungunya virus (CHIKV), whose genomes were >99% identical to each other and to a Bangladeshi strain only previously recognized to cause febrile illness in 2017. CHIKV-specific qPCR of all remaining stored CSF samples from children who presented with idiopathic meningitis in 2017 (n = 472) revealed 17 additional CHIKV meningitis cases, exposing an unrecognized meningitis outbreak. Orthogonal molecular confirmation, case-based clinical data, and patient follow-up substantiated the findings. Case-control CSF mNGS surveys can complement conventional diagnostic methods to identify etiologies of meningitis, conduct surveillance, and predict outbreaks. The improved patient- and population-level data can inform evidence-based policy decisions.

Seasonal variation and etiologic inferences of childhood pneumonia and diarrhea mortality in India

Control of pneumonia and diarrhea mortality in India requires understanding of their etiologies. We combined time series analysis of seasonality, climate region, and clinical syndromes from 243,000 verbal autopsies in the nationally representative Million Death Study. Pneumonia mortality at 1 month-14 years was greatest in January (Rate ratio (RR) 1.66, 99% CI 1.51-1.82; versus the April minimum). Higher RRs at 1-11 months suggested respiratory syncytial virus (RSV) etiology. India's humid subtropical region experienced a unique summer pneumonia mortality. Diarrhea mortality peaked in July (RR 1.66, 1.48-1.85) and January (RR 1.37, 1.23-1.48), while deaths with fever and bloody diarrhea (indicating enteroinvasive bacterial etiology) showed little seasonality. Combining mortality at ages 1-59 months with prevalence surveys, we estimate 40,600 pneumonia deaths from Streptococcus pneumoniae, 20,700 from RSV, 12,600 from influenza, and 7200 from Haemophilus influenzae type b and 24,700 diarrheal deaths from rotavirus occurred in 2015. Careful mortality studies can elucidate etiologies and inform vaccine introduction.

Invasive Pneumococcal Infections in Children with Nephrotic Syndrome in Bangladesh

INTRODUCTION

Children with nephrotic syndrome are susceptible to invasive bacterial infections. In this study, we aimed to: (1) determine the pathogens associated with infections in children with nephrotic syndrome and (2) describe antimicrobial susceptibility and serotype distribution of Streptococcus pneumoniae to guide evidence-based treatment and prevention policies.

METHODS

From June 2013 to March 2015, we collected blood and/or ascitic fluid from children hospitalized with nephrotic syndrome and suspected bacterial disease in the largest pediatric hospital of Bangladesh. We cultured all samples and performed polymerase chain reaction (PCR) and immunochromatographic test on ascitic fluid for detection of S. pneumoniae. Pneumococcal isolates were tested for antibiotic susceptibility using disc diffusion and serotyped using Quellung reaction and PCR.

RESULTS

We identified 1342 children hospitalized with nephrotic syndrome. Among them, 608 children had suspected bacterial disease from whom blood and/or ascitic fluid were collected. A pathogen was identified in 8% (48/608) of cases, 94% (45/48) of which were S. pneumoniae. Most (73%, 33/45) pneumococcal infections were identified through culture of blood and ascitic fluid and 27% (12/45) through immunochromatographic test and PCR of ascitic fluid. In total, 24 different pneumococcal serotypes were detected; 51% are covered by PCV10 (+6A), 53% by PCV13 and 60% by PPSV23. All pneumococcal isolates were susceptible to penicillin.

CONCLUSIONS

Because S. pneumoniae was the primary cause of invasive infections, pneumococcal vaccines may be considered as a preventive intervention in children with nephrotic syndrome. Additionally, penicillin can be used to prevent and treat pneumococcal infections in children with nephrotic syndrome in Bangladesh.

Spatial analysis of pneumococcal meningitis in São Paulo in the pre- and post-immunization era

OBJECTIVE

To analyze the pneumococcal meningitis incidence rates in the State of São Paulo, Brazil, by age group, municipalities and micro-regions, as well as the spatial distribution of pneumococcal meningitis incidence rates among children under 5 years old in the pre- (2005-2009) and post-vaccination (2011-2013) periods and its associations with socioeconomic variables and vaccination coverage.

METHODS

The data source was the Brazilian Notifiable Diseases Information System. For the pre- and post-vaccination periods, thematic maps were built for pneumococcal meningitis incidence in under-5 children, by São Paulo state micro-regions, vaccination coverage and socioeconomic variables, using QGIS 2.6.1 software. Scan statistics performed by the SatScan 9.2 software were used to analyze spatial and spatiotemporal clusters in São Paulo municipalities and micro-regions. A Bayesian inference for latent Gaussian model with zero-inflated Poisson model through the integrated nested Laplace approximation was used in the spatial analysis to evaluate associations between pneumococcal meningitis incidence rates and socioeconomic variables of interest in São Paulo micro-regions.

RESULTS

From 2005 to 2013, 3,963 pneumococcal meningitis cases were reported in São Paulo. Under-5 children were the most affected in the whole period. In the post-vaccination period, pneumococcal meningitis incidence rates decreased among this population, particularly among infants (from 4.17/100,000 in 2005 to 2.54/100,000 in 2013). Two clusters were found in pre-vaccination - one of low risk for pneumococcal meningitis, in the northwest of the state (OR = 0.45, p = 0.0003); and another of high risk in the southeast (OR = 1.62, p = 0.0000). In the post-vaccination period, only a high-risk cluster remained, in the southeast (RR = 1.97, p = 0.0570). In Bayesian analysis, wealth was the only variable positively associated to pneumococcal meningitis (RR = 1.026, 95%CI 1.002-1.052).

CONCLUSIONS

Pneumococcal meningitis is probably underdiagnosed and underreported in São Paulo. Differentiated rates of pneumococcal meningitis diagnosis and reporting in each microregion, according to the São Paulo Index of Social Responsibility, might explain our results.

Spatial analysis of pneumococcal meningitis in São Paulo in the pre- and post-immunization era

OBJECTIVE

To analyze the pneumococcal meningitis incidence rates in the State of São Paulo, Brazil, by age group, municipalities and micro-regions, as well as the spatial distribution of pneumococcal meningitis incidence rates among children under 5 years old in the pre- (2005-2009) and post-vaccination (2011-2013) periods and its associations with socioeconomic variables and vaccination coverage.

METHODS

The data source was the Brazilian Notifiable Diseases Information System. For the pre- and post-vaccination periods, thematic maps were built for pneumococcal meningitis incidence in under-5 children, by São Paulo state micro-regions, vaccination coverage and socioeconomic variables, using QGIS 2.6.1 software. Scan statistics performed by the SatScan 9.2 software were used to analyze spatial and spatiotemporal clusters in São Paulo municipalities and micro-regions. A Bayesian inference for latent Gaussian model with zero-inflated Poisson model through the integrated nested Laplace approximation was used in the spatial analysis to evaluate associations between pneumococcal meningitis incidence rates and socioeconomic variables of interest in São Paulo micro-regions.

RESULTS

From 2005 to 2013, 3,963 pneumococcal meningitis cases were reported in São Paulo. Under-5 children were the most affected in the whole period. In the post-vaccination period, pneumococcal meningitis incidence rates decreased among this population, particularly among infants (from 4.17/100,000 in 2005 to 2.54/100,000 in 2013). Two clusters were found in pre-vaccination - one of low risk for pneumococcal meningitis, in the northwest of the state (OR = 0.45, p = 0.0003); and another of high risk in the southeast (OR = 1.62, p = 0.0000). In the post-vaccination period, only a high-risk cluster remained, in the southeast (RR = 1.97, p = 0.0570). In Bayesian analysis, wealth was the only variable positively associated to pneumococcal meningitis (RR = 1.026, 95%CI 1.002-1.052).

CONCLUSIONS

Pneumococcal meningitis is probably underdiagnosed and underreported in São Paulo. Differentiated rates of pneumococcal meningitis diagnosis and reporting in each microregion, according to the São Paulo Index of Social Responsibility, might explain our results.

Quadruple valve infective endocarditis presenting with suspected Austrian syndrome: a case report and a case series of quadruple valve infective endocarditis

OBJECTIVES

Austrian syndrome comprises the triad of pneumonia, meningitis, and endocarditis secondary to Streptococcus pneumonia. We present what we believe to be the first reported case of Austrian syndrome with quadruple heart valve involvement and review the literature detailing cases of quadruple valve infective endocarditis.

CASE PRESENTATION AND RESULTS

A case is presented of a patient with radiographic evidence of a left lower lobe pneumonia. Sequential transthoracic followed by transesophageal echocardiogram done to evaluate the presence of a cardiac murmur revealed the presence of quadruple valve vegetations. Multiple blood cultures were persistently negative. The patient went on to develop seizures secondary to proven meningitis. Microbiological diagnosis was eventually established through positive Streptococcus pneumoniae antigen (Alere BinaxNOW®) from cerebrospinal fluid, establishing a presumptive clinical diagnosis of Austrian syndrome. A computerized PubMed search for reports of quadruple valve infective endocarditis and their references was collated. A total of 22 patients were found, including our patient. The median age of presentation was 47.5 years. Five patients had a history of intravenous drug abuse, another 5 had underlying congenital heart disease, and 1 had both. Two patients (9.1%) had 2 microorganisms isolated. Staphylococcus aureus and Streptococcus viridans (3 cases, 13.6% each) were the most commonly implicated microorganism. Heart failure was the commonest complication, afflicting 11 patients (50.0%). Ten patients (45.5%) underwent surgery. Overall case fatality rate was 50.0%. Cardiac surgery was of statistical significance in predicting survival (P = 0.009).

CONCLUSION

Quadruple valve endocarditis is associated with a high mortality rate, and cardiac surgery may be protective.

Incidence and aetiology of bacterial meningitis among children aged 1-59 months in South Asia: systematic review and meta-analysis

BACKGROUND

Bacterial meningitis is a significant cause of morbidity and mortality worldwide among children aged 1-59 months. We aimed to describe its burden in South Asia, focusing on vaccine-preventable aetiologies.

METHODS

We searched five databases for studies published from January 1, 1990, to April 25, 2017. We estimated incidence and aetiology-specific proportions using random-effects meta-analysis. In secondary analyses, we described vaccine impact and pneumococcal meningitis serotypes.

RESULTS

We included 48 articles cumulatively reporting 20,707 cases from 1987 to 2013. Mean annual incidence was 105 (95% confidence interval [CI], 53-173) cases per 100,000 children. On average, Haemophilus influenzae type b (Hib) accounted for 13% (95% CI, 8-19%) of cases, pneumococcus for 10% (95% CI, 6-15%), and meningococcus for 1% (95% CI, 0-2%). These meta-analyses had substantial between-study heterogeneity (I² > 78%, P < 0.0001). Among studies reporting only confirmed cases, these three bacteria caused a median of 78% cases (IQR, 50-87%). Hib meningitis incidence declined by 72-83% at sentinel hospitals in Pakistan and Bangladesh, respectively, within two years of implementing nationwide vaccination. On average, PCV10 covered 49% (95% CI, 39-58%), PCV13 covered 51% (95% CI, 40-61%), and PPSV23 covered 74% (95% CI, 67-80%) of pneumococcal meningitis serotypes. Lower PCV10 and PCV13 serotype coverage in Bangladesh was associated with higher prevalence of serotype 2, compared to India and Pakistan.

CONCLUSIONS

South Asia has relatively high incidence of bacterial meningitis among children aged 1-59 months, with vaccine-preventable bacteria causing a substantial proportion. These estimates are likely underestimates due to multiple epidemiological and microbiological factors. Further research on vaccine impact and distribution of pneumococcal serotypes will inform vaccine policymaking and implementation.

Frequent Community Use of Antibiotics among a Low-Economic Status Population in Manila, the Philippines: A Prospective Assessment Using a Urine Antibiotic Bioassay

The widespread unregulated use of antibiotics without medical consultation contributes to the burden of antibiotic resistance in Southeast Asian countries. This study investigated antibiotic use before hospital consultation. In a prospective observational study from February 2, 2015, to July 2, 2015, we enrolled febrile patients attending the emergency room in San Lazaro Hospital, Manila, the Philippines. A urine sample was collected and a bioassay was used to detect antibiotic activity in urine using Bacillus stearothermophilus (ATCC7953), Escherichia coli (ATCC25922), and Streptococcus pyogenes (ATCC19615). Patients or caregivers reported their medication history, clinical information, and socioeconomic status. During the study period, 410 patients were enrolled. The median (interquartile range) age was 14 (7-23) years and 158 (39%) reported prior antibiotic use, predominantly a beta-lactam antibiotic. A total of 164 (40%, 95% confidence interval [CI]: 35-45) patients were urine bioassay positive with any of three organisms. The Bacillus assay was the most sensitive, detecting 162 (99%, 95% CI: 96-100) cases. Among bioassay positive patients, dengue (N = 91, 55%, 95% CI: 48-63) was the most frequent diagnosis, followed by other viral infections, including measles, rubella, and mumps (N = 17, 10%, 95% CI: 6-16). Patients with a positive bioassay were significantly more likely to be from the lowest-income group (adjusted odds ratio [AOR]: 1.7; 95% CI: 1.1-2.6) and required hospital admission (AOR: 2.1; 95% CI: 1.3-3.5). Unnecessary antibiotic use for febrile illnesses before hospital consultation is common in a low-income, highly populated urban community in Manila. Education targeting this group should be implemented to reduce unnecessary antibiotic use.

Loop-Mediated Isothermal Amplification Methods for Diagnosis of Bacterial Meningitis

The rapid, accurate, and efficient identification of an infectious disease is critical to ensure timely clinical treatment and prevention in public health settings. In 2015, meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis was responsible for 379,200 (range: 322,700-444,700) deaths. Clinical features alone cannot determine whether bacterial meningitis is present; an analysis of cerebrospinal fluid (CSF) is essential. Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method offering an alternative to polymerase chain reaction (PCR). LAMP-based assays for detection of three leading bacteria in CSF for diagnosis of meningitis have been established. The typing assays using LAMP for detection of meningococcal serogroups A, B, C, W, X, and Y as well as H. influenzae serotypes a, b, c, d, e, and f were launched. In comparative analysis of the meningitis pathogen assays, LAMP assays did not yield false negative results, and the detection rate of LAMP assays was superior compared with PCR or conventional culture methods. LAMP assays provide accurate and rapid test results to detect major bacterial meningitis pathogens. Accumulating evidence suggests that LAMP assays have the potential to provide urgently needed diagnostics for bacterial meningitis in resource-limited settings of both developed and developing countries.

Central Nervous System Infections

This chapter provides an overview of infectious syndromes, pathogens, and diagnostic testing modalities for central nervous system infections in the immunocompromised host.

Rapid diagnostic test for respiratory infections

Acute respiratory infections are the second cause of morbidity and mortality in children and adults worldwide, being viruses, bacteria and fungi involved in their aetiology. The rapid diagnosis allows for a better clinical management of the patient, for adopting public health measures and for controlling possible outbreaks. The main etiologic agents can be diagnosed within the first hours after the onset of symptoms with antigen detection techniques, primarily immunochromatography. Results are obtained in 15–30 min, with 70–90% sensitivity and >95% specificity for the diagnosis of Streptococcus pneumoniae and Legionella pneumophila serogroup O1 infections from urine, Streptococcus pyogenes from throat swabs and respiratory syncytial virus from nasopharyngeal aspirates. Worse results are obtained for influenza viruses and Pneumocystis jirovecii with these techniques; however, other easy-to-perform molecular techniques are available for the rapid diagnosis of these microorganisms. In general, these techniques should not be used for monitoring the outcome or response to treatment.

[Rapid diagnostic test for respiratory infections]

Acute respiratory infections are the second cause of morbidity and mortality in children and adults worldwide, being viruses, bacteria and fungi involved in their etiology. The rapid diagnosis allows for a better clinical management of the patient, for adopting public health measures and for controlling possible outbreaks. The main etiologic agents can be diagnosed within the first hours after the onset of symptoms with antigen detection techniques, primarily immunochromatography. Results are obtained in 15-30minutes, with 70-90% sensitivity and >95% specificity for the diagnosis of Streptococcus pneumoniae and Legionella pneumophila serogroup O1 infections from urine, Streptococcus pyogenes from throat swabs and respiratory syncytial virus from nasopharyngeal aspirates. Worse results are obtained for influenza viruses and Pneumocystis jirovecii with these techniques; however, other easy-to-perform molecular techniques are available for the rapid diagnosis of these microorganisms. In general, these techniques should not be used for monitoring the outcome or response to treatment.

Real-time qPCR improves meningitis pathogen detection in invasive bacterial-vaccine preventable disease surveillance in Fiji

As part of the World Health Organization Invasive Bacterial-Vaccine Preventable Diseases (IB-VPD) surveillance in Suva, Fiji, cerebrospinal fluid (CSF) samples from suspected meningitis patients of all ages were examined by traditional methods (culture, Gram stain, and latex agglutination for bacterial antigen) and qPCR for Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. Of 266 samples tested, pathogens were identified in 47 (17.7%). S. pneumoniae was the most common pathogen detected (n = 17) followed by N. meningitidis (n = 13). The use of qPCR significantly increased detection of IB-VPD pathogens (P = 0.0001): of 35 samples that were qPCR positive for S. pneumoniae, N. meningitidis, and H. influenzae, only 10 were culture positive. This was particularly relevant for N. meningitidis, as only 1/13 cases was culture positive. Molecular serotyping by microarray was used to determine pneumococcal serotypes from 9 of 16 (56%) of samples using DNA directly extracted from CSF specimens. Results indicate that qPCR significantly increases detection of S. pneumoniae, N. meningitidis, and H. influenzae in CSF, and that application of molecular diagnostics is a feasible way to enhance local and global surveillance for IB-VPD.

PCR-Based Serotyping of Streptococcus pneumoniae from Culture-Negative Specimens: Novel Primers for Detection of Serotypes within Serogroup 18

Six multiplex-compatible PCR primers were designed to distinguish Streptococcus pneumoniae serotypes within serogroup 18 from culturable/nonculturable pneumococcal specimens, with no cross-reactivity with other serotypes and respiratory organisms. These primers will aid in the generation of better data on vaccine/nonvaccine serotypes in invasive and carriage pneumococcal surveillance and contribute to future vaccine formulation and impact studies.

Epidemiology of Invasive Pneumococcal Disease in Bangladeshi Children Before Introduction of Pneumococcal Conjugate Vaccine

BACKGROUND

Because Bangladesh intended to introduce pneumococcal conjugate vaccine (PCV)-10 in 2015, we examined the baseline burden of invasive pneumococcal disease (IPD) to measure impact of PCV.

METHODS

During 2007-2013, we performed blood and cerebrospinal fluid cultures in children <5 years old with suspected IPD identified through active surveillance at 4 hospitals. Isolates were serotyped by quellung and tested for antibiotic susceptibility by disc diffusion and E-test. Serotyping of culture-negative cases, detected by Binax or polymerase chain reaction, was done by sequential multiplex polymerase chain reaction. Trends in IPD case numbers were analyzed by serotype and clinical syndrome.

RESULTS

The study identified 752 IPD cases; 78% occurred in children <12 months old. Serotype information was available for 78% (442/568), including 197 of 323 culture-negative cases available for serotyping. We identified 50 serotypes; the most common serotypes were 2 (16%), 1 (10 %), 6B (7%), 14 (7%) and 5 (7%). PCV-10 and PCV-13 serotypes accounted for 46% (range 29%-57% by year) and 50% (range 37%-64% by year) of cases, respectively. Potential serotype coverage for meningitis and nonmeningitis cases was 45% and 49% for PCV-10, and 48% and 57% for PCV-13, respectively. Eighty-two percent of strains were susceptible to all antibiotics except cotrimoxazole.

CONCLUSION

The distribution of serotypes causing IPD in Bangladeshi children is diverse, limiting the proportion of IPD cases PCV can prevent. However, PCV introduction is expected to have major benefits as the country has a high burden of IPD-related mortality, morbidity and disability.

South Asia symposium on pneumococcal disease and the promise of vaccines - Meeting report

Despite the licensure of the pneumococcal conjugate vaccine (PCV) in the US and other Western countries for over 14 years, as of September 2014 only 4 South Asian countries were using PCV in their universal immunization program. To generate momentum toward addressing this issue a "South Asia symposium on pneumococcal disease and the promise of vaccines" was organized just prior to the 9th international symposium on pneumococci and pneumococcal diseases held in India recently. Leading scientists, program managers, and decision makers including ministry officials from the region participated in the meeting. The participants discussed available data on pneumococcal disease burden in South Asia, surveillance methods, efficacy and safety of pneumococcal conjugate vaccines (PCV), the status of PCV introduction, programmatic challenges in introducing PCV and available data on the impact of PCV in South Asia and globally. There was a strong consensus that available data on disease burden and the global experience with PCV justified the introduction PCV in all Asian countries in order to accelerate the gains in child survival in the region.

Improving diagnosis of pneumococcal disease by multiparameter testing and micro/nanotechnologies

The diagnosis and management of pneumococcal disease remains challenging, in particular in children who often are asymptomatic carriers, and in low-income countries with a high morbidity and mortality from febrile illnesses where the broad range of bacterial, viral and parasitic cases are in contrast to limited, diagnostic resources. Integration of multiple markers into a single, rapid test is desirable in such situations. Likewise, the development of multiparameter tests for relevant arrays of pathogens is important to avoid overtreatment of febrile syndromes with antibiotics. Miniaturization of tests through use of micro- and nanotechnologies combines several advantages: miniaturization reduces sample requirements, reduces the use of consumables and reagents leading to a reduction in costs, facilitates parallelization, enables point-of-care use of diagnostic equipment and even reduces the amount of potentially infectious disposables, characteristics that are highly desirable in most healthcare settings. This critical review emphasizes our vision on the importance of multiparametric testing for diagnosing pneumococcal infections in patients with fever and examines recent relevant developments in micro/nanotechnologies to achieve this goal.

Enhanced Diagnosis of Pneumococcal Bacteremia Using Antigen- and Molecular-Based Tools on Blood Specimens in Mali and Thailand: A Prospective Surveillance Study

Prior antibiotic use, contamination, limited blood volume, and processing delays reduce yield of blood cultures for detection of Streptococcus pneumoniae. We performed immunochromatographic testing (ICT) on broth from incubated blood culture bottles and real-time lytA polymerase chain reaction (PCR) on broth and whole blood and compared findings to blood culture in patients with suspected bacteremia. We selected 383 patients in Mali and 586 patients in Thailand based on their blood culture results: 75 and 31 were positive for pneumococcus, 100 and 162 were positive for other pathogens, and 208 and 403 were blood culture negative, respectively. ICT and PCR of blood culture broth were at least 87% sensitive and 97% specific compared with blood culture; whole blood PCR was 75–88% sensitive and 96–100% specific. Pneumococcal yields in children < 5 years of age increased from 2.9% to 10.7% in Mali with > 99% of additional cases detected by whole blood PCR, and from 0.07% to 5.1% in Thailand with two-thirds of additional cases identified by ICT. Compared with blood culture, ICT and lytA PCR on cultured broth were highly sensitive and specific but their ability to improve pneumococcal identification varied by site. Further studies of these tools are needed before widespread implementation.

Time window for positive cerebrospinal fluid broad-range bacterial PCR and Streptococcus pneumoniae immunochromatographic test in acute bacterial meningitis

BACKGROUND

Reliable microbiological tests are essential for the diagnosis of acute bacterial meningitis (ABM). In this study we investigated the time period after the start of antibiotic therapy during which culture, polymerase chain reaction (PCR) and the immunochromatographic test (ICT) are able to detect bacteria in cerebrospinal fluid (CSF).

METHODS

The study was performed on CSF samples from adults with ABM admitted to the Department of Infectious Diseases, Sahlgrenska University Hospital, Gothenburg, Sweden, from January 2007 to April 2014. In addition to the initial lumbar puncture (LP), the participants underwent one or two more LPs during 10 days following the start of antibiotics. The analyses performed on the CSF samples were culture, PCR and ICT.

RESULTS

The study comprised 70 CSF samples from 25 patients with ABM. A bacterium could be identified by CSF culture in 44%, by blood culture in 58% and by PCR in 100% of the patients. There were no positive CSF cultures in samples taken later than the day of starting antibiotics. PCR was positive in 89% on days 1-3, 70% on days 4-6 and 33% on days 7-10. For cases of pneumococcal meningitis, the ICT was positive in 88% on days 1-3, 90% on days 4-6 and 75% on days 7-10.

CONCLUSIONS

This study shows that PCR is highly sensitive for bacterial detection in CSF samples taken up to 1 week into antibiotic therapy. The ICT is highly sensitive for the detection of pneumococci in CSF samples taken during the first week of antibiotic treatment.

Methods of rapid diagnosis for the etiology of meningitis in adults

Infectious meningitis may be due to bacterial, mycobacterial, fungal or viral agents. Diagnosis of meningitis must take into account numerous items of patient history and symptomatology along with regional epidemiology and basic cerebrospinal fluid testing (protein, etc.) to allow the clinician to stratify the likelihood of etiology possibilities and rationally select additional diagnostic tests. Culture is the mainstay for diagnosis in many cases, but technology is evolving to provide more rapid, reliable diagnosis. The cryptococcal antigen lateral flow assay (Immuno-Mycologics) has revolutionized diagnosis of cryptococcosis and automated nucleic acid amplification assays hold promise for improving diagnosis of bacterial and mycobacterial meningitis. This review will focus on a holistic approach to diagnosis of meningitis as well as recent technological advances.

Aetiology of paediatric pneumonia with effusion in the Dominican Republic and the potential impact of pneumococcal conjugate vaccines

Pleural effusion is a serious complication of pneumonia, and Streptococcus pneumoniae is a leading cause. We describe the aetiology of pneumonia with effusion among children in the Dominican Republic before the introduction of the 13-valent pneumococcal conjugate vaccine (PCV) in 2013 and the performance characteristics of a rapid immunochromatographic test (ICT) for detecting S. pneumoniae in pleural fluid. From July 2009 to June 2011, we enrolled children <15 years old admitted with pneumonia and pleural effusion to Robert Reid Cabral Children’s Hospital, Dominican Republic. Pleural fluid was tested by culture, polymerase chain reaction (PCR) for bacterial (S. pyogenes, S. pneumoniae) and viral (respiratory syncytial virus and human rhinovirus) pathogens, and by ICT for S. pneumoniae. We calculated the performance of ICT and culture compared with PCR. Among 121 cases, the median age was 31 months (range 1 week to 14 years). Pleural fluid culture (n = 121) and PCR testing (n = 112) identified an aetiology in 85 (70.2%) cases, including 62 S. pneumoniae (51.2%) and 19 Staphylococcus aureus (15.7%). The viruses tested were not detected. The most prevalent pneumococcal serotypes were 14 (n = 20), 1 (n = 13), and 3 (n = 12). Serotype coverage of the 10- and 13-valent PCVs would be 70.5% and 95.1%, respectively. The sensitivity of point-of-care ICT was 100% (95% confidence interval [CI] 94.1%–100%), while specificity was 86.3% (95% CI 73.7%–94.3%). S. pneumoniae caused more than half of paediatric pneumonia with effusion cases; introduction of PCV in the Dominican Republic could reduce the burden by 36–49%. ICT is a practical, valid diagnostic tool for clinical care and surveillance in settings with limited laboratory capacity.

Impact of introduction of the Haemophilus influenzae type b conjugate vaccine into childhood immunization on meningitis in Bangladeshi infants

OBJECTIVES

Some Asian countries have been reluctant to adopt Haemophilus influenzae type b (Hib) conjugate vaccination because of uncertainty over disease burden. We assessed the impact of introduction of Hib conjugate vaccine into the Expanded Program on Immunization in Bangladesh on purulent and laboratory-confirmed H influenzae meningitis.

STUDY DESIGN

Within a well-defined catchment area around 2 surveillance hospitals in Dhaka, Bangladesh, we compared the incidence of Hib meningitis confirmed by culture, latex agglutination, and polymerase chain reaction assay among infants 1 year before and 1 year after introduction of Hib conjugate vaccine. We adjusted the incidence rate for the proportion of children who sought care at the surveillance hospitals.

RESULTS

Among infants, the incidence of confirmed Hib meningitis decreased from 92-16 cases per 100,000 within 1 year of vaccine introduction (vaccine preventable incidence = 76; 95% CI 18, 135 per 100,000). The incidence of purulent meningitis decreased from 1659-1159 per 100,000 (vaccine preventable incidence = 500; 95% CI: 203, 799 per 100,000). During the same time period, there was no significant difference in the incidence of meningitis due to Streptococcus pneumoniae.

CONCLUSIONS

Introduction of conjugate Hib conjugate vaccine into Bangladesh Expanded Program on Immunization markedly reduced the burden of Hib and purulent meningitis.

Rapid diagnostic tests for neurological infections in central Africa

Infections are a leading cause of life-threatening neuropathology worldwide. In central African countries affected by endemic diseases such as human African trypanosomiasis, tuberculosis, HIV/AIDS, and schistosomiasis, delayed diagnosis and treatment often lead to avoidable death or severe sequelae. Confirmatory microbiological and parasitological tests are essential because clinical features of most neurological infections are not specific, brain imaging is seldom feasible, and treatment regimens are often prolonged or toxic. Recognition of this diagnostic bottleneck has yielded major investment in application of advances in biotechnology to clinical microbiology in the past decade. We review the neurological pathogens for which rapid diagnostic tests are most urgently needed in central Africa, detail the state of development of putative rapid diagnostic tests for each, and describe key technical and operational challenges to their development and implementation. Promising field-suitable rapid diagnostic tests exist for the diagnosis of human African trypanosomiasis and cryptococcal meningoencephalitis. For other infections-eg, syphilis and schistosomiasis-highly accurate field-validated rapid diagnostic tests are available, but their role in diagnosis of disease with neurological involvement is still unclear. For others-eg, tuberculosis-advances in research have not yet yielded validated tests for diagnosis of neurological disease.

Pleural fluid nucleic acid testing enhances pneumococcal surveillance in children

BACKGROUND AND OBJECTIVE

National surveillance of invasive pneumococcal disease (IPD) includes serotyping Streptococcus pneumoniae (SP) isolates from sterile site cultures. PCR is more sensitive and can identify more SP serotypes (STs) in culture-negative samples. The aim of this study was to determine whether enhanced surveillance of childhood empyema, using PCR, provides additional serotype information compared with conventional surveillance.

METHODS

Pleural fluid (PF) from children with empyema were cultured and tested by PCR to identify SP, targeting the autolysin gene (lytA). Multiplex PCR-based reverse line blot assay was used to identify SP STs. Corresponding IPD surveillance and serotype data were obtained from the National Notifiable Diseases Surveillance System (NNDSS).

RESULTS

Eighty-nine children with empyema, aged ≤16 years, were recruited between April 2008 and March 2009, inclusive. SP was isolated from 5/84 (5.9%) PF cultures and by PCR in 43/79 (54.4%) PF samples. Serotypes were unidentifiable in 15 samples. The frequency of six serotypes (or serotype pairs) identified in 28 samples, including one with two serotypes, were: ST1, n = 4/29 (13.8%); ST3, n = 9/29 (31.0%); ST19A, n = 12/29 (41.4%); ST7F/7A, n = 1/29 (3.4%); ST9V/9A, n = 1/29 (3.4%); ST22F/22A, n = 2/29 (6.9%). Over the same period, 361 IPD patients, aged 16 years or less, were notified to NNDSS. Among 331 serotypeable NNDSS isolates (71.5% from blood), the frequencies of ST1 and 3 were significantly lower than in PF samples: ST1, n = 8/331 (2.4%; P < 0.05); ST3, n = 13/331 (3.9%; P < 0.0001).

CONCLUSIONS

The use of PCR to identify and serotype SP in culture-negative specimens provides additive information.

Meningitis in children in Fiji: etiology, epidemiology, and neurological sequelae

OBJECTIVES

To describe the etiology, epidemiology, neurological sequelae, and quality of life of children aged 1 month to less than 5 years admitted with meningitis to the Colonial War Memorial Hospital (CWMH), Suva, Fiji.

METHODS

Over a 3-year period, all eligible children with suspected meningitis admitted to CWMH had blood drawn for culture. Of these children, those for whom is was possible were tested for a four-fold rise in antibody titers to Haemophilus influenzae type b (Hib) and pneumococcal surface adhesin A (PsaA). Cerebrospinal fluid (CSF) was taken for bacteriological culture and antigen testing. CSF was also tested by PCR for Streptococcus species, Neisseria meningitidis, Hib, Mycobacterium tuberculosis, and enterovirus. Pneumococcal isolates were serotyped using multiplex-PCR reverse-line blot hybridization. Following discharge, cases underwent a neurological assessment, audiometry, and quality of life assessment (Pediatric Quality of Life Inventory (PedsQL) tool).

RESULTS

There were 70 meningitis cases. Meningitis was more common in indigenous Fijian than Indo-Fijian children. Enterovirus was the most common etiological agent and appeared to be outbreak-associated. Streptococcus pneumoniae was the most common bacterial cause of meningitis with an annual incidence of 9.9 per 100 000 under 5 years old (95% confidence interval 4.9-17.7) and a case fatality rate of 36%. With the exception of deafness, neurological sequelae were more frequent in cases of bacterial meningitis than in viral meningitis (18.5% vs. 0%, p=0.04). Quality of life at follow-up was significantly lower in patients with bacterial meningitis than in those with viral meningitis (p=0.003) or meningitis of unknown etiology (p=0.004).

CONCLUSIONS

During the study period an outbreak of enterovirus occurred making it the most common etiological agent identified. However in the absence of this outbreak, S. pneumoniae was the most common cause of childhood meningitis in Fiji. Bacterial meningitis is associated with serious sequelae and a reduced quality of life.

Burden of pneumonia and meningitis caused by Streptococcus pneumoniae in China among children under 5 years of age: a systematic literature review

BACKGROUND AND METHODS

To understand the burden and epidemiology of Streptococcus pneumoniae disease among children between 1 and 59 months of age in China, we conducted a review of literature published between 1980 and 2008 applying standardized algorithms. Because of the absence of population-based surveillance for pneumococcal disease (PD), we identified all-cause pneumonia, bacteremia and meningitis burden, syndromes most commonly associated with S. pneumoniae, and applied the proportion of disease attributable to S. pneumoniae from studies that determined the etiology of these three syndromes to calculate PD burden. Because of the microbiologic difficulties in identifying S. pneumoniae-attributable pneumonia which likely underestimates the pneumonia burden, we also used the proportion obtained from vaccine efficacy trials.

RESULTS

Between 1980 and 2008, there were 12,815 cases/100,000/year of all-cause pneumonia among children between 1 month and 59 months, with 526 deaths/100,000 annually. There were 14 meningitis cases/100,000/year. We estimate that as of 2000, there were 260,768 (113,000 to 582,382) and 902 (114-4,463) cases of pneumococcal pneumonia and meningitis, respectively with 10,703 (4,638-23,904) and 75 (9-370) pneumococcal pneumonia and meningitis deaths, respectively. Pneumococcal pneumonia cases and deaths were more than two-fold higher, 695,382 (173,845-1,216,918) and 28,542 (7,136-49,949), respectively, when parameters from efficacy trials were used. Serotypes 19F, 19A and 14 were the most common serotypes obtained from pneumonia/meningitis patients. Currently available vaccines are expected to cover 79.5% to 88.4% of the prevalent serotypes. With high antibiotic resistance, introducing pneumococcal vaccines to the routine immunization program should be considered in China. Population-based studies are warranted.

Improving the sensitivity of blood culture for Streptococcus pneumoniae

Isolation of Streptococcus pneumoniae is jeopardized by low sensitivity of blood culture, autolysis and contamination with fast-growing organism(s). We performed an immunochromatographic (ICT) test for S. pneumoniae on chocolatized blood culture bottles and also sub-cultured contaminated bottles on a selective medium, thus identifying an additional eight and three cases, respectively, and improving the detection of pneumococcus by 23% (48% vs. 59%). Prescreening of culture bottles in a blinded fashion could rationalize the use of ICT with ~99% accuracy. These two approaches can aid microbiology laboratories in resource-poor countries to substantially improve rates of detection of S. pneumoniae.