https://publications.hse.ru/mirror/pubs/share/folder/myodg9xfxt/direct/143360779.pdf

Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: A systematic analysis for the Global Burden of Disease Study 2013

https://www.who.int/immunization/diseases/pneumococcal/GBD_pneumococcus.pdf

Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates

Summary Background Lower respiratory infections are a leading cause of morbidity and mortality around the world The Global Burden of Diseases, Injuries, and Risk Factors (GBD) Study 2016, provides an up-to-date analysis of the burden of lower respiratory infections in 195 countries This study assesses cases, deaths, and aetiologies spanning the past 26 years and shows how the burden of lower respiratory infection has changed in people of all ages Methods We used three separate modelling strategies for lower respiratory infections in GBD 2016: a Bayesian hierarchical ensemble modelling platform (Cause of Death Ensemble model), which uses vital registration, verbal autopsy data, and surveillance system data to predict mortality due to lower respiratory infections; a compartmental meta-regression tool (DisMod-MR), which uses scientific literature, population representative surveys, and health-care data to predict incidence, prevalence, and mortality; and modelling of counterfactual estimates of the population attributable fraction of lower respiratory infection episodes due to Streptococcus pneumoniae, Haemophilus influenzae type b, influenza, and respiratory syncytial virus We calculated each modelled estimate for each age, sex, year, and location We modelled the exposure level in a population for a given risk factor using DisMod-MR and a spatio-temporal Gaussian process regression, and assessed the effectiveness of targeted interventions for each risk factor in children younger than 5 years We also did a decomposition analysis of the change in LRI deaths from 2000–16 using the risk factors associated with LRI in GBD 2016 Findings In 2016, lower respiratory infections caused 652 572 deaths (95% uncertainty interval [UI] 586 475–720 612) in children younger than 5 years (under-5s), 1 080 958 deaths (943 749–1 170 638) in adults older than 70 years, and 2 377 697 deaths (2 145 584–2 512 809) in people of all ages, worldwide Streptococcus pneumoniae was the leading cause of lower respiratory infection morbidity and mortality globally, contributing to more deaths than all other aetiologies combined in 2016 (1 189 937 deaths, 95% UI 690 445–1 770 660) Childhood wasting remains the leading risk factor for lower respiratory infection mortality among children younger than 5 years, responsible for 61·4% of lower respiratory infection deaths in 2016 (95% UI 45·7–69·6) Interventions to improve wasting, household air pollution, ambient particulate matter pollution, and expanded antibiotic use could avert one under-5 death due to lower respiratory infection for every 4000 children treated in the countries with the highest lower respiratory infection burden Interpretation Our findings show substantial progress in the reduction of lower respiratory infection burden, but this progress has not been equal across locations, has been driven by decreases in several primary risk factors, and might require more effort among elderly adults By highlighting regions and populations with the highest burden, and the risk factors that could have the greatest effect, funders, policy makers, and programme implementers can more effectively reduce lower respiratory infections among the world's most susceptible populations Funding Bill & Melinda Gates Foundation

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

https://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(10)62225-8.pdf

Serotype replacement in disease after pneumococcal vaccination

The British Thoracic Society first published management guidelines for community acquired pneumonia in children in 2002 and covered available evidence to early 2000. These updated guidelines represent a review of new evidence since then and consensus clinical opinion where evidence was not found. This document incorporates material from the 2002 guidelines and supersedes the previous guideline document.

https://thorax.bmj.com/content/thoraxjnl/66/Suppl_2/ii1.full.pdf

British Thoracic Society guidelines for the management of community acquired pneumonia in children: update 2011

Background and aim Influenza diagnostics play a critical role informing in clinical management decisions and defining the global epidemiology of the disease to support public health responses. Use of influenza diagnostics within most low-income and middle-income countries remains limited, including in the Philippines, where they are currently used only for epidemiologic surveillance. The aim of this study was to define key considerations, including product characteristics, which may influence future adoption, uptake, and integration of influenza diagnostics into public and private clinical settings in this emerging Asian market. Methods Our study was conducted using a convenience sample of public and private hospital laboratories in Metro Manila. A usability assessment was conducted that included interviews with decision-makers and direct observation of laboratory end users using 2 platforms representative of emerging diagnostic products: (1) a point-of-care antigen-based rapid immunoassay diagnostic test paired with a reader and (2) a molecular diagnostic platform intended for decentralized use. Data were analyzed to assess user errors and device failure modes with each platform and to determine key considerations related to product adoption and uptake. Results The most difficult test step for most users on both platforms involved sample preparation. When deciding to adopt a new test, priority product attributes include performance, potential volume of demand from clinicians, equipment cost, and ease of use. Demand for new tests is likely going to be driven by clinicians, and policies and guidelines will be needed to support the introduction of new products. Conclusion Adoption of influenza diagnostics in Metro Manila is feasible but will require affordable products capable of satisfying needs for use in both epidemiologic surveillance and clinical management.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/hsr2.75

Understanding user requirements to improve adoption of influenza diagnostics in clinical care within Metro Manila.

Large outbreaks of measles occurred in the Philippines in 2010 and 2011. Genetic analysis was performed to identify the genotype of measles virus (MeV) that was responsible for the large outbreaks. A total of 114 representative MeVs that were detected in the Philippines from 2008 to 2011 were analyzed by sequencing the C-terminal region of nucleocapsid (N) gene and partial hemagglutinin (H) gene and by inferring the phylogenetic trees. Genetic analysis showed that genotype D9 was the predominant circulating strain during the 4-year study period. Genotype D9 was detected in 23 samples (92%) by N gene sequencing and 93 samples (94%) by H gene analysis. Sporadic cases of genotype G3 MeV were identified in 2 samples (8%) by N gene sequencing and 6 samples (6%) by H gene analysis. Genotype G3 MeV was detected mainly in Panay Island in 2009 and 2010. Molecular clock analysis of N gene showed that the recent genotype D9 viruses that caused the big outbreaks in 2010 and 2011 diverged from a common ancestor in 2005 in one of the neighboring Southeast Asian countries, where D9 was endemic. These big outbreaks of measles resulted in a spillover and were associated with genotype D9 MeV importation to Japan and the USA. Genotype D9 MeV became endemic and caused two big outbreaks in the Philippines in 2010 and 2011. Genotype G3 MeV was detected sporadically with limited geographic distribution. This study highlights the importance of genetic analysis not only in helping with the assessment of measles elimination program in the country but also in elucidating the transmission dynamics of measles virus.

/pdf/genetic-characterization-of-measles-virus-in-the-philippines-16x4knq76d.pdf

Genetic characterization of measles virus in the Philippines, 2008–2011

Research activities and responding to typhoon Haiyan (Yolanda): Tohoku-RITM collaborating research center in the Philippines

Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory infection, and therefore, a major threat to global health. This study determined the epidemiological and molecular characteristics of RSV among cases of influenza‐like illness (ILI) and severe acute respiratory infection (SARI) among children in the Philippines.

https://doi.org/10.22541/au.164453014.41772108/v1

Genotyping of respiratory syncytial virus among influenza‐like illness and severe acute respiratory infection cases of children in the Philippines from 2006 to 2016

Introduction. SThe National External Quality Assessment Scheme (NEQAS) has been established by the Department of Health–Philippines (DOH) to provide DOH-approved external quality assessment programs, including the Proficiency Test (PT) for Bacteriology to clinical laboratories. The PT for Bacteriology aims to monitor and evaluate laboratory capabilities in the identification of clinically important pathogens through proficiency testing. Since then, participation in the NEQAS has been a requirement for clinical laboratories to obtain a license to operate from the DOH–Health Facilities and Services Regulatory Bureau (HFSRB). Objective. The objective of this report is to summarize and examine the results of the PT for Bacteriology from 2009 to 2015 and the performances of participating clinical laboratories throughout the Philippines. Methodology. The Research Institute for Tropical Medicine National Reference Laboratory (RITM-NRL) conducted orientation seminars between 2008 and 2009 to introduce clinical laboratories to the NEQAS. Laboratories submitted their accomplished enrolment forms to RITM–NRL and paid the fees to enroll in the PT. Participating laboratories were required to identify three analytes and perform antimicrobial susceptibility test (AST) on one assigned analyte. Results. A total of 468 laboratories participated over the seven-year period. The number of participating laboratories obtaining a passing score of 80% and above had significantly increased from 2009 to 2015. Out of the 144 laboratories consistently enrolled over the seven-year period, the proportion of participants with scores of 80% and above had increased. Of the 468 participating laboratories throughout 2009 to 2015, 33.3% were good performers; 6.6% were fair performers; and 60.0% were poor performers. Conclusion. The increasing number of participating laboratories obtaining passing scores over the years suggests overall improvement of the performance of clinical laboratories in bacteriology. Corrective actions are still needed to address the situation regarding the poor performing laboratories. The assessments done in 2008 and 2013 found that poorly performing laboratories lack trained personnel, resources, and implementation of quality assurance procedures for bacteriological testing.

Socorro Lupisan

Papers

Understanding user requirements to improve adoption of influenza diagnostics in clinical care within Metro Manila.

Genetic characterization of measles virus in the Philippines, 2008–2011

Research activities and responding to typhoon Haiyan (Yolanda): Tohoku-RITM collaborating research center in the Philippines

Genotyping of respiratory syncytial virus among influenza‐like illness and severe acute respiratory infection cases of children in the Philippines from 2006 to 2016

Proficiency Testing of Clinical Laboratories for Bacteriology in the Philippines, 2009–2015