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Objective:To determine the bacterial etiology, clinical presentation and risk factors for outcome of serious community-acquired infections in young infants.Study Design:Infants younger than 60 days, admitted for severe pneumonia or suspected sepsis/meningitis were prospectively evaluated using complete blood count, blood culture, chest radiograph, cerebrospinal fluid (CSF) culture in suspected meningitis. chi (2) or Fisher's exact test and stepwise logistic regression were used for analysis.Results:Thirty-four of 767 enrolled infants had a positive blood or CSF culture. Gram-negative bacteria were more frequent than Gram positive: overall (P=0.004), in those below 7 days of age (P=0.002) and among home deliveries (P=0.012). Case fatality rates were higher among infants below 1 week old (OR 4.14, P<0.001), those with dense (OR 2.92, P<0.001) or diffuse radiographic infiltrates (OR 2.79, P=0.003).Conclusions:Gram-negative enteric bacteria are the predominant causes of community-acquired infections in Filipino infants below 2 months old. Age below 7 days and radiographic pneumonia predicted death. [ABSTRACT FROM AUTHOR]

Introduction: The high burden of respiratory syncytial virus (RSV) infection in young children disproportionately occurs in low- and middle-income countries (LMICs). The PROUD (Preventing RespiratOry syncytial virUs in unDerdeveloped countries) Taskforce of 24 RSV worldwide experts assessed key needs for RSV prevention in LMICs, including vaccine and newer preventive measures., Methods: A global, survey-based study was undertaken in 2021. An online questionnaire was developed following three meetings of the Taskforce panellists wherein factors related to RSV infection, its prevention and management were identified using iterative questioning. Each factor was scored, by non-panellists interested in RSV, on a scale of zero (very-low-relevance) to 100 (very-high-relevance) within two scenarios: (1) Current and (2) Future expectations for RSV management., Results: Ninety questionnaires were completed: 70 by respondents (71.4% physicians; 27.1% researchers/scientists) from 16 LMICs and 20 from nine high-income (HI) countries (90.0% physicians; 5.0% researchers/scientists), as a reference group. Within LMICs, RSV awareness was perceived to be low, and management was not prioritised. Of the 100 factors scored, those related to improved diagnosis particularly access to affordable point-of-care diagnostics, disease burden data generation, clinical and general education, prompt access to new interventions, and engagement with policymakers/payers were identified of paramount importance. There was a strong need for clinical education and local data generation in the lowest economies, whereas upper-middle income countries were more closely aligned with HI countries in terms of current RSV service provision., Conclusion: Seven key actions for improving RSV prevention and management in LMICs are proposed., Competing Interests: The reviewer PAP declared a past co-authorship with the author(s) FMT to the handling. XCE and BP have received research funding and/or compensation as advisor/lecturer from AbbVie and AstraZeneca. JF and BRG, working for Violicom and former company, have previously received payment from AbbVie and AstraZeneca for work on various projects. MCN reports grants from the Bill & Melinda Gates Foundation, European & Developing Countries Clinical Trials Partnership, Pfizer, AstraZeneca and Sanofi-Pasteur; and personal fees from Pfizer and Sanofi-Pasteur. RTS has received fees for Advisory Board meetings and lectures for Sanofi-Pasteur, AstraZeneca, Janssen, and AbbVie. QB serves in the Independent Data Monitoring Committee (IDMC) for Respiratory Syncytial Virus (RSV) vaccine development for the protection of infants (since October 2015) (GlaxoSmithKline -GSK). JP reports grants to his institution from MedImmune, Merck, Sanofi Pasteur and AbbVie, and personal fees from AbbVie, Merck and AstraZeneca. JMP reports grants to his institution from MedImmune. HJZ has received funding for RSV-related research studies from Pfizer, AstraZeneca, Merck and the Bill & Melinda Gates Foundation. AM has received research funding from Merck and Janssen and compensation as advisor/lecturer from Sanofi-Pasteur and AstraZeneca. IM has been an investigator on studies funded by MedImmune, Regeneron, and Boehringer. MAS has received research funding from Janssen and compensation as advisor/lecturer from AbbVie, Sanofi-Pasteur and AstraZeneca. All declarations made by authors outside of the submitted work. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2022 Carbonell-Estrany, Simões, Bont, Gentile, Homaira, Scotta, Stein, Torres, Sheikh, Broor, Khuri-Bulos, Nokes, Munywoki, Bassat, Sharma, Basnet, Garba, De Jesus-Cornejo, Lupisan, Nunes, Divarathna, Fullarton, Rodgers-Gray, Keary, Reñosa, Verwey, Moore, Noordeen, Kabra, do Vale, Paternina-De La Ossa, Mariño, Figueras-Aloy, Krilov, Berezin, Zar, Paudel, Safadi, Dbaibo, Jroundi, Jha, Rafeek, Pinheiro, Bracht, Muthugala, Lanari, Martinón-Torres, Mitchell, Irimu, Pandey, Krishnan, Mejias, Santos Corrêa Da Costa, Shrestha, Pernica, Cotrim de Carvalho, Jalango, Ibrahim, Ewa, Ensinck, Ulloa-Gutierrez, Miralha, Lucion, Hassan, Akhtar, Aleem, Chowdhury, Rojo, Sande, Musau, Zaman, Arlant, Ghimire, Price, Subedi, Brenes-Chacon, Goswami, Rahman, Hossain, Chisti, Vain, Lim, Chiu, Papenburg, Juarez, Senaratne, Arunasalam, Strand, Ayuk, Ogunrinde, Tavares, Garba, Garba, Dawa, Gordon, Osoro, Agoti, Nyawanda, Ngama, Tabu, Mathew, Cornacchia, Rai, Jain, Giongo and Paes.)

Background: Rhinoviruses (RVs) are among the most frequently detected viruses from hospitalized children with severe acute respiratory infections, being classified into RV-A, RV-B, and RV-C (4 clades: C, GAC1, GAC2, and A2). This study aimed to compare the clinical characteristics and respiratory tract illness severity between the RV species and RV-C clades in children in primary care and hospital settings in rural communities in the Philippines., Methods: Clinical samples and information of children <5 years old in the Philippines were collected from 2014 to 2016. The samples were tested by reverse-transcription polymerase chain reaction (RT-PCR) targeting the 5'-untranslated region. PCR-positive samples were sequenced, and RV species were identified by phylogenetic analysis., Results: Overall, 3680 respiratory tract illness episodes in 1688 cohort children were documented; 713 of those were RV positive and identified as RV-A (n = 271), RV-B (n = 47), and RV-C (n = 395: C [n = 76], GAG1 [n = 172], GAG2 [n = 8], A2 [n = 138], and unidentified [n = 1]). Severe illnesses, low oxygen saturation, cough, and wheezing were more common in patients with RV-C, especially with GAC1, than in those with RV-A or RV-B. Furthermore, severe illness was significantly more common in RV-C (GAC1)-positive cases than in RV-A-positive cases (odds ratio, 2.61 [95% CI, 1.17-4.13])., Conclusions: Children infected with RV-C had more severe illnesses than children infected with RV-A and RV-B. Moreover, emerging clades of RV-C were associated with increased severity., Competing Interests: Potential conflicts of interest. The authors: No reported conflicts of interest., (© The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

We report 19 nearly complete genome sequences of influenza C virus isolated from clinical samples recovered from children in the Philippines between 2014 and 2019.

Complete genome sequences were determined for 4 clade A and 12 clade D enterovirus D68 strains detected in nasopharyngeal swabs from children with acute respiratory illness in the Philippines. These sequence data will be useful for future epidemiological monitoring, including watching for viral evolution.

Rotaviruses are the major cause of severe acute diarrhea in infants and young children. Rotaviruses exhibit zoonosis and thereby infect both humans and animals. Viruses detected in urban rivers possibly reflect the presence of circulating viruses in the catchment. The present study investigates the genetic diversity of species A rotaviruses detected from river water and stool of hospitalized children with acute diarrhea in Tacloban City, the Philippines. Species A rotaviruses were detected by real-time RT-PCR and their genotypes were identified by multiplex PCR and sequencing of partial regions of VP7 and VP4. Rotaviruses were detected in 85.7% (30/35) of the river water samples and 62.7% (151/241) of the clinical samples. Genotypes of VP7 in the river water samples were G1, G2, G3, G4, G5, and G9, and those of VP4 were P[3], P[4], P[6], P[8], and P[13]. Genotypes of viruses from the clinical samples were G2P[4], G1P[8], G3P[8], G4P[6], G5P[6], and G9P[8]. Among those, G2P[4] in clinical samples (77.9%, 81/104) and P[4] of VP4 in river water samples (67.5%, 56/83)) were the most frequently detected rotavirus genotypes. However, G5 was the more frequently detected than G2 in the river water samples (42% vs. 13%) which may be originated from porcine rotavirus. Sequence analyses of eleven gene segments revealed one G5P[6] and two G4P[6] rotaviruses in the clinical samples, wherein, several gene segments were closely related to porcine rotaviruses. The constellation of these rotavirus genes suggests the emergence of reassortment between human and porcine rotavirus due to interspecies transmission. Although two commercial rotavirus vaccines are available now, these vaccines are designed to confer immunity against the major human rotaviruses. Constant monitoring of viral variety in populated areas where humans and domestic animals live in close proximity provides vital information related to the diversity of rotaviruses in a human population., (Copyright © 2020. Published by Elsevier B.V.)

Background and Objectives: Despite a substantial reduction in the mortality rate of children under 5 years in the past 25 years, pneumonia remains the single-largest infectious cause of child deaths worldwide. This study explored the chronological order of visited healthcare facilities and practitioners, and the factors affecting mothers' intention to seek care before the hospitalisation of children with pneumonia., Methods and Analysis: A qualitative research design was employed using theory of planned behaviour as a framework for the analysis. Using purposive sampling technique, 11 mothers, whose children under 5 years old were hospitalised with severe pneumonia, were recruited for individual semi-structured interviews. Their socio-demographic information was analysed using descriptive statistics., Results: Mothers brought their sick children to multiple facilities, and 1 to 19 days had passed before hospitalisation. We identified four major factors determining mothers' intentions: (1) doing something useful for the sick child, (2) expecting the child to receive the necessary assessment and treatment, (3) accepting advice to visit a healthcare facility and be referred to a hospital and (4) considering issues and benefits associated with hospitalisation. Mothers noticed their children's unusual symptoms and monitored them while applying home remedies. They also took their children to traditional healers despite knowing that the treatments were not necessarily effective. Mothers expected children to be checked by health professionals and listened to advice from family members regarding the facilities to visit, and from healthcare staff to be referred to a hospital. Financial issues and the double burden of housework and caring for the hospitalised child were mothers' major concerns about hospitalisation., Conclusion: Children were hospitalised after several days because they visited multiple healthcare facilities, including traditional healers. Improving care quality at healthcare facilities and reducing financial and mothers' burden may reduce the hospitalisation delay for children with pneumonia., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

The IL-8 luciferase reporter cell line, THP-G8 cells, used in the in vitro sensitization test, OECD442E, can respond to a variety of stimuli other than haptens, such as lipopolysaccharide (LPS), other bacterial toxins, and detergents. Considering these characteristics, we examined the ability of the IL-8 luciferase assay using THP-G8 cells to evaluate water pollution. We first stimulated THP-G8 cell with various Toll-like receptor (TLR) agonists and nucleotide-binding oligomerization domain-like receptor (NLR) agonists, and found that TLR1, 2, 4, 5, 6 agonists and NOD 1, 2 agonists significantly augmented IL-8 luciferase activity (IL8LA). Then, we examined the detection threshold of LPS by THP-G8 cells, and found it 0.4 EU/ml. Next, we examined whether THP-G8 cells can differently respond to a variety of sources of environmental water around Sendai, Japan and Manila, Philippine and whether there is a correlation between the IL8LA of different sources of water and their level of endotoxin assessed by the LAL assay. There was a clear trend that the IL8LA was lower in the upper stream and higher in the downstream in both Japan and Philippine. Moreover, there was a strong correlation between the IL8LA of the environmental water and its endotoxin level. Finally, using N-acetyl-L-cysteine, an antioxidant/radical scavenger, and polymyxin B that neutralizes endotoxin, we demonstrated that there was a difference in the suppressive effects by them between the water from Japan and that from Philippine. These data suggest the potential of the IL-8 luciferase assay for evaluating environmental water pollution both quantitatively and qualitatively., (Copyright © 2020 Kimura et al.)

Background: Respiratory syncytial virus (RSV) is one of the main viral causes of lower respiratory tract illness (LRTI), especially in young children. RSV vaccines, including maternal and infant vaccines, are under development; however, more epidemiological studies are needed to develop effective vaccination strategies., Objectives: To estimate detailed age-specific incidence rates and severity of RSV-associated LRTI (RSV-LRTI) using data from a community-based prospective cohort study in the Philippines., Patients/methods: Cohort children who visited health facilities due to acute respiratory symptoms were identified, and nasopharyngeal swabs were collected to detect RSV. The severity of RSV-LRTI was assessed using the severity definition proposed by the World Health Organization. Risk factors for developing RSV-LRTI and contribution of SpO 2 measurement were also evaluated., Results: A total of 395 RSV episodes which occurred in children aged 2-59 months were categorised as 183 RSV-LRTI, 72 as severe RSV-LRTI and 29 as very severe RSV-LRTI. Children aged 3-5 months had the highest incidence rate of RSV-LRTI, at 207.4 per 1000 child-years (95% CI: 149.0-279.5). Younger age group, place of living and low educational level of caregivers were associated with developing RSV-LRTI. Clinical manifestations had low levels of agreement with hypoxaemia as measured by pulse oximeter., Conclusion: The highest burden of RSV was observed in young infants aged 3-5 months, whereas the burden was also high in those aged 12-20 months. Future vaccination strategies should consider the protection of older children, especially those aged one year, as well as young infants., (© 2019 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.)

Objective: Pneumonia remains the leading cause of hospitalisations and deaths among children aged <5 years. Diverse respiratory pathogens cause acute respiratory infections, including pneumonia. Here, we analysed viral and bacterial pathogens and risk factors associated with death of hospitalised children., Design: A 9-year case series study., Setting: Two secondary-care hospitals, one tertiary-care hospital and one research centre in the Philippines., Participants: 5054 children aged <5 years hospitalised with severe pneumonia., Methods: Nasopharyngeal swabs for virus identification, and venous blood samples for bacterial culture were collected. Demographic, clinical data and laboratory findings were collected at admission time. Logistic regression analyses were performed to identify the factors associated with death., Results: Of the enrolled patients, 57% (2876/5054) were males. The case fatality rate was 4.7% (238/5054), showing a decreasing trend during the study period (p<0.001). 55.0% of the patients who died were either moderately or severely underweight. Viruses were detected in 61.0% of the patients, with respiratory syncytial virus (27.0%) and rhinovirus (23.0%) being the most commonly detected viruses. In children aged 2-59 months, the risk factors significantly associated with death included age of 2-5 months, sensorial changes, severe malnutrition, grunting, central cyanosis, decreased breath sounds, tachypnoea, fever (≥38.5°C), saturation of peripheral oxygen <90%, infiltration, consolidation and pleural effusion on chest radiograph.Among the pathogens, adenovirus type 7, seasonal influenza A (H1N1) and positive blood culture for bacteria were significantly associated with death. Similar patterns were observed between the death cases and the aforementioned factors in children aged <2 months., Conclusion: Malnutrition was the most common factor associated with death and addressing this issue may decrease the case fatality rate. In addition, chest radiographic examination and oxygen saturation measurement should be promoted in all hospitalised patients with pneumonia as well as bacteria detection to identify patients who are at risk of death., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Hepatitis A virus (HAV) is a common infectious etiology of acute hepatitis worldwide. The Philippines remains highly endemic for hepatitis A, but there is still a lack of information about HAV in the country. To evaluate the HAV contamination in environmental water in the Philippines, we conducted the detection and genetic analyses of HAV RNA in samples from river water. Twelve water samples were collected at 6 sampling sites of 3 rivers in Metro Manila, in both the dry and wet seasons in 2012 and 2013. The HAV RNA was detected in all the 6 samples collected in the dry season, and in one sample from the wet season. Phylogenetic analysis confirmed that the HAV strains detected in the river water included multiple sequences belonging to subgenotypes IA and IIIA. This indicates that at least 2 genotypes of the HAV strains are circulating in the environment in the Philippines, posing a risk of HAV infection to not only residents, but also tourists, especially in the dry season.

Complete genome sequences were determined for 12 human respiratory syncytial virus strains collected from nasopharyngeal samples obtained from children with repeated subgroup B infections. Eight common amino acid polymorphisms in the G, F, and L proteins were identified between the viruses detected in initial and subsequent infections.

Background: Human respiratory syncytial virus (RSV) is the leading cause of severe acute respiratory infection in infants and young children, which is characterized by repeated infections. However, the role of amino acid substitutions in repeated infections remains unclear. Hence, this study aimed to elucidate the genetic characteristics of RSV in children with repeated infections using molecular analyses of F and G genes., Methods: We conducted a cohort study of children younger than 5 years in the Philippines. We collected nasopharyngeal swabs from children with acute respiratory symptoms and compared F and G sequences between initial and subsequent RSV infections., Results: We examined 1802 children from May 2014 to January 2016 and collected 3471 samples. Repeated infections were observed in 25 children, including 4 with homologous RSV-B reinfections. Viruses from the 4 pairs of homologous reinfections had amino acid substitutions in the G protein mostly at O-glycosylation sites, whereas changes in the F protein were identified at antigenic sites V (L173S) and θ (Q209K), considered essential epitopes for the prefusion conformation of the F protein., Conclusions: Amino acid substitutions in G and F proteins of RSV-B might have led to antigenic changes, potentially contributing to homologous reinfections observed in this study.

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.

Background: Respiratory syncytial virus (RSV) infection is an important cause of pneumonia mortality in young children. However, clinical data for fatal RSV infection are scarce. We aimed to identify clinical and socioeconomic characteristics of children aged younger than 5 years with RSV-related mortality using individual patient data., Methods: In this retrospective case series, we developed an online questionnaire to obtain individual patient data for clinical and socioeconomic characteristics of children aged younger than 5 years who died with community-acquired RSV infection between Jan 1, 1995, and Oct 31, 2015, through leading research groups for child pneumonia identified through a comprehensive literature search and existing research networks. For the literature search, we searched PubMed for articles published up to Feb 3, 2015, using the key terms "RSV", "respiratory syncytial virus", or "respiratory syncytial viral" combined with "mortality", "fatality", "death", "died", "deaths", or "CFR" for articles published in English. We invited researchers and clinicians identified to participate between Nov 1, 2014, and Oct 31, 2015. We calculated descriptive statistics for all variables., Findings: We studied 358 children with RSV-related in-hospital death from 23 countries across the world, with data contributed from 31 research groups. 117 (33%) children were from low-income or lower middle-income countries, 77 (22%) were from upper middle-income countries, and 164 (46%) were from high-income countries. 190 (53%) were male. Data for comorbidities were missing for some children in low-income and middle-income countries. Available data showed that comorbidities were present in at least 33 (28%) children from low-income or lower middle-income countries, 36 (47%) from upper middle-income countries, and 114 (70%) from high-income countries. Median age for RSV-related deaths was 5·0 months (IQR 2·3-11·0) in low-income or lower middle-income countries, 4·0 years (2·0-10·0) in upper middle-income countries, and 7·0 years (3·6-16·8) in high-income countries., Interpretation: This study is the first large case series of children who died with community-acquired RSV infection. A substantial proportion of children with RSV-related death had comorbidities. Our results show that perinatal immunisation strategies for children aged younger than 6 months could have a substantial impact on RSV-related child mortality in low-income and middle-income countries., Funding: Bill & Melinda Gates Foundation., (Copyright © 2017 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Background: We have previously estimated that respiratory syncytial virus (RSV) was associated with 22% of all episodes of (severe) acute lower respiratory infection (ALRI) resulting in 55 000 to 199 000 deaths in children younger than 5 years in 2005. In the past 5 years, major research activity on RSV has yielded substantial new data from developing countries. With a considerably expanded dataset from a large international collaboration, we aimed to estimate the global incidence, hospital admission rate, and mortality from RSV-ALRI episodes in young children in 2015., Methods: We estimated the incidence and hospital admission rate of RSV-associated ALRI (RSV-ALRI) in children younger than 5 years stratified by age and World Bank income regions from a systematic review of studies published between Jan 1, 1995, and Dec 31, 2016, and unpublished data from 76 high quality population-based studies. We estimated the RSV-ALRI incidence for 132 developing countries using a risk factor-based model and 2015 population estimates. We estimated the in-hospital RSV-ALRI mortality by combining in-hospital case fatality ratios with hospital admission estimates from hospital-based (published and unpublished) studies. We also estimated overall RSV-ALRI mortality by identifying studies reporting monthly data for ALRI mortality in the community and RSV activity., Findings: We estimated that globally in 2015, 33·1 million (uncertainty range [UR] 21·6-50·3) episodes of RSV-ALRI, resulted in about 3·2 million (2·7-3·8) hospital admissions, and 59 600 (48 000-74 500) in-hospital deaths in children younger than 5 years. In children younger than 6 months, 1·4 million (UR 1·2-1·7) hospital admissions, and 27 300 (UR 20 700-36 200) in-hospital deaths were due to RSV-ALRI. We also estimated that the overall RSV-ALRI mortality could be as high as 118 200 (UR 94 600-149 400). Incidence and mortality varied substantially from year to year in any given population., Interpretation: Globally, RSV is a common cause of childhood ALRI and a major cause of hospital admissions in young children, resulting in a substantial burden on health-care services. About 45% of hospital admissions and in-hospital deaths due to RSV-ALRI occur in children younger than 6 months. An effective maternal RSV vaccine or monoclonal antibody could have a substantial effect on disease burden in this age group., Funding: The Bill & Melinda Gates Foundation., (Copyright © 2017 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Background: Estimation of the incidences of influenza and respiratory syncytial virus (RSV) infection is important for disease control. Previous estimate in the city showed a substantial burden of influenza in both outpatients and inpatients while it did not account for individuals who do not seek medical attention nor RSV., Patients/methods: A total of 17 674 influenza-like illness (ILI) and 13 242 severe acute respiratory illness (SARI) cases were recruited, and samples were collected from 6267 and 2962 of ILI and SARI cases, respectively. RT-PCR assays were performed to detect influenza and RSV in the samples. A health-seeking behavior survey was conducted from February 2014 to April 2014 to estimate the fraction of infected individuals who did not seek medical attention between rainy and dry season., Results: Average influenza and RSV incidence rates in outpatients were 1.6 and 1.4 per 1000 individuals, respectively, and the highest incidence rate for both viruses was found in the of 6-23 month age group. Average influenza and RSV hospitalization incidence rates were 1.7 and 1.9 per 1000 individuals, respectively. Further, we estimated that the incidence rates of influenza and RSV in individuals who did not seek medical attention were threefold and 1.6-fold those in the medically attended population., Conclusions: Respiratory syncytial virus and influenza pose a substantial disease burden, particularly in hospitalized cases. The implementation of either a community-based approach or an enhanced surveillance system in combination with a community survey will allow a better understanding of the disease burdens of RSV and influenza in the Philippines., (© 2017 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.)

Background: Both vaccine trials and surveillance studies typically use passive surveillance systems to monitor study outcomes, which may lead to under-reporting of study outcomes in areas with poor access to care. This detection bias can have an adverse effect on conventional estimates of pneumonia risk derived from vaccine trials., Methods: We conducted a secondary analysis of a randomized, placebo-controlled, double-blind vaccine trial that examined the efficacy of an 11-valent pneumococcal vaccine (PCV) among children less than 2 years of age in Bohol, Philippines. Trial data were linked to the residential location of each participant using a geographical information system. The study was conducted using 11 729 children who received three doses of any study vaccine (PCV11) or placebo. Multivariate Cox proportional hazards models were used to examine major risk factors for pneumonia diagnosis and the relationship between distance to Bohol Regional Hospital (BRH) and vaccination with PCV with risk for pneumonia diagnosis., Results: There was a significant interaction effect between distance from BRH and vaccination with PCV11 on pneumonia risk. Among children living 12 km from BRH, vaccination with PCV11 was associated with a decreased hazard ratio for radiographic pneumonia, compared with vaccination with the study placebo [0.57, 95% confidence interval (CI) 0.37-0.86). However, for children living 1 km from BRH, there was little difference in risk of radiographic pneumonia diagnosis between children vaccinated with PCV11 and those given the study placebo., Conclusion: Children living close to BRH had no documented reduction in the primary study outcome from PCV11, whereas those at greater distance experienced a substantial reduction. Because of detection bias caused by distance to BRH, in spatial analysis of vaccine trial results it may be necessary to adjust estimates of pneumonia risk and vaccine efficacy. Failure to consider the geographical dimension of trials may lead to underestimates of efficacy which might influence public health planning efforts., (© The Author 2016; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association)

Introduction: Typhoon Yolanda (Haiyan) hit the central part of the Philippines on November 8, 2013. To identify possible outbreaks of communicable diseases after the typhoon, nasopharyngeal swabs, stool and blood samples were collected from patients who visited the Eastern Visayas Regional Medical Center due to acute respiratory infection (ARI), acute gastroenteritis (AGE) or other febrile illness (OFI) including suspected dengue fever, between November 28, 2013 and February 5, 2014.   Methods: Samples were tested on-site for selected pathogens using rapid diagnostic tests. Confirmation and further analysis were conducted at the Research Institute for Tropical Medicine (RITM) in Manila using polymerase chain reaction (PCR) and sequencing. Residues of the rapid diagnostic tests and samples collected in the filter papers (FTATM card) were transported to Manila under suboptimal conditions. PCR results were compared between the kit residues and the filter papers.   Results: A total of 185 samples were collected. Of these, 128 cases were ARI, 17 cases were AGE and 40 cases were OFI. For nasopharyngeal swab samples, detection rates for enterovirus and rhinovirus residues were higher than the filter papers. For stool samples, rotavirus positive rate for the filter paper was higher than the kit residues. We also managed to obtain the sequence data from some of the kit residues and filter papers.   Discussion: Our results confirmed the importance of PCR for the laboratory diagnosis of infectious diseases in post-disaster situations when  diagnostic options are limited.

Background: WU and KI are human polyomaviruses initially detected in the respiratory tract, whose clinical significance remains uncertain., Objectives: To determine the epidemiology, viral load and clinical characteristics of WU and KI polyomaviruses., Study Design: We tested respiratory specimens collected during a randomized, placebo-controlled pneumococcal conjugate vaccine trial and related epidemiological study in the Philippines. We analyzed 1077 nasal washes from patients aged 6 weeks to 5 years who developed lower respiratory tract illness using quantitative real-time PCR for WU and KI. We collected data regarding presenting symptoms, signs, radiographic findings, laboratory data and coinfection., Results: The prevalence and co-infection rates for WU were 5.3% and 74% respectively and 4.2% and 84% respectively for KI. Higher KI viral loads were observed in patients with severe or very severe pneumonia, those presenting with chest indrawing, hypoxia without wheeze, convulsions, and with KI monoinfection compared with co-infection. There was no significant association between viral load and clinical presentation for WU., Conclusions: These findings suggest a potential pathogenic role for KI, and that there is an association between KI viral load and illness severity., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Background: Human sapovirus (SaV) is a causative agent of acute gastroenteritis. Recently, SaV detection has been increasing worldwide due to the emerging SaV genotype I.2. However, SaV infection has not been reported in the Philippines., Objectives: To evaluate the prevalence and genetic diversity of SaV in hospitalized children aged less than 5 years with acute gastroenteritis., Study Design: Stool samples were collected from children with acute gastroenteritis at three hospitals in the Philippines from June 2012 to August 2013. SaV was detected by reverse transcription real-time PCR, and the polymerase and capsid gene sequences were analyzed. Full genome sequencing and recombination analysis were performed on possible recombinant viruses., Results: SaV was detected in 7.0% of the tested stool samples (29/417). In 10 SaV-positive cases, other viruses were also detected, including rotavirus (n=6), norovirus (n=2), and human astrovirus (n=2). Four known SaV genotypes (GI.1 [7], GI.2 [2], GII.1 [12], and GV [2]) and one novel recombinant (n=3) were identified by polymerase and capsid gene sequence analysis. Full genome sequencing revealed that the 5' nontranslated region (NTR) and nonstructural protein region of the novel recombinant were closely related to the GII.1 Bristol/98/UK variant, whereas the structural protein region and 3' NTR were closely related to the GII.4 Kumamoto6/Mar2003/JPN variant., Discussion and Conclusions: SaV was regularly detected in hospitalized children due to acute gastroenteritis during the study period. A novel recombinant, SaV GII.1/GII.4, was identified in three cases at two different study sites., (Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.)

Objectives: The present study was designed to determine the genotypes of circulating Bordetella pertussis in the Philippines by direct molecular typing of clinical specimens., Methods: Nasopharyngeal swabs (NPSs) were collected from 50 children hospitalized with pertussis in three hospitals during 2012-2014. Multilocus variable-number tandem repeat analysis (MLVA) was performed on the DNA extracts from NPSs. B. pertussis virulence-associated allelic genes (ptxA, prn, and fim3) and the pertussis toxin promoter, ptxP, were also investigated by DNA sequence-based typing., Results: Twenty-six DNA extracts yielded a complete MLVA profile, which were sorted into 10 MLVA types. MLVA type 34 (MT34), which is rare in Australia, Europe, Japan, and the USA, was the predominant strain (50%). Seven MTs (MT29, MT32, MT33, and MT283-286, total 42%) were single-locus variants of MT34, while two (MT141 and MT287, total 8%) were double-locus variants of MT34. All MTs had the combination of virulence-associated allelic genes, ptxP1-ptxA1-prn1-fim3A., Conclusions: The B. pertussis population in the Philippines comprises genetically related strains. These strains are markedly different from those found in patients from other countries where acellular pertussis vaccines are used. The differences in vaccine types between these other countries and the Philippines, where the whole-cell vaccine is still used, may select for distinct populations of B. pertussis., (Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.)

From November 2009 to December 2013 in the Philippines, 15 influenza C viruses were isolated, using MDCK cells, from specimens obtained from children with severe pneumonia and influenza-like illness (ILI). This is the first report of influenza C virus isolation in the Philippines. In addition, from January 2008 to December 2013, 7 influenza C viruses were isolated from specimens that were obtained from children with acute respiratory illness (ARI) in Sendai city, Japan. Antigenic analysis with monoclonal antibodies to the hemagglutinin-esterase (HE) glycoprotein showed that 19 strains (12 from the Philippines and 7 from Japan) were similar to the influenza C virus reference strain C/Sao Paulo/378/82 (SP82). Phylogenetic analysis of the HE gene showed that the strains from the Philippines and Japan formed distinct clusters within an SP82-related lineage. The clusters that included the Philippine and Japanese strains were shown to have diverged from a common ancestor around 1993. In addition, phylogenetic analysis of the internal genes showed that all strains isolated in the Philippines and Japan had emerged through reassortment events. The composition of the internal genes of the Philippine strains was different from that of the Japanese strains, although all strains were classified into an SP82-related lineage by HE gene sequence analysis. These observations suggest that the influenza C viruses analyzed here had emerged through different reassortment events; however, the time and place at which the reassortment events occurred were not determined., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Enterovirus D68 (EV-D68) has been recognized as an important cause of acute respiratory infections. Here we report the molecular epidemiology of EV-D68 in Philippines from 2013 to 2014; we found cases in areas affected by Typhoon Haiyan and found new strains in the country., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

To understand the hepatitis E virus (HEV)-pollution status in the environment in the Philippines, a total of 12 water samples were collected from rivers in Manila City for detection of HEV RNA. Three of 12 samples were positive for HEV RNA indicating that HEV is circulating in the Philippines. Phylogenetic analysis classified all of the HEV sequences into genotype 3.

Pneumococcal conjugate vaccines (PCVs) have demonstrated efficacy against childhood pneumococcal disease in several regions globally. We demonstrate how spatial epidemiological analysis of a PCV trial can assist in developing vaccination strategies that target specific geographic subpopulations at greater risk for pneumococcal pneumonia. We conducted a secondary analysis of a randomized, placebo-controlled, double-blind vaccine trial that examined the efficacy of an 11-valent PCV among children less than 2 y of age in Bohol, Philippines. Trial data were linked to the residential location of each participant using a geographic information system. We use spatial interpolation methods to create smoothed surface maps of vaccination rates and local-level vaccine efficacy across the study area. We then measure the relationship between distance to the main study hospital and local-level vaccine efficacy, controlling for ecological factors, using spatial autoregressive models with spatial autoregressive disturbances. We find a significant amount of spatial variation in vaccination rates across the study area. For the primary study endpoint vaccine efficacy increased with distance from the main study hospital from -14% for children living less than 1.5 km from Bohol Regional Hospital (BRH) to 55% for children living greater than 8.5 km from BRH. Spatial regression models indicated that after adjustment for ecological factors, distance to the main study hospital was positively related to vaccine efficacy, increasing at a rate of 4.5% per kilometer distance. Because areas with poor access to care have significantly higher VE, targeted vaccination of children in these areas might allow for a more effective implementation of global programs.

β-Lactamases, including extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases, are major resistance mechanisms of Enterobacteriaceae. Emergence of plasmid-mediated quinolone resistance (PMQR) determinants in ESBL-producing isolates poses a global threat. The molecular characterisitcs of ESBL and PMQR determinants in the Philippines are not well characterized. In this study, we investigated ESBLs and AmpC β-lactamases in clinical isolates of Enterobacteriaceae from the Philippines, and analyzed the association between ESBL and PMQR genes. A total of 91 amoxicilin non-susceptible Enterobacteriaceae were collected at the Research Institute for Tropical Medicine of the Philippines from 2006 to 2008. AmpC- or ESBL-producing isolates were screened by detecting a zone diameter for cefoxitin ≤ 14 mm or cefpodoxime ≤ 20 mm, respectively. Possible ESBL-producing strains were assessed by the ESBL confirmation test of the Clinical and Laboratory Standards Institute. PCR and sequencing were performed to detect the ESBL and PMQR genes. The number of ESBL-producers and AmpC-producers confirmed phenotypically was 17 (18.7%) and 61 (67.0%), respectively. Of 17 phenotypic ESBL-producers, 14 isolates had ESBL genes, including 6 of Escherichia coli, 3 of Enterobacter cloacae, 2 of Enterobacter aerogenes, 2 of Klebsiella pneumoniae, and 1 of Klebsiella ozaenae. Among these isolates, there were 13, 4, and 12 with bla(CTX-M), bla(SHV), and bla(TEM), respectively. Of the bla(CTX-M)-positive isolates, bla(CTX-M-15) shows the highest prevalence, followed by bla(CTX-M-3) and bla(CTX-M-14). Of 14 ESBL-producers identified by PCR, 4, 6, and 7 isolates were positive for qnrB, qnrS, and aac(6')-Ib-cr, respectively. The frequency of aac(6')-Ib-cr positivity was significantly higher among CTX-M-15-producing isolates. Thus, we identified bla(CTX-M), aac(6')-Ib-cr, and qnr in ESBL-producing Enterobacteriaceae from the Philippines, and revealed a significant association between bla(CTX-M-15) and aac(6')-Ib-cr. Local epidemiological data are important for implementing appropriate antimicrobial therapy and effective infection control measures. Continuous monitoring of antimicrobial resistance genes in the Philippines will be required., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Several novel viruses have been recently identified in respiratory samples. However, the epidemiology of these viruses in tropical countries remains unclear. The aim of the present study was to provide an overview of the epidemiology of novel respiratory viruses, including human metapneumovirus, human bocavirus, new subtypes of human coronavirus (NL63 and HKU1), KI virus, WU virus, and Melaka virus in the Philippines, a tropical country. Nasopharyngeal aspirates from 465 patients with influenza-like illness were collected in 2006 and 2007. Reverse transcription polymerase chain reaction (RT-PCR) and PCR were performed to detect viruses from culture-negative specimens. Human metapneumovirus, human bocavirus, human coronavirus HKU1, KI virus, and WU virus were detected for the first time in the Philippines; Melaka virus was not found., ((c) 2010 Wiley-Liss, Inc.)

Objective: To determine predictors of death among children 2-59 months old admitted to hospital with severe pneumonia., Methods: Prospective observational study from April 1994 to May 2000 to investigate serious infections in children less than 5 years old admitted to a tertiary care government hospital in a rural province in central Philippines. The quality of clinical and laboratory work was monitored. The WHO classification for severe pneumonia was used for patient enrolment., Results: There were 1249 children with severe pneumonia and no CNS infection. Thirty children died. Using univariate analysis, the following factors were significantly associated with death: age 2-5 months, dense infiltrates on chest radiography and presence of definite bacterial pathogens in the blood. Stepwise logistic regression analysis revealed the following independent predictors of death: age 2-5 months, weight for age z-score less than -2 SD, dense infiltrates on chest radiography and definite pathogens isolated in the blood. When the results of chest radiographs and blood cultures were not included to mimic facilities available at first-level facilities, age 2-5 months and weight for age z-score less than -2 SD remained independent predictors of death., Conclusion: When resources are limited, children with lower chest wall indrawing (severe pneumonia) who are 2-5 months old or moderately to severely malnourished should be referred for immediate higher-level care.

Over 6 years, 1667 children aged 2-59 months admitted for pneumonia [1287 severe and 380 very severe] were studied. The case fatality rate (CFR) in children with severe pneumonia was 2.1% and 14.3% with CNS infection, with very severe pneumonia the CFR was 18.9%, 10.4% in those with hypoxemia and 43.6% with CNS infection. High CFRs were associated with CNS infection and inability to drink/cyanosis. The appropriate management of children with very severe pneumonia should include cerebrospinal fluid examination, oxygen monitoring and possibly ventilated support, suggesting that these are minimal standards of care at the district hospital.

This paper describes the clinical profile and aetiology of bacterial meningitis in infants and children less than 5 y old admitted to a rural general hospital in the Philippines. A total of 989 infants and children 0-59 months old with suspected meningitis using a standardized guideline based on clinical signs and symptoms were prospectively enrolled from April 1994 to May 2000. Blood and CSF were drawn on admission for culture, antigen testing and cell count. All had blood cultures and 623 (63%) had CSF samples. Bacterial aetiology was found in 54 (5%). The most common bacterial pathogens were H. influenzae type b (Hib) (20, 37%) and S. pneumoniae (Pnc) (10, 18%). All of the Hib infections and 8 (80%) Pnc infections were in infants less than 1 y old. 12 (22%) of the subjects with bacterial meningitis died. All strains of S. pneumoniae and H. influenzae were sensitive to chloramphenicol, cotrimoxazole and ampicillin. In conclusion, S. pneumoniae and H. influenzae type b are the most common aetiological agents of bacterial meningitis in a rural area in the Philippines, and occur especially in infants less than 1 y old. Aetiological agents were susceptible to the currently recommended antimicrobial agents.

Epidemiological features of blood culture confirmed typhoid fever and antibiotic sensitivity of isolated Salmonella typhi strains were investigated in Bohol Province in Central Philippines from where no earlier information of these was avialable. Typhoid fever is endemic elsewhere in the Philippines (eg Metropolitan Manila and surroundings) where also multidrug resistant S. typhi strains have been detected. A laboratory for surveillance of invasive bacterial infections was established in a tertiary care government hospital, in Bohol, Central Philippines, in 1994. Patients with suspected typhoid fever or other serious infection were managed and blood cultures from them were taken according to clinicians' judgment. Blood cultures were processed and the isolated bacteria identified using generally accepted methods. S. typhi and other Salmonella isolates were identified using commercial antisera. Patient data were collected from hospital records. Of a total of 4,699 blood cultures done during a period of 3 3/4 years, 1,530 (32%) were requested for suspected typhoid fever. S. typhi was the most common pathogen isolated from 422 patients (8.9%), followed by S. paratyphi A from 55 patients (1%). Most patients were young adults (43%) and school age children (28%). Male:female ratio was 1.5:1. Among the 422 patients, there were 9 (2%) deaths due to typhoid fever, all with complications. All S. typhi isolates were sensitive to chloramphenicol, cotrimoxazole, and ampicillin. Our observation on blood culture confirmed typhoid fever demonstrates its importance as a major infectious disease in Bohol and gives a sound basis for treatment of typhoid patients and for further clinical and epidemiologic studies of typhoid fever and for following antibiotic sensitivity of S. typhi in Bohol and elsewhere in the Philippines.

The etiology of invasive bacterial infections was studied among 956 Filipino children less than five years old who fulfilled the World Health Organization criteria for severe or very severe pneumonia or had suspected meningitis or sepsis. The most common invasive infections were due to Streptococcus pneumoniae (12 [1.3%]) and Haemophilus influenzae (12 [1.3%]); including four cases of pneumococcal meningitis and 11 cases of H. influenzae meningitis. Type 1 was the most common (six of the 12 isolates) of the pneumococcal serotypes. Serotypes/groups 1, 6, 14, and 23 accounted for 91.7% of the invasive isolates. The majority of the H. influenzae strains from blood (10 out of 10) and cerebrospinal fluid (6 out of 7) were type b. Almost all of the invasive S. pneumoniae (9 out of 12) and H. influenzae (11 out of 12) infections were seen before one year of age, which stresses the need to investigate early immunization of children for H. influenzae type b and S. pneumoniae, as well as maternal immunization to maximize the potential of immunoprophylaxis.