ORCID Profile
0000-0002-9807-1821
Current Organisation
University of Oxford
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Publisher: Public Library of Science (PLoS)
Date: 27-06-2019
Publisher: American Society of Tropical Medicine and Hygiene
Date: 03-05-2017
Publisher: Oxford University Press (OUP)
Date: 23-09-2017
Publisher: F1000 Research Ltd
Date: 26-08-2202
DOI: 10.12688/WELLCOMEOPENRES.17263.2
Abstract: This article summarises a recent virtual meeting organised by the Oxford University Clinical Research Unit in Vietnam on the topic of climate change and health, bringing local partners, faculty and external collaborators together from across the Wellcome and Oxford networks. Attendees included invited local and global climate scientists, clinicians, modelers, epidemiologists and community engagement practitioners, with a view to setting priorities, identifying synergies and fostering collaborations to help define the regional climate and health research agenda. In this summary paper, we outline the major themes and topics that were identified and what will be needed to take forward this research for the next decade. We aim to take a broad, collaborative approach to including climate science in our current portfolio where it touches on infectious diseases now, and more broadly in our future research directions. We will focus on strengthening our research portfolio on climate-sensitive diseases, and supplement this with high quality data obtained from internal studies and external collaborations, obtained by multiple methods, ranging from traditional epidemiology to innovative technology and artificial intelligence and community-led research. Through timely agenda setting and involvement of local stakeholders, we aim to help support and shape research into global heating and health in the region.
Publisher: F1000 Research Ltd
Date: 05-09-2022
DOI: 10.12688/WELLCOMEOPENRES.17263.3
Abstract: This article summarises a recent virtual meeting organised by the Oxford University Clinical Research Unit in Vietnam on the topic of climate change and health, bringing local partners, faculty and external collaborators together from across the Wellcome and Oxford networks. Attendees included invited local and global climate scientists, clinicians, modelers, epidemiologists and community engagement practitioners, with a view to setting priorities, identifying synergies and fostering collaborations to help define the regional climate and health research agenda. In this summary paper, we outline the major themes and topics that were identified and what will be needed to take forward this research for the next decade. We aim to take a broad, collaborative approach to including climate science in our current portfolio where it touches on infectious diseases now, and more broadly in our future research directions. We will focus on strengthening our research portfolio on climate-sensitive diseases, and supplement this with high quality data obtained from internal studies and external collaborations, obtained by multiple methods, ranging from traditional epidemiology to innovative technology and artificial intelligence and community-led research. Through timely agenda setting and involvement of local stakeholders, we aim to help support and shape research into global heating and health in the region.
Publisher: F1000 Research Ltd
Date: 17-08-2120
DOI: 10.12688/WELLCOMEOPENRES.17263.1
Abstract: This article summarises a recent virtual meeting organised by the Oxford University Clinical Research Unit in Vietnam on the topic of climate change and health, bringing local partners, faculty and external collaborators together from across the Wellcome and Oxford networks. Attendees included invited local and global climate scientists, clinicians, modelers, epidemiologists and community engagement practitioners, with a view to setting priorities, identifying synergies and fostering collaborations to help define the regional climate and health research agenda. In this summary paper, we outline the major themes and topics that were identified and what will be needed to take forward this research for the next decade. We aim to take a broad, collaborative approach to including climate science in our current portfolio where it touches on infectious diseases now, and more broadly in our future research directions. We will focus on strengthening our research portfolio on climate-sensitive diseases, and supplement this with high quality data obtained from internal studies and external collaborations, obtained by multiple methods, ranging from traditional epidemiology to innovative technology and artificial intelligence and community-led research. Through timely agenda setting and involvement of local stakeholders, we aim to help support and shape research into global heating and health in the region.
Publisher: Oxford University Press (OUP)
Date: 02-06-2020
Abstract: The extent to which influenza recurrence depends upon waning immunity from prior infection is undefined. We used antibody titers of Ha-Nam cohort participants to estimate protection curves and decay trajectories. Households (270) participated in influenza-like–illness (ILI) surveillance and provided blood at intervals spanning laboratory–confirmed virus transmission. Sera were tested in hemagglutination inhibition assay. Infection was defined as influenza virus-positive ILI and/or seroconversion. Median protective titers were estimated using scaled-logistic regression to model pretransmission titer against infection status in that season, limiting analysis to households with infection(s). Titers were modelled against month since infection using mixed-effects linear regression to estimate decay and when titers fell below protection thresholds. From December 2008–2012, 295 and 314 participants were infected with H1N1pdm09-like and A/Perth/16/09-like (H3N2Pe09) viruses, respectively. The proportion protected rose more steeply with titer for H1N1pdm09 than for H3N2Pe09, and estimated 50% protection titers were 19.6 and 37.3, respectively. Postinfection titers started higher against H3N2Pe09 but decayed more steeply than against H1N1pdm09. Seroprotection was estimated to be sustained against H1N1pdm09 but to wane by 8-months for H3N2Pe09. Estimates indicate that infection induces durable seroprotection against H1N1pdm09 but not H3N2Pe09, which could in part account for the younger age of A(H1N1) versus A(H3N2) cases.
Publisher: SAGE Publications
Date: 07-2012
DOI: 10.3851/IMP2098
Publisher: MDPI AG
Date: 25-02-2022
DOI: 10.3390/V14030470
Abstract: Prior vaccination can alternately enhance or attenuate influenza vaccine immunogenicity and effectiveness. Analogously, we found that vaccine immunogenicity was enhanced by prior A(H3N2) virus infection among participants of the Ha Nam Cohort, Viet Nam, but was attenuated by prior vaccination among Australian Health Care Workers (HCWs) vaccinated in the same year. Here, we combined these studies to directly compare antibody titers against 35 A(H3N2) viruses spanning 1968–2018. Participants received licensed inactivated vaccines containing A/HongKong/4801/2014 (H3N2). The analysis was limited to participants aged 18–65 Y, and compared those exposed to A(H3N2) viruses circulating since 2009 by infection (Ha Nam) or vaccination (HCWs) to a reference group who had no recent A(H3N2) infection or vaccination (Ha Nam). Antibody responses were compared by fitting titer/titer-rise landscapes across strains, and by estimating titer ratios to the reference group of 2009–2018 viruses. Pre-vaccination, titers were lowest against 2009–2014 viruses among the reference (no recent exposure) group. Post-vaccination, titers were, on average, two-fold higher among participants with prior infection and two-fold lower among participants with 3–5 prior vaccinations compared to the reference group. Titer rise was negligible among participants with 3–5 prior vaccinations, poor among participants with 1–2 prior vaccinations, and equivalent or better among those with prior infection compared to the reference group. The enhancing effect of prior infection versus the incrementally attenuating effect of prior vaccinations suggests that these exposures may alternately promote and constrain the generation of memory that can be recalled by a new vaccine strain.
Publisher: Public Library of Science (PLoS)
Date: 08-08-2016
Publisher: Springer Science and Business Media LLC
Date: 09-06-2015
Publisher: Public Library of Science (PLoS)
Date: 03-05-2010
Publisher: Springer Science and Business Media LLC
Date: 13-06-2023
DOI: 10.1186/S12879-023-08300-1
Abstract: Acute encephalitis syndrome (AES) differs in its spatio-temporal distribution in Vietnam with the highest incidence seen during the summer months in the northern provinces. AES has multiple aetiologies, and the cause remains unknown in many cases. While vector-borne disease such as Japanese encephalitis and dengue virus and non-vector-borne diseases such as influenza and enterovirus show evidence of seasonality, associations with climate variables and the spatio-temporal distribution in Vietnam differs between these. The aim of this study was therefore to understand the spatio-temporal distribution of, and risk factors for AES in Vietnam to help hypothesise the aetiology. The number of monthly cases per province for AES, meningitis and diseases including dengue fever influenza-like-illness (ILI) hand, foot, and mouth disease (HFMD) and Streptococcus suis were obtained from the General Department for Preventive Medicine (GDPM) from 1998–2016. Covariates including climate, normalized difference vegetation index (NDVI), elevation, the number of pigs, socio-demographics, JEV vaccination coverage and the number of hospitals were also collected. Spatio-temporal multivariable mixed-effects negative binomial Bayesian models with an outcome of the number of cases of AES, a combination of the covariates and harmonic terms to determine the magnitude of seasonality were developed. The national monthly incidence of AES declined by 63.3% over the study period. However, incidence increased in some provinces, particularly in the Northwest region. In northern Vietnam, the incidence peaked in the summer months in contrast to the southern provinces where incidence remained relatively constant throughout the year. The incidence of meningitis, ILI and S. suis infection temperature, relative humidity with no lag, NDVI at a lag of one month, and the number of pigs per 100,000 population were positively associated with the number of cases of AES in all models in which these covariates were included. The positive correlation of AES with temperature and humidity suggest that a number of cases may be due to vector-borne diseases, suggesting a need to focus on vaccination c aigns. However, further surveillance and research are recommended to investigate other possible aetiologies such as S. suis or Orientia tsutsugamushi .
Publisher: Springer Science and Business Media LLC
Date: 05-2018
DOI: 10.1038/S41598-018-24767-4
Abstract: HPIVs are serologically and genetically grouped into four species that account for up to 10% of all hospitalizations due to acute respiratory infection in children under the age of five. Genetic and epidemiological data for the four HPIVs derived from two pediatric cohorts in Viet Nam are presented. Respiratory s les were screened for HPIV1–4 by real-time PCR. Demographic and clinical data of patients infected with different HPIV were compared. We used a hemi-nested PCR approach to generate viral genome sequences from HPIV-positive s les and conducted a comprehensive phylogenetic analysis. In total, 170 s les tested positive for HPIV. HPIV3 was most commonly detected in our cohort and 80 co-detections of HPIV with other respiratory viruses were found. Phylogenetic analyses suggest local endemic circulation as well as punctuated introductions of new HPIV lineages. Viral gene flow analysis revealed that Viet Nam is a net importer of viral genetic ersity. Epidemiological analyses imply similar disease severity for all HPIV species. HPIV sequences from Viet Nam formed local clusters and were interspersed with sequences from erse geographic regions. Combined, this new knowledge will help to investigate global HPIV circulation patterns in more detail and ultimately define more suitable vaccine strains.
Publisher: Springer Science and Business Media LLC
Date: 07-07-2016
Publisher: SAGE Publications
Date: 07-2012
DOI: 10.3851/IMP2092
Abstract: Access to antiretroviral therapy (ART) for HIV-infected in iduals in Vietnam is rapidly expanding, but there are limited data on HIV drug resistance (HIVDR) to guide ART strategies. We retrospectively conducted HIVDR testing in 220 ART-naive in iduals recruited to a randomized controlled trial of immediate versus deferred ART in in iduals with HIV-associated tuberculous meningitis in Ho Chi Minh City (HCMC) from 2005–2008. HIVDR mutations were identified by population sequencing of the HIV pol gene and were defined based on 2009 WHO surveillance drug resistance mutations (SDRMs). We successfully sequenced 219/220 plasma s les of subjects prior to ART 218 were subtype CRF01_AE and 1 was subtype B. SDRMs were identified in 14/219 (6.4%) subjects 8/14 were resistant to nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs T69D, L74V, V75M, M184V/I and K219R), 5/14 to non-nucleoside reverse transcriptase inhibitors (NNRTIs K103N, V106M, Y181C, Y188C and G190A), 1/14 to both NRTIs and NNRTIs (D67N and Y181C) and none to protease inhibitors. After 6 months of ART, eight subjects developed protocol-defined virological failure. HIVDR mutations were identified in 5/8 subjects. All five had mutations with high-level resistance to NNRTIs and three had mutations with high-level resistance to NRTIs. Due to a high early mortality rate (58%), the effect of pre-existing HIVDR mutations on treatment outcome could not be accurately assessed. The prevalence of WHO SDRMs in ART-naive in iduals with HIV-associated tuberculous meningitis in HCMC from 2005–2008 is 6.4%. The SDRMs identified conferred resistance to NRTIs and/or NNRTIs, reflecting the standard first-line ART regimens in Vietnam.
Publisher: Elsevier BV
Date: 03-2019
Publisher: Wiley
Date: 23-04-2015
DOI: 10.1111/IRV.12307
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.IJID.2022.07.018
Abstract: In this study, we aimed to conduct a systematic review to characterize antimicrobial resistance (AMR) patterns for bacterial causes of febrile illness in Africa and Asia. We included published literature from 1980-2015 based on data extracted from two recent systematic reviews of nonmalarial febrile illness from Africa, South Asia, and Southeast Asia. Selection criteria included articles with full bacterial identification and antimicrobial susceptibility testing (AST) results for key normally sterile site pathogen-drug combinations. Pooled proportions of resistant isolates were combined using random effects meta-analysis. Study data quality was graded using the Microbiology Investigation Criteria for Reporting Objectively (MICRO) framework. Of 3475 unique articles included in the previous reviews, 371 included the target pathogen-drug combinations. Salmonella enterica tested against ceftriaxone and ciprofloxacin were the two highest reported combinations (30,509 and 22,056 isolates, respectively). Pooled proportions of resistant isolates were high for third-generation cephalosporins for Klebsiella pneumoniae and Escherichia coli in all regions. The MICRO grading showed an overall lack of standardization. This review highlights a general increase in AMR reporting and in resistance over time. However, there were substantial problems with diagnostic microbiological data quality. Urgent strengthening of laboratory capacity, standardized testing, and reporting of AST results is required to improve AMR surveillance.
Publisher: Springer Science and Business Media LLC
Date: 02-2022
DOI: 10.1038/S41591-022-01690-W
Abstract: Studies of successive vaccination suggest that immunological memory against past influenza viruses may limit responses to vaccines containing current strains. The impact of memory induced by prior infection is rarely considered and is difficult to ascertain, because infections are often subclinical. This study investigated influenza vaccination among adults from the Ha Nam cohort (Vietnam), who were purposefully selected to include 72 with and 28 without documented influenza A(H3N2) infection during the preceding 9 years (Australian New Zealand Clinical Trials Registry 12621000110886). The primary outcome was the effect of prior influenza A(H3N2) infection on hemagglutinin-inhibiting antibody responses induced by a locally available influenza vaccine administered in November 2016. Baseline and postvaccination sera were titrated against 40 influenza A(H3N2) strains spanning 1968-2018. At each time point (baseline, day 14 and day 280), geometric mean antibody titers against 2008-2018 strains were higher among participants with recent infection (34 (29-40), 187 (154-227) and 86 (72-103)) than among participants without recent infection (19 (17-22), 91 (64-130) and 38 (30-49)). On days 14 and 280, mean titer rises against 2014-2018 strains were 6.1-fold (5.0- to 7.4-fold) and 2.6-fold (2.2- to 3.1-fold) for participants with recent infection versus 4.8-fold (3.5- to 6.7-fold) and 1.9-fold (1.5- to 2.3-fold) for those without. One of 72 vaccinees with recent infection versus 4 of 28 without developed symptomatic A(H3N2) infection in the season after vaccination (P = 0.021). The range of A(H3N2) viruses recognized by vaccine-induced antibodies was associated with the prior infection strain. These results suggest that recall of immunological memory induced by prior infection enhances antibody responses to inactivated influenza vaccine and is important to attain protective antibody titers.
Publisher: JMIR Publications Inc.
Date: 02-10-2020
DOI: 10.2196/19762
Abstract: Reporting cumulative antimicrobial susceptibility testing data on a regular basis is crucial to inform antimicrobial resistance (AMR) action plans at local, national, and global levels. However, analyzing data and generating a report are time consuming and often require trained personnel. This study aimed to develop and test an application that can support a local hospital to analyze routinely collected electronic data independently and generate AMR surveillance reports rapidly. An offline application to generate standardized AMR surveillance reports from routinely available microbiology and hospital data files was written in the R programming language (R Project for Statistical Computing). The application can be run by double clicking on the application file without any further user input. The data analysis procedure and report content were developed based on the recommendations of the World Health Organization Global Antimicrobial Resistance Surveillance System (WHO GLASS). The application was tested on Microsoft Windows 10 and 7 using open access ex le data sets. We then independently tested the application in seven hospitals in Cambodia, Lao People’s Democratic Republic, Myanmar, Nepal, Thailand, the United Kingdom, and Vietnam. We developed the AutoMated tool for Antimicrobial resistance Surveillance System (AMASS), which can support clinical microbiology laboratories to analyze their microbiology and hospital data files (in CSV or Excel format) onsite and promptly generate AMR surveillance reports (in PDF and CSV formats). The data files could be those exported from WHONET or other laboratory information systems. The automatically generated reports contain only summary data without patient identifiers. The AMASS application is downloadable from www.amass.website/. The participating hospitals tested the application and deposited their AMR surveillance reports in an open access data repository. The AMASS is a useful tool to support the generation and sharing of AMR surveillance reports.
Publisher: Elsevier BV
Date: 2012
Publisher: JMIR Publications Inc.
Date: 03-05-2020
Abstract: eporting cumulative antimicrobial susceptibility testing data on a regular basis is crucial to inform antimicrobial resistance (AMR) action plans at local, national, and global levels. However, analyzing data and generating a report are time consuming and often require trained personnel. his study aimed to develop and test an application that can support a local hospital to analyze routinely collected electronic data independently and generate AMR surveillance reports rapidly. n offline application to generate standardized AMR surveillance reports from routinely available microbiology and hospital data files was written in the R programming language (R Project for Statistical Computing). The application can be run by double clicking on the application file without any further user input. The data analysis procedure and report content were developed based on the recommendations of the World Health Organization Global Antimicrobial Resistance Surveillance System (WHO GLASS). The application was tested on Microsoft Windows 10 and 7 using open access ex le data sets. We then independently tested the application in seven hospitals in Cambodia, Lao People’s Democratic Republic, Myanmar, Nepal, Thailand, the United Kingdom, and Vietnam. e developed the AutoMated tool for Antimicrobial resistance Surveillance System (AMASS), which can support clinical microbiology laboratories to analyze their microbiology and hospital data files (in CSV or Excel format) onsite and promptly generate AMR surveillance reports (in PDF and CSV formats). The data files could be those exported from WHONET or other laboratory information systems. The automatically generated reports contain only summary data without patient identifiers. The AMASS application is downloadable from www.amass.website/. The participating hospitals tested the application and deposited their AMR surveillance reports in an open access data repository. he AMASS is a useful tool to support the generation and sharing of AMR surveillance reports.
Publisher: Cambridge University Press (CUP)
Date: 17-10-2017
DOI: 10.1017/S0950268817002333
Abstract: Strongyloidiasis is a neglected tropical disease caused by the roundworm Strongyloides stercoralis affecting 30–100 million people worldwide. Many Southeast-Asian countries report a high prevalence of S. stercoralis infection, but there are little data from Vietnam. Here, we evaluated the seroprevalence of S. stercoralis related to geography, sex and age in Vietnam through serological testing of anonymized sera. Sera ( n = 1710, 1340 adults and 270 children) from an anonymized age-stratified serum bank from four regions in Vietnam between 2012 and 2013 were tested using a commercial Strongyloides ratti immunoglobulin G ELISA. Seroreactivity was found in 29·1% (390/1340) of adults and 5·5% (15/270) of children. Male adults were more frequently seroreactive than females (33·3% vs. 24·9%, P = 0·001). The rural central highlands had the highest seroprevalence (42·4% of adults). Seroreactivity in the other regions was 29·9% (Hue) and 26·0% and 18·2% in the large urban centres of Hanoi and Ho Chi Minh City, respectively. We conclude that seroprevalence of S. stercoralis was high in the Vietnamese adult population, especially in rural areas.
Publisher: Public Library of Science (PLoS)
Date: 13-07-2010
Publisher: F1000 Research Ltd
Date: 11-05-2018
DOI: 10.12688/WELLCOMEOPENRES.11558.2
Abstract: Background: Since 1962, enterovirus D68 (EV-D68) has been implicated in multiple outbreaks and sporadic cases of respiratory infection worldwide, especially in the USA and Europe with an increasing frequency between 2010 and 2014. We describe the detection, associated clinical features and molecular characterization of EV-D68 in central and southern Viet Nam between 2009 and 2015. Methods: Enterovirus/rhinovirus PCR positive respiratory or CSF s les taken from children and adults with respiratory/central nervous system infections in Viet Nam were tested by an EV-D68 specific PCR. The included s les were derived from 3 different observational studies conducted at referral hospitals across central and southern Viet Nam 2009 2015. Whole-genome sequencing was carried out using a MiSeq based approach. Phylogenetic reconstruction and estimation of evolutionary rate and recombination were carried out in BEAST and Recombination Detection Program, respectively. Results: EV-D68 was detected in 21/625 (3.4%) enterovirus/rhinovirus PCR positive respiratory s les but in none of the 15 CSF. All the EV-D68 patients were young children (age range: 11.8 – 24.5 months) and had moderate respiratory infections. Phylogenetic analysis suggested that the Vietnamese sequences clustered with those from Asian countries, of which 9 fell in the B1 clade, and the remaining sequence was identified within the A2 clade. One intra sub-clade recombination event was detected, representing the second reported recombination within EV-D68. The evolutionary rate of EV-D68 was estimated to be 5.12E -3 substitutions/site/year. Phylogenetic analysis indicated that the virus was imported into Viet Nam in 2008. Conclusions: We have demonstrated for the first time EV-D68 has been circulating at low levels in Viet Nam since 2008, associated with moderate acute respiratory infection in children. EV-D68 in Viet Nam is most closely related to Asian viruses, and clusters separately from recent US and European viruses that were suggested to be associated with acute flaccid paralysis.
Publisher: Public Library of Science (PLoS)
Date: 08-06-2010
Publisher: American Society for Microbiology
Date: 29-12-2016
Abstract: To document the viral zoonotic risks in Vietnam, fecal s les were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 04-2018
Publisher: F1000 Research Ltd
Date: 16-08-2023
DOI: 10.12688/WELLCOMEOPENRES.19210.2
Abstract: Background : Antimicrobial resistance surveillance is essential for empiric antibiotic prescribing, infection prevention and control policies and to drive novel antibiotic discovery. However, most existing surveillance systems are isolate-based without supporting patient-based clinical data, and not widely implemented especially in low- and middle-income countries (LMICs). Methods : A Clinically-Oriented Antimicrobial Resistance Surveillance Network (ACORN) II is a large-scale multicentre protocol which builds on the WHO Global Antimicrobial Resistance and Use Surveillance System to estimate syndromic and pathogen outcomes along with associated health economic costs. ACORN-healthcare associated infection (ACORN-HAI) is an extension study which focuses on healthcare-associated bloodstream infections and ventilator-associated pneumonia. Our main aim is to implement an efficient clinically-oriented antimicrobial resistance surveillance system, which can be incorporated as part of routine workflow in hospitals in LMICs. These surveillance systems include hospitalised patients of any age with clinically compatible acute community-acquired or healthcare-associated bacterial infection syndromes, and who were prescribed parenteral antibiotics. Diagnostic stewardship activities will be implemented to optimise microbiology culture specimen collection practices. Basic patient characteristics, clinician diagnosis, empiric treatment, infection severity and risk factors for HAI are recorded on enrolment and during 28-day follow-up. An R Shiny application can be used offline and online for merging clinical and microbiology data, and generating collated reports to inform local antibiotic stewardship and infection control policies. Discussion : ACORN II is a comprehensive antimicrobial resistance surveillance activity which advocates pragmatic implementation and prioritises improving local diagnostic and antibiotic prescribing practices through patient-centred data collection. These data can be rapidly communicated to local physicians and infection prevention and control teams. Relative ease of data collection promotes sustainability and maximises participation and scalability. With ACORN-HAI as an ex le, ACORN II has the capacity to accommodate extensions to investigate further specific questions of interest.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 04-2015
Publisher: Elsevier BV
Date: 03-2010
Publisher: Cold Spring Harbor Laboratory
Date: 20-11-2022
DOI: 10.1101/2022.11.19.22282535
Abstract: Blood culture (BC) s ling is recommended for all suspected sepsis patients prior to antibiotic administration. Here, we aimed to identify barriers and enablers to BC s ling in three Southeast Asian countries. We conducted a systematic review of studies evaluating barriers/enablers to BC s ling from 1900 to 2020 globally (PROSPERO, CRD42020206557). Using the findings of the systematic review, we developed and conducted a Theoretical Domains Framework (TDF)-based survey with a case scenario question among doctors and final-year medical students in Indonesia, Thailand and Vietnam. In the systematic review, we identified 6,175 unique records from the databases, of which 25 met the eligibility criteria. Studies were conducted in 37 high-income countries (HICs) and 41 low-and middle-income countries (LMICs). Of 14 TDF domains, three and seven were not assessed in HICs and LMICs by the studies included in the systematic review, respectively. 1,070 medical doctors and 238 final-year medical students completed the survey. The proportion of respondents who would definitely take BC in the case scenario was 89.8% for Thai, 50.5% for Vietnamese and 31.3% for Indonesians (p .001). Eight TDF domains were considered key in influencing BC s ling, including ‘no awareness of guideline [TDF-knowledge]’, ‘low priority of BC [TDF-goals]’, ‘no intention to follow guidelines [TDF-intention]’, ‘level of doctors who can order or initiate an order for BC [TDF-social professional role and identity]’, ‘no norms of BC s ling [TDF-social influence]’, ‘perceived cost-effectiveness of BC [TDF-environmental context and resources]’, ‘regulation on cost reimbursement [TDF-behavioural regulation]’ and ‘consequences that discourage BC s ling [TDF-reinforcement].’ However, there was substantial heterogeneity between the countries across most domains. Evidence on barriers and enablers to BC s ling is limited globally. We identified in idual, socio-cultural and environmental barriers/enablers to BC s ling across different countries, which represent potential targets for interventions. Context-specific multifaceted interventions at both hospital and policy levels are required to improve diagnostic stewardship practices. Wellcome Trust, UK (220557/Z/20/Z).
Publisher: F1000 Research Ltd
Date: 09-01-2017
DOI: 10.12688/WELLCOMEOPENRES.10042.2
Abstract: As part of an ongoing effort to generate complete genome sequences of hand, foot and mouth disease-causing enteroviruses directly from clinical specimens, two complete coding sequences and two partial genomic sequences of human bocavirus 1 (n=3) and 2 (n=1) were co- lified and sequenced, representing the first genome sequences of human bocaviruses from Vietnam. The sequences may aid future study aiming at understanding the evolution of the virus.
Publisher: F1000 Research Ltd
Date: 21-04-2023
DOI: 10.12688/WELLCOMEOPENRES.19210.1
Abstract: Background : Antimicrobial resistance surveillance is essential for empiric antibiotic prescribing, infection prevention and control policies and to drive novel antibiotic discovery. However, most existing surveillance systems are isolate-based without supporting patient-based clinical data, and not widely implemented especially in low- and middle-income countries (LMICs). Methods : A Clinically-Oriented Antimicrobial Resistance Surveillance Network (ACORN) II is a large-scale multicentre protocol which builds on the WHO Global Antimicrobial Resistance and Use Surveillance System to estimate syndromic and pathogen outcomes along with associated health economic costs. ACORN-healthcare associated infection (ACORN-HAI) is an extension study which focuses on healthcare-associated bloodstream infections and ventilator-associated pneumonia. Our main aim is to implement an efficient clinically-oriented antimicrobial resistance surveillance system, which can be incorporated as part of routine workflow in hospitals in LMICs. These surveillance systems include hospitalised patients of any age with clinically compatible acute community-acquired or healthcare-associated bacterial infection syndromes, and who were prescribed parenteral antibiotics. Diagnostic stewardship activities will be implemented to optimise microbiology culture specimen collection practices. Basic patient characteristics, clinician diagnosis, empiric treatment, infection severity and risk factors for HAI are recorded on enrolment and during 28-day follow-up. An R Shiny application can be used offline and online for merging clinical and microbiology data, and generating collated reports to inform local antibiotic stewardship and infection control policies. Discussion : ACORN II is a comprehensive antimicrobial resistance surveillance activity which advocates pragmatic implementation and prioritises improving local diagnostic and antibiotic prescribing practices through patient-centred data collection. These data can be rapidly communicated to local physicians and infection prevention and control teams. Relative ease of data collection promotes sustainability and maximises participation and scalability. With ACORN-HAI as an ex le, ACORN II has the capacity to accommodate extensions to investigate further specific questions of interest.
Publisher: European Centre for Disease Control and Prevention (ECDC)
Date: 15-11-2018
DOI: 10.2807/1560-7917.ES.2018.23.46.1800590
Abstract: Since January 2018, over 53,000 hospitalisations and six deaths due to hand, foot and mouth disease (HFMD) have occurred across Vietnam with most cases from September onward. In a large tertiary referral hospital, Ho Chi Minh City, enterovirus A71 subgenogroup C4 was predominant, while B5 was only sporadically detected. The re-emergence of C4 after causing a severe HFMD outbreak with 200 deaths in 2011–12 among susceptible young children raises concern of another impending severe outbreak.
Publisher: Frontiers Media SA
Date: 24-06-2021
DOI: 10.3389/FMICB.2021.689658
Abstract: Background: Hand, Foot and Mouth Disease (HFMD) is a major public health concern in the Asia-Pacific region. Most recent HFMD outbreaks have been caused by enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), CVA10, and CVA6. There has been no report regarding the epidemiology and genetic ersity of CVA16 in Vietnam. Such knowledge is critical to inform the development of intervention strategies. Materials and Methods: From 2011 to 2017, clinical s les were collected from in- and outpatients enrolled in a HFMD research program conducted at three referral hospitals in Ho Chi Minh City (HCMC), Vietnam. Throat or rectal swabs positive for CVA16 with sufficient viral load were selected for whole genome sequencing and evolutionary analysis. Results: Throughout the study period, 320 CVA16 positive s les were collected from 2808 HFMD patients (11.4%). 59.4% of patients were male. The median age was 20.8 months (IQR, 14.96–31.41). Patients resided in HCMC (55.3%), Mekong Delta (22.2%), and South East Vietnam (22.5%). 10% of CVA16 infected patients had moderately severe or severe HFMD. CVA16 positive s les from 153 patients were selected for whole genome sequencing, and 66 complete genomes were obtained. Phylogenetic analysis demonstrated that Vietnamese CVA16 strains belong to a single genogroup B1a that clusters together with isolates from China, Japan, Thailand, Malaysia, France and Australia. The CVA16 strains of the present study were circulating in Vietnam some 4 years prior to its detection in HFMD cases. Conclusion: We report for the first time on the molecular epidemiology of CVA16 in Vietnam. Unlike EV-A71, which showed frequent replacement between subgenogroups B5 and C4 every 2–3 years in Vietnam, CVA16 displays a less pronounced genetic alternation with only subgenogroup B1a circulating in Vietnam since 2011. Our collective findings emphasize the importance of active surveillance for viral circulation in HFMD endemic countries, critical to informing outbreak response and vaccine development.
Publisher: Public Library of Science (PLoS)
Date: 24-03-2011
Publisher: Elsevier BV
Date: 08-2019
Publisher: Cold Spring Harbor Laboratory
Date: 20-03-2021
DOI: 10.1101/2021.03.20.436248
Abstract: The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on within-host virus ersity of infections in otherwise healthy adults based on single timepoint data. Here, we analysed the within-host evolution of 82 longitudinally-s led in iduals, mostly young children, infected with A/H3N2 or A/H1N1pdm09 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous changes were common early in infection but decreased or remained constant throughout infection. For A/H3N2 viruses, early infection was dominated by purifying selection. However, as infections progressed, nonsynonymous variants increased in frequencies even though within-host virus titres decreased, leading to the maintenance of virus ersity via mutation-selection balance. Our findings suggest that this maintenance of genetic ersity in these children combined with their longer duration of infection may provide important opportunities for within-host virus evolution.
Publisher: Oxford University Press (OUP)
Date: 03-2017
Publisher: Oxford University Press (OUP)
Date: 07-2018
DOI: 10.1093/VE/VEY035
Abstract: The Coronaviridae family of viruses encompasses a group of pathogens with a zoonotic potential as observed from previous outbreaks of the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Accordingly, it seems important to identify and document the coronaviruses in animal reservoirs, many of which are uncharacterized and potentially missed by more standard diagnostic assays. A combination of sensitive deep sequencing technology and computational algorithms is essential for virus surveillance, especially for characterizing novel- or distantly related virus strains. Here, we explore the use of profile Hidden Markov Model-defined Pfam protein domains (Pfam domains) encoded by new sequences as a Coronaviridae sequence classification tool. The encoded domains are used first in a triage to identify potential Coronaviridae sequences and then processed using a Random Forest method to classify the sequences to the Coronaviridae genus level. The application of this algorithm on Coronaviridae genomes assembled from agnostic deep sequencing data from surveillance of bats and rats in Dong Thap province (Vietnam) identified thirty-four Alphacoronavirus and eleven Betacoronavirus genomes. This collection of bat and rat coronaviruses genomes provided essential information on the local ersity of coronaviruses and substantially expanded the number of coronavirus full genomes available from bat and rats and may facilitate further molecular studies on this group of viruses.
Publisher: Springer Science and Business Media LLC
Date: 13-10-2016
Publisher: Springer Science and Business Media LLC
Date: 12-04-2018
Publisher: Research Square Platform LLC
Date: 15-06-2021
DOI: 10.21203/RS.3.RS-569330/V1
Abstract: Background The controversial hypothesis that recalled immunological memory limits responses to variant virus strains has been revived by recent reports linking poor vaccine effectiveness against A(H3N2) influenza viruses with prior vaccination. The impact of memory induced by prior infection is rarely considered, and is difficult to ascertain because infections are often sub-clinical. This study investigates influenza vaccine immunogenicity among participants who had been monitored for 9 years for clinical influenza infection or seroconversion. Methods In 2007, 269 households from Ha Nam, Viet Nam commenced ongoing monitoring for influenza infection. In 2016, 72 adult participants with documented prior A(H3N2) infection and 28 without infection received trivalent inactivated influenza vaccine for the first time. Serological responses were assessed by hemagglutination inhibition assay against 40 A(H3N2) viruses spanning 1968-2018. Effects of prior infection were determined by comparing geometric mean titres and titre rises. Generalized additive and lowess models were used to fit, and compare, titre landscapes across strains. Findings Participants with documented prior A(H3N2) virus infection had higher pre-vaccine titres against strains circulating since 2004 compared to those without prior infection. Moreover, they had higher titre rises on days 7, 14, 21 and 280 post-vaccination against vaccine and subsequently circulating strains. Accordingly, 1/72 versus 4/28 of vaccinees with and without documented prior infection experienced illness due to A(H3N2) in the season after vaccination (p = 0.021). The range of A(H3N2) virus clades recognized by vaccine-induced antibodies was associated with the clade that last caused infection, indicating that recalled immunity drove antibody production against shared epitopes. Interpretation These results suggest that immunological memory from prior infection drives and shapes antibody production induced by inactivated influenza vaccine, and underpins the capacity for vaccine to induce sufficient antibody for protection.
Publisher: Springer Science and Business Media LLC
Date: 14-02-2018
Publisher: American Society for Microbiology
Date: 15-01-2012
DOI: 10.1128/JVI.05985-11
Abstract: Little is known about the rate at which genetic variation is generated within intrahost populations of dengue virus (DENV) and what implications this ersity has for dengue pathogenesis, disease severity, and host immunity. Previous studies of intrahost DENV variation have used a low frequency of s ling and/or experimental methods that do not fully account for errors generated through lification and sequencing of viral RNAs. We investigated the extent and pattern of genetic ersity in sequence data in domain III (DIII) of the envelope (E) gene in serial plasma s les ( n = 49) taken from 17 patients infected with DENV type 1 (DENV-1), totaling some 8,458 clones. Statistically rigorous approaches were employed to account for artifactual variants resulting from lification and sequencing, which we suggest have played a major role in previous studies of intrahost genetic variation. Accordingly, nucleotide sequence ersities of viral populations were very low, with conservative estimates of the average levels of genetic ersity ranging from 0 to 0.0013. Despite such sequence conservation, we observed clear evidence for mixed infection, with the presence of multiple phylogenetically distinct lineages present within the same host, while the presence of stop codon mutations in some s les suggests the action of complementation. In contrast to some previous studies we observed no relationship between the extent and pattern of DENV-1 genetic ersity and disease severity, immune status, or level of viremia.
Publisher: Elsevier BV
Date: 11-2016
Publisher: Elsevier BV
Date: 04-2015
Publisher: SAGE Publications
Date: 2014
DOI: 10.33151/AJP.11.5.59
Abstract: Over 9,500 people die annually in Australia from sudden cardiac arrest, with strong evidence suggesting early high quality CPR and early counter shock being paramount for improving survival from cardiac arrest. It has also been shown that first responder programs have been able to reduce response times and increase survival rates for out-of-hospital cardiac arrest. The objective of this study was to examine data from the first seven years of an Australian out-of-hospital cardiac arrest first responder program where fire fighters provided basic life support. This study was a retrospective cohort study of all cardiac arrests attended by the Metropolitan Fire and Emergency Services Board (MFESB) as part of the Emergency Medical Response program over a seven-year period in Melbourne, Victoria, Australia. The MFESB attended 4,450 cardiac arrests. The majority of patients presented in asystole 669 (63.7%) with just 243 (23.1%) presenting in a shockable rhythm. The majority of patients in cardiac arrest were males (64.2%) and the mean age of the patients was 67.5 years. The MFESB median response time during the study period was 5.7 minutes (IQR 2.25 minutes), range of 0.15 minutes to 31.7 minutes, which remained stable over the seven years. Patients spent a median time of 4.6 minutes (0.02 seconds to 36.5 minutes) in the care of fire fighters prior to the arrival of EMS. The rhythm on handover to paramedics was asystole in 787 (75.1%) cases with no shockable rhythms. One in three (31.3%) patients received bystander CPR, with a significant rise in the rate of bystander CPR occurring over the last two years. This study demonstrated acceptable response times to cardiac arrests and a low bystander CPR rate prior to arrival of the MFESB. The incidence of a shockable rhythm on arrival of the MFESB was low with the main rhythm being asystole. The main rhythm on handover to paramedics was asystole with non-shockable rhythms. Further research is required to determine the effect on patient outcomes.
Publisher: Cold Spring Harbor Laboratory
Date: 22-02-2022
DOI: 10.1101/2022.02.20.22271261
Abstract: A major driver of antimicrobial resistance (AMR) and poor clinical outcomes is suboptimal antibiotic use, although data are lacking in low-resource settings. We reviewed studies on systemic antibiotic use (WHO ATC/DDD category J01) for human health in Indonesia, and synthesized available evidence to identify opportunities for intervention. We systematically searched five international and national databases for eligible peer-reviewed articles, in English and Indonesian, published between 1 January 2000 and 1 June 2021 including: 1) antibiotic consumption 2) prescribing appropriateness 3) antimicrobial stewardship (AMS) 4) perceptions among consumers and providers. Two independent reviewers included studies and extracted data. Study-level data were summarized using random-effects model meta-analysis for consumption and prescribing appropriateness, effect direction analysis for AMS interventions, and qualitative synthesis for perception surveys. (PROSPERO CRD42019134641) Of 9323 search hits, we included 100 reports on antibiotic consumption (20), prescribing appropriateness (49), AMS (13), and/or perception (25) (8 categorized in domain). The pooled estimate of overall antibiotic consumption was 110.1 DDD/100 patient-days (95%CI98.5-121.6), with ceftriaxone, icillin and levofloxacin being most consumed. Pooled estimates for overall appropriate prescribing (according to Gyssens method) were 33.5% (95%CI18.1-53.4%) in hospitals and 49.4% (95%CI23.7-75.4%) in primary care. Pooled estimates for appropriate prescribing (according to reference guidelines) were, in hospitals, 99.7% (95%CI97.4-100%) for indication, 84.9% (95%CI38.5-98.0%) for drug choice, and 6.1% (95%CI0.2-63.2%) for overall appropriateness, and, in primary care, 98.9% (95%CI60.9-100%) for indication, 82.6% (95%CI50.5%-95.7%) for drug choice and 10.5% (95%CI0.8-62.6%) for overall appropriateness. The few AMS intervention studies conducted to date suggested potential to reduce antibiotic consumption and improve prescribing appropriateness. Key themes identified in perception surveys were lack of antibiotic knowledge among consumers and non-prescription antibiotic self-medication. Context-specific strategies are urgently needed to improve rational antibiotic use in Indonesian hospitals and communities, with critical evidence gaps concerning private and informal health providers. What is already known? • Indonesia is a potential AMR hotspot, where, based on pharmaceutical sales data, antibiotic consumption increased 2.5-fold between 2000 and 2015, mostly driven by broad-spectrum penicillins, fluoroquinolones and cephalosporins. • Representative contemporary data on antibiotic use are lacking, although anecdotal data suggest antibiotic overuse in the healthcare system, widespread over-the-counter use in communities, and high rates of AMR mostly among common Gram-negative bacteria. • A comprehensive review on antibiotic use in human health in Indonesia has not been conducted to date. What are the new findings? • Available data spanning the past 20 years, suggested that only 34% and 49% of antibiotics were appropriately prescribed in hospital and primary care settings, respectively, although the quality of the evidence was low. • Publications evaluating AMS interventions have been sparse to date, demonstrating the need to strengthen the local research base to develop context-specific and sustainable AMS models. • Community surveys suggested important gaps in antibiotic knowledge, and that non-prescription antibiotic self-medication is common practice, although data to quantify this problem and its drivers are lacking. What do the new findings imply? • Available evidence synthesised in this Review provides important insights in the magnitude and patterns of antibiotic use, and associated patient and health system factors, which helps define opportunities for optimising responsible antibiotic use. • Critical evidence gaps exist on informal and formal private health care providers, geographic areas outside of Java Island, as well as effective AMS models that consider country-specific socio-cultural, economic and political circumstances. • Optimization of antimicrobial use as a means to tackle AMR should be a priority of the national agenda for universal health coverage.
Publisher: Wiley
Date: 13-10-2015
DOI: 10.1111/IRV.12326
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 02-2020
Publisher: Oxford University Press (OUP)
Date: 27-09-2017
Publisher: Microbiology Society
Date: 12-2015
DOI: 10.1099/JGV.0.000298
Abstract: Human respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children 2 years of age. Little is known about RSV intra-host genetic ersity over the course of infection or about the immune pressures that drive RSV molecular evolution. We performed whole-genome deep-sequencing on 53 RSV-positive s les (37 RSV subgroup A and 16 RSV subgroup B) collected from the upper airways of hospitalized children in southern Vietnam over two consecutive seasons. RSV A NA1 and RSV B BA9 were the predominant genotypes found in our s les, consistent with other reports on global RSV circulation during the same period. For both RSV A and B, the M gene was the most conserved, confirming its potential as a target for novel therapeutics. The G gene was the most variable and was the only gene under detectable positive selection. Further, positively selected sites in G were found in close proximity to and in some cases overlapped with predicted glycosylation motifs, suggesting that selection on amino acid glycosylation may drive viral genetic ersity. We further identified hotspots and coldspots of intra-host genetic ersity in the RSV genome, some of which may highlight previously unknown regions of functional importance.
Publisher: Elsevier BV
Date: 09-2016
Publisher: Oxford University Press (OUP)
Date: 07-2016
DOI: 10.1093/VE/VEW027
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 04-2019
Publisher: Oxford University Press (OUP)
Date: 13-06-2019
DOI: 10.1093/OFID/OFZ284
Abstract: Hand, foot, and mouth disease (HFMD) has become a major public health concern in the Asia-Pacific region. Knowledge of its economic burden is essential for policy makers in prioritizing the development and implementation of interventions. A multi-hospital-based study was prospectively conducted at 3 major hospitals in Ho Chi Minh City, Vietnam, during 2016–2017. Data on direct and productivity costs were collected alongside clinical information and s les and demographic information from study participants. A total of 466 patients were enrolled. Two hundred three of 466 (43.6%) patients lived in Ho Chi Minh City, and 72/466 (15.5%) had severe HFMD. An enterovirus was identified in 74% of 466 patients, with EV-A71, CV-A6, CV-A10, and CV-A16 being the most common viruses identified (236/466, 50.6%). The mean economic burden per case was estimated at US$400.80 (95% confidence interval [CI], $353.80–$448.90), of which the total direct (medical) costs accounted for 69.7%. There were considerable differences in direct medical costs between groups of patients with different clinical severities and pathogens (ie, EV-A71 vs non-EV-A71). In Vietnam, during 2016–2017, the economic burden posed by HFMD was US$90 761 749 (95% CI, $79 033 973–$103 009 756). Our findings are of public health significance because for the first time we demonstrate that HFMD causes a substantial economic burden in Vietnam, and although multivalent vaccines are required to control HFMD, effective EV-A71 vaccine could substantially reduce the burden posed by severe HFMD. The results will be helpful for health policy makers in prioritizing resources for the development and implementation of intervention strategies to reduce the burden of HFMD.
Publisher: Wiley
Date: 18-04-2017
DOI: 10.1111/ZPH.12362
Publisher: American Society for Microbiology
Date: 28-04-2016
Abstract: A large measles virus outbreak occurred across Vietnam in 2014. We identified and obtained complete measles virus genomes in stool s les collected from two diarrheal pediatric patients in Dong Thap Province. These are the first complete genome sequences of circulating measles viruses in Vietnam during the 2014 measles outbreak.
Publisher: Wiley
Date: 09-06-2017
DOI: 10.1111/ZPH.12364
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for H Rogier van Doorn.