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A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
Immunogenicity of third dose COVID-19 vaccine strategies in patients who are immunocompromised with suboptimal immunity following two doses (OCTAVE-DUO): an open-label, multicentre, randomised, controlled, phase 3 trial.
BackgroundThe humoral and T-cell responses to booster COVID-19 vaccine types in multidisease immunocompromised individuals who do not generate adequate antibody responses to two COVID-19 vaccine doses, is not fully understood. The OCTAVE DUO trial aimed to determine the value of third vaccinations in a wide range of patients with primary and secondary immunodeficiencies.MethodsOCTAVE-DUO was a prospective, open-label, multicentre, randomised, controlled, phase 3 trial investigating humoral and T-cell responses in patients who are immunocompromised following a third vaccine dose with BNT162b2 or mRNA-1273, and of NVX-CoV2373 for those with lymphoid malignancies. We recruited patients who were immunocompromised from 11 UK hospitals, aged at least 18 years, with previous sub-optimal responses to two doses of SARS-CoV-2 vaccine. Participants were randomly assigned 1:1 (1:1:1 for those with lymphoid malignancies), stratified by disease, previous vaccination type, and anti-spike antibody response following two doses. Individuals with lived experience of immune susceptibility were involved in the study design and implementation. The primary outcome was vaccine-specific immunity defined by anti-SARS-CoV-2 spike antibodies (Roche Diagnostics UK and Ireland, Burgess Hill, UK) and T-cell responses (Oxford Immunotec, Abingdon, UK) before and 21 days after the third vaccine dose analysed by a modified intention-to-treat analysis. The trial is registered with the ISRCTN registry, ISRCTN 15354495, and the EU Clinical Trials Register, EudraCT 2021-003632-87, and is complete.FindingsBetween Aug 4, 2021 and Mar 31, 2022, 804 participants across nine disease cohorts were randomly assigned to receive BNT162b2 (n=377), mRNA-1273 (n=374), or NVX-CoV2373 (n=53). 356 (45%) of 789 participants were women, 433 (55%) were men, and 659 (85%) of 775 were White. Anti-SARS-CoV-2 spike antibodies measured 21 days after the third vaccine dose were significantly higher than baseline pre-third dose titres in the modified intention-to-treat analysis (median 1384 arbitrary units [AU]/mL [IQR 4·3-7990·0] compared with median 11·5 AU/mL [0·4-63·1]; p<0·001). Of participants who were baseline low responders, 380 (90%) of 423 increased their antibody concentrations to more than 400 AU/mL. Conversely, 166 (54%) of 308 baseline non-responders had no response after the third dose. Detectable T-cell responses following the third vaccine dose were seen in 494 (80%) of 616 participants. There were 24 serious adverse events (BNT612b2 eight [33%] of 24, mRNA-1273 12 [50%], NVX-CoV2373 four [17%]), two (8%) of which were categorised as vaccine-related. There were seven deaths (1%) during the trial, none of which were vaccine-related.InterpretationA third vaccine dose improved the serological and T-cell response in the majority of patients who are immunocompromised. Individuals with chronic renal disease, lymphoid malignancy, on B-cell targeted therapies, or with no serological response after two vaccine doses are at higher risk of poor response to a third vaccine dose.FundingMedical Research Council, Blood Cancer UK.
Detection of florfenicol resistance in opportunistic Acinetobacter spp. infections in rural Thailand.
Florfenicol (Ff) is an antimicrobial agent belonging to the class amphenicol used for the treatment of bacterial infections in livestock, poultry, and aquaculture (animal farming). It inhibits protein synthesis. Ff is an analog of chloramphenicol, an amphenicol compound on the WHO essential medicine list that is used for the treatment of human infections. Due to the extensive usage of Ff in animal farming, zoonotic pathogens have developed resistance to this antimicrobial agent. There are numerous reports of resistance genes from organisms infecting or colonizing animals found in human pathogens, suggesting a possible exchange of genetic materials. One of these genes is floR, a gene that encodes for an efflux pump that removes Ff from bacterial cells, conferring resistance against amphenicol, and is often associated with mobile genetic elements and other resistant determinants. In this study, we analyzed bacterial isolates recovered in rural Thailand from patients and environmental samples collected for disease monitoring. Whole genome sequencing was carried out for all the samples collected. Speciation and genome annotation was performed revealing the presence of the floR gene in the bacterial genome. The minimum inhibitory concentration (MIC) was determined for Ff and chloramphenicol. Chromosomal and phylogenetic analyses were performed to investigate the acquisition pattern of the floR gene. The presence of a conserved floR gene in unrelated Acinetobacter spp. isolated from human bacterial infections and environmental samples was observed, suggesting multiple and independent inter-species genetic exchange of drug-resistant determinants. The floR was found to be in the variable region containing various mobile genetic elements and other antibiotic resistance determinants; however, no evidence of HGT could be found. The floR gene identified in this study is chromosomal for all isolates. The study highlights a plausible impact of antimicrobials used in veterinary settings on human health. Ff shares cross-resistance with chloramphenicol, which is still in use in several countries. Furthermore, by selecting for floR-resistance genes, we may be selecting for and facilitating the zoonotic and reverse zoonotic exchange of other flanking resistance markers between human and animal pathogens or commensals with detrimental public health consequences.
Malaria epidemiology, surveillance and response for elimination in Lao PDR.
BackgroundLao PDR has made significant progress in malaria control. The National Strategic Plans outline ambitious targets, aiming for the elimination of Plasmodium falciparum and P. vivax malaria from all northern provinces by 2025 and national elimination by 2030. This article presents an overview of malaria epidemiology, surveillance, and response systems in Lao PDR, emphasizing experiences and achievements in transmission reduction.MethodsData on surveillance, monitoring and evaluation systems, human resources, infrastructure, and community malaria knowledge during 2010-2020 were systematically gathered from the national program and relevant documents. The collected information was synthesized, and discussions on challenges and future prospects were provided.ResultsMalaria control and elimination activities in Lao PDR were implemented at various levels, with a focus on health facility catchment areas. There has been significant progress in reducing malaria transmission throughout the country. Targeted interventions, such as case management, vector control, and community engagement, using stratification of control interventions by catchment areas have contributed to the decline in malaria cases. In elimination areas, active surveillance strategies, including case and foci investigation, are implemented to identify and stop transmission. The surveillance system has facilitated timely detection and response to malaria cases, enabling these targeted interventions in higher-risk areas.ConclusionsThe malaria surveillance and response system in Lao PDR has played a crucial role in reducing transmission and advancing the country towards elimination. Challenges such as importation, drug resistance, and sustaining support require ongoing efforts. Further strengthening surveillance, improving access to services, and addressing transmission determinants are key areas of focus to achieve malaria elimination and enhance population health in Lao PDR.
Antenatal corticosteroids reduce neonatal mortality in settings without assisted ventilatory support: a retrospective cohort study of early preterm births on the Thailand-Myanmar border.
BackgroundPrematurity is the highest risk for under-five mortality globally. The aim of the study was to assess the effect of antenatal dexamethasone on neonatal mortality in early preterm in a resource-constrained setting without assisted ventilation.MethodsThis retrospective (2008-2013) cohort study in clinics for refugees/migrants on the Thai-Myanmar border included infants born <34 weeks gestation at home, in, or on the way to the clinic. Dexamethasone, 24 mg (three 8 mg intramuscular doses, every 8 hours), was prescribed to women at risk of preterm birth (28 to <34 weeks). Appropriate newborn care was available: including oxygen but not assisted ventilation. Mortality and maternal fever were compared by the number of doses (complete: three, incomplete (one or two), or no dose). A sub-cohort participated in neurodevelopmental testing at one year.ResultsOf 15,285 singleton births, 240 were included: 96 did not receive dexamethasone and 144 received one, two or three doses (56, 13 and 75, respectively). Of live-born infants followed to day 28, (n=168), early neonatal and neonatal mortality/1,000 livebirths (95%CI) with complete dosing was 217 (121-358) and 304 (190-449); compared to 394 (289-511) and 521 (407-633) with no dose. Compared to complete dosing, both incomplete and no dexamethasone were associated with elevated adjusted ORs 4.09 (1.39 to 12.00) and 3.13 (1.14 to 8.63), for early neonatal death. By contrast, for neonatal death, while there was clear evidence that no dosing was associated with higher mortality, adjusted OR 3.82 (1.42 to 10.27), the benefit of incomplete dosing was uncertain adjusted OR 1.75 (0.63 to 4.81). No adverse impact of dexamethasone on infant neurodevelopmental scores (12 months) or maternal fever was observed.ConclusionsNeonatal mortality reduction is possible with complete dexamethasone dosing in pregnancies at risk of preterm birth in settings without capacity to provide assisted ventilation.
Exploring community participation in vectorborne disease control in Southeast Asia: a scoping review protocol.
IntroductionVector borne diseases (VBDs) present significant public health challenges in Southeast Asia (SEA), and the increasing number of cases threatens vulnerable communities. Inadequate vector control and management have been linked to the spread of VBDs. To address these issues, community participation has been proposed as a promising approach to enhance health programmes and control of VBDs. This article outlines a protocol for a scoping review of the published literature on community-participation approaches to control VBDs in the SEA region. The primary research question is 'How does community participation complement the control of VBDs in SEA?' This review aims to provide an overview of various approaches and identify barriers and facilitators to effective implementation.Methods and analysisThe research questions will guide the scoping review. In stage 1, peer-reviewed publications from PubMed, Web of Science and Scopus will be searched using predefined search terms related to community-based approaches and VBDs in the SEA region, English, Indonesian and Malay published between 2012 and 2022. In stage 2, the references from relevant articles will be screened for eligibility. In stage 3, eligible articles will be charted in Microsoft Excel to facilitate the review process, and studies will be characterised based on the investigated diseases; this review will also highlight the methodological context of these studies. In stage 4, a thematic analysis will be conducted to derive meaningful findings from the dataset relevant to the research inquiry, followed by writing the results in stage 5. This scoping review aims to be the first to explore community participation in VBD control in the SEA population, providing valuable insights for future research and stakeholders involved in disease control.Ethics and disseminationThis scoping review does not require ethical approval because the methodology synthesises information from available articles. This review is planned for dissemination in academic journals, conference presentations and shared with stakeholders as part of knowledge sharing among those involved in VBD control.
Spatial Analysis of Drug-Susceptible and Multidrug-Resistant Cases of Tuberculosis, Ho Chi Minh City, Vietnam, 2020-2023.
We characterized the spatial distribution of drug-susceptible (DS) and multidrug-resistant (MDR) tuberculosis (TB) cases in Ho Chi Minh City, Vietnam, a major metropolis in southeastern Asia, and explored demographic and socioeconomic factors associated with local TB burden. Hot spots of DS and MDR TB incidence were observed in the central parts of Ho Chi Minh City, and substantial heterogeneity was observed across wards. Positive spatial autocorrelation was observed for both DS TB and MDR TB. Ward-level TB incidence was associated with HIV prevalence and the male proportion of the population. No ward-level demographic and socioeconomic indicators were associated with MDR TB case count relative to total TB case count. Our findings might inform spatially targeted TB control strategies and provide insights for generating hypotheses about the nature of the relationship between DS and MDR TB in Ho Chi Minh City and the wider southeastern region of Asia.
The relationship between viral clearance rates and disease progression in early symptomatic COVID-19: a systematic review and meta-regression analysis
Abstract Background Effective antiviral drugs accelerate viral clearance in acute COVID-19 infections; the relationship between accelerating viral clearance and reducing severe clinical outcomes is unclear. Methods A systematic review was conducted of randomized controlled trials (RCTs) of antiviral therapies in early symptomatic COVID-19, where viral clearance data were available. Treatment benefit was defined clinically as the relative risk of hospitalization/death during follow-up (≥14 days), and virologically as the SARS-CoV-2 viral clearance rate ratio (VCRR). The VCRR is the ratio of viral clearance rates between the intervention and control arms. The relationship between the clinical and virological treatment effects was assessed by mixed-effects meta-regression. Results From 57 potentially eligible RCTs, VCRRs were derived for 44 (52 384 participants); 32 had ≥1 clinical endpoint in each arm. Overall, 9.7% (R2) of the variation in clinical benefit was explained by variation in VCRRs with an estimated linear coefficient of −0.92 (95% CI: −1.99 to 0.13; P = 0.08). However, this estimate was highly sensitive to the inclusion of the recent very large PANORAMIC trial. Omitting this outlier, half the variation in clinical benefit (R2 = 50.4%) was explained by variation in VCRRs [slope −1.47 (95% CI −2.43 to −0.51); P = 0.003], i.e. higher VCRRs were associated with an increased clinical benefit. Conclusion Methods of determining viral clearance in COVID-19 studies and the relationship to clinical outcomes vary greatly. As prohibitively large sample sizes are now required to show clinical treatment benefit in antiviral therapeutic assessments, viral clearance is a reasonable surrogate endpoint.
The PreQuine Platform: A novel diagnostic tool for measuring glucose-6-phosphate dehydrogenase (G6PD) activity and hemoglobin concentration
Quantitative diagnosis of glucose-6-phosphate dehydrogenase (G6PD) deficiency is essential for the safe administration of 8-aminoquinoline based radical cure for the treatment of Plasmodium vivax infections. Here, we present the PreQuine Platform (IVDS, USA), a quantitative biosensor that uses a dual-analyte assay for the simultaneous measurement of Hemoglobin (Hgb) levels and G6PD enzyme activity within the same sample. The platform relies on a downloadable mobile application. The device requires 10μl of whole blood and works with a reflectance-based meter. Comparing the G6PD measurement normalized by Hgb of 12 samples from the PreQuine Platform with reference measurements methods (spectrophotometry, Pointe Scientific, USA and hemoglobin meter, HemoCue, Sweden) showed a positive and significant agreement with a slope of 1.0091 and an intercept of -0.0379 under laboratory conditions. Next steps will be to conduct field trials in Bangladesh, Cambodia, and the USA to assess diagnostic performance, user friendliness and acceptance.
Antenatal corticosteroids reduce neonatal mortality in settings without assisted ventilatory support: a retrospective cohort study of early preterm births on the Thailand-Myanmar border
Background Prematurity is the highest risk for under-five mortality globally. The aim of the study was to assess the effect of antenatal dexamethasone on neonatal mortality in early preterm in a resource-constrained setting without assisted ventilation. Methods This retrospective (2008-2013) cohort study in clinics for refugees/migrants on the Thai-Myanmar border included infants born <34 weeks gestation at home, in, or on the way to the clinic. Dexamethasone, 24 mg (three 8 mg intramuscular doses, every 8 hours), was prescribed to women at risk of preterm birth (28 to <34 weeks). Appropriate newborn care was available: including oxygen but not assisted ventilation. Mortality and maternal fever were compared by the number of doses (complete: three, incomplete (one or two), or no dose). A sub-cohort participated in neurodevelopmental testing at one year. Results Of 15,285 singleton births, 240 were included: 96 did not receive dexamethasone and 144 received one, two or three doses (56, 13 and 75, respectively). Of live-born infants followed to day 28, (n=168), early neonatal and neonatal mortality/1,000 livebirths (95%CI) with complete dosing was 217 (121–358) and 304 (190–449); compared to 394 (289–511) and 521 (407–633) with no dose. Compared to complete dosing, both incomplete and no dexamethasone were associated with elevated adjusted ORs 4.09 (1.39 to 12.00) and 3.13 (1.14 to 8.63), for early neonatal death. By contrast, for neonatal death, while there was clear evidence that no dosing was associated with higher mortality, adjusted OR 3.82 (1.42 to 10.27), the benefit of incomplete dosing was uncertain adjusted OR 1.75 (0.63 to 4.81). No adverse impact of dexamethasone on infant neurodevelopmental scores (12 months) or maternal fever was observed. Conclusions Neonatal mortality reduction is possible with complete dexamethasone dosing in pregnancies at risk of preterm birth in settings without capacity to provide assisted ventilation.
Case Report: A case of disseminated cutaneous listeriosis following appendicitis from Lao PDR
Background Listeria monocytogenes is a food-borne pathogen that is a rare cause of bacteraemia and meningitis in immunosuppressed patients, and carries a high mortality rate. Cutaneous manifestations of listeriosis are rare, and are usually associated with direct inoculation of the skin. Case A 41-year-old woman who initially presented to a hospital in Laos with appendicitis was diagnosed with disseminated listeriosis with cutaneous involvement. Intra-abdominal pathology probably contributed to bacterial bloodstream invasion. Initial treatment with meropenem was switched to ampicillin based on best practice, however our patient died 5 days after diagnosis. Conclusions This case highlights listeriosis as an important cause of mortality in low- and middle-income countries, exacerbated by poor availability of laboratory diagnostics and ineffective empiric antibiotic regimens. Improvements in food hygiene, surveillance, and increased laboratory capacity are important strategies to reduce rates of infection and clinical outcomes.
Frequency and mortality rate following antimicrobial-resistant bloodstream infections in tertiary-care hospitals compared with secondary-care hospitals.
There are few studies comparing proportion, frequency, mortality and mortality rate following antimicrobial-resistant (AMR) infections between tertiary-care hospitals (TCHs) and secondary-care hospitals (SCHs) in low and middle-income countries (LMICs) to inform intervention strategies. The aim of this study is to demonstrate the utility of an offline tool to generate AMR reports and data for a secondary data analysis. We conducted a secondary-data analysis on a retrospective, multicentre data of hospitalised patients in Thailand. Routinely collected microbiology and hospital admission data of 2012 to 2015, from 15 TCHs and 34 SCHs were analysed using the AMASS v2.0 (www.amass.website). We then compared the burden of AMR bloodstream infections (BSI) between those TCHs and SCHs. Of 19,665 patients with AMR BSI caused by pathogens under evaluation, 10,858 (55.2%) and 8,807 (44.8%) were classified as community-origin and hospital-origin BSI, respectively. The burden of AMR BSI was considerably different between TCHs and SCHs, particularly of hospital-origin AMR BSI. The frequencies of hospital-origin AMR BSI per 100,000 patient-days at risk in TCHs were about twice that in SCHs for most pathogens under evaluation (for carbapenem-resistant Acinetobacter baumannii [CRAB]: 18.6 vs. 7.0, incidence rate ratio 2.77; 95%CI 1.72-4.43, p<0.001; for carbapenem-resistant Pseudomonas aeruginosa [CRPA]: 3.8 vs. 2.0, p = 0.0073; third-generation cephalosporin resistant Escherichia coli [3GCREC]: 12.1 vs. 7.0, p<0.001; third-generation cephalosporin resistant Klebsiella pneumoniae [3GCRKP]: 12.2 vs. 5.4, p<0.001; carbapenem-resistant K. pneumoniae [CRKP]: 1.6 vs. 0.7, p = 0.045; and methicillin-resistant Staphylococcus aureus [MRSA]: 5.1 vs. 2.5, p = 0.0091). All-cause in-hospital mortality (%) following hospital-origin AMR BSI was not significantly different between TCHs and SCHs (all p>0.20). Due to the higher frequencies, all-cause in-hospital mortality rates following hospital-origin AMR BSI per 100,000 patient-days at risk were considerably higher in TCHs for most pathogens (for CRAB: 10.2 vs. 3.6,mortality rate ratio 2.77; 95%CI 1.71 to 4.48, p<0.001; CRPA: 1.6 vs. 0.8; p = 0.020; 3GCREC: 4.0 vs. 2.4, p = 0.009; 3GCRKP, 4.0 vs. 1.8, p<0.001; CRKP: 0.8 vs. 0.3, p = 0.042; and MRSA: 2.3 vs. 1.1, p = 0.023). In conclusion, the burden of AMR infections in some LMICs might differ by hospital type and size. In those countries, activities and resources for antimicrobial stewardship and infection control programs might need to be tailored based on hospital setting. The frequency and in-hospital mortality rate of hospital-origin AMR BSI are important indicators and should be routinely measured to monitor the burden of AMR in every hospital with microbiology laboratories in LMICs.
A pharmacokinetic randomised interventional study to optimise dihydroartemisinin-piperaquine dosing for malaria preventive treatment in Malawian infants: A protocol for the OPTIMAL study
Background A newer malaria preventive treatment, dihydroartemisinin-piperaquine (DP), has been identified as an effective alternative to sulfadoxine-pyrimethamine, to which malaria parasites are increasingly becoming resistant. However, how best to dose DP to safely prevent malaria in infants when aligned with routine health facility visits remains unresolved. As infants are usually excluded from participating in early dose optimisation clinical trials, the present study seeks to shift the paradigm and develop optimised DP dosing strategies for malaria preventive treatment in infants. Methods A randomised, single-blind, placebo-controlled, two-arm, interventional study will be conducted in southern Malawi. At 10 weeks (2.5 months) of age, 220 eligible infants will be randomised to receive DP (intervention group, n=110) or placebo (control group, n=110) with routine vaccines. They will be followed until 12 months of age and receive three further DP or placebo treatment courses at 14 weeks, six- and nine months. Infants in the intervention group will contribute capillary samples for piperaquine concentrations pre-dose and at three-, seven-, 14- and 28-days post-DP dosing as well as capillary samples pre-dose and on day 28 post-DP to quantify malaria parasitaemia using microscopy and quantitative PCR. In the control group, infants will contribute capillary blood samples for malaria parasitaemia at the same time points as the intervention group. Malaria incidence and adverse events will be compared between the two groups. Population pharmacokinetic-pharmacodynamic modelling techniques will be applied to derive feasible, optimised, efficacious, and safe DP dosing strategies for malaria preventive treatment in infancy. Conclusions The findings will provide the much-needed evidence to inform DP dosing for malaria preventive treatment in infants when administered with routine health facility visits. Additionally, they will help inform optimal DP dosing for malaria treatment in infants. The trial was registered with the Pan African Clinical Trials Registry; (PACTR202211575727659) on 8 November 2022. Protocol version 3.1, dated 29 September 2022.
Novel estimation of African swine fever transmission parameters within smallholder villages in Lao P.D.R.
African Swine Fever (ASF) disease transmission parameters are crucial for making response and control decisions when faced with an outbreak, yet they are poorly quantified for smallholder and village contexts within Southeast Asia. Whilst disease-specific factors - such as latent and infectious periods - should remain reasonably consistent, host, environmental and management factors are likely to affect the rate of disease spread. These differences are investigated using Approximate Bayesian Computation with Sequential Monte-Carlo methods to provide disease parameter estimates in four naïve pig populations in villages of Lao People's Democratic Republic. The villages represent smallholder pig farmers of the Northern province of Oudomxay and the Southern province of Savannakhet, and the model utilised field mortality data to validate the transmission parameter estimates over the course of multiple model generations. The basic reproductive number between-pigs was estimated to range from 3.08 to 7.80, whilst the latent and infectious periods were consistent with those published in the literature for similar genotypes in the region (4.72 to 6.19 days and 2.63 to 5.50 days, respectively). These findings demonstrate that smallholder village pigs interact similarly to commercial pigs, however the spread of disease may occur slightly slower than in commercial study groups. Furthermore, the findings demonstrated that despite diversity across the study groups, the disease behaved in a consistent manner. This data can be used in disease control programs or for future modelling of ASF in smallholder contexts.