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SummaryBackgroundMelioidosis is a grossly neglected but often-fatal tropical disease. The disease is named “a great mimicker” after its broad clinical manifestations, which makes disease diagnosis challenging and time-consuming. To improve diagnosis, we developed and evaluated the performance of the CRISPR-Cas12a system called “CRISPR-BP34” to detectBurkholderia pseudomalleiDNA across clinical specimens from patients suspected to have melioidosis.MethodsWe documented time taken for diagnosis, antibiotics prescribed during the waiting period, and infection outcomes in 875 melioidosis patients treated in a hospital in northeast Thailand between October 2019 and December 2022. In the last six months, we performed CRISPR-BP34 detection on clinical specimens (blood, urine, respiratory secretion, pus and other body fluids) collected from 330 patients with suspected melioidosis and compared its performance to the current gold-standard culture-based method. Discordant results were validated by three independent qPCR tests.FindingsA window of 3-4 days was required for gold-standard culture diagnosis, which resulted in delayed treatment. 199 [22·7%] of 875 patients died prior to diagnosis results while 114 [26·3%] of 433 follow-up cases had been diagnosed, treated, but died within 28 days of admission. A shorter sample-to-diagnosis time of less than 4 hours offered by CRISPR-BP34 technology could lead to faster administration of correct treatment. We demonstrated an improved sensitivity of CRISPR-BP34 (106 [93·0%] of 114 positive cases, 95% CI 86·6 - 96·9) compared to the culture approach (76 [66·7%] of 114 positive cases, 95% CI 57·2 - 75·2); while maintaining similar specificity (209 [96·8%] of 216 negative cases, 95% CI 93·4-98·7) to the culture (216 [100 %] of 216 negative cases, 95% CI 98·3-100·0).InterpretationThe sensitivity, specificity, speed, window of clinical intervention, and ease of operation offered by the CRISPR-BP34 support its use as a point-of-care diagnostic for melioidosis.FundingChiang Mai University Thailand and Wellcome Trust UKResearch in contextEvidence before this studyMelioidosis is an often-severe infectious disease caused by the bacteriumBurkholderia pseudomallei. It is estimated to affect 165,000 individuals annually worldwide, of which 89,000 cases are fatal. The disease diagnosis is challenging due to diverse clinical presentations, low awareness, limited diagnostic options, or even a lack of diagnostic tests. A PubMed search conducted from the database inception to 6 May 2023, using the terms “melioidosis” AND “diagnosis test,” yielded 207 results, 40 of which presented clinical evaluations of rapid melioidosis diagnostic tests. Antigen-based diagnostic tests, which detect the presence ofB. pseudomallei, reported high specificity (median = 98·6%, IQR 94·0 - 100·0), but low sensitivity (median = 57·1%, IQR = 44·3 - 82·5). The test sensitivity suffers from the often-low concentration of the bacterial antigens in patients’ samples, which can vary by specimen type and stage of infection. Antibody-based diagnostic tests that detect host antibodies againstB. pseudomalleitypically exhibit satisfactory specificity (median = 94·5%, IQR = 88·6 - 96·2) but poor sensitivity (median = 80·2%, IQR = 71·0 - 88·1). These tests are often impacted by variations in antibody responses toB. pseudomalleiand the duration required for antibody production. Furthermore, standardisation remains challenging due to the influence of different serum titres on sensitivity and background of the tests. Likewise, quantitative PCR exhibits a high degree of specificity (median = 99·8%, IQR = 91·6-100·0), but an observed low sensitivity for melioidosis (median = 77·1%, IQR = 20·8-97·8), which is likely attributed to the genetic heterogeneity ofB. pseudomalleigenomes. Additionally, these studies consistently reported a demand for improved speed and ease of implementation in resource-limited settings where melioidosis is endemic. With the limitations of current diagnostic methods, a culture-confirmed approach with 60% sensitivity, 100% specificity, and a diagnosis time of 2-7 days still stands as the gold standard for melioidosis diagnosis.Added value of this studyTo date, no study has measured the impact of delayed diagnosis on melioidosis. We assessed the number of deaths occurring prior to culture-confirmed diagnosis (22·7%) and those after diagnosis but within 28 days post-admission (26·3%), highlighting the urgent need for prompt action. To address this, we developed the CRISPR-BP34 test, which utilises isothermal amplification of a nucleic acid target followed by site-specific detection using a CRISPR-Cas12a enzyme. We successfully implemented this assay in a resource-limited setting in northeast Thailand, where the disease prevalence is among the highest in the world. The assay achieved a diagnostic sensitivity and specificity of 93·0% and 96·8%, respectively, with a limit of detection ranging from 50-250 cfu/mL. Early diagnosis can be achieved within four hours of patient admission, which is significantly faster than the gold-standard test that typically takes several days. Moreover, the ultrasensitivity of the CRISPR-BP34 assay enabled the detection of low levels ofB. pseudomalleiin hemoculture bottles, which could be missed due to mixed infections, poor aseptic technique, or other causes, leading to undiagnosed melioidosis.Implications of all available evidenceThe CRISPR-BP34 test holds great promise for the management and control of melioidosis. Its minimal setup and shallow learning curve make it well-suited for resource-limited settings. Additionally, its speed and high sensitivity enable early diagnosis and treatment, which are crucial for saving patients’ lives.

Background: Favipiravir, an anti-influenza drug, has in vitro antiviral activity against SARS-CoV-2. Clinical trial evidence to date is inconclusive. Favipiravir has been recommended for the treatment of COVID-19 in some countries. Methods: In a multicentre open-label, randomised, controlled, adaptive platform trial, low-risk adult patients with early symptomatic COVID-19 were randomised to one of ten treatment arms including high dose oral favipiravir (3.6g on day 0 followed by 1.6g daily to complete 7 days treatment) or no study drug. The primary outcome assessed in a modified intention-to-treat population (mITT) was the rate of viral clearance (derived under a linear mixed-effects model from the daily log10 viral densities in standardised duplicate oropharyngeal swab eluates taken daily over 8 days [18 swabs per patient]). The safety population included all patients who received at least one dose of the allocated intervention. This ongoing adaptive platform trial is registered at ClinicalTrials.gov (NCT05041907). Results: In the final analysis, the mITT population contained data from 114 patients randomised to favipiravir and 126 patients randomised concurrently to no study drug. Under the linear mixed-effects model fitted to all oropharyngeal viral density estimates in the first 8 days from randomisation (4,318 swabs), there was no difference in the rate of viral clearance between patients administered favipiravir and patients receiving no study drug -1% (95% CI: -14 to 14% change). High dose favipiravir was well tolerated. Interpretation: Favipiravir does not accelerate viral clearance in early symptomatic COVID-19.

BackgroundPrimaquine is the only widely available treatment to prevent relapses ofPlasmodium vivaxmalaria, but is underused because of concerns over haemolysis in glucose-6-phosphate dehydrogenase deficient (G6PDd) individuals. G6PDd is common in malaria endemic areas but testing is often not available.MethodsWe conducted a pharmacometric study to characterise the relationship between primaquine dose and haemolysis in G6PDd. The aim was to explore shorter and safer pri-maquine radical cure regimens compared to those currently recommended, potentially obviating the need for G6PD testing. Hemizygous G6PDd healthy adult Thai male volunteers were admitted to the Hospital for Tropical Diseases in Bangkok. In Part 1, volunteers were given ascending dose primaquine regimens whereby daily doses were increased from 7.5 mg up to 45 mg over 15 to 20 days. In Part 2, a single primaquine 45 mg dose was given.Results24 volunteers were enrolled in Part 1, and 16 in Part 2 (13 participated in both studies). In three volunteers the ascending dose regimen was stopped because of primaquine related safety concerns (two had increased levels of transaminases, one haemolysis). Other-wise the ascending regimens were well tolerated with no drug-related serious adverse events. In Part 1, haemoglobin concentrations fell 3.7 g/dL (median; range: 2.1 to 5.9; relative fall of -26% [range: -15 to 40%]). Primaquine doses up to 0.87 mg/kg/day were tolerated subsequently without clinically significant further falls in haemoglobin. In Part 2, the haemoglobin concentrations fell by 1.7 g/dL (median; range -0.9 to 4.1; relative fall of 12% [range: 7 to 30%]). The ascending dose primaquine regimens gave 7 times more drug but resulted in only double the haemoglobin fall.Conclusions and InterpretationIn patients with Southeast Asian G6PDd variants full radical cure treatment can be given in under three weeks compared with the current 8 week regimen.FundingMRC (MR/R015252/1); Wellcome (223099/Z/21/Z)

There are few studies comparing proportion, frequency, mortality and mortality rate of antimicrobial-resistant (AMR) bacterial infections between tertiary-care hospitals (TCHs) and secondary-care hospitals (SCHs) in low and middle-income countries (LMICs) to inform infection control strategies. We evaluated bloodstream infections (BSIs) from 2012 to 2015 in 15 TCHs and 34 SCHs in Thailand. There were differences in the proportions (%) of BSI caused by AMR strains for some pathogens between TCHs and SCHs. Of 19,665 patients with AMR BSI, 6,746 (34.3%) died. Among patients with AMR BSI, there were no or minimal differences in mortality proportion for all AMR pathogens between TCHs and SCHs. However, the frequency and mortality rates of AMR BSI were considerably higher in TCHs for most pathogens. For example, the mortality rate of hospital-origin carbapenem-resistantAcinetobacter baumanniiBSI in TCHs was nearly three times higher than that in SCHs (10.2 vs. 3.6 per 100,000 patient-days at risk, mortality rate ratio 2.77; 95% confidence interval 1.71 to 4.48, p

BackgroundUncertainty over the therapeutic benefit provided by parenteral remdesivir in COVID-19 has resulted in varying treatment guidelines. Early in the pandemic the monoclonal antibody cocktail, casirivimab/imdevimab, proved highly effective in clinical trials but because of weak or absentin vitroactivity against the SARS-CoV-2 Omicron BA.1 subvariant, it is no longer recommended.MethodsIn a multicenter open label, randomized, controlled adaptive platform trial, low-risk adult patients with early symptomatic COVID-19 were randomized to one of eight treatment arms including intravenous remdesivir (200mg followed by 100mg daily for five days), casirivimab/imdevimab (600mg/600mg), and no study drug. The primary outcome was the viral clearance rate in the modified intention-to-treat population derived from daily log10viral densities (days 0-7) in standardized duplicate oropharyngeal swab eluates. This ongoing adaptive trial is registered atClinicalTrials.gov(NCT05041907).ResultsAcceleration in mean estimated SARS-CoV-2 viral clearance, compared with the contemporaneous no study drug arm (n=64), was 42% (95%CI 18 to 73%) for remdesivir (n=67). Acceleration with casirivimab/imdevimab was 58% (95%CI: 10 to 120) in Delta (n=13), and 20% (95%CI: 3 to 43) in Omicron variant (n=61) infections compared with contemporaneous no study drug arm (n=84). In apost hocsubgroup analysis viral clearance was accelerated by 8% in BA.1 (95%CI: −21 to 59) and 23% (95%CI: 3 to 49) in BA.2 and BA.5 Omicron subvariants.ConclusionsParenteral remdesivir accelerates viral clearance in early symptomatic COVID-19. Despite substantially reducedin vitroactivities, casirivimab/imdevimab retainsin vivoantiviral activity against COVID-19 infections caused by currently prevalent Omicron subvariants.Brief summaryIn early symptomatic COVID-19 remdesivir accelerated viral clearance by 42% while the monoclonal antibody cocktail casirivimab/imdevimab accelerated clearance by approximately 60% in SARS-CoV-2 Delta variant infections, and by approximately 25% in infections with Omicron subvariants BA.2 and BA.5.

BackgroundThere is no generally accepted methodology for in vivo assessment of antiviral activity in SARS-CoV-2 infection. Ivermectin has been recommended widely as a treatment of COVID-19, but whether it has significant antiviral activity in vivo is uncertain.MethodsIn a multicentre open label, randomized, controlled adaptive platform trial, adult patients with early symptomatic COVID-19 were randomized to one of six treatment arms including high dose ivermectin (600µg/kg daily for seven days), the monoclonal antibodies casirivimab and imdevimab (600mg/600mg), and no study drug. Viral clearance rates were derived from daily duplicate oropharyngeal quantitative PCR measurements. This ongoing trial is registered at ClinicalTrials.gov (NCT05041907).ResultsRandomization to the ivermectin arm was stopped after enrolling 205 patients into all arms, as the prespecified futility threshold was reached. Compared with the no study drug arm, the mean estimated SARS-CoV-2 viral clearance following ivermectin was 9.1% slower [95%CI -27.2% to +11.8%; n=45 versus n=41], whereas in a preliminary analysis of the casirivimab/imdevimab arm it was 52.3% faster [95%CI +7.0% to +115.1%; n=10 (Delta variant) versus n=41].ConclusionsHigh dose ivermectin did not have measurable antiviral activity in early symptomatic COVID-19. Measured in this way viral clearance rate is a valuable pharmacodynamic measure in assessing antiviral COVID-19 therapeutics in vivo.Funding“Finding treatments for COVID-19: A phase 2 multi-centre adaptive platform trial to assess antiviral pharmacodynamics in early symptomatic COVID-19 (PLAT-COV)” is funded by the Wellcome Therapeutics Accelerator (223195/Z/21/Z).ImpactRate of viral clearance determined from daily duplicate oropharyngeal swabs over one week is an efficient measure of antiviral efficacy in early COVID-19 infection.High dose ivermectin did not demonstrate measurable antiviral activity in early symptomatic COVID-19 infection.

Summary Background Artemisinin and partner-drug resistance in Plasmodium falciparum are major threats to malaria control and elimination. Triple artemisinin-based combination therapies (TACTs), which combine existing co-formulated ACTs with a second partner drug that is slowly eliminated, might provide effective treatment and delay emergence of antimalarial drug resistance. Methods In this multicentre, open-label, randomised trial, we recruited patients with uncomplicated P falciparum malaria at 18 hospitals and health clinics in eight countries. Eligible patients were aged 2–65 years, with acute, uncomplicated P falciparum malaria alone or mixed with non-falciparum species, and a temperature of 37·5°C or higher, or a history of fever in the past 24 h. Patients were randomly assigned (1:1) to one of two treatments using block randomisation, depending on their location: in Thailand, Cambodia, Vietnam, and Myanmar patients were assigned to either dihydroartemisinin–piperaquine or dihydroartemisinin–piperaquine plus mefloquine; at three sites in Cambodia they were assigned to either artesunate–mefloquine or dihydroartemisinin–piperaquine plus mefloquine; and in Laos, Myanmar, Bangladesh, India, and the Democratic Republic of the Congo they were assigned to either artemether–lumefantrine or artemether–lumefantrine plus amodiaquine. All drugs were administered orally and doses varied by drug combination and site. Patients were followed-up weekly for 42 days. The primary endpoint was efficacy, defined by 42-day PCR-corrected adequate clinical and parasitological response. Primary analysis was by intention to treat. A detailed assessment of safety and tolerability of the study drugs was done in all patients randomly assigned to treatment. This study is registered at ClinicalTrials.gov, NCT02453308, and is complete. Findings Between Aug 7, 2015, and Feb 8, 2018, 1100 patients were given either dihydroartemisinin–piperaquine (183 [17%]), dihydroartemisinin–piperaquine plus mefloquine (269 [24%]), artesunate–mefloquine (73 [7%]), artemether–lumefantrine (289 [26%]), or artemether–lumefantrine plus amodiaquine (286 [26%]). The median age was 23 years (IQR 13 to 34) and 854 (78%) of 1100 patients were male. In Cambodia, Thailand, and Vietnam the 42-day PCR-corrected efficacy after dihydroartemisinin–piperaquine plus mefloquine was 98% (149 of 152; 95% CI 94 to 100) and after dihydroartemisinin–piperaquine was 48% (67 of 141; 95% CI 39 to 56; risk difference 51%, 95% CI 42 to 59; p

BackgroundFever is a common presenting symptom in low- and middle-income countries (LMICs). It was previously assumed that malaria was the cause in such patients, but its incidence has declined rapidly. The urgent need to develop point-of-care tests for the most important causes of non-malarial acute febrile illness is hampered by the lack of robust epidemiological data. We sought to obtain expert consensus on analytes which should be prioritized for inclusion in fingerprick blood-based multiplex lateral flow rapid diagnostic tests (LF-RDTs) targeted towards four categories of patients with acute non-malarial fever in South and Southeast Asian LMICs, stratified by age (paediatric vs. adult) and care setting (primary vs. secondary care).Methodology/Principal FindingsWe conducted a two-round modified e-Delphi survey. A total of 84 panellists were invited, consisting of seven each from 12 countries, divided into three regional panels (Mainland Southeast Asia, Maritime Southeast Asia, and South Asia). Panellists were asked to rank their top seven analytes for inclusion in LF-RDTs to be used in each patient category, justify their choices, and indicate whether such LF-RDTs should be incorporated into algorithm-based clinical decision support tools. Thirty-six panellists (43%) participated in the first round and 44 (52%) in the second. There was consensus that such LF-RDTs should be incorporated into clinical decision support tools. At a minimum, these LF-RDTs should be able to diagnose dengue and enteric fever in all patient categories. There was a clear preference to develop LF-RDTs for pathogens not readily detected by existing technologies, and for direct diagnosis through antigen detection. Pathogen biomarkers were prioritized over host inflammatory biomarkers, with CRP being the only one ranked consistently highly.Conclusions/SignificanceOur results provide guidance on prioritizing analytes for inclusion in context-specific multiplex LF-RDTs and similar platforms for non-malarial acute febrile illness, for which there is an urgent unmet need.AUTHOR SUMMARYIn rural South and Southeast Asia, most acute febrile illness was previously attributable to malaria but the incidence of malaria is declining. To aid diagnosis and prognosis in patients presenting with the common symptom of acute fever with no localising features but in whom malaria has been excluded, there is an urgent need to develop minimally-invasive rapid diagnostic tests (RDTs) which can test for multiple pathogen and host biomarkers. Obtaining expert consensus opinions on what biomarkers these tests should detect will contribute greatly to their development, but there is a paucity of robust epidemiological data on the diverse non-malarial causes of acute fever. We determined the biomarkers which should be included in region-specific fingerprick blood-based RDTs tailored to four patient categories differentiated by age and level of care, in the form of seven-item lists ranked in decreasing order of priority. To provide context for these rank lists, we ascertained the principal factors influencing expert priority-setting and explored perceptions of the clinical utility of such RDTs. Our results provide essential region-specific guidance to aid development of RDTs for acute non-malarial fever, for which there was strong consensus for their inclusion in clinical decision-making tools for low- and semi-skilled healthcare staff.

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

The emergence and spread of artemisinin resistant Plasmodium falciparum, first in the Greater Mekong Subregion (GMS), and now in East Africa, is a major threat to global malaria eliminations ambitions. To investigate the artemisinin resistance mechanism, transcriptome analysis was conducted of 577 P. falciparum isolates collected in the GMS between 2016-2018. A specific artemisinin resistance-associated transcriptional profile was identified that involves a broad but discrete set of biological functions related to proteotoxic stress, host cytoplasm remodeling and REDOX metabolism. The artemisinin resistance-associated transcriptional profile evolved from initial transcriptional responses of susceptible parasites to artemisinin. The genetic basis for this adapted response is likely to be complex.One sentence summaryThe transcriptional profile that characterize artemisinin resistant infections with malaria parasites Plasmodium falciparum originates in the initial transcriptional response to the drug.

In rural areas of South and Southeast Asia malaria is declining but febrile illnesses still account for substantial morbidity and mortality. Village health workers (VHWs) are often the first point of contact with the formal health system, and for patients with febrile illnesses they can provide early diagnosis and treatment of malaria. However, for the majority of febrile patients, VHWs lack the training, support and resources to provide further care. Consequently, treatable bacterial illnesses are missed, antibiotics are overused and poorly targeted, and patient attendance wanes along with declining malaria. This Open Letter announces the start of a new initiative, the Rural Febrile Illness (RFI) project, the first in a series of projects to be implemented as part of the South and Southeast Asian Community-based Trials Network (SEACTN) research programme. This multi-country, multi-site project will begin in Bangladesh, Cambodia, Lao PDR, and Myanmar and will define the epidemiological baseline of febrile illness in five remote and underserved areas of Asia where malaria endemicity is declining and access to health services is limited. The RFI project aims to determine the incidence, causes and outcomes of febrile illness; understand the opportunities, barriers and appetite for adjustment of the role of VHWs to include management of non-malarial febrile illnesses; and establish a network of community healthcare providers and facilities capable of implementing interventions designed to triage, diagnose and treat patients presenting with febrile illnesses within these communities in the future.

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

X-linked glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzymopathy. The severe Mediterranean variant (G6PD Med) found across Europe and Asia is thought to confer protection against malaria, but its effect is unclear. We fitted a Bayesian statistical model to observed G6PD Med allele frequencies in 999 Pashtun patients presenting with acute Plasmodium vivax malaria and 1408 population controls. G6PD Med was associated with reductions in symptomatic P. vivax malaria incidence of 76% (95% credible interval [CI], 58–88) in hemizygous males and homozygous females combined and 55% (95% CI, 38–68) in heterozygous females. Unless there is very large population stratification within the Pashtun (confounding these results), the G6PD Med genotype confers a very large and gene-dose proportional protective effect against acute vivax malaria. The proportion of patients with vivax malaria at risk of haemolysis following 8-aminoquinoline radical cure is substantially overestimated by studies measuring G6PD deficiency prevalence in healthy subjects.

BACKGROUND 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. OBJECTIVE 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. METHODS 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 example 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. RESULTS 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 https://www.amass.website/. The participating hospitals tested the application and deposited their AMR surveillance reports in an open access data repository. CONCLUSIONS The AMASS is a useful tool to support the generation and sharing of AMR surveillance reports.

Case fatality rates in severe falciparum malaria depend on the pattern and degree of vital organ dysfunction. Recent large-scale case-control analyses of pooled severe malaria data reported that glucose-6-phosphate dehydrogenase deficiency (G6PDd) was protective against cerebral malaria but increased the risk of severe malarial anaemia. A novel formulation of the balancing selection hypothesis was proposed as an explanation for these findings, whereby the selective advantage is driven by the competing risks of death from cerebral malaria and death from severe malarial anaemia. We re-analysed these claims using causal diagrams and showed that they are subject to collider bias. A simulation based sensitivity analysis, varying the strength of the known effect of G6PDd on anaemia, showed that this bias is sufficient to explain all of the observed association. Future genetic epidemiology studies in severe malaria would benefit from the use of causal reasoning.

To determine household and health-care provider costs associated withWe collected cost data alongside three multicentre clinical trials ofThe mean total household costs ranged from 8.7 United States dollars (US$; standard deviation, SD: 4.3) in Afghanistan to US$ 254.7 (SD: 148.4) in Colombia. Across all countries, productivity losses were the largest household cost component, resulting in mean indirect costs ranging from US$ 5.3 (SD: 3.0) to US$ 220.8 (SD: 158.40). The range of health-care provider costs for routine care was US$ 3.6-6.6. The cost of administering a glucose-6-phosphate-dehydrogenase rapid diagnostic test, ranged from US$ 0.9 to 13.5, consistently lower than the costs of the widely-used fluorescent spot test (US$ 6.3 to 17.4).An episode ofDéterminer les coûts, pour les ménages et les prestataires de soins, associés à l'infection parNous avons recueilli des données sur les coûts à l'occasion de trois essais cliniques multicentres relatifs au traitement contreLes coûts totaux moyens pour les ménages allaient de 8,7 dollars des États-Unis ($ US; écart type, ET: 4,3) en Afghanistan à 254,7 $ US (ET: 148,4) en Colombie. Tous pays confondus, les pertes de productivité étaient la principale composante des coûts pour les ménages, puisqu'elles entraînaient des coûts indirects moyens allant de 5,3 $ US (ET: 3,0) à 220,8 $ US (ET: 158,40). En ce qui concerne les prestataires de soins, le coût des soins courants allait de 3,6 à 6,6 $ US. Le coût de réalisation d'un test de diagnostic rapide basé sur le glucose-6-phosphate-déshydrogénase variait de 0,9 $ US à 13,5 $ US, un coût toujours inférieur à celui du très répandu test par fluorescence (6,3 $ US à 17,4 $ US).Un épisode de paludisme àDeterminar los costos del hogar y de los proveedores de atención de la salud asociados con la infección porSe recopilaron datos de costos junto con tres ensayos clínicos multicéntricos del tratamiento conLos costos totales promedio de los hogares oscilaron entre 8,7 dólares estadounidenses (USD; desviación estándar, DE: 4,3) en Afganistán y 254,7 USD (DE: 148,4) en Colombia. En todos los países, las pérdidas de productividad fueron el mayor componente del costo del hogar, lo que dio lugar a costos indirectos promedios que oscilaron entre 5,3 y 220,8 USD. El rango de los costos de los proveedores de atención de la salud para la atención de rutina fue de 3,6 a 6,6 USD. El costo por administrar una prueba de diagnóstico rápido de la glucosa-6-fosfato-deshidrogenasa, varió de 0,9 a 13,5 USD, consistentemente más bajo que los costos de la prueba de fluorescencia aleatoria ampliamente utilizada (6,3 a 17,4 USD).Un episodio de malaria porتحديد تكاليف مزود الرعاية الصحية والتكاليف الأسرية المرتبطة بعدوى بلازموديوم فيفاكس عبر مجموعة من الأوضاع الوبائية.قمنا بتجميع بيانات التكلفة إلى جانب ثلاث تجارب سريرية متعددة المراكز لعلاج بلازموديوم فيفاكس في كل من إثيوبيا وأفغانستان وإندونيسيا والبرازيل والفلبين وبيرو وتايلند وفييت نام وكولومبيا، تمت ما بين أبريل/نيسان 2014 إلى ديسمبر/كانون أول 2017. وحصلنا على التكاليف الأسرية من مسوح للمشاركين في التجربة تم إجراؤها عند التسجيل، ثم مرة أخرى بعد أسبوعين من تحديد تكاليف العلاج والنقل، وعدد الأيام التي لم يتمكن فيها المرضى ومقدمو الرعاية المنزلية من القيام بأنشطتهم المعتادة. قمنا بتحديد تكاليف الرعاية الروتينية من جانب مقدمي الرعاية الصحية عن طريق تقدير التكاليف الدقيقة للموارد المستخدمة لتشخيص وعلاج بلازموديوم فيفاكس في مواقع الدراسة. النتائج تراوح متوسط ​​إجمالي تكاليف الأسرة من 8.7 دولاراً أمريكياً (دولار أمريكي؛ الانحراف المعياري: 4.3) في أفغانستان إلى 254.7 دولاراً أمريكياً (الانحراف المعياري: 148.4) في كولومبيا. في كل البلدان، كانت خسائر الإنتاجية هي أكبر عنصر في التكلفة الأسرية، مما أسفر عن أن يتراوح متوسط التكاليف غير المباشرة من 5.3 دولار أمريكي (الانحراف المعياري: 3.0) إلى 220.8 دولاراً أمريكياً (الانحراف المعياري: 158.40). كان نطاق تكاليف مقدم الرعاية الصحية للرعاية الروتينية يتراوح بين 3.6 و6.6 دولاراً أمريكياً. تراوحت تكلفة إجراء الاختبار التشخيصي السريع للجلوكوز 6 فوسفات ديهيدروجينيز، ما بين 0.9 إلى 13.5 دولارًا أمريكيًا، وهي أقل بشكل متسق عن تكاليف اختبار بقعة الفلورسنت المستخدم بشكل شائع (6.3 دولار أمريكي إلى 17.4 دولاراً أمريكياً).تؤدي نوبة الإصابة بملاريا确定多个流行国家我们收集了从 2014 年 4 月至 2017 年 12 月在阿富汗、埃塞俄比亚、秘鲁、巴西、菲律宾、哥伦比亚、泰国、印度尼西亚和越南进行的三项各国的平均家庭总成本分别从阿富汗的 8.7 美元(美元;标准差:4.3)至哥伦比亚的 254.7 美元(标准差:148.4)不等。在所有国家中,生产力下降是家庭成本中最主要的部分,从而导致平均间接成本从 5.3 美元(标准差:3.0)至 220.8 美元(标准差:158.40)不等。医疗护理提供者进行一般性医疗的费用范围是 3.6–6.6 美元。进行葡萄糖-6-磷酸脱氢酶快速诊断测试的费用从 0.9 美元至 13.5 美元不等,比普遍使用的荧光点试验的费用(6.3 美元至 17.4 美元)要低。.Определение затрат поставщиков услуг в сфере здравоохранения и семей пациентов при всплесках малярии, вызваннойАвторы собрали данные по затратам для трех многоцентровых клинических исследований по лечению инфекцииСредняя общая величина затрат семьи находилась в диапазоне от 8,7 долл. США (среднеквадратичное отклонение, СО 4,3) в Афганистане до 254,7 долл. США (СО 148,4) в Колумбии. Во всех странах потеря трудоспособности составляла наибольший компонент затрат семьи, при этом средние косвенные затраты составляли от 5,3 долл. США (СО 3,0) до 220,8 долл. США (СО 158,4). Затраты медицинских учреждений на обеспечение стандартного набора медицинских услуг составляли от 3,6 до 6,6 долл. США. Затраты на проведение экспресс-теста для диагностики заболевания по глюкозо-6-фосфат-дегидрогеназе составляли от 0,9 до 13,5 долл. США, что было во всех случаях ниже затрат на широко используемый тест флуоресцентного пятна (от 6,3 до 17,4 долл. США).Вспышка заболеваемости малярией, вызванной

Summary Background Potentially untreatable Plasmodium falciparum malaria threatens the Greater Mekong subregion. A previous series of pilot projects in Myanmar, Laos, Cambodia, and Vietnam suggested that mass drug administration was safe, and when added to provision of early diagnosis and treatment, could reduce the reservoir of P falciparum and interrupts transmission. We examined the effects of a scaled-up programme of this strategy in four townships of eastern Myanmar on the incidence of P falciparum malaria. Methods The programme was implemented in the four townships of Myawaddy, Kawkareik, Hlaingbwe, and Hpapun in Kayin state, Myanmar. Increased access to early diagnosis and treatment of malaria was provided to all villages through community-based malaria posts equipped with rapid diagnostic tests, and treatment with artemether–lumefantrine plus single low-dose primaquine. Villages were identified as malarial hotspots (operationally defined as >40% malaria, of which 20% was P falciparum ) with surveys using ultrasensitive quantitative PCR either randomly or targeted at villages where the incidence of clinical cases of P falciparum malaria remained high (ie, >100 cases per 1000 individuals per year) despite a functioning malaria post. During each survey, a 2 mL sample of venous blood was obtained from randomly selected adults. Hotspots received targeted mass drug administration with dihydroartemisinin–piperaquine plus single-dose primaquine once per month for 3 consecutive months in addition to the malaria posts. The main outcome was the change in village incidence of clinical P falciparum malaria, quantified using a multivariate, generalised, additive multilevel model. Malaria prevalence was measured in the hotspots 12 months after mass drug administration. Findings Between May 1, 2014, and April 30, 2017, 1222 malarial posts were opened, providing early diagnosis and treatment to an estimated 365 000 individuals. Incidence of P falciparum malaria decreased by 60 to 98% in the four townships. 272 prevalence surveys were undertaken and 69 hotspot villages were identified. By April 2017, 50 hotspots were treated with mass drug administration. Hotspot villages had a three times higher incidence of P falciparum at malarial posts than neighbouring villages (adjusted incidence rate ratio [IRR] 2·7, 95% CI 1·8–4·4). Early diagnosis and treatment was associated with a significant decrease in P falciparum incidence in hotspots (IRR 0·82, 95% CI 0·76–0·88 per quarter) and in other villages (0·75, 0·73–0·78 per quarter). Mass drug administration was associated with a five-times decrease in P falciparum incidence within hotspot villages (IRR 0·19, 95% CI 0·13–0·26). By April, 2017, 965 villages (79%) of 1222 corresponding to 104 village tracts were free from P falciparum malaria for at least 6 months. The prevalence of wild-type genotype for K13 molecular markers of artemisinin resistance was stable over the three years (39%; 249/631). Interpretation Providing early diagnosis and effective treatment substantially decreased village-level incidence of artemisinin-resistant P falciparum malaria in hard-to-reach, politically sensitive regions of eastern Myanmar. Targeted mass drug administration significantly reduced malaria incidence in hotspots. If these activities could proceed in all contiguous endemic areas in addition to standard control programmes already implemented, there is a possibility of subnational elimination of P falciparum . Funding The Bill & Melinda Gates Foundation, the Regional Artemisinin Initiative (Global Fund against AIDS, Tuberculosis and Malaria), and the Wellcome Trust.

Coagulase-negative staphylococci (CoNS) are a leading cause of sepsis in the neonatal intensive care unit (NICU) setting. To evaluate the hypothesis that isolates of CoNS associated with disease belong to hypervirulent clones, as opposed to being drawn randomly from the neonatal unit carriage flora, we conducted a prospective, case-controlled study in a busy NICU. Using pulsed-field gel electrophoresis (PFGE), we compared the population structures of CoNS isolates associated with bacteremia with isolates from the skin of healthy and infected neonates and with blood culture contaminants. Endemic clones of CoNS were identified, but there was no difference in the distribution of the 6 species or 73 PFGE types between the carriage and disease isolate groups; this suggests that hypervirulent clones with an enhanced ability to cause disease were not present in this NICU setting.

Coagulase-negative staphylococci (CoNS) are a major cause of sepsis in the neonatal intensive care unit (NICU). We evaluated the hypothesis that the ica operon and biofilm production are associated with CoNS disease in this setting. CoNS associated with bacteremia or blood culture contamination and from the skin of infants with CoNS bacteremia or healthy controls were obtained during a prospective case-control study on a busy NICU. A total of 180 strains were identified, of which 122 (68%) were Staphylococcus epidermidis and the remainder were S. capitis ( n = 29), S. haemolyticus ( n = 11), S. hominis ( n = 9), S. warneri ( n = 8), and S. auricularis ( n = 1). The presence of the genes icaA, icaB, icaC , and icaD was determined by PCR, and biofilm production was examined using qualitative (Congo red agar [CRA]) and quantitative (microtiter plate) techniques. There were no significant differences in the presence of the ica operon or CRA positivity among the four groups of strains. However, quantitative biofilm production was significantly greater in strains isolated from either the blood or the skin of neonates with S. epidermidis bacteremia. We conclude that the quantity of biofilm produced may be associated with the ability to cause CoNS infection. This conclusion suggests that the regulation of biofilm expression may play a central role in the disease process.

Introduction Antimalarial resistance, particularly artemisinin resistance, is a major threat to P. falciparum malaria elimination efforts worldwide. Urgent intervention is required to tackle artemisinin resistance but field data on which to base planning of strategies are limited. The aims were to collect available field data and develop population level mathematical models of P. falciparum malaria treatment and artemisinin resistance in order to determine the optimal strategies for elimination of artemisinin resistant malaria in Cambodia and treatment of pre-hospital and severe malaria in Cambodia and Bangladesh. Methods Malaria incidence and parasite clearance data from Cambodia and Bangladesh were collected and analysed and modelling parameters derived. Population dynamic mathematical models of P. falciparum malaria were produced. Results The modelling demonstrated that elimination of artemisinin resistant P. falciparum malaria would be achievable in Cambodia in the context of artemisinin resistance using high coverages with ACT treatment, ideally combined with LLITNs and adjunctive single dose primaquine. Sustained efforts would be necessary to achieve elimination and effective surveillance is essential, both to identify the baseline malaria burden and to monitor parasite prevalence as interventions are implemented. A modelled policy change to rectal and intravenous artesunate in the context of pre-existing artemisinin resistance would not compromise the efficacy of ACT for malaria elimination. Conclusions By being developed rapidly in response to specific questions the models presented here are helping to inform planning efforts to combat artemisinin resistance. As further field data become available, their planned on-going development will produce increasingly realistic and informative models which can be expected to play a central role in planning efforts for years to come.

Multilocus sequence typing (MLST) of Staphylococcus aureus is well suited to the study of global or long-term epidemiology, but its role in local epidemiology has not been defined. The present study has compared MLST with pulsed-field gel electrophoresis (PFGE) by using S. aureus isolates associated with carriage and disease in a busy regional renal unit. One hundred forty-four patients were prospectively recruited, of whom 103 were receiving hemodialysis and 41 were on continuous ambulatory peritoneal dialysis. Three nasal swab specimens were obtained 1 month apart on entering the study. A nasal swab was positive for S. aureus on at least one occasion in 50 patients (35%). Typing of the 104 carriage isolates demonstrated 21 PFGE types and 21 sequence types (STs). Thirty-one carriers had two or more positive nasal swabs; of these, the isolates in all swabs from a given carrier had identical PFGE types for 29 carriers; the isolates in all of the same 29 swabs had identical STs. The carriage strain in two patients changed both PFGE type and STs during the period of swabbing. Eight patients (6%) had an episode of S. aureus bacteremia during the 12-month study period, and two of these were nasal carriers. One of these invasive isolates had the same PFGE type and ST as the carriage isolate. There were no differences between Simpson's index of diversity for PFGE and Simpson's index of diversity for MLST for both invasive and carriage isolates, suggesting that the two methods have very similar discriminatory abilities. We conclude that PFGE and MLST performed equally in this study.