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Improving the reproducibility of biomedical research is a major challenge. Transparent and accurate reporting is vital to this process; it allows readers to assess the reliability of the findings and repeat or build upon the work of other researchers. The ARRIVE guidelines (Animal Research: Reporting In Vivo Experiments) were developed in 2010 to help authors and journals identify the minimum information necessary to report in publications describing in vivo experiments. Despite widespread endorsement by the scientific community, the impact of ARRIVE on the transparency of reporting in animal research publications has been limited. We have revised the ARRIVE guidelines to update them and facilitate their use in practice. The revised guidelines are published alongside this paper. This explanation and elaboration document was developed as part of the revision. It provides further information about each of the 21 items in ARRIVE 2.0, including the rationale and supporting evidence for their inclusion in the guidelines, elaboration of details to report, and examples of good reporting from the published literature. This document also covers advice and best practice in the design and conduct of animal studies to support researchers in improving standards from the start of the experimental design process through to publication., The NC3Rs developed the ARRIVE guidelines in 2010 to help authors and journals identify the minimum information necessary to report in publications describing in vivo experiments. This article explains the rationale behind each item in the revised and updated ARRIVE guidelines 2019, clarifying key concepts and providing illustrative examples.

Background HIV self-testing (HIVST) has the potential to increase coverage of HIV testing, but concerns exist about intended users’ ability to correctly perform and interpret tests, especially in poor communities with low literacy rates. We assessed the clinical performance of the 2016 prototype OraQuick® HIV Self-Test in rural and urban communities in Zambia to assess the sensitivity and specificity of the test compared to the national HIV rapid diagnostic test (RDT) algorithm and a laboratory reference standard using 4th generation enzyme immunoassays and HIV RNA detection. Methods Participants were recruited from randomly selected rural and urban households and one urban health facility between May 2016 and June 2017. Participants received a brief demonstration of the self-test, and then self-tested without further assistance. The research team re-read the self-test, repeated the self-test, drew blood for the laboratory reference, and conducted RDTs following the national HIV testing algorithm (Determine™ HIV1/2 (Alere) confirmed using Unigold™ HIV1/2 (Trinity Biotech)). Selected participants (N = 85) were videotaped whilst conducting the testing to observe common errors. Results Initial piloting showed that written instructions alone were inadequate, and a demonstration of self-test use was required. Of 2,566 self-test users, 2,557 (99.6%) were able to interpret their result. Of participants who were videoed 75/84 (89.3%) completed all steps of the procedure correctly. Agreement between the user-read result and the researcher-read result was 99.1%. Compared to the RDT algorithm, user-conducted HIVST was 94.1% sensitive (95%CI: 90.2–96.7) and 99.7% specific (95%CI: 99.3–99.9). Compared to the laboratory reference, both user-conducted HIVST (sensitivity 87.5%, 95%CI: 82.70–91.3; specificity 99.7%, 95%CI: 99.4–99.9) and the national RDT algorithm (sensitivity 93.4%, 95%CI: 89.7–96.1%; specificity 100% (95%CI: 99.8–100%) had considerably lower sensitivity. Conclusions Self-testers in Zambia who used OraQuick® HIV Self-Test achieved reasonable clinical performance compared to the national RDT algorithm. However, sensitivity of the self-test was reduced compared to a laboratory reference standard, as was the national RDT algorithm. In-person demonstration, along with the written manufacturer instructions, was needed to obtain accurate results. Programmes introducing self-care diagnostics should pilot and optimise support materials to ensure they are appropriately adapted to context.

The scientific community has responded to the coronavirus disease 2019 (COVID-19) pandemic by rapidly undertaking research to find effective strategies to reduce the burden of this disease. Encouragingly, researchers from a diverse array of fields are collectively working towards this goal. Research with infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is undertaken in high-containment laboratories; however, it is often desirable to work with samples at lower-containment levels. To facilitate the transfer of infectious samples from high-containment laboratories, we have tested methods commonly used to inactivate virus and prepare the sample for additional experiments. Incubation at 80°C, a range of detergents, Trizol reagents, and UV energies were successful at inactivating a high titer of SARS-CoV-2. Methanol and paraformaldehyde incubation of infected cells also inactivated the virus. These protocols can provide a framework for in-house inactivation of SARS-CoV-2 in other laboratories, ensuring the safe use of samples in lower-containment levels., SARS-CoV-2 research requires the safe use of samples in low-containment laboratories. Heat, UV, and chemical reagents inactivated high titers of virus in solution and cells. These methods will facilitate use of once-infectious samples in downstream procedures.

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. Here, we introduce ARRIVE 2.0. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the “ARRIVE Essential 10,” which constitutes the minimum requirement, and the “Recommended Set,” which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration (E&E) document, which serves (1) to explain the rationale behind each item in the guidelines, (2) to clarify key concepts, and (3) to provide illustrative examples. We aim, through these changes, to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility., The ARRIVE guidelines detail key information to include in any publication describing animal research. This Perspective article describes how the guidelines have been updated and reorganised to facilitate their use in practice.

8 páginas, 4 figuras, 1 tabla, Four peptides with cytotoxic activity against BRIN-BD11 rat clonal β-cells were purified from the venom of the black-necked spitting cobra Naja nigricollis using reversed-phase HPLC. The peptides were identified as members of the three-finger superfamily of snake toxins by ESI-MS/MS sequencing of tryptic peptides. The most potent peptide (cytotoxin-1N) showed strong cytotoxic activity against three human tumor-derived cell lines (LC50 = 0.8 ± 0.2 μM for A549 non-small cell lung adenocarcinoma cells; LC50 = 7 ± 1 μM for MDA-MB-231 breast adenocarcinoma cells; and LC50 = 9 ± 1 μM for HT-29 colorectal adenocarcinoma cells). However, all the peptides were to varying degrees cytotoxic against HUVEC human umbilical vein endothelial cells (LC50 in the range 2-22 μM) and cytotoxin-2N was moderately hemolytic (LC50 = 45 ± 3 μM against mouse erythrocytes). The lack of differential activity against cells derived from non-neoplastic tissue limits their potential for development into anti-cancer agents. In addition, two proteins in the venom, identified as isoforms of phospholipase A2, effectively stimulated insulin release from BRIN-BD11 cells (an approximately 6-fold increase in rate compared with 5.6 mM glucose alone) at a concentration (1 μM) that was not cytotoxic to the cells suggesting possible application in therapy for Type 2 diabetes., This work was partly supported by the Ministerio de Ciencia, Innovacion � y Universidades, Madrid, Spain (grant number BFU 2017- 89103-P) to JJC.

Antimicrobial resistance (AMR) is a major threat to human health globally. Surveillance is a key activity to determine AMR burden, impacts, and trends and to monitor effects of interventions. Surveillance systems require efficient capture and onward sharing of high-quality laboratory data. Substantial investment is being made to improve laboratory capacity, particularly in low-income and middle-income countries (LMICs) with high disease burdens. However, building capacity for effective laboratory data management remains an under-resourced area, which, unless addressed, will limit progress towards comprehensive AMR surveillance in LMICs. The lack of a fit-for-purpose and open-source laboratory information management system software is of particular concern. In this Personal View, we summarise the technical requirements for microbiology laboratory data management, provide a snapshot of laboratory data management in LMIC laboratories, and describe the key steps required to improve the situation. Without action to improve information technology infrastructure and data management systems in microbiology laboratories, the ongoing efforts to develop capacity for AMR surveillance in LMICs might not realise their full potential.

Background: Results from an increasing number of studies suggest that mosquito excreta/feces (E/F) testing has considerable potential to serve as a supplement for traditional molecular xenomonitoring techniques. However, as the catalogue of possible use-cases for this methodology expands, and the list of amenable pathogens grows, a number of fundamental methods-based questions remain. Answering these questions is critical to maximizing the utility of this approach and to facilitating its successful implementation as an effective tool for molecular xenomonitoring.\ud Methods: Utilizing E/F produced by mosquitoes or tsetse flies experimentally exposed to Brugia malayi, Plasmodium falciparum, or Trypanosoma brucei brucei, factors such as limits of detection, throughput of testing, adaptability to use with competent- and incompetent-vector species, and effects of additional blood feedings post parasite-exposure were evaluated. Two platforms for the detection of pathogen signal (quantitative real-time PCR and digital PCR [dPCR]) were also compared, with strengths and weaknesses examined for each. \ud Results: Experimental results indicated that high throughput testing is possible when evaluating mosquito E/F for the presence of either B. malayi or P. falciparum from both competent- and incompetent-vector mosquito species. Furthermore, following exposure to pathogen, providing mosquitoes with a second, uninfected bloodmeal did not expand the temporal window for E/F collection during which pathogen detection was possible. However, this collection window did appear longer in E/F collected from tsetse flies following exposure to T. b. brucei. Testing also suggested that dPCR may facilitate detection through its increased sensitivity. Unfortunately, logistical obstacles will likely make the large-scale use of dPCR impractical for this purpose.\ud Conclusions: By examining many E/F testing variables, expansion of this technology to a field-ready platform has become increasingly feasible. However, translation of this methodology from the lab to the field will first require the completion of field-based pilot studies aimed at assessing the efficacy of E/F screening.

Background: Xpert MTB/RIF (GX) for tuberculosis (TB) diagnosis is often located in reference laboratories, and sputum needs to be transported using a cold chain. Transport media to preserve sputum are available, but performance data under programmatic conditions are limited. Methods: Sputum samples were collected from patients with presumptive TB in Nigeria. One sputum was transported in a cold chain, tested immediately with GX and cultured. One sputum was swabbed and stored in PrimeStore-Molecular-Transport-Medium (Primestore), and the remainder was stored in OMNIGene-sputum (Omnigene), kept for seven days and tested with GX. Results: Of 248 patients, 63 were fresh-sputum culture-positive and 56 GX-positive (sensitivity 88.9%, 95% CI: 78.4&ndash, 95.4%). Four of 185 culture-negative patients were GX-positive (specificity 97.8%, 94.6&ndash, 99.4%). Omnigene GX and Primestore GX were positive in 56/62 (90.3%, 80.1&ndash, 96.4%) and 49/62 (79.0%, 66.8&ndash, 88.3%) culture-positive, respectively, and 1/185 (99.5%, 97.0&ndash, 100.0%) and 3/185 (98.4%, 95.3&ndash, 99.7%) were culture-negative patients. 14 Human Immunodeficiency Virus (HIV)-infected and 44 HIV-uninfected patients were culture-positive. Omnigene and Primestore detected 12/14 (85.7%, 57.2&ndash, 98.2%) and 5/14 (35.7%, 12.8&ndash, 64.9%) HIV-infected and 41/44 (93.2%, 81.3&ndash, 98.6%) HIV-uninfected culture-positive patients. Interpretation: Omnigene stored and fresh sputum samples had similar GX results. The GX results of Primestore-stored samples were similar to those found in the fresh sputum of non-HIV infected patients, but GX-positivity was lower in HIV-infected patients. This was likely due to the lower amount of bacilli collected by the swab and transferred to PrimeStore.

Background: Strengthening capacity for public health research is essential to the generation of high-quality, reliable scientific data. This study focuses on a research capacity strengthening project supporting seven test facilities in Africa conducting studies on mosquito vector control products towards Good Laboratory Practice (GLP) certification. It captures the primary effects of the project on each facility�s research capacity, the secondary effects at the individual and institutional level, and the ripple effects that extend beyond the research system. The relationships between effects at different levels are identified and compared to an existing framework for the evaluation of research capacity strengthening initiatives. Methods: To capture the views of individuals engaged in the project at all levels within each facility, a maximum-variation purposive sampling strategy was used. This allowed triangulation between different data sources. Semi-structured interviews were conducted with individuals in three facilities and a combination of email and remote video-call interviews were conducted with individuals at two further facilities. Results: We found that, despite a focus of the GLP certification project at the institutional level, the project had effects also at individual (including enhanced motivation, furtherment of careers) and national/international levels (including development of regional expertise). In addition, we detected ripple effects of the project which extended beyond the research system. Conclusion: This study shows that research capacity strengthening interventions that are focussed on institutional level goals require actions also at individual and national/international levels. The effects of engagement at all three levels can be amplified by collaborative actions at the national/international level. These findings show that research capacity strengthening projects must develop plans that address and evaluate impact at all three levels. Capturing the ripple effects of investment in research capacity strengthening should also be planned for from the beginning of projects to support further engagement of all stakeholders.

Background:With increasing insecticide resistance in malaria-endemic countries there is an urgent need for safe and effective novel vector control products. To improve the capacity of facilities that test insecticides in sub-Saharan Africa, a programme is supporting seven facilities towards Good Laboratory Practice (GLP) certification, the globally recognized standard for quality management system (QMS) for the conduct of non-clinical and environmental studies. The World Health Organization (WHO) GLP Handbook provides guidance on a stepwise approach to implement a GLP compliant QMS. This study assesses auditor GLP checklists and timings outlined in the WHO GLP Handbook in the real-life context of a Tanzanian insecticide-testing facility, evaluating their implementation in this context.Methods and Principle Findings:We conducted document review and semi-structured interviews with staff at all levels of the test facility to explore factors that influenced progress towards GLP certification. We found that while auditor GLP checklists underemphasised computer systems, they were otherwise broadly applicable. Factors that delayed time to completion of GLP certification included the need for extensive infrastructure improvements, the availability of regional expertise related to GLP, the capacity of national and regional external systems and services to meet GLP compliance requirements, and training development required for Standard Operating Procedure implementation.Conclusion:The standards required for full GLP compliance are rigorous, with an expected completion timeline to implementation of 24 months. This study shows that in low and middle-income countries this timeline may be unrealistic due to challenges related to infrastructure development and lack of regional capacity and expertise. We recommend a comprehensive gap analysis when starting a project, including these areas which are beyond those recommended by the WHO GLP Handbook. These challenges can be successfully overcome and the experience in Tanzania provides key lessons for other facilities seeking GLP certification or the development of similar QMS.

Background: Results from an increasing number of studies suggest that mosquito excreta/feces (E/F) testing has considerable potential to serve as a supplement for traditional molecular xenomonitoring techniques. However, as the catalogue of possible use-cases for this methodology expands, and the list of amenable pathogens grows, a number of fundamental methods-based questions remain. Answering these questions is critical to maximizing the utility of this approach and to facilitating its successful implementation as an effective tool for molecular xenomonitoring.Methods: Utilizing E/F produced by mosquitoes or tsetse flies experimentally exposed toBrugia malayi,Plasmodium falciparum, orTrypanosoma brucei brucei, factors such as limits of detection, throughput of testing, adaptability to use with competent and incompetent vector species, and effects of additional blood feedings post parasite-exposure were evaluated. Two platforms for the detection of pathogen signal (quantitative real-time PCR and digital PCR (dPCR)) were also compared, with strengths and weaknesses examined for each. Results: Experimental results indicated that high throughput testing is possible when evaluating mosquito E/F for the presence of eitherB. malayiorP. falciparumfrom both competent and incompetent vector mosquito species. Furthermore, following exposure to pathogen, providing mosquitoes with a second, uninfected bloodmeal did not expand the temporal window for E/F collection during which pathogen detection was possible. However, this collection window did appear longer in E/F collected from tsetse flies following exposure toT. b. brucei. Testing also suggested that dPCR may facilitate detection through its increased sensitivity. Unfortunately, logistical obstacles will likely make the large-scale use of dPCR impractical for this purpose.Conclusions: By examining many E/F testing variables, expansion of this technology to a field-ready platform has become increasingly feasible. However, translation of this methodology from the lab to the field will first require field-based pilot studies aimed at assessing the efficacy of E/F screening.

To better understand envenoming and to facilitate the development of new therapies for snakebite victims, rapid, sensitive, and robust methods for assessing the toxicity of individual venom proteins are required. Metalloproteinases comprise a major protein family responsible for many aspects of venom-induced haemotoxicity including coagulopathy, one of the most devastating effects of snake envenomation, and is characterized by fibrinogen depletion. Snake venoms are also known to contain anti-fibrinolytic agents with therapeutic potential, which makes them a good source of new plasmin inhibitors. The protease plasmin degrades fibrin clots, and changes in its activity can lead to life-threatening levels of fibrinolysis. Here, we present a methodology for the screening of plasmin inhibitors in snake venoms and the simultaneous assessment of general venom protease activity. Venom is first chromatographically separated followed by column effluent collection onto a 384-well plate using nanofractionation. Via a post-column split, mass spectrometry (MS) analysis of the effluent is performed in parallel. The nanofractionated venoms are exposed to a plasmin bioassay, and the resulting bioassay activity chromatograms are correlated to the MS data. To study observed proteolytic activity of venoms in more detail, venom fractions were exposed to variants of the plasmin bioassay in which the assay mixture was enriched with zinc or calcium ions, or the chelating agents EDTA or 1,10-phenanthroline were added. The plasmin activity screening system was applied to snake venoms and successfully detected compounds exhibiting antiplasmin (anti-fibrinolytic) activities in the venom of Daboia russelii, and metal-dependent proteases in the venom of Crotalus basiliscus. Graphical abstract ᅟ.

Background\ud \ud The success of the sterile insect technique depends, among other things, on continuous releases of sexually competitive sterile males within the target area. Several factors (including high rearing density and physical manipulation, such as larvae and pupae separation) can influence the quality of males produced in mass-rearing facilities. The different steps in mass production in the laboratory may modify the behaviour of mosquitoes, directly or through loss of natural characters as a result of adaptation to lab rearing, and lead to the competitiveness of sterile male being reduced. In the present study, the objective was to evaluate the effect of mass-rearing conditions on sterile male sexual competitiveness in semi-field cages compared to routine small scale laboratory rearing methods.\ud \ud Methods\ud \ud Anopheles arabiensis immature stages were reared both on a large scale using a rack and tray system developed by the FAO/IAEA (MRS), and on a small scale using standard laboratory rearing trays (SRS). Mosquito life history traits such as pupation rate, emergence rate, adult size as well as the effect of irradiation on adult longevity were evaluated. Moreover, 5–6 day old mosquitoes were released into field cages and left for two nights to mate and the mating competitiveness between sterile mass-reared males and fertile males reared on a small scale when competing for small scale reared virgin females was investigated. Resulting fertility in a treatment ratio of 1:1:1 (100 irradiated males: 100 non-irradiated males: 100 virgin females) was compared to control cages with 0:100:100 (non-irradiated control) and 100:0:100 (irradiated control).\ud \ud Results\ud \ud No significant differences in life history parameters were observed between rearing methods. The competitiveness index of mass reared males (0.58) was similar to males reared on a small scale (0.59). A residual fertility rate of 20% was observed in the irradiated control (100:0:100), measured as the percentage of eggs collected from the cages which developed to adulthood. No significant difference was observed (t = 0.2896, df = 4, P = 0.7865) between the rearing treatments (MRS and SRS) in the fertility rate, a measure of mating competitiveness.\ud \ud Conclusions\ud \ud The results showed that the FAO/IAEA mass-rearing process did not affect mosquito life history parameters or the mating competitiveness of males.

Saline irrigation of the nasal cavity and paranasal sinuses has a recognised role in the management of chronic rhinosinusitis. However, bacterial recontamination of irrigation bottles through backflow from the sinonasal cavity is a concern in recurrent sinus cavity infections. While patients are encouraged to clean the irrigation bottles regularly, there remains significant concern that the use of contaminated bottles may perpetuate chronic rhinosinusitis. This study assesses the optimal microwave duration to achieve decontamination for each irrigation bottle component part (reservoir, tube and nozzle) using a standard, commercially available microwave. In addition, the irrigation fluid was also tested for contamination after each microwave cycle.Laboratory-based experimental study.No patients were involved in this study.The percentage in vitro decontamination of the bottles' components was determined following 30, 60, 90, 120, 150 seconds of microwave cycles.Complete decontamination of the bottles was not achieved at any of the tested microwave cycles. Levels of decontamination differed for the different bottle components, and the greatest degree of decontamination for all bottle components occurred at 90 seconds. Although higher levels of decontamination were observed at microwave durations exceeding 90 seconds, this was at the expense of thermal degradation and deformation of the reservoir plastic component of the irrigation bottle. Similarly, lowest contamination of irrigation fluid was observed at 120 seconds.This study highlights the importance of establishing precise decontamination procedures and recommends a microwave cycle of 90 seconds for optimal decontamination.

Setting\ud A high proportion of notified tuberculosis cases in the Philippines are clinically diagnosed (63%) as opposed to bacteriologically confirmed. Better understanding of this phenomenon is required to improve tuberculosis control.\ud \ud Objectives\ud To determine the percentage of smear negative presumptive tuberculosis patients that would be diagnosed by GeneXpert; compare clinical characteristics of patients diagnosed as tuberculosis cases; and review the impact that the current single government physician and a reconstituted Tuberculosis Diagnostic committee (expert panel) may have on tuberculosis over-diagnosis.\ud \ud Design\ud This a cross-sectional study of 152 patients 15–85 years old with two negative Direct Sputum Smear Microscopy results, with abnormal chest X-ray who underwent GeneXpert testing and review by an expert panel.\ud \ud Results\ud Thirty-two percent (48/152) of the sample were Xpert positive and 93% (97/104) of GeneXpert negatives were clinically diagnosed by a single physician. Typical symptoms and X-ray findings were higher in bacteriologically confirmed tuberculosis. When compared to the GeneXpert results the Expert panel’s sensitivity for active tuberculosis was high (97.5%, 39/40), specificity was low (40.2%, 35/87).\ud \ud Conclusion\ud Using the GeneXpert would increase the level of bacteriologically confirmed tuberculosis substantially among presumptive tuberculosis. An expert panel will greatly reduce over-diagnosis usually seen when a decision is made by a single physician.

BACKGROUND\ud \ud Malaria in pregnancy poses a major public health problem in Indonesia with an estimated six million pregnancies at risk of Plasmodium falciparum or Plasmodium vivax malaria annually. In 2010, Indonesia introduced a screen and treat policy for the control of malaria in pregnancy at first antenatal visit using microscopy or rapid diagnostic tests (RDTs). A diagnostic study was conducted in Sumba, Indonesia to compare the performance of four different RDTs in predominately asymptomatic pregnant women under field condition.\ud \ud METHODS\ud \ud Women were screened for malaria at antenatal visits using field microscopy and four HRP-2/pLDH combination RDTs (Carestart™, First-Response(®), Parascreen(®) and SD-Bioline(®)). The test results were compared with expert microscopy and nested PCR. End user experience of the RDTs in the field was assessed by questionnaire.\ud \ud RESULTS\ud \ud Overall 950 were recruited and 98.7 % were asymptomatic. The prevalence of malaria was 3.0-3.4 % by RDTs, and 3.6, 5.0 and 6.6 % by field microscopy, expert microscopy and PCR, respectively. The geometric-mean parasite density was low (P. falciparum = 418, P. vivax = 147 parasites/µL). Compared with PCR, the overall sensitivity of the RDTs and field microscopy to detect any species was 24.6-31.1 %; specificities were >98.4 %. Relative to PCR, First-Response(®) had the best diagnostic accuracy (any species): sensitivity = 31.1 %, specificity = 98.9 % and diagnostic odds ratio = 39.0 (DOR). The DOR values for Carestart™, Parascreen(®), SD-Bioline(®), and field microscopy were 23.4, 23.7, 23.5 and 29.2, respectively. The sensitivity of Pan-pLDH bands to detect PCR confirmed P. vivax mono-infection were 8.6-13.0 %. The sensitivity of the HRP-2 band alone to detect PCR confirmed P. falciparum was 10.3-17.9 %. Pan-pLDH detected P. falciparum cases undetected by the HRP-2 band resulting in a better test performance when both bands were combined. First Response(®) was preferred by end-users for the overall practicality.\ud \ud CONCLUSION\ud \ud The diagnostic accuracy to detect malaria among mostly asymptomatic pregnant women and perceived ease of use was slightly better with First-Response(®), but overall, differences between the four RDTs were small and performance comparable to field microscopy. Combination RDTs are a suitable alternative to field microscopy to screen for malaria in pregnancy in rural Indonesia. The clinical relevance of low density malaria infections detected by PCR, but undetected by RDTs or microscopy needs to be determined.

Background\ud \ud Accurate and rapid tests for tuberculosis (TB) drug resistance are critical for improving patient care and decreasing the transmission of drug-resistant TB. Genotype®MTBDRsl (MTBDRsl) is the only commercially-available molecular test for detecting resistance in TB to the fluoroquinolones (FQs; ofloxacin, moxifloxacin and levofloxacin) and the second-line injectable drugs (SLIDs; amikacin, kanamycin and capreomycin), which are used to treat patients with multidrug-resistant (MDR-)TB.\ud \ud Objectives\ud \ud To obtain summary estimates of the diagnostic accuracy of MTBDRsl for FQ resistance, SLID resistance and extensively drug-resistant TB (XDR-TB; defined as MDR-TB plus resistance to a FQ and a SLID) when performed (1) indirectly (ie on culture isolates confirmed as TB positive) and (2) directly (ie on smear-positive sputum specimens).\ud To compare summary estimates of the diagnostic accuracy of MTBDRsl for FQ resistance, SLID resistance and XDR-TB by type of testing (indirect versus direct testing).\ud The populations of interest were adults with drug-susceptible TB or drug-resistant TB. The settings of interest were intermediate and central laboratories.\ud \ud Search methods\ud \ud We searched the following databases without any language restriction up to 30 January 2014: Cochrane Infectious Diseases Group Specialized Register; MEDLINE; EMBASE; ISI Web of Knowledge; MEDION; LILACS; BIOSIS; SCOPUS; the metaRegister of Controlled Trials; the search portal of the World Health Organization International Clinical Trials Registry Platform; and ProQuest Dissertations & Theses A&I.\ud \ud Selection criteria\ud \ud We included all studies that determined MTBDRsl accuracy against a defined reference standard (culture-based drug susceptibility testing (DST), genetic testing or both). We included cross-sectional and diagnostic case-control studies. We excluded unpublished data and conference proceedings.\ud \ud Data collection and analysis\ud \ud For each study, two review authors independently extracted data using a standardized form and assessed study quality using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We performed meta-analyses to estimate the pooled sensitivity and specificity of MTBDRsl for FQ resistance, SLID resistance, and XDR-TB. We explored the influence of different reference standards. We performed the majority of analyses using a bivariate random-effects model against culture-based DST as the reference standard.\ud \ud Main results\ud \ud We included 21 unique studies: 14 studies reported the accuracy of MTBDRsl when done directly, five studies when done indirectly and two studies that did both. Of the 21 studies, 15 studies (71%) were cross-sectional and 11 studies (58%) were located in low-income or middle-income countries. All studies but two were written in English. Nine (43%) of the 21 included studies had a high risk of bias for patient selection. At least half of the studies had low risk of bias for the other QUADAS-2 domains.\ud As a test for FQ resistance measured against culture-based DST, the pooled sensitivity of MTBDRsl when performed indirectly was 83.1% (95% confidence interval (CI) 78.7% to 86.7%) and the pooled specificity was 97.7% (95% CI 94.3% to 99.1%), respectively (16 studies, 1766 participants; 610 confirmed cases of FQ-resistant TB; moderate quality evidence). When performed directly, the pooled sensitivity was 85.1% (95% CI 71.9% to 92.7%) and the pooled specificity was 98.2% (95% CI 96.8% to 99.0%), respectively (seven studies, 1033 participants; 230 confirmed cases of FQ-resistant TB; moderate quality evidence). For indirect testing for FQ resistance, four (0.2%) of 1766 MTBDRsl results were indeterminate, whereas for direct testing 20 (1.9%) of 1033 were MTBDRsl indeterminate (P < 0.001).\ud As a test for SLID resistance measured against culture-based DST, the pooled sensitivity of MTBDRsl when performed indirectly was 76.9% (95% CI 61.1% to 87.6%) and the pooled specificity was 99.5% (95% CI 97.1% to 99.9%), respectively (14 studies, 1637 participants; 414 confirmed cases of SLID-resistant TB; moderate quality evidence). For amikacin resistance, the pooled sensitivity and specificity were 87.9% (95% CI 82.1% to 92.0%) and 99.5% (95% CI 97.5% to 99.9%), respectively. For kanamycin resistance, the pooled sensitivity and specificity were 66.9% (95% CI 44.1% to 83.8%) and 98.6% (95% CI 96.1% to 99.5%), respectively. For capreomycin resistance, the pooled sensitivity and specificity were 79.5% (95% CI 58.3% to 91.4%) and 95.8% (95% CI 93.4% to 97.3%), respectively. When performed directly, the pooled sensitivity for SLID resistance was 94.4% (95% CI 25.2% to 99.9%) and the pooled specificity was 98.2% (95% CI 88.9% to 99.7%), respectively (six studies, 947 participants; 207 confirmed cases of SLID-resistant TB, 740 SLID susceptible cases of TB; very low quality evidence). For indirect testing for SLID resistance, three (0.4%) of 774 MTBDRsl results were indeterminate, whereas for direct testing 53 (6.1%) of 873 were MTBDRsl indeterminate (P < 0.001).\ud As a test for XDR-TB measured against culture-based DST, the pooled sensitivity of MTBDRsl when performed indirectly was 70.9% (95% CI 42.9% to 88.8%) and the pooled specificity was 98.8% (95% CI 96.1% to 99.6%), respectively (eight studies, 880 participants; 173 confirmed cases of XDR-TB; low quality evidence).\ud \ud Authors' conclusions\ud \ud In adults with TB, a positive MTBDRsl result for FQ resistance, SLID resistance, or XDR-TB can be treated with confidence. However, MTBDRsl does not detect approximately one in five cases of FQ-resistant TB, and does not detect approximately one in four cases of SLID-resistant TB. Of the three SLIDs, MTBDRsl has the poorest sensitivity for kanamycin resistance. MTBDRsl will miss between one in four and one in three cases of XDR-TB. The diagnostic accuracy of MTBDRsl is similar when done using either culture isolates or smear-positive sputum. As the location of the resistance causing mutations can vary on a strain-by-strain basis, further research is required on test accuracy in different settings and, if genetic sequencing is used as a reference standard, it should examine all resistance-determining regions. Given the confidence one can have in a positive result, and the ability of the test to provide results within a matter of days, MTBDRsl may be used as an initial test for second-line drug resistance. However, when the test reports a negative result, clinicians may still wish to carry out conventional testing.

Malaria parasite infections that are only detectable by molecular methods are highly prevalent and represent a potential transmission reservoir. The methods used to detect these infections are not standardized, and their operating characteristics are often unknown. We designed a proficiency panel of Plasmodium spp. in order to compare the accuracy of parasite detection of molecular protocols used by labs in a clinical trial consortium. Ten dried blood spots (DBSs) were assembled that contained P. falciparum , P. vivax , P. malariae , and P. ovale ; DBSs contained either a single species or a species mixed with P. falciparum . DBS panels were tested in 9 participating laboratories in a masked fashion. Of 90 tests, 68 (75.6%) were correct; there were 20 false-negative results and 2 false positives. The detection rate was 77.8% (49/63) for P. falciparum , 91.7% (11/12) for P. vivax , 83.3% (10/12) for P. malariae , and 70% (7/10) for P. ovale . Most false-negative P. falciparum results were from samples with an estimated ≤5 parasites per μl of blood. Between labs, accuracy ranged from 100% to 50%. In one lab, the inability to detect species in mixed-species infections prompted a redesign and improvement of the assay. Most PCR-based protocols were able to detect P. falciparum and P. vivax at higher densities, but these assays may not reliably detect parasites in samples with low P. falciparum densities. Accordingly, formal quality assurance for PCR should be employed whenever this method is used for diagnosis or surveillance. Such efforts will be important if PCR is to be widely employed to assist malaria elimination efforts.

This is the protocol for a review and there is no abstract. The objectives are as follows:\ud \ud To obtain summary estimates of the diagnostic accuracy of GenoType® MTBDRsl for detection of resistance to the fluoroquinolones in patient specimens or culture isolates confirmed as TB positive.\ud \ud To obtain summary estimates of the diagnostic accuracy of GenoType® MTBDRsl for detection of resistance to second-line injectable drugs in patient specimens or culture isolates confirmed as TB positive.\ud \ud To obtain summary estimates of the diagnostic accuracy of GenoType® MTBDRsl for detection of XDR-TB in patient specimens or culture isolates confirmed as TB positive.\ud \ud Purpose of index test: GenoType® MTBDRsl used as an initial test replacing phenotypic culture-based DST as the initial test.\ud \ud We plan to investigate heterogeneity in relation to the reference tests (genetic sequencing, culture-based DST, and culture-based DST followed by genetic sequencing), as well as by type of testing (indirect or direct). We also plan to investigate heterogeneity in relation to HIV status, conditions of the specimens (fresh or frozen, volume of specimen) and patient population (patients suspected of having MDR-TB or XDR-TB).

Objectives: A future treatment for uncomplicated malaria will contain at least one component that exerts a rapid rate of kill. We describe here the validation and application of a simple, robust and rapid bioluminescence-based assay for the determination of the initial rate of kill in intra-erythrocytic asexual stages of Plasmodium falciparum.\ud \ud Methods: A modification to the concentration–response bioluminescence [here termed bioluminescence relative rate of kill (BRRoK)] assay, utilizing exposure to fold-IC50 concentrations (0.33× to 9×), was used to monitor the immediate cytocidal effect of 372 open-source compounds for antimalarial drug discovery available through the Medicines for Malaria Venture Malaria Box.\ud \ud Results: Antimalarial drugs that exert a rapid cytocidal effect produce a concentration-dependent loss of bioluminescence signal that correlates with available in vitro and in vivo estimates of parasite clearance time and parasite reduction ratio. Following the measurement of IC50 for the Malaria Box compounds in Dd2luc, the BRRoK assay was used to identify and rank 372 compounds for their initial cytocidal activity. Fifty-three compounds in the Malaria Box show an initial relative rate of kill greater than that of chloroquine, with 17 of these having an initial relative rate of kill greater than that of dihydroartemisinin.\ud \ud Conclusions: The BRRoK assay provides a rapid assay format for the estimation of a key pharmacodynamic property of antimalarial drug action. The simplicity and robustness of the assay suggests it would be readily scalable for high-throughput screening and a critical decision-making tool for antimalarial drug development.

Background Malaria mortality is mainly a direct consequence of inadequate and/or delayed diagnosis and case management. Some important control interventions (e.g. long-lasting insecticidal nests) have contributed to reduce malaria morbidity and mortality in different parts of the world. Moreover, the development and effective use of rapid diagnostic tests (RDTs) hold promise to further enhance the control and elimination of malaria, particularly in areas where health services are deficient. The aim of this study was to determine knowledge, attitudes, practices and beliefs in relation to RDTs for malaria in rural Côte d’Ivoire. Methods One hundred individuals from Bozi and Yoho who sought care at the health centre in Bozi and were offered an RDT for malaria were interviewed in April 2010 using a pre-tested questionnaire on practice and perceptions in relation to RDTs for malaria. The relationships between acceptance of RDTs and factors related to opinions were identified, using generalized linear mixed models. Qualitative data from open-ended questions complemented the quantitative analysis. Results Only 34 out of 100 patients who were offered an RDT for malaria were willing to undergo the test. People who perceived blood as a sacred body fluid were less likely to comply with an RDT. The concurrent availability and use of RDTs for HIV and malaria was associated with an unwilling attitude towards RDTs for malaria (Fisher’s exact test, p Conclusion Socio-cultural factors might be barriers for accepting RDTs in general health services. There are social representations of malaria and HIV/AIDS, symbolic for blood or experiences in relation to blood taking and blood-related diseases in relation to the introduction and routine use of RDTs. Special attention should be given to these barriers as otherwise the promotion of RDTs for prompt and effective diagnosis and subsequent management of malaria is hampered.

Background Resource-limited tropical countries are home to numerous infectious pathogens of both human and zoonotic origin. A capability for early detection to allow rapid outbreak containment and prevent spread to non-endemic regions is severely impaired by inadequate diagnostic laboratory capacity, the absence of a “cold chain” and the lack of highly trained personnel. Building up detection capacity in these countries by direct replication of the systems existing in developed countries is not a feasible approach and instead requires “leapfrogging” to the deployment of the newest diagnostic systems that do not have the infrastructure requirements of systems used in developed countries. Methods A laboratory for molecular diagnostics of infectious agents was established in Bo, Sierra Leone with a hybrid solar/diesel/battery system to ensure stable power supply and a satellite modem to enable efficient communication. An array of room temperature stabilization and refrigeration technologies for reliable transport and storage of reagents and biological samples were also tested to ensure sustainable laboratory supplies for diagnostic assays. Results The laboratory demonstrated its operational proficiency by conducting an investigation of a suspected avian influenza outbreak at a commercial poultry farm at Bo using broad range resequencing microarrays and real time RT-PCR. The results of the investigation excluded influenza viruses as a possible cause of the outbreak and indicated a link between the outbreak and the presence of Klebsiella pneumoniae. Conclusions This study demonstrated that by application of a carefully selected set of technologies and sufficient personnel training, it is feasible to deploy and effectively use a broad-range infectious pathogen detection technology in a severely resource-limited setting.

The Republic of Angola is a priority country for onchocerciasis and lymphatic filariasis (LF) elimination, however, the co-distribution of loiasis, caused by the filarial parasite Loa loa, is a significant impediment. This is due to the increasing risk of severe adverse effects (SAEs) associated with ivermectin treatment(s) when used in mass drug administration (MDA) campaigns in Loa loa endemic areas. In Bengo province, Angola a putative high-risk, but under-surveyed, endemic zone for loiasis exists where alternative intervention(s) may need to be implemented. Within this province, the presence and geographical overlap(s) of the three filarial infections are not well defined. \ud Furthermore, knowledge gaps in the vector biology of Loa loa exist. To this end, I undertook a twophased epidemiological investigation of the three filarial diseases and I provided an upto-date assessment of the biology of Chrysops, the insect vector of loiasis. In the latter I placed special focus upon opportunities to develop better vector control.\ud In Phase 1, 2007 individuals from 29 communities from Bengo province were surveyed. Community prevalence estimates were determined by Rapid Assessment Procedure for Loiasis (RAPLOA) and Rapid Epidemiological Mapping of Onchocerciasis (REMO) together with two questions on LF clinical manifestations (presence of lymphoedema and\ud hydrocoele). Overall, low levels of endemicity, with different overlapping distributions were found. Loiasis was found in 18 communities with a prevalence of 2.0% (31/1571). This contrasted to previous results which predicted this area to be a high-risk zone. Onchocerciasis prevalence was 5.3% (49/922) in eight communities, and lymphatic filariasis prevalence was 0.4% for lymphoedema (8/2007) and 2.6% for hydroceles (20/761 males) in seven and twelve communities, respectively. The clinical mapping survey method helped to highlight that all three filarial infections are present in this zone of Bengo province and their fine scale spatial patterns. \ud In Phase 2, a novel combination of clinical, serological and DNA \ud diagnostics was applied, where additional information was collected on participants' duration of residency, access to mass drug administration, knowledge of insect vectors and use of bednets. A total of 1616 individuals (38.1% male, 61.9% female), with an average age of 43 years, were examined. For Loa loa, 6.2% (n = 100/1616) individuals were found to have eyeworm, based on the rapid assessment procedure for loiasis (RAPLOA) surveys, and 11.5% (n=178/1543) based on nested PCR analyses of venous blood. Loa loa prevalence in longterm residents (>10 years) and older individuals (>60 years) were significantly higher, 5\ud and older men with eyeworm were better informed about Chrysops vectors. For O. volvulus, 4.7% (n = 74/1567) individuals were found to be positive by enzyme-linked immunosorbent assay (Ov16 ELISA), with only three individuals reporting to have ever taken ivermectin. For W. bancrofti, no infection was found using the antigen-based immunochromatographic test (ICT) and real-time PCR analysis; however, 27 individuals presented with LF related clinical conditions (lymphoedema = 11, hydrocoele = 14, both = 2). Just under half (45.5%) of the participants owned a bednet, with the majority (71.1%) sleeping under it the night before. Our approach of using combination diagnostics reveals the age-prevalence of loiasis alongside low endemicity of\ud onchocerciasis and LF. Future research foci should be on identifying opportunities for more cost-effective ways to eliminate onchocerciasis and to develop innovative surveillance modalities for clinical LF for individual disease management and disability prevention. Taken as a whole, my results evidence that the utility of the earlier RAPLOA\ud derived maps, based on surveys undertaken over a decade ago, are in need of revision and updating given the extent of population movement and environmental change, particularly deforestation. In future, further fine scale micro-mapping is required to more precisely delineate most appropriate interventions required for these complex co-endemic\ud diseases.

Clinical trials of treatments for Plasmodium falciparum are an integral aspect of a continually evolving evidence base that informs public health policy with the aim of reducing malaria morbidity, mortality, preventing the emergence of parasite resistance to drugs and, eventually, permitting elimination of the disease. Despite their importance, obtaining useful information from in vivo trials can be hindered through methodological gaps that make it difficult to obtain or analyse results (through an inability to quantify important parameters in vivo), cost, required patient numbers or ethical considerations. \ud This thesis uses a computer modelling approach to address two key research problems relating to in vivo trials: Firstly, it quantifies the accuracy failure rate estimates obtained during trials for routine monitoring of artemisinin-based combination therapy (ACT) efficacy in cases of uncomplicated malaria, noting that currently available methods for genotyping patient blood samples are imperfect, and that patients can be infected by new parasite clones (termed reinfection) during the follow-up period which may share (by chance) genetic data with clones present at the time of treatment. Consequently, it is possible for drug failure to be misclassified as a reinfection or vice versa, inducing error in drug failure rate estimates. The true drug failure rate cannot be known in vivo so the accuracy of each method is not known. The results presented here show that currently used methods (length-polymorphic markers and microsatellite markers) are under-estimating true drug failure rate and preventing the detection of failing drugs (~10% failure rate). Accuracy of failure rate estimates was greatly improved by using alternative statistical algorithms or through use of novel Amplicon Sequencing techniques for genotyping blood samples. \ud Secondly, clinical trials of severe malaria generally use reduction in circulating parasite numbers as a clinical endpoint but sequestered - not circulating - parasites are responsible for pathology in severe malaria. A mathematical model was developed to quantify the pathology of severe malaria in an in silico patient population based on sequestered parasite numbers. Results from this model then indicated that a simplified treatment regimen was generally non-inferior to the World Health Organization (WHO) recommended regimen, though specific sub-groups of patients may be at increased risk. Model results also indicated that the emergence of resistance to artesunate in parasite early ring-stages would have severe consequences for patient prognosis in cases of severe malaria.