Dissertations / Theses on the topic 'Rapid Diagnostic Test (RDT)'

Diagnosis of schistosomiasis is still widely reliant on traditional parasitological methods, i.e. the Kato-Katz faecal smear for Schistosoma mansoni and urine filtration for S. haematobium. Since these methods are insensitive, relatively laborious and expensive to perform, much effort has been expended into developing alternative ways of diagnosing the disease. Antibody-detection is the best method for diagnosis in areas of low endemicity. It has the merit of high sensitivity and is likely to be useful for schistosomiasis control as programmes are expanded and accelerated towards meeting the WHO's 2020 goals for neglected tropical diseases (NTDs). A rapid diagnostic test (RDT) for use at the point-of-care (POC) is much more likely to be useful in low-middle income countries than the current assays that are available for antibody-detection. Work has therefore begun towards developing such a test that incorporates S. mansoni cercarial transformation fluid (SmCTF) for the detection of anti -schistosome antibodies in human blood. Here it is demonstrated that SmCTF performs equivalently to S. mansoni soluble egg antigens (SmSEA) in an enzyme-linked immunosorbent assay (ELlSA) format for the detection of anti -So mansoni, anti-So haematobium and anti-So japonicum antibodies.

Les tests de diagnostic rapide (TDR) sont aujourd’hui des outils indispensables pour une réponse urgente en pathologie infectieuse. De nombreux tests sont disponibles pour rechercher différents agents pathogènes (VIH, streptocoque du groupe A, plasmodium …) dans des prélèvements biologiques variés (urine, liquide cérébrospinal ou LCS, sang …). L’avantage de ce mode de diagnostic est leur rapidité, leur simplicité de mise en œuvre, y compris par des non-spécialistes ou à l’extérieur d’une structure de laboratoire, et leur coût raisonnable. Dans ce travail de thèse CIFRE, nous présentons trois TDR que nous avons contribué à développer et à évaluer, basés sur l’immunochromatographie à flux latéral (LFIA). Le premier TDR cible Neisseria meningitidis dans le LCS, bactérie responsable de redoutables épidémies de méningites dans les pays à ressources limitées. Ce TDR est le seul test commercial de type LFIA qui permette de détecter 5 des 6 principaux sérogroupes impliqués dans la maladie (A/C/W/X/Y). Une étude publiée sous l’égide du CNR des méningocoques à l’Institut Pasteur de Paris montre les excellentes performances de ce test sur près de 560 échantillons de LCS provenant de 6 pays. Le deuxième TDR cible Streptococcus pneumoniae dans l’urine et le LCS, également dans le cadre du diagnostic des méningites bactériennes. Ce test, couplé au précédent, fait l’objet d’une étude multicentrique en Afrique de l’ouest sous couvert de l’OMS. Le troisième TDR est un avatar du précédent dédié aux sécrétions respiratoires. Dénommé PneumoResp, il introduit le concept de TDR semi-quantitatif en proposant d’effectuer le test sur sécrétions non diluées et, en cas de résultat positif, sur sécrétions diluées au 1 :100ème. Nous proposons un algorithme (qui fait l’objet d’un brevet en cours d’expertise) qui vise à différencier le portage de l’infection invasive à S. pneumoniae chez l’enfant. Par rapport aux techniques conventionnelles (culture semi-quantitative et qPCR), nous montrons sur quelque 200 échantillons respiratoires une excellente sensibilité et une très bonne valeur prédictive négative de ce test pour exclure ou suspecter une infection active à S. pneumoniae chez l’enfant dès le premier jour
Nowadays, Rapid Diagnostic Tests (RDTs) are essential tools for an urgent response in infectious diseases. Many tests are available to search for different pathogens (HIV, group A streptococcus, plasmodium ...) in various biological samples (urine, cerebrospinal fluid or CSF, blood ...). The main advantages of this mode of diagnosis are speed, simplicity of implementation, including by non-specialists or outside a laboratory structure, and reasonable cost. In this “CIFRE” (industrial) thesis, we present three RDTs based on lateral flow immunochromatography (LFIA) that we contributed to develop and evaluate.The first TDR targets Neisseria meningitidis, a bacterium responsible for severe outbreaks of meningitis in resource-limited countries, in CSF samples. This RDT is the only LFIA-type commercial test that can detect 5 of the 6 major serogroups involved in the disease (A/C/W/X/Y). A study published under the authority of the meningococci reference centre at the Institut Pasteur of Paris showed the excellent performances of this test on nearly 560 CSF samples collected from 6 countries including 5 in Africa.The second TDR targets Streptococcus pneumoniae in urine and CSF; it is also intended to the diagnosis of bacterial meningitis. This test, coupled with the previous one, is the object of a multicentric study presently conducted in West Africa under cover of WHO.The third TDR is an avatar of the previous one but was dedicated to respiratory secretions. Called PneumoResp, it introduces the concept of semi-quantitative RDT. It proposes to perform the test on undiluted secretions and, in the case of positive result, on 1:100-diluted secretions. We present an algorithm (which is the object of a patent pending appraisal) that aims to differentiate S. pneumoniae carriage from invasive infection by this germ in children. Compared to conventional techniques (semi-quantitative culture and qPCR assays), the test performed on 196 respiratory specimens showed an excellent sensitivity and a very good negative predictive value, allowing to exclude or suspect an active S. pneumoniae infection as soon as the first day

La prevenció i el control de les malalties transmissibles depenen, en gran mesura, de la detecció ràpida i eficaç. Els mètodes convencionals per a la detecció d'un patogen, com ara el cultiu microbiològic, generalment requereixen molt de temps, són laboriosos, necessiten personal qualificat i no són aptes com a eines de diagnòstic en el punt d'atenció. El desenvolupament de mètodes de diagnòstic ràpid en el marc dels criteris ASSURED, de l'anglès (A) Affordable, (SS) Sensitive i Didàctiques, (O) User-friendly, (R) Rapid and Robust, (I) Equipment free, and (d) Deliverable to those who need it, Affordable, descrits per l'Organització Mundial de la Salut (OMS), es troben en l'actualitat sota intens estudi. Per tant, la present tesi aborda el disseny i desenvolupament d'estratègies, mètodes i materials per millorar les prestacions analítiques i simplificar el procediment en proves de diagnòstic ràpid, incloses noves estratègies de preconcentració en fase sòlida, mètodes d'amplificació i materials avançats, així com la seva integració en diferents plataformes (principalment biosensors basats en detecció electroquímica i proves en paper amb lectura òptica). En tots els casos, les aplicacions seleccionades es centren en malalties transmissibles, inclosos els patògens transmesos pels aliments i els micobacteris. Amb aquesta finalitat, es comparen dues plataformes basades en paper en diferents configuracions (flux lateral i vertical) en termes de rendiment analític per a la detecció de Mycobacterium. Per aconseguir una millora addicional en el límit de detecció, s'estudia la preconcentració prèvia dels bacteris per separació immunomagnètica. En segon lloc, s'avaluen i es comparen en termes del seu rendiment analític la detecció simultània de Salmonella i E. coli mitjançant flux lateral d'àcid nucleic amb lectura visual i genosensors electroquímics. Si bé aquests mètodes requereixen PCR de doble etiquetatge per a l'amplificació, es poden adaptar fàcilment a termocicladors portàtils que funcionen amb bateries per poder ser realitzats en entorns amb recursos limitats per satisfer les demandes de diagnòstic ASSURED. A més, també es presenta en aquesta tesi la síntesi de polímers magnètics impresos molecularment, per tal de reemplaçar les partícules magnètiques biològicament modificades, i prenent com a model la detecció de biotina i de molècules biotinilades. A més, es realitza la caracterització del material mitjançant diferents tècniques analítiques i es compara, en tots els casos, amb el polímer no imprès. Aquest material biomimètic mostra un gran potencial per a la preconcentració i detecció d'una àmplia gamma d'analits. Malgrat tot els progressos, les tècniques d'amplificació d'àcid nucleic segueixen essent necessàries per assolir els límits de detecció requerits en algunes malalties transmissibles. En aquest sentit, les tècniques d'amplificació isotèrmiques són bons candidats per dur a terme proves de diagnòstic en entorns on la PCR pot ser una barrera. En concret, es descriu en aquest treball la detecció d' E.coli mitjançant un genosensor electroquímic basat en l'amplificació isotèrmica. En aquest cas, s'optimitza la lectura electroquímica per voltamperometria d'ona quadrada en elèctrodes d'un sol ús comparant dues estratègies de marcatge del producte amplificat. És important ressaltar que totes aquestes estratègies apunten a ser utilitzades com a eines per millorar les proves de diagnòstic ràpid en entorns de baixos recursos, per interrompre la cadena d'infecció de malalties transmissibles i permetre, per tant, un tractament precoç.
La prevención y el control de las enfermedades transmisibles dependen, en gran medida, de la detección rápida y eficaz. Los métodos convencionales para la detección de un patógeno, como el cultivo microbiológico, generalmente requieren mucho tiempo, son laboriosos, necesitan personal cualificado y no son aptos como herramientas de diagnóstico en el punto de atención. El desarrollo de métodos de diagnóstico rápido en el marco de los criterios ASSURED, del inglés (A) Affordable, (SS) Sensitive and Specific, (U) User-friendly, (R) Rapid and Robust, (E) Equipment free, and (D) Deliverable to those who need it, Affordable, descritos por la Organización Mundial de la Salud (OMS), se encuentran en la actualidad bajo intenso estudio. Por lo tanto, la presente tesis aborda el diseño y desarrollo de estrategias, métodos y materiales para mejorar las prestaciones analíticas y simplificar el procedimiento en pruebas de diagnóstico rápido, incluidas nuevas estrategias de preconcentración en fase sólida, métodos de amplificación y materiales avanzados, así como su integración en diferentes plataformas (principalmente biosensores basados en detección electroquímica y pruebas en papel con lectura óptica). En todos los casos, las aplicaciones seleccionadas se centran en enfermedades transmisibles, incluidos los patógenos transmitidas por los alimentos y las micobacterias. Con este fin, se comparan dos plataformas basadas en papel en diferentes configuraciones (flujo lateral y vertical) en términos del rendimiento analítico para la detección de Mycobacterium. Para lograr una mejora adicional en el límite de detección, se estudia la preconcentración previa de las bacterias por separación inmunomagnética. En segundo lugar, se evalúan y se comparan en términos de su rendimiento analítico la detección simultánea de Salmonella y E. coli mediante flujo lateral de ácido nucleico con lectura visual y genosensores electroquímicos. Si bien estos métodos requieren PCR de doble etiquetado para la amplificación, se pueden adaptar fácilmente a termocicladores portátiles que funcionan con baterías para poder ser realizados en entornos con recursos limitados para satisfacer las demandas de diagnóstico ASSURED. Además, también se presenta en esta disertación la síntesis de polímeros magnéticos impresos molecularmente, con el objeto de reemplazar las partículas magnéticas biológicamente modificadas, y tomando como modelo la detección de biotina y moléculas biotiniladas. Además, se realiza la caracterización del material mediante diferentes técnicas analíticas y se compara, en todos los casos, con el polímero no impreso. Este material biomimético muestra un gran potencial para la preconcentración y detección de una amplia gama de analitos. A pesar de todo este progreso, las técnicas de amplificación de ácido nucleico siguen siendo necesarias para alcanzar los límites de detección requeridos en algunas enfermedades transmisibles. Las técnicas de amplificación isotérmica son buenos candidatos para llevar pruebas de diagnóstico en entornos donde la PCR puede ser una barrera. En concreto, se describe en esta disertación la detección de E. coli mediante un genosensor electroquímico basada en la amplificación isotérmica. En este caso, se optimiza la lectura electroquímica por voltamperometría de onda cuadrada en electrodos desechables comparando dos estrategias de marcaje del producto amplificado. Es importante resaltar que todas estas estrategias apuntan a ser utilizadas como herramientas para mejorar las pruebas de diagnóstico rápido en entornos de bajos recursos, para interrumpir la cadena de infección de enfermedades transmisibles y permitir, por tanto, un tratamiento precoz.
The prevention and control of communicable disease rely, to a large extent, on effective and early detection approaches. Conventional methods for the detection of a pathogen, such as microbiological culture, are usually time-consuming, laborious, need skilled personnel and are non-amenable to point-of-care diagnostic tools. The development of rapid diagnostic methods in the framework of the ASSURED criteria as (A) Affordable, (SS) Sensitive and Specific, (U) User-friendly, (R) Rapid and Robust, (E) Equipment free, and (D) Deliverable to those who need it, outlined by the World Health Organization (WHO), are under intensive study. Therefore, the present dissertation addresses the design and development of strategies, methods and materials to improve the analytical performance and to simplify the analytical procedure in rapid diagnostic tests, including novel solid-phase preconcentration strategies, amplification methods and advanced materials, as well as their integration in different platforms (mainly biosensors based on electrochemical detection and paper-based strips for optical readout). In all instances, the applications selected are focused on communicable diseases, including foodborne pathogens and mycobacteria. Therefore, two paper-based platforms in different configurations (nucleic acid lateral and vertical flow) are compared in terms of the analytical performance for the detection of Mycobacterium. In order to achieve a further improvement in the limit of detection, the preconcentration of the bacteria is performed by immunomagnetic separation. Secondly, the simultaneous detection of Salmonella and E. coli by nucleic acid lateral flow with visual readout and electrochemical genosensing are evaluated and compared in terms of their analytical performance. Although these methods required double-tagging PCR for amplification, portable, battery-powered thermocyclers can easily be adapted for resource-constrained settings to meet the demands for ASSURED diagnosis. Furthermore, the synthesis of Magnetic Molecularly Imprinted Polymers, in order to replace biological-modified magnetic particles is also presented in this dissertation, taking as a model the detection of biotin and biotinylated molecules with outstanding performance. Moreover, the characterization of the material is performed by different analytical techniques and compared, in all instances, with the non-imprinted polymer. This biomimetic material shows a great potential for the preconcentration and detection of a huge range of analytes. Despite all these progress, nucleic acid amplification techniques are still necessary to reach the challenging limits of detection required in some communicable disease. Isothermal amplification techniques are good candidates to bring sensitive diagnostic tests in places where the PCR can be a barrier. In detail, the electrochemical genosensing of E. coli based on isothermal amplification is also described in this dissertation. In this approach, the electrochemical readout by square-wave voltammetry on disposable electrodes is optimized comparing two different labelling approaches. It is important to highlight that all these strategies aim to be used as tools for the improvement of rapid diagnostic test in low resource settings, to interrupt the chain of infection of communicable diseases and enabling the rapid treatment.

Aim: This thesis aimed to evaluate the performance and usage of ICT Pf Malaria Rapid Diagnostic Test (MRDT), in an operational setting in the Limpopo Province, South Africa. Methods: Four studies were conducted to: assess factors affecting MRDT use (exploratory study- conducted as part of formative work); determine ICT Pf accuracy (cross-sectional study amongst 405 patients with prospective observational cohort component for follow-up); determine the performance of MRDT end-users (crosssectional observational study) and assess the suitability of using positive control antigen wells (PCWs) for routine quality control. Results: Key informants reported that MRDT accuracy, end-user proficiency and MRDT quality affect MRDT use and impact. The accuracy study found that sensitivity, specificity, positive and negative predictive values of ICT Pf test were 99.48% (99% Cl; 96.17-100.00%), 96.26% (99% Cl; 94.7-100%) 98.48 (99% Cl 98.41 -100.00%) and 96.26% (99% Cl 91.53-98.79%) respectively. Febrile patients with 'sweating' were 5 times more likely to be ICT Pf positive than those without sweating. Among the 68 patients who returned for day-seven follow up 23 (33%) were ICT Pf positive; however all were microscopy-negative. End-user proficiency: of the 15 recommended steps for MRDT use, 50% of end-users performed 11 or more steps correctly; 50% of end-users interpreted 90% of pre-prepared tests correctly. The false negative interpretation rate was 15%. The quality control study revealed that diluting PCWs with MRDT-negative blood gave better signals than diluting with citrate buffer. PCWs maintain signal strength when stored up to 30 days at 25°C at rural health clinics. Conclusions: Although ICT Pf MRDT can be used for malaria diagnosis in Limpopo, test sensitivity at low level parasitaemias in field settings need to be established. The ICT Pf test should not be used for assessing cure post-treatment. End-user proficiency needs improvement. PCWs can be used to monitor MRDT quality at PHC level.

La dengue est une maladie virale des régions tropicales et subtropicales, transmise par les moustiques du genre Aedes. Le virus de la dengue (DENV) appartient à la famille des Flaviviridae, genre Flavivirus. Si la plupart des infections sont asymptomatiques ou se traduisent par un syndrome fébrile sans gravité, le virus peut aussi causer une maladie plus sévère caractérisée par une fuite plasmatique, avec ou sans hémorragie. Sans prise en charge adéquate, les formes les plus sévères peuvent évoluer vers un syndrome de choc, potentiellement mortel. Il n’existe pas de traitement spécifique de la dengue mais une réhydratation adaptée et débutée précocement permet de réduire la survenue de formes sévères de la maladie. Malheureusement, les symptômes initiaux de la dengue avant la survenue des éventuelles complications ne sont pas spécifiques et seul un diagnostic biologique basé sur la détection du génome viral, de l’antigène NS1 ou des anticorps anti-DENV dans le sang des patients permet de confirmer la nature exacte de l’infection. La dengue constitue à l’heure actuelle un problème majeur de santé publique du fait de son expansion mondiale et de l’augmentation annuelle du nombre de cas sévères. Pour assurer la surveillance épidémiologique et le contrôle de la maladie, il est indispensable de développer des outils diagnostiques performants et faciles à mettre en œuvre, à la fois utilisables par les médecins de toutes les structures médicales, des simples centres de soins de santé primaire aux centres de référence, et utilisables lors d’enquêtes épidémiologiques pour l’investigation de nouvelles épidémies. Le travail de cette thèse a porté sur plusieurs aspects de cette problématique. Dans une première partie, un test commercial de diagnostic rapide (TDR) permettant la détection simultanée de la NS1 et des IgG et IgM anti-DENV, a été évalué, en laboratoire spécialisé et sur le terrain, afin de comparer, à partir des mêmes échantillons, les performances du test dans deux situations différentes. La sensibilité s’est révélée plus faible lors de l’utilisation sur le terrain que lors de l’utilisation en laboratoire de référence. La majorité des discordances a été observées pour la détection des IgG et des IgM. L’impact de la mise à disposition du test sur la prise en charge des patients a également été évalué et il s’est avéré qu’au cours de cette étude les pédiatres cambodgiens ont ignorés les résultats du test rapide et ont préféré suivre leur instinct clinique.Un second volet a porté sur la faisabilité d’utiliser les urines et la salive en remplacement du sang veineux pour les tests employés en routine pour le diagnostic de la dengue. Les urines et la salive sont des fluides biologiques plus faciles à prélever que le sang veineux ce qui présente un avantage majeur pour les enquêtes épidémiologiques mais peut également secourir les médecins lorsqu’un prélèvement de sang veineux est difficile à obtenir, par exemple chez les enfants. Bien que les performances des différentes méthodes de diagnostic ne soient pas aussi bonnes avec de l’urine et la salive qu’avec du plasma, les résultats obtenus par PCR en temps réel et avec les ELISAs de détection des anticorps anti-DENV démontrent l’intérêt potentiel de ces deux fluides biologiques pour détecter les infections par le DENV lorsqu’il est difficile d’obtenir du sang veineux. Plusieurs TDR commerciaux développés pour permettre la détection de la NS1 et des anticorps anti-DENV (IgM, IgG et IgA) dans les urines et la salive ont été évalués mais les performances obtenues se sont révélées peu satisfaisantes.Une dernière partie du travail a été consacrée à l’étude de la protéinurie comme marqueur pronostic potentiel de sévérité de la dengue. Ce marqueur biologique ne s’est pas révélé être utile pour diagnostiquer précocement les formes sévères de la maladie
Dengue is a viral disease transmitted by Aedes species mosquitoes, in tropical and subtropical regions. Dengue virus (DENV) belongs to the family Flaviviridae, genus Flavivirus. Although most DENV infections are asymptomatic or result in a self-limited febrile illness, severe diseases characterized by plasma leakage, with or without hemorrhage, can also occur. Patients with a severe dengue can rapidly progress into a life-threatening shock syndrome if no efficient clinical management is provided. There is no specific treatment available for dengue but an accurate and early fluid therapy substantially reduces the occurrence of severe forms of the disease. Dengue symptoms are typically non-specific until or unless complications develop. Only a biologic diagnosis based on DENV genome, NS1 antigen or anti-DENV antibodies detection enables to confirm dengue cases. Dengue is now a major public health problem due to both its geographical spread and the increase in the number of severe cases. New diagnostic tools are necessary to ensure epidemiological surveillance and control of the disease. These tools need to be effective and easy to use in every medical settings, from the smallest primary health centers to the biggest reference centers, and also usable for epidemiologic studies, e.g. for epidemic investigations. The work presented in this thesis was dedicated to this problematic.In a first part of the work, a rapid diagnostic test (RDT), designed to detect NS1 antigen, anti-DENV IgG and IgM, was evaluated, both in a specialized laboratory and in the field, in order to compare the test performances in two different settings, with the same samples. Interestingly, sensitivity was lower when the test was used in the field compared to the sensitivity of the test when performed in the specialized laboratory. Discordances were mainly observed for IgM and IgG detection. Impact of the use of the RDT on clinical management was also assessed during the field study and it revealed that Cambodian pediatricians ignored the results of the RDT and followed their clinical instinct.A second part of the work was dedicated to the assessment of the usefulness of urine and saliva for dengue diagnostic. Dengue diagnostic normally requires a venous blood sample that can be difficult to obtain in certain conditions such as in children or during epidemiological studies. Urine and saliva are easier to collect as the procedure is non-invasive. We showed that, although the performances of the different diagnostic methods were not as good in saliva and urine as in plasma specimens, the results obtained by qRT-PCR and by anti-DENV antibody ELISA could well justify the use of these two body fluids to detect dengue infection in situations when the collection of blood samples is difficult. Performances of commercial RDTs developed for NS1 and anti-DENV antibodies (IgM, IgG and IgA) detection in urine and saliva specimens were not satisfactory.In the last part of the thesis, the potential use of proteinuria as a prognostic marker of severity was assessed but it didn’t prove to be a useful marker for risk prediction

Thesis: S.M. in Technology and Policy, Massachusetts Institute of Technology, Engineering Systems Division, 2015.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 162-168).
Diagnosis of malaria is important in order to ensure early and effective treatment, to facilitate public health surveillance, and to prevent drug resistance. Rapid diagnostic tests (RDTs) are an important tool in resource-constrained settings, as they do not rely on costly lab equipment and specially trained personnel. In Uganda's private sector clinics and drug shops, which is where the majority of patients first seek care, diagnosis of malaria is often presumptive and patients receive neither RDT nor microscopy. Several studies have focused on the patient perspective (e.g. willingness to pay and willingness to be tested) but much less is understood about the supplier perspective (e.g. willingness to stock). This study aimed to understand the preferences and priorities of agents across the malaria RDT supply chain in Uganda on stocking the devices using multi-criteria decision analysis. This methodology was adapted to be relevant and understandable for agents in Uganda so that it was possible to analyze business decisions incorporating a multiplicity of attributes such as selling price, purchase cost, sales volume, complexity of regulations, waste management, and training available. Data surveys and semistructured interviews were collected from 28 private sector retailers (i.e., shopkeepers, pharmacists, clinic managers), two first line buyers, and three distributors. Analysis of the data resulted in the construction of value functions for all agents, the relative weights (therefore the tradeoffs) among decision criteria, and the calculation of an overall value for the decision about whether or not to stock RDTs for the different supply chain agents. Results indicate that the best option for one level of the supply chain is not necessarily the best for another. A discussion offers insights on how to align value across the supply chain, which is important for facilitating public health interventions.
by Corinne M. Carland.
S.M. in Technology and Policy

Le paludisme est un problème de santé public dans de nombreux pays. Cinq espèces infectent l'homme : P. falciparum, responsable de la grande majorité des décès, et P. vivax, P. ovale, P. malariae et P. knowlesi qui provoquent des formes bénignes de la maladie. Le diagnostic qui fait partie des moyens de lutte, est une urgence médicale. Les tests de diagnostic rapides (TDRs) dont l'usage est recommandés par l'OMS, sont donc de plus en plus employés. Cependant, la détection et l'identification des espèces non P. falciparum par ces tests est insuffisante. Le besoin en nouveaux couples « antigènes-anticorps » est une nécessité pour améliorer les TDRs. Au cours de ce travail, de nouveaux anticorps anti LDH de P.malariae ont été produits.Une recherche de nouveaux antigènes a également été entreprise. Pour cela, certaines enzymes de la voie de la glycolyse ont été étudiées. Pour la première fois des séquences des enzymes de cette voie ont été obtenues pour P. ovale et P. malariae. Elles ont permis de déterminer de nombreux épitopes cibles potentiels spécifiques et ceux communs à toutes les espèces. Dans un deuxième temps, une recherche en protéomique a été menée pour identifier des biomarqueurs parasitaires. L'étude du culot globulaire et du plasma de patients infectés a permis la sélection de 8 protéines cibles originales. Ces travaux préparent la fabrication et la commercialisation par la société Whidiag d'une nouvelle génération de TDRs pour le paludisme
Malaria is a public health problem in many countries. Five species infect humans: P. falciparum, responsible for the vast majority of deaths, and P. vivax, P. ovale, P. malariae and P. knowlesi causing mild forms of the disease. The diagnostic is a means of control and a medical emergency. The rapid diagnostic tests (RDT) whose are recommended by WHO, are increasingly used. However, the detection and identification of not P. falciparum species is insufficient. New "antigen-antibody" couples are a need to improve the RDTs performance. In this work, new anti LDH antibodies from P. malariae were produced. A search for new antigens was also undertaken. For this purpose, some enzyme of glycolysis pathway were studied. For the first time the sequences of the enzymes from this pathway were obtained for P. ovale and P. malariae. We identified many potential target epitopes specific and common to all those species. In a second step, a proteomics approches has been conducted to identify parasites biomarkers. The study of red blood cells and plasma of infected patients has led to the selection of 8 original target proteins. This work prepares the manufacturing and marketing of a new generation of RDTs for malaria by the company Whidiag

Introduction: The Home-based Management of Malaria (HMM) is a cornerstone of malaria control in sub-Saharan Africa (SSA) and is recommended by WHO to provide prompt access to antimalarial treatment for children in under-served areas. Although HMM has been shown to reduce malaria morbidity and mortality with chloroquine, it has not been examined previously in the era of artemisinin-based combination therapies. The objectives of this study were to determine whether HMM reduced: 1] the time from when a mother or guardian realized her child was ill to the time when the child was brought for treatment and 2] malaria morbidity in children less than 5 years of age.

Methodology: This cross-sectional retrospective study (2008-2014) was performed in intervention villages (receiving HMM) and control villages (not receiving HMM) to examine the effectiveness of HMM.

Key Results: More mothers and guardians were informed about the malaria control activities performed (98% vs. 24%) in intervention than control villages (p < 0.001). Consistent with that result, mothers and guardians in intervention villages sought care for their sick children earlier than mothers in control villages (p < 0.001) and were more likely to obtain treatment from community health workers (CHWs) in their home villages. In contrast, more children were referred for malaria treatment to health posts and health centers from control than intervention villages (p < 0.001). Likewise, more children with complicated malaria were referred for treatment from control villages (p < 0.001), although those conclusions were limited by the small numbers of complicated (severe) malaria cases.

Conclusions: These results indicate HMM shortens the time mothers wait before taking their children to receive treatment. Because more children with uncomplicated or complicated malaria are referred for treatment from control than intervention villages, these results indicate that the availability of HMM treatment in the child’s home village reduces morbidity (the risk of severe malarial disease). However, additional studies with larger numbers of subjects will be necessary to determine if HMM reduces mortality.

Pseudomonassp. CBB1 degraded caffeine via C-8 oxidation. Previously, a novel quinone-dependent caffeine dehydrogenase (Cdh) was shown to catalyze the oxidation of caffeine to 1,3,7-trimethyluric acid (TMU). Initial metabolite analysis using resting cells and partially purified extract of CBB1 identified transient accumulation 1,3,7-trimethyl-5-hydroxyisourate (TM-HIU), and 3,6,8-trimethylallantoin (TMA). TMA structure was confirmed; chiral analysis revealed that it was racemic. In contrast, a time-course reaction showed that one of the enantiomers of TMA accumulated nine times, and racemized in three hours. Based on this, it was proposed that TMU was converted to TM-HIU and enantiomeric TMA. A 43-kDa NADH-dependent TMU mononxygenase (TmuM) was purified and shown to convert TMU to unstable TM-HIU. The enzyme belonged to a new family of FAD-dependent monooxygenases. The enzyme was specific for methyluric acid with no activity on uric acid. Homology model of TmuM revealed a larger, more hydrophobic active site compared to analogous uricase in the uric acid pathway. Genes encoding heterotrimeric Cdh (cdhA,B,C) and TmuM (tmuM), were located on a 25.2-kb fragment in CBB1 genome. Gene cluster analysis relative to similar cluster in uric acid degrading organisms identified five more putative genes of the C-8 oxidation pathway, namely tmuH, tmuD, orf1, orf2, and orf3. First three genes were assigned encoding TM-HIU hydrolase (TM-HIU to TM-OHCU), TM-OHCU decarboxylase (TM-OHCU to stereospecific TMA (proposed S-(+)-TMA)), and trimethylallantoinase (stereospecific TMA to TMAA), respectively. Further, orf2 and orf3 are proposed to encode for YlbA and ArgE like hydrolase and deacetylase, which convert TMAA to glyoxylate, di- and monomethylurea. This is the first report of (a) TMA structure (b) TMU monooxygenase and TM-HIU (hydroxylation product of TMU), and (c) complete delineation of C-8 oxidation pathway by a combination of enzymology and cluster analysis. Excessive consumption of caffeine in various forms has created a need for a rapid diagnostic test, esp. for nursing mothers and infants. Cdh was hypothesized to be suitable for this test. Sensitivity of the test was shown to be 1 ppm. A colorimetric test with partially purified Cdh and INT-dye was optimized to detect within a minute, caffeine in drugs, nursing mother's milk, and differentiate decaffeinated beverages.

Introduction – La place des tests de diagnostic rapide (TDR) et des règles de décision cliniques (RDC) pour le diagnostic des pharyngites à streptocoque du groupe A (SGA) chez l’enfant varie selon les recommandations internationales en raison de doutes sur la stabilité des performances diagnostiques du TDR et d’une validation insuffisante des RDC. Méthodes – Dans une étude prospective multicentrique (n=17) ambulatoire réalisée au sein du réseau clinique pédiatrique ACTIV de 2009 à 2011, 1776 enfants avec pharyngite ou sains ont été soumis à des prélèvements de gorge pour réaliser un TDR et une mise en culture (test de référence). Nous avons étudié l’effet indépendant de variables liées aux patients et aux médecins sur les performances diagnostiques du TDR, exploré systématiquement les faux-Positifs (FP) du TDR et réalisé une validation externe et une comparaison des RDC existantes. Résultats – La sensibilité du TDR (en moyenne 87%) variait selon la présentation clinique (âge, signes cliniques), l’inoculum bactérien et le phénomène de portage (paramètres aussi liés entre eux), et selon des variables liées aux médecins (dont le type d’activité clinique). La valeur prédictive négative du TDR était élevée (autour de 90%) et stable. Les FP du TDR étaient positifs pour le SGA en PCR. Aucune RDC n’était satisfaisante en termes de calibration et de discrimination. Conclusion – Le TDR est suffisant pour le diagnostic de pharyngite à SGA si les cliniciens évaluent leurs propres performances et les améliorent si besoin. Aucune RDC ne peut être recommandée en pratique clinique en pédiatrie
Background – The roles of rapid antigen detection tests (RADT) and clinical prediction rules (CPR) for the diagnosis of group A streptococcus (GAS) in children with pharyngitis vary across international clinical guidelines. This might be related to unstable diagnostic accuracy of RADTs and insufficient validation of CPRs. Methods – In a prospective multicenter (n=17) office-Based study that took place in France within the ACTIV network between 2009 and 2011, 1776 children with pharyngitis or healthy controls underwent throat swabs to perform a RADT and a throat culture (reference standard). We assessed the independent effect of patient- and physician-Level characteristics on the accuracy of a RADT, systematically re-Analyzed RADT false-Positive results, and externally validated and compared existing CPRs. Results – RADT sensitivity (overall 87%) varied according to clinical signs and symptoms, bacterial inoculum size and GAS throat carriage (factors also related to each other), and according to physician-Level characteristics (including type of clinical practice). RADT negative predictive value was high (about 90%) and stable. RADT false-Positives were positive for GAS when using a new PCR technique. No CPR had sufficient performances regarding calibration and discrimination. Conclusions – RADTs are sufficient for diagnosing GAS pharyngitis if clinicians accept diagnostic accuracy monitoring and adequate training when needed. No CPR can be recommended for use in pediatrics

Introduction Nigeria has the highest malaria burden worldwide. The 2010 and 2015 Nigeria Malaria Indicator Surveys (NMIS) suggest an improvement in malaria indicators, with the North West zone lagging behind. This study aimed to identify the individual and household-level malaria determinants in north-west and southern Nigeria, using Rapid Diagnostic Testing (RDT) and microscopy for malaria diagnosis. Methods Data on 3,358 children aged 6-59 months from north-west and southern Nigeria from the 2015 NMIS was used. The two populations were compared using chi-square tests, and logistic regression analysis was done for determinants of malaria infection, based on RDT and microscopic malaria test results. Results Malaria prevalence by RDT in the north-west and south was 55.8% and 29.2%, respectively (37.0% and 14.9%, respectively by microscopy). In both populations, a higher age, positive RDT in an additional household member and rural residence increased the odds of malaria infection; while higher education of the head of household and greater household wealth lowered the odds of malaria infection. Household clustering of RDT-positive cases appeared to be stronger in the south compared to the north-west. There were no statistically significant differences between the results using RDT or microscopy. Conclusion Irrespective of the diagnostic tool used, malaria determinants were similar in north-west and southern Nigeria. However, poorer social circumstances were observed in the north-west, and may account for the delayed progress in malaria control in the region. There may be a need to intensify malaria control efforts, particularly in the north-west, while awaiting socio-economic development.

Entre juin et septembre 2009, nous avons réalisé une étude transversale pour évaluer l'état de la prise en charge du paludisme chez la femme enceinte à Bangui. Les résultats de cette évaluation ont montré que dans les services de consultation prénatale (CPN) de Bangui, 28,8% des femmes enceintes reçoivent à titre curatif au moins une prescription de médicament antipaludique pendant leur grossesse. La quinine et les combinaisons à base d'artémisinine, antipaludiques compatibles avec la grossesse, sont prescrites dans des proportions de 56,7% et 26,8% respectivement. Par contre, la confirmation du paludisme par un examen de laboratoire est réalisée seulement dans 18,9% des cas avant la prescription du traitement. Les deux doses recommandées de traitement préventif intermittent du paludisme par la sulfadoxine-pyrimethamine (TPIsp) sont administrées à 30,5% des femmes pendant leur grossesse. Les moustiquaires imprégnées d'insecticide à longue durée (MIILD) sont utilisées par 42,4% des femmes enceintes. Malgré ce, la prévalence de la parasitémie placentaire à l'accouchement est relativement faible (4%). Ces données nous ont amené à réaliser une étude dont l'objectif était d'évaluer l'intérêt de l'introduction d'un test de diagnostic rapide (TDR) sur la rationalisation du traitement du paludisme chez les femmes enceintes lors des CPN. Entre octobre 2009 et octobre 2011, nous avons réalisé une étude sur une cohorte de 76 femmes enceintes. Le nombre de traitements antipaludiques après confirmation du paludisme par TDR Paracheck-Pf® lors des CPN a été déterminé sur cette cohorte
From June to September 2009, we designed a cross-sectional study aiming to assess malaria management during pregnancy in antenatal health care in Bangui. Our findings showed that antimalarials are prescribed to 28.8% of pregnant women attending antenatal clinics (ANCs) in Bangui. Quinine and artemisinin combined therapies are widely used (56.7% and 26.8% respectively). However, laboratory diagnosis of malaria infection is performed for solely 18.9% of consultants. The recommended two doses of intermittent preventive treatment with sulfadoxine-pyrimethamine (IPTsp) are given to 30.5% of pregnant women, while 42.4% of them use the insecticides treated nets (ITNs). Nonetheless, the prevalence of placental malaria at delivery is relatively low (4%). From those preliminary data of our study we assessed the impact of a systematic rapid diagnosis test (RDT) of malaria during pregnancy on antimalarials prescription, during the period from October 2009 and October 2011. The proportions of antimalarial treatment episodes were compared in two groups of women: a cohort of 76 pregnant women presenting at their ANCs visits, in which a systematic screening of malaria with the RDT Paracheck-Pf® was performed and a control group of women who delivered in the same period. Our findings showed that in the cohort, there was a proportion of 13.8 % of positive RDT, hence requiring antimalarial treatment, while the proportion of antimalarials prescriptions in the control group was 26.3% (P = 0.0001). The avoidable rate of unnecessary antimalarials prescriptions was estimated at 47%

Introduction: Ensuring universal access to primary health care (PHC) is a key component of the Ethiopian nationalhealth policy. The policy also emphasises promoting and enhancing national self-reliance in health development bymobilizing and efficiently utilizing resources including community participation. To this end, the government introducedthe accelerated expansion of the PHC strategy through a comprehensive health extension programme (HEP). HEP is afamily and community-based health care delivery system institutionalised at health post level which combines carefullyselected high impact promotive, preventive and basic curative interventions. All HEP interventions are promotive and preventive except the malaria intervention which, in addition, incorporates a curative service. In the country, malaria is a leading disease. Unlike most Sub-Saharan African countries where P. falciparum accounts for almost all malaria infections, in Ethiopia both P. falciparum and P. vivax are co-dominant. Considering this peculiar epidemiological nature, the national guideline recommends alternative diagnosis and treatment strategies. Rationale: The lack of adequate resources and the efficiency with which available resources are being utilised are the main challenges in any health care setting. Therefore, if the HEP which consumes consideral amount of resource desires to reach its intended goal, monitoring and improving its efficiency is of great public heath importance. HEP has been successful in improving access to PHC including the malaria diagnosis and treatment service. Though this is a crucial measure, its quality ought to be considered. For the malaria curative service, studying the cost-effectiveness of the available strategy and patients’ adherence to the treatment regimen can be considered as proxy measures of quality for which local evidence is lacking. However, none of the existing studies in this field of research has addressed the Ethiopian malaria epidemiological context and its diagnosis and treatment guideline. In Tigray, for more than two decades, access to malaria early diagnosis and prompt treatment was facilitated by volunteer community healthworkers (CHWs). However, with the introduction of artemether-lumefantrine (AL) the service was compromised mainly for reasons of cost, safety and logistic. Therefore, it was important to explore the feasibility and the impact of community deployment of AL with rapid diagnostic tests (RDTs). The aim: to explore the overall performance of HEP and particularly the access to and quality of malaria early diagnosis and prompt treatment in the Tigray region of Ethiopia. Methods: Different study designs and populations were used for each of the four specific objectives. Data envelop analysis (DEA) was applied to assess the HEP efficiency. For this, register data for the output variables and primary data for the input and the environmental factors were collected. A health provider perspective cost-effectiveness analysis was used to determine which among the currently available diagnostic and treatment strategies is best for the country. Effectiveness data were generated from a stratified cross-sectional survey and secondary data were used to calculate the cost. For measuring adherence to the six-dose AL regimen, an assessment questionnaire and pill count was employed at patients´ home. To determine whether deploying AL with RDT at community level was feasible and effective, a number of designs were used: longitudinal follow-up, cross-sectional surveys, cost analysis, verbal autopsyquestionnaires and focal group discussions. Main findings: More than three-quarters of the health posts were found to be technically inefficient with an average score of 42%, which implies potentially they could improve their efficiency by 58%. Scale of operation was not a cause of inefficiency. None of the considered environmental factors was associated with efficiency. The Parascreen-based strategy (multispecies RDT-BS) was found to be the most cost-effective strategy, which allowed treating correctly an additional 65% of patients with less cost than the paracheck-BS. Presumptive-BS was highly dominated. Among P.falciparum positive patients to whom AL was prescribed, more than a quarter did not finish their treatment. The main reasons for interrupting the dose were ‘too many tablets’ and ‘felt better before finishing the dose’. The ownership of aradio, the belief that malaria cannot be treated traditionally and a delay of more than one day in seeking treatment after the onset of fever were significantly associated with being adherent. Deploying AL with RDT at community level was demonstrated to be effective and feasible. In the intervention district, almost 60% of suspected cases were managed by CHWs. Malaria transmission was lower at least threefold and malaria mortality risk by around 40% compared to the control district. The use of RDTs reduced cost and possibly the risk of drug resistance development. Conclusion: Though improving access to health care is important, it should be considered a means, not an end. Themore accessible a system is the more people could utilise it to improve their health. Thus, ensuring the access obtainedthrough HEP is maintained, its quality is improved and efficiently utilised to its optimal productivity level is a necessarytask. The DEA study revealed a high level of inefficiency where majority of the health posts needed improvement.This thesis also found parascreen-BS to be the most cost-effective strategy and that there is no epidemiological andeconomical contextual justification to keep both, the presumptive-BS and the RDT-BS specific only to P.falciparum.The high poor adherence levels raises great concern as it leads to recurrent malaria attacks of the patient, speed upthe development and spread of drug resistance strains and reduces the effect of the drug on the transmission. Therefore,providing effective drug alone is not sufficient; assessing and monitoring adherence to the treatment is by faressential. Deployment of AL with RDT through a community-based service has shown an enormous impact in termsof cost, transmission, morbidity and mortality. However, it is worth noting that this results came from an area wherea community-based service has been involved in the PHC system for more than three decades.

Fin avril 2009, un nouveau virus grippal A/H1N1 d'origine porcine émerge dans le monde causant la première pandémie grippale du XXIème siècle. Les différents travaux présentés dans cette thèse retracent la gestion de cette situation au laboratoire de virologie des hôpitaux publics de Marseille. D'avril 2009 à avril 2010, nous avons analysé plus de 13 000 prélèvements issus de cas suspects. Nous avons dû adapter continuellement les moyens mis en œuvre pour effectuer le diagnostic et la mise en place d'une stratégie 'Point of Care' s'est avérée très utile. Nos résultats montrent que l'usage des tests rapides en complément de la RT-PCR en temps réel permet de réduire significativement le délai de rendu des résultats pour les patients infectés. Les données épidémiologiques sur les nombreux cas suspects dépistés ont également permis d'obtenir en temps réel des informations précieuses sur l'épidémiologie de cette pandémie comme l'estimation de l'incidence par classe d'âge, la proportion de patients hospitalisés et la mortalité. Enfin, nous avons réalisé une étude de séroprévalence qui montre qu'environ 12% de la population française a été infectée par ce nouveau virus en 2009-2010 et que les taux d'attaque les plus élevés ont été observés chez les enfants et les jeunes adultes
In late April 2009, a new swine-origin A/H1N1 Influenza virus emerged and spread rapidly worldwide causing the first influenza pandemic of the 21st century. This work describes how we coped with this emergency situation in the virology laboratory of Marseille public hospitals. From April 2009 to April 2010, we analyzed more than 13,000 samples from suspected cases. We needed to adapt continuously the organization to maintain diagnostic capacity and the implementation of a point of care strategy revealed very useful to achieve this goal. Our results support the use of rapid Influenza detection tests in combination with real-time RT-PCR because it reduces significantly the delay from sample to result for positive cases, thus giving the opportunity to improve patient management. Epidemiological data from all suspected cases tested allowed us to obtain timely precious information about the epidemiology of this pandemic as the estimation of (i) the incidence by age group, (ii) the rate of hospitalization and (iii) the mortality rate among tested patients. Finally, we set up a serological study and showed that around 12% of the French population had been infected by this new virus in 2009-2010 with higher attack rates observed in children and young adults

Made available in DSpace on 2011-05-04T12:42:03Z (GMT). No. of bitstreams: 0 Previous issue date: 2009
As infecções de transmissão sexual, em especial a sífilis, são um dos problemasde saúde mais comuns e ainda se desconhece sua real magnitude, inclusive no Brasil. Algumas explicações podem ser descritas pela insuficiência de recursos humanos e materiais necessários ao seu diagnóstico em zonas de difícil acesso, em diversos países. Nessas circunstancias, exames de diagnóstico denominados testes rápidos têm um papel importante para a identificação da doença, e, na tentativa de demonstrar sua aplicabilidade e seu papel na gestão de políticas públicas este trabalho atuou em quatro frentes de pesquisa: Primeira - validação das características operacionais, de quatro diferentes testes rápidos treponêmicos em clínica especializada em Doenças Sexualmente Transmissíveis (DST), em Manaus, comparado-os com o FTA-Abs como padrão ouro e a avaliação da aceitabilidade dos testes junto aos profissionais e clientela testada. Segundo- Validação multicêntrica com outros três países participantes do estudo. Terceira Estudos dirigidos a subgrupos de pessoas que habitualmente não acedem, de maneira espontânea, os serviços regulares de saúde. E, por fim Estudos junto a populações de diferentes prevalências para a sífilis. Onde somadas as quatro etapas comprovou-se as principais virtudes desta nova geração de testes, rapidez e facilidade na execução e interpretação; aceitabilidade pelos pacientes e profissionais de saúde; favorecimento da decisão do tratamento imediato; dispensar energia elétrica ou profissional especializado. As evidências levantadas por estas investigações enfatizam o papel que os testes rápidos jogarão nos próximos anos, para o controle da sífilis.
Sexually Transmitted Infections, particularly syphilis, are one of the most common health problems worldwide and its real magnitude is still unknown, including in Brazil. The lack of skilled human resources and basic laboratory infrastructure in areas of difficult access in many parts of the world contribute to explain it. Under these circumstances rapid tests represent a promising and valuable alternative to traditional syphilis diagnostic. To demonstrate the test's applicability and its role for public policy, this thesis explored four different research fronts: First- the validation of the performance characteristics and the operability of different syphilis rapid tests were carried out in a Sexually Transmitted Infection clinic in Manaus, Brazil. Four treponemical syphilis rapid tests were compared against the “gold standard” FTA-Abs. This portion of the research also includes a study on the acceptability of the rapid tests by the health professionals, as well as patients. Second- Validation of syphilis rapid tests with three other countries participating in a multicentric study. Third- Studies on the use and acceptability of the tests for target groups which do not have regular or easy access to health services and are also difficult to reach locations. Lastly, the rapid tests were tested in target groups with different Syphilis prevalence. These different phases of the research proved the virtues of this new generation of tests: speed and ease of use and interpretation of results, patient and health professional acceptability, the test increases the likelihood of immediate treatment, and it does not require electric power or specialized professionals. The results obtained emphasize and evidence the importance of the role that rapid tests have in the diagnosis and control of syphilis.

Yes
Background: Tuberculosis (TB) is the highest-mortality infectious disease in the world and the main cause of death related to antimicrobial resistance, yet its surveillance is still paper-based. Rifampicin-resistant TB (RR-TB) is an urgent public health crisis. The World Health Organization has, since 2010, endorsed a series of rapid diagnostic tests (RDTs) that enable rapid detection of drug-resistant strains and produce large volumes of data. In parallel, most high-burden countries have adopted connectivity solutions that allow linking of diagnostics, real-time capture, and shared repository of these test results. However, these connected diagnostics and readily available test results are not used to their full capacity, as we have yet to capitalize on fully understanding the relationship between test results and specific rpoB mutations to elucidate its potential application to real-time surveillance. Objective: We aimed to validate and analyze RDT data in detail, and propose the potential use of connected diagnostics and associated test results for real-time evaluation of RR-TB transmission. Methods: We selected 107 RR-TB strains harboring 34 unique rpoB mutations, including 30 within the rifampicin resistance–determining region (RRDR), from the Belgian Coordinated Collections of Microorganisms, Antwerp, Belgium. We subjected these strains to Xpert MTB/RIF, GenoType MTBDRplus v2.0, and Genoscholar NTM + MDRTB II, the results of which were validated against the strains’ available rpoB gene sequences. We determined the reproducibility of the results, analyzed and visualized the probe reactions, and proposed these for potential use in evaluating transmission. Results: The RDT probe reactions detected most RRDR mutations tested, although we found a few critical discrepancies between observed results and manufacturers’ claims. Based on published frequencies of probe reactions and RRDR mutations, we found specific probe reactions with high potential use in transmission studies: Xpert MTB/RIF probes A, Bdelayed, C, and Edelayed; Genotype MTBDRplus v2.0 WT2, WT5, and WT6; and Genoscholar NTM + MDRTB II S1 and S3. Inspection of probe reactions of disputed mutations may potentially resolve discordance between genotypic and phenotypic test results. Conclusions: We propose a novel approach for potential real-time detection of RR-TB transmission through fully using digitally linked TB diagnostics and shared repository of test results. To our knowledge, this is the first pragmatic and scalable work in response to the consensus of world-renowned TB experts in 2016 on the potential of diagnostic connectivity to accelerate efforts to eliminate TB. This is evidenced by the ability of our proposed approach to facilitate comparison of probe reactions between different RDTs used in the same setting. Integrating this proposed approach as a plug-in module to a connectivity platform will increase usefulness of connected TB diagnostics for RR-TB outbreak detection through real-time investigation of suspected RR-TB transmission cases based on epidemiologic linking.
KCN was supported by Erasmus Mundus Joint Doctorate Fellowship grant 2016-1346, and BCdJ, LR, and CJM were supported by European Research Council-INTERRUPTB starting grant 311725.

Aim: To develop an antigen detection test that would quickly exclude H. ducreyi infection in individuals with genital ulcers. Materials and Methods: H. ducreyi strains A54 and A68 were grown on Modified Bieling (MB) agar plates and in MB broth under microaerophilic conditions. The 58.5 kDa GroEL Heat Shock Protein (HSP) was extracted from H. ducreyi strain A54 by means of sonication. The purified HSP was used to raise antibodies in rabbits. HSP determination and separation was done on SDS PAGE gels and protein was eluted by means of a passive elution process. Antibody was purified by affinity chromatography and a fraction of the antibody was conjugated to a chromogen to be used as a detection antibody. An ELISA was developed to evaluate the antibody response to the HSP. A second ELISA was developed to evaluate test parameters. Results: A good immune response was achieved with the crude serum of one of the three rabbits when tested against the antigen by means of ELISA. However, after purification of the IgG from the serum of the same rabbit no antigen-antibody binding was observed. Anti-rabbit IgG was able to recognise the antibodies. Discussion and Conclusion: While the Fc portion of the purified IgG remained active, the Fab portion of the antibody had lost biological activity. This loss of biological activity of antibody can be attributed to the low pH of the elution buffers used during the purification steps. Alternative antibody purification systems need to be explored. The use of monoclonal antibodies also needs to be considered.
Thesis (M.Med.)-University of KwaZulu-Natal, Durban, 2010.

The transmission of malaria is among the leading public health problems in Ethiopia. From the total area of Ethiopia, more than 75% is malarious. Identifying the infectiousness of malaria by socio-economic, demographic and geographic risk factors based on the malaria rapid diagnosis test (RDT) survey results has several advantages for planning, monitoring and controlling, and eventual malaria eradication effort. Such a study requires thorough understanding of the diseases process and associated factors. However such studies are limited. Therefore, the aim of this study was to use different statistical tools suitable to identify socioeconomic, demographic and geographic risk factors of malaria based on the malaria rapid diagnosis test (RDT) survey results in Ethiopia. A total of 224 clusters of about 25 households were selected from the Amhara, Oromiya and Southern Nation Nationalities and People (SNNP) regions of Ethiopia. Accordingly, a number of binary response statistical analysis models were used. Multiple correspondence analysis was carried out to identify the association among socioeconomic, demographic and geographic factors. Moreover a number of binary response models such as survey logistic, GLMM, GLMM with spatial correlation, joint models and semi-parametric models were applied. To test and investigate how well the observed malaria RDT result, use of mosquito nets and use of indoor residual spray data fit the expectations of the model, Rasch model was used. The fitted models have their own strengths and weaknesses. Application of these models was carried out by analysing data on malaria RDT result. The data used in this study, which was conducted from December 2006 to January 2007 by The Carter Center, is from baseline malaria indicator survey in Amhara, Oromiya and Southern Nation Nationalities and People (SNNP) regions of Ethiopia. The correspondence analysis and survey logistic regression model was used to identify predictors which affect malaria RDT results. The effect of identified socioeconomic, demographic and geographic factors were subsequently explored by fitting a generalized linear mixed model (GLMM), i.e., to assess the covariance structures of the random components (to assess the association structure of the data). To examine whether the data displayed any spatial autocorrelation, i.e., whether surveys that are near in space have malaria prevalence or incidence that is similar to the surveys that are far apart, spatial statistics analysis was performed. This was done by introducing spatial autocorrelation structure in GLMM. Moreover, the customary two variables joint modelling approach was extended to three variables joint effect by exploring the joint effect of malaria RDT result, use of mosquito nets and indoor residual spray in the last twelve months. Assessing the association between these outcomes was also of interest. Furthermore, the relationships between the response and some confounding covariates may have unknown functional form. This led to proposing the use of semiparametric additive models which are less restrictive in their specification. Therefore, generalized additive mixed models were used to model the effect of age, family size, number of rooms per person, number of nets per person, altitude and number of months the room sprayed nonparametrically. The result from the study suggests that with the correct use of mosquito nets, indoor residual spraying and other preventative measures, coupled with factors such as the number of rooms in a house, are associated with a decrease in the incidence of malaria as determined by the RDT. However, the study also suggests that the poor are less likely to use these preventative measures to effectively counteract the spread of malaria. In order to determine whether or not the limited number of respondents had undue influence on the malaria RDT result, a Rasch model was used. The result shows that none of the responses had such influences. Therefore, application of the Rasch model has supported the viability of the total sixteen (socio-economic, demographic and geographic) items for measuring malaria RDT result, use of indoor residual spray and use of mosquito nets. From the analysis it can be seen that the scale shows high reliability. Hence, the result from Rasch model supports the analysis carried out in previous models.
Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

In the year of 2020, an international pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has afflicted tens of millions of people’s life also disrupting global economics. Diagnostic testing is an important part of ensuring public health until a vaccine that has been shown to be safe and effective is made available to the general public. Most tests for detecting COVID-19 utilize quantitative polymerase chain reaction (qPCR) assays, which is a specific and relatively simple quantitative assay that could provide adequate sensitivity for diagnosing early infection. Although powerful, these lab-based molecular assays have a significant lag time, usually several days before receiving results. To satisfy the needs of different purposes (diagnostics, screening, and surveillance), a unified approach is impractical. This thesis presents an alternative testing method supporting the current procedure of point of care (POC) testing and in community testing. This paper-based test overcomes the limitations of current testing methods by utilizing reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and receiving the result on-site by a color change in the presence of the virus within 60 minutes. The test utilizes untreated freshly collected saliva, a less invasive specimen, as the sample and possesses a limit of detection (LoD) of 200 copies of virus per microliter of whole saliva with an analytical sensitivity of 97% and analytical specificity of 100%. The test requires minimal operator training and could be fabricated on a large-scale using roll-to-roll methods. Since the test is based on nucleic acids, the testing platform itself lends to further applications including food safety monitoring, animal diagnostic, etc. simply by changing the specific primers.

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfillment of the requirements for the degree of Master of Dentistry. Johannesburg, 2018.
Background: Accurate HIV diagnosis is critical and can be life-saving. A Rapid Test (RT) is considered key to HIV prevention and management. Some studies have found RT to be comparable with ELISA whilst others have reported on lower sensitivity. Aim and study design: The aim of this retrospective comparative descriptive study was to evaluate the sensitivity and specificity of the Tri-line HIV rapid test device in comparison to ELISA on patient records from Wits Oral Health Centre (WOHC) between 2014 and 2016 Method: The study population comprised records of patients older than18 months who had Tri-Line HIV RT and blood drawn for ELISA on the same day. Descriptive analysis of the data was carried out. Results: The sensitivity of Tri-line was 80% (CI: 59-93%) and specificity was 100% (CI: 83-100%). The PPV was 100% (CI: 83-100%) and NPV was 80% (CI: 65-90%). ROC area of 0.9 at 95% CI was determined. Conclusion: Due to a low sample size in this study a definitive conclusion could not be drawn. However on the basis of the results obtained, although the tri-line RT showed lower sensitivity it was shown to be a clinically useful test.
LG2018

acase@tulane.edu
Introduction: The Home-based Management of Malaria (HMM) is a cornerstone of malaria control in sub-Saharan Africa (SSA) and is recommended by WHO to provide prompt access to antimalarial treatment for children in under-served areas. Although HMM has been shown to reduce malaria morbidity and mortality with chloroquine, it has not been examined previously in the era of artemisinin-based combination therapies. The objectives of this study were to determine whether HMM reduced: 1] the time from when a mother or guardian realized her child was ill to the time when the child was brought for treatment and 2] malaria morbidity in children less than 5 years of age. Methodology: This cross-sectional retrospective study (2008-2014) was performed in intervention villages (receiving HMM) and control villages (not receiving HMM) to examine the effectiveness of HMM. Key Results: More mothers and guardians were informed about the malaria control activities performed (98% vs. 24%) in intervention than control villages (p < 0.001). Consistent with that result, mothers and guardians in intervention villages sought care for their sick children earlier than mothers in control villages (p < 0.001) and were more likely to obtain treatment from community health workers (CHWs) in their home villages. In contrast, more children were referred for malaria treatment to health posts and health centers from control than intervention villages (p < 0.001). Likewise, more children with complicated malaria were referred for treatment from control villages (p < 0.001), although those conclusions were limited by the small numbers of complicated (severe) malaria cases. Conclusions: These results indicate HMM shortens the time mothers wait before taking their children to receive treatment. Because more children with uncomplicated or complicated malaria are referred for treatment from control than intervention villages, these results indicate that the availability of HMM treatment in the child’s home village reduces morbidity (the risk of severe malarial disease). However, additional studies with larger numbers of subjects will be necessary to determine if HMM reduces mortality.
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Ibrahima SECK