Recent Advances and Potential Future Applications of MALDI-TOF Mass Spectrometry for Identification of Helminths

Helminth infections caused by nematodes, trematodes, and cestodes are major neglected tropical diseases and of great medical and veterinary relevance. At present, diagnosis of helminthic diseases is mainly based on microscopic observation of different parasite stages, but microscopy is associated with limited diagnostic accuracy. Against this background, recent studies described matrixassisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry as a potential, innovative tool for helminth identification and differentiation. MALDI-TOF mass spectrometry is based on the analysis of spectra profiles generated from protein extracts of a given pathogen. It requires an available spectra database containing reference spectra, also called main spectra profiles (MSPs), which are generated from well characterized specimens. At present, however, there are no commercially available databases for helminth identification using this approach. In this narrative review, we summarize recent developments and published studies between January 2019 and September 2022 that report on the use of MALDI-TOF mass spectrometry for helminths. Current challenges and future research needs are identified and briefly discussed

Evaluation of the Qvella FAST System and the FAST-PBC cartridge for rapid species identification and antimicrobial resistance testing directly from positive blood cultures

Blood culture diagnostics require rapid and accurate identification (ID) of pathogens and antimicrobial susceptibility testing (AST). Standard procedures, involving conventional cultivation on agar plates, may take up to 48 hours or more until AST completion. Recent approaches aim to shorten the processing time of positive blood cultures (PBC). The FAST System is a new technology, capable of purifying and con centrating bacterial/fungal pathogens from positive blood culture media and produc ing a bacterial suspension called “liquid colony” (LC), which can be further used in downstream analyses (e.g., ID and AST). Here, we evaluated the performance of the FAST System LC generated from PBC in comparison to our routine workflow includ ing ID by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using Sepsityper, AST by automatized MicroScan WalkAway plus and directly inocula ted disk diffusion (DD), and MICRONAUT-AM for yeast/fungi. A total of 261 samples were analyzed, of which 86.6% (226/261) were eligible for the comparative ID and AST analyses. In comparison to the reference technique (culture-grown colonies), ID concordance of the FAST System LC and Sepsityper was 150/154 (97.4%) and 123/154 (79.9%), respectively, for Gram positive; 67/70 (95.7%) and 64/70 (91.4%), respectively, for Gram negative. For AST, categorical agreement (CA) of the FAST System LC in comparison to the routine workflow for Gram-positive bacteria was 96.1% and 98.7% for MicroScan and DD, respectively. Similar results were obtained for Gram-negative bacteria with 96.6% and 97.5% of CA for MicroScan and DD, respectively. Taken together, the FAST System LC allowed the laboratory to significantly reduce the time to obtain correct ID and AST (automated MicroScan) results 1 day earlier and represents a promising tool to expedite the processing of PBC

Programme d’Accélération de la Cadence de l’Agriculture Sénégalaise (PRACAS) et dynamique des espaces agricoles sénégalais: Cas du bassin de l’Anambe

The PRACAS, which was designed as a part of the agricultural policy of the Emerging Senegal Plan (PSE) as the main tool for public policy planning in Senegal, was based on participatory and inclusive approach. It was initiated in 2014 by the Senegalese government with a view to increasing agricultural production and thus achieving national food self-sufficiency. This program has led to dynamics across the Anambe basin. The program, which is designed to implement annual irrigated dual crop, is a privileged area for this program to achieve food self-sufficiency, particularly in the upper Casamance. This study assesses the impacts of PRACAS on the agricultural environment of the Anambe basin. It is based on field surveys, interviews with resource persons (technicians, managers of hydraulics union and the economic interest group) but also an analysis of agricultural statistics collected from the agricultural and industrial development society of Senegal (SODAGRI). It is clear from this work that PRACAS, despite the persistence of food insecurity, has allowed the rehabilitation of the land area, the reception of agricultural equipment and the increase in areas and production of rice. These results prompted the State of Senegal to extend the SODAGRI intervention zone to the entire southern region of the country. Keywords: PRACAS, rural area dynamics, food insecurity, rice production, Anambe BassinLe Programme d’Accélération de la Cadence de l’Agriculture Sénégalaise (PRACAS), conçu comme une déclinaison de la politique agricole du Plan Sénégal Émergent (PSE) principal outil de planification des politiques publiques sénégalaises, témoigne d’une rupture de par sa démarche participative et inclusive. Il a été initié en 2014 par le gouvernement sénégalais dans l’optique d’accroître les productions agricoles et par conséquent d’atteindre une autonomie alimentaire nationale. Ce programme a entraîné des dynamiques à l’échelle du bassin de l’Anambé. Ce dernier, aménagé dans une perspective de double culture irriguée annuelle, constitue un terrain privilégié de ce programme pour l’atteinte de l’autosuffisance alimentaire, notamment en Haute Casamance. Cette étude évalue les impacts du PRACAS sur l’environnement agricole du bassin de l’Anambé. Elle s’appuie sur des enquêtes de terrain, des entretiens auprès de personnes ressources (techniciens, responsables d’Unions hydrauliques et de Groupement d’Intérêt Économique) mais également sur une analyse de statistiques agricoles collectées au niveau de la Société de Développement Agricole et Industriel du Sénégal (SODAGRI). Il ressort de ce travail que le PRACAS, malgré la persistance de l’insécurité alimentaire, a permis la réhabilitation du périmètre, la réception de matériel agricole et l’augmentation des superficies et des productions rizicoles dans la zone. Ces résultats ont incité l’État du Sénégal à étendre la zone d’intervention de la SODAGRI à toute la zone Sud du pays. Mots clés: PRACAS, dynamique des espaces ruraux, insécurité alimentaire, productions rizicoles, bassin de l’Anamb

Vulnérabilités et stratégies d’adaptation des paysans face aux changements socio-environnementaux en Haute Casamance (Sud-Sénégal)

La sécurité alimentaire a toujours été le vœu des plus hautes autorités politiques sénégalaises. De l’indépendance à nos jours, différentes politiques agricoles ont été proposées pour satisfaire au moins la demande alimentaire du pays. La Haute Casamance constitue l’une des régions devant permettre l’atteinte de cet objectif. Toutefois, dans cette région, les perspectives de développement de l’agriculture sont très incertaines du fait de la conjonction de nombreux aléas pédoclimatiques, socio-économiques, technologiques, organisationnels et politiques qui empêchent encore de porter la production et la productivité agricoles à des niveaux satisfaisants. L’objectif de cette étude est d’analyser la vulnérabilité et l’adaptabilité des paysans face aux dynamiques socio-environnementales en Haute Casamance. L’ampleur des changements est mesurée grâce à une approche géographique globale et multi-scalaire, qui intègre à la fois des outils de la géomatique et des travaux de terrain (observations directes, enquêtes auprès de 441 ménages répartis dans 12 communes et analyse de perceptions). Cette approche a conduit à l’identification des facteurs de vulnérabilité qui tournent autour des obstacles pédoclimatiques, des contraintes politico-techniques et organisationnelles. Aussi, l’analyse des stratégies développées pour remédier à la baisse des productions agricoles a montré que la rotation et la jachère effectuées respectivement par 91 % et 38 % des producteurs, l’association culturale ainsi que les aménagements hydroagricoles sont les techniques culturales utilisées pour redresser l’agriculture.Food security is an old wish of the highest political authorities in Senegal. From independence to the present day, various agricultural policies have been proposed to satisfy at least the country’s food demand. The Upper Casamance is one of the regions which should enable this objective to be achieved. However, in this region the prospects for agricultural development are very uncertain due to the combination of many soil, socio-economic and technological hazards. The European Union is also committed to the development of the European Agricultural Area. The objective of this study is to analyse the vulnerability and adaptability of farmers in the face of socio-environmental dynamics in Upper Casamance. The magnitude of change is measured through a comprehensive and multi-scaled geographic approach that integrates both geomatics tools (GIS, GPS point surveys) and fieldwork (direct observations, surveys of 441 households in 12 communes and analysis of perceptions). This approach led to the identification of vulnerability factors that revolve around soil-climatic obstacles, political-technical and organisational constraints. Also, analysis of mitigation strategies showed that rotation (91%), fallow land (38%), crop association, hydroagricultural development are the techniques used to increase production

Variabilité pluviométrique et développement de l’activité agricole dans la région de Kolda (Sénégal)

L’agriculture familiale s’affiche indéniablement comme un pilier de la sécurité alimentaire nationale sénégalaise. Elle représente près de 80 % des exploitations en Afrique sub-saharienne et emploie 75 % des actifs. Elle se caractérise par l’importance des cultures pluviales (96 % des plantes cultivées), témoignant ainsi de sa dépendance à la pluviométrie saisonnière. Or, le climat est sujet à une variabilité interannuelle et certains parlent même de changement climatique. Cette étude analyse la variabilité pluviométrique et permet d’identifier les stratégies d’adaptation mises en œuvre pour tenter de maintenir un niveau de production permettant de satisfaire les besoins alimentaires des populations. L’étude s’appuie sur le traitement de données agro-climatiques, sur des travaux de terrain (enquêtes et entretien) et sur des tests de corrélation (nuage de points et Analyse en Composantes Principales). Les résultats l’ACP révèlent que l’influence de la pluviométrie sur la variation des productions est faible, car le R2 (pluviométrie et rendements agricoles) est inférieur à 0,1. Globalement, l’analyse comparative entre les deux périodes de références (1951-1980 et 1981-2010) révèle un raccourcissement de la durée de la saison des pluies à la station de Kolda. Des stratégies telles que l’adoption de variétés à cycle court, le recalage du calendrier cultural selon le contexte climatique en vigueur ont été identifiées.Family farming is undeniably a pillar of Senegalese national food security. It accounts for nearly 80% of farms in sub-Saharan Africa and employs 75% of the workforce. It is characterized by the importance of rain fed crops (96% of cultivated plants), thus testifying to its dependence on seasonal rainfall. However, climate is subject to inter-annual variability and some even talk about climate change. This study analyses rainfall variability and identifies adaptation strategies implemented to try to maintain a level of production that allows them to meet their food needs. The study is based on agro-climatic data processing, fieldwork (surveys and maintenance) and Principal Component Analysis (PCA). The results show that rainfall was in surplus from 1951 to 1970, in deficit from 1971 to 1990 and irregular (alternating between dry and wet years) from 1991 to the present. As for exits from the ACP, it turns out that rainfall is not the only factor responsible for the variation in production. Strategies such as the adoption of short-cycle varieties, the recalculation of the crop calendar according to the current climate context have been identified

Evaluating Different Storage Media for Identification of Taenia saginata Proglottids Using MALDI-TOF Mass Spectrometry

Taenia saginata is a helminth that can cause taeniasis in humans and cysticercosis in cattle. A species-specific diagnosis and differentiation from related species (e.g., Taenia solium) is crucial for individual patient management and disease control programs. Diagnostic stool microscopy is limited by low sensitivity and does not allow discrimination between T. saginata and T. solium. Molecular diagnostic approaches are not routinely available outside research laboratories. Recently, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) was proposed as a potentially suitable technique for species-specific helminth diagnosis. However, standardized protocols and commercial databases for parasite identification are currently unavailable, and pre-analytical factors have not yet been assessed. The purpose of this study was to employ MALDI-TOF MS for the identification of T. saginata proglottids obtained from a human patient, and to assess the effects of different sample storage media on the technique’s diagnostic accuracy. We generated T. saginata-specific main spectral profiles and added them to an in-house database for MALDI-TOF MS-based diagnosis of different helminths. Based on protein spectra, T. saginata proglottids could be successfully differentiated from other helminths, as well as bacteria and fungi. Additionally, we analyzed T. saginata proglottids stored in (i) LC–MS grade water; (ii) 0.45% sodium chloride; (iii) 70% ethanol; and (iv) 37% formalin after 2, 4, 6, 8, 12, and 24 weeks of storage. MALDITOF MS correctly identified 97.2–99.7% of samples stored in water, sodium chloride, and ethanol, with log-score values ≥2.5, thus indicating reliable species identification. In contrast, no protein spectra were obtained for samples stored in formalin. We conclude that MALDI-TOF-MS can be successfully employed for the identification of T. saginata, and that water, sodium chloride, and ethanol are equally effective storage solutions for prolonged periods of at least 24 weeks