Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis.

The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most population genetic studies in P. falciparum focus on regions of high transmission where parasite populations are large and genetically diverse, such as sub-Saharan Africa. Understanding population dynamics in low transmission settings, however, is of particular importance as these are often where drug resistance first evolves. Here, we use the Pacific Coast of Colombia and Ecuador as a model for understanding the population structure and evolution of Plasmodium parasites in small populations harboring less genetic diversity. The combination of low transmission and a high proportion of monoclonal infections means there are few outcrossing events and clonal lineages persist for long periods of time. Yet despite this, the population is evolutionarily labile and has successfully adapted to changes in drug regime. Using newly sequenced whole genomes, we measure relatedness between 166 parasites, calculated as identity by descent (IBD), and find 17 distinct but highly related clonal lineages, six of which have persisted in the region for at least a decade. This inbred population structure is captured in more detail with IBD than with other common population structure analyses like PCA, ADMIXTURE, and distance-based trees. We additionally use patterns of intra-chromosomal IBD and an analysis of haplotypic variation to explore past selection events in the region. Two genes associated with chloroquine resistance, crt and aat1, show evidence of hard selective sweeps, while selection appears soft and/or incomplete at three other key resistance loci (dhps, mdr1, and dhfr). Overall, this work highlights the strength of IBD analyses for studying parasite population structure and resistance evolution in regions of low transmission, and emphasizes that drug resistance can evolve and spread in small populations, as will occur in any region nearing malaria elimination.

Barreras para la eliminación de la malaria en Guapi-Cauca, Colombia / Obstacles to malaria elimination in Guapi-Cauca, Colombia

RESUMEN Objetivo Explicar las barreras para la eliminación de la malaria en Guapi (Cauca, Colombia), según la percepción de la comunidad. Método Se realizó un estudio cualitativo descriptivo de tipo exploratorio en Guapi, de octubre a noviembre de 2016, a través del análisis de contenido de grupos focales de ocho mujeres voluntarias y de análisis inductivo e interpretativo. Resultados Basadas en las respuestas de las voluntarias, se construyeron tres categorías, de las cuales se originaron cinco subcategorías relacionadas con barreras (tema) para la eliminación de la malaria que incluyen determinantes sociales del municipio tales como las barreras ambientales, culturales y de atención en salud. Todas ellas requieren de la intervención integral por parte de las diferentes dependencias del Estado, con la inclusión de las características propias de la comunidad guapireña. Conclusión Se identificó que la falta de planeación e infraestructura deficiente en el municipio obstaculiza no solo la eliminación de la malaria sino también la de otras enfermedades transmisibles. El desarrollo de actividades económicas como la minería, las prácticas de automedicación, la poca adherencia a las medidas de prevención por parte de la comunidad, la falta de contratación de profesionales y microscopistas y el difícil acceso a los servicios de salud constituyen las principales barreras para la eliminación de la malaria en este municipio de la región pacífica colombiana.

ABSTRACT Objetive To explain the obstacles for malaria elimination in Guapi (Cauca, Colombia), considering the community perception. Method A qualitative, descriptive and exploratory research was carried out in Guapi, from October to November 2016, through the content analysis of eight female volunteer's focus groups. Inductive and interpretive analyses were also performed. Results Based on the volunteers' responses, three categories were built, from which five subcategories related to obstacles (issue) for malaria elimination emerged; these included municipality social determinants such as environmental, cultural and health care barriers. All of them require of comprehensive interventions by different state agencies and inclusion of the specific characteristics of the local community. Conclusion We found that lack of planning and municipal poor infrastructure limits the elimination of malaria and other communicable diseases alike. Economic activities such as mining, self-medication practices, community poor adherence to prevention measures, lack of professional and microscopists hiring and the difficulties for accessing to health services are the main obstacles for malaria elimination in this municipality of the Colombian Pacific Coast.

[Obstacles to malaria elimination in Guapi-Cauca, Colombia]. / Barreras para la eliminación de la malaria en Guapi-Cauca, Colombia.

OBJETIVE: To explain the obstacles for malaria elimination in Guapi (Cauca, Colombia), considering the community perception. METHOD: A qualitative, descriptive and exploratory research was carried out in Guapi, from October to November 2016, through the content analysis of eight female volunteer's focus groups. Inductive and interpretive analyses were also performed. RESULTS: Based on the volunteers' responses, three categories were built, from which five subcategories related to obstacles (issue) for malaria elimination emerged; these included municipality social determinants such as environmental, cultural and health care barriers. All of them require of comprehensive interventions by different state agencies and inclusion of the specific characteristics of the local community. CONCLUSION: We found that lack of planning and municipal poor infrastructure limits the elimination of malaria and other communicable diseases alike. Economic activities such as mining, self-medication practices, community poor adherence to prevention measures, lack of professional and microscopists hiring and the difficulties for accessing to health services are the main obstacles for malaria elimination in this municipality of the Colombian Pacific Coast.

OBJETIVO: Explicar las barreras para la eliminación de la malaria en Guapi (Cauca, Colombia), según la percepción de la comunidad. MÉTODO: Se realizó un estudio cualitativo descriptivo de tipo exploratorio en Guapi, de octubre a noviembre de 2016, a través del análisis de contenido de grupos focales de ocho mujeres voluntarias y de análisis inductivo e interpretativo. RESULTADOS: Basadas en las respuestas de las voluntarias, se construyeron tres categorías, de las cuales se originaron cinco subcategorías relacionadas con barreras (tema) para la eliminación de la malaria que incluyen determinantes sociales del municipio tales como las barreras ambientales, culturales y de atención en salud. Todas ellas requieren de la intervención integral por parte de las diferentes dependencias del Estado, con la inclusión de las características propias de la comunidad guapireña. CONCLUSIÓN: Se identificó que la falta de planeación e infraestructura deficiente en el municipio obstaculiza no solo la eliminación de la malaria sino también la de otras enfermedades transmisibles. El desarrollo de actividades económicas como la minería, las prácticas de automedicación, la poca adherencia a las medidas de prevención por parte de la comunidad, la falta de contratación de profesionales y microscopistas y el difícil acceso a los servicios de salud constituyen las principales barreras para la eliminación de la malaria en este municipio de la región pacífica colombiana.

Estrategias para la eliminación de malaria: una perspectiva afro-colombiana / Strategies for malaria elimination: an Afro-Colombian perspective

RESUMEN Objetivo Describir las estrategias para la eliminación de la malaria a partir de la percepción de pobladores afro-colombianos residentes en Guapi en el contexto de la Estrategia de Gestión Integrada para la promoción, prevención y control de las Enfermedades Transmitidas por Vectores en Colombia (EGI). Métodos Estudio de tipo cualitativo basado en el análisis de discurso de grupos focales. Ocho participantes residentes en zona urbana de Guapi, divididas en dos grupos: el primero correspondió a tres mujeres auxiliares de enfermería, denominadas "mujeres con mayor experiencia", trabajadoras en el actual sistema de salud y funcionarias del antiguo Servicio de Erradicación de la Malaria. El segundo correspondió a cinco mujeres auxiliares de enfermería, denominadas "mujeres con limitada experiencia", trabajadoras en el actual sistema de salud y no tuvieron formación directa con el programa de malaria. Análisis inductivo e interpretativo. Resultados Emergieron ocho subcategorias enmarcadas en la EGI, con énfasis en la promoción y prevención orientadas a disminuir la malaria, especialmente en el área rural. El abordaje del problema debe hacerse de forma integral incluyendo otras problemáticas en salud y determinantes sociales que los afectan como: saneamiento básico, acceso al servicio de salud, falta de educación, uso de tratamientos populares, fragilidad de infraestructura, entre otros. Conclusión Las participantes consideran que la malaria en Guapi se puede reducir pero no eliminar. Se requiere abordar este problema desde una perspectiva institucional y comunitaria, teniendo en cuenta las diferencias culturales, a partir de estrategias que incluyan el empoderamiento comunitario y fortalecimiento administrativo e institucional del programa.(AU)

ABSTRACT Objective To describe strategies for malaria elimination based on the perception of Afro-Colombian residents in Guapi, in the context of the Integrated Management Strategy for the Promotion, Prevention and Control of Vector-Borne Diseases in Colombia (EGI-ETV). Materials and Methods Qualitative study based on focus group discourse analysis. Eight participants from the urban area of Guapi were divided into two groups. The first group included three female nursing assistants, and was called "women with more experience"; they were workers in the current health system and former Malaria Eradication Service officers. The second group was made up of female nursing assistants, and was called "women with limited experience"; they were workers in the current health system and were not directly trained in the malaria program. An inductive and interpretative analysis was performed. Results Eight subcategories emerged, framed in the EGI-EVT, making emphasis on promotion and prevention aimed at reducing malaria, especially in rural areas. This problem must be addressed comprehensively, including other health issues and social determinants that affect them, such as: basic sanitation, access to health services, lack of education, use of popular treatments, and lack of infrastructure, among others. Conclusion Participants consider that malaria in Guapi can be reduced but not eliminated. This problem needs to be addressed from an institutional and community perspective, taking into account cultural differences, based on strategies that include community empowerment and administrative and institutional strengthening of the program.(AU)

[Strategies for malaria elimination: an Afro-Colombian perspective]. / Estrategias para la eliminación de malaria: una perspectiva afro-colombiana.

OBJECTIVE: To describe strategies for malaria elimination based on the perception of Afro-Colombian residents in Guapi, in the context of the Integrated Management Strategy for the Promotion, Prevention and Control of Vector-Borne Diseases in Colombia (EGI-ETV). MATERIALS AND METHODS: Qualitative study based on focus group discourse analysis. Eight participants from the urban area of Guapi were divided into two groups. The first group included three female nursing assistants, and was called "women with more experience"; they were workers in the current health system and former Malaria Eradication Service officers. The second group was made up of female nursing assistants, and was called "women with limited experience"; they were workers in the current health system and were not directly trained in the malaria program. An inductive and interpretative analysis was performed. RESULTS: Eight subcategories emerged, framed in the EGI-EVT, making emphasis on promotion and prevention aimed at reducing malaria, especially in rural areas. This problem must be addressed comprehensively, including other health issues and social determinants that affect them, such as: basic sanitation, access to health services, lack of education, use of popular treatments, and lack of infrastructure, among others. CONCLUSION: Participants consider that malaria in Guapi can be reduced but not eliminated. This problem needs to be addressed from an institutional and community perspective, taking into account cultural differences, based on strategies that include community empowerment and administrative and institutional strengthening of the program.

OBJETIVO: Describir las estrategias para la eliminación de la malaria a partir de la percepción de pobladores afro-colombianos residentes en Guapi en el contexto de la Estrategia de Gestión Integrada para la promoción, prevención y control de las Enfermedades Transmitidas por Vectores en Colombia (EGI). MÉTODOS: Estudio de tipo cualitativo basado en el análisis de discurso de grupos focales. Ocho participantes residentes en zona urbana de Guapi, divididas en dos grupos: el primero correspondió a tres mujeres auxiliares de enfermería, denominadas "mujeres con mayor experiencia", trabajadoras en el actual sistema de salud y funcionarias del antiguo Servicio de Erradicación de la Malaria. El segundo correspondió a cinco mujeres auxiliares de enfermería, denominadas "mujeres con limitada experiencia", trabajadoras en el actual sistema de salud y no tuvieron formación directa con el programa de malaria. Análisis inductivo e interpretativo. RESULTADOS: Emergieron ocho subcategorias enmarcadas en la EGI, con énfasis en la promoción y prevención orientadas a disminuir la malaria, especialmente en el área rural. El abordaje del problema debe hacerse de forma integral incluyendo otras problemáticas en salud y determinantes sociales que los afectan como: saneamiento básico, acceso al servicio de salud, falta de educación, uso de tratamientos populares, fragilidad de infraestructura, entre otros. CONCLUSIÓN: Las participantes consideran que la malaria en Guapi se puede reducir pero no eliminar. Se requiere abordar este problema desde una perspectiva institucional y comunitaria, teniendo en cuenta las diferencias culturales, a partir de estrategias que incluyan el empoderamiento comunitario y fortalecimiento administrativo e institucional del programa.

Preservación de huevos de Necator americanus con acetato de sodio-ácido acético-formalina (SAF). Estudio de caso / Preservation of Necator americanus eggs with sodium acetate-acetic acid-formalin(SAF). Case study

Resumen Introducción. La técnica de Kato Katz es el método recomendado para realizar el recuento de huevos en materia fecal y determinar la intensidad parasitaria por helmintos. La calidad de los resultados se ve afectada por la tardanza en el procesamiento de la muestra, por lo que se requiere de preservantes que faciliten la lectura posterior a las 24 horas de recolección de la muestra. Objetivo. Demostrar validez de la solución con acetato de sodio-ácido acético-formalina (SAF) como preservante de huevos de Necator americanus por medio del estudio de un caso clinico. Materiales y métodos. Descripción de caso clínico con diagnóstico de parásitos intestinales por coprológico, intensidad de la infección por la técnica de Kato Katz, evaluación de la presencia de huevos N. americanus por la técnica de Kato Katz durante 10 meses en muestra preservada en SAF y determinación de especie de Uncinaria sp. por qPCR. Resultados. Los huevos de N. americanus se conservan de manera adecuada en morfología durante los primeros cinco meses. Conclusiones. A fin de ejecutar la técnica de Kato Katz, la fijación con SAF demostró ser adecuada para el mantenimiento de la intensidad parasitaria y morfología de los huevos de N. americanus en un período de hasta cinco meses.

Abstract Introduction: The Kato Katz technique is the recommended method for fecal egg counts and determining the intensity of parasitic helminths. The quality of the results is affected by the delay in the analysis of the sample. Therefore, fixatives are necessary to make the reading easier 24 hours after sample collection. Objective: To prove the usefulness of sodium acetate-acetic acid-formalin (SAF) solution as a fixative for Necator americanus eggs by means of a clinical case study. Materials and methods: Clinical case description and intestinal parasites diagnosis by direct stool microscopic analysis and parasite infection intensity by means of the Kato Katz technique. N. americanus eggs were detected by Kato Katz method for 10 months on a SAF-fixed stool sample. Identification of Uncinaria sp. by qPCR. Results: N. americanus eggs are adequately preserved in SAF during the first five months. Conclusions: SAF fixative is suitable for Kato Katz method and proved to be capable of maintaining parasite intensity and N. americanus egg morphology over a period of up to five months.

Baseline in vivo, ex vivo and molecular responses of Plasmodium falciparum to artemether and lumefantrine in three endemic zones for malaria in Colombia.

Background: Colombia began using artemisinin-based combination therapies for the treatment of uncomplicated Plasmodium falciparum malaria in 2006. It is necessary to implement resistance surveillance to antimalarial drugs in order to promptly detect changes in parasite susceptibility. The aim of this study was to establish a susceptibility baseline of P. falciparum to artemether-lumefantrine using three monitoring tools. Methods: Patients with uncomplicated malaria treated with artemether-lumefantrine underwent clinical and parasitological follow-up over 28 days. Ex vivo test was performed using the microtest technique for chloroquine, arthemeter, dihydroartemisinin and lumefantrine. Pfmdr1 copy number and polymorphisms in Pfk13, Pfatp6, Pfcrt and Pfmdr1 genes were analyzed. Results: From a total of 150 screened patients, 49 completed follow-up for 28 days. All treated patients had adequate clinical and parasitological responses. Parasitic clearance showed a drastic reduction of parasite biomass at 24 hours and complete elimination at 48 hours. One hundred eleven isolates were processed, all exhibited high susceptibility to artemisinins and a slight decrease in susceptibility to lumefantrine. No genetic polymorphisms associated with resistance to artemisinin were found. Conclusion: This study generated a susceptibility baseline in response to therapy with Coartem (artemether-lumefantrine) with numerical reference values, which will allow data comparison with future studies to systematically monitor changes in the parasite and to provide an early alert to the health authorities.

Perfil clínico y parasitológico de la malaria por Plasmodium falciparum y Plasmodium vivax no complicada en Córdoba, Colombia / Clinical and parasitological profiles of patients with non-complicated Plasmodium falciparum and Plasmodium vivax malaria in northwestern Colombia

Antecedentes. En Colombia existen pocos estudios que buscan encontrar diferencias clínicas y parasitológicas en la malaria causada por Plasmodium falciparum y Plasmodium vivax. Objetivo. Describir el perfil clínico y parasitológico de las malarias por Plasmodium falciparum y Plasmodium vivax no complicadas en Tierralta, Córdoba, Colombia. Materiales y métodos. Se evaluaron pacientes con paludismo no complicado por Plasmodium falciparum y Plasmodium vivax según los protocolos estandarizados por la Organización Panamericana de la Salud y se recolectó información clínica y parasitológica. De igual forma, se utilizó análisis multivariado por correspondencias múltiples para describir diferentes perfiles de pacientes con paludismo no complicado por estas dos especies antes de recibir tratamiento. Resultados. Se evaluaron 112 pacientes con edad entre 6 y 64 años, 59 (52.7%) con Plasmodium falciparum y 53 (47.3%) con Plasmodium vivax. Los síntomas más frecuentes fueron fiebre en 111 pacientes (99.1%; IC 95%: 81.5-100), sudoración en 105 (93.8%; IC 95%: 76.7-100) y dolor osteomuscular en 105 (93.8%; IC 95%: 76.7-100). Se presentaron con mayor frecuencia, y con diferencia significativa, en las infecciones por Plasmodium falciparum: diarrea en 18 pacientes (30.5%; IC 95%: 18.1-48.2); decaimiento en 49 (83%; IC 95%: 61.4-109.8); palidez palmar en 39 (66.1%; IC 95%: 47-90.4) y sequedad de mucosas en 12 (20.3%; IC 95%: 10.5-35.5). El escalofrío se presentó con mayor frecuencia en Plasmodium vivax (98.1%; IC 95%: 73.4-128.1). El análisis multivariado agrupó las variables en cuatro perfiles distintos de presentaciones clínicas así: 1) síntomas clínicos y su relación con el recuento parasitario, 2) características clínicas en relación con la edad y sexo, 3) antecedentes de malaria en relación con características demográficas y clínicas y 4) especie del parásito en relación con antecedentes, clínica y variables demográficas. Conclusión. Se identificaron algunas diferencias clínicas entre los enfermos con Plasmodium vivax y los enfermos con Plasmodium falciparum, y las variables estudiadas se agruparon en cuatro perfiles que permiten una variedad de interpretaciones.

Background. There are few studies in Colombia that have aimed at finding clinical and parasitological differences between Plasmodium falciparum and Plasmodium vivax malaria. Objective. To describe the clinical and parasitological profile of non-complicated malaria caused by Plasmodium falciparum and Plasmodium vivax in Tierralta, Cordoba, Colombia. Materials and Methods. Patients with non-complicated malaria caused by Plasmodium falciparum and Plasmodium vivax were evaluated according to standardized protocols recommended by the Pan American Health Organization. Both clinical and parasitological information was collected. A multiple correspondence multivariate analysis was used to describe the different profiles of patients suffering non-complicated malaria caused by these two species before the administration of the required treatment. Results. One hundred and twelve patients aged 6 to 64 were evaluated, 59 (52.7%) suffering Plasmodium falciparum malaria and 53 (47.3%), Plasmodium vivax malaria. The most frequent symptoms were fever in 111 (99.1%; 95% CI: 81.5- 100), sweating in 105 (93.8%; 95% CI: 76.7-100) and musculoskeletal pain in 105 (93.8%; IC 95%: 76.7-100). Regarding the Plasmodium falciparum infections there was a higher frequency, with significant difference, in the following clinical manifestations: diarrhea: 18 patients (30.5%; 95%: 18.1-48.2); asthenia: 49 patients (83%; 95% CI: 61.4-109.8); palmar pallor: 39 patients (66.1%; 95% CI: 47-90.4); mucosal dryness: 12 patients (20.3%; 95%CI: 10.5-35.5). The chills appeared with higher frequency in Plasmodium vivax malaria (98.1%; 95%CI: 73.4-128.1). The multivariate analysis grouped the variables into four different profiles of clinical presentations: Clinical symptoms and their relation to the parasite count; clinical characteristics in relation to age and sex; history of malaria regarding demographic and clinical characteristics; and parasite species in relation to historic, clinical and demographic variables. Conclusions. Some clinical differences between patients with Plasmodium vivax and patients with Plasmodium falciparum were identified and the studied variables were grouped into four profiles which allow for a variety of interpretations.