Effects of therapeutic zno and antibiotics and its withdrawal on the microbiome of weaned pigs

Resumen

1. Introducción o motivación de la tesis: La diarrea pos-destete (PWD, del inglés post-weaning diarrhoea) es una enfermedad infecciosa que causa pérdidas productivas y económicas en producción porcina y que a menudo requiere el uso de antimicrobianos. El uso profiláctico y metafiláctico de estos antimicrobianos para el tratamiento de la PWD está sujeto a cada vez más restricciones, especialmente en la UE, debido al riesgo de resistencias antimicrobianas. El óxido de zinc (ZnO) usado en concentraciones de 1500 a 3000ppm (referidas como concentraciones terapéuticas o farmacológicas) también se usa como un tratamiento eficaz para prevenir la PWD. Su uso se prohibió el 28 de julio de 2022 en la UE debido al riesgo ambiental de contaminación del suelo asociado a su uso. Encontrar estrategias alternativas al uso de los antibióticos y del ZnO es crucial para mantener los niveles óptimos de salud y bienestar animal, así como la rentabilidad de las granjas, asegurando la producción de alimentos de alta calidad. Un primer paso clave para encontrar estas estrategias alternativas a los antibióticos y el ZnO es entender en detalle sus efectos de en el microbioma y en el animal. Esta tesis se centrar en los efectos en el microbioma. El principal agente causal de la PWD es Escherichia coli enterotoxigénica. El ZnO y los antibióticos son efectivos para controlar el crecimiento excesivo de E. coli durante este período, aunque el mecanismo de acción exacto del ZnO no está totalmente claro. Por otro lado, la disbiosis del microbioma que ocurre en los días posteriores al destete es uno de los nuevos posibles factores de riesgo y a su vez consecuencias descritas de la PWD. Se cree que el ZnO estabiliza el microbioma intestinal, pero hasta el momento, los cambios taxonómicos y funcionales exactos que provoca no están bien caracterizados. En esta tesis, utilizamos la secuenciación del metagenoma completo para caracterizar el efecto que tanto el ZnO como los antibióticos tienen en el microbioma intestinal del cerdo tanto a nivel taxonómico como funcional, en las primeras semanas posteriores al destete. 2.Contenido de la investigación: En el capítulo 2, estudiamos el efecto del ZnO y de la apramicina en la respuesta del microbioma intestinal del cerdo al destete una semana pos-destete. Ambos tuvieron efectos marcados en la taxonomía y funcionalidad del microbioma intestinal. Los cerdos alimentados con dieta control sin ZnO ni antibióticos (Ct) exhibieron una gran abundancia de E. coli, que portaba varios factores de virulencia en animales que no mostraban signos clínicos de diarrea. Este estudio se realizó en una granja experimental de baja patología con altos niveles de higiene y bioseguridad en la que también se evaluaron los efectos de diferentes procedimientos de limpieza. El tratamiento fue el factor con mayor efecto en el microbioma, mientras que los procedimientos de limpieza no tuvieron efectos notables. Dados los resultados observados en el primer estudio, los siguientes estudios descritos en los capítulos 3 y capítulo 4 se realizaron en granjas comerciales para explorar los efectos de los antibióticos y el ZnO en entornos comerciales y la variabilidad entre granjas en la composición del microbioma intestinal. En el capítulo 3, se compararon granjas que usaban antibióticos y ZnO con granjas que los habían retirado. El microbioma de las granjas que utilizaban ZnO y antibióticos exhibió diferencias en los días 7 y 14 posteriores al destete, tanto a nivel de taxonómico como funcional; diferencias más evidentes en muestras de diarrea de 7 días post destete. El análisis del microbioma ambiental reveló una contribución débil al microbioma de los lechones, que compartían algunas especies consideradas como “core” que permanecían en el ambiente limpio de la sala de destete y en muestras iniciales y recogidas a las 2 semanas pos-destete. En el capitulo 4 se estudió el impacto de la retirada de los antibióticos y ZnO en el microbioma porcino en granjas que utilizaban habitualmente antimicrobianos de forma profiláctica y metafiláctica al destete. Los resultados mostraron que los antibióticos, y sobretodo el ZnO, mantienen la composición del microbioma estable (taxonómica y funcionalmente), inhibiendo el crecimiento excesivo de E. coli tanto en condiciones normales como en diarrea. La retirada de ZnO y antibióticos en estas granjas generó un aumento en la abundancia de E. coli, así como genes relacionados con la virulencia asociados a la mayor abundancia de E. coli. Por último, en el capítulo 5, discutimos la utilidad de la secuenciación por medio de “Shotgun” en el estudio de los cambios en el microbioma causados por el ZnO y la diarrea, que podrían desencadenarse por efectos antimicrobianos y no antimicrobianos asociados al ZnO (tanto taxonómica como funcionalmente), y los efectos de ZnO manteniendo la estabilidad del microbioma intestinal durante el período más crítico de la etapa posterior al destete. 3.Conclusión: De los resultados obtenidos en esta tesis, el autor concluye que el destete induce una transición brusca de un microbioma de lechón lactante a un microbioma de cerdo adulto. 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