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Analysis of genotypic and phenotypic AMR in Salmonella spp. isolates from food-producing animals in Denmark
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A resistência aos antimicrobianos (RAM) é um dos maiores desafios globais de saúde pública e exige abordagens integradas no âmbito da Uma Só Saúde. Salmonella spp. é um dos agentes zoonóticos prioritários da União Europeia e um organismo sentinela importante para a vigilância da RAM. Embora a Sequenciação Total do Genoma (STG) esteja a ser progressivamente incorporada nos programas de monitorização, a correspondência entre determinantes genotípicos de resistência e resultados fenotípicos de suscetibilidade obtidos através de métodos padronizados permanece insuficientemente caracterizada. Este estudo avaliou a concordância entre perfis fenotípicos e genotípicos de RAM em isolados de Salmonella spp. provenientes de animais de produção e carnes comerciais monitorizados pelo DANMAP entre 2018 e 2023. No total, 967 isolados foram testados pelo método fenotípico de microdiluição em caldo e 3.011 foram sequenciados por STG, dos quais 769 apresentaram dados emparelhados completos. As fontes incluíram suínos, aves, bovinos e carnes de porco, vaca e pato. A resistência e a multirresistência foram mais elevadas em suínos e carne de porco, incluindo um aumento acentuado em isolados domésticos em 2023. Nas aves, os resultados foram mais diversos, dependendo da origem e do serovar. Apesar de sempre importada, a carne de pato apresentou um perfil diferente, notável pela resistência a antimicrobianos de importância crítica (AICs). Os bovinos e a carne de vaca revelaram níveis de resistência mais baixos. A análise genotípica com ResFinder e AMRFinderPlus demonstrou resultados semelhantes, com discrepâncias sobretudo associadas a beta-lactamases e fluoroquinolonas. A concordância genótipo-fenótipo foi geralmente elevada, principalmente para tetraciclinas e sulfonamidas, e mais moderada para beta-lactâmicos e quinolonas. De forma geral, os resultados reforçam a importância de combinar abordagens fenotípicas e genotípicas na vigilância da RAM, evidenciando o potencial do STG, mas também a necessidade de atualização contínua das bases de dados e de melhoria na interpretação funcional dos determinantes de resistência
Antimicrobial resistance (AMR) is one of the major global public health challenges and requires integrated approaches within the One Health framework. Salmonella spp. remains one of the European Union's priority zoonotic agents and is a key sentinel organism for AMR surveillance. Although Whole Genome Sequencing (WGS) is being increasingly incorporated into national monitoring programs, correspondence between genotypic resistance determinants and phenotypic susceptibility results obtained using standardized methods remains insufficiently characterized. The present study aimed to assess the phenotypic and genotypic AMR profile concordance for Salmonella spp. isolates obtained from food-producing animals and retail meats under DANMAP monitoring from 2018 to 2023. A total of 967 isolates were tested by the broth microdilution phenotypic method, and 3,011 were sequenced by WGS, of which 769 had complete paired data. The sources included swine, poultry, cattle, pork, beef, and duck meat. Resistance and multidrug resistance were the highest in pigs and pork, including a significant increase in domestic isolates in 2023. In poultry, results were more heterogeneous, depending on origin and diversity of serovars. Although always imported, duck meat presented a distinct profile, standing out for its resistance to critically important antimicrobials (CIAs). Cattle and beef generally showed lower resistance levels. Genotypic analysis using ResFinder and AMRFinderPlus demonstrated high agreement, with discrepancies mostly associated with beta-lactamases and determinants of resistance to fluoroquinolones. The genotype-phenotype concordance was generally high, especially for tetracyclines and sulfonamides, but more moderate for beta-lactams and quinolones. Overall, the findings emphasize the importance of combining phenotypic and genotypic approaches in AMR surveillance, illustrating the potential of WGS along with a need for ongoing curation of databases and improvement in functional interpretation of resistance determinants
Antimicrobial resistance (AMR) is one of the major global public health challenges and requires integrated approaches within the One Health framework. Salmonella spp. remains one of the European Union's priority zoonotic agents and is a key sentinel organism for AMR surveillance. Although Whole Genome Sequencing (WGS) is being increasingly incorporated into national monitoring programs, correspondence between genotypic resistance determinants and phenotypic susceptibility results obtained using standardized methods remains insufficiently characterized. The present study aimed to assess the phenotypic and genotypic AMR profile concordance for Salmonella spp. isolates obtained from food-producing animals and retail meats under DANMAP monitoring from 2018 to 2023. A total of 967 isolates were tested by the broth microdilution phenotypic method, and 3,011 were sequenced by WGS, of which 769 had complete paired data. The sources included swine, poultry, cattle, pork, beef, and duck meat. Resistance and multidrug resistance were the highest in pigs and pork, including a significant increase in domestic isolates in 2023. In poultry, results were more heterogeneous, depending on origin and diversity of serovars. Although always imported, duck meat presented a distinct profile, standing out for its resistance to critically important antimicrobials (CIAs). Cattle and beef generally showed lower resistance levels. Genotypic analysis using ResFinder and AMRFinderPlus demonstrated high agreement, with discrepancies mostly associated with beta-lactamases and determinants of resistance to fluoroquinolones. The genotype-phenotype concordance was generally high, especially for tetracyclines and sulfonamides, but more moderate for beta-lactams and quinolones. Overall, the findings emphasize the importance of combining phenotypic and genotypic approaches in AMR surveillance, illustrating the potential of WGS along with a need for ongoing curation of databases and improvement in functional interpretation of resistance determinants
Descrição
Dissertação de Mestrado Integrado em Medicina Veterinária, área científica de Sanidade Animal
Palavras-chave
Salmonella spp. Resistência aos antimicrobianos Sequenciação genómica Multirresistência Animais de produção Salmonella spp. Antimicrobial resistance Genome sequencing Multidrug resistance Food-producing animals