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Enterobacterales from the pork production chain in Portugal are key reservoirs of antibiotic resistance and virulence genes
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Enterobacterales representam muitas vezes uma ameaça à saúde pública devido à sua capacidade de adquirir e disseminar genes de resistência a antibióticos. Enterobacterales resistentes aos carbapenemos (CRE) são importantes causadores de infeções em Portugal e no mundo. Os animais utilizados para a produção de alimentos têm sido descritos como reservatórios de CRE e de determinantes de resistência aos antibióticos. No entanto, a extensão de disseminação de CRE e seus genes de resistência, entre a cadeia de produção de alimentos e o hospital, têm sido pouco explorados. Este estudo pretende compreender se a cadeia de produção de suínos constitui um reservatório de genes de resistência a antibióticos, bem como de Enterobacterales resistentes a antibióticos e clinicamente relevantes.
Para este estudo foram recolhidos isolados pertencentes à Ordem Enterobacterales num matadouro em Portugal, em 2019. Estes isolados foram caracterizados quanto ao seu perfil de suscetibilidade a antibióticos; e isolados representativos foram caracterizados através da sequenciação total do genoma. O seu conteúdo genómico foi determinado através da análise dos dados de sequenciação, utilizando ferramentas bioinformáticas. A identificação do género/espécie foi confirmada pela sequenciação do gene 16S rRNA e pelo método Average Nucleotide Identity (ANI). Os tipos clonais foram identificados pelo método de multilocus sequence typing (MLST) in silico.
Foi identificado uma grande variedade de Enterobacterales, sendo que 79,5% foram consideradas multirresistentes. Além disso, 45% apresentaram resistência à colistina (MIC> 8 mg/L). A análise genómica mostrou que a maioria dos Enterobacterales apresentava uma diversidade de β-lactamases da classe C, classe A e classe B, tendo sido algumas delas encontradas em CRE causadoras de infeções em humanos. Dos 10 isolados resistentes à colistina que foram sequenciados, três continham o gene mcr-10. Foram também descritos 264 fatores de virulência relacionados com motilidade (41,7%), quimiotaxia (3,8%), sistema de secreção (22,3%), aquisição de ferro (10,6%), cápsula (9,8%), toxinas (7,5%), bombas de efluxo (2,75%) e
porinas (1,1%). Também identificamos dois isolados que pertencem a tipos clonais previamente associados a infeções em humanos (Escherichia coli ST410 e Klebsiella pneumoniae ST60).
No geral, os nossos resultados sugerem que Enterobacterales existentes na cadeia de produção de suínos constituem um reservatório de genes de resistência a antibióticos e de bactérias patogénicas para os humanos.
Enterobacterales are a major public health threat due to their capacity to spread antibiotic resistance genes. Carbapenem resistant Enterobacterales (CRE) are important causes of infections in Portugal and worldwide. Food production animals have been described as reservoirs of CRE and resistance determinants. However, the extent of dissemination of CRE and their resistance genes between food production chain and hospitals is limited explored. We aimed to understand if the pork production chain in Portugal was a reservoir of clinically relevant antibiotic resistance genes and resistant Enterobacterales. Enterobacterales collected from a slaughterhouse in Portugal, in 2019 were characterized for their antibiotic susceptibility profile by disk diffusion and microdilution and the whole genome of a representative collection of isolates was sequenced. Moreover, their content in antimicrobial resistance and virulence genes was determined by analysis of whole-genome sequencing data using bioinformatics tools. Enterobacterales genus/species were identified by 16S rRNA gene sequencing and confirmed by determining the average nucleotide identity (ANI). Clonal types were identified by in silico multilocus sequence typing. We identified a wide variety of Enterobacterales, 79.5% of which were multidrug-resistant. Moreover, 45% showed resistance to colistin (MIC>8 mg/L). Genomic analysis showed that the great majority of Enterobacterales (74%) carried a diversity of class C β-lactamases, class A and class B - some previously associated to CRE causing infections in humans. Out of the 10 colistin- resistant isolates that were sequenced, three carried the mcr-10 gene. A total of 264 different virulence factors were identified related to motility (41.7%), chemotaxis (3.8%), secretion system (22.3%), iron acquisition (10.6%), capsule (9.8%), toxins (7.5%), efflux pumps (2.75%) and porins (1.1%). Two isolates belonged to clonal types previously found causing infections in humans (Escherichia coli ST410 and Klebsiella pneumoniae ST60). Our results suggest that Enterobacterales from the pig meat production chain constitute a reservoir of antibiotic resistance genes and resistant bacteria pathogenic to humans.
Enterobacterales are a major public health threat due to their capacity to spread antibiotic resistance genes. Carbapenem resistant Enterobacterales (CRE) are important causes of infections in Portugal and worldwide. Food production animals have been described as reservoirs of CRE and resistance determinants. However, the extent of dissemination of CRE and their resistance genes between food production chain and hospitals is limited explored. We aimed to understand if the pork production chain in Portugal was a reservoir of clinically relevant antibiotic resistance genes and resistant Enterobacterales. Enterobacterales collected from a slaughterhouse in Portugal, in 2019 were characterized for their antibiotic susceptibility profile by disk diffusion and microdilution and the whole genome of a representative collection of isolates was sequenced. Moreover, their content in antimicrobial resistance and virulence genes was determined by analysis of whole-genome sequencing data using bioinformatics tools. Enterobacterales genus/species were identified by 16S rRNA gene sequencing and confirmed by determining the average nucleotide identity (ANI). Clonal types were identified by in silico multilocus sequence typing. We identified a wide variety of Enterobacterales, 79.5% of which were multidrug-resistant. Moreover, 45% showed resistance to colistin (MIC>8 mg/L). Genomic analysis showed that the great majority of Enterobacterales (74%) carried a diversity of class C β-lactamases, class A and class B - some previously associated to CRE causing infections in humans. Out of the 10 colistin- resistant isolates that were sequenced, three carried the mcr-10 gene. A total of 264 different virulence factors were identified related to motility (41.7%), chemotaxis (3.8%), secretion system (22.3%), iron acquisition (10.6%), capsule (9.8%), toxins (7.5%), efflux pumps (2.75%) and porins (1.1%). Two isolates belonged to clonal types previously found causing infections in humans (Escherichia coli ST410 and Klebsiella pneumoniae ST60). Our results suggest that Enterobacterales from the pig meat production chain constitute a reservoir of antibiotic resistance genes and resistant bacteria pathogenic to humans.
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Palavras-chave
Enterobacterales Carbapenem-resistance Pig production chain Colistin