基于测序的西班牙食品加工设施微生物组分析揭示了优势类群和抗生素抗性基因的环境特异性变异。

Adrián Alvarez-Molina, José F Cobo-Díaz, Elena A Alexa, Fiona Crispie, Miguel Prieto, Mercedes López, Paul D Cotter, Avelino Alvarez-Ordóñez
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引用次数: 0

摘要

近年来,高通量测序技术的进步为扩大食品加工设施中的环境监测活动开辟了可能性,为以无目标的方式表征食品和食品加工环境(FPE)的微生物组和耐药性提供了更多的机会,在食品安全管理系统中具有巨大的潜在优势。在这里,通过对每个设施的2个复合样本进行全宏基因组测序,评估了屠宰场(n=3)、乳制品(n=12)和肉类(n=10)加工厂的FPE的微生物组和耐药性,分别包括从食物接触表面采集的10个FPE拭子和从非食物接触表面获取的10个FPE样本。屠宰场的FPE具有更多样的微生物组和抗性组,而乳制品加工厂的FPE显示出最高的β-分散性,与更异质的微生物组及抗性组组成一致。主要细菌属取决于行业类型,假单胞菌和Psychrobacter在屠宰场和肉类行业的表面上高度占主导地位,而不同的乳酸菌在乳制品行业占主导地位。发现的最丰富的抗微生物耐药性基因(ARG)与氨基糖苷类、四环素类和季铵化合物(QAC)的耐药性有关。与氨基糖苷类和四环素类耐药性相关的ARGs在屠宰场比在食品加工厂更普遍,而QAC抗性基因在乳制品和肉类加工厂的一些食品接触表面特别丰富,这表明,在一些设施中,在次优条件下的日常卫生可能是对耐受这些杀生物剂的持久微生物群的选择。ARG的分类图谱表明,特定的细菌属,如大肠杆菌、芽孢杆菌或葡萄球菌,是最相关的抗性决定簇的携带者。大约63%的ARG读数被分配给被归类为质粒相关的重叠群,这表明FPE的抗性组可能通过移动遗传元件的传播而强烈形成。总的来说,FPE作为ARG库的相关性得到了证实,并证明了下一代测序技术能够深入表征食品工业环境中微生物和抗微生物耐药性决定因素的来源和传播途径,有望纳入监测和食品安全管理计划。
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Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes.

In the last years, advances in high throughput sequencing technologies have opened the possibility to broaden environmental monitoring activities in facilities processing food, offering expanded opportunities for characterizing in an untargeted manner the microbiome and resistome of foods and food processing environments (FPE) with huge potential benefits in food safety management systems. Here the microbiome and resistome of FPE from slaughterhouses (n = 3), dairy (n = 12) and meat (n = 10) processing plants were assessed through whole metagenome sequencing of 2 composite samples for each facility, comprising 10 FPE swabs taken from food contact surfaces and 10 FPE samples from non-food contact surfaces, respectively. FPE from slaughterhouses had more diverse microbiomes and resistomes, while FPE from dairy processing plants showed the highest β-dispersion, consistent with a more heterogeneous microbiome and resistome composition. The predominant bacterial genera depended on the industry type, with Pseudomonas and Psychrobacter being highly dominant in surfaces from slaughterhouses and meat industries, while different lactic acid bacteria predominated in dairy industries. The most abundant antimicrobial resistance genes (ARG) found were associated with resistance to aminoglycosides, tetracyclines and quaternary ammonium compounds (QAC). ARGs relating to resistance to aminoglycosides and tetracyclines were significantly more prevalent in slaughterhouses than in food processing plants, while QAC resistance genes were particularly abundant in some food contact surfaces from dairy and meat processing plants, suggesting that daily sanitation under suboptimal conditions may be selecting for persistent microbiota tolerant to these biocides in some facilities. The taxonomic mapping of ARG pointed to specific bacterial genera, such as Escherichia, Bacillus, or Staphylococcus, as carriers of the most relevant resistance determinants. About 63% of all ARG reads were assigned to contigs classified as plasmid-associated, indicating that the resistome of FPE may be strongly shaped through the spread of mobile genetic elements. Overall, the relevance of FPE as reservoirs of ARG was confirmed and it was demonstrated that next generation sequencing technologies allowing a deep characterisation of sources and routes of spread of microorganisms and antimicrobial resistance determinants in food industry settings hold promise to be integrated in monitoring and food safety management programmes.

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