Departamento de Producción Animal Y Ciencia de Los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Departamento de Producción Animal Y Ciencia de Los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain.
Food Res Int. 2024 Oct;193:114842. doi: 10.1016/j.foodres.2024.114842. Epub 2024 Jul 31.
Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted monitoring. This study assessed the microbiome and resistome in a poultry burger processing line using culturing techniques and whole metagenomic sequencing (WMS). Samples included meat, burgers, and expired burgers, and different work surfaces. Microbiome analysis revealed spoilage microorganisms as the main microbiota, with substantial shifts observed during the shelf-life period. Core microbiota of meat and burgers included Pseudomonas spp., Psychrobacter spp., Shewanella spp. and Brochothrix spp., while expired burgers were dominated by Latilactobacillus spp. and Leuconostoc spp. Cleaning and disinfection (C&D) procedures altered the microbial composition of work surfaces, which still harbored Hafnia spp. and Acinetobacter spp. after C&D. Resistome analysis showed a low overall abundance of resistance genes, suggesting that effective interventions during processing may mitigate their transmission. However, biocide resistance genes were frequently found, indicating potential biofilm formation or inefficient C&D protocols. This study demonstrates the utility of combining culturing techniques and WMS for comprehensive of the microbiome and resistome characterization in food processing lines.
传统上，食品产品和食品加工环境的监测计划主要集中在目标病原体和耐药基因上。高通量测序的最新进展允许更全面和非靶向的监测。本研究使用培养技术和全宏基因组测序（WMS）评估了家禽汉堡加工线的微生物组和耐药组。样本包括肉、汉堡和过期汉堡以及不同的工作表面。微生物组分析显示，腐败微生物是主要的微生物群，在保质期内观察到明显的变化。肉和汉堡的核心微生物群包括假单胞菌属、嗜冷杆菌属、希瓦氏菌属和布鲁氏菌属，而过期汉堡则主要由乳酸杆菌属和肠球菌属。清洗和消毒（C&D）程序改变了工作表面的微生物组成，即使在 C&D 之后，工作表面仍含有哈夫尼亚菌属和不动杆菌属。耐药组分析显示，耐药基因的总体丰度较低，这表明在加工过程中进行有效的干预可能会减轻它们的传播。然而，经常发现杀生物剂耐药基因，表明可能形成生物膜或 C&D 方案效率低下。本研究表明，结合培养技术和 WMS 对食品加工线的微生物组和耐药组进行全面分析是有用的。
