Table_2_Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets (Oncorhynchus mykiss).XLSX

The rise of antibiotic resistance is not only a challenge for human and animal health treatments, but is also posing the risk of spreading among bacterial populations in foodstuffs. Farmed fish-related foodstuffs, the food of animal origin most consumed worldwide, are suspected to be a reservoir of antibiotic resistance genes and resistant bacterial hazards. However, scant research has been devoted to the possible sources of diversity in fresh fillet bacterial ecosystems (farm environment including rivers and practices, and factory environment). In this study bacterial communities and the antibiotic resistance genes of fresh rainbow trout fillet were described using amplicon sequencing of the V3-V4 region of the 16S rRNA gene and high-throughput qPCR assay. The antibiotic residues were quantified using liquid chromatography/mass spectrometry methods. A total of 56 fillets (composed of muscle and skin tissue) from fish raised on two farms on the same river were collected and processed under either factory or laboratory sterile filleting conditions. We observed a core-bacterial community profile on the fresh rainbow trout fillets, but the processing conditions of the fillets has a great influence on their mean bacterial load (3.38 ± 1.01 log CFU/g vs 2.29 ± 0.72 log CFU/g) and on the inter-individual diversity of the bacterial community. The bacterial communities were dominated by Gamma- and Alpha-proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The most prevalent genera were Pseudomonas, Escherichia-Shigella, Chryseobacterium, and Carnobacterium. Of the 73 antibiotic residues searched, only oxytetracycline residues were detected in 13/56 fillets, all below the European Union maximum residue limit (6.40–40.20 μg/kg). Of the 248 antibiotic resistance genes searched, 11 were found to be present in at least 20% of the fish population (tetracycline resistance genes tetM and tetV, β-lactam resistance genes blaDHA and blaACC, macrolide resistance gene mphA, vancomycin resistance genes vanTG and vanWG and multidrug-resistance genes mdtE, mexF, vgaB and msrA) at relatively low abundances calculated proportionally to the 16S rRNA gene.

抗生素耐药性的兴起不仅对人类和动物的健康治疗构成挑战，而且对食品中细菌群体的传播风险亦日益凸显。养殖鱼类相关的食品，作为全球消费量最大的动物源性食品，被怀疑是抗生素耐药基因和耐药细菌危害的储存库。然而，针对新鲜鱼片细菌生态系统（包括养殖环境如河流及养殖实践，以及工厂环境）多样性的潜在来源，研究投入甚微。本研究通过16S rRNA基因V3-V4区域的扩增子测序和高通量qPCR检测，对新鲜彩虹鲑鱼片中的细菌群落及其抗生素耐药基因进行了描述。采用液相色谱/质谱联用法对抗生素残留物进行了定量分析。共收集并处理了来自同一条河流上两个养殖场的56块鱼片（由肌肉和皮肤组织组成），在工厂或实验室无菌切片条件下进行处理。我们在新鲜彩虹鲑鱼片上观察到核心细菌群落特征，但鱼片的处理条件对其平均细菌负荷（3.38 ± 1.01 log CFU/g vs 2.29 ± 0.72 log CFU/g）以及细菌群落的个体间多样性产生了显著影响。细菌群落主要由伽马-和阿尔法-变形菌、拟杆菌门、厚壁菌门和放线菌门组成。最常见的属为铜绿假单胞菌、大肠杆菌-志贺菌、黄杆菌和肉毒杆菌。在搜索的73种抗生素残留物中，仅在13/56块鱼片中发现四环素残留，所有残留量均低于欧盟的最大残留限量（6.40–40.20 μg/kg）。在搜索的248种抗生素耐药基因中，有11种在至少20%的鱼群中发现（四环素耐药基因tetM和tetV、β-内酰胺耐药基因blaDHA和blaACC、大环内酯耐药基因mphA、万古霉素耐药基因vanTG和vanWG以及多重耐药基因mdtE、mexF、vgaB和msrA），其丰度相对较低，按16S rRNA基因的比例计算。