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 bla_DHA and bla_ACC, 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.

抗生素抗性的提高不仅是对人类和动物健康治疗的挑战，而且还构成了在食品中细菌种群中传播的风险。养殖鱼类相关食品，是全世界范围内最消耗的动物源性食品，被怀疑是抗生素抗性基因和抗性细菌危害的储藏库。但是，鲜有研究致力于新鲜鱼片细菌生态系统（包括河流和耕作的农业环境以及工厂环境）中可能的多样性来源。在这项研究中，使用16S rRNA基因的V3-V4区域的扩增子测序和高通量qPCR分析描述了新鲜虹鳟鱼片的细菌群落和抗生素抗性基因。使用液相色谱/质谱法定量抗生素残留。在工厂或实验室无菌鱼片加工条件下，收集并加工了来自在同一条河上两个农场养殖的鱼的56个鱼片（由肌肉和皮肤组织组成）。我们在新鲜的虹鳟鱼片上观察到核心细菌群落特征，但是鱼片的加工条件对其平均细菌载量有很大影响（3.38±1.01 log CFU / g vs 2.29±0.72 log CFU / g）和细菌群落的个体间多样性。细菌群落主要由γ-和α-变形杆菌，拟杆菌，Firmicutes和放线杆菌组成。最普遍的属是 在工厂或实验室无菌鱼片加工条件下，收集并加工了来自在同一条河上两个农场养殖的鱼的56个鱼片（由肌肉和皮肤组织组成）。我们在新鲜的虹鳟鱼片上观察到核心细菌群落特征，但是鱼片的加工条件对其平均细菌载量有很大影响（3.38±1.01 log CFU / g vs 2.29±0.72 log CFU / g）和细菌群落的个体间多样性。细菌群落主要由γ-和α-变形杆菌，拟杆菌，Firmicutes和放线杆菌组成。最普遍的属是 在工厂或实验室无菌鱼片加工条件下，收集并加工了来自在同一条河上两个农场养殖的鱼的56个鱼片（由肌肉和皮肤组织组成）。我们在新鲜的虹鳟鱼片上观察到核心细菌群落特征，但是鱼片的加工条件对其平均细菌载量有很大影响（3.38±1.01 log CFU / g vs 2.29±0.72 log CFU / g）和细菌群落的个体间多样性。细菌群落主要由γ-和α-变形杆菌，拟杆菌，Firmicutes和放线杆菌组成。最普遍的属是 但是鱼片的加工条件对其平均细菌载量（3.38±1.01 log CFU / g与2.29±0.72 log CFU / g）和细菌群落的个体多样性有很大影响。细菌群落主要由γ-和α-变形杆菌，拟杆菌，Firmicutes和放线杆菌组成。最普遍的属是 但是鱼片的加工条件对其平均细菌载量（3.38±1.01 log CFU / g与2.29±0.72 log CFU / g）和细菌群落的个体多样性有很大影响。细菌群落主要由γ-和α-变形杆菌，拟杆菌，Firmicutes和放线杆菌组成。最普遍的属是假单胞菌， 埃希氏菌属--志贺氏菌， 金细菌和 食肉杆菌。在搜索的73种抗生素残留中，仅在13/56个鱼片中检出了土霉素残留，均低于欧盟最大残留限量（6.40–40.20μg/ kg）。在搜索的248种抗生素抗性基因中，发现至少有20％的鱼类种群中存在11种（四环素抗性基因泰特 和 电视，β-内酰胺抗性基因 bla_DHA和bla_ACC，大环内酯抗性基因每小时，万古霉素耐药基因 VanTG 和 vanWG 和多药耐药基因 mdtE， 墨西哥， vgaB 和 密码）以相对较低的丰度与16S rRNA基因成比例计算。