Abstract：
Hundreds of tons of antibiotics are widely used in aquaculture to prevent microbial infections and promote fish growth. However, the overuse of antibiotics and chemical products can lead to the selection and spreading of antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), which are of great concern considering the threat to public health worldwide. Here, in-depth metagenome sequencing was performed to explore the environmental resistome and ARB distribution across farming stages in shrimp farms and examine anthropogenic effects in nearby coastal waters. A genome-centric analysis using a metagenome binning approach allowed us to accurately investigate the distribution of pathogens and ARG hosts in shrimp farms. The diversity of resistomes was higher in shrimp farms than in coastal waters, and the distribution of resistomes was dependent on the farming stage. In particular, the tetracycline resistance gene was found mainly at the early post-larval stage regardless of the farm. The metagenome-assembled genomes of Vibrio spp. were dominant at this stage and harbored tet34, which is known to confer resistance to oxytetracycline. In addition, opportunistic pathogens such as Francisella, Mycoplasma, Photobacterium, and Vibrio were found in abundance in shrimp farms, which had multiple virulence factors. This study highlights the increased resistance diversity and environmental selection of pathogens in shrimp farms. The use of environmental pollutants on farms may cause an increase in resistome diversity/abundance and the transmission of pathogens to the surrounding environment, which may pose future risks to public health and aquatic organisms.
摘要：
数百吨抗生素广泛用于水产养殖，以防止微生物感染并促进鱼类生长。然而,抗生素和化学产品的过度使用可能导致抗生素抗性细菌（ARB）和抗微生物药物抗性基因（ARGs）的选择和传播，考虑到对全球公共卫生的威胁，这是非常令人担忧的。这里,进行了深入的宏基因组测序，以探索对虾养殖场养殖阶段的环境抗性和ARB分布，并检查附近沿海水域的人为影响。使用宏基因组分类方法进行的以基因组为中心的分析使我们能够准确地调查对虾养殖场中病原体和ARG宿主的分布。对虾养殖场的抗性体多样性高于沿海水域，抗性体的分布取决于耕作阶段。特别是,无论在哪个农场，四环素抗性基因主要在幼虫后早期发现。弧菌的宏基因组组装基因组。在此阶段占主导地位，并带有tet34，已知tet34赋予土霉素抗性。此外,机会性病原体，如Francisella，支原体,光细菌,在虾养殖场发现了大量的弧菌，具有多种毒力因子。这项研究强调了对虾养殖场中病原体的抗性多样性和环境选择的增加。在农场使用环境污染物可能会导致耐药性多样性/丰度的增加以及病原体向周围环境的传播，这可能会对公共健康和水生生物构成未来的风险。
