Abstract：
Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including blaTEM-1B, blaFOX-18, aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.
摘要：
水产养殖环境可以通过周围环境成为抗性基因的热点。我们的目标是研究耐药组，分离的革兰氏阴性菌的病毒组和动员体，使用WGS方法。66株革兰氏阴性菌株(Aeromonadaceae，肠杆菌科,哈夫尼科,莫甘草科，假竹科,Shewanellaceae,弧菌科，和Yersiniaceae家族）被选择用于基因组表征。确定了物种和MLST，和抗生素/消毒剂/重金属抗性基因，毒力决定因素，MGE,和对人类的致病性进行了研究。我们的研究揭示了新的序列类型（例如，气单胞菌属。ST879、ST880、ST881、ST882、ST883、ST887、ST888；希瓦氏菌属。ST40,ST57,ST58,ST60,ST61,ST62;弧菌属。ST206、ST205)。>140个不同的基因被鉴定在海牛和双壳软体动物的抗性组，包括与β-内酰胺相关的基因，四环素,氨基糖苷类,喹诺酮类药物,磺胺类药物,甲氧苄啶,酚类化合物,大环内酯类和磷霉素抗性。消毒剂抗性基因qacE型，发现了sitABCD型和FormA型。重金属抗性基因MDT,acr和sil是最常见的。大多数抗性基因与水产养殖环境中常用的抗生素/消毒剂/重金属相关。我们还鉴定了25个与毒力增加相关的不同基因，即与坚持有关，殖民,毒素生产，红细胞裂解，铁代谢，逃离宿主的免疫系统。此外，74.2%的分析菌株被认为对人类有致病性。我们调查了几种抗生素抗性基因的遗传环境，包括blaTEM-1B,blaFOX-18,aph(3″)-Ib,dfrA型,aadA1,catA1-type,tet(A)/(E),qnrB19和sul1/2。我们的分析还集中在识别这些基因（例如IntI1，质粒和TnAs）附近的MGE，这可能会促进细菌在不同环境中的耐药性传播。这项研究全面考察了可以转移到人类和环境中的抗性基因的多样性，认识到水产养殖和更广泛的环境在这个复杂的传输网络中起着重要的中介作用。
