宏基因组学方法揭示了非集约化水产养殖环境与人类之间抗生素抗性基因的迁移和共存。

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human.

机构信息

College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China.

The University of Hong Kong Shenzhen Institute of Research and Innovation, HKU SIRI, Shenzhen, Guangdong, 518057, China.

出版信息

Microbiome. 2024 Jun 14;12(1):107. doi: 10.1186/s40168-024-01824-x.

DOI:10.1186/s40168-024-01824-x

PMID:38877573

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11179227/

Abstract

BACKGROUND

Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health.

RESULTS

The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer.

CONCLUSIONS

The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.

摘要

背景

水产养殖是全球重要的食物来源。在集约化大规模养殖场中广泛使用抗生素导致了耐药性的产生。非集约化水产养殖是另一种有利于生态保护且与自然环境密切相关的水产养殖模式。然而，非集约化水产养殖中的耐药基因（Resistome）传播尚未得到很好的描述。此外，还需要进一步了解水产养殖耐药基因对人类健康的影响。在这里，采用宏基因组学方法来鉴定水产养殖耐药基因的可移动性，并评估其对人类健康的潜在风险。

结果

结果表明，抗生素耐药基因（ARGs）广泛存在于非集约化水产养殖系统中，其中多药耐药类型最为丰富，占 34%。非集约化水产养殖环境中的 ARGs 主要由微生物群落塑造，占 51%。根据网络分析，77 个属和 36 个移动遗传元件（MGEs）与 23 种 ARG 类型显著相关（p<0.05）。根据丰度排名，有 6 种 ARG 被定义为核心 ARGs（最丰富的前 3%，出现频率>80%），它们占据了鱼类肠道样本中 ARG 丰度的 40%。鉴定出 71 个携带 ARG 的连续基因序列（Contigs），其中 75%同时携带 MGEs。qacEdelta1 和 sul1 形成了稳定的组合，并在水产养殖环境和人类中同时被检测到。此外，还回收了 475 个高质量的宏基因组组装基因组（MAGs），其中 81 个 MAGs 携带 ARGs。MAGs 携带的 ARG 类型以多药和杆菌肽耐药基因最为丰富。值得注意的是，在水产养殖系统和人类肠道中都发现了携带 ARGs 和 MGEs 的 Fusobacterium_A（机会性人类病原体），这表明 ARG 转移的潜在风险。