摘要
      细胞外和细胞内抗生素抗性基因（eARGs和iARGs）共同构成了环境中的整个抗性组。然而，对eARGs和iARGs的系统分析仍然不足。分析了牲畜粪便、污水污泥和湖泊沉积物三种环境，揭示了eARGs和iARGs的综合特征。根据宏基因组数据，eARGs和iARGs的多样性、相对丰度和组成相似。细胞外和细胞内整合素和插入序列（IS）也没有显示出任何显著差异。然而，整合子/IS和ARGs的总相对丰度之间的相关性程度和显著性在细胞外低于在细胞内。在粪便和污泥样本中扩增了1类整合子携带的基因盒，测序结果表明，细胞外和细胞内鉴定的ARGs是不同的。通过分析遗传背景，发现大多数ARG位于染色体上。然而，质粒携带的ARGs的比例在细胞外增加。qPCR用于量化sul1、sul2、tetO和tetW的绝对丰度，并且在污泥样品中发现它们的细胞外比例最高。这些发现共同提出了在风险评估和移除管理方面分别考虑eARG和iARG的要求。
Abstract
The extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) together constitute the entire resistome in environments. However, the systematic analysis of eARGs and iARGs was still inadequate. Three kinds of environments, i.e., livestock manure, sewage sludge, and lake sediment, were analyzed to reveal the comprehensive characteristics of eARGs and iARGs. Based on the metagenomic data, the diversities, relative abundances, and compositions of eARGs and iARGs were similar. The extracellular and intracellular integrons and insertion sequences (ISs) also did not show any significant differences. However, the degree and significance of the correlation between total relative abundances of integrons/ISs and ARGs were lower outside than inside the cells. Gene cassettes carried by class 1 integron were amplified in manure and sludge samples, and sequencing results showed that the identified ARGs extracellularly and intracellularly were distinct. By analyzing the genetic contexts, most ARGs were found located on chromosomes. Nevertheless, the proportion of ARGs carried by plasmids increased extracellularly. qPCR was employed to quantify the absolute abundances of sul1, sul2, tetO, and tetW, and their extracellular proportions were found highest in sludge samples. These findings together raised the requirements of considering eARGs and iARGs separately in terms of risk evaluation and removal management.

https://www.sciencedirect.com/science/article/abs/pii/S0304389422000632