摘要

       临床环境中抗生素耐药性 (AR) 的增加是现代全球最大的公共卫生问题之一，因此，由于其对治疗过程和患者存活率的影响，了解其机制、进化和全球分布是当务之急。除了在临床菌株中阐明 AR 机制的所有努力外，对其在环境不可培养微生物中的流行和进化知之甚少。在这项研究中，来自 TARA 海洋项目的 293 个宏基因组和 10 个宏转录组样本用于使用现代机器学习工具检测和量化环境抗生素抗性基因 (ARG)。经过大量的人工管理，我们展示了它们的全球分布、丰度、分类学和系统发育、它们被质粒或病毒水平转移的潜力以及它们与环境和地理参数的相关性。经过人工管理，我们总共确定了 99,205 个环境 ORF 作为潜在的 ARG。这些 ORF 属于 560 个 ARG 家族，它们赋予对 26 种抗生素类别的抗性。共有 149 个 ORF 被归类为病毒序列。此外，在归类为质粒序列的重叠群中发现了 24,567 个 ORF，表明移动遗传元件在 ARG 传播动力学中的重要性。从通过所有定量分析标准的 13,163 个鉴定出的 ARG 中，4,224 个在 10 个宏转录组样本中的至少一个中表达（FPKM > 5）。此外，还发现了 4,804 个具有超过 2 个 ARG 的重叠群，包括具有 5 个不同 ARG 的 2 个质粒，突出了自然环境和/或不受人类存在海洋影响的多重抗性微生物的潜在存在，以及水平基因的可能性临床和自然环境之间的转移 (HGT)。 293 个样本中 ARG 的丰度显示出不同的分布模式，其中一些类别在沿海生物群落中显着更丰富。最后，我们确定了对一些最相关的临床抗生素具有抗性的 ARG，揭示了来自最近发现的 MCR-1 家族的 15 个 ARG 在极地生物群落中的高丰度。 Psychrobacter 属中总共存在 5 个 MCR-1 ORF，Psychrobacter 是一种可导致人类致命感染的机会性细菌。我们的结果以 MySQL 数据库转储格式在 Zenodo 上可用，用于分析的所有代码，包括 jupyter notebooks 都可以在 github (https://github.com/rcuadrat/ocean_resistome) 上访问。

The rise of antibiotic resistance (AR) in clinical settings is one of the biggest modern global public health concerns, therefore, the understanding of its mechanisms, evolution and global distribution is a priority due to its impact on the treatment course and patient survivability. Besides all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental uncultivable microorganisms. In this study, 293 metagenomic and 10 metatranscriptomic samples from the TARA oceans project were used to detect and quantify environmental Antibiotic Resistance Genes (ARGs) using modern machine learning tools. After extensive manual curation, we show their global distribution, abundance, taxonomy and phylogeny, their potential to be horizontally transferred by plasmids or viruses and their correlation with environmental and geographical parameters. After manual curation, we identified a total of 99,205 environmental ORFs as potential ARGs. These ORFs belong to 560 ARG families that confer resistance to 26 antibiotic classes. A total of 149 ORFs were classified as viral sequences. In addition, 24,567 ORFs were found in contigs classified as plasmidial sequences, suggesting the importance of mobile genetic elements in the dynamics of ARGs transmission. From the 13,163 identified ARGs passing all the criteria for quantification analysis, 4,224 were expressed in at least one of the 10 metatranscriptomic samples (FPKM >5). Moreover, 4,804 contigs with more than 2 ARGs were found, including 2 plasmids with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in natural environment and/or non-impacted by human presence oceans, together with the possibility of Horizontal Gene Transfer (HGT) between clinical and natural environments. The abundance of ARGs in 293 samples showed different patterns of distribution, with some classes being significatively more abundant in Coastal Biomes. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs from the recently discovered MCR-1 family with high abundance on Polar Biomes. A total of 5 MCR-1 ORFs are present in the genus Psychrobacter, an opportunistic bacteria that can cause fatal infections in humans. Our results are available on Zenodo in MySQL database dump format and all the code used for the analyses, including jupyter notebooks can be accessed on github (https://github.com/rcuadrat/ocean_resistome).

https://www.biorxiv.org/content/10.1101/765446v1.abstract