Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
Doctoral School of Biology, University of Szeged, Szeged, Hungary.
Nat Microbiol. 2023 Mar;8(3):410-423. doi: 10.1038/s41564-023-01320-2. Epub 2023 Feb 9.
Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.
功能宏基因组学是一种强大的实验工具，可用于鉴定环境中的抗生素抗性基因（ARGs），但合适的宿主细菌种类有限。这种限制影响了鉴定出的 ARGs 的范围及其临床相关性的解释。在这里，我们提出了一种称为经重编程噬菌体颗粒辅助多物种功能宏基因组学（DEEPMINE）的功能宏基因组学方法。该方法结合并改进了 T7 噬菌体的使用，利用交换的尾部纤维和靶向诱变来扩大噬菌体的宿主特异性和功能宏基因组学的效率。这些经过修饰的噬菌体颗粒被用于将大型宏基因组质粒文库引入临床相关的细菌病原体中。通过针对 13 种抗生素筛选土壤和肠道微生物组以及临床基因组中的 ARGs，我们证明这种方法大大扩展了鉴定出的 ARGs 列表。许多 ARGs 对耐药性具有种特异性影响；它们在一种细菌物种中提供了高水平的耐药性，但在相关物种中产生的耐药性非常有限。最后，我们鉴定了针对目前处于临床开发或最近获得批准的抗生素的移动 ARGs。总的来说，DEEPMINE 扩展了用于研究微生物群落的功能宏基因组学工具包。
