Identification of antimicrobial reagents against TB and ESKAPE pathogens from bacteria collected in Vietnam

抗生素的发现几十年来一直是天然产物(NP)研究的目标。成为世界上 细菌是对抗细菌感染的天然对手，事实证明，细菌本身是很好的抗生素生产者。 然而，由于广泛的探索，从细菌中发现NP一直受到冗余的瓶颈。至 克服了这一点，新的方法被发现，包括多样化的采样，培养条件筛选， 创新的代谢组检测技术以及利用基因组挖掘寻找新的生物活性 NPS。然而，建立细菌文库的方式并没有太大的变化，这需要花费大量的人力和财力 所需流程，直接影响下游NP调查。在本研究中，我们将采用工作流 对于优先使用IDBac管道的细菌菌株，然后是两种互补的方法(1)改进 传统的生物活性导向的NP分离和(2)基于基因组学的研究以鉴定抗菌剂 针对结核病和ESKAPE病原体，世界各地，特别是越南的抗生素耐药性线索。 通过分析基质辅助激光解吸电离质谱仪(MALDI-MS)指纹图谱 生物信息学工具IDBac，我们可以从水生和洞穴中产生最小重叠的细菌集 环境作为NP发现的输入材料。在我们创新的双面琼脂平板(DAPA)试验的指导下， 似乎对结核病和ESKAPE病原体有抑制作用的菌株随后将接受传统分离 用于识别活动组件的流程。此外，基因组挖掘和Fosid文库生成将提供 一种替代的、但又互补的方法，用于阐明有希望的生物合成基因簇和编码的 针对结核病和ESKAPE病原体的抗生素(以及药物靶标)。

Antibiotics discovery has been the target of natural product (NP) investigation for decades. Being one of the natural rivals against bacterial infection, bacteria themselves have shown to be good antibiotic producers. However, due to extensive exploration, NP discovery from bacteria has been bottlenecked by redundancy. To overcome this, new approaches have been discovered including diverse sampling, culture condition screening, innovative metabolomic detection techniques as well as the usage of genome mining to seek for new bioactive NPs. However, there hasn’t much changed in the way of establishing bacterial library, a costly and manpower required process, which directly affects downstream NP investigation. In this study, we will employ a workflow for prioritizing bacteria strains using the IDBac pipeline followed by two complementary approaches (1) improved traditional bioactivity-guided NP isolation and (2) genomics-based studies to identify antimicrobial reagents against TB and ESKAPE pathogens, antibiotic resistance threads worldwide and in Vietnam in particular. Through analyzing matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) fingerprints using the bioinformatic tool IDBac, we can generate a minimum overlap set of bacteria from aquatic and cave environments as input materials for NP discovery. Guided by our innovative dual-sided agar plate (DAPA) assay, strains which appear to inhibit TB and ESKAPE pathogens will be subsequently submitted to traditional isolation processes to identify the active components. Moreover, genome mining and fosmid library generation will offer an alternative, yet complement, approach for elucidating promising biosynthetic gene clusters and the encoded antibiotics (as well as the drug targets) for TB and ESKAPE pathogens.