生物合成基因簇（BGCs）是存在于各种生物体内用于产生特异代谢物（SMs）的一组连续基因的子集。这些SMs正成为生产多种药物，包括抗菌和抗癌剂的基石。天然产物（NPs）在增强ESKAPE病原体（Enterococcus faecium、Staphylococcus aureus、Klebsiella pneumoniae、Acinetobacter baumannii、Pseudomonas aeruginosa和Enterobacter spp.）的毒力方面也起着关键作用，这些病原体代表了全球的健康威胁。我们的目标是对属于埃及临床环境中的三个不同ESKAPE致病物种的66株菌株进行BGCs的测序和计算分析：21株A. baumannii、28株K. pneumoniae和17株P. aeruginosa菌株。使用QIAamp DNA Mini试剂盒提取DNA，并使用Illumina NextSeq 550进行全基因组测序。序列经fastp质量过滤，用Unicycler进行组装。使用antiSMASH、BAGEL、GECCO和PRISM检测BGCs，并使用Clinker进行比对。在P. aeruginosa中检测到最高数量的BGCs（590个），其次是K. pneumoniae（146个），A. baumannii菌株数量最少（133个）。P. aeruginosa分离株主要共享非核糖体肽合成酶（NRPS）类型，K. pneumoniae分离株主要共享核糖体合成和翻译后修饰的肽类（RiPP-like）类型，而A. baumannii分离株主要共享铁载体类型。大多数分离株携带非核糖体肽（NRP）BGCs，少数K. pneumoniae分离株编码多酮类BGCs。Sactipeptides和bottromycin BGCs是最常检测到的RiPP簇。我们假设每个物种的BGC特征赋予其毒力。未来的实验将把已检测到的簇与其物种联系起来，并确定编码的SMs是否会产生并导致其毒力。重要性：我们的研究分析了来自Acinetobacter baumannii、Klebsiella pneumoniae和Pseudomonas aeruginosa菌株的66个ESKAPE病原体分离物组装中存在的生物合成基因簇（BGCs）。我们报告了它们的测序和组装，然后使用多种生物信息学工具对其BGCs进行了分析。然后，我们重点讨论了每个物种中最丰富的BGC类型，并讨论了它们在每个物种毒力中的潜在作用。这项研究对于进一步建立其在毒力、可能的抗菌效果以及编码的特异代谢物（SMs）的表征方面的实验工作至关重要。该研究强调了研究“有害”BGCs的重要性，以及理解这些物种的致病性和毒力的重要性，以及如果SMs被用作抗菌剂可能带来的好处。这可能是埃及的首项类似研究，将为了解来自埃及的ESKAPE病原体的BGCs提供光明。

Biosynthetic gene clusters (BGCs) are a subset of consecutive genes present within a variety of organisms to produce specialized metabolites (SMs). These SMs are becoming a cornerstone to produce multiple medications including antibacterial and anticancer agents. Natural products (NPs) also play a pivotal role in enhancing the virulence of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which represent a global health threat. We aimed to sequence and computationally analyze the BGCs present in 66 strains pertaining to three different ESKAPE pathogenic species: 21 A. baumannii, 28 K. pneumoniae, and 17 P. aeruginosa strains recovered from clinical settings in Egypt. DNA was extracted using QIAamp DNA Mini kit and Illumina NextSeq 550 was used for whole-genome sequencing. The sequences were quality-filtered by fastp and assembled by Unicycler. BGCs were detected by antiSMASH, BAGEL, GECCO, and PRISM, and aligned using Clinker. The highest abundance of BGCs was detected in P. aeruginosa (590), then K. pneumoniae (146) and the least in A. baumannii strains (133). P. aeruginosa isolates shared mostly the non-ribosomal peptide synthase (NRPS) type, K. pneumoniae isolates shared the ribosomally synthesized and post-translationally modified peptide-like (RiPP-like) type, while A. baumannii isolates shared the siderophore type. Most of the isolates harbored non-ribosomal peptide (NRP) BGCs with few K. pneumoniae isolates encoding polyketide BGCs. Sactipeptides and bottromycin BGCs were the most frequently detected RiPP clusters. We hypothesize that each species' BGC signature confers its virulence. Future experiments will link the detected clusters with their species and determine whether the encoded SMs are produced and cause their virulence. IMPORTANCE Our study analyzes the biosynthetic gene clusters (BGCs) present in 66 assemblies from clinical ESKAPE pathogen isolates pertaining to Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa strains. We report their sequencing and assembly followed by the analysis of their BGCs using several bioinformatics tools. We then focused on the most abundant BGC type in each species and we discussed their potential roles in the virulence of each species. This study is pivotal to further build on its experimental work that deciphers the role in virulence, possible antibacterial effects, and characterization of the encoded specialized metabolites (SMs). The study highlights the importance of studying the "harmful" BGCs and understanding the pathogenicity and virulence of those species, as well as possible benefits if the SMs were used as antibacterial agents. This could be the first study of its kind from Egypt and would shed light on BGCs from ESKAPE pathogens from Egypt.