Differential analysis of whole genome sequencing (WGS) of Staphylococcus aureus 25923 in presence and absence of PPEF

PPEF is a known antibacterial agent that acts as a type IA topoisomerase inhibitor. We have observed PPEF as a potent molecule which could inhibit the growth of different bacteria irrespective of the nature of their cell wall. The efficacy of antimicrobial activity of PPEF against methicillin-sensitive S. aureus (MSSA), MRSA, and vancomycin-resistant S. aureus (VRSA) is reflected by its low MIC and MBC. The S. aureus strain ATCC 25923 has been evolved in a dose-dependent manner against PPEF. Over 440 generations, its MIC90 increased to 16-fold denoted as Staphylococcus aureus PPEF Resistance (SA-PR). Whole genome analysis was performed for SA-PR in comparison with SA-GC (Staphylococcus aureus Growth Control). S. aureus ATCC 25923 (MSSA), a closely related non-pathogenic species, were pivotal in the identification of protein-coding genes essential for PPEF resistance. However, no comprehensive comparison has focused on the non-coding genome. The SA-PR became sensitive to commercial antibiotics. Overall, this study provides insights into the existence of diverse evolutionary pathways of S. aureus for tolerance and resistance development against PPEF. PPEF synthesis and its bactericidal effects are published in JMC (Synthesis and biological evaluation of novel bisbenzimidazoles as Escherichia coli topoisomerase IA inhibitors and potential antibacterial agents. Nimesh H, Sur S, Sinha D, Yadav P, Anand P, Bajaj P, Virdi JS, Tandon V.J Med Chem. 2014 Jun 26;57:5238-57.), Scientific Reports (Synergistic efficacy of Bisbenzimidazole and Carbonyl Cyanide 3-Chlorophenylhydrazone combination against MDR bacterial strains. Sinha D, Pandey S, Singh R, Tiwari V, Sad K, Tandon V. Sci Rep. 2017 Mar 17;7:44419.) and Communication Biology (Unraveling topoisomerase IA gate dynamics in presence of PPEF and its preclinical evaluation against multidrug-resistant pathogens. Maurya V, Singh R, Singh RK, Pandey S, Yadav P, Parashar P, Gaind R, Dubey KD, Naresh Patwari G, Tandon V., 2023 Feb 18;6(1):195.) by our group.

PPEF是一种已知抗菌剂，可作为IA型拓扑异构酶（type IA topoisomerase）抑制剂。本团队观察到，PPEF是一种强效抗菌分子，可抑制不同细菌的生长，且不受细菌细胞壁类型的影响。PPEF对甲氧西林敏感金黄色葡萄球菌（methicillin-sensitive S. aureus，简称MSSA）、耐甲氧西林金黄色葡萄球菌（methicillin-resistant Staphylococcus aureus，简称MRSA）及耐万古霉素金黄色葡萄球菌（vancomycin-resistant S. aureus，简称VRSA）的抗菌活性效力，可通过其较低的最低抑菌浓度（minimum inhibitory concentration，简称MIC）与最低杀菌浓度（minimum bactericidal concentration，简称MBC）得以体现。
金黄色葡萄球菌菌株ATCC 25923已通过剂量依赖式传代筛选，进化出对PPEF的耐药性。经过440余代的传代培养，其90%菌株的最低抑菌浓度（MIC90）升至初始水平的16倍，该耐药菌株被命名为PPEF耐药金黄色葡萄球菌（Staphylococcus aureus PPEF Resistance，简称SA-PR）。
我们以SA-GC（金黄色葡萄球菌生长对照组，Staphylococcus aureus Growth Control）为对照，对SA-PR开展了全基因组分析。作为亲缘关系相近的非致病性菌株，金黄色葡萄球菌ATCC 25923（MSSA）在鉴定PPEF耐药相关的必需蛋白编码基因方面发挥了关键作用。但目前尚无针对其非编码基因组的全面比较研究。
SA-PR菌株对商用抗生素重新恢复了敏感性。综上，本研究为解析金黄色葡萄球菌针对PPEF产生耐受性与耐药性的多样化进化路径提供了新的研究视角。
本团队已将PPEF的合成及其杀菌活性相关研究成果发表于以下期刊：
1. 《新型双苯并咪唑类化合物作为大肠杆菌（Escherichia coli）IA型拓扑异构酶抑制剂及潜在抗菌剂的合成与生物学评价》，作者：Nimesh H、Sur S、Sinha D、Yadav P、Anand P、Bajaj P、Virdi JS、Tandon V，发表于《药物化学杂志》（Journal of Medicinal Chemistry，简称JMC），2014年6月26日，第57卷：5238-57；
2. 《双苯并咪唑与羰基氰化物间氯苯腙联用对多重耐药（multidrug-resistant，简称MDR）菌株的协同抗菌效力》，作者：Sinha D、Pandey S、Singh R、Tiwari V、Sad K、Tandon V，发表于《科学报告》（Scientific Reports），2017年3月17日，第7卷：44419；
3. 《解析PPEF存在下的IA型拓扑异构酶闸门动力学及其针对多重耐药病原体的临床前评价》，作者：Maurya V、Singh R、Singh RK、Pandey S、Yadav P、Parashar P、Gaind R、Dubey KD、Naresh Patwari G、Tandon V，发表于《通讯生物学》（Communication Biology），2023年2月18日，第6卷第1期：195。