Nageeb Wedad M, AlHarbi Nada, Alrehaili Amani A, Zakai Shadi A, Elfadadny Ahmed, Hetta Helal F
Department of Medical Microbiology and Immunology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.
Front Microbiol. 2023 Oct 6;14:1271733. doi: 10.3389/fmicb.2023.1271733. eCollection 2023.
Although carbapenemases are frequently reported in resistant clinical isolates, other chromosomally mediated elements of resistance that are considered essential are frequently underestimated. Having a wide substrate range, multidrug efflux pumps frequently underlie antibiotic treatment failure. Recognizing and exploiting variations in multidrug efflux pumps and penicillin-binding proteins (PBPs) is an essential approach in new antibiotic drug discovery and engineering to meet the growing challenge of multidrug-resistant Gram-negative bacteria.
A total of 980 whole genome sequences of were analyzed. Nucleotide sequences for the genes studied were queried against a custom database of FASTA sequences using the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) system. The correlation between different variants and carbapenem Minimum Inhibitory Concentrations (MICs) was studied. PROVEAN and I-Mutant predictor suites were used to predict the effect of the studied amino acid substitutions on protein function and protein stability. Both PsiPred and FUpred were used for domain and secondary structure prediction. Phylogenetic reconstruction was performed using SANS serif and then visualized using iTOL and Phandango.
Exhibiting the highest detection rate, codes for an important efflux-pump structural protein. T48V, T584I, and P660Q were important variants identified in the -predicted multidrug efflux transporter pore domains. These can act as probable targets for designing new efflux-pump inhibitors. Each of Q239L and D167N can also act as probable targets for restoring carbapenem susceptibility. Membrane proteins appear to have lower predictive potential than efflux pump-related changes. OprB and OprD changes show a greater effect than OmpA, OmpW, Omp33, and CarO changes on carbapenem susceptibility. Functional and statistical evidence make the variants T636A and S382N at PBP1a good markers for imipenem susceptibility and potential important drug targets that can modify imipenem resistance. In addition, PBP3_370, PBP1a_T636A, and PBP1a_S382N may act as potential drug targets that can be exploited to counteract imipenem resistance.
The study presents a comprehensive epidemiologic and statistical analysis of potential membrane proteins and efflux-pump variants related to carbapenem susceptibility in , shedding light on their clinical utility as diagnostic markers and treatment modification targets for more focused studies of candidate elements.
尽管碳青霉烯酶在耐药临床分离株中经常被报道，但其他被认为至关重要的染色体介导的耐药元件却常常被低估。多药外排泵具有广泛的底物范围，常常是抗生素治疗失败的原因。识别和利用多药外排泵及青霉素结合蛋白（PBPs）的变异是新抗生素药物研发和工程中的关键方法，以应对日益严峻的多重耐药革兰氏阴性菌挑战。
共分析了980个全基因组序列。使用细菌和病毒生物信息学资源中心（BV-BRC）系统，将所研究基因的核苷酸序列与一个定制的FASTA序列数据库进行比对。研究了不同变异与碳青霉烯最低抑菌浓度（MICs）之间的相关性。使用PROVEAN和I-Mutant预测工具来预测所研究的氨基酸替换对蛋白质功能和蛋白质稳定性的影响。PsiPred和FUpred都用于结构域和二级结构预测。使用SANS serif进行系统发育重建，然后使用iTOL和Phandango进行可视化。
编码一种重要的外排泵结构蛋白，检测率最高。T48V、T584I和P660Q是在预测的多药外排转运体孔结构域中鉴定出的重要变异。这些可作为设计新型外排泵抑制剂的潜在靶点。Q239L和D167N各自也可作为恢复碳青霉烯敏感性的潜在靶点。膜蛋白的预测潜力似乎低于与外排泵相关的变化。OprB和OprD的变化对碳青霉烯敏感性的影响大于OmpA、OmpW、Omp33和CarO的变化。功能和统计证据表明，PBP1a上的T636A和S382N变异是亚胺培南敏感性的良好标志物，也是可改变亚胺培南耐药性的潜在重要药物靶点。此外，PBP3_370、PBP1a_T636A和PBP1a_S382N可能作为潜在的药物靶点，可用于对抗亚胺培南耐药性。
本研究对与碳青霉烯敏感性相关的潜在膜蛋白和外排泵变异进行了全面的流行病学和统计分析，揭示了它们作为诊断标志物和治疗调整靶点的临床效用，以便对候选元件进行更有针对性的研究。
