Renz2021 - Collection of 13 SBML L3V1 constraint-based models (FBC Version 2) of Staphylococcus aureus

Staphylococcus aureus is a high-priority pathogen causing severe infections with high morbidity and mortality worldwide. Many S. aureus strains are methicillin-resistant (MRSA) or even multi-drug resistant. It is one of the most successful and prominent modern pathogens. An effective fight against S. aureus infections requires novel targets for antimicrobial and antistaphylococcal therapies. Recent advances in whole-genome sequencing and high-throughput techniques facilitate the generation of genome-scale metabolic models (GEMs). Among the multiple applications of GEMs is drug-targeting in pathogens. Hence, comprehensive and predictive metabolic reconstructions of S. aureus could facilitate the identification of novel targets for antimicrobial therapies. This review aims at giving an overview of all available GEMs of multiple S. aureus strains. We downloaded all 114 available GEMs of S. aureus for further analysis. The scope of each model was evaluated, including the number of reactions, metabolites, and genes. Furthermore, all models were quality-controlled using Mᴇᴍᴏᴛᴇ, an open-source application with standardized metabolic tests. Growth capabilities and model similarities were examined. This review should lead as a guide for choosing the appropriate GEM for a given research question. With the information about the availability, the format, and the strengths and potentials of each model, one can either choose an existing model or combine several models to create models with even higher predictive values. This facilitates model-driven discoveries of novel antimicrobial targets to fight multi-drug resistant S. aureus strains.

金黄色葡萄球菌（Staphylococcus aureus）是全球范围内引发重症感染、具有高发病率与高死亡率的优先防控病原体。诸多金黄色葡萄球菌菌株为耐甲氧西林（MRSA）甚至多药耐药菌株，它亦是目前最成功且备受关注的现代病原体之一。有效对抗金黄色葡萄球菌感染，亟需开发抗菌与抗葡萄球菌治疗的新型靶点。全基因组测序与高通量技术的近期进展，推动了基因组规模代谢模型（genome-scale metabolic models, GEMs）的构建。基因组规模代谢模型的多项应用之一便是对病原体开展药物靶点研究。因此，构建全面且具备预测能力的金黄色葡萄球菌代谢重建模型，将有助于识别抗菌治疗的新型靶点。本综述旨在系统梳理目前已公开的所有金黄色葡萄球菌菌株的基因组规模代谢模型。我们共下载了114个公开可用的金黄色葡萄球菌GEMs用于后续分析。对每一款模型的研究范围进行了评估，涵盖反应数、代谢物数与基因数。此外，所有模型均通过采用标准化代谢测试的开源应用Mᴇᴍᴏᴛᴱ完成质量控制，并对模型的生长能力与相似性进行了分析。本综述可为针对特定研究需求选择合适的基因组规模代谢模型提供参考指南。依托每款模型的可用性、格式及其优势与应用潜力信息，研究人员既可以选用已有的模型，也可整合多款模型以构建预测性能更优的模型，从而助力基于模型驱动发现对抗多药耐药金黄色葡萄球菌菌株的新型抗菌靶点。