Microbiology and Molecular Genetics (MMG) Program, Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia, USA.
Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA.
mSphere. 2021 Jan 13;6(1):e01263-20. doi: 10.1128/mSphere.01263-20.
is a human pathogen that causes serious diseases, ranging from skin infections to septic shock. Bacteriophages (phages) are both natural killers of , offering therapeutic possibilities, and important vectors of horizontal gene transfer (HGT) in the species. Here, we used high-throughput approaches to understand the genetic basis of strain-to-strain variation in sensitivity to phages, which defines the host range. We screened 259 diverse strains covering more than 40 sequence types for sensitivity to eight phages, which were representatives of the three phage classes that infect the species. The phages were variable in host range, each infecting between 73 and 257 strains. Using genome-wide association approaches, we identified putative loci that affect host range and validated their function using USA300 transposon knockouts. In addition to rediscovering known host range determinants, we found several previously unreported genes affecting bacterial growth during phage infection, including , , , , , and We used the data from our host range matrix to develop predictive models that achieved between 40% and 95% accuracy. This work illustrates the complexity of the genetic basis for phage susceptibility in but also shows that with more data, we may be able to understand much of the variation. With a knowledge of host range determination, we can rationally design phage therapy cocktails that target the broadest host range of strains and address basic questions regarding phage-host interactions, such as the impact of phage on evolution. is a widespread, hospital- and community-acquired pathogen, many strains of which are antibiotic resistant. It causes diverse diseases, ranging from local to systemic infection, and affects both the skin and many internal organs, including the heart, lungs, bones, and brain. Its ubiquity, antibiotic resistance, and disease burden make new therapies urgent. One alternative therapy to antibiotics is phage therapy, in which viruses specific to infecting bacteria clear infection. In this work, we identified and validated genes that influence phage host range-the number of strains a phage can infect and kill-by testing strains representative of the diversity of the species for phage host range and associating the genome sequences of strains with host range. These findings together improved our understanding of how phage therapy works in the bacterium and improve prediction of phage therapy efficacy based on the predicted host range of the infecting strain.
是一种人类病原体，可导致从皮肤感染到败血性休克等严重疾病。噬菌体（phages）既是 的天然杀伤者，提供了治疗的可能性，也是该物种水平基因转移（HGT）的重要载体。在这里，我们使用高通量方法来了解菌株间对噬菌体敏感性的遗传基础，这决定了宿主范围。我们筛选了 259 株多样化的 菌株，以检测对 8 株噬菌体的敏感性，这 8 株噬菌体代表了感染该物种的三种噬菌体类。噬菌体在宿主范围上存在差异，每种噬菌体感染的菌株数在 73 到 257 株之间。使用全基因组关联方法，我们确定了影响宿主范围的假定基因座，并使用 USA300 转座子敲除来验证其功能。除了重新发现已知的宿主范围决定因素外，我们还发现了几个以前未报道的基因，这些基因在噬菌体感染期间影响细菌生长，包括 、 、 、 、 和 。我们使用宿主范围矩阵中的数据开发了预测模型，这些模型的准确性在 40%到 95%之间。这项工作说明了 噬菌体敏感性的遗传基础的复杂性，但也表明随着更多的数据，我们可能能够理解大部分的变异。有了宿主范围决定因素的知识，我们就可以合理地设计靶向最广泛的 菌株宿主范围的噬菌体治疗鸡尾酒，并解决噬菌体-宿主相互作用的基本问题，例如噬菌体对 的进化影响。 是一种广泛存在的、医院和社区获得性病原体，许多菌株对抗生素具有耐药性。它引起多种疾病，从局部到全身感染，影响皮肤和许多内部器官，包括心脏、肺部、骨骼和大脑。其普遍性、抗生素耐药性和疾病负担使得新的治疗方法变得迫切。抗生素替代疗法之一是噬菌体疗法，即用特异性感染细菌的病毒清除感染。在这项工作中，我们通过测试代表 物种多样性的菌株对噬菌体宿主范围的检测，并将菌株的基因组序列与宿主范围相关联，鉴定和验证了影响噬菌体宿主范围的 基因-噬菌体可以感染和杀死的菌株数量。这些发现共同提高了我们对噬菌体在细菌中如何发挥作用的理解，并提高了基于感染菌株预测的宿主范围预测噬菌体治疗效果的能力。
