生物
微生物学
病菌
细菌
金黄色葡萄球菌
噬菌体
大肠杆菌
败血症
细菌细胞结构
葡萄球菌
人口
人类病原体
细菌遗传学
DNA
病毒学
遗传学
免疫学
基因
医学
环境卫生
作者
Naomi L. Haddock,Layla J. Barkal,Nikhil Ram-Mohan,Gernot Kaber,Charles Y. Chiu,Ami S. Bhatt,Samuel Yang,Paul L. Bollyky
出处
期刊:Nature microbiology
日期:2023-06-12
卷期号:8 (8): 1495-1507
被引量:15
标识
DOI:10.1038/s41564-023-01406-x
摘要
Bacteriophages, viruses that infect bacteria, have great specificity for their bacterial hosts at the strain and species level. However, the relationship between the phageome and associated bacterial population dynamics is unclear. Here we generated a computational pipeline to identify sequences associated with bacteriophages and their bacterial hosts in cell-free DNA from plasma samples. Analysis of two independent cohorts, including a Stanford Cohort of 61 septic patients and 10 controls and the SeqStudy cohort of 224 septic patients and 167 controls, reveals a circulating phageome in the plasma of all sampled individuals. Moreover, infection is associated with overrepresentation of pathogen-specific phages, allowing for identification of bacterial pathogens. We find that information on phage diversity enables identification of the bacteria that produced these phages, including pathovariant strains of Escherichia coli. Phage sequences can likewise be used to distinguish between closely related bacterial species such as Staphylococcus aureus, a frequent pathogen, and coagulase-negative Staphylococcus, a frequent contaminant. Phage cell-free DNA may have utility in studying bacterial infections.
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