The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data

PeerJ

article

Sandeep J. Joseph¹  Ben Li³  Robert A. Petit III¹  Zhaohui S. Qin³  Lyndsey Darrow²  Timothy D. Read¹ 

[1] Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine;Department of Epidemiology, Rollins School of Public Health, Emory University;Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University;Department of Human Genetics, Emory University School of Medicine

关键词: Staphylococcus aureus;    Microbiome;    Metagenomics;   

DOI  :  10.7717/peerj.2571

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

In this study we developed a genome-based method for detecting Staphylococcus aureus100,000 known S. aureus94% specificity at 0.025X coverage for S. aureus. We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S. aureus0.025. In both projects, CC8 and CC30 were the most common S. aureus clonal complexes encountered. We found evidence that the subtype composition at different body sites of the same individual were more similar than random sampling and more limited evidence that certain body sites were enriched for particular subtypes. One surprising finding was the apparent high frequency of CC398, a lineage often associated with livestock, in samples from the tongue dorsum. Epidemiologic analysis of the HMP subject population suggested that high BMI (body mass index) and health insurance are possibly associated with S. aureus carriage but there was limited power to identify factors linked to carriage of even the most common subtype. In the NYC subway data, we found a small signal of geographic distance affecting subtype clustering but other unknown factors influence taxonomic distribution of the species around the city.

【 授权许可】

CC BY