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

• Type of Material: Article
• Authors: Sandeep J. Joseph, Emory University; Ben Li, Emory University; Robert A. Petit, Emory University; Zhaohui Qin, Emory University; Lyndsey Darrow, Emory University; Timothy Read, Emory University
• Language: English
• Date: 2016-10-18
• Publisher: PeerJ
• Publication Version: Final Published Version
• Copyright Statement: © 2016 Joseph et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.7717/peerj.2571
• Title of Journal or Parent Work: PeerJ
• ISSN: 2167-8359
• Volume: 4
• Issue: 10
• Start Page: e2571
• End Page: e2571
• Grant/Funding Information: This work was funded through development funds from Emory University School of Medicine.; Funding support for the development of NIH Human Microbiome Project—Core Microbiome Sampling Protocol A (HMP-A) was provided by the NIH Roadmap for Medical Research.
• Keywords: IDENTIFICATION; Science & Technology; Metagenomics; NASAL CARRIAGE; DIVERSITY; COMMUNITY; BACTERIAL STRAINS; Multidisciplinary Sciences; Staphylococcus aureus; MRSA; PHYLOGENETIC ANALYSIS; COLONIZATION; INFECTIONS; Microbiome; UNITED-STATES
• Research Categories: Health Sciences, Epidemiology; Biology, Genetics; Biology, Bioinformatics

Abstract

In this study we developed a genome-based method for detecting Staphylococcus aureus subtypes from metagenome shotgun sequence data. We used a binomial mixture model and the coverage counts at > 100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of 40 subtypes in metagenome samples. We were able to obtain > 87% sensitivity and > 94% 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. aureus at genome coverage > 0.025. 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.