USA300 Staphylococcus aureus persists on multiple body sites following an infection

• Type of Material: Article
• Authors: Timothy Read, Emory University; Robert A. Petit, III, Emory University; Zachary Yin, University of Chicago; Tuyaa Montgomery, University of Chicago; Moira C. McNulty, University of Chicago; Michael Z. David, University of Pennsylvania
• Language: English
• Date: 2018-12-05
• Publisher: BMC (part of Springer Nature)
• Publication Version: Final Published Version
• Copyright Statement: © 2018 The Author(s).
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1186/s12866-018-1336-z
• Title of Journal or Parent Work: BMC Microbiology
• ISSN: 1471-2180
• Volume: 18
• Issue: 1
• Start Page: 206
• End Page: 206
• Grant/Funding Information: The funder had no role in the design of the study; in the collection, interpretation, or analysis of the data; nor in the writing of the manuscript.; TDR was supported by NIH grant AI121860; MZD was supported by NIH grant AI095361–01.
• Keywords: DIVERSITY; USA300; EPIDEMIOLOGY; TRANSMISSION; NASAL CARRIAGE; MRSA; SKIN; Colonization; RESISTANCE; Antibiotic resistance; EMERGENCE; EVOLUTION; Staphylococcus aureus; Life Sciences & Biomedicine; Microbiology; Plasmids; Science & Technology; GENOME; SSTI; Phage
• Research Categories: Biology, Microbiology; Biology, Genetics; Biology, Virology

Abstract

Background: USA300 methicillin-resistant Staphylococcus aureus (MRSA) is a community- and hospital-acquired pathogen that frequently causes infections but also can survive on the human body asymptomatically as a part of the normal microbiota. We devised a comparative genomic strategy to track colonizing USA300 at different body sites after an initial infection. We sampled ST8 S. aureus from subjects at the site of a first known MRSA infection. Within 60 days of this infection and again 12 months later, each subject was tested for asymptomatic colonization in the nose, throat and perirectal region. 93 S. aureus strains underwent whole genome shotgun sequencing. Results: Among 28 subjects at the initial sampling time, we isolated S. aureus from the nose, throat and perirectal sites from 15, 11 and 15 of them, respectively. Twelve months later we isolated S. aureus from 9 subjects, with 6, 3 and 3 strains from the nose, throat and perirectal area, respectively. Genome sequencing revealed that 23 patients (ages 0-66 years) carried USA300 intra-subject lineages (ISLs), defined as having an index infection isolate and closely related colonizing strains. Pairwise distance between strains in different ISLs was 48 to 162 single nucleotide polymorphisms (SNPs) across the core regions of the chromosome, whereas within the same ISL it was 0 to 26 SNPs. Strains in ISLs from the same subject differed in plasmid and prophage content, and contained deletions that removed the mecA-containing SCCmec and ACME regions. Five strains contained frameshift mutations in agr toxin-regulating genes. Persistence of an ISL was not associated with clinical or demographic subject characteristics. We inferred that colonization with the ISL occurred about 18 weeks before the first assessment of asymptomatic colonization. Conclusions: Clonal lineages of USA300 may continue to colonize people at one or more anatomic sites up to a year after an initial infection and experience loss of the SCCmec, loss and gain of other mobile genetic elements, and mutations in the agr operon.