Applying a New Technology to an Old Question: Whole-Genome Sequencing and Staphylococcus aureus Acquisition in an Intensive Care Unit

Phenotypic and genotypic characteristics of Staphylococcus aureus have long been used to determine the relatedness of isolates obtained from patients with epidemiologic evidence of a prior common risk factor for infection. In the 1940s, at the dawn of the era of the use of antimicrobial agents, the antibiogram of 2 isolates was compared to suggest isolate relatedness. In the 1950s, staphylococcal bacteriophage typing systems [1, 2] often enabled infection control practitioners in outbreak investigations to relate strains to one another. For example, with phage typing in hospitals, a virulent and rapidly disseminated S. aureus strain type known as the phage 80/81 type was recognized and tracked [3]. In the early 1960s, methicillin resistance in S. aureus (MRSA) was recognized, a genetic trait with the phenotype of resistance to β-lactam antibiotics. The MRSA phenotype provided epidemiologists in the healthcare setting a means of studying outbreaks and monitoring epidemiologic trends. Restriction endonuclease–based typing of strains, used increasingly in the early 1990s, changed practices for outbreak investigations. In particular, pulsed-field gel electrophoresis (PFGE), with improvements in analytical software, led to the development of standardized S. aureus national typing classification schemes, such as the US Centers for Disease Control and Prevention’s USA100-USA1100 scheme [4]. As novel MRSA backgrounds emerged in community settings in the 1980s in Australia and in the 1990s elsewhere, PFGE contributed to an improved understanding of the epidemiology of MRSA, both inside and outside healthcare settings. Since 1999, with increasing use of polymerase chain reaction (PCR) and a decrease in the cost of Sanger sequencing, DNA sequence–based genotyping methods were introduced for S. aureus. These provide a reproducible method for defining and identifying strain types of S. aureus isolates. Multilocus sequence typing, which requires the assessment of 7 partial “housekeeping” (ie, universally present) gene sequences, and protein A (spa) typing, which requires sequencing of a single PCR amplicon in a hypervariable region of the spa gene, are sequence-based classification systems that use Web-based algorithms to determine the likely relatedness of isolates. These techniques have transformed epidemiologic research by providing a common language for S. aureus genotyping, whether researchers work in New York, Copenhagen, Nairobi, Perth, or Hong Kong. With this common genotyping “language,” researchers have a framework for more detailed genetic, proteomic, and other studies on the determinants of virulence and fitness in circulating S. aureus isolates. All of the genotyping schemes described above share a common weakness: There is an assumption that the isolates having the same strain type also share many other, unmeasured, genetic characteristics. However, mobile genetic elements may or may not be present, making up the so-called accessory genome of a given S. aureus isolate. There is also a continuous evolutionary process of point mutation in the core and accessory genome of S. aureus. Either source of variation can undermine the assumption of close isolate relatedness. Consequences of this critical limitation in sequence-based genotyping schemes were demonstrated in the article by Price Received 20 November 2013; accepted 22 November 2013; electronically published 12 December 2013. Correspondence: Robert S. Daum, MD, The University of Chicago, Department of Pediatrics, 5841 S Maryland Ave, MC6054, Chicago, IL 60637 (rdaum@peds.bsd.uchicago.edu). Clinical Infectious Diseases 2014;58(5):619–21 © The Author 2013. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals. permissions@oup.com. DOI: 10.1093/cid/cit812