Open Access Research article

Rapid PCR/ESI-MS-based molecular genotyping of Staphylococcus aureus from nasal swabs of emergency department patients

Aleksandar Kecojevic1*, Ray Ranken3, David J Ecker3, Christian Massire3, Rangarajan Sampath3, Lawrence B Blyn3, Yu-Hsiang Hsieh2, Richard E Rothman24 and Charlotte A Gaydos24

Author Affiliations

1 Department of Community Health and Prevention, Drexel University School of Public Health, Philadelphia, PA, USA

2 Department of Emergency Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA

3 Ibis Biosciences, an Abbott Company, Carlsbad, CA, USA

4 Department of Medicine, Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, USA

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BMC Infectious Diseases 2014, 14:16  doi:10.1186/1471-2334-14-16

Published: 9 January 2014



A limitation of both culture-based and molecular methods of screening for staphylococcal infection is that current tests determine only the presence or absence of colonization with no information on the colonizing strain type. A technique that couples polymerase chain reaction to mass spectrometry (PCR/ESI-MS) has recently been developed and an assay validated to identify and genotype S. aureus and coagulase-negative staphylococci (CoNS).


This study was conducted to determine the rates, risk factors, and molecular genotypes of colonizing Staphylococcus aureus in adult patients presenting to an inner-city academic emergency department. Participants completed a structured questionnaire to assess hospital and community risks for infection with methicillin-resistant S. aureus (MRSA). Nasal swabs were analyzed by PCR/ESI-MS to identify and genotype S. aureus and CoNS.


Of 200 patients evaluated, 59 were colonized with S. aureus; 27 of these were methicillin-resistant strains. Twenty-four of the 59 S. aureus carriers were co-colonized with a CoNS and 140 of the 200 patients were colonized exclusively with CoNS. The molecular genotypes of the 59 S. aureus strains were diverse; 21 unique molecular genotypes belonging to seven major clonal complexes were identified. Eighty-five of 200 patients carried strains with high-level mupirocin resistance. Of these eighty-five participants, 4 were colonized exclusively with S. aureus, 16 were co-colonized with S. aureus and CoNS, and 65 were colonized exclusively with CoNS.


The prevalence of S. aureus and methicillin-resistant S. aureus colonization in a random sample of patients seeking care in Emergency Department was 29.5% and 13.5%, respectively. A substantial fraction of the S. aureus-colonized patients were co-colonized with CoNS and high-level mupirocin-resistant CoNS. Determining the molecular genotype of S. aureus during intake screening may prove valuable in the future if certain molecular genotypes become associated with increased infection risk.