Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing.

Nicholas Chia,Kyung-Hwa Park,Priya Sampathkumar,Heidi Nelson,Kerryl E. Greenwood-Quaintance,James R. Uhl,Patricio R. Jeraldo,Scott A. Cunningham,Robin Patel,Herminia de Lencastre

doi:10.1371/journal.pone.0179003

Nicholas Chia, Kyung-Hwa Park

Open Access

https://doi.org/10.1371/journal.pone.0179003

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Abstract

Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB) is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated. Herein, we examined the epidemiology of SAB using whole genome sequencing (WGS). 152 SAB isolates collected over the course of 2015 at a single large Minnesota medical center were studied. Staphylococcus protein A (spa) typing was performed by PCR/Sanger sequencing; multilocus sequence typing (MLST) and core genome MLST (cgMLST) were determined by WGS. Forty-eight isolates (32%) were methicillin–resistant S. aureus (MRSA). The isolates encompassed 66 spa types, clustered into 11 spa clonal complexes (CCs) and 10 singleton types. 88% of 48 MRSA isolates belonged to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA) isolates were more genotypically diverse, with 61% distributed across four spa CCs (CC-002, CC-012, CC-008 and CC-084). By MLST, there was 31 sequence types (STs), including 18 divided into 6 CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST clones were CC5 (23%), CC30 (19%), CC8 (15%) and CC15 (11%). Common MRSA clones were CC5 (67%) and CC8 (25%); there were no MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9 allelic differences between two isolates, with the remaining 150 isolates differing from each other by over 40 alleles. The two isolates were retroactively epidemiologically linked by medical record review. Overall, cgMLST analysis resulted in higher resolution epidemiological typing than did multilocus sequence or spa typing.

Highlights

Staphylococcus aureus is responsible for a high percentage of hospital- and communityacquired infections worldwide
By multilocus sequence typing (MLST) analysis, CC45 and CC30 contained only Methicillin-susceptible S. aureus (MSSA) isolates, and common methicillin-resistant S. aureus (MRSA) clones were CC5 and CC8. core genome MLST (cgMLST) results yielded higher resolution typing results compared to MLST or spa typing, and demonstrated a single episode of possible hospital-based transmission of S. aureus bacteremia
There are no standardized thresholds for interpreting clonality with cgMSLT, we recently proposed that using the scheme applied for S. aureus, 8 allelic differences be considered related, 9–29 allelic differences be considered possibly related and 30 or more allelic differences be considered unrelated [22]

Summary

Introduction

Staphylococcus aureus is responsible for a high percentage of hospital- and communityacquired infections worldwide. It is a leading cause of bacteremia, often associated with metastatic infections and significant morbidity and mortality. The epidemiology of S. aureus infection has changed over the past decade and a half, with methicillin-resistant S. aureus (MRSA) being increasingly identified in community settings. This has led to interest in attempting to understand the genetic background of the pathogen across different geographic regions and care settings [1,2,3]. To inform IPAC strategies within individual institutions, it is helpful to understand the molecular epidemiology of infection, including whether particular strains are prevalent, and whether or not there is evidence of patient to patient transmission

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