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

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.

Fig 1. spa clustering of 148 Staphylococcus aureus bacteremia isolates using PCR/Sanger sequencing-based spa typing.

MRSA, methicillin-resistant S. aureus; HO, hospital onset; HCA, healthcare-associated; CA, community-associated. Values in parentheses are the numbers of isolates of a given spa type.

Fig 2. Minimum spanning network built from the core genome MLST allelic profiles of 152 Staphylococcus aureus bacteremia isolates with MLST clonal complexes (CCs) overlain.

Each circle represents a single genotype, i.e., an allelic profile based on up to 1,861 target genes present in the isolates with the “pairwise ignoring missing values” option turned on in the SeqSphere⁺ software during comparison. The circles are named with the sample ID and MLST ST and color coded as MSSA (white) or MRSA (black). The numbers on the connecting lines indicate the numbers of different alleles between the connected genotypes. MSSA, methicillin-susceptible S. aureus; MRSA, methicillin-resistant S. aureus; N.A, not available. The MRSA isolates with 9 allelic differences, MZ51 and MZ81, are highlighted in gray. CC30 by MLST corresponds to spa CC-012, CC5 corresponds to spa CC-002, and CC8 corresponds to spa CC-008.

Fig 3. Phylogenetic tree of cgMLST analysis generated using the neighbor-joining method compared to MLST (ST) and traditional spa typing (spa) for 152 Staphylococcus aureus bacteremia isolates.

cgMLST analysis was based on allelic profiles as determined using SeqSphere+ software. N.A., not available. Methicillin-resistant isolates are highlighted in black.