Evolution of community-associated MRSA: a 20-year genomic and epidemiological study in Region Örebro County, Sweden

Abstract

Background: Methicillin-resistant Staphylococcus aureus (MRSA) has been an issue in healthcare since the 1960s. It was initially found only in healthcare facilities, but in the late 1990s it began to be seen with no healthcare connexion. The mechanisms of intercontinental and national spread are not fully understood, as sometimes novel outbreaks occur without any identifiable source or connexion to locally dominant clonal clusters.

Methods: This study investigated the epidemiology and genomics of community-associated MRSA in Region Örebro County, Sweden, through 330 isolates collected between 2000 and 2019.

Results: A shift in the dominant sequence type (ST) from ST80 to ST22 occurred in 2011-2019, along with an increase in the prevalence of STs belonging to clonal complexes CC5 and CC22. Both ST8 and ST80 isolates seemed to give way to emerging ST22 isolates, also indicated by the declining presence of the USA300 clone. The staphylococcal chromosomal cassette mec (SCCmec) type IV Remained dominant.

Conclusions: The SCCmec type IV characteristic appears to be relatively geographically stable, possibly due to its low fitness cost and transductal capabilities. This warrants further studies of SCCmec type IV variant's survival mechanics as well as the effects of migratory flow on local epidemiology, in preparation for future possible outbreaks.

Keywords: CA-MRSA; MLST; SCCmec; Staphylococcus aureus; clonal complex; epidemiology.

Figure 1

Workflow of bioinformatic analysis from raw sequence data.

Figure 2

Heat map showing country of origin for cases of community-acquired methicillin-resistant Staphylococcus aureus in Region Örebro County during 2000–2019 with presumed origin of infection outside of Sweden.

Figure 3

Variation in (A) sequence type, (B) clonal complex, and (C) SCCmec among 330 isolates of primary cases of community-acquired methicillin-resistant Staphylococcus aureus collected in Region Örebro County during 2000–2019. Recombination events are defined as isolates that showed presence of some SCCmec genes and other recombinase complexes, indicating a recombination event.

Figure 4

Phylogenetic neighbour joining tree using 1,861 core genome multilocus sequence typing (cgMLST) genes of isolates from primary cases of community-acquired methicillin-resistant Staphylococcus aureus in Region Örebro County during 2000–2019, divided into two cohorts: 2000–2010 (n = 107) and 2011–2019 (n = 223). Each leaf represents an isolate. Scale presents the percentage difference between the 1,861 cgMLST genes analysed.