Whole genome sequencing reveals new links between spa t172/CC59 methicillin-resistant Staphylococcus aureus cases in low-endemicity region of Southwest Finland, 2007‒2016

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) rates have remained relatively low in Finland. In Southwest Finland, however, annual MRSA incidence increased from 12 to 25/100,000 between 2007 and 2016 with spa t172 strain causing one fourth (237/983) of all cases. This provoked us to study the molecular epidemiology of t172-MRSA, aiming to better understand the transmission of this strain type. We combined epidemiological data and whole genome sequencing (WGS) of a set of 64 (27%, 64/237) t172-MRSA isolates covering 10 years. Isolates represented sporadic and index cases of all identified healthcare-associated outbreaks (HAOs) and family clusters (FCs). Among the included 62 isolates, core-genome MLST analysis revealed eight genomic clusters comprising 24 (38.7%) isolates and 38 (61.3%) non-clustered isolates. Cluster 1 comprised ten and the remaining seven clusters two isolates each, respectively. Two epidemiologically distinct HAOs were linked in cluster 1. FCs were involved in all clusters. All strains were associated with epidemic clonal complex CC59. We were able to confirm the spread of several successful t172-MRSA subclones in regional healthcare and the community. WGS complemented routine surveillance by revealing undetected links between t172-MRSA cases. Targeted, WGS-based typing could enhance MRSA surveillance without the need for routine WGS diagnostics.

Figure 1

Annual number of MRSA cases caused by the four most common or other spa types and the proportion of t172, Hospital District of Southwest Finland, years 2007–2016 (n = 976).

Figure 2

Epidemiological classification and the total number of index/sporadic t172 MRSA cases (n = 273) in the Hospital District of Southwest Finland, years 2007–2016. All t172 index cases and sporadic cases were selected for the WGS based analysis (bold). Healthcare-associated/Community-associated (HA/CA).

Figure 3

(a)Minimum spanning tree based on single nucleotide variants (SNVs) between the core-genome alleles of 75 spa t172 MRSA isolates, Hospital District of Southwest Finland, years 2007–2016. Each node represents one or two isolates as stated in the node. 62 isolates represent index cases from healthcare-associated outbreaks (HAO, n = 9) and family clusters (FC, n = 37) and sporadic cases (n = 16). The rest, 13 isolates, are from other additional HAO cases acquired via clinical HAO investigations. Clusters are highlighted with grey background, distance threshold 15 SNVs. Epidemiological case data shown by the colour scheme as stated in the figure legends: blue indicates community (CA-MRSA) origin, with additional parameters: dark blue family cluster (FC) index case and light blue sporadic case. Red indicates healthcare (HA-MRSA) origin: dark red HAO index case and, light red FC index case and pale red other HAO case. (b) Isolate detection year shown by the colour scheme. *Clusters including isolates from clinical HAO investigations (legend: HAO other) marked with asterisk.