Next generation sequencing of enhanced surveillance Staphylococcus aureus bacteraemias across Scottish Health Boards in 2015

Background: Staphylcoccus aureus bacteraemia (SAB) is the second most common bacteraemia in Scotland, and in 2015 there were 1,587 reported cases. In October 2014 the national enhanced surveillance of SAB was introduced in Scotland for the identification of sources of infection and associated risk factors. 540 strains were sampled and sequenced from the first complete year of surveillance, 2015. The aim was to link genomic data from the infecting organism with the national surveillance results to understand the contributions of bacterial and host factors in SAB.

Materials/methods: 540 bloodstream Staphylcoccus aureus isolates were selected, from across the 15 National Health Service (NHS) boards in Scotland, from the collection of all 2015 SAB isolates (n=1587) held at the Scottish MRSA Reference Laboratory (SMRSARL). The mandatory SAB surveillance programme metadata was provided by Health Protection Scotland. Whole genome sequencing was performed using the Illumina HiSeq platform at Sanger Institute, Cambridge.

Results: Seven main sequences types (ST) were identified: ST5, ST45, ST30, ST8, ST22, ST15 and ST1. The STs were distributed evenly across the Healthboards. Likewise the distribution of AMR and virulence genes showed no predispositions for particular Healthboards. A population of methicillin and fluoroquinolone ST22s were identified along with fusidic acid resistant ST1s and Toxic Shock Syndrome Toxin (TSST) positive ST30s. Network analysis showed antibiogram results correlated with closely their respective AMR genes and six antibiotics (clindamycin, erythromycin, ciprofloxacin, trimethoprim, gentamycin and mupirocin) were closely associated together. ST22 were found predominantly in healthcare associated infections while ST1 were community-associated. The rep16, rep19 and rep5 plasmid replicon types were common across the majority of STs. Surveillance data identified specific STs responsible for cellulitis and eczema skin infections. Reoccurrence and transmission events were detected and were associated with the use of vascular access and other medical devices.

Conclusions: The device risk factors obtained from surveillance reports could lead to transmission and reoccurrence events. Next generation sequencing of SAB strains with concurrent enhanced surveillance data provides an unparalleled understanding of the responsible bacterial and host factors.