Microbial strain typing in surveillance and outbreak investigation: past, present and future

Abstract

It is estimated that 180 000 cases of hospital-acquired infections occur in Australian hospitals each year(1). Many of these follow colonisation of patients by nosocomial bacterial pathogens. Identifying these acquisition events is necessary to target infection control interventions and to accurately estimate the burden of hospital-acquired infections on our healthcare system. Strain typing is required to reliably monitor these nosocomial acquisition events, particularly for organisms with high background incidence like Staphylococcus aureus. Traditional strain typing methods have been used in a limited, retrospective fashion to confirmsuspected outbreaks, but newer technologies allow routine, prospective strain typing to detect transmission soon after it occurs and whole genome sequencing allows the identification of the direction of transmission chains.