Undetected carriage explains apparent Staphylococcus aureus acquisition in a non-outbreak healthcare setting

•Five of seven apparent acquisitions identified during hospital admission can be explained by pre-existing carriage in this study.•Augmented screening increases detection of pre-healthcare S. aureus carriage by 19% and one in five people who are continuously culture negative by culture-based screening of nose, groin and any wound carry S. aureus undetected.•Enhanced culture does not detect difficult-to-culture organisms but identifies a minority of colonised individuals (including one case of MRSA) who are undetected by routine and comprehensive detection methods.•Molecular testing alone detected S. aureus carriage undetected by routine or augmented measures in 3 patients exhibiting discontinuously detected carriage.•Nearly one third of patients who become culture-negative during admission have S. aureus genomic material detected at discharge. Previous studies have been unable to identify patient or staff reservoirs for the majority of the nosocomial S. aureus acquisitions which occur in the presence of good infection control practice. We set out to establish the extent to which undetected pre-existing carriage explains apparent nosocomial S. aureus acquisition. Over two years elective cardiothoracic admissions were screened for S. aureus carriage before and during hospital admission. Routine screening (nose/groin/wound sampling), was supplemented by sampling additional body sites (axilla/throat/rectum) and culture-based methods optimised to detect fastidious phenotypes (small colony variants, cell wall deficient variants) and molecular identification by PCR. 35% of participants (53/151) were S. aureus carriers according to routine pre-healthcare screening; increasing to 42% (63/151) when additional body sites and enhanced cultures were employed. 71% (5/7) of apparent acquisitions were explained by pre-existing carriage using augmented measures. Enhanced culture identified a minority of colonised individuals (3/151 including 1 MRSA carrier) who were undetected by routine and additional screening cultures. 4/14 (29%) participants who became culture-negative during admission had S. aureus genomic material detected at discharge. Conventional sampling under-estimates carriage of S. aureus and this explains the majority of apparent S. aureus acquisitions among elective cardiothoracic patients.