Evaluation of an "all-in-one" seven-day WGS solution in the investigation of a Staphylococcus aureus outbreak in a neonatal Intensive Care Unit.

BACKGROUND: Meticillin-susceptible and resistant Staphylococcus aureus (MSSA and MRSA) are responsible for outbreaks in intensive care units. MSSA infections have the same morbidity and mortality rate as MRSA infections but are less often studied. Whole genome sequencing (WGS) is increasingly used for outbreak monitoring but still requires specific installation and trained personnel to obtain and analyse the data.

AIM: To evaluate the workflow and the benefits of the bioMerieux Episeq® (bioMerieux, France) solution in exploring an increased incidence of S. aureus bloodstream infections in a neonatal intensive care unit (NICU).

METHODS: Four bacteraemia and 27 colonizing S. aureus isolates from January to July 2016 were submitted to the "all in one solution" Episeq® (whole genome sequencing, quality data assessment, MLST, spa type, virulome, resistome and phylogenetic tree construction). More in-depth analyses were performed (wgMLST and wgSNP analysis) with BioNumerics software (Applied Maths, Belgium).

FINDINGS: Nine different STs and 13 different spa types were found among the 31 isolates studied. Among those isolates, n=11 (7 patients) were ST146 spa type t002, n=5 (4 patients) ST30 and n=4 (4 patients) ST398. The eleven ST146 isolates had a maximum of 7 pairwise SNP differences.

CONCLUSION: The use of the Episeq solution allowed us to quickly demonstrate the polyclonal profile of the MSSA population in neonates and thus rule out the suspicion of a global outbreak. However, wgSNP analysis showed the transmission and persistence of one ST over 6 months in the NICU and enabled the infection control team to adapt its response.