An emergence of multidrug-resistant (MDR)
Staphylococcus haemolyticus
has been observed in the neonatal intensive care unit (NICU) of Nîmes University Hospital in southern France. A case–control analysis was conducted on 96 neonates, to identify risk factors associated with
S. haemolyticus
infection, focusing on clinical outcomes. Forty-eight MDR
S. haemolyticus
strains, isolated from neonates between October 2019 and July 2022, were investigated using routine
in vitro
procedures and whole-genome sequencing. Additionally, five
S. haemolyticus
isolates from adult patients were sequenced to identify clusters circulating within the hospital environment. The incidence of neonatal
S. haemolyticus
was significantly associated with low birth weight, lower gestational age, and central catheter use (
p
< 0.001). Sepsis was the most frequent clinical manifestation in this series (20/46, 43.5%) and was associated with five deaths. Based on whole-genome analysis, three
S. haemolyticus
genotypes were predicted: ST1 (6/53, 11%), ST25 (3/53, 5.7%), and ST29 (44/53, 83%), which included the subcluster II-A, predominantly emerging in the neonatal department. All strains were profiled
in silico
to be resistant to methicillin, erythromycin, aminoglycosides, and fluoroquinolones, consistent with
in vitro
antibiotic susceptibility tests. Moreover,
in silico
prediction of biofilm formation and virulence-encoding genes supported the association of ST29 with severe clinical outcomes, while the persistence in the NICU could be explained by the presence of antiseptic and heavy metal resistance-encoding genes. The clonality of
S. haemolyticus
ST29 subcluster II-A isolates confirms healthcare transmission causing severe infections. Based on these results, reinforced hygiene measures are necessary to eradicate the nosocomial transmission of MDR strains.