NRCS-A Staphylococcus capitis NICU sequencing. Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey

Background: S. capitis NRCS-A strain has emerged as a global cause of late onset sepsis in neonatal intensive care units (NICUs). Identifying outbreaks is critical for improving patient safety, antimicrobial stewardship and infection prevention. Methods: Demographic and clinical data for 45 neonates from Hospital 1 with S. capitis and 90 with other coagulase-negative staphylococci (CoNS) from sterile sites were reviewed and clinical significance determined by two clinicians. S. capitis isolated from sterile site samples in 27 neonates at two hospitals between 2017-2022 underwent sequencing of culture-derived bacterial DNA with long read (ONT) sequencing (n=27) and short read (Illumina) sequencing (n=18). These were compared with S. capitis sequenced from blood cultures isolates from other adult and paediatric patients in the same hospitals (n=6), S. capitis isolated from surface swabs (n=5), rectal swabs (n=2) in NICU patients, NICU environmental samples (n=5), and two well characterised reference strains. Reads from all samples were mapped to a hybrid assembly of a local sterile site strain, forming a newly created complete UK NRCS-A reference strain, for genomic analysis of the outbreak. Results: S. capitis bacteraemia was associated with lower gestational age (26 vs 27 weeks; p = 0.047) and increased age at sample (day 22 vs 12; p = 0.01). Phylogeny of sequenced S. capitis revealed that 25/27 sterile site isolates from neonates formed a cluster, which also included 3/5 superficial, 2/2 rectal and 1/5 environmental isolates. No isolates from other adult or paediatric wards belonged to this cluster. Comparison with published sequences confirmed the cluster were NRCS-A outbreak strain, but found relatively high genomic diversity indicative of multiple sub-lineages. S. capitis in superficial culture did not correlate with neonatal bacteraemia, but both neonates with rectal S. capitis carriage identified also experienced S. capitis bacteraemia. Conclusions: S. capitis bacteraemia occurred in patients with longer NICU admission than other CoNS. Genomic analysis confirms clinically significant infections with the NRCS-A S. capitis strain, distinct from S. capitis detected in non-NICU clinical samples, which demonstrated multiple introductions to the NICU setting. This has important implications for infection control measures and antimicrobial stewardship on the NICU.