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

The NRCS-A strain has emerged as a global cause of late-onset sepsis associated with outbreaks in neonatal intensive care units (NICUs) whose transmission is incompletely understood. Demographic and clinical data for 45 neonates with and 90 with other coagulase-negative staphylococci (CoNS) isolated from sterile sites were reviewed, and clinical significance was determined. isolated from 27 neonates at 2 hospitals between 2017 and 2022 underwent long-read (ONT) (=27) and short-read (Illumina) sequencing (=18). These sequences were compared with sequenced from blood culture isolates from other adult and paediatric patients in the same hospitals (=6), isolated from surface swabs (found in 5/150 samples), rectal swabs (in 2/69 samples) in NICU patients and NICU environmental samples (in 5/114 samples). Reads from all samples were mapped to a hybrid assembly of a local sterile site strain, forming a complete UK NRCS-A reference genome, for outbreak analysis and comparison with 826 other from the UK and Germany. bacteraemia was associated with increased length of NICU stay at sampling (median day 22 vs day 12 for other CoNS isolated; =0.05). A phylogeny of sequenced revealed a cluster comprised of 25/27 neonatal sterile site isolates and 3/5 superficial, 2/2 rectal and 1/5 environmental isolates. No isolates from other wards belonged to this cluster. Phylogenetic comparison with published sequences confirmed that the cluster was NRCS-A outbreak strain but found a relatively high genomic diversity (mean pairwise distance of 84.9 SNPs) and an estimated NRCS-A molecular clock of 5.1 SNPs/genome/year (95% credibility interval 4.3-5.9). The presence of in superficial cultures did not correlate with neonatal bacteraemia, but both neonates with rectal NRCS-A carriage identified also experienced bacteraemia. bacteraemia occurred in patients with longer NICU admission than other CoNS. Genomic analysis confirms clinically significant infections with the NRCS-A strain, distinct from non-NICU clinical samples. Multiple introductions of , rather than prolonged environmental persistence, were seen over 5 years of infections.