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

Abstract

Background. The Staphylococcus capitis 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.Methods. Demographic and clinical data for 45 neonates with S. capitis and 90 with other coagulase-negative staphylococci (CoNS) isolated from sterile sites were reviewed, and clinical significance was determined. S. capitis isolated from 27 neonates at 2 hospitals between 2017 and 2022 underwent long-read (ONT) (n=27) and short-read (Illumina) sequencing (n=18). These sequences were compared with S. capitis sequenced from blood culture isolates from other adult and paediatric patients in the same hospitals (n=6), S. capitis 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 S. capitis from the UK and Germany.Results. S. capitis bacteraemia was associated with increased length of NICU stay at sampling (median day 22 vs day 12 for other CoNS isolated; P=0.05). A phylogeny of sequenced S. capitis 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 S. capitis molecular clock of 5.1 SNPs/genome/year (95% credibility interval 4.3-5.9). The presence of S. capitis in superficial cultures did not correlate with neonatal bacteraemia, but both neonates with rectal NRCS-A 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 non-NICU clinical samples. Multiple introductions of S. capitis, rather than prolonged environmental persistence, were seen over 5 years of infections.

Keywords: Staphylococcus capitis; antimicrobial resistance; infection control; late-onset sepsis; neonates.

Fig. 1.. (a) Vancomycin MIC and (b) antibiograms with available results from S. capitis clinical isolates, demonstrating a pattern consistent with that seen for the NRCS-A clone (fluoroquinolone and rifampicin susceptibility, beta-lactam, fusidic acid and gentamicin resistance and vancomycin heteroresistance).

Fig. 2.. ML phylogeny of S. capitis isolates from two hospitals including isolates from non-NICU settings in both hospitals. Year of isolation, clinical origin, ward location hospital and presence of the NRCS-A marker nsr gene are denoted in legend. Samples in the local NICU cluster are labelled in red, and non-cluster samples are labelled in black. CSF, cerebrospinal fluid; Line, vascular line tip; AICU, adult intensive care unit. Scale bar represents an evolutionary distance of 10⁻⁴ (one ten thousandth of the genome length, ~260 bp).

Fig. 3.. Pairwise distance matrix of 31 closely related S. capitis strains from clinical and environmental samples found in NICU (all confirmed as NRCS-A clone). Samples 32 and 35 are from the same patient (line tip culture and rectal swab culture). Samples 34 and 37 are from the same patient (blood culture and rectal swab culture).