Detection, survival, and persistence of Staphylococcus capitis NRCS-A in neonatal units in England

Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates

OBJECTIVE

Staphylococcus capitis is part of the human microbiome and an opportunistic pathogen known to cause catheter-associated bacteraemia, prosthetic joint infections, skin and wound infections, among others. Detection of S. capitis in normally sterile body sites saw an increase over the last decade in England, where a multidrug-resistant clone, NRCS-A, was widely identified in blood samples from infants in neonatal intensive care units. To address a lack of complete genomes and antibiograms of S. capitis in public databases, we performed long- and short-read whole-genome sequencing, hybrid genome assembly, and antimicrobial susceptibility testing of 22 diverse isolates.

DATA DESCRIPTION

We present complete genome assemblies of two S. capitis type strains (subspecies capitis: DSM 20326; subspecies urealyticus: DSM 6717) and 20 clinical isolates (NRCS-A: 10) from England. Each genome is accompanied by minimum inhibitory concentrations of 13 antimicrobials including vancomycin, teicoplanin, daptomycin, linezolid, and clindamycin. These 22 genomes were 2.4-2.7 Mbp in length and had a GC content of 33%. Plasmids were identified in 20 isolates. Resistance to teicoplanin, daptomycin, gentamicin, fusidic acid, rifampicin, ciprofloxacin, clindamycin, and erythromycin was seen in 1-10 isolates. Our data are a resource for future studies on genomics, evolution, and antimicrobial resistance of S. capitis.

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. 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.

Two-step or one-step - are all methods for neonatal incubator decontamination equal?

Healthcare-associated pathogens, including Staphylococcus capitis, can contaminate incubator surfaces and are of significant concern in neonatal intensive care units (NICUs). Effective incubator decontamination is essential for infection prevention and control, with submersion decontamination often recommended. This may not always be achievable, with wipe decontamination seen as an alternative. Here we compare the ability of a two-step (submersion in enzymatic detergent followed by wiping with hypochlorite-based wipes) with a one-step (wiping with quaternary ammonium compound-impregnated wipes) decontamination procedure to remove microbial surrogate markers from neonatal incubator surfaces. Three cauliflower-mosaic-virus-derived microbial surrogate markers were inoculated on to the fan, a mattress seam and the external arm port door clips of two Giraffe™ Omnibed™ Carestation™ incubators. Incubators were decontaminated either by the one-step or the two-step decontamination process. Swab samples were collected from 28 sites on each incubator and surrounding environment, with marker presence determined by qPCR. Following two-step decontamination, three of 28 (11%) sample sites were positive for any marker, compared with 12 of 28 (43%) after one-step decontamination. Markers were transferred to several incubator surfaces and recovered from the originally inoculated sites following one-step decontamination, with the marker inoculated on door clips having the greatest transfer. Markers inoculated on to the mattress persisted through both decontamination strategies. In conclusion, microbial surrogate markers were not completely removed from incubator surfaces by one-step decontamination alone. Two-step decontamination was the most effective method and removed markers from submergible surfaces, but not from the mattress. These findings indicate that micro-organisms can persist after incubator terminal decontamination, particularly on mattresses and when a two-step decontamination process is not used. This highlights the importance of effective decontamination practices to mitigate micro-organism persistence on incubator surfaces.

Staphylococcus capitis Central-Line-Associated Bloodstream Infections in the Neonatal Intensive Care Unit: A Single-Center, Four-Year Experience in Central-Line Management during Sepsis Treatment

Coagulase-negative staphylococci (CoNS) are reportedly responsible for 50-60% of bloodstream infections in very preterm (<1500 g) infants in neonatal intensive care units (NICUs). Staphylococcus capitis is an increasingly prevalent pathogen in the neonatal setting, frequently causing central-line-associated bloodstream infections (CLABSIs) that can be difficult to eradicate. Central venous catheter (CVC) removal versus in situ treatment with CoNS CLABSIs is a controversial treatment strategy with no clear consensus. We reviewed all S. capitis CLABSIs in our NICU between 2019 and 2022, focusing on the role of catheter removal in eradication. Among the 25 patients, 17 CVCs were removed after diagnosis, leading to a 76.5% eradication rate in this group. Three infants had a persistently positive blood culture after CVC substitution. A new catheter was then inserted after a 48 h washout period, resulting in resolution of the infection. Only two of the eight patients (25%) who retained their catheter after diagnosis achieved infection eradication with antibiotic therapy alone. When feasible, catheter removal seems to be the most effective strategy for eradicating S. capitis CLABSIs, sometimes even requiring a 48 h washout period before reinsertion. Further studies on this topic are needed to better standardize the management of this type of infection.