Unraveling the secrets of the prevalent Staphylococcus strain

In a recent study published in Microbial Genomics, researchers investigated the genomes of a group of Staphylococcus capitis isolates from neonates.

Background

NRCS-A, a clone of S. capitis, is prevalent among newborns, a vulnerable population prone to late-onset sepsis. This NAS, a prevalent cause of late-onset sepsis (LOS), lengthens hospital stays, requires invasive procedures, and requires antibiotic treatments, all of which have a severe influence on newborn babies’ long-term health.

Despite a significant incidence of the strain in neonatal intensive care units (NICUs) globally, the mechanisms of NRCS-A are unknown.

About the study

In the present study, researchers analyzed staphylococci isolates obtained from a longitudinal assessment of NAS from gut and skin swabs of NICU-admitted babies.

The study included neonates admitted to neonatal ICUs of Norfolk and Norwich University Hospital (NNUH, United Kingdom) or University Children’s Hospital (Germany) throughout 10-week intervals in 2017 and 2018. The UK unit enrollment occurred between November 2017 and January 2018, whereas the German unit enrollment occurred between January and March 2018.

The researchers examined S. capitis-colonizing neonates admitted to the two NICUs and pathological clinical isolates. Swabs are regularly collected from neonates upon hospitalization and during their stays at both locations for monitoring methicillin-resistant Staphylococcus aureus (MRSA).

Duplicate swab specimens were collected for the current investigation, and staphylococci were isolated. Isolates were obtained from positive cerebrospinal fluid, blood, wound cultures, and urine during the research, and those obtained subsequently were also included.

On admission and every week until discharge, Amie charcoal swabs were used for isolating microorganisms from newborns.

Swabs obtained from the nose, ear, groin, axilla, and stomach were streaked on horse blood agar before incubating at room temperature for 24 hours, and coagulase-negative Staphylococcal organisms were identified following mannitol-salt agar (MSA) sub-cultures, coagulase testing, and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry.

Clinically relevant S. capitis isolates detected by local departments during routine practice during the investigation period were included, as were further anonymized clinical isolates obtained during regular hematological tests from neonates suspected of having sepsis from the NNUH neonatal ICU in 2018 (seven neonates) and from June to May 2022 (five neonates).

A 15 Staphylococcus capitis-panel was isolated from pre-existing Staphylococcal collections using Amies swabs, and isolates were obtained from adult hematological cultures (in cases of suspected infection) and prosthetic joint infections (PJIs).

Isolates were cultured overnight at 37 °C in Brain Heart Infusion (BHI) broth, and deoxyribonucleic acid (DNA) was isolated, measured, and submitted to polymerase chain reaction (PCR) and whole-genome sequencing.

The pangenome of 138 isolates was evaluated after genome analysis. The phylogeny of Staphylococcus capitis isolates was studied to find traits related to NRCS-A isolates. The National Center for Biotechnology Information (NCBI) protein database was searched for nsr and tarJ gene homologs. Antimicrobial susceptibility tests and pH sensitivity studies were also carried out.

Results

The team discovered 102 S. capitis isolates from four body locations in 159 regular swabs from NICU newborns in the United Kingdom and Germany, 12 from neonates with illness, 11 from blood, and one from skin. The average genome size of all 129 strains was 2.5 Mbp, with 33% GC content.

The team found a three-group population structure: non-NRCS-A strains, NRCS-A strains, and ‘proto-NRCS-A’ strains closely linked to the NRCS-A strains but unrelated to neonatal infections. All bloodstream isolates belonged to the NRCS-A group and were indistinguishable from skin or gut strains.

NRCS-A strains were more resistant to antibiotics and chlorhexidine than other Staphylococcus capitis isolates and could proliferate at higher pH levels. Both the NRCS-A and proto groups had characteristic tarJ and nsr genes. Only NRCS-A isolates exhibited the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein (Cas) system and increased expression genes involved in metal uptake and transport.

The researchers discovered evidence of Staphylococcus capitis NRCS-A transmission in the neonatal ICU, with related strains transferred between newborns and repeated acquisitions by a few neonates. NRCS-A isolates colonized uninfected neonates in the NICU, indicating a possible reservoir for infection.

Researchers discovered genes involved in the higher disease potential of the NRCS-A isolate, including antimicrobial peptide resistance, metal uptake and detoxification, and phage defense.

The genes enabled NRCS-A to persist in the gut, which might explain its success. Multiple antimicrobial resistance (AMR) genes were found in NRCS-A isolates, including fusB (fusidic acid resistance), blaZ (beta-lactamase), mecA (penicillin/methicillin resistance), and AAC(6′)-la-APH(2′)-la (aminoglycoside resistance).

Antiseptic susceptibility differed by geographical location, with S. capitis isolates being more sensitive to octenidine than chlorhexidine. The 50% minimum inhibitory concentration (MIC₅₀) values for octenidine and chlorhexidine were lower in German isolates, whereas they were greater in UK isolates for gentamicin, penicillin, and fusidic acid. No vancomycin resistance was detected; however, roughly a quarter of the patients showed intermediate susceptibility.

Conclusions

Overall, the study findings showed that the most prevalent neonatal strain detected on the skin and gut of uninfected newborns was NRCS-A, which was transmitted and survived in the NICU. The isolate was linked to CRISPR genes and has a full CRISPR-Cas type III-A system.

Carriage isolates were indistinguishable from blood cultures, suggesting that carriage can occur before infection. Strategies to prevent gut colonization may help reduce NRCS infections. The ability to live in the stomach and on the skin aided transmission, and metal uptake and tolerance may be important in NRCS-A biology. Further research is required to devise infection control protocols for NRCS-A.