Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis

Abstract

Coagulase-negative staphylococci (CoNS), such as Staphylococcus capitis, are major causes of bloodstream infections in neonatal intensive care units (NICUs). Recently, a distinct clone of S. capitis (designated S. capitis NRCS-A) has emerged as an important pathogen in NICUs internationally. Here, 122 S. capitis isolates from New Zealand (NZ) underwent whole-genome sequencing (WGS), and these data were supplemented with publicly available S. capitis sequence reads. Phylogenetic and comparative genomic analyses were performed, as were phenotypic assessments of antimicrobial resistance, biofilm formation, and plasmid segregational stability on representative isolates. A distinct lineage of S. capitis was identified in NZ associated with neonates and the NICU environment. Isolates from this lineage produced increased levels of biofilm, displayed higher levels of tolerance to chlorhexidine, and were multidrug resistant. Although similar to globally circulating NICU-associated S. capitis strains at a core-genome level, NZ NICU S. capitis isolates carried a novel stably maintained multidrug-resistant plasmid that was not present in non-NICU isolates. Neonatal blood culture isolates were indistinguishable from environmental S. capitis isolates found on fomites, such as stethoscopes and neonatal incubators, but were generally distinct from those isolates carried by NICU staff. This work implicates the NICU environment as a potential reservoir for neonatal sepsis caused by S. capitis and highlights the capacity of genomics-based tracking and surveillance to inform future hospital infection control practices aimed at containing the spread of this important neonatal pathogen.

Keywords: coagulase-negative staphylococci; genomics; multidrug resistance; neonates; plasmids.

FIG 1

Maximum likelihood (ML) trees demonstrating the population structure of Staphylococcus capitis. ML trees were inferred from core-genome single nucleotide polymorphisms (SNPs) and rooted using the minimal ancestor deviation method (29). (A) ML tree of all 135 included S. capitis isolates, with metadata indicating source, highest level BAPS grouping, and presence/absence of antimicrobial resistance (AMR) genes (mecA and plasmid-carried fusB, aadD, and qacA) and embp. (B) ML tree of isolates classified as part of BAPS group 3, with metadata indicating source and BAPS grouping of isolates within BAPS group 3 (indicated in panel A).

FIG 2

(A) Comparison of representative S. capitis chromosome sequences relative to S. capitis NZ-SC16875, illustrating a high level of conservation among the international NICU-associated S. capitis BP3 isolates (inner six rings). Variable regions are annotated in the outer ring. These regions include two putative bacteriophages (phage 1 and phage 2), the SCCcad-SCCars-SCCcop region, and the embp gene (B) Schematic diagram illustrating the genetic organization of the composite SCCcad-SCCars-SCCcop element in BP3 lineage S. capitis isolates NZ-SC16875 and CR01. Also included are the SCCmec V elements of S. schleiferi TSCC54, S. pseudintermedius 06-3228, S. aureus JCSC6944, and MRSA P126, and S. haemolyticus NW19A, as well as the SCCcad-SCCars-SCCcop regions of S. haemolyticus S167 and SH621 and S. simulans FDAARGOS_124 for comparison. Green and yellow arrows indicate sequences present within SCCmec V regions; orange arrows are CRISPR-associated genes; and blue, purple, and red arrows indicate genes within SCCcad-SCCars-SCCcop regions. The direction of the arrows indicates the direction of transcription for open reading frames. Only coding sequences of >200 bp are shown. Shaded areas represent regions that share >99% nucleotide sequence identity (pink denotes the same orientation, and blue denotes the reverse orientation). Note that the S. capitis NZ-SC16875 region is shown at the top and bottom of the figure for ease of comparison.