Carriage prevalence and genomic epidemiology of Staphylococcus aureus among Native American children and adults in the Southwestern USA

Abstract

Native American individuals in the Southwestern USA experience a higher burden of invasive Staphylococcus aureus disease than the general population. However, little is known about S. aureus carriage in these communities. A cross-sectional study was conducted to determine the carriage prevalence, risk factors and genomic epidemiology of S. aureus among Native American children (<5 years, n=121) and adults (≥18 years, n=167) in the Southwestern USA. Short- and long-read sequencing data were generated using Illumina and Oxford Nanopore Technology platforms to produce high-quality hybrid assemblies, and antibiotic-resistance, virulence and pangenome analyses were performed. S. aureus carriage prevalence was 20.7 % among children, 30.2 % among adults 18-64 years and 16.7 % among adults ≥65 years. Risk factors among adults included recent surgery, prior S. aureus infection among household members, and recent use of gyms or locker rooms by household members. No risk factors were identified among children. The bacterial population structure was dominated by clonal complex 1 (CC1) (21.1 %), CC5 (22.2 %) and CC8 (22.2 %). Isolates from children and adults were intermixed throughout the phylogeny. While the S. aureus population was diverse, the carriage prevalence was comparable to that in the general USA population. Genomic and risk-factor data suggest household, community and healthcare transmission are important components of the local epidemiology.

Keywords: Native American; Staphylococcus aureus; carriage; genome epidemiology; phylogeny.

Fig. 1.

Maximum-likelihood phylogeny of the S.aureus isolates (n=90) inferred from an alignment of 80 116 SNPs present in the core genome. The tip colours indicate strains with meticillin susceptibility (MSSA; grey) or resistance (MRSA; black). Bootstrap values indicating statistical support of dominant clades in the phylogeny are shown on the branches. Lineages identified through statistical analysis of population structure are highlighted. Clades are annotated with multilocus ST. The heatmap around the tree shows the CC, where identifiable, and age group associated with the isolate. The scale bar indicates genetic distance.

Fig. 2.

Maximum-likelihood phylogeny illustrating population structure, phenotypic antibiotic susceptibility, and genotypic virulence and antibiotic-resistance determinants. Dominant clades identified through analysis of population structure are highlighted with MLST type annotated. Strains identified as MRSA or MSSA are indicated by circular and square tip shapes, respectively, with SCCmec type shown by the tip colour of MRSA strains. The heatmap to the right shows the phenotypic antibiotic (Abx) susceptibility results, genotypic antibiotic determinants and virulence determinants. Phenotypic antibiotic testing is reported for erythromycin (erm), clindamycin (clinda), trimethoprim/sulfamethoxazole (TMP_SMX), ciprofloxacin (cipro), gentamicin (gent), tetracycline (tet) and oxacillin. The presence of genotypic antibiotic-resistance determinants is indicated by light pink. Antibiotic-resistance determinants include: aminoglycoside resistance (AadD, Aph3.III, Sat4A, Spc), β-lactam resistance (BlaZ, Dha1), fosfomycin resistance (FosfB), macrolide resistance (ErmA, ErmC, MphC, MsrA), fluoroquinolone resistance (NorA) and tetracycline resistance (TetM). Virulence factor presence is indicated in purple, and includes: (i) adherence – collagen binding protein (Cna); (ii) toxin – PVL Panton-Valentine leucocidin (LukF-PV), staphylococcal enterotoxin (enterotoxin), exfoliative toxin b (Etb), toxic shock syndrome toxin-1 (TSST-1); (iii) exoenzyme – von Willebrand factor-binding protein (vWbp), staphylocoagulase (Coa); (iv) immune evasion – CHIPS chemotaxis inhibitory protein of staphylococcus (Chp), SCIN staphylococcal complement inhibitor (Scn); - plasminogen activator – staphylokinase (Sak). The scale bar indicates genetic distance.

Fig. 3.

Population structure of the S. aureus isolates carried (a) and five dominant lineages (b–f). (a) The maximum-likelihood phylogeny from Fig. 1, with the dominant lineages indicated. (b–f) Lineage (ST or CC), number of core genes, nucleotide length of the core genome and the mean pairwise SNP diversity are shown. The tips of the phylogeny are coloured according to meticillin susceptibility (MSSA; black) or resistance (MRSA; grey). Bootstrap statistical support values are annotated on the branches of the phylogeny and the branch length scales are shown at the bottom of each panel. The heatmap to the right shows the age group and deidentified study site associated with the isolate. The clades annotated with a star have a mean SNP difference of 0 SNPs (CC30) and 306 SNPs (ST188). The scale bar indicates genetic distance.