The impact of Staphylococcus aureus genomic variation on clinical phenotype of children with acute hematogenous osteomyelitis

Abstract

BackgroundChildren with acute hematogenous osteomyelitis (AHO) have a broad spectrum of illness ranging from mild to severe. The purpose of this study is to evaluate the impact of genomic variation of Staphylococcus aureus on clinical phenotype of affected children and determine which virulence genes correlate with severity of illness.MethodsDe novo whole genome sequencing was conducted for a strain of Community Acquired Methicillin Resistant Staphylococcus aureus (CA-MRSA), using PacBio Hierarchical Genome Assembly Process (HGAP) from 6 Single Molecule Real Time (SMRT) Cells, as a reference for DNA library assembly of 71 Staphylococcus aureus isolates from children with AHO. Virulence gene annotation was based on exhaustive literature review and genomic data in NCBI for Staphylococcus aureus. Clinical phenotype was assessed using a validated severity score. Kruskal-Wallis rank sum test determined association between clinical severity and virulence gene presence using False Discovery Rate (FDR), significance <0.01.ResultsPacBio produced an assembled genome of 2,898,306 bp and 2054 Open Reading Frames (ORFs). Annotation confirmed 201 virulence genes. Statistical analysis of gene presence by clinical severity found 40 genes significantly associated with severity of illness (FDR ≤0.009). MRSA isolates encoded a significantly greater number of virulence genes than did MSSA (p < 0.0001). Phylogenetic analysis by maximum likelihood (PAML) demonstrated the relatedness of genomic distance to clinical phenotype.ConclusionsThe Staphylococcus aureus genome contains virulence genes which are significantly associated with severity of illness in children with osteomyelitis. This study introduces a novel reference strain and detailed annotation of Staphylococcus aureus virulence genes. While this study does not address bacterial gene expression, a platform is created for future transcriptome investigations to elucidate the complex mechanisms involved in childhood osteomyelitis.

Delayed diagnosis and treatment of pediatric calcaneal acute hematogenous osteomyelitis: A case report

“…Additional studies have shown similar incidence in the calcaneus, ranging from 3-12% (3,4,5). Staphylococcus aureus (S. aureus) is the most commonly isolated organism in cases of AHO worldwide, cultured in upwards of 80% of culture-positive cases (1,6). Due to its prevalence, antibiotic therapy should be targeted against S. aureus while awaiting culture results and culture negative cases, which account for 33-55% of all cultures (1,3).…”

Contemporary clinical isolates ofStaphylococcus aureusfrom pediatric osteomyelitis patients display unique characteristics in a mouse model of hematogenous osteomyelitis

“…8B and C). Next, 173 virulence-associated genes within each isolate were grouped by function and examined for the presence of polymorphisms, as compared to their respective reference strain (31). TI2 shows more polymorphisms in genes related to adhesins and immune evasion than Tl1 or TI3 ( Fig.…”

“…Clinical isolate polymorphisms by gene. 173 virulence associated genes (modified from (31)) and their presence, absence, and sequence relative to the reference strain. USA300_FPR3757 is the USA300 reference genome, and N315 is the USA100 reference genome.…”

“…No reuse allowed without permission. Collins et al 2018) and their presence, absense, and seqence relative to the reference strain. USA300_FPR3757 is the USA300 reference genome, and N315 is the USA100 reference genome.…”

The Continuing Evolution of Community-Associated MRSA ST93-IV in Australia

“…To determine the association between gene content and disease, genome-wide association studies (GWAS) can be performed by analysing single nucleotide polymorphisms (SNPs), and the accessory genes provided by WGS data. For example, GWAS performed on isolates from children with acute S. aureus osteomyelitis identi ed an association in the number of virulence genes present and the severity of disease (8). In contrast, when applied to S. aureus bacteraemia isolates, no obvious associations in the number of virulence genes present in isolates from patients with and without S. aureus infective endocarditis were identi ed (9).…”