Streptococcus pyogenes transcriptome changes in inflammatory environment of necrotizing fasciitis

Streptococcus pyogenes is a major cause of necrotizing fasciitis, a life-threatening subcutaneous soft-tissue infection. At the host infection site, the local environment and interactions between the host and bacteria have effects on bacterial gene-expression profiles, while the gene-expression pattern of S. pyogenes related to this disease remains unknown. In this study, we used a mouse model of necrotizing fasciitis and performed RNA-sequencing (RNA-seq) analysis of S. pyogenes M1T1 strain 5448 by isolating total RNA from infected hindlimbs obtained at 24, 48, and 96 h post-infection. RNA-seq analysis results identified 483 bacterial genes whose expression was consistently altered in the infected hindlimbs as compared to their expression under in vitro conditions. Genes showing consistent enrichment during infection included 306 encoding molecules involved in virulence, carbohydrate utilization, amino acid metabolism, trace-metal transport, and the vacuolar ATPase transport system. Surprisingly, drastic upregulation of 3 genes, encoding streptolysin S precursor (sagA), cysteine protease (speB), and secreted DNase (spd), was noted in the present mouse model (log2 fold-change: >6.0, >9.4, and >7.1, respectively). Conversely, the number of consistently downregulated genes was 177, including those associated with oxidative-stress response and cell division. These results suggest that in necrotizing fasciitis, S. pyogenes shows an altered metabolism, decreased cell proliferation, and upregulation of expression of major toxins. Our findings are considered to provide critical information for developing novel treatment strategies and vaccines for necrotizing fasciitis. Importance Necrotizing fasciitis, a life-threatening subcutaneous soft-tissue infection, is principally caused by Streptococcus pyogenes. The inflammatory environment at the site of infection causes global gene expression changes for survival of the bacterium and pathogenesis. However, no known study regarding transcriptomic profiling of S. pyogenes in cases of necrotizing fasciitis has been presented. We identified 483 bacterial genes whose expression was consistently altered during infection. Our results showed that S. pyogenes infection induces drastic upregulation of the expression of virulence-associated genes and shifts metabolic-pathway usage. In particular, high-level expressions of toxins, such as cytolysins, proteases, and nucleases, were observed at infection sites. In addition, genes identified as consistently enriched included those related to metabolism of arginine and histidine, as well as carbohydrate uptake and utilization. Conversely, genes associated with oxidative-stress response and cell division were consistently downregulated during infection. The present findings provide useful information necessary for establishing novel treatment strategies.