Genome-Wide Analysis of Group A Streptococci Reveals a Mutation That Modulates Global Phenotype and Disease Specificity

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Abstract
Many human pathogens produce phenotypic variants as a means to circumvent the host immune system and enhance survival and, as a potential consequence, exhibit increased virulence. For example, it has been known for almost 90 y that clinical isolates of the human bacterial pathogen group A streptococci (GAS) have extensive phenotypic heterogeneity linked to variation in virulence. However, the complete underlying molecular mechanism(s) have not been defined. Expression microarray analysis of nine clinical isolates identified two fundamentally different transcriptomes, designated pharyngeal transcriptome profile (PTP) and invasive transcriptome profile (ITP). PTP and ITP GAS differed in approximately 10% of the transcriptome, including at least 23 proven or putative virulence factor genes. ITP organisms were recovered from skin lesions of mice infected subcutaneously with PTP GAS and were significantly more able to survive phagocytosis and killing by human polymorphonuclear leukocytes. Complete genome resequencing of a mouse-derived ITP GAS revealed that the organism differed from its precursor by only a 7-bp frameshift mutation in the gene (covS) encoding the sensor kinase component of a two-component signal transduction system implicated in virulence. Genetic complementation, and sequence analysis of covR/S in 42 GAS isolates confirmed the central role of covR/S in transcriptome, exoproteome, and virulence modulation. Genome-wide analysis provides a heretofore unattained understanding of phenotypic variation and disease specificity in microbial pathogens, resulting in new avenues for vaccine and therapeutics research. Phenotypic heterogeneity within an infecting population is a strategy commonly used by bacterial pathogens to evade the host immune system and enhance survival. Such phenotypic variation has been observed for the human pathogen group A streptococci (GAS), which can cause a wide range of diseases with differing severity. However, the underlying mechanisms that control this variation, and the survival- and virulence-associated effects of this variation, have not been fully elucidated. By assaying total gene expression the authors found that clinical GAS isolates from invasive and pharyngeal diseases had distinct gene expression patterns during growth in standard laboratory media. These two gene expression patterns conferred distinct virulence-associated attributes on the expressing GAS strain, as assessed using bacteremia and soft-tissue infection models of disease. Likewise, the ability to survive the bactericidal activity of human neutrophils was significantly different between GAS strains with the two distinct expression patterns. Transition from one gene expression pattern to the other required the mutation of the two-component signal transduction system CovRS (control of virulence R/S). The authors conclude that the ability of GAS to remodel its transcriptome plays a major contribution in its ability to colonize distinct niches of the human body and cause disease.