Genomic Characterization of a Pattern D Streptococcus pyogenes emm53 Isolate Reveals a Genetic Rationale for Invasive Skin Tropicity

Abstract

The genome of an invasive skin-tropic strain (AP53) of serotype M53 group A Streptococcus pyogenes (GAS) is composed of a circular chromosome of 1,860,554 bp and carries genetic markers for infection at skin locales, viz., emm gene family pattern D and FCT type 3. Through genome-scale comparisons of AP53 with other GAS genomes, we identified 596 candidate single-nucleotide polymorphisms (SNPs) that reveal a potential genetic basis for skin tropism. The genome of AP53 differed by ϳ30 point mutations from a noninvasive pattern D serotype M53 strain (Alab49), 4 of which are located in virulence genes. One pseudogene, yielding an inactive sensor kinase (CovS ؊ ) of the two-component transcriptional regulator CovRS, a major determinant for invasiveness, severely attenuated the expression of the secreted cysteine protease SpeB and enhanced the expression of the hyaluronic acid capsule compared to the isogenic noninvasive AP53/CovS ؉ strain. The collagen-binding protein transcript sclB differed in the number of 5=-pentanucleotide repeats in the signal peptides of AP53 and Alab49 (9 versus 15), translating into different lengths of their signal peptides, which nonetheless maintained a full-length translatable coding frame. Furthermore, GAS strain AP53 acquired two phages that are absent in Alab49. One such phage (⌽AP53.2) contains the known virulence factor superantigen exotoxin gene tandem speK-slaA. Overall, we conclude that this bacterium has evolved in multiple ways, including mutational variations of regulatory genes, short-tandem-repeat polymorphisms, large-scale genomic alterations, and acquisition of phages, all of which may be involved in shaping the adaptation of GAS in specific infectious environments and contribute to its enhanced virulence. IMPORTANCEInfectious strains of S. pyogenes (GAS) are classified by their serotypes, relating to the surface M protein, the emm-like subfamily pattern, and their tropicity toward the nasopharynx and/or skin. It is generally agreed that M proteins from pattern D strains, which also directly bind human host plasminogen, are skin tropic. We have sequenced and characterized the genome of an invasive pattern D GAS strain (AP53) in comparison to a very similar strain (Alab49) that is noninvasive and developed a genomic rationale as to possible reasons for the skin tropicity of these two strains and the greater invasiveness of AP53. G roup A Streptococcus pyogenes (GAS) is a beta-hemolytic, Gram-positive, human-pathogenic bacterium that infects multiple epithelial surfaces and, in some cases, is able to invade deeper soft tissue and cause severe disease (1). An estimated 700 million cases of GAS infection occur worldwide per year (2), ranging from benign treatable clinical conditions, e.g., pharyngitis and impetigo, to more invasive and potentially lethal infections, including necrotizing fasciitis (NF), streptococcal toxic shock syndrome (STSS), acute rheumatic fever (ARF), and acute glomerulonephritis (AGN) (3, 4). The wide range of infectious niches and broad varianc...

Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps

“…The calculation shows that there is no significant difference in the sequence diversity within and between the sublineages SI and ARF ( p -value > 0.07, t -test), indicative of the absence of complete genetic barriers to horizontal gene transfer between the two sublineages. A prominent example for horizontal gene transfer between the sublineages SI and ARF is the FCT locus (encoding Fibronectin-binding proteins, Collagen-binding proteins and T-antigens), where several strains associated with SI and ARF share the same pattern of gene organization43. The surface proteins encoded by the locus facilitate the adherence of bacteria to host cells, and the host cell surfaces in turn may provide venues for the bacteria to disseminate gene contents between the strains.…”

The Streptococcal Protease SpeB Antagonizes the Biofilms of the Human PathogenStaphylococcus aureusUSA300 through Cleavage of the Staphylococcal SdrC Protein

“…AP53CovS+ is a M53 GAS strain belonging to the emm pattern D subgroup (34), members of which are skin-trophic and have higher levels of SpeB secretion than A-C emm pattern strains (21). To evaluate the effects of SpeB production by the GAS strain AP53CovS+, we first generated an isogenic speB deletion mutant.…”

“…The GAS strain AP53 was described by Berge in 1993 (51) and its whole genome sequence determined in 2016 (34). In 2013, it was discovered that the original clinical isolate contained a mutated two-component signal protein (CovS), which was not expressed (AP53CovS-).…”

“…Compared to the large number of host-based studies of SpeB, little research has been on September 16, 2020 by guest http://jb.asm.org/ Downloaded from 6 conducted on potential roles of SpeB against other microorganisms in a polymicrobial environment. Another human pathogen and skin colonizer, Staphylococcus aureus, can occupy similar niches to the S. pyogenes strain AP53CovS+, a skin-trophic, noninvasive GAS strain (34,35). S. aureus is clinically important due to its ability to cause human disease in the form of skin infections, sepsis, and pneumonia (36)(37)(38)(39).…”

Comparative pathogenomic characterization of a non-invasive serotype M71 strain Streptococcus pyogenes NS53 reveals incongruent phenotypic implications from distinct genotypic markers

“…Previously, we proposed that the emm pattern D strains with skin tropicity have subtype FCT-3 (Bao et al 2016a). Based on this correlation, serotype M71 strains should be probably more disposed to cause skin infection.…”