Biological characteristics and whole-genome sequencing analysis of an alpha-hemolytic Streptococcus pyogenes strain

Background Streptococcus pyogenes is a major human pathogen. Recently, alpha-hemolytic isolates—unusual for this typically beta-hemolytic species—have emerged, but their virulence, antibiotic resistance, and evolution are poorly understood. This study used an alpha-hemolytic pyogenic streptococcus isolated from erysipelas skin secretions and used whole-genome sequencing, phenotypic testing, and bioinformatics to characterize its virulence, resistance, and phylogeny. Methods A clinical isolate of alpha-hemolytic streptococcus was obtained from a tertiary care hospital. Species identification was conducted using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and the VITEK® II Compact system. Antimicrobial susceptibility testing was performed using the disk diffusion method and E-test strips. Whole-genome sequencing was carried out by Beijing Novogene Co., Ltd., followed by genome assembly, functional gene annotation, phylogenetic tree construction, multilocus sequence typing (MLST), and emm gene typing. Comprehensive bioinformatic analyses were conducted to identify antibiotic resistance genes and virulence-associated genes. Results Both MALDI-TOF MS and biochemical assays confirmed the isolate as Streptococcus pyogenes . Antimicrobial susceptibility testing revealed resistance to macrolides and tetracycline, while sensitivity was maintained to penicillins, cephalosporins, and other tested agents. MLST assigned the strain to sequence type ST176, and emm typing identified it as emm58.7. Resistance genes including tet(M), mef(A), and msr(D) were detected. Additionally, multiple virulence factor-encoding genes—such as fbp54, hylA, hasA, hasB, hasC, ideS/mac, slo, sagA, speB, speC, speG, speJ, and smeZ—were identified in the genome. Conclusion This S. pyogenes isolate exhibited atypical alpha-hemolysis rather than the classical beta-hemolytic phenotype on Columbia blood agar, resembling the hemolytic pattern of viridans group streptococci.The alpha-hemolytic phenotype may be attributed to a substitution at position 215 of the sagB gene, where serine (S) is replaced by proline (P), potentially disrupting the functional expression of streptolysin S (SLS) and thereby leading to alpha-hemolysis. However, this phenotypic variation did not compromise its accurate microbiological identification, virulence potential, or antimicrobial susceptibility profile. Due to morphological and hemolytic similarities with commensal flora, there is a risk of clinical underdetection. Integrating antigen detection, serological antibody testing, and molecular diagnostic methods can enhance the detection rate of such atypically presenting S. pyogenes strains, thereby reducing the likelihood of misdiagnosis or missed diagnosis.