[Genomic characteristics and drug resistance features of Group A Streptococcus in children from a district in Beijing City from 2012 to 2024].

Objective: To investigate the genomic characteristics, virulence genes, and drug resistance features of Group A Streptococcus (GAS) isolates in Huairou District, Beijing, from 2012 to 2024. Methods: Throat swab specimens were collected from pediatric outpatients and emergency cases clinically diagnosed with scarlet fever or pharyngeal infections in maternal and child health hospitals in Huairou District between May and July each year from 2012 to 2024. GAS isolates were identified and subjected to whole-genome sequencing to analyze M protein gene types (emm) and multilocus sequence typing (MLST). A phylogenetic tree was constructed based on core genomes. Antimicrobial resistance genes and virulence genes were identified and analyzed, and antibiotic susceptibility testing was performed. Results: A total of 1 776 throat swab specimens were collected, and 121 GAS isolates were obtained (6.81%, 121/1 776). Four emm genotypes were identified: emm1, emm3, emm6, and emm12. The most prevalent type was emm12 (54.55%, 66/121). From 2012 to 2019, the predominant type was emm1 (61.18%, 52/85), while from 2023 to 2024, the predominant type was emm12 (97.22%, 35/36). Among the 121 GAS isolates, five ST types were identified: ST36 (54.55%, 66/121), ST1274 (24.79%, 30/121), ST28 (19.01%, 23/121), one isolate of ST15, and one isolate of ST382. Phylogenetic analysis showed a strong consistency between the emm types and ST types. Besides emm genes, 56 virulence genes were detected in the 121 GAS isolates, with an average of 44.42 and 42.53 virulence genes carried by emm12 and emm1 GAS isolates, respectively (Z=-3.691, P<0.001). Nine streptococcal superantigen genes were identified, among which speA and speJ showed statistically significant differences in the carriage rates of GAS in emm1 (26.42%, 24.53%, respectively) and emm12 (59.09%, 57.58%, respectively) (χ²=11.60 and χ²=13.11, respectively; both P<0.05). Among the 121 GAS isolates, 120 exhibited drug resistance, with high resistance rates of erythromycin (99.17%, 120/121), tetracycline (97.52%, 118/121), and clindamycin (99.17%, 120/121). Additionally, 97.52% (118/121) of GAS isolates showed triple resistance to erythromycin, tetracycline, and clindamycin. Four resistance genes were detected: lmrP (100%, 121/121), ermB (99.17%, 120/121), mef(E) (99.17%, 120/121), and tet(M) (97.52%, 118/121). The genotype and phenotype of drug resistance were closely aligned. Conclusion: The predominant GAS types in children in this district of Beijing from 2012 to 2024 are emm12 and emm1, with strong concordance between emm and ST types. GAS isolates demonstrate high resistance to erythromycin, tetracycline, and clindamycin, and resistance genotypes align well with their phenotypes.