Antimicrobial resistance of Group A Streptococcus isolates from patients in Shenzhen, China during COVID-19 pandemic

Group A Streptococcus (GAS) is a bacterial pathogen causing various infections and autoimmune diseases, with humans as its only host. Transmission occurs mainly via airborne droplets and skin mucous membrane contact. While previous surveillance studies from our group (2016–2018) established baseline resistance profiles and genotype distributions of GAS in Shenzhen, the profound societal and healthcare disruptions caused by the COVID-19 pandemic presented a unique natural experiment to investigate potential shifts in bacterial epidemiology. This study aimed to conduct a comparative molecular epidemiological analysis of GAS isolates from pediatric patients (0–18 years) in Shenzhen during the pandemic years (2019–2020), specifically focusing on temporal changes in antimicrobial resistance patterns, emm type prevalence, and Multilocus sequence types (MLST). We hypothesized that pandemic control measures might have altered GAS transmission dynamics, potentially leading to changes in the circulating strain population and its associated resistance profiles. GAS strains isolated from outpatients and wards between January 2019 and December 2020 were collected. Antimicrobial susceptibility testing was performed according to CLSI guidelines. Macrolide and tetracycline resistance genes, emm typing, and MLST were analyzed by PCR. All 124 GAS strains were sensitive to penicillin, with 95.2% sensitive to levofloxacin. Most strains were resistant to clindamycin, azithromycin, clarithromycin, erythromycin, and tetracycline (resistance rates: 73.4%-78.2%). Chloramphenicol resistance was low (3.2%). Macrolide resistance genes were detected in 79.8% (ermB), 44.0% (ermA), and 45.1% (mefA) of strains. Tetracycline resistance genes were found in 46.7% (tetO) and 80.6% (tetM). Twelve emm types were identified, with emm1, emm3, emm4, and emm12 being common in both years. Resistance rates slightly increased in 2020 compared to 2019. Despite a reduction in GAS isolates collected during the pandemic, a significant increase in resistance rates to clindamycin, macrolides, and tetracycline was observed in 2020 compared to 2019 (P < 0.05). Continuous surveillance of GAS antimicrobial resistance and clonal dynamics is crucial to inform evidence-based antibiotic stewardship policies and to optimize empirical treatment strategies in clinical practice.