Background: Streptococcus pyogenes is a major cause of community-acquired and nosocomial infections linked with morbidity and mortality worldwide. Clindamycin resistance is rare globally in streptococci and is associated with specific lineages. We investigated the emergence and outbreak of a globally rare multidrug-resistant S. pyogenes emm93.0, ST-10 among iGAS infections in Israel.
Methods: Invasive group A streptococcal (iGAS) disease is notifiable is Israel and all isolates are analyzed for emm types at the Streptococcus national reference center. emm93.0 outbreak strains were tested for antibiotic susceptibility. Whole genome sequences were analyzed for phylogeny, resistance and virulence determinants.
Results: During 2014-2019 a total of 2,947 iGAS isolates were classified and analyzed (blood-51.3%, wounds-21.7%). Molecular assignment into 180 emm types revealed emergence of successful lineages. The incidence of iGAS ranged between 4-7 cases/100,000 population per year. An increasing trend in incidence was observed during 2016-2019. During this period, emm93.0 was the cause of 116 infections and became the leading type during 2018 (N=59). Following this period this type remained prevalent (2020-N=23, 2021-N=14). Cases were geographically disseminated, male (76%), adults ≥18 years (94.7%), bacteremia (75%).
Notably, multidrug resistance was observed for clindamycin, tetracycline and trimethoprim/sulfamethoxazole. WGS-based phylogeny confirmed clonality among geographically disseminated isolates and a novel genomic island harboring the resistance genes lsa(E),lnu(B), ant(6)-Ia aph(3')-III was identified.
Conclusions: The increasing prevalence of clindamycin resistance in iGAS infection highlights susceptibility testing as a guide for effective treatment. Further phenotypic and genomic studies are required to determine the prevalence of this resistance element in other iGAS types.