Emerging Threat of Antimicrobial Resistance in β-Hemolytic Streptococci

Abstract

Highly variable resistance rates to erythromycin and clindamycin have been reported in the β-hemolytic streptococcal species Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus dysgalactiae, depending on geographic and temporal context. In the present study we aimed to examine the longitudinal trends of antimicrobial resistance in these three species in a northern European setting. Furthermore, we used whole genome sequencing to identify resistance determinants and the mobile genetic elements involved in their dissemination, as well as elucidate phylogenetic relationships. All cases of invasive β-hemolytic streptococcal diseases in Health Region Bergen, western Norway, in the period 2004 to 2018 were retrospectively identified, comprising 271, 358, and 280 cases of S. pyogenes, S. agalactiae, and S. dysgalactiae, respectively. Antimicrobial susceptibility testing revealed a gradual but significant increase in erythromycin and clindamycin resistance for S. agalactiae and S. dysgalactiae during the study period. Whole genome sequencing of the erythromycin and clindamycin resistant bacterial population revealed a substantial phylogenetic diversity in S. agalactiae and S. dysgalactiae. However, the mobile genetic elements harboring the resistance determinants showed remarkable intra- and interspecies similarities, suggesting a dissemination of antimicrobial resistance predominantly through conjugative transfer rather than clonal expansion of resistant strains in these two species. Conversely, antimicrobial resistance in S. pyogenes remained low, apart from a transient outbreak of a clindamycin and erythromycin resistant emm11/ST403-clone in 2010-2012. Increased epidemiological attentiveness is warranted to monitor the emerging threat of antimicrobial resistance in β-hemolytic streptococci, particularly in S. agalactiae and S. dysgalactiae.

Keywords: Streptococcus agalactiae; Streptococcus dysgalactiae; Streptococcus pyogenes; antimicrobial resistance; β-hemolytic streptococci.

FIGURE 1

Temporal trends of erythromycin and clindamycin resistance in BHS. Resistance to erythromycin (A) and clindamycin (B) increased significantly in Streptococcus agalactiae (GBS) and Streptococcus dysgalactiae (SD) during the study period. In Streptococcus pyogenes (GAS) resistance to erythromycin and clindamycin remained low, apart from a transient outbreak of resistance to both agents in the period 2010–2012.

FIGURE 2

Phylogenetic trees of the resistant BHS – population. The phylogenetic trees are based on core-genome SNP-analysis of S. pyogenes (A), S. agalactiae (B), and S. dysgalactiae (C) isolates displaying reduced susceptibility to erythromycin and/or clindamycin. The scale indicates substitutions per site. Isolates clustering with >97% similarity have been highlighted with colored rectangular boxes. The circular node tips have been assigned color coding according to the mobile genetic element harboring the MLS_B-resistance gene in the respective isolates. Red indicates ICEsp2907, blue color has been assigned to Tn3872, yellow indicates ICESa2603, isolates carrying the bacteriophage 1207.3 are white, and all other elements are depicted in black. The red asterisk indicates the two isolates co-harboring lsa(C).

FIGURE 3

Genetic composition of the mobile genetic element IMEsp2907 in three BHS. Mauve was used for the sequence alignment of the mobile genetic element. Panel (A) depicts a comparison of IMEsp2907 detected in the invasive BHS isolates iGAS302 (S. pyogenes), iGBS485 (S. agalactiae), and iSDSE357 (S. dysgalactiae). The integrative mobilizable element displayed a conserved genetic architecture and highly similar nucleotide sequences in these three species. Genes involved in mobilization and integration accounted for the majority of the discrepancies. The gene immediately downstream from erm(A) is annotated by RAST as a spectinomycin resistance gene based on sequence similarities, but has not been experimentally verified. Panel (B) displays an alignment of Tn3872 detected in two GBS isolates and one SD isolate. The ICE Tn3872 is composed of an erm(B) module (highlighted in a pink box) integrated into a Tn916 element.