Genomic Surveillance of Streptococcus pyogenes Strains Causing Invasive Disease, United States, 2016–2017

Abstract

Background: Streptococcus pyogenes is a major cause of severe, invasive infections in humans. The bacterial pathogen harbors a wide array of virulence factors and exhibits high genomic diversity. Rapid changes of circulating strains in a community are common. Understanding the current prevalence and dynamics of S. pyogenes lineages could inform vaccine development and disease control strategies. Methods: We used whole-genome sequencing (WGS) to characterize all invasive S. pyogenes isolates obtained through the United States Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs) in 2016 and 2017. We determined the distribution of strain features, including emm type, antibiotic resistance determinants, and selected virulence factors. Changes in strain feature distribution between years 2016 and 2017 were evaluated. Phylogenetic analysis was used to identify expanding lineages within emm type. Results: Seventy-one emm types were identified from 3873 isolates characterized. The emm types targeted by a 30-valent M protein-based vaccine accounted for 3230 (89%) isolates. The relative frequencies of emm types collected during the 2 years were similar. While all isolates were penicillin-susceptible, erythromycin-resistant isolates increased from 273 (16% of 2016 isolates) to 432 (23% of 2017 isolates), mainly driven by increase of the erm-positive emm types 92 and 83. The prevalence of 24 virulence factors, including 11 streptococcal pyrogenic toxins, ranged from 6 to 90%. In each of three emm types (emm 49, 82, and 92), a subgroup of isolates significantly expanded between 2016 and 2017 compared to isolates outside of the subgroup (Pvalues < 0.0001). Specific genomic sequence changes were associated with these expanded lineages.

Identification of epidemic scarlet fever group A Streptococcus strains in the paediatric population of Houston, TX, USA

“…From the 300 emm12 GAS isolates from Houston, TX screened for antimicrobial resistance, a total of 14 (5 %) were identified with resistance to erythromycin or tetracycline and a single isolate (TSPY1687 – pharyngitis from 2018) was identified to be resistant to both antibiotics. Consistent with previous reports on GAS [ 12 ], we saw complete congruence between resistance phenotype and genotype for all Houston, TX strains analysed. For comparison, we also queried the genomes of all emm12 GAS isolates sequenced by the CDC ABCs and discovered three additional isolates with erythromycin and tetracycline resistance genes (CDC1–3, Fig.…”

Invasive Multidrug-Resistant emm93.0 Streptococcus pyogenes Strain Harboring a Novel Genomic Island, Israel, 2017–2019

“…The potential coverage of multivalent vaccines was low in Israel compared with other industrialized countries ( 21 ). The yearly predicted coverage of the 26-valent S. pyogenes vaccine was 36.7%–44.6% of the invasive strains, and 40.7% for the entire period.…”

Nonimmune antibody interactions of Group A Streptococcus M and M-like proteins

“…Nonimmune binding of IgG, IgA, or both is conserved in a wide variety of M protein types, Mrps, and PrtH. Mrps are encoded in almost 90% of Strep A isolates as surveyed from a globally representative collection [ 48 ], and PrtH is encoded in 30% of M1 Strep A strains, with M1 being the most prevalent M type in industrialized nations and the most prevalent cause of invasive disease in the United States [ 81 , 82 ]. It is therefore more likely than not that a Strep A strain interacts in nonimmune fashion with IgG, IgA, or both.…”