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

Abstract

Scarlet fever (SF) has recently been associated with group A streptococcal (GAS) strains possessing multidrug resistance and specific streptococcal exotoxins. We screened a local surveillance collection of GAS emm12 strains in Houston, TX, USA for antimicrobial resistance and identified a single isolate matching the antimicrobial resistance pattern previously reported for SF clones. Using whole-genome sequencing and combining genome sequence data derived from national surveillance databases, we identified additional emm12 GAS clones similar to those associated with prior SF outbreaks, emphasizing the need for continued surveillance for epidemic emergence in the USA.

Keywords: antimicrobial resistance; emm12; group A Streptococcus; paediatric; scarlet fever.

Fig. 1.

(a) Comparison of Houston/US SF-like emm12 GAS strains to previously described SF outbreak strains. Phylogenetic reconstruction of 670 emm12 GAS strains (Table 1) based on 7159 core genome biallelic SNP loci relative to the reference strain MGAS2096 using RAxML. Disease type, country, resistance genotype and exotoxin/DNase content are indicated in the vertical bars on the right. Strains mentioned in the text are labelled. (b) Comparison of TSPY1687 to reference emm12 GAS genomes. The complete genome of TSPY1687 was resolved using a combination of short- and long-read sequences and annotated (PGAP at NCBI). blast comparisons to HKU16 (AFRY01000001), SP1336 (CP031738) and MGAS2096 (CP000261) are indicated in red, orange and yellow rings (inside to outside), respectively. Ring legend (inside to outside): (1) GC content, (2) GC skew, (3) SNPs relative to HKU16, (4) HKU16 blast comparison, (5) SNPs relative to SP1336, (6) SP1336 blast comparison, (7) SNPs relative to MGAS2096, (8) MGAS2096 blast comparison, (9) genomic features of TSPY1687 including prophage (blue), ICE (red) and exotoxin/DNase genes (black).

Fig. 2.

Comparison of exotoxin and antimicrobial resistance encoding MGE between TSPY1687 and HKU16. progressiveMauve alignments of: (top alignment) ICE-TSPY1687 (TSPY1687) compared to ICE-emm12 (HKU16) with antimicrobial resistance genes boxed and labelled and (bottom alignment) 1687.2 (TSPY1687) relative to ϕHKU.vir (HKU16) with exotoxin genes boxed and labelled. Bar at the top of each alignment indicates degree of homology: green (100%), yellow (>30 %), none (absent in one genome). Additionally, black markings on solid bar below annotations indicate nucleotide differences.