AUTHOR=Li Yuan , Rivers Joy , Mathis Saundra , Li Zhongya , Velusamy Srinivasan , Nanduri Srinivas A. , Van Beneden Chris A. , Snippes-Vagnone Paula , Lynfield Ruth , McGee Lesley , Chochua Sopio , Metcalf Benjamin J. , Beall Bernard 

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

JOURNAL=Frontiers in Microbiology

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.01547

DOI=10.3389/fmicb.2020.01547

ISSN=1664-302X

ABSTRACT=<sec><title>Background</title><p><italic>Streptococcus pyogenes</italic> 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 <italic>S. pyogenes</italic> lineages could inform vaccine development and disease control strategies.</p></sec><sec><title>Methods</title><p>We used whole-genome sequencing (WGS) to characterize all invasive <italic>S. pyogenes</italic> 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 <italic>emm</italic> 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 <italic>emm</italic> type.</p></sec><sec><title>Results</title><p>Seventy-one <italic>emm</italic> types were identified from 3873 isolates characterized. The <italic>emm</italic> types targeted by a 30-valent M protein-based vaccine accounted for 3230 (89%) isolates. The relative frequencies of <italic>emm</italic> 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 <italic>erm</italic>-positive <italic>emm</italic> types 92 and 83. The prevalence of 24 virulence factors, including 11 streptococcal pyrogenic toxins, ranged from 6 to 90%. In each of three <italic>emm</italic> types (<italic>emm</italic> 49, 82, and 92), a subgroup of isolates significantly expanded between 2016 and 2017 compared to isolates outside of the subgroup (<italic>P</italic>-values &lt; 0.0001). Specific genomic sequence changes were associated with these expanded lineages.</p></sec><sec><title>Conclusions</title><p>While the overall population structure of invasive <italic>S. pyogenes</italic> isolates in the United States remained stable, some lineages, including several that were antibiotic-resistant, increased between 2016 and 2017. Continued genomic surveillance can help monitor and characterize bacterial features associated with emerging strains from invasive infections.</p></sec>