Genomic Characterization of Group A Streptococci Causing Pharyngitis and Invasive Disease in Colorado, USA, June 2016- April 2017

Abstract

Background: The genomic features and transmission link of circulating Group A Streptococcus (GAS) strains causing different disease types, such as pharyngitis and invasive disease, are not well understood.

Methods: We used whole-genome sequencing to characterize GAS isolates recovered from persons with pharyngitis and invasive disease in the Denver metropolitan area from June 2016 to April 2017.

Results: The GAS isolates were cultured from 236 invasive and 417 pharyngitis infections. Whole-genome sequencing identified 34 emm types. Compared with pharyngitis isolates, invasive isolates were more likely to carry the erm family genes (23% vs 7.4%, P<.001), which confer resistance to erythromycin and clindamycin (including inducible resistance), and covS gene inactivation (7% vs 0.5%, P<.001). Whole-genome sequencing identified 97 genomic clusters (433 isolates; 2-65 isolates per cluster) that consisted of genomically closely related isolates (median single-nucleotide polymorphism=3 [interquartile range, 1-4] within cluster). Thirty genomic clusters (200 isolates; 31% of all isolates) contained both pharyngitis and invasive isolates and were found in 11 emm types.

Conclusions: In the Denver metropolitan population, mixed disease types were commonly seen in clusters of closely related isolates, indicative of overlapping transmission networks. Antibiotic-resistance and covS inactivation was disproportionally associated with invasive disease.

Keywords: Group A streptococcus; antimicrobial resistance; genomic cluster; invasive disease; pharyngitis.

Figure 1.

emm types identified in pharyngitis and invasive Group A Streptococcus isolates, Colorado, June 2016 to April 2017. (A) Number of isolates recovered from each month of the study period. (B) Number of isolates for each of the emm types identified. (C) Each point represents an emm type for which the x- and y-axis values indicate the proportion of invasive and pharyngitis isolates belonging to the emm type, respectively. The dotted line indicates where the 2 proportions are equal. Text labels under points are the emm types. emm types 49, 82, 92, and 76 (red) were significantly more common in invasive isolates, whereas emm types 4, 12, 3, 6, and 87 (blue) were significantly more common in pharyngitis isolates. (D) The same as (C) except that 57 invasive isolates that were recovered from people who injected drugs or who experienced homeless were removed.

Figure 2.

Distribution of antibiotic resistance genes by emm type. Within in individual emm type, the proportion of pharyngitis (blue) or invasive (red) isolates that were positive for the erm genes (A) or the tet genes (B) is shown. The x-axis is ordered by decreasing y-values of the invasive (red) group. The point size is proportion to isolate count. No pharyngitis isolates were emm 92; therefore, the corresponding proportion was absent. Only the 15 most frequent emm types each containing 10 or more isolates are shown.

Figure 3.

Distribution of virulence-related factors by emm type. The proportion of pharyngitis (blue) or invasive (red) isolates that were positive for inactivating mutations in the covS gene (COVS_NULL) (A), the Pnga 3 - Clade 3 up-regulated promoter of the nga operon (PNGA3) (B), and streptococcal pyrogenic exotoxin C (SPE_C) (C) is shown. The x-axis is ordered by decreasing y-values of the invasive (red) group. The point size is proportional to the isolate count. There were no emm92 pharyngitis isolates so no proportion existed. Only the 15 most frequent emm types each containing 10 or more isolates are shown.

Figure 4.

Clusters of genomically closely related pharyngitis and invasive Group A streptococcus isolates, Colorado, June 2016 to April 2017. (A) Distribution of single-nucleotide polymorphism (SNP) distance between a pair of emm-matched isolates that were within a same cluster (red, 3340 pairs) or nonclustered (blue, 1316 pairs). (B) Box-plot of cluster size (number of isolates within a cluster) by cluster type. (C) Clustered isolates within individual emm types. Each rectangle represents a cluster containing 2 or more isolates. Each spot within the rectangle indicates a pharyngitis isolate (blue) or an invasive isolate (red). An asterisk indicates a mixed cluster. The percentage of clustered isolates in each emm is shown at the end of the row. Only emm types in which at least 1 cluster was detected are shown. (D) Clustered isolates among invasive disease cases from people who injected drugs ([PWID] n = 45), who were experiencing homelessness (PEH, n = 23), and who had either of the 2 conditions (high risk, n = 57). Percentages of isolates that belong to a cluster among these patients are shown.