Overall, 1320 GAS isolates were collected during the 32-month study period, 904 from HD1 and 416 from HD2, respectively. This represents 14% of all GAS-positive pharyngitis cultures performed in these two laboratories during this period: 22% (of 4023 isolates) in HD1 and 7.4% (of all 5597 isolates) in HD2, respectively (Fig. 1 A).

A The number of pharyngitis GAS isolates collected to our study by season from Hospital District 1 between March 2018 and December 2020 (bar chart) in relation to all GAS-positive pharyngitis findings from the same period collected in the same hospital district (line chart). Sample collection was halted for 6 weeks in Spring 2020 (16.3–26.4.2020). The vertical black bar marks the start of the COVID-19 pandemic (Spring 2020). Data is shown for each 3-month period; however, Winter 2021 includes only the month of December. The aim was to collect 10 isolates per week. The fulfilment was on average 7 isolates per week (range 0–19). B and C Seasonal fluctuations of main emm types (B) and emm clusters (C) among GAS pharyngitis isolates collected in Hospital District 1. Isolates collected after March 2020 (black bar) were not included in the seasonality analysis. *Significant difference (p < 0.05) observed for emm12, emm75, emm89 and the group ”others”

The median number of weekly collected strains was seven (range 0–19). Before the COVID-19 pandemic, the proportion of collected isolates in relation to all GAS isolates varied between 6.0 % (spring 2018, 52/865) and 40% (autumn 2019, 117/293). After the start of COVID-19 pandemic, the amount of isolates decreased, but the proportion remained high (37%, 146/392, Fig. 1 A).

The median age of patients was 17 years (range < 1–81 years). The most common age group was under 10-year-olds (298/904, 33% of all) and 71% of these were 5–9-year-olds (212/904, 23% of all). 58 % of the study subjects were female (526/904, 58%). The age distribution was significantly different between genders (p < 0.0001). Median age of males was 11 years (range 1–72 years), whereas within females it was 21 years (range < 1–81 years). Within males, most cases occurred in the age group under 10 years (177/378, 47%). Within females, the distribution was more uniform until age of 40 years (20–23% of the cases in each of the 10-year age group), whereas within males the distribution was skewed to right (Fig. 2).

The age distribution in years (y) by gender, male (n = 378) and female (n = 526), of GAS pharyngitis cases in Hospital District 1 between March 2018 and December 2020. The age distribution was significantly different between genders (p < 0.0001)

Altogether, 34 different emm types were identified (Fig. 3 A, Online Resource 1). The four most common types were emm12 (20%), emm28 (19%), emm89 (16%) and emm1 (15%), and they covered 70% of the isolates. Two major emm subtypes dominated within emm1; emm1.0 (n = 96, 11% of all) and emm1.25 (n = 29, 3.2%), respectively, and within emm12; emm12.0 (n = 83, 9.2%) and emm12.37 (n = 63, 7.0%), respectively. Five of the most common emm cluster patterns were E4 (367/904 isolates, 41%), A-C4 (n = 178, 20%), A-C3 (n = 132, 15%), E1 (n = 95, 11%) and E6 (n = 79, 8.7%) (Online resorce 1).

Emm types and cumulative percentage of GAS pharyngitis isolates collected A in Hospital District 1 (n = 904) and B in Hospital District 2 (n = 416) during the study period

97% of the isolates shared emm types putatively covered by the 30-valent GAS M-protein-based vaccine [14].

Age group was associated with prevalence of emm28 (p = 0.005) and emm89 (p = 0.028). emm28 was most common in the age group of 20–29 years. Compared to the rarest group among > 60 years old, the OR for the age group of 20–29 years is 7.0 (95%CI [2.5–19.6]). Also, all other age groups between 10 and 39 years old differed from the rarest age group (> 60 years old). emm89 was most common at the age group < 10 years; statistically significant difference was to all age groups between 20–49 years, ORs varying from 0.4 to 0.5 (Online Resource 2). No other statistical difference was observed between any of the identified emm type and age group or gender.

The emm-type distributions varied over time (Fig. 4). Frequency of emm1 decreased during the study (n = 60 (58%) in 2018, n = 11 (11%) in 2020), whereas emm12 increased (n = 41 (23%) vs n = 59 (33%)), respectively.

A Distribution of emm types among GAS pharyngitis isolates collected in Hospital District (HD) 1 (n = 904) and HD2 (n = 416) by year. The annual number of isolates is shown under each column. B Distribution of emm types of invasive GAS isolates reported from HD1 (n = 64) and HD2 (n = 93) during 2018–2020. The total number of isolates is shown under the column. In group “others” in iGAS isolates, the proportion of emm77 isolates was high in HD2 (13% of the isolates) and emm84 in HD1 (7.8%). Seven most common emm types (emm1, emm1.25, emm4, emm12, emm28, emm75 and emm89) were studied individually and the rest jointly under the group “others”

The number of isolates varied significantly in relation to season (p < 0.001, Fig. 1 A). Most isolates were collected during autumn (n = 246, 27% of all) and winter (n = 248, 27%). As to emm types, seasonality was noted to be significant within emm12 (p < 0.0001), emm75 (p = 0.003), emm89 (p = 0.003) and the group “others” (p = 0.0007) (Fig. 1 B). Most of the emm12 isolates were observed in winter (n = 76, 43%), emm75 in autumn (n = 23, 40%), emm89 in winter (n = 45, 32%) and “others” in autumn (n = 36, 38%). For emm1, emm1.25, emm4 and emm28, there was no statistically significant changes between seasons. Of note is the rise of the group “others” during the COVID-19 pandemic months.

In total, 21 emm types were identified among the 416 isolates collected (Fig. 3 B, Online Resource 1). The four most common emm types were emm1 (38%), emm12 (18%), emm28 (17%) and emm89 (9.6%) covering 75% of the isolates. Two major emm1 subtypes dominated: emm1.0 (n = 119, 29%) and emm1.25 (n = 31, 7.5%). The annual distribution of emm types differed (Fig. 4A). emm1 decreased (n = 39 (31%) in 2018 vs n = 10 (18%) in 2020) and emm12 increased (n = 18 (14%) vs n = 20 (36%)), respectively. Five of the most common emm cluster patterns were A-C3 (n = 156, 38% of all), E4 (n = 124, 30%), A-C4 (n = 74, 18%), E6 (n = 23, 5.5%) and E1 (n = 15, 3.6%). One emm type (emm240.3) did not belong to any known emm cluster (Online resorce 1).

Ninety-seven percent of the isolates shared emm types putatively covered by the 30-valent GAS M-protein-based vaccine (14).

Altogether, 157 iGAS cases were reported (64 in HD1 and 93 in HD2) between 2018–2020. The four most common emm types in HD1 were emm1 (30%), emm28 (28%), emm4 (9.3%) and emm84 (7.8%) and in HD2 emm1 (24%), emm28 (14%), emm77 (13%) and emm89 (12%) (Fig. 4 B). Compared by source of specimen, emm12 was found to be more common among pharyngitis than iGAS isolates in both hospital districts (Figs. 3 and 4 B). While emm77 and emm84 were common in iGAS, they were rare among pharyngitis isolates (grouped to “others”).