Detection of asymptomatic group A <i>Streptococcus</i> throat carriage and respiratory viruses during pharyngitis outbreaks in two daycare centers

ABSTRACT This study aimed to characterize the frequency of asymptomatic group A Streptococcus (GAS) carriage and respiratory virus detection, and to assess the utility of GAS nucleic acid amplification tests (NAATs) as a microbiological screening method during pharyngitis outbreaks. In this observational cross-sectional study, we recruited healthy children and daycare employees from two daycare centers experiencing GAS pharyngitis outbreaks. One throat swab was collected for GAS culture and NAAT, and another for respiratory virus NAAT. All GAS isolates underwent whole-genome sequencing (WGS). A total of 87 individuals were enrolled: 68 children and 19 adults. GAS was detected in 19/87 (22%) participants by culture, and 36/87 (41%) by NAAT. Most isolates were emm1.0 in outbreak 1 (5/7, 71%) and emm4.0 in outbreak 2 (10/12, 83%). WGS demonstrated high genetic similarity within each outbreak (median 1.3–3 SNP differences). Respiratory virus detection rates were similar between GAS-positive (10/19, 53%) and GAS-negative (33/68, 49%) individuals. In outbreak 1, enteroviruses were more common among GAS-positive participants (4/7, 57%) than GAS-negative participants (4/37, 11%; unadjusted P = 0.014). In conclusion, substantial asymptomatic GAS carriage was observed. The contribution of concurrent respiratory virus circulation to GAS transmission remains uncertain. However, enterovirus detection was more frequent among GAS-positive individuals in one outbreak. The high sensitivity of GAS NAATs, which detect nucleic acids rather than viable bacteria, may complicate efforts to balance outbreak control with antimicrobial stewardship. IMPORTANCE Group A Streptococcus (GAS) is an increasingly important respiratory pathogen, causing illnesses ranging from life-threatening infections to pharyngitis and asymptomatic carriage. The factors influencing GAS transmission remain poorly defined, and, in the absence of a GAS vaccine, identifying determinants that may guide outbreak-control strategies is essential. In this observational cross-sectional study, substantial asymptomatic carriage was observed among children and adults in daycare centers experiencing GAS outbreaks: 22% by throat culture and 41% by nucleic acid amplification testing (NAAT). Co-detection of respiratory viruses was also common, and in one outbreak, enterovirus detection was more frequent among GAS-positive individuals. These findings provide preliminary insight into the complex dynamics of GAS transmission and highlight asymptomatic carriage and viral co-infections as potential intervention targets. However, the increased sensitivity of GAS NAATs compared with culture may complicate outbreak management by potentially driving unnecessary antimicrobial use.