Virulence gene profiling of pharyngeal Group A streptococci isolated in Central Italy during the 2012 epidemic wave

Objectives Pharyngitis caused by Group A streptococcus (GAS) is a common disease and, though self-limiting, may be associated to suppurative tonsillar-pharyngeal or non-suppurative immunological sequelae. The aim of this work was to isolate GAS during the 2012 epidemic wave of pharyngitis and characterize their virulence genetic profile. Methods We collected one hundred seven (n = 107) GAS isolates between January and May 2012 in three different cities located in the central part of Italy. Their emm-type has been determined by sequencing following the CDC Streptococcus Laboratory guidelines. We applied a PCR screening to evaluate the presence of genes encoding the main GAS virulence factors, namely speA, speC, ssa, sdn, sla, speH, speI, speL, speM, speK, speB, and smeZ. Also the genetic structure of the GAS FCT region was screened by PCR. Results Twelve emm-types represented more than 90% of the isolates. emm4 was the most frequent type (13%), followed by emm1 (12%), emm12 (10%), emm6 (10%), emm89 (9%), emm29 (7%), and emm44 (7%). More than 30% of the isolates possessed an emm-type not included in the 26-valent vaccine under clinical evaluation. As long as the profile of virulence genes is concerned, we observed a high degree of clonality (Simpson index of diversity = 0.993 - CI95% = 0.989-0.997). On the average, the overall number of the considered virulence genes per isolate was 3 (SD = 1.7). Among the emm-types associated with the highest mean number of virulence genes per isolates we found emm4 and emm44, which are not considered among the types of the 26-valent vaccine. The more frequent FCT-types were FCT-4 (22%), FCT-5 (19%), and FCT-3 (12%). Interestingly, almost 19% of isolates could not be assigned to a known FCT-type. Conclusion The GAS population under study is highly polyclonal. This feature is the clear result of a significant rate of genetic variation playing a great role in the evolution and dissemination of this pathogen. As a consequence, a high degree of diversification continuously challenges the efficacy of a vaccine against GAS infections