Molecular characterisation and clonal analysis of group A streptococci causing pharyngitis among paediatric patients in Palermo, Italy

Global Streptococcus pyogenes strain diversity, disease associations, and implications for vaccine development: a systematic review

The high strain diversity of Streptococcus pyogenes serves as a major obstacle to vaccine development against this leading global pathogen. We did a systematic review of studies in PubMed, MEDLINE, and Embase that reported the global distribution of S pyogenes emm-types and emm-clusters from Jan 1, 1990, to Feb 23, 2023. 212 datasets were included from 55 countries, encompassing 74 468 bacterial isolates belonging to 211 emm-types. Globally, an inverse correlation was observed between strain diversity and the UNDP Human Development Index (HDI; r=-0·72; p<0·0001), which remained consistent upon subanalysis by global region and site of infection. Greater strain diversity was associated with a lower HDI, suggesting the role of social determinants in diseases caused by S pyogenes. We used a population-weighted analysis to adjust for the disproportionate number of epidemiological studies from high-income countries and identified 15 key representative isolates as vaccine targets. Strong strain type associations were observed between the site of infection (invasive, skin, and throat) and several streptococcal lineages. In conclusion, the development of a truly global vaccine to reduce the immense burden of diseases caused by S pyogenes should consider the multidimensional diversity of the pathogen, including its social and environmental context, and not merely its geographical distribution.

Evolution of macrolide resistance in Streptococcus pyogenes over 14 years in an area of central Italy

We evaluated temporal fluctuations in macrolide resistance rates, analysing genetic determinants of resistance and clonal evolution in a population of 2744 S. pyogenes isolates collected in the period 2000-2013. The total resistance rate to erythromycin of the isolates was 17.9 %. A maximum of erythromycin resistance emerged in 2000 (38.6 %), followed by a significant decrease to 5.2 % in 2012 (P < 0.0001). Molecular analysis revealed the presence and co-presence of known genetic resistance determinants mefA, mefE, ermTR and ermB, in line with phenotypes. PFGE analysis identified genetically related groups in 2000 and 2007-2008, mainly the MLS and M phenotypes, respectively. The most prevalent emm types among a representative subset of resistant isolates were emm2, emm75 and emm77. All emm2 and 88.2 % of the strains harbouring the emm75 gene were only recorded in M-phenotype strains, whilst all emm77-positive strains had the inducible MLS phenotype. The analysed susceptible isolates showed several emm types partially shared with resistant ones. Our results suggest that changes in bacterial population clonality, rather than horizontal transfer of resistance determinants, plays a major epidemiological role in S. pyogenes. Continuous monitoring of microbiological epidemiology seems to be crucial for correct and effective management of streptococcal infections.

Molecular epidemiology and genomics of group A Streptococcus

Streptococcus pyogenes (group A Streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed.

Decline in macrolide resistance rates among Streptococcus pyogenes causing pharyngitis in children isolated in Italy

Macrolides are often used to treat group A streptococcus (GAS) infections, but their resistance rates reached high proportions worldwide. The aim of the present study was to give an update on the characteristics and contemporary prevalence of macrolide-resistant pharyngeal GAS in Central Italy. A total of 592 isolates causing pharyngitis in children were collected in the period 2012–2013. Clonality was assessed by emm typing and pulsed-field gel electrophoresis (PFGE) for all macrolide-resistant strains and for selected susceptible isolates. Genetic determinants of resistance were screened by polymerase chain reaction (PCR). Forty-four GAS were erythromycin-resistant (7.4 %). Among them, 52.3 % and 50 % were clindamycin- and tetracycline-resistant, respectively. erm(B)-positive isolates (52.3 %) expressed the constitutive cMLS_B phenotype. mef(A) and its associated M phenotype were recorded in 40.9 % of the cases. The remaining erm(A)-positive isolates expressed the iMLS_B phenotype. Seventeen tetracycline-resistant isolates carried tet(M) and five isolates carried tet(O). Twenty-five emm types were found among all strains, with the predominance of emm types 12, 89, 1, and 4. Eleven emm types and 12 PFGE clusters characterized macrolide-resistant strains, with almost two-thirds belonging to emm12, emm4, and emm11. Macrolide-susceptible and -resistant emm types 12, 89, 11, and 4 shared related PFGE profiles. There was a dramatic decline in macrolide resistance in Central Italy among pharyngeal GAS isolates in 2012–2013 when compared to previous studies from the same region (p < 0.05), although macrolide consumption remained stable over the past 15 years. We observed a decrease in the proportion of macrolide-resistant strains within emm types commonly associated with macrolide resistance in the past, namely emm12, 1, and 89.

Evaluation of emm gene types, toxin gene profiles and clonal relatedness of group A streptococci

The aim of this study is to evaluate antibiotic susceptibilities, emm gene types, toxin gene profiles and clonal relatedness of group A streptococci (GAS) isolates obtained from patients and carriers. A total of 79 clinical isolates from patients and 60 isolates from carriers were included in the study. Emm typing, toxin gene detection for speA, speB, speC, speG and smeZ genes and pulsed-field gel electrophoresis (PFGE) was performed. Twenty-one distinct emm types were detected; the most common types were emm12, emm89, emm1, emm77, emm4 and emm3. The detection rates of both emm types and the toxin genes didn't differ significantly between patients and carriers. The presence of speA and smeZ was significantly higher in emm1 and speG was significantly lower in emm4 when compared to the other emm types. The rate of clustering obtained with PFGE wasn't significantly different in patients and carriers. As a result, twelve of the 21 emm types detected in this study were covered by the 26-valent vaccine, constituting 77.7% of the emm typeable isolates; however the emm4 type which is one of the most common types in the present study is not among this coverage.

Distribution of phage-associated virulence genes in pharyngeal group a streptococcal strains isolated in Italy

The presence and assortment of 16 known virulence/resistance genetic determinants carried by prophages or prophage-like elements were tested in 212 clinical group A Streptococcus (GAS) strains and related to available data from SmaI macrorestriction/pulsed-field gel electrophoresis analysis and emm typing. A strong correlation existed among the three analyses. This finding supports the substantial contribution to the evolution and diversification of the GAS genome attributed to phages.