Genomic Characterization of Streptococcus  dysgalactiae subsp. equisimilis Associated with Respiratory Tract Infections

Filipe Barbosa Valcovo

Key information

Authors:

Filipe Barbosa Valcovo (Filipe Barbosa Valcovo)

Supervisors:

Marcos Daniel Caetano Borges de Pinho; Leonilde de Fátima Morais Moreira (Leonilde de Fátima Morais Moreira)

Published in

12/02/2022

Abstract

Human infections caused by Streptococcus dysgalactiae subsp. equisimilis (SDSE) have been rising in recent decades. Typing of the emm gene, which encodes an important virulence factor in SDSE, revealed two emm types to be almost exclusively associated with respiratory tract (RT) infections in Portugal. This motivated the characterisation of 199 RT isolates recovered in Portugal in the years 2011 to 2019 to define the main clonal lineages responsible for RT infection, to determine antimicrobial resistance, and employ high throughput sequencing to determine emm types, multilocus sequence typing (MLST) and core genome MLST (cgMLST) allele profiles, known virulence factors and to perform a genome-wide association study (GWAS) to explore possibly unknown virulence factors. RT infections in Portugal were more frequent among younger patients. Typing of the emm gene found 31 distinct emm types, of which stC36 and stC839 were almost exclusively associated with RT infections. MLST revealed 121 sequence types (ST) distributed among 37 clonal complexes (CC) and 72 singletons, with 3 distantly related lineages, CC3, CC49 and CC68, being almost exclusively associated with RT infection. While some CCs had a diverse variety of emm types, the CCs associated with the RT were associated with the RT emm types. Among known streptococcal virulence factors, mf3, a phage-associated extracellular nuclease, was almost exclusively associated to RT CCs. GWAS revealed that RT CCs lacked several CRISPR-associated proteins, which serve important roles in protection against phages, and possessed several phage genes, which may affect virulence.