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Cryptic prophages within a Streptococcus pyogenes genotype emm4 lineage.
Alex Remmington1, Samuel Haywood1, Julia Edgar1,2
1Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, UK.
Microbial Genomics
|November 27, 2020
Summary
Streptococcus pyogenes emm4 isolates show significant prophage gene loss, retaining key virulence factors. This degradation impacts mobile genetic elements and varies geographically between the US and UK.
Area of Science:
- Microbiology
- Genomics
- Evolutionary Biology
Background:
- Streptococcus pyogenes is a major human pathogen.
- Mobile genetic elements, including prophages, often carry virulence genes in S. pyogenes.
- Previous studies highlight the role of mobile genetic elements in bacterial evolution and pathogenicity.
Purpose of the Study:
- To investigate the genomic characteristics of emm4 Streptococcus pyogenes isolates.
- To analyze the extent and impact of gene loss in prophage regions and chromosomal islands.
- To explore the geographical distribution and potential fitness consequences of these genomic alterations.
Main Methods:
- Whole-genome sequencing of longitudinal S. pyogenes isolates.
- Comparative genomic analysis focusing on prophage regions and the SpyCIM4 island.
- Experimental induction of prophage elements where possible.
Main Results:
- Identified an emm4 lineage (MEW427-like) with substantial gene loss in prophage regions, affecting lysogeny and regulatory modules.
- Prophage-encoded superantigen and DNase genes were retained despite gene loss.
- Observed gene loss in the SpyCIM4 island, though the mismatch repair operon remained functional; prophages were not experimentally inducible in degraded isolates.
Conclusions:
- An international emm4 S. pyogenes lineage is characterized by degraded prophage elements.
- The USA population is predominantly MEW427-like, while the UK has both MEW427-like and MGAS10750-like isolates.
- Degraded mobile genetic elements may have significant phenotypic and fitness implications for S. pyogenes, warranting further investigation into population dynamics.
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