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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Comparative genomics reveals polyphyletic emergence of methicillin-resistant Staphylococcus aureus ST152 from a
Brown Beckley1,2, Vincent Amarh3, Adesola Olalekan4
1Department of Medical Biochemistry, University of Ghana Medical School, Accra, Ghana. brownbeckley94@gmail.com.
Background:
Staphylococcus aureus is a major public health threat in Ghana, with the Sequence Type 152 (ST152) lineage emerging as a dominant, Panton-Valentine leukocidin toxin (PVL)-positive lineage. This study investigates the evolutionary dynamics and emergence of methicillin resistance within the ST152 population in Ghana.
Methods:
We analyzed 285 publicly available S. aureus whole-genome sequences (WGS) from Ghana, encompassing isolates of human and animal origin. Comprehensive genomic characterization was performed using the StaphScope pipeline, followed by detailed pangenome and phylogenetic analyses of 80 ST152 isolates.
Results:
ST152 was the most prevalent lineage (28.1%). Phylogenetic analysis revealed patterns consistent with polyphyletic emergence of methicillin-resistant S. aureus (MRSA) ST152 through multiple independent acquisitions of the staphylococcal cassette chromosome mec (SCCmec). Despite these multiple origins, a single MRSA-enriched sublineage has become dominant. This successful clade is characterized by the significant enrichment of additional resistance genes (catA, tet(K)), a specific plasmid replicon (rep7a_5_repD(pTZ4)), and the collagen adhesin gene (cna), which may enhance host colonization and transmission. Interestingly, methicillin-susceptible S. aureus (MSSA) isolates were found phylogenetically embedded within MRSA clusters, indicating a highly dynamic resistance landscape.
Conclusions:
The emergence of MRSA ST152 in Ghana is a complex, multi-origin process. The dominance of a specific sublineage harboring enhanced virulence and resistance markers suggests a specialized adaptation that facilitates its epidemiological success. These findings underscore the critical need for sustained genomic surveillance to monitor the evolution and spread of high-risk MRSA lineages in West Africa.
Insights
Methicillin-resistant Staphylococcus aureus (MRSA) ST152 in Ghana emerged from multiple origins. A dominant sublineage with enhanced resistance and virulence factors drives its spread, necessitating genomic surveillance.
Area of Science:
- Microbiology
- Genomics
- Evolutionary Biology
Background:
- Staphylococcus aureus is a significant public health concern in Ghana.
- The Panton-Valentine leukocidin (PVL)-positive Sequence Type 152 (ST152) lineage is a dominant strain.
- Understanding methicillin resistance emergence in ST152 is crucial.
Purpose of the Study:
- Investigate the evolutionary dynamics of Staphylococcus aureus ST152 in Ghana.
- Determine the origins and emergence patterns of methicillin resistance within this lineage.
- Identify factors contributing to the success of methicillin-resistant S. aureus (MRSA) ST152.
Main Methods:
- Analyzed 285 publicly available S. aureus whole-genome sequences (WGS) from Ghana.
- Utilized the StaphScope pipeline for genomic characterization.
- Conducted pangenome and phylogenetic analyses on 80 ST152 isolates.
Main Results:
- ST152 was the most prevalent lineage (28.1%).
- Methicillin-resistant S. aureus (MRSA) ST152 emerged polyphyletically through multiple staphylococcal cassette chromosome mec (SCCmec) acquisitions.
- A dominant MRSA-enriched sublineage possesses enhanced resistance genes (catA, tet(K)), a specific plasmid replicon, and the collagen adhesin gene (cna).
- Methicillin-susceptible S. aureus (MSSA) isolates were found within MRSA clusters, indicating a dynamic resistance landscape.
Conclusions:
- MRSA ST152 emergence in Ghana is a complex, multi-origin process.
- A specialized, adapted sublineage drives the epidemiological success of MRSA ST152.
- Sustained genomic surveillance is essential for monitoring high-risk MRSA evolution in West Africa.
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Clinical Significance of Antibiotic Resistance
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Evolution of Microbial Genome
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