Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana

Grace Kpeli; Andrew H Buultjens; Stefano Giulieri; Evelyn Owusu-Mireku; Samuel Y Aboagye; Sarah L Baines; Torsten Seemann; Dieter Bulach; Anders Gonçalves da Silva; Ian R Monk; Benjamin P Howden; Gerd Pluschke; Dorothy Yeboah-Manu; Timothy Stinear

doi:10.7717/peerj.3047

Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana

PeerJ. 2017 Feb 28:5:e3047. doi: 10.7717/peerj.3047. eCollection 2017.

Affiliations

¹ Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana; Department of Molecular Parasitology and Immunology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
² Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia.
³ Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana , Accra , Ghana.
⁴ Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; University of Melbourne, Victorian Life Sciences Computation Initiative, Melbourne, VIC, Australia.
⁵ Department of Microbiology and Immunology, Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; Department of Microbiology and Immunology, Microbiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, VIC, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia.
⁶ Department of Molecular Parasitology and Immunology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.

Abstract

Background: The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an "African" CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide.

Methods: We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages.

Results: We show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β-lactams, tetracycline and chloramphenicol.

Discussion: This study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone.

Keywords: CA-MRSA; Comparative genomics; MRSA; Phylogeography; ST88; Staphylococcus aureus; Whole genome sequencing.

Associated data

figshare/10.6084/m9.figshare.3863475

Grants and funding

This work was supported by the Stop Buruli initiative of the UBS Optimus foundation and the Volkswagen Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.