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

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

doi:10.7717/peerj.3047

Abstract

BackgroundThe 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.MethodsWe 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.ResultsWe 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.DiscussionThis 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.

Highlights

Since the 1990s, community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) infections have been increasing worldwide (Centers for Disease Control and Prevention, 2013; de Kraker et al, 2011)
We 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
This study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana

Summary

Introduction

Since the 1990s, community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) infections have been increasing worldwide (Centers for Disease Control and Prevention, 2013; de Kraker et al, 2011). Studies from Angola (Conceicao et al, 2014), Cameroon (Breurec et al, 2011), Gabon (Ngoa et al, 2012; Schaumburg et al, 2011), Ghana (Amissah et al, 2015; Egyir et al, 2013, 2014), Madagascar (Breurec et al, 2011), Niger (Breurec et al, 2011), Nigeria (Ghebremedhin et al, 2009; Raji et al, 2013; Shittu et al, 2012) and Senegal (Breurec et al, 2011) have identified it as a major circulating clone within both hospital and community settings It was detected in children from West Africa who underwent surgery in Switzerland but had been hospitalized in their home countries prior to surgical treatment.

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