Skip to content

Research at St Andrews

Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic

Research output: Research - peer-reviewArticle

DOI

Open Access permissions

Open

Author(s)

Dorota M. Jamrozy, Simon R. Harris, Naglaa Mohamed, Sharon J. Peacock, Charles Y. Tan, Julian Parkhill, Annaliesa S. Anderson, Matthew T. G. Holden

School/Research organisations

Abstract

Staphylococcus aureus USA300 represents the dominant community-associated methicillin-resistant S. aureus lineage in the USA, where it is a major cause of skin and soft tissue infections. Previous comparative genomic studies have described the population structure and evolution of USA300 based on geographically restricted isolate collections. Here, we investigated the USA300 population by sequencing genomes of a geographically distributed panel of 191 clinical S. aureus isolates belonging to clonal complex 8 (CC8), derived from the Tigecycline Evaluation and Surveillance Trial program. Isolates were collected at 12 healthcare centres across nine USA states in 2004, 2009 or 2010. Reconstruction of evolutionary relationships revealed that CC8 was dominated by USA300 isolates (154/191, 81 %), which were heterogeneous and demonstrated limited phylogeographic clustering. Analysis of the USA300 core genomes revealed an increase in median pairwise SNP distance from 62 to 98 between 2004 and 2010, with a stable pattern of above average dN/dS ratios. The phylogeny of the USA300 population indicated that early diversification events led to the formation of nested clades, which arose through cumulative acquisition of predominantly non-synonymous SNPs in various coding sequences. The accessory genome of USA300 was largely homogenous and consisted of elements previously associated with this lineage. We observed an emergence of SCCmec negative and ACME negative USA300 isolates amongst more recent samples, and an increase in the prevalence of ϕSa5 prophage. Together, the analysed S. aureus USA300 collection revealed an evolving pan-genome through increased core genome heterogeneity and temporal variation in the frequency of certain accessory elements.
Close

Details

Original languageEnglish
Pages (from-to)1-14
Number of pages14
JournalMicrobial Genomics
Volume2
Issue number5
Early online date31 May 2016
DOIs
StatePublished - 31 May 2016

    Research areas

  • MRSA, USA300, Evolution

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Distinct evolutionary patterns of Neisseria meningitidis serogroup B disease outbreaks at two universities in the USA

    Hao, L., Holden, M. T. G., Wang, X., Andrew, L., Wellnitz, S., Hu, F., Whaley, M., Sammons, S., Knipe, K., Frace, M., McNamara, L. A., Liberator, P. & Anderson, A. S. 4 Apr 2018 In : Microbial Genomics. 10 p., 4

    Research output: Research - peer-reviewArticle

  2. Proposal of serovars 17 and 18 of Actinobacillus pleuropneumoniae based on serological and genotypic analysis

    Bossé, J. T., Li, Y., Sárközi, R., Fodor, L., Lacouture, S., Gottschalk, M., Amoribieta, M. C., Angen, Ø., Nedbalcova, K., Holden, M. T. G., Maskell, D. J., Tucker, A. W., Wren, B. W., Rycroft, A. N., Langford, P. R. & on behalf of the BRaDP1T consortium Apr 2018 In : Veterinary Microbiology. 217, p. 1-6

    Research output: Research - peer-reviewArticle

  3. Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing

    Parcell, B. J., Oravcova, K., Pinheiro, M., Holden, M. T. G., Phillips, G., Turton, J. F. & Gillespie, S. H. Mar 2018 In : Journal of Hospital Infection. 98, 3, p. 282-288 7 p.

    Research output: Research - peer-reviewArticle

  4. The microevolution and epidemiology of Staphylococcus aureus colonization during atopic eczema disease flare

    Harkins, C. P., Pettigrew, K. A., Oravcová, K., Gardner, J., Hearn, R. M. R., Rice, D., Mather, A. E., Parkhill, J., Brown, S. J., Proby, C. M. & Holden, M. T. G. Feb 2018 In : Journal of Investigative Dermatology. 138, 2, p. 336-343

    Research output: Research - peer-reviewArticle

  5. Genomic investigation unmasks evidence of transmission across mycobacterium abscessus cystic fibrosis patients

    Alateah, S., Peters, C., Dhasmana, D. J., Pettigrew, K., Fallon, R., Seagar, A., Sloan, D. J., Laurenson, I. F., Holden, M. & Gillespie, S. 15 Dec 2017 In : Thorax. 72, Suppl 3, p. A56-A56

    Research output: Research - peer-reviewAbstract

Related by journal

  1. Distinct evolutionary patterns of Neisseria meningitidis serogroup B disease outbreaks at two universities in the USA

    Hao, L., Holden, M. T. G., Wang, X., Andrew, L., Wellnitz, S., Hu, F., Whaley, M., Sammons, S., Knipe, K., Frace, M., McNamara, L. A., Liberator, P. & Anderson, A. S. 4 Apr 2018 In : Microbial Genomics. 10 p., 4

    Research output: Research - peer-reviewArticle

  2. Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island

    Sarovich, D. S., Chapple, S. N. J., Price, E. P., Mayo, M., Holden, M. T. G., Peacock, S. J. & Currie, B. J. 31 Aug 2017 In : Microbial Genomics. 3, 8, 7 p., e000117

    Research output: Research - peer-reviewArticle

  3. Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns

    Donker, T., Reuter, S., Scriberras, J., Reynolds, R., Brown, N. M., Török, M. E., James, R., Network, E. O. E. M. R., Aanensen, D. M., Bentley, S. D., Holden, M. T. G., Parkhill, J., Spratt, B. G., Peacock, S. J., Feil, E. J. & Grundmann, H. 9 Jul 2017 In : Microbial Genomics. 3, 7, 12 p., e000113

    Research output: Research - peer-reviewArticle

  4. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

    Argimón, S., Abudahab, K., Goater, R. J. E., Fedosejev, A., Bhai, J., Glasner, C., Feil, E. J., Holden, M. T. G., Yeats, C. A., Grundmann, H., Spratt, B. G. & Aanensen, D. M. 30 Nov 2016 In : Microbial Genomics. 2, 11, 11 p.

    Research output: Research - peer-reviewArticle

  5. Whole-genome sequencing of a quarter-century melioidosis outbreak in temperate Australia uncovers a region of low-prevalence endemicity

    Chapple, S. N. J., Sarovich, D. S., Holden, M. T. G., Peacock, S. J., Buller, N., Golledge, C., Currie, B. J., Mayo, M. & Price, E. P. 11 Jul 2016 In : Microbial Genomics. 2, 7, 10 p.

    Research output: Research - peer-reviewArticle

ID: 243159670