Extensive Genomic Diversity among Bovine-Adapted Staphyloco…

RESEARCH ARTICLE Extensive Genomic Diversity among Bovine- Adapted Staphylococcus aureus : Evidence for a Genomic Rearrangement within CC97 Kathleen E. Budd 1,2 , Finola McCoy 3 , Stefan Monecke 4 , Paul Cormican 1 , Jennifer Mitchell 2 , Orla M. Keane 1 * 1 Animal & Bioscience Department, AGRIC, Teagasc, Grange, Dunsany, Co. Meath, Ireland, 2 School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland, 3 Animal Health Ireland, Carrick- on-Shannon, Co. Leitrim, Ireland, 4 Alere Technologies GmbH, Löbstedter Straße 103 – 105, D-07749 Jena, Germany Abstract Staphylococcus aureus is an important pathogen associated with both human and veterinary disease and is a common cause of bovine mastitis. Genomic heterogeneity exists between S . aureus strains and has been implicated in the adaptation of specific strains to colonise particular mammalian hosts. Knowledge of the factors required for host specificity and virulence is impor- tant for understanding the pathogenesis and management of S . aureus mastitis. In this study, a panel of mastitis-associated S . aureus isolates (n = 126) was tested for resistance to antibiotics commonly used to treat mastitis. Over half of the isolates (52%) demonstrated resistance to penicillin and ampicillin but all were susceptible to the other antibiotics tested. S . aureus isolates were further examined for their clonal diversity by Multi-Locus Sequence Typing (MLST). In total, 18 different sequence types (STs) were identified and eBURST analysis demonstrated that the majority of isolates grouped into clonal complexes CC97, CC151 or sequence type (ST) 136. Analysis of the role of recombination events in determining S . aureus population struc- ture determined that ST diversification through nucleotide substitutions were more likely to be due to recombination compared to point mutation, with regions of the genome possibly acting as recombination hotspots. DNA microarray analysis revealed a large number of differences amongst S . aureus STs in their variable genome content, including genes associated with cap- sule and biofilm formation and adhesion factors. Finally, evidence for a genomic arrangement was observed within isolates from CC97 with the ST71-like subgroup showing evidence of an IS431 insertion element having replaced approximately 30 kb of DNA including the ica operon and histidine biosynthesis genes, resulting in histidine auxotrophy. This genomic rearrangement may be responsible for the diversification of ST71 into an emerging bovine adapted subgroup. * orla.keane@teagasc.ie

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Citation: Budd KE, McCoy F, Monecke S, Cormican P, Mitchell J, Keane OM (2015) Extensive Genomic Diversity among Bovine-Adapted Staphylococcus aureus : Evidence for a Genomic Rearrangement within CC97. PLoS ONE 10(8): e0134592. doi:10.1371/journal.pone.0134592 Editor: Willem van Schaik, University Medical Center Utrecht, NETHERLANDS

Received: February 2, 2015

Accepted: July 11, 2015

Published: August 28, 2015

Copyright: © 2015 Budd et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files with the exception of sequence files which are available from the NCBI Sequence Read Archive with accession number SRP050409. Funding: Funding from the Teagasc Walsh Fellowship Scheme (grant number 6082) is gratefully acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Alere Technologies GmbH provided support in the form of salaries for authors (SM), but did not have any

Introduction Mastitis, which encompasses any inflammatory process that occurs in the mammary gland, is predominantly caused by bacterial infection [ 1 ]. Bovine mastitis pathogens are classically

PLOS ONE | DOI:10.1371/journal.pone.0134592 August 28, 2015

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