Genomic Analysis of Companion Rabbit Staphylococcus aureus

RESEARCH ARTICLE Genomic Analysis of Companion Rabbit Staphylococcus aureus Mark A. Holmes1, Ewan M. Harrison2, Elizabeth A. Fisher3, Elizabeth M. Graham4, Julian Parkhill5, Geoffrey Foster6, Gavin K. Paterson3* 1 Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom, 2 Department of Medicine, University of Cambridge, Cambridge, United Kingdom, 3 School of Biological, Biomedical and Environmental Sciences, University of Hull, Kingston upon Hull, United Kingdom, 4 School of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom, 5 The Wellcome Trust Sanger Institute, Wellcome Trust, Genome Campus, Hinxton, United Kingdom, 6 Scottish Agricultural College Consulting Veterinary Services, Inverness, United Kingdom * [email protected] Abstract OPEN ACCESS Citation: Holmes MA, Harrison EM, Fisher EA, Graham EM, Parkhill J, Foster G, et al. (2016) Genomic Analysis of Companion Rabbit Staphylococcus aureus. PLoS ONE 11(3): e0151458. doi:10.1371/journal.pone.0151458 Editor: Axel Cloeckaert, Institut National de la Recherche Agronomique, FRANCE Received: November 13, 2015 Accepted: February 29, 2016 Published: March 10, 2016 Copyright: © 2016 Holmes 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 sequence data are available from the European Nucleotide Archive (accession numbers: ERR387096, ERR387097, ERR387166, ERR387195, ERR387196, ERR387256, ERR387257, ERR494744, ERR494745, ERR494746). Funding: This project was supported by internal funding from the School of Biological, Biomedical and Environmental Sciences, University of Hull (GKP), a Medical Research Council (MRC) Partnership Grant (G1001787/1) (MAH and JP), and the Wellcome Trust, Grant number 098051 (JP). The funders had In addition to being an important human pathogen, Staphylococcus aureus is able to cause a variety of infections in numerous other host species. While the S. aureus strains causing infection in several of these hosts have been well characterised, this is not the case for companion rabbits (Oryctolagus cuniculus), where little data are available on S. aureus strains from this host. To address this deficiency we have performed antimicrobial susceptibility testing and genome sequencing on a collection of S. aureus isolates from companion rabbits. The findings show a diverse S. aureus population is able to cause infection in this host, and while antimicrobial resistance was uncommon, the isolates possess a range of known and putative virulence factors consistent with a diverse clinical presentation in companion rabbits including severe abscesses. We additionally show that companion rabbit isolates carry polymorphisms within dltB as described as underlying host-adaption of S. aureus to farmed rabbits. The availability of S. aureus genome sequences from companion rabbits provides an important aid to understanding the pathogenesis of disease in this host and in the clinical management and surveillance of these infections. Introduction Staphylococcus aureus is a major human and veterinary pathogen, responsible for a wide range of diseases. Among economically important livestock animals these diseases include mastitis in dairy cows and small ruminants, lameness in commercial broiler chickens and virulent epidemics of skin abscesses, mastitis and septicaemia in farmed rabbits (Oryctolagus cuniculus). S. aureus colonisation and infection of animals is not only important from the perspective of animal wellbeing and economic impact but may also lead to zoonotic infection of humans [1, 2]. Although also recognised as a versatile and virulent pathogen among companion rabbits, in particular as a cause of severe abscesses [3], few data are available on the S. aureus strains causing disease in this host. This is despite the popularity of rabbits as a companion animal; for PLOS ONE | DOI:10.1371/journal.pone.0151458 March 10, 2016 1/9 Staphylococcus aureus in Companion Rabbits no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. instance the population of companion rabbits in the UK is estimated at ~ 1 million [4]. Furthermore S. aureus, including methicillin-resistant S. aureus (MRSA) is a well-documented pathogen among other companion animals such as cats, dogs and horses, [5–7]. Interest in the S. aureus population among companion rabbits is further heightened by the discovery of emergent mecC MRSA in a farmed rabbit [8], and sporadic reports of MRSA in companion rabbits [9], including livestock-associated clonal complex 398 MRSA [10] and Panton-Valentine Leucocidin-positive isolates [11]. Furthermore, rabbits are a frequently used experimental model for S. aureus infections and a better understanding of the natural bacterial-host interactions in this setting may facilitate improved model systems. In order to address this paucity of data on the S. aureus population among companion rabbits we have genome sequenced a collection of companion and research unit S. aureus from this host species in the United Kingdom. This novel genome-level study provides insight into host-pathogen interactions, antimicrobial resistance and the phylogenetics of S. aureus among rabbits. These data will inform clinical management in rabbits and the future surveillance of this widespread and important pathogen. Materials and Methods Bacterial isolates and antimicrobial susceptibility A request for S. aureus isolates from companion rabbits was made to personal contacts and veterinary diagnostic laboratories in the UK. Isolates where collected by veterinary microbiology laboratories in the course of their routine diagnostic work, with the study approved by the Department of Veterinary Medicine, University of Cambridge Ethics and Welfare Committee (reference: CR76 Collection of S. aureus isolates from domestic and wild animals for genome sequencing). The resultant ten isolates that were collected and their associated details are shown in Table 1. Antimicrobial susceptibility testing was performed using the Staph AST-P620 card on the Vitek 2 system (bioMérieux, Basingstoke, UK) following the manufacturer’s instructions with S. aureus NCTC6571 and NCTC12493 as control strains. Genome sequencing and analysis Genomic DNA was extracted using the MasterPure™ Gram Positive DNA Purification Kit (Cambio, Dry Drayton, UK) from overnight cultures grown from single colonies in 5 ml of tryptic soy broth overnight at 37°C. Illumina library preparation was carried out as described previously [12], and genome sequencing using Hi-Seq 2000 performed following the manufacturer’s standard protocols (Illumina, Little Chesterfield, UK). Nucleotide sequences been deposited in the European Nucleotide Archive, accession numbers provided in Table 1. Genome assembly was performed de novo using Velvet [13] and antimicrobial resistance genes and virulence factors identified using BLAST and ResFinder [14]. Genome-derived multi-locus sequence types (MLST) were assigned as described previously [15]. The phylogenetic relationships among the isolates was assessed using core genome (cg)MLST using SeqSphere+ software (Ridom GmbH, Münster Germany) as described previously [16] and including twenty-eight reference genomes to place the rabbit isolates within the context of the wider S. aureus population. 1475 core genome loci found in all isolates were used. spa typing was performed using Sanger sequencing of PCR products using primers spa-1113f (5'- TAA AGA CGA TCC TTC GGT GAG C -3') and spa-1514r (5'- CAG CAG TAG TGC CGT TTG CTT -3') as per Ridom GmbH (Würzburg, Germany). PLOS ONE | DOI:10.1371/journal.pone.0151458 March 10, 2016 2/9 PLOS ONE | DOI:10.1371/journal.pone.0151458 March 10, 2016 Table 1. Rabbit isolates included in this study. Biosample Assembly Accessions Geographical location Site of isolation Date of isolation ST1 CC2 spa type3 Phenotypic resistance4 Resistance genes/ mutations Additional notes 163x SAMEA1929514 FJNS01000001-FJNS01000044 Manchester area, England Not known Apr-2013 30 30 t021 benzylpenicillin blaZ, tet(38), norA same animal as FP02 ERR387097 156x SAMEA1929515 FJNW01000001-FJNW01000043 Manchester area, England Not known Apr-2013 30 30 t021 benzylpenicillin blaZ, tet(38), norA same animal as FP01 557472 ERR387166 113x SAMEA1929647 FJNT01000001-FJNT01000024 England Ventral vulva abscess Jun-2013 3126 291 t1614 benzylpenicillin blaZ, tet(38), norA M1970/98/ 1 ERR387195 160x SAMEA1929516 FJNU01000001-FJNU01000024 Scotland Lesion 1998 3120 425 t13114 susceptible tet(38), norA M503044/ 99/1 ERR387196 147x SAMEA1929517 FJNP01000001-FJNP01000029 Scotland Sub-cutaneous abscess 1999 121 121 t645 susceptible tet(38), norA 543471 ERR387256 90x SAMEA1929646 FJNQ01000001-FJNQ01000011 England Darcocystitis Feb-2013 6 6 t5413 benzylpenicillin, fusidic acid blaZ, tet(38), norA; H457Y in elongation factor G 559622 ERR387257 101x SAMEA1929648 FJNN01000001-FJNN01000024 England Skin infection Jun-2013 15 15 t2574 benzylpenicillin blaZ, tet(38), norA 61908 ERR494744 134x SAMEA2298602 FJNO01000001-FJNO01000014 Stirlingshire, Scotland Nasal sample at postmortem Sep-2009 3092 425 t15410 susceptible tet(38), norA feral rabbit 68850 ERR494745 144x SAMEA2298603 FJNV01000001-FJNV01000032 Glasgow, Scotland Chest cavity abscess Jun-2012 39 30 t15409 benzylpenicillin blaZ, tet(38), norA experimental research unit 68901 ERR494746 130x SAMEA2298604 FJNR01000001-FJNR01000031 Glasgow, Scotland Lower jaw abscess Jun-2012 2257 22 t1977 benzylpenicillin blaZ, tet(38), norA experimental research unit Isolate name ERA Accession FP01 ERR387096 FP02 1 3 Multi-locus sequenced type (new multi-locus sequence types shown in bold) MLST clonal complex assigned by e-Burst New spa types shown in bold 4 Tested against: benzylpenicillin, cefoxitin, oxacillin, ciprofloxacin, erythromycin, chloramphenicol, daptomycin, fusidic acid, gentamicin, linezolid, mupirocin, nitrofurantoin, rifampicin, teicoplanin, tetracycline, tigecycline, trimethoprim, vancomycin and clindamycin as well as inducible resistance to clindamycin. doi:10.1371/journal.pone.0151458.t001 3/9 Staphylococcus aureus in Companion Rabbits 2 Coverage Staphylococcus aureus in Companion Rabbits Fig 1. Clonal relationships among rabbit S. aureus and their context within the wider S. aureus population. A phylogenetic dendrogram (UPGMA) generated from the allelic profiles of 1475 cgMLST target genes, based on (16) and comprising the ten rabbit isolates from this study and twenty-eight reference S. aureus genomes from Genbank. Rabbit isolates are denoted by *, isolate name and Genbank accession provided for the reference genomes. The last figure in the text line indicates the multi-locus sequence type of each isolate, where available. The scale bar indicates the number of differing alleles comprising the calculated distance. doi:10.1371/journal.pone.0151458.g001 Results Study strains, multi-locus sequence types and spa types Ten rabbit S. aureus isolates collected between 1998 and 2013 in the UK were included in this study, Table 1. Eight were from companion rabbits including two isolates from the same rabbit, with a further two isolates from research unit rabbits. MLST showed the ten isolates belonged to nine different sequence types, the only duplication of ST being the two isolates from the same rabbit which both belonged to ST30. Three new ST were identified in this study; ST3092 and ST3120 being single locus variants (SLV) of ST425 in aroE and tpi respectively, whilst ST3126 is a SLV of ST291 in tpi. These STs belonged to eight clonal complexes, Table 1. Similarly to MLST, nine different spa types were found among the ten isolates, the only duplication again being the two isolates from the same rabbit. Two new spa types, t15409 and t15410 were found. PLOS ONE | DOI:10.1371/journal.pone.0151458 March 10, 2016 4/9 Staphylococcus aureus in Companion Rabbits Table 2. Distribution of virulence factors and dltB mutations among rabbit S. aureus. fnbA fnbB sdrD sdrE efb cna sea seb sec seg sei sen seo sep pvlFS tsst sak scn dltB polymorphisms1 FP01 + - - - + + + + - - + + + + - + + + I227V Y346H FP02 + - - - + + + + - - + + + + - + + + S48F Y346H 557472 - + - - + - + - - - - - - + - - + + *405Q M1970/98/ 1 + + + + - + - - - - - - - + - - - - G5S Q231R *405Q M503044/ 99/1 - + + - - + + - + - + + - - - - - - T113K Y250H *405Y 543471 + + - + - + + - - - - - - + - - + + Y346H 559622 + + + + + - - - - - - - - - - - - - L127S F221L Y346C 61908 + - - + - + - - - - - - - + - - - - T113K *405Q 68850 + - - - + + - - - - - + + - - - - V328M Y346H 68901 + + + + + + - - - + - + + - - - - Y346C + 1 as ascribed by comparison to MRSA252 dltB (locus tag SAR_RS04555 Accession NC_002952 REGION: 931760.932974). New mutations, not described previously by Viana et al. (2015) shown in bold. Further genes present in all ten isolates but not displayed in table: coa, nuc, spa, clfA, clfB, icaRABC, hla, hlb, hlgACB, eta, isb, sdrH, ebh, fib, ebpS, sdrC doi:10.1371/journal.pone.0151458.t002 Whole genome phylogenetic analysis In agreement with the diversity indicated by MLST, whole genome analysis using cgMLST across 1475 loci showed a diverse population among rabbit isolates, Fig 1. The average pairwise difference in allele profile between rabbit isolates was 1271 alleles, representing 86% of the core genome loci assessed. The two isolates from the same rabbit, FP01 and FP02 differed in 51 alleles and the largest pairwise difference in profile was 1402 (95% of the 475 core loci analysed). Inclusion in the analysis of twenty-eight reference S. aureus genomes showed the rabbit isolates to be distributed across the wider S. aureus population, Fig 1 Antimicrobial Resistance and resistance determinates Resistance to benzylpenicillin occurred in seven of the isolates and correlated with the presence of blaZ, Table 1. Resistance to other antimicrobials was restricted to a single isolate, 543471, showing fusidic acid resistance, Table 1. This resistance correlated with a single amino acid substitution, H457Y in elongation factor G. Whilst no other phenotypic resistance was seen, all ten isolates were positive for the efflux pump genes tet(38) and norA. Virulence factors and markers of host adaption The sequenced rabbit isolates were assessed for the presence or absence of S. aureus virulence factors, Table 2. Several genes, including those encoding α-(hla), β-(hlb) and γ-haemolysins (hlgACB) were present in all the isolates with others present in a subset, Table 2. None of the ten isolates possessed the genes encoding for Panton-Valentine Leucocidin but isolates FP01 and FP02 were both positive for toxic shock syndrome toxin-1. Four of the strains were positive for the phage-encoded immune evasion genes, sak and scn which are taken as indicative of strains of human origin. Among clinical rabbit isolates from commercial rabbitries in mainland Europe, Viana et al. have demonstrated a critical role in host adaption for polymorphisms in dltB, encoding the D-alanine teichoic acid esterification protein [17]. We therefore compared PLOS ONE | DOI:10.1371/journal.pone.0151458 March 10, 2016 5/9 Staphylococcus aureus in Companion Rabbits the DltB sequence in our isolates to that from human isolated S. aureus. Every rabbit isolate in our collection had at least one amino acid polymorphism in DltB, Table 2. These comprised both novel and previously described polymorphisms including the experimentally validated T113K dltB mutation [17]. Discussion To gain insight into the molecular epidemiology and disease pathogenesis of rabbit staphylococcosis we have genome sequenced a collection of S. aureus isolates from companion rabbits. Strain typing by MLST and spa typing showed a diverse population of isolates with no duplication of ST or spa type between isolates from different animals and minimal overlap even at the level of MLST clonal complex. This finding of a diverse S. aureus population able to infect rabbits was further supported by the use of high-resolution whole genome analysis using cgMLST. Bacterial diversity extended to two isolates from the same individual rabbit which differed by 51 alleles and demonstrates that the within host diversity of S. aureus described previously in humans and dogs [18–21] extends to the rabbit host also. This diversity among the isolates indicates that a variety of S. aureus lineages are able to cause disease in companion rabbits, with no strong suggestion that any lineages are predominant, albeit based on a relatively small sample. However, the finding that this relatively small collection led to the identification of three novel STs and two novel spa types strongly indicates that the S. aureus population among this host has been poorly sampled to date and includes strains rare in humans and other animals. With the exception of penicillin resistance, present in the majority of isolates and which correlated with the possession of blaZ, antimicrobial resistance was scarce. No MRSA isolates were found and the only additional phenotypic resistance was a single isolate resistant to fusidic acid. This isolate possessed a single amino acid substitution in elongation factor G which has previously been found associated with fusidic acid resistance in naturally occurring clinical isolates and in experimentally selected resistance mutants [22–25]. Furthermore, when introduced into a susceptible strain on a plasmid, this mutant fusA allele confers fusidic acid resistance [22]. All ten strains were positive for norA, a multidrug efflux pump which confers resistance to ciprofloxacin among a broad spectrum of agents [26] and tet(38), an efflux pump conferring tetracycline resistance [27]. In both cases however, phenotypic resistance is associated with mutations leading to over-expression which likely explains the absence of phenotypic resistance in these rabbit isolates [26, 27]. The presence of these genes in rabbit isolates, however, indicates the potential for such resistance to manifest in the future. The importance of dltB polymorphisms in host adaption of S. aureus to rabbits has been demonstrated previously with a single amino acid substitution (T113K) sufficient to confer virulence in rabbits to a human ST121 isolate otherwise avirulent in that host [17]. Furthermore, while dltB is highly conserved in human isolates, thirty-nine rabbit isolates belonging to a range of STs and CCs all contained one or more non-synonymous SNPs in dltB thus suggesting convergent evolution among rabbit-adapted S. aureus [17]. All ten rabbit isolates in our collection carried at least one amino acid polymorphism in DltB with each strain encoding a different pattern of polymorphism(s) to each other. Two isolates belonging to ST121 and ST15 carried the experimentally validated T113K substitution. A second distinct dltB allele containing two SNPs and associated with the S. aureus ST96 rabbit clone was also shown experimentally to confer virulence in rabbits [17]. While one of those two SNPs,  405Q, was present in some of the isolates reported here, the second SNP, K402R, was not. We show therefore that host-adaption via dltB polymorphism occurs in companion rabbit isolates and provide further evidence for convergent evolution at this locus across diverse S. aureus lineages infecting PLOS ONE | DOI:10.1371/journal.pone.0151458 March 10, 2016 6/9 Staphylococcus aureus in Companion Rabbits rabbits. In addition to the DltB polymorphisms described previously we have identified six novel amino acid substitutions, Table 1. Using a predicted membrane topology model of the DltB protein, Viana et al. noted that the majority of mutations they described were predicted to be in the extracellular loops or proximal to the outer surface of the membrane [17]. Using that model, while none of the novel mutations described here appear to be located extracellularly, four are predicted to be proximal to the outer surface of the membrane (data not shown). Interestingly, the pattern of distinct polymorphisms between the isolates included the two related ST30 isolates, FP01 and FP02, cultured from the same animal. These two isolates shared one amino acid insertion but had a distinct second amino acid substitution. This suggests that the selective pressure exerted on dltB by the rabbit host may be acting to drive divergent evolution within clones within the same individual host. Although the independent acquisition of two related strains with divergent dltB alleles cannot be excluded. To conclude, we have used antimicrobial susceptibility testing and whole genome sequencing to characterise S. aureus isolates from companion rabbit. Isolates came from a diverse bacterial population, including three new STs and two new spa types. While antimicrobial resistance was uncommon, except for penicillin resistance, isolates possessed a number of virulence factors consistent with the ability to cause severe abscesses in companion rabbits. The availability of these genome sequences will underpin improved understanding of disease pathogenesis, clinical management and pathogen surveillance in this popular companion animal. Acknowledgments This project was supported by internal funding from the School of Biological, Biomedical and Environmental Sciences, University of Hull, a Medical Research Council (MRC) Partnership Grant (G1001787/1), and the Wellcome Trust, Grant number 098051. The help of the core sequencing and informatics team at the Wellcome Trust Sanger Institute is gratefully acknowledged. Author Contributions Conceived and designed the experiments: GKP MAH. Performed the experiments: GKP EMH EAF. Analyzed the data: MAH GKP. Contributed reagents/materials/analysis tools: MAH JP EMG GF. Wrote the paper: GKP. Contributed to the drafting and approval of final manuscript: MAH EMH EAF EMG JP GF GKP. References 1. Harrison EM, Paterson GK, Holden MTG, Larsen J, Stegger M, Larsen AR, et al. Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC. EMBO Molecular Medicine. 2013; 5(4):509–15. doi: 10.1002/emmm.201202413 PMID: WOS:000317070200005. 2. Price LB, Stegger M, Hasman H, Aziz M, Larsen J, Andersen PS, et al. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. MBio. 2012; 3(1):00305–11. PMID: 22354957. 3. Harcourt-Brown F. Textbook of Rabbit Medicine. Oxford, UK: Butterworth-Heinemann 2001. 4. PFMA. Pet Food Manufacturers' Association Pet Population 2014 [cited 2015 02.07.2015]. Available from: http://www.pfma.org.uk/pet-population-2014/. 5. Harrison EM, Weinert LA, Holden MTG, Welch JJ, Wilson K, Morgan FJE, et al. A Shared Population of Epidemic Methicillin-Resistant Staphylococcus aureus 15 Circulates in Humans and Companion Animals. Mbio. 2014; 5(3). doi: 10.1128/mBio.00985-13 PMID: WOS:000338875900029. 6. Vincze S, Stamm I, Kopp PA, Hermes J, Adlhoch C, Semmler T, et al. Alarming Proportions of Methicillin-Resistant Staphylococcus aureus (MRSA) in Wound Samples from Companion Animals, Germany 2010–2012. PLoS ONE. 2014; 9(1):e85656. doi: 10.1371/journal.pone.0085656 PMID: 24465637 PLOS ONE | DOI:10.1371/journal.pone.0151458 March 10, 2016 7/9 Staphylococcus aureus in Companion Rabbits 7. Weese JS. Methicillin-Resistant Staphylococcus aureus in Animals. ILAR Journal. 2010; 51(3):233–44. doi: 10.1093/ilar.51.3.233 PMID: 21131724 8. Paterson GK, Larsen AR, Robb A, Edwards GE, Pennycott TW, Foster G, et al. The newly described mecA homologue, mecA(LGA251), is present in methicillin-resistant Staphylococcus aureus isolates from a diverse range of host species. Journal of Antimicrobial Chemotherapy. 2012; 67(12):2809–13. doi: 10.1093/jac/dks329 PMID: WOS:000311312100006. 9. Rich M, Roberts L. MRSA in companion animals. Veterinary Record. 2006; 159(16):535–6. doi: 10. 1136/vr.159.16.535 PMID: 17041070 10. Loncaric I, Künzel F. Sequence type 398 meticillin-resistant Staphylococcus aureus infection in a pet rabbit. Veterinary Dermatology. 2013; 24(3):370–e84. doi: 10.1111/vde.12023 PMID: 23551846 11. Rankin S, Roberts S, O'Shea K, Maloney D, Lorenzo M, Benson CE. Panton valentine leukocidin (PVL) toxin positive MRSA strains isolated from companion animals. Veterinary Microbiology. 2005; 108(1– 2):145–8. http://dx.doi.org/10.1016/j.vetmic.2005.02.013. PMID: 15917142 12. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, et al. A large genome center's improvements to the Illumina sequencing system. Nat Meth. 2008; 5(12):1005–10. http://www.nature. com/nmeth/journal/v5/n12/suppinfo/nmeth.1270_S1.html. 13. Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research. 2008; 18(5):821–9. doi: 10.1101/gr.074492.107 PMID: WOS:000255504600014. 14. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. Journal of Antimicrobial Chemotherapy. 2012; 67(11):2640– 4. doi: 10.1093/jac/dks261 PMID: 22782487 15. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, et al. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria. Journal of Clinical Microbiology. 2012; 50(4):1355–61. doi: 10.1128/jcm.06094-11 PMID: 22238442 16. Leopold SR, Goering RV, Witten A, Harmsen D, Mellmann A. Bacterial Whole-Genome Sequencing Revisited: Portable, Scalable, and Standardized Analysis for Typing and Detection of Virulence and Antibiotic Resistance Genes. Journal of Clinical Microbiology. 2014; 52(7):2365–70. doi: 10.1128/jcm. 00262-14 PMID: 24759713 17. Viana D, Comos M, McAdam PR, Ward MJ, Selva L, Guinane CM, et al. A single natural nucleotide mutation alters bacterial pathogen host tropism. Nat Genet. 2015; 47(4):361–6. doi: 10.1038/ng.3219 http://www.nature.com/ng/journal/v47/n4/abs/ng.3219.html#supplementary-information. PMID: 25685890 18. Gullberg E, Cao S, Berg OG, Ilback C, Sandegren L, Hughes D, et al. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog. 2011; 7(7):e1002158. PMID: 21811410. doi: 10.1371/ journal.ppat.1002158 19. Paterson GK, Harrison EM, Murray GGR, Welch JJ, Warland JH, Holden MTG, et al. Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nat Commun. 2015; 6(6560). doi: 10.1038/ncomms7560 20. Stanczak-Mrozek KI, Manne A, Knight GM, Gould K, Witney AA, Lindsay JA. Within-host diversity of MRSA antimicrobial resistances. Journal of Antimicrobial Chemotherapy. 2015. doi: 10.1093/jac/ dkv119 21. Harris SR, Cartwright EJ, Torok ME, Holden MT, Brown NM, Ogilvy-Stuart AL, et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis. 2012; 9(12):70268–2. PMID: 23158674. 22. Besier S, Ludwig A, Brade V, Wichelhaus TA. Molecular analysis of fusidic acid resistance in Staphylococcus aureus. Molecular Microbiology. 2003; 47(2):463–9. doi: 10.1046/j.1365-2958.2003.03307.x PMID: 12519196 23. Nagaev I, Björkman J, Andersson DI, Hughes D. Biological cost and compensatory evolution in fusidic acid-resistant Staphylococcus aureus. Molecular Microbiology. 2001; 40(2):433–9. doi: 10.1046/j. 1365-2958.2001.02389.x PMID: 11309125 24. O’Neill AJ, Bostock JM, Morais Moita A, Chopra I. Antimicrobial activity and mechanisms of resistance to cephalosporin P1, an antibiotic related to fusidic acid. Journal of Antimicrobial Chemotherapy. 2002; 50(6):839–48. doi: 10.1093/jac/dkf248 PMID: 12461002 25. O'Neill AJ, Larsen AR, Henriksen AS, Chopra I. A Fusidic Acid-Resistant Epidemic Strain of Staphylococcus aureus Carries the fusB Determinant, whereas fusA Mutations Are Prevalent in Other Resistant Isolates. Antimicrobial Agents and Chemotherapy. 2004; 48(9):3594–7. doi: 10.1128/aac.48.9.3594– 3597.2004 PMID: 15328136 26. Kaatz GW, Seo SM. Inducible NorA-mediated multidrug resistance in Staphylococcus aureus. Antimicrobial Agents and Chemotherapy. 1995; 39(12):2650–5. PMID: PMC163006. PLOS ONE | DOI:10.1371/journal.pone.0151458 March 10, 2016 8/9 Staphylococcus aureus in Companion Rabbits 27. Truong-Bolduc QC, Dunman PM, Strahilevitz J, Projan SJ, Hooper DC. MgrA Is a Multiple Regulator of Two New Efflux Pumps in Staphylococcus aureus. Journal of Bacteriology. 2005; 187(7):2395–405. doi: 10.1128/JB.187.7.2395–2405.2005 PMID: PMC1065235. PLOS ONE | DOI:10.1371/journal.pone.0151458 March 10, 2016 9/9