Staphylococcus aureus is the causative agent of multiple infections, including bacteremia, infective endocarditis, osteomyelitis, septic arthritis, and prosthetic device infections. We report here the first whole-genome sequence for four S. aureus sequence type 398 isolates from clinical cases of osteomyelitis in four goats with a history of orthopedic surgery

Abouelkhair, Mohamed A

Anderson, David A

Bemis, David A.

Biris, Alexandru S

Grzeskowiak, Remiqiusz M

Kania, Stephen A

Rifkin, Rebecca E

English

University of Tennessee, Knoxville: Trace

University of Tennessee, KnoxvilleTrace: Tennessee Research and CreativeExchangeFaculty Publications and Other Works -- Biomedicaland Diagnostic SciencesVeterinary Medicine -- Faculty Publications andOther WorksWinter 9-27-2018Complete Genome Sequences of FourStaphylococcus aureus Sequence Type 398 Isolatesfrom Four Goats with OsteomyelitisMohamed A. AbouelkhairUniversity of Tennessee, KnoxvilleStephen A. KaniaUniversity of Tennessee, KnoxvilleDavid A. BemisUniversity of Tennessee, KnoxvilleRebecca E. RifkinUniversity of Tennessee, KnoxvilleRemiqiusz M. GrzeskowiakUniversity of Tennessee, KnoxvilleSee next page for additional authorsFollow this and additional works at: https://trace.tennessee.edu/utk_compmedpubsPart of the Veterinary Medicine CommonsThis Article is brought to you for free and open access by the Veterinary Medicine -- Faculty Publications and Other Works at Trace: TennesseeResearch and Creative Exchange. It has been accepted for inclusion in Faculty Publications and Other Works -- Biomedical and Diagnostic Sciences byan authorized administrator of Trace: Tennessee Research and Creative Exchange. For more information, please contact trace@utk.edu.Recommended CitationAbouelkhair, Mohamed A.; Kania, Stephen A.; Bemis, David A.; Rifkin, Rebecca E.; Grzeskowiak, Remiqiusz M.; Biris, Alexandru S.;and Anderson, David A., "Complete Genome Sequences of Four Staphylococcus aureus Sequence Type 398 Isolates from Four Goatswith Osteomyelitis" (2018). Faculty Publications and Other Works -- Biomedical and Diagnostic Sciences.https://trace.tennessee.edu/utk_compmedpubs/116AuthorsMohamed A. Abouelkhair, Stephen A. Kania, David A. Bemis, Rebecca E. Rifkin, Remiqiusz M. Grzeskowiak,Alexandru S. Biris, and David A. AndersonThis article is available at Trace: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/utk_compmedpubs/116Complete Genome Sequences of Four Staphylococcus aureusSequence Type 398 Isolates from Four Goats withOsteomyelitisMohamed A. Abouelkhair,a Rebecca E. Rifkin,b Remiqiusz M. Grzeskowiak,b Alexandru S. Biris,c David E. Anderson,bDavid A. Bemis,a Stephen A. KaniaaaDepartment of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee,Knoxville, Tennessee, USAbDepartment of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee,Knoxville, Tennessee, USAcCenter for Integrative Nanotechnology Sciences, University of Arkansas at Little Rock, Little Rock, Arkansas, USAABSTRACT Staphylococcus aureus is the causative agent of multiple infections, in-cluding bacteremia, infective endocarditis, osteomyelitis, septic arthritis, and pros-thetic device infections. We report here the first whole-genome sequence for four S.aureus sequence type 398 isolates from clinical cases of osteomyelitis in four goatswith a history of orthopedic surgery.Staphylococcus aureus is a Gram-positive bacterium commonly found as a compo-nent of the human and animal normal flora (1–3). S. aureus is an importantopportunistic pathogen in human medicine and is an emerging problem in veterinarypractice (1, 2, 4).Here, we report draft genome sequences of four methicillin-susceptible S. aureus(MSSA) sequence type 398 (ST398) isolates obtained from goats that underwentorthopedic surgery at the College of Veterinary Medicine, University of Tennessee(Table 1). The goats were 5 to 6 years old, weighed between 41 and 61 kg, and werefree of underlying disease at the time of surgery. The goats had undergone orthopedicsurgery a mean of 45 days prior (range, 30 to 90 days) to clinical manifestation ofosteomyelitis. Clinical signs included nonhealing wounds, deep surgical site infections,and prolific bone formation. This work was approved by the University of TennesseeIACUC and conducted under protocol 2383-1215.A single bacterial colony of each strain grown on blood agar plates was inoculatedinto 5 ml of sterile Trypticase soy broth (TSB) (BD Biosciences, USA; cat. no. RS1-011-21)and incubated overnight at 37°C with shaking at 225 rpm using an Excella E24 incu-bator shaker (New Brunswick Scientific, USA). DNA was extracted using the MasterPureDNA purification kit (Epicentre, USA; cat. no. MCD85201) according to the manu-facturer’s instructions.Sequencing libraries were constructed using the Nextera DNA sample prep kit(Illumina, Inc., USA) according to the manufacturer’s instructions. The genomes weresequenced using a MiSeq platform (Illumina, Inc.) with a single-end read length of150 bp at the University of Tennessee Genomics Core facility. Sequences were trimmedusing BBDuk and de novo assembled using Geneious version 11.0.3 (5). Annotation wasperformed by the NCBI Prokaryotic Genome Annotation Pipeline version 4.6 (https://www.ncbi.nlm.nih.gov/genome/annotation_prok) using the best-placed reference pro-tein set with GenMarkS. The numbers of reads and contigs, N50 values, GC contentvalues, and the total lengths of the draft genome sequences are listed in (Table 1).In the genome sequence of S. aureus strain MI18-33, there are 2,793 putativeReceived 22 August 2018 Accepted 4September 2018 Published 27 September2018Citation Abouelkhair MA, Rifkin RE,Grzeskowiak RM, Biris AS, Anderson DE, BemisDA, Kania SA. 2018. Complete genomesequences of four Staphylococcus aureussequence type 398 isolates from four goatswith osteomyelitis. Microbiol Resour Announc7:e01174-18. https://doi.org/10.1128/MRA.01174-18.Editor Catherine Putonti, Loyola UniversityChicagoCopyright © 2018 Abouelkhair et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Stephen A. Kania,skania@utk.edu.GENOME SEQUENCEScrossmVolume 7 Issue 12 e01174-18 mra.asm.org 1 on November 5, 2018 by guesthttp://mra.asm.org/Downloaded from protein-coding genes out of 2,905 predicted genes with 112 pseudogenes. StrainMI18-34 contained 2,793 putative protein-coding genes and 109 pseudogenes out of2,902 predicted genes. Strain MI18-935 had 2,793 putative protein-coding genes out of2,904 predicted genes with 111 pseudogenes. In strain MI18-1974, there are 2,790putative protein-coding genes and 111 pseudogenes out of 2,901 predicted genes.This work used the S. aureus MLST database at the University of Oxford (https://pubmlst.org/saureus) for whole-genome multilocus sequence typing (6). All isolateswere identified as ST398.The genome sequences will facilitate identification of the genetic relatedness ofthese isolates with previously published S. aureus strains and may help to elucidate apathomechansim involved in bone infections, healing, and regeneration (7–9).Data availability. The whole-genome shotgun sequencing projects of isolates S.aureus MI18-33 (UTCVM 1), MI18-34 (UTCVM 2), MI18-935 (UTCVM 3), and MI18-1974(UTCVM 4) have been deposited at DDBJ/ENA/GenBank and the Sequence Read Archive(SRA) under the accession numbers listed in Table 1.ACKNOWLEDGMENTSThese studies were partially funded by U.S. Army Medical Research and MaterielCommand (USAMRMC) grant W81XWH-15-1-0666.We acknowledge the Bacteriology Lab, College of Veterinary Medicine, University ofTennessee, for technical assistance.REFERENCES1. Weese JS. 2010. Methicillin-resistant Staphylococcus aureus in animals.ILAR J 51:233–244. https://doi.org/10.1093/ilar.51.3.233.2. Burstiner LC, Faires M, Weese JS. 2010. Methicillin-resistant Staphylococcusaureus colonization in personnel attending a veterinary surgery confer-ence. Vet Surg 39:150–157. https://doi.org/10.1111/j.1532-950X.2009.00638.x.3. Weese JS, van Duijkeren E. 2010. Methicillin-resistant Staphylococcus au-reus and Staphylococcus pseudintermedius in veterinary medicine. VetMicrobiol 140:418–429. https://doi.org/10.1016/j.vetmic.2009.01.039.4. Kottler S, Middleton JR, Perry J, Weese JS, Cohn LA. 2010. Prevalence ofStaphylococcus aureus and methicillin-resistant Staphylococcus aureus car-riage in three populations. J Vet Intern Med 24:132–139. https://doi.org/10.1111/j.1939-1676.2009.0424.x.5. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S,Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, DrummondA. 2012. Geneious Basic: an integrated and extendable desktop softwareplatform for the organization and analysis of sequence data. 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Holden MT, Feil EJ, Lindsay JA, Peacock SJ, Day NP, Enright MC, Foster TJ,Moore CE, Hurst L, Atkin R, Barron A, Bason N, Bentley SD, ChillingworthC, Chillingworth T, Churcher C, Clark L, Corton C, Cronin A, Doggett J,Dowd L, Feltwell T, Hance Z, Harris B, Hauser H, Holroyd S, Jagels K, JamesKD, Lennard N, Line A, Mayes R, Moule S, Mungall K, Ormond D, Quail MA,Rabbinowitsch E, Rutherford K, Sanders M, Sharp S, Simmonds M, StevensK, Whitehead S, Barrell BG, Spratt BG, Parkhill J. 2004. Complete genomesof two clinical Staphylococcus aureus strains: evidence for the rapidevolution of virulence and drug resistance. Proc Natl Acad Sci U S A101:9786–9791. https://doi.org/10.1073/pnas.0402521101.9. Zubair S, Fischer A, Liljander A, Meens J, Hegerman J, Gourle H, Bishop RP,Roebbelen I, Younan M, Mustafa MI, Mushtaq M, Bongcam-Rudloff E,Jores J. 2015. Complete genome sequence of Staphylococcus aureus,strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel. StandGenomic Sci 10:109. https://doi.org/10.1186/s40793-015-0098-6.TABLE 1 Strain characteristicsCharacteristicData for isolate:UTCVM 1 UTCVM 2 UTCVM 3 UTCVM 4Laboratory accession no. MI18-33 MI18-34 MI18-935 MI18-1974GenBank accession no. QQZR00000000 QQZS00000000 QQZU00000000 QQZX00000000No. of reads 552,318 760,362 735,277 920,750No. of contigs 29 28 27 28N50 (bp) 193,883 227,498 380,234 228,010Genome length (bp) 2,835,200 2,834,945 2,835,359 2,836,056GC content (%) 32.9 32.9 32.9 32.9No. of predicted codingsequences2,793 2,793 2,793 2,790No. of predictedRNAs76 75 77 78SRA accession no. SRR7765197 SRR7765198 SRR7765195 SRR7765196Abouelkhair et al.Volume 7 Issue 12 e01174-18 mra.asm.org 2 on November 5, 2018 by guesthttp://mra.asm.org/Downloaded from 

Complete Genome Sequences of Four Staphylococcus aureus Sequence Type 398 Isolates from Four Goats with Osteomyelitis

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Complete Genome Sequences of Four Staphylococcus aureus Sequence Type 398 Isolates from Four Goats with Osteomyelitis

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