Staphylococcus epidermidis is a Gram-positive bacterium that is resistant to many antibiotics. Here, we present the 2.5-Mb draft genome of S. epidermidis UMB7765, isolated from a voided urine sample from a female with recurrent urinary tract infections

Kemper, Lucy

Miller-Ensminger, Taylor

Putonti, Catherine

Voukadinova, Adelina

Wolfe, Alan J

English

Loyola eCommons

Loyola University Chicago Loyola eCommons Bioinformatics Faculty Publications Faculty Publications and Other Works by Department 5-14-2020 Draft Genome Sequence of Staphylococcus epidermidis UMB7765, Isolated from the Urobiome of a Woman with Recurrent Urinary Tract Infection Lucy Kemper Loyola University Chicago Taylor Miller-Ensminger Loyola University Chicago Adelina Voukadinova Loyola University Chicago Alan J. Wolfe Loyola University Chicago, awolfe@luc.edu Catherine Putoni Loyola University Chicago, cputonti@luc.edu Follow this and additional works at: https://ecommons.luc.edu/bioinformatics_facpub  Part of the Bioinformatics Commons, and the Biology Commons Recommended Citation Kemper, Lucy; Miller-Ensminger, Taylor; Voukadinova, Adelina; Wolfe, Alan J.; and Putoni, Catherine. Draft Genome Sequence of Staphylococcus epidermidis UMB7765, Isolated from the Urobiome of a Woman with Recurrent Urinary Tract Infection. Microbiology Resource Announcements, 9, : , 2020. Retrieved from Loyola eCommons, Bioinformatics Faculty Publications, http://dx.doi.org/10.1128/MRA.00417-20 This Article is brought to you for free and open access by the Faculty Publications and Other Works by Department at Loyola eCommons. It has been accepted for inclusion in Bioinformatics Faculty Publications by an authorized administrator of Loyola eCommons. For more information, please contact ecommons@luc.edu. This work is licensed under a Creative Commons Attribution 4.0 License. © Kemper et al., 2020. Draft Genome Sequence of Staphylococcus epidermidisUMB7765, Isolated from the Urobiome of a Woman withRecurrent Urinary Tract InfectionLucy Kemper,a Taylor Miller-Ensminger,b Adelina Voukadinova,b Alan J. Wolfe,c Catherine Putontia,b,c,daDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USAbBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USAcDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USAdDepartment of Computer Science, Loyola University Chicago, Chicago, Illinois, USAABSTRACT Staphylococcus epidermidis is a Gram-positive bacterium that is resistantto many antibiotics. Here, we present the 2.5-Mb draft genome of S. epidermidisUMB7765, isolated from a voided urine sample from a female with recurrent urinarytract infections.While Staphylococcus epidermidis primarily colonizes human skin (1), it has alsobeen found to be a native member of the microbiota of other organs (2, 3). Whileoften harmless, S. epidermidis is an opportunistic pathogen; it can cause seriousinfections of implanted medical devices (such as catheters and pacemakers) (4, 5).Treatment of S. epidermidis infections is complicated by the species’ often high levelsof antibiotic resistance and ability to form biofilms (6, 7). Here, we present the genomesequence of S. epidermidis UMB7765, isolated from a voided urine sample from awoman with recurrent urinary tract infection (UTI). While S. epidermidis has on rareoccasions been associated with UTIs (8), we do not have definitive evidence that thisstrain was the cause of UTI symptoms for this individual.S. epidermidis UMB7765 was isolated using the expanded quantitative urine culture(EQUC) method (3) as part of a prior institutional review board (IRB)-approved study(University of California, San Diego, IRB no. 170077AW). The genus and species for thisisolate were determined by matrix-assisted laser desorption ionization–time of flight(MALDI-TOF) mass spectrometry following protocols detailed previously (3). The isolatewas stored at 80°C until sequencing. The freezer stock was first streaked onto aColumbia nalidixic acid (CNA) agar plate and incubated at 35°C with 5% CO2 for 24 h.Tryptone soy liquid medium was inoculated with a single colony from the plate andincubated overnight at 37°C. DNA extraction was done using the Qiagen DNeasy bloodand tissue kit with the following modifications to the Gram-positive protocol: thebacteria were lysed using 230 l of lysis buffer (180 l of 20 mM Tris-Cl, 2 mMsodium EDTA, and 1.2% Triton X-100 and 50 l of lysozyme) in step 2, and theincubation time in step 5 was altered to 10 min. The purified DNA was quantifiedusing a Qubit fluorometer. DNA sequencing was done at the Microbial GenomeSequence Center at the University of Pittsburgh, where the DNA was fragmentedusing an Illumina tagmentation enzyme. Indices were attached using PCR andsequenced on the Illumina NextSeq 550 platform. Sequencing yielded 1,950,209pairs of 150-bp reads. Unless otherwise noted, default parameters were used for allsoftware tools. Reads were trimmed using Sickle v1.33 (https://github.com/najoshi/sickle). The reads were assembled using SPAdes v3.13.0 with the “only-assembler”option for k values of 55, 77, 99, and 127 (9). The genome coverage was calculatedusing BBMap v38.47 (https://sourceforge.net/projects/bbmap/). NCBI’s Prokaryotic Ge-Citation Kemper L, Miller-Ensminger T,Voukadinova A, Wolfe AJ, Putonti C. 2020. Draftgenome sequence of Staphylococcusepidermidis UMB7765, isolated from theurobiome of a woman with recurrent urinarytract infection. Microbiol Resour Announc9:e00417-20. https://doi.org/10.1128/MRA.00417-20.Editor Frank J. Stewart, Georgia Institute ofTechnologyCopyright © 2020 Kemper et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Catherine Putonti,cputonti@luc.edu.Received 15 April 2020Accepted 27 April 2020Published 14 May 2020GENOME SEQUENCEScrossmVolume 9 Issue 20 e00417-20 mra.asm.org 1 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from nome Annotation Pipeline (PGAP) v4.11 was used to annotate the publicly availablegenome sequences (10).The draft genome sequence is 2,530,547 bp long, assembled into 68 contigs with anN50 value of 158,051 bp and 190 coverage. The GC content of the assembled genomeis 31.93%, which is consistent with that of other publicly available S. epidermidisgenomes. PGAP annotation includes 2,475 genes total, 2,361 encoding proteins, and 56tRNAs. We analyzed the genome assembly using the Center for Genomic Epidemiol-ogy’s Web tool ResFinder v3.2 (11) and identified resistance genes for aminoglycosides,beta-lactams, fosfomycin, macrolides, and tetracycline. Frequently, antibiotics are pre-scribed for recurrent UTIs, and antibiotic resistance is likely (12). We can thusspeculate that the multiple genes associated with antibiotic resistance encoded byS. epidermidis UMB7765 were acquired through repeated antibiotic exposure.Data availability. This whole-genome shotgun project has been deposited inGenBank under the accession no. JAAUWD000000000. The version described in thispaper is the first version, JAAUWD010000000. The raw sequencing reads have beendeposited in the SRA under the accession no. SRR11441034.ACKNOWLEDGMENTSThis work was conducted as part of the Bacterial Genomics course at LoyolaUniversity Chicago’s Department of Biology. For prior patient recruitment, we acknowl-edge the Loyola Urinary Education and Research Collaborative (LUREC) and the patientswho provided the samples for this study.REFERENCES1. Byrd AL, Belkaid Y, Segre JA. 2018. The human skin microbiome. Nat RevMicrobiol 16:143–155. https://doi.org/10.1038/nrmicro.2017.157.2. Aujoulat F, Roudière L, Picaud J-C, Jacquot A, Filleron A, Neveu D, BaumT-P, Marchandin H, Jumas-Bilak E. 2014. Temporal dynamics of the verypremature infant gut dominant microbiota. BMC Microbiol 14:325.https://doi.org/10.1186/s12866-014-0325-0.3. Hilt EE, McKinley K, Pearce MM, Rosenfeld AB, Zilliox MJ, Mueller ER,Brubaker L, Gai X, Wolfe AJ, Schreckenberger PC. 2014. Urine is notsterile: use of enhanced urine culture techniques to detect residentbacterial flora in the adult female bladder. J Clin Microbiol 52:871– 876.https://doi.org/10.1128/JCM.02876-13.4. Otto M. 2009. Staphylococcus epidermidis—the “accidental” pathogen.Nat Rev Microbiol 7:555–567. https://doi.org/10.1038/nrmicro2182.5. Fluckiger U, Ulrich M, Steinhuber A, Doring G, Mack D, Landmann R,Goerke C, Wolz C. 2005. Biofilm formation, icaADBC transcription, andpolysaccharide intercellular adhesin synthesis by staphylococci in adevice-related infection mode. Infect Immun 73:1811–1819. https://doi.org/10.1128/IAI.73.3.1811-1819.2005.6. Sabaté Brescó M, Harris LG, Thompson K, Stanic B, Morgenstern M,O’Mahony L, Richards RG, Moriarty TF. 2017. Pathogenic mechanismsand host interactions in Staphylococcus epidermidis device-related in-fection. Front Microbiol 8:1401. https://doi.org/10.3389/fmicb.2017.01401.7. Lee JYH, Monk IR, Gonçalves da Silva A, Seemann T, Chua KYL, Kearns A,Hill R, Woodford N, Bartels MD, Strommenger B, Laurent F, Dodémont M,Deplano A, Patel R, Larsen AR, Korman TM, Stinear TP, Howden BP. 2018.Global spread of three multidrug-resistant lineages of Staphylococcusepidermidis. Nat Microbiol 3:1175–1185. https://doi.org/10.1038/s41564-018-0230-7.8. Lozano V, Fernandez G, Spencer PL, Taylor SL, Hatch R. 2015. Staphylo-coccus epidermidis in urine is not always benign: a case report ofpyelonephritis in a child. J Am Board Fam Med 28:151–153. https://doi.org/10.3122/jabfm.2015.01.140118.9. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV,Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a newgenome assembly algorithm and its applications to single-cell sequenc-ing. J Comput Biol 19:455– 477. https://doi.org/10.1089/cmb.2012.0021.10. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP,Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBIProkaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614 – 6624. https://doi.org/10.1093/nar/gkw569.11. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O,Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobialresistance genes. J Antimicrob Chemother 67:2640 –2644. https://doi.org/10.1093/jac/dks261.12. Albert X, Huertas I, Pereiro II, Sanfélix J, Gosalbes V, Perrotta C. 2004.Antibiotics for preventing recurrent urinary tract infection in non-pregnant women. Cochrane Database Syst Rev 3:CD001209. https://doi.org/10.1002/14651858.CD001209.pub2.Kemper et al.Volume 9 Issue 20 e00417-20 mra.asm.org 2 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from 

Draft Genome Sequence of Staphylococcus epidermidis UMB7765, Isolated from the Urobiome of a Woman with Recurrent Urinary Tract Infection

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Draft Genome Sequence of Staphylococcus epidermidis UMB7765, Isolated from the Urobiome of a Woman with Recurrent Urinary Tract Infection

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