Proteus mirabilis is a Gram-negative motile and rod-shaped bacterium that is a common pathogen of the urinary tract. Here, we report the draft genome sequence of P. mirabilis UMB0038, which was isolated from a woman without lower urinary tract symptoms

Gallian, Noreen

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 5-21-2020 Draft Genome Sequence of Proteus mirabilis Strain UMB0038, Isolated from the Female Bladder Noreen Gallian 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 Gallian, Noreen; Miller-Ensminger, Taylor; Voukadinova, Adelina; Wolfe, Alan J.; and Putoni, Catherine. Draft Genome Sequence of Proteus mirabilis Strain UMB0038, Isolated from the Female Bladder. Microbiology Resource Announcements, 9, : , 2020. Retrieved from Loyola eCommons, Bioinformatics Faculty Publications, http://dx.doi.org/10.1128/MRA.00401-20 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. © Gallian et al., 2020 Draft Genome Sequence of Proteus mirabilis Strain UMB0038,Isolated from the Female BladderNoreen Gallian,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 Proteus mirabilis is a Gram-negative motile and rod-shaped bacteriumthat is a common pathogen of the urinary tract. Here, we report the draft genomesequence of P. mirabilis UMB0038, which was isolated from a woman without lowerurinary tract symptoms.Proteus mirabilis is well known for its prominent flagella, allowing it to move acrosssurfaces. Unique virulence factors such as urease production, fimbriae, iron and zincacquisition, toxins, and biofilm formation allow it to overtake many other species withwhich it comes into contact, allowing it to be a common pathogen within the urinarytract (1). P. mirabilis is commonly seen in complicated urinary tract infection (UTI) casesthat include long-term catheterization (2). Catheter-associated UTIs are frequentlycaused by P. mirabilis biofilm formation on the catheter surface, blocking urine flow.Therefore, much research has gone into methods for inhibiting biofilm formation (seereviews [3, 4]). Here, we present the draft genome sequence of a P. mirabilis strain,UMB0038, isolated from a catheterized urine sample obtained from a “healthy” womanwithout lower urinary tract symptoms.P. mirabilis was collected as part of prior institutional review board (IRB)-approvedstudies (5–8) using the expanded quantitative urine culture (EQUC) protocol (8). Thegenus and species for this isolate were determined through matrix-assisted laserdesorption ionization–time of flight (MALDI-TOF) mass spectrometry (8) prior to storageat 80°C. From the freezer stock, the P. mirabilis isolate was streaked onto a Columbianalidixic acid (CNA) plate and incubated for 24 h at 35°C in 5% CO2. A single colony wasselected from the plate, added to liquid tryptic soy broth (TSB) and incubated for 48 hat 37°C with shaking. DNA was extracted using the Qiagen DNeasy blood and tissue kitfollowing the protocol for Gram-positive bacteria with minor modification. An adjustedamount of 230 l of lysis buffer (180 l of 20 mM Tris-Cl, 2 mM sodium EDTA, and 1.2%Triton X-100 and 50 l of lysozyme) was used, with an incubation time of 10 min afterthe addition of buffer AL. DNA was quantified using a Qubit fluorometer and then sentto the Microbial Genome Sequencing Center (MiGS) at the University of Pittsburgh forsequencing on the Illumina NextSeq 550 platform. There the DNA was enzymaticallyfragmented using an Illumina tagmentation enzyme, and indices were attached usingPCR. A total of 1,565,124 pairs of 150-bp reads were produced. Raw reads were trimmedusing Sickle v1.33 (https://github.com/najoshi/sickle) and assembled using SPAdesv3.13.0 with the only-assembler option for k values of 55, 77, 99, and 127 (9). Thegenome coverage for the assembly was 103 and was calculated using BBMap v38.47(https://sourceforge.net/projects/bbmap). Genome quality assessment and annotationwere conducted with PATRIC v3.6.3 (10). The NCBI Prokaryotic Genome AnnotationCitation Gallian N, Miller-Ensminger T,Voukadinova A, Wolfe AJ, Putonti C. 2020. Draftgenome sequence of Proteus mirabilis strainUMB0038, isolated from the female bladder.Microbiol Resour Announc 9:e00401-20.https://doi.org/10.1128/MRA.00401-20.Editor Vincent Bruno, University of MarylandSchool of MedicineCopyright © 2020 Gallian et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Catherine Putonti,cputonti@luc.edu.Received 13 April 2020Accepted 28 April 2020Published 21 May 2020GENOME SEQUENCEScrossmVolume 9 Issue 21 e00401-20 mra.asm.org 1 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from Pipeline (PGAP) v4.8 (11) also was used to annotate the genome sequence. Defaultparameters were used for each software tool unless previously stated.The P. mirabilis UMB0038 draft genome was assembled into 57 contigs. It is3,946,388 bp long with an N50 value of 164,741 bp and a GC content of 38.6%. The sizeand GC content are similar to those of other strains of this species in GenBank. PGAPidentified 3,533 protein-coding genes in the genome assembly. PHASTER (12) foundthree incomplete phages and one intact phage within this genome. The intact phageis of particular interest, because very few P. mirabilis-infecting phages are known (13)and phages are one strategy currently being explored to combat P. mirabilis biofilms(3). Additional analysis of this strain and genome will provide insight into how uniquevirulence factors contribute to UTIs.Data availability. This whole-genome shotgun project has been deposited inGenBank under the accession no. JAAUWO000000000. The version described in thispaper is the first version, JAAUWO010000000. The raw sequencing reads have beendeposited in the SRA under the accession no. SRR11441037.ACKNOWLEDGMENTSThis work was conducted as part of the Loyola University Chicago’s Department ofBiology Bacterial Genomics course. For prior patient recruitment, we acknowledge theLoyola Urinary Education and Research Collaborative and the patients who providedthe samples for this study.REFERENCES1. Schaffer J, Pearson M. 2015. Proteus mirabilis and urinary tract infections.Microbiol Spectr 3:UTI-0017–2013. https://doi.org/10.1128/microbiolspec.UTI-0017-2013.2. Stickler D, Ganderton L, King J, Nettleton J, Winters C. 1993. Proteusmirabilis biofilms and the encrustation of urethral catheters. Urol Res21:407– 411. https://doi.org/10.1007/bf00300077.3. Siddiq DM, Darouiche RO. 2012. New strategies to prevent catheter-associated urinary tract infections. Nat Rev Urol 9:305–314. https://doi.org/10.1038/nrurol.2012.68.4. Tenke P, Mezei T, Bőde I, Köves B. 2017. Catheter-associated urinary tractinfections. Eur Urol Suppl 16:138 –143. https://doi.org/10.1016/j.eursup.2016.10.001.5. Pearce MM, Hilt EE, Rosenfeld AB, Zilliox MJ, Thomas-White K, Fok C,Kliethermes S, Schreckenberger PC, Brubaker L, Gai X, Wolfe AJ. 2014.The female urinary microbiome: a comparison of women with andwithout urgency urinary incontinence. mBio 5:e01283-14. https://doi.org/10.1128/mBio.01283-14.6. Pearce MM, Zilliox MJ, Rosenfeld AB, Thomas-White KJ, Richter HE, NagerCW, Visco AG, Nygaard IE, Barber MD, Schaffer J, Moalli P, Sung VW,Smith AL, Rogers R, Nolen TL, Wallace D, Meikle SF, Gai X, Wolfe AJ,Brubaker L. 2015. The female urinary microbiome in urgency urinaryincontinence. Am J Obstet Gynecol 213:347.e1–347.e11. https://doi.org/10.1016/j.ajog.2015.07.009.7. Thomas-White KJ, Hilt EE, Fok C, Pearce MM, Mueller ER, Kliethermes S,Jacobs K, Zilliox MJ, Brincat C, Price TK, Kuffel G, Schreckenberger P, GaiX, Brubaker L, Wolfe AJ. 2016. Incontinence medication response relatesto the female urinary microbiota. Int Urogynecol J 27:723–733. https://doi.org/10.1007/s00192-015-2847-x.8. 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.02876-13.9. 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. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N,Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, MachiD, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, OverbeekR, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H,Stevens RL. 2017. Improvements to PATRIC, the all-bacterial Bioinformat-ics Database and Analysis Resource Center. Nucleic Acids Res 45:D535–D542. https://doi.org/10.1093/nar/gkw1017.11. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, ZaslavskyL, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI ProkaryoticGenome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569.12. Arndt D, Grant J, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS. 2016.PHASTER: a better, faster version of the PHAST phage search tool.Nucleic Acids Res 44:W16 –W21. https://doi.org/10.1093/nar/gkw387.13. Alves DR, Nzakizwanayo J, Dedi C, Olympiou C, Hanin A, Kot W, HansenL, Lametsch R, Gahan CGM, Schellenberger P, Ogilvie LA, Jones BV. 2019.Genomic and ecogenomic characterization of Proteus mirabilis bacterio-phages. Front Microbiol 10:1783. https://doi.org/10.3389/fmicb.2019.01783.Gallian et al.Volume 9 Issue 21 e00401-20 mra.asm.org 2 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from 

Draft Genome Sequence of Proteus mirabilis Strain UMB0038, Isolated from the Female Bladder

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Draft Genome Sequence of Proteus mirabilis Strain UMB0038, Isolated from the Female Bladder

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