Here, we present the draft genome sequence for Klebsiella pneumoniae strain UMB8492, isolated from a urine sample from a female patient with overactive bladder (OAB) symptoms. The assembled genome has a length of 5,660,575 bp, a G+C content of 57.19%, and an N50 value of 136,315 bp

Gondi, Suma

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 Klebsiella pneumoniae UMB8492, Isolated from the Female Urinary Tract Suma Gondi 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 Gondi, Suma; Miller-Ensminger, Taylor; Voukadinova, Adelina; Wolfe, Alan J.; and Putoni, Catherine. Draft Genome Sequence of Klebsiella pneumoniae UMB8492, Isolated from the Female Urinary Tract. Microbiology Resource Announcements, 9, : , 2020. Retrieved from Loyola eCommons, Bioinformatics Faculty Publications, http://dx.doi.org/10.1128/MRA.00405-2 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. © Gondi et al., 2020. Draft Genome Sequence of Klebsiella pneumoniae UMB8492,Isolated from the Female Urinary TractSuma Gondi,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 Here, we present the draft genome sequence for Klebsiella pneumoniaestrain UMB8492, isolated from a urine sample from a female patient with overactivebladder (OAB) symptoms. The assembled genome has a length of 5,660,575 bp, aGC content of 57.19%, and an N50 value of 136,315 bp.Klebsiella pneumoniae is a Gram-negative bacterium that is commonly found in thegastrointestinal tract of healthy animals and humans (1, 2). It can also cause urinarytract, respiratory tract, and bloodstream infections (3). K. pneumoniae is a major causeof hospital-acquired infections, and surveys from several different countries estimatethat K. pneumoniae accounts for 2 to 6% of hospital-acquired UTIs (3, 4). K. pneumoniaeis also classified as a multidrug-resistant (MDR) pathogen, and thus there are limitedtreatment options (1). Here, we present the draft genome of K. pneumoniae UMB8492,isolated from a catheterized urine sample. While K. pneumoniae is frequently associatedwith UTIs, the woman from whom it was isolated did not have a UTI but rather hadsymptoms of overactive bladder (OAB).K. pneumoniae UMB8492 was isolated from a previously conducted institutionalreview board (IRB)-approved study (Loyola University Chicago, IRB no. LU207102) usingthe expanded quantitative urinary culture (EQUC) protocol (5). The genus and speciesof Klebsiella pneumoniae were confirmed using matrix-assisted laser desorption ioniza-tion–time of flight (MALDI-TOF) mass spectrometry before the culture was frozen at80°C. The EQUC method was also used to isolate strains of Lactobacillus jensenii,Corynebacterium coyleae, Lactobacillus iners, Corynebacterium aurimucosum, and Staph-ylococcus epidermidis from this same woman’s urinary microbiome. From the freezerstock of UMB8492, an aliquot was streaked onto a Columbia nalidixic acid (CNA) agarplate and incubated at 35°C with 5% CO2 for 24 h. A single colony was isolated, andliquid LB medium was inoculated and grown overnight with shaking at 37°C. DNA wasisolated from this liquid culture using the Qiagen DNeasy blood and tissue kit followingthe Gram-positive protocol with the following exceptions. We used 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 oflysozyme) in step 2 and incubated the sample at 56°C for 10 minutes in step 5. The DNAquality was determined using a Qubit fluorometer. DNA was sent to the MicrobialGenome Sequencing Center (MiGS) at the University of Pittsburgh for sequencing. MiGSprepared the libraries using the Illumina Nextera kit and sequenced the library on theNextSeq 550 platform. In total, 1,712,978 pairs of 2  150-bp reads were generated.These raw reads were trimmed using Sickle v1.33 (https://github.com/najoshi/sickle),using default parameters, and assembled using SPAdes v3.13.0 with the “only-assembler” option for k values of 55, 77, 99, and 127 (6). The genome assembly wasannotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.11 (7).Citation Gondi S, Miller-Ensminger T,Voukadinova A, Wolfe AJ, Putonti C. 2020. Draftgenome sequence of Klebsiella pneumoniaeUMB8492, isolated from the female urinarytract. Microbiol Resour Announc 9:e00405-20.https://doi.org/10.1128/MRA.00405-20.Editor David A. Baltrus, University of ArizonaCopyright © 2020 Gondi 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 27 April 2020Published 14 May 2020GENOME SEQUENCEScrossmVolume 9 Issue 20 e00405-20 mra.asm.org 1 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from The genome coverage was calculated using BBMap v38.47 (https://sourceforge.net/projects/bbmap/) with default parameters.K. pneumoniae UMB8492 has a draft genome size of 5,660,575 bp, assembled into127 contigs with an N50 value of 136,315 bp, and a GC content of 57.19%. Thegenome coverage is 77. PGAP annotation identified 5,508 protein-coding genes and79 tRNAs. This genome sequence provides an additional genome resource for the studyof uropathogens.Data availability. This whole-genome shotgun project has been deposited inGenBank under accession no. JAAUVU000000000. The version described in this paperis the first version, JAAUVU010000000. The raw sequencing reads have been depositedin the SRA under accession no. SRR11441023.ACKNOWLEDGMENTSThis work was conducted as part of the Bacterial Genomics course at LoyolaUniversity Chicago’s Department of Biology.For prior patient recruitment, we acknowledge the Loyola Urinary Education andResearch Collaborative (LUEREC) and the patients who provided the samples for thisstudy.REFERENCES1. Navon-Venezia S, Kondratyeva K, Carattoli A. 2017. Klebsiella pneumoniae: amajor worldwide source and shuttle for antibiotic resistance. FEMS MicrobiolRev 41:252–275. https://doi.org/10.1093/femsre/fux013.2. Wyres KL, Holt KE. 2018. Klebsiella pneumoniae as a key trafficker of drugresistance genes from environmental to clinically important bacteria. CurrOpin Microbiol 45:131–139. https://doi.org/10.1016/j.mib.2018.04.004.3. Paczosa MK, Mecsas J. 2016. Klebsiella pneumoniae: going on the offensewith a strong defense. Microbiol Mol Biol Rev 80:629 – 661. https://doi.org/10.1128/MMBR.00078-15.4. Meatherall BL, Gregson D, Ross T, Pitout JD, Laupland KB. 2009. Incidence,risk factors, and outcomes of Klebsiella pneumoniae bacteremia. Am J Med122:866 – 873. https://doi.org/10.1016/j.amjmed.2009.03.034.5. Hilt EE, McKinley K, Pearce MM, Rosenfeld AB, Zilliox MJ, Mueller ER,Brubaker L, Gai X, Wolfe AJ, Schreckenberger PC. 2014. Urine is not sterile:use of enhanced urine culture techniques to detect resident bacterialflora in the adult female bladder. J Clin Microbiol 52:871– 876. https://doi.org/10.1128/JCM.02876-13.6. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, LesinVM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N,Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome as-sembly algorithm and its applications to single-cell sequencing. J ComputBiol 19:455– 477. https://doi.org/10.1089/cmb.2012.0021.7. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L,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.Gondi et al.Volume 9 Issue 20 e00405-20 mra.asm.org 2 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from 

Draft Genome Sequence of Klebsiella pneumoniae UMB8492, Isolated from the Female Urinary Tract

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Draft Genome Sequence of Klebsiella pneumoniae UMB8492, Isolated from the Female Urinary Tract

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