Pseudomonas aeruginosa is a Gram-negative bacterium that has the ability to survive in and readily adapt to a variety of environmental conditions. Here, we report 2 genome sequences of P. aeruginosa strains, UMB1046 and UMB5686, isolated from the female urogenital tract

Johnson, Genevieve

Mores, Carine R

Putonti, Catherine

Wolfe, Alan J

English

Loyola eCommons

Loyola University Chicago Loyola eCommons Bioinformatics Faculty Publications Faculty Publications and Other Works by Department 1-2-2020 Draft Genome Sequences of Two Pseudomonas aeruginosa Isolates from the Female Urogenital Tract Genevieve Johnson Loyola University Chicago Carine R. Mores 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 Johnson, Genevieve; Mores, Carine R.; Wolfe, Alan J.; and Putoni, Catherine. Draft Genome Sequences of Two Pseudomonas aeruginosa Isolates from the Female Urogenital Tract. Microbiology Resource Announcements, 9, : , 2020. Retrieved from Loyola eCommons, Bioinformatics Faculty Publications, http://dx.doi.org/10.1128/MRA.01378-19 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. © Johnson et al., 2020. Draft Genome Sequences of Two Pseudomonas aeruginosaIsolates from the Female Urogenital TractGenevieve Johnson,a Carine R. Mores,b,c Alan J. Wolfe,b Catherine Putontia,b,c,daDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USAbDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USAcBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USAdDepartment of Computer Science, Loyola University Chicago, Chicago, Illinois, USAABSTRACT Pseudomonas aeruginosa is a Gram-negative bacterium that has theability to survive in and readily adapt to a variety of environmental conditions. Here,we report 2 genome sequences of P. aeruginosa strains, UMB1046 and UMB5686,isolated from the female urogenital tract.Pseudomonas aeruginosa is an opportunistic pathogen in compromised hosts but isharmless to healthy individuals. P. aeruginosa is associated with chronic lunginfections in individuals with cystic fibrosis (1), as well as nosocomial urinary tractinfections (2). While it is not frequently found within the urogenital microbiota ofhealthy women (3, 4), strains have been isolated from women with lower urinary tractsymptoms (3, 5, 6). Here, we present the genomes of two P. aeruginosa strains isolatedfrom two different women. P. aeruginosa UMB5686 was isolated from a vaginal swabsample obtained from a woman with overactive bladder (OAB) symptoms after12 weeks of treatment with a vaginal estrogen cream (5). P. aeruginosa UMB1046 wasisolated from a catheterized urine sample obtained from a woman with a urinary tractinfection (6).P. aeruginosa UMB1046 and UMB5686 were isolated from prior institutional reviewboard (IRB)-approved studies (5, 6) using the expanded quantitative urinary culture(EQUC) protocol (5). Briefly, vaginal swabs were collected using the BD liquid Amieselution swab (ESwab) collection system and cultured as previously described (5);catheterized urine samples were cultured as previously described (6). The genus andspecies for these isolates were determined via matrix-assisted laser desorption ioniza-tion–time of flight (MALDI-TOF) mass spectrometry prior to storage at – 80°C. Fromthese freezer stocks, each P. aeruginosa isolate was first streaked on an LB agar plateand incubated at 37°C for 24 hours. A single colony was selected from each plate toinoculate LB broth and incubated at 37°C with shaking for 24 hours. DNA was extractedusing the Qiagen DNeasy UltraClean microbial kit and quantified using the Qubitfluorometer. DNA was sent to the Microbial Genomic Sequencing Center (MiGS) at theUniversity of Pittsburgh for sequencing, where the DNA was first enzymatically frag-mented using an Illumina tagmentation enzyme. Indices were attached using PCR andsequenced using an Illumina NextSeq 500 flow cell, producing 938,702 and 1,641,347pairs of 151-bp reads for UMB1046 and UMB5686, respectively. Raw reads weretrimmed using Sickle v1.33 (https://github.com/najoshi/sickle) and assembled usingSPAdes v3.13.0 with the “only-assembler” option for k values of 55, 77, 99, and 127(7). Genome coverage was calculated using BBMap v38.47 (https://sourceforge.net/projects/bbmap/). The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.8 (8)was used to annotate the genome sequences. Unless previously noted, default param-eters were used for each software tool.Citation Johnson G, Mores CR, Wolfe AJ,Putonti C. 2020. Draft genome sequences oftwo Pseudomonas aeruginosa isolates from thefemale urogenital tract. Microbiol ResourAnnounc 9:e01378-19. https://doi.org/10.1128/MRA.01378-19.Editor David A. Baltrus, University of ArizonaCopyright © 2020 Johnson 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 3 November 2019Accepted 14 November 2019Published 2 January 2020GENOME SEQUENCEScrossmVolume 9 Issue 1 e01378-19 mra.asm.org 1 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from The P. aeruginosa UMB1046 genome is 6,513,817 bp long in 161 contigs with a GCcontent of 64%, genome coverage of 34.03, and an N50 score of 64,232 bp. The P.aeruginosa UMB5686 genome has a similar size, 6,684,697 bp, with a GC content of63%. The UMB5686 assembly includes 98 contigs with a coverage of 58.48 and an N50score of 120,243 bp. PGAP annotation identified 6,257 and 6,351 protein-coding genesfor UMB1046 and UMB5686, respectively. The strains vary in their number of rRNAoperons and tRNAs; UMB1046 carries 3 rRNA operons and 58 tRNAs, whereas UMB5686carries 4 rRNA operons and 59 tRNAs. Future analyses of these strains and genomes willfurther our understanding of this opportunistic pathogen within the female urogenitaltract.Data availability. This whole-genome shotgun (WGS) project has been deposited inGenBank under the accession numbers WHVN00000000 and WHVM00000000 for P.aeruginosa UMB1046 and UMB5686, respectively. The raw sequence reads have beendeposited under accession numbers SRR10336114 and SRR10336113 for P. aeruginosaUMB1046 and UMB5686, respectively. The WGS and SRA records are associated withBioProject number PRJNA316969.ACKNOWLEDGMENTSWe thank the authors of the prior studies that isolated the bacteria. For prior patientrecruitment, we acknowledge the Loyola Urinary Education and Research Collaborative(LUEREC), specifically Mary Tulke, Linda Brubaker, Elizabeth Mueller, Cynthia Brincat,Susanne Taege, and Tanaka Dune, and the patients who provided the samples for thisstudy.G.J. is partially supported by a Mulcahy research fellowship from Loyola UniversityChicago.REFERENCES1. Faure E, Kwong K, Nguyen D. 2018. Pseudomonas aeruginosa in chroniclung infections: how to adapt within the host? Front Immunol 9:2416.https://doi.org/10.3389/fimmu.2018.02416.2. Djordjevic Z, Folic MM, Zivic Z, Markovic V, Jankovic SM. 2013. Nosocomialurinary tract infections caused by Pseudomonas aeruginosa and Acineto-bacter species: sensitivity to antibiotics and risk factors. Am J InfectControl 41:1182–1187. https://doi.org/10.1016/j.ajic.2013.02.018.3. 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.02876-13.4. Ma B, Forney LJ, Ravel J. 2012. The vaginal microbiome: rethinking healthand diseases. Annu Rev Microbiol 66:371–389. https://doi.org/10.1146/annurev-micro-092611-150157.5. Thomas-White K, Forster SC, Kumar N, Van Kuiken M, Putonti C, StaresMD, Hilt EE, Price TK, Wolfe AJ, Lawley TD. 2018. Culturing of femalebladder bacteria reveals an interconnected urogenital microbiota. NatCommun 9:1557. https://doi.org/10.1038/s41467-018-03968-5.6. Price TK, Dune T, Hilt EE, Thomas-White KJ, Kliethermes S, Brincat C,Brubaker L, Wolfe AJ, Mueller ER, Schreckenberger PC. 2016. The clinicalurine culture: enhanced techniques improve detection of clinically rele-vant microorganisms. J Clin Microbiol 54:1216 –1222. https://doi.org/10.1128/JCM.00044-16.7. 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.2012.0021.8. 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.Johnson et al.Volume 9 Issue 1 e01378-19 mra.asm.org 2 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from 

Draft Genome Sequences of Two Pseudomonas aeruginosa Isolates from the Female Urogenital Tract

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Draft Genome Sequences of Two Pseudomonas aeruginosa Isolates from the Female Urogenital Tract

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