Here, we introduce the 2.8-Mbp draft genome of Enterococcus faecalis strain UMB0843, isolated from the female urinary tract. E. faecalis is a leading cause of nosocomial infections, and many strains are often resistant to multiple antibiotics. We focus our genome analysis on the multiple genes involved in antibiotic resistance in this strain

Miller-Ensminger, Taylor

Purta, Natalia

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 Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract Natalia Purta 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 Purta, Natalia; Miller-Ensminger, Taylor; Voukadinova, Adelina; Wolfe, Alan J.; and Putoni, Catherine. Draft Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, 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.00407-20 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. © Purta et al., 2020 Draft Genome Sequence of Antibiotic-Resistant Enterococcusfaecalis Strain UMB0843, Isolated from the Female UrinaryTractNatalia Purta,a Taylor Miller-Ensminger,b Adelina Voukadinova,b Alan J. Wolfe,c Catherine Putontib,c,d,eaNeuroscience Program, 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 Biology, Loyola University Chicago, Chicago, Illinois, USAeDepartment of Computer Science, Loyola University Chicago, Chicago, Illinois, USAABSTRACT Here, we introduce the 2.8-Mbp draft genome of Enterococcus faecalisstrain UMB0843, isolated from the female urinary tract. E. faecalis is a leading causeof nosocomial infections, and many strains are often resistant to multiple antibiotics.We focus our genome analysis on the multiple genes involved in antibiotic resis-tance in this strain.Enterococcus faecalis lives in the gastrointestinal tract of many organisms (1) and hasrecently emerged as a leading cause of nosocomial infections due to its increasedresistance to many antibiotics (2, 3). E. faecalis is often a primary cause of surgicalinfections, infections within the bloodstream, and urinary tract infections (UTIs) (3, 4).Recently, we isolated E. faecalis strain UMB0843 from a urine sample obtained from apregnant female. Here, we present the draft genome sequence of this isolate and theantibiotic resistance genes found within the genome.E. faecalis UMB0843 was collected as part of a previous institutional review board(IRB)-approved study (5) and cultured using the expanded quantitative urine culture(EQUC) protocol (6). To determine the genus and species of each isolate, matrix-assistedlaser desorption ionization–time of flight (MALDI-TOF) mass spectrometry was used,following a protocol detailed previously (6), prior to storage of the isolates at 80°C.From the freezer stocks, E. faecalis was streaked onto a Columbia nalidixic acid (CNA)agar plate and incubated at 35°C in 5% CO2 for 24 h. A single colony was selected,inoculated in brain heart infusion (BHI) broth (premixed BBL brain heart infusion; BD),and incubated under the same conditions described above. DNA was extracted usingthe Qiagen DNeasy blood and tissue kit and quantified using the fluorescence-basedQubit. The Gram-positive extraction protocol was followed with the following excep-tion: 230 l of lysis buffer was used (180 l of 20 mM Tris-Cl, 2 mM sodium EDTA, and1.2% Triton X-100 and 50 l of lysozyme). The extracted DNA was sent to the MicrobialGenome Sequencing Center (MiGS) at the University of Pittsburgh for sequencing. TheDNA was first enzymatically fragmented using the Illumina tagmentation enzyme, andthen indices were attached using PCR. Sequencing was performed using an IlluminaNextSeq 550 flow cell, and 1,590,783 pairs of 150-bp reads were generated. The rawreads were trimmed using Sickle v1.33 (https://github.com/najoshi/sickle) and assem-bled using SPAdes v3.13.0 with the “only-assembler” option for k values of 55, 77, 99,and 127 (7). BBMap v38.47 (https://sourceforge.net/projects/bbmap/) was used tocalculate the genome coverage. Genome sequences were annotated using PATRICv3.6.3 (8), while the publicly available genome was annotated using the NCBI Prokary-Citation Purta N, Miller-Ensminger T,Voukadinova A, Wolfe AJ, Putonti C. 2020. Draftgenome sequence of antibiotic-resistantEnterococcus faecalis strain UMB0843, isolatedfrom the female urinary tract. Microbiol ResourAnnounc 9:e00407-20. https://doi.org/10.1128/MRA.00407-20.Editor John J. Dennehy, Queens CollegeCopyright © 2020 Purta 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 e00407-20 mra.asm.org 1 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from otic Genome Annotation Pipeline (PGAP) v4.11 (9). Unless stated otherwise, defaultparameters were used for all software.The E. faecalis UMB0843 draft genome is 2,805,168 bp long, assembled into 20contigs with a genome coverage of 147 and an N50 score of 284,798 bp. The genomehas a GC content of 38%, similar to that of other genomes of the species. PGAPidentified 2,611 protein-coding regions. Both annotation tools found 51 tRNAs and 5complete rRNA gene sequences (3 5S, 1 16S, and 1 23S). While resistance of this strainwas not experimentally tested, PATRIC reported 39 genes associated with antibioticresistance. Upon further investigation using ResFinder v3.2 (10), only antibiotic resis-tance to macrolides was detected [resistance gene, lsa(A)]. Our analysis suggests thatthis strain is susceptible to vancomycin, commonly used as the last line of defense.Vancomycin-resistant strains of E. faecalis emerged in the United States first in 1989 (11)and have become a significant concern for UTI treatment (12).Data availability. This whole-genome shotgun project has been deposited inDDBJ/ENA/GenBank under the accession no. JAAUWL000000000. The version describedin this paper is the first version, JAAUWL010000000. The raw sequencing reads havebeen deposited in the SRA under the accession no. SRR11441019.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 (LUEREC) and thepatients who provided the samples for this study.REFERENCES1. Lawley TD, Walker AW. 2013. Intestinal colonization resistance. Immu-nology 138:1–11. https://doi.org/10.1111/j.1365-2567.2012.03616.x.2. Gilmore MS, Lebreton F, van Schaik W. 2013. Genomic transition ofenterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era. Curr Opin Microbiol16:10 –16. https://doi.org/10.1016/j.mib.2013.01.006.3. Jett BD, Huycke MM, Gilmore MS. 1994. Virulence of enterococci. ClinMicrobiol Rev 7:462– 478. https://doi.org/10.1128/cmr.7.4.462.4. Hidron AI, Edwards JR, Patel J, Horan TC, Sievert DM, Pollock DA, FridkinSK, National Healthcare Safety Network Team, Participating NationalHealthcare Safety Network Facilities. 2008. 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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.2012.0021.8. 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/gkw1017.9. 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/gkw569.10. 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/dks261.11. Sahm DF, Kissinger J, Gilmore MS, Murray PR, Mulder R, Solliday J, ClarkeB. 1989. In vitro susceptibility studies of vancomycin-resistant Entero-coccus faecalis. Antimicrob Agents Chemother 33:1588 –1591. https://doi.org/10.1128/aac.33.9.1588.12. Shrestha LB, Baral R, Khanal B. 2019. Comparative study of antimicrobialresistance and biofilm formation among Gram-positive uropathogensisolated from community-acquired urinary tract infections and catheter-associated urinary tract infections. Infect Drug Resist 12:957–963. https://doi.org/10.2147/IDR.S200988.Purta et al.Volume 9 Issue 20 e00407-20 mra.asm.org 2 on October 30, 2020 by guesthttp://mra.asm.org/Downloaded from 

Draft Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract

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Draft Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract

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