The presence of bacteria in urine can pose significant risks during pregnancy. However, there are few reference genome strains for many common urinary bacteria. We isolated 12 urinary strains of Streptococcus, Staphylococcus, Citrobacter, Gardnerella, and Lactobacillus. These strains and their genomes are now available to the research community

Deitzler, Grace E

Hallsworth-Pepin, Kymberlie

Lewis, Amanda L

Lewis, Warren G

Mitreva, Makedonka

Park, SoEun

Robinson, Lloyd S

Weimer, Cory M

Wollam, Aye

Genome Announcements

English

PubMed

Digital Commons@Becker

Washington University School of MedicineDigital Commons@BeckerOpen Access Publications2016Genome sequences of 12 bacterial isolatesobtained from the urine of pregnant womenCory M. WeimerWashington University School of Medicine in St. LouisGrace E. DeitzlerWashington University School of Medicine in St. LouisLloyd S. RobinsonWashington University School of Medicine in St. LouisSoEun ParkWashington University School of Medicine in St. LouisKymberlie Hallsworth-PepinWashington University School of Medicine in St. LouisSee next page for additional authorsFollow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubsThis Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in OpenAccess Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact engeszer@wustl.edu.Recommended CitationWeimer, Cory M.; Deitzler, Grace E.; Robinson, Lloyd S.; Park, SoEun; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva,Makedonka; Lewis, Warren G.; and Lewis, Amanda L., ,"Genome sequences of 12 bacterial isolates obtained from the urine ofpregnant women." Genome Announcements.4,5. e00882-16. (2016).https://digitalcommons.wustl.edu/open_access_pubs/5628AuthorsCory M. Weimer, Grace E. Deitzler, Lloyd S. Robinson, SoEun Park, Kymberlie Hallsworth-Pepin, AyeWollam, Makedonka Mitreva, Warren G. Lewis, and Amanda L. LewisThis open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/5628Genome Sequences of 12 Bacterial Isolates Obtained from the Urineof Pregnant WomenCory M. Weimer,a,d Grace E. Deitzler,a,d Lloyd S. Robinson,a,d SoEun Park,a,d Kymberlie Hallsworth-Pepin,c,e Aye Wollam,c,eMakedonka Mitreva,c,e Warren G. Lewis,c,d Amanda L. Lewisa,b,dDepartment of Molecular Microbiology,a Department of Obstetrics and Gynecology,b Department of Medicine,c Center for Women’s Infectious Disease Research,d andMcDonnell Genome Institute,e Washington University School of Medicine, St. Louis, Missouri, USAFor a commentary on this article, see doi:10.1128/genomeA.00890-16.The presence of bacteria in urine can pose significant risks during pregnancy. However, there are few reference genome strainsfor many common urinary bacteria. We isolated 12 urinary strains of Streptococcus, Staphylococcus, Citrobacter, Gardnerella,and Lactobacillus. These strains and their genomes are now available to the research community.Received 29 June 2016 Accepted 28 July 2016 Published 29 September 2016CitationWeimer CM, Deitzler GE, Robinson LS, Park S, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG, Lewis AL. 2016. Genome sequences of 12 bacterial isolates obtainedfrom the urine of pregnant women. Genome Announc 4(5):e00882-16. doi:10.1128/genomeA.00882-16.Copyright © 2016 Weimer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Warren G. Lewis, WarrenGLewisPhD@gmail.com, or Amanda L. Lewis, allewis@wustl.edu.Nearly 8million urinary tract infections (UTIs) occur each yearin the United States alone (1). During pregnancy, dilation ofthe renal pelvis and ureters makes womenmore prone to bacterialinfection of the kidney. Landmark studies by Mittendorf andcoworkers employed a randomized placebo-controlled trialshowing that 40% of women with persistent (untreated) asymp-tomatic bacteriuria (ASB) went on to experience pyelonephritis,while none of the antibiotic-treated women went on experiencethis outcome (2). Due to the risks posed by pyelonephritis to preg-nancy, it is now common practice in the United States to screenand treat pregnant women for asymptomatic bacteriuria.Escherichia coli is the most common and best-studied cause ofUTI. However, other less common bacteria are not well studied,despite being responsible for tens of thousands of cases in theUnited States alone. For example, group B Streptococcus (GBS) is acommon vaginal bacterium responsible for ~1% of UTIs (1)among young sexually active women (~80,000 cases/year). GBS isalso a leading cause of newborn sepsis (3) and commonly causesstillbirth (4) and placental infections in pregnant women (5).However, little is known about how GBS causes UTIs, and thereare few urine isolates with sequenced genomes.Similarly, there is an emerging understanding that the bladderis home to a surprising variety of bacteria, or at least that thebladder is frequently exposed to bacteria from nearby mucosalreservoirs (6). However, urinary strains from many taxa withinthese phyla are not readily available.Here, we isolated and performed genome sequencing for 12new strains of urinary bacteria. Briefly, clean-catch urine sam-ples were provided by pregnant women as part of the Womenand Infants’ Health Specimen Consortium (WIHSC) accord-ing to Washington University institutional review board (IRB)-approved protocol 20110382. Sampleswere sent from theOb/Gynclinic to the Barnes Jewish Hospital microbiology laboratory foridentification of suspected uropathogens. Species identificationwas confirmed by full-length 16S rRNA gene sequence analysis.Genomic DNA was obtained using the Wizard purification kit(Promega). Genome assembly and annotation was performed asdescribed more fully in the companion paper published in thisTABLE 1 Strain identifiers and nucleotide accession numbersGenus/species Strain BEI catalog no. Nucleotide accession no.Streptococcus agalactiae PSS_7632A HMS-1244 LRQM00000000Streptococcus agalactiae PSS_7632B HMS-1245 LRQN00000000Streptococcus agalactiae PSS_7625 HMS-1246 LRQL00000000Streptococcus agalactiae PSS_7568 HMS-1247 LRQK00000000Streptococcus agalactiae PSS_7678 HMS-1248 LRQO00000000Streptococcus agalactiae PSS_7722 HMS-1249 LRQP00000000Streptococcus agalactiae PSS_7736 HMS-1250 LRQQ00000000Citrobacter koseri PSS_7778B HMS-1275 LRPT00000000Gardnerella vaginalis PSS_7772B HMS-1276 LRQB00000000Lactobacillus crispatus PSS7772C HMS-1277 LSQY00000000Lactobacillus gasseri PSS7772D HMS-1278 LRQD00000000Staphylococcus aureus PSS7673 HMS-1279 LRQH00000000crossmarkGenome AnnouncementsSeptember/October 2016 Volume 4 Issue 5 e00882-16 genomea.asm.org 1 on February 28, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from issue (“Genome sequences of 11 human vaginal Actinobacteria”).Briefly, genomes were assembled de novo using the One ButtonVelvet assembly pipeline (version 1.1.06) (7). Gene productswere predicted/annotated using GeneMark, Glimmer3 (8, 9),NCBI’s nonredundant bacterial (NR) database, and Pfam (10),tRNAscan-SE (11), RNAmmer (12), and Rfam (13).Accession number(s). These whole-genome shotgun projectshave been deposited in GenBank under the accession numberslisted in Table 1. The sequences described in this paper are the firstversions. To facilitate future research in this field, we have alsomade the strains available to the research community by deposit-ing them with the Biodefense and Emerging Infections (BEI) Re-search Resource Repository (see BEI numbers in Table 1).ACKNOWLEDGMENTSWe thank Deborah Frank for editorial assistance, theWomen and InfantsHealth Specimen Consortium (WIHSC) for consenting and collectingspecimens from patients, the Barnes Jewish Microbiology lab for provid-ing isolates, and BEI Resources for providing the isolates to other investi-gators. We also gratefully acknowledge the patients who provided urinesamples.This work was funded in part by NIDDK DK092586-01A1 (A.L.L.),P50 DK064540-11 (A.L.L., project II), the Children’s Discovery Insti-tute (W.G.L. and A.L.L.), and the Human Microbiome Project5U54HG00496804. A summer stipend was provided by the PlanningCenter for Research in Benign Urology Summer Research ProgramP20DK097798 (G.E.D.).FUNDING INFORMATIONThis work, including the efforts of Makedonka Mitreva, was fundedby HHS | National Institutes of Health (NIH) (5U54HG00496804).This work, including the efforts of Amanda L. Lewis, was funded byHHS | NIH | National Institute of Diabetes and Digestive and KidneyDiseases (NIDDK) (DK092586-01A1 and P50 DK064540-11). Thiswork, including the efforts of Grace E. Deitzler, was funded by HHS| NIH | National Institute of Diabetes and Digestive and KidneyDiseases (NIDDK) (P20DK097798). This work, including the effortsof Amanda L. Lewis and Warren G. Lewis, was funded by Children’sDiscovery Institute (CDI).REFERENCES1. Foxman B. 2003. Epidemiology of urinary tract infections: incidence,morbidity, and economic costs. DIS Mon 49:53–70. http://dx.doi.org/10.1067/mda.2003.7.2. Mittendorf R, Williams MA, Kass EH. 1992. Prevention of pretermdelivery and low birth weight associated with asymptomatic bacteriuria.Clin Infect Dis 14:927–932. http://dx.doi.org/10.1093/clinids/14.4.927.3. Edmond KM, Kortsalioudaki C, Scott S, Schrag SJ, Zaidi AK, CousensS, Heath PT. 2012. Group B streptococcal disease in infants aged youngerthan 3months: systematic review andmeta-analysis. Lancet 379:547–556.http://dx.doi.org/10.1016/S0140-6736(11)61651-6.4. Nan C, Dangor Z, Cutland CL, Edwards MS, Madhi SA, CunningtonMC. 2015. Maternal group B streptococcus-related stillbirth: a system-atic review. BJOG 122:1437–1445. http://dx.doi.org/10.1111/1471-0528.13527.5. Horvath B, Lakatos F, Tóth C, Bödecs T, Bódis J. 2014. Silent chorio-amnionitis and associated pregnancy outcomes: a review of clinical datagathered over a 16-year period. J Perinat Med 42:441–447. http://dx.doi.org/10.1515/jpm-2013-0186.6. Kline KA, Lewis AL. 2016. Gram positive uropathogens, polymicro-bial urinary tract infection, and the emerging microbiota of the urinarytract. Microbiol Spectr 4, in press. http://dx.doi.org/10.1128/microbiolspec.UTI-0012-2012.7. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short readassembly using de Bruijn graphs. Genome Res 18:821–829. http://dx.doi.org/10.1101/gr.074492.107.8. Borodovsky M, Mills R, Besemer J, Lomsadze A. 2003. Prokaryoticgene prediction using GeneMark and GeneMark.Hmm. Curr ProtocBioinformatics Chapter 4:Unit4.5. http://dx.doi.org/10.1002/0471250953.bi0405s01.9. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improvedmicrobial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641. http://dx.doi.org/10.1093/nar/27.23.4636.10. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G,Forslund K, Eddy SR, Sonnhammer EL, Bateman A. 2008. The Pfamprotein families database. Nucleic Acids Res 36:D281–D288. http://dx.doi.org/10.1093/nar/gkm960.11. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detec-tion of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. http://dx.doi.org/10.1093/nar/25.5.0955.12. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, UsseryDW. 2007. RNAmmer: consistent and rapid annotation of ribosomalRNA genes. Nucleic Acids Res 35:3100–3108. http://dx.doi.org/10.1093/nar/gkm160.13. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, BatemanA. 2005. Rfam: annotating non-coding RNAs in complete genomes. Nu-cleic Acids Res 33:D121–D124. http://dx.doi.org/10.1093/nar/gki081.Weimer et al.Genome Announcements2 genomea.asm.org September/October 2016 Volume 4 Issue 5 e00882-16 on February 28, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from 

Genome sequences of 12 bacterial isolates obtained from the urine of pregnant women

ABSTRACT
          
            The presence of bacteria in urine can pose significant risks during pregnancy. However, there are few reference genome strains for many common urinary bacteria. We isolated 12 urinary strains of
            Streptococcus, Staphylococcus, Citrobacter, Gardnerella
            , and
            Lactobacillus
            . These strains and their genomes are now available to the research community.
          </jats:p

Cory M. Weimer

Grace E. Deitzler

Lloyd S. Robinson

SoEun Park

Kymberlie Hallsworth-Pepin

Aye Wollam

Makedonka Mitreva

Warren G. Lewis

Amanda L. Lewis

Crossref

Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women

http://dx.doi.org/10.1128/genomeA.00882-16

Genome sequences of 12 bacterial isolates obtained from the urine of pregnant women

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