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Genome Sequences

Draft Genome Sequence of Streptococcus agalactiae UMB7782, Isolated from the Female Urinary Tract

Linda M. Salgado, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Julie C. Dunning Hotopp, Editor
Linda M. Salgado
aDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USA
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Taylor Miller-Ensminger
bBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
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Adelina Voukadinova
bBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
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Alan J. Wolfe
cDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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Catherine Putonti
aDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USA
bBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
cDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
dDepartment of Computer Science, Loyola University Chicago, Chicago, Illinois, USA
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Julie C. Dunning Hotopp
University of Maryland School of Medicine
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DOI: 10.1128/MRA.00423-20
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ABSTRACT

Streptococcus agalactiae is a Gram-positive bacterium common to the human gut and vaginal microbiota. Here, we report the 2.1-Mbp draft genome sequence of S. agalactiae UMB7782, isolated from a urine sample from a woman with a recurrent urinary tract infection.

ANNOUNCEMENT

Streptococcus agalactiae, also known as a group B Streptococcus, is known as both a commensal bacterium and a pathogen in humans and animals (see reviews [1, 2]). While sometimes pathogenic (2), S. agalactiae is found in 20 to 40% of healthy women, colonizing the urogenital and/or lower gastrointestinal tract (3–6). While a part of the normal urogenital flora of many women, S. agalactiae can cause urinary tract infections (UTIs) (2). The rise of antibiotic-resistant strains of S. agalactiae is a pressing concern for this emerging uropathogen (2, 7). Here, we present the draft genome of S. agalactiae UMB7782, isolated from a voided urine sample obtained from a female with a recurrent UTI.

S. agalactiae UMB7782 was isolated from a previous institutional review board (IRB)-approved study (University of California, San Diego, IRB no. 170077AW) using the expanded quantitative urinary culture (EQUC) protocol (8). The sample was collected from a patient at the Women’s Pelvic Medicine Center at the University of California, San Diego, California, in August 2017. The genus and species of the isolate was determined by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (8) before storage at −80°C. The isolate was streaked onto a Columbia nalidixic acid (CNA) agar plate and incubated at 35°C with 5% CO2 for 24 h. A single colony was selected and grown overnight in blood heart infusion (BHI) liquid medium under the same conditions. DNA was extracted using the Qiagen DNeasy blood and tissue kit’s Gram-positive extraction protocol and quantified using a Qubit fluorometer. The extraction protocol was slightly modified; we used 230 μl of lysis buffer (180 μl 20 mM Tris-Cl, 2 mM sodium EDTA, and 1.2% Triton X-100 and 50 μl of lysozyme) in step 2 and reduced the incubation time in step 5 to 10 min. DNA was sent to the Microbial Genome Sequencing Center (MiGS) at the University of Pittsburgh for library preparation and sequencing. There the DNA was first enzymatically fragmented using an Illumina tagmentation enzyme, and indices were attached via PCR. The library was sequenced on the Illumina NextSeq 550 platform, producing 1,612,404 pairs of 150-bp reads. The raw reads were trimmed using Sickle v1.33 (https://github.com/najoshi/sickle). The reads were assembled using SPAdes v3.13.0 with the “only-assembler” option for k values of 55, 77, 99, and 127 (9). Genome coverage was calculated using BBMap v38.47 (https://sourceforge.net/projects/bbmap/). Additionally, the NCBI PGAP v4.11 (10) was used to annotate the sequence. Unless specifically noted, default parameters were used for each software tool.

The S. agalactiae UMB7782 draft genome is 2,136,704 bp long with a GC content of 35.11%. It was assembled into 32 contigs with a genome coverage of 197× and an N50 score of 147,539 bp. The PGAP annotation found 2,051 protein-coding genes, 47 tRNAs, and 5 rRNAs. The genome assembly also was examined using the ResFinder Web server v3.2 (11). Resistances to macrolides and tetracycline were predicted. Both have previously been reported for other members of the species (2). Further analysis will help us better understand the pathogenic nature of this species in the female urinary tract.

Data availability.This whole-genome shotgun project has been deposited in GenBank under the accession no. JAAUVX000000000. The version described in this paper is the first version, JAAUVX010000000. The raw sequencing reads have been deposited in the SRA under the accession no. SRR11441028.

ACKNOWLEDGMENTS

This work was conducted as part of the Bacterial Genomics course at Loyola University Chicago’s Department of Biology. For prior patient recruitment, we acknowledge the Loyola Urinary Education and Research Collaborative (LUEREC) and the patients who provided the samples for this study.

FOOTNOTES

    • Received 15 April 2020.
    • Accepted 28 April 2020.
    • Published 14 May 2020.
  • Copyright © 2020 Salgado et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Chen SL
    . 2019. Genomic insights into the distribution and evolution of group B streptococcus. Front Microbiol 10:1447. doi:10.3389/fmicb.2019.01447.
    OpenUrlCrossRef
  2. 2.↵
    1. Raabe VN,
    2. Shane AL
    . 2019. Group B streptococcus (Streptococcus agalactiae). Microbiol Spectr 7. doi:10.1128/microbiolspec.GPP3-0007-2018.
    OpenUrlCrossRef
  3. 3.↵
    1. Schuchat A
    . 1998. Epidemiology of group B streptococcal disease in the United States: shifting paradigms. Clin Microbiol Rev 11:497–513. doi:10.1128/CMR.11.3.497.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Campbell JR,
    2. Hillier SL,
    3. Krohn MA,
    4. Ferrieri P,
    5. Zaleznik DF,
    6. Baker CJ
    . 2000. Group B streptococcal colonization and serotype-specific immunity in pregnant women at delivery. Obstet Gynecol 96:498–503. doi:10.1016/s0029-7844(00)00977-7.
    OpenUrlCrossRefPubMedWeb of Science
  5. 5.↵
    1. Bliss SJ,
    2. Manning SD,
    3. Tallman P,
    4. Baker CJ,
    5. Pearlman MD,
    6. Marrs CF,
    7. Foxman B
    . 2002. Group B Streptococcus colonization in male and nonpregnant female university students: a cross-sectional prevalence study. Clin Infect Dis 34:184–190. doi:10.1086/338258.
    OpenUrlCrossRefPubMedWeb of Science
  6. 6.↵
    1. Manning SD,
    2. Neighbors K,
    3. Tallman PA,
    4. Gillespie B,
    5. Marrs CF,
    6. Borchardt SM,
    7. Baker CJ,
    8. Pearlman MD,
    9. Foxman B
    . 2004. Prevalence of group B streptococcus colonization and potential for transmission by casual contact in healthy young men and women. Clin Infect Dis 39:380–388. doi:10.1086/422321.
    OpenUrlCrossRefPubMedWeb of Science
  7. 7.↵
    1. Gizachew M,
    2. Tiruneh M,
    3. Moges F,
    4. Tessema B
    . 2019. Streptococcus agalactiae maternal colonization, antibiotic resistance and serotype profiles in Africa: a meta-analysis. Ann Clin Microbiol Antimicrob 18:14. doi:10.1186/s12941-019-0313-1.
    OpenUrlCrossRef
  8. 8.↵
    1. Hilt EE,
    2. McKinley K,
    3. Pearce MM,
    4. Rosenfeld AB,
    5. Zilliox MJ,
    6. Mueller ER,
    7. Brubaker L,
    8. Gai X,
    9. Wolfe AJ,
    10. Schreckenberger PC
    . 2014. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol 52:871–876. doi:10.1128/JCM.02876-13.
    OpenUrlAbstract/FREE Full Text
  9. 9.↵
    1. Bankevich A,
    2. Nurk S,
    3. Antipov D,
    4. Gurevich AA,
    5. Dvorkin M,
    6. Kulikov AS,
    7. Lesin VM,
    8. Nikolenko SI,
    9. Pham S,
    10. Prjibelski AD,
    11. Pyshkin AV,
    12. Sirotkin AV,
    13. Vyahhi N,
    14. Tesler G,
    15. Alekseyev MA,
    16. Pevzner PA
    . 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Tatusova T,
    2. DiCuccio M,
    3. Badretdin A,
    4. Chetvernin V,
    5. Nawrocki EP,
    6. Zaslavsky L,
    7. Lomsadze A,
    8. Pruitt KD,
    9. Borodovsky M,
    10. Ostell J
    . 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi:10.1093/nar/gkw569.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Zankari E,
    2. Hasman H,
    3. Cosentino S,
    4. Vestergaard M,
    5. Rasmussen S,
    6. Lund O,
    7. Aarestrup FM,
    8. Larsen MV
    . 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640–2644. doi:10.1093/jac/dks261.
    OpenUrlCrossRefPubMedWeb of Science
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Draft Genome Sequence of Streptococcus agalactiae UMB7782, Isolated from the Female Urinary Tract
Linda M. Salgado, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Microbiology Resource Announcements May 2020, 9 (20) e00423-20; DOI: 10.1128/MRA.00423-20

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Draft Genome Sequence of Streptococcus agalactiae UMB7782, Isolated from the Female Urinary Tract
Linda M. Salgado, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Microbiology Resource Announcements May 2020, 9 (20) e00423-20; DOI: 10.1128/MRA.00423-20
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