1887

Abstract

species are common inhabitants of the ‘healthy’ female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 strains, including 16 paired urogenital samples from the same participant. These strains represent five different species: , , , , and . Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the same participant were performed. We conducted simulations of genome assemblies and ANI comparisons and present a statistical method to distinguish between unrelated, related, and identical strains. We found that 50 % of the paired samples have identical strains, evidence that the urinary and vaginal communities are connected. Additionally, we found evidence of strains sharing a common ancestor. These results establish that microbial sharing between the urinary tract and vagina is not limited to uropathogens. Knowledge that these two anatomical sites can share lactobacilli in females can inform future clinical approaches.

Funding
This study was supported by the:
  • Loyola University Chicago
    • Principle Award Recipient: HaleyAtkins
  • National Institutes of Health (US) (Award R25DK122954)
    • Principle Award Recipient: CatherinePutonti
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-07-01
2024-07-23
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References

  1. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK et al. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A 2011; 108:4680–4687 [View Article] [PubMed]
    [Google Scholar]
  2. Price TK, Hilt EE, Thomas-White K, Mueller ER, Wolfe AJ et al. The urobiome of continent adult women: a cross-sectional study. BJOG 2020; 127:193–201 [View Article] [PubMed]
    [Google Scholar]
  3. Pearce MM, Hilt EE, Rosenfeld AB, Zilliox MJ, Thomas-White K et al. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. mBio 2014; 5:e01283-14 [View Article] [PubMed]
    [Google Scholar]
  4. Smith SB, Ravel J. The vaginal microbiota, host defence and reproductive physiology. J Physiol 2017; 595:451–463 [View Article] [PubMed]
    [Google Scholar]
  5. Gupta K, Stapleton AE, Hooton TM, Roberts PL, Fennell CL et al. Inverse association of H2O2-producing lactobacilli and vaginal Escherichia coli colonization in women with recurrent urinary tract infections. J Infect Dis 1998; 178:446–450 [View Article] [PubMed]
    [Google Scholar]
  6. Atassi F, Brassart D, Grob P, Graf F, Servin AL. Vaginal Lactobacillus isolates inhibit uropathogenic Escherichia coli. FEMS Microbiol Lett 2006; 257:132–138 [View Article] [PubMed]
    [Google Scholar]
  7. Hütt P, Lapp E, Štšepetova J, Smidt I, Taelma H et al. Characterisation of probiotic properties in human vaginal lactobacilli strains. Microb Ecol Health Dis 2016; 27:30484 [View Article] [PubMed]
    [Google Scholar]
  8. Butler D, Silvestroni A, Stapleton A. Cytoprotective effect of Lactobacillus crispatus CTV-05 against uropathogenic E. coli. Pathogens 2016; 5:27 [View Article]
    [Google Scholar]
  9. Singh AK, Hertzberger RY, Knaus UG. Hydrogen peroxide production by lactobacilli promotes epithelial restitution during colitis. Redox Biol 2018; 16:11–20 [View Article] [PubMed]
    [Google Scholar]
  10. Abdul-Rahim O, Wu Q, Price TK, Pistone G, Diebel K et al. Phenyl-lactic acid is an active ingredient in bactericidal supernatants of Lactobacillus crispatus. J Bacteriol 2021; 203:e0036021 [View Article] [PubMed]
    [Google Scholar]
  11. Navarro S, Abla H, Colmer-Hamood JA, Ventolini G, Hamood AN. Under conditions closely mimicking vaginal fluid, Lactobacillus jensenii strain 62B produces a bacteriocin-like inhibitory substance that targets and eliminates Gardnerella species. Microbiology 2023; 169:001409 [View Article] [PubMed]
    [Google Scholar]
  12. Petrova MI, Lievens E, Malik S, Imholz N, Lebeer S. Lactobacillus species as biomarkers and agents that can promote various aspects of vaginal health. Front Physiol 2015; 6:81 [View Article] [PubMed]
    [Google Scholar]
  13. Eschenbach DA, Davick PR, Williams BL, Klebanoff SJ, Young-Smith K et al. Prevalence of hydrogen peroxide-producing Lactobacillus species in normal women and women with bacterial vaginosis. J Clin Microbiol 1989; 27:251–256 [View Article] [PubMed]
    [Google Scholar]
  14. Al-Mushrif S, Jones BM. A study of the prevalence of hydrogen peroxide generating Lactobacilli in bacterial vaginosis: the determination of H2O2 concentrations generated, in vitro, by isolated strains and the levels found in vaginal secretions of women with and without infection. J Obstet Gynaecol 1998; 18:63–67 [View Article] [PubMed]
    [Google Scholar]
  15. Abou Chacra L, Fenollar F, Diop K. Bacterial vaginosis: what do we currently know?. Front Cell Infect Microbiol 2021; 11:672429 [View Article] [PubMed]
    [Google Scholar]
  16. Chee WJY, Chew SY, Than LTL. Vaginal microbiota and the potential of Lactobacillus derivatives in maintaining vaginal health. Microb Cell Fact 2020; 19:203 [View Article] [PubMed]
    [Google Scholar]
  17. Zheng N, Guo R, Wang J, Zhou W, Ling Z. Contribution of Lactobacillus iners to vaginal health and diseases: a systematic review. Front Cell Infect Microbiol 2021; 11:792787 [View Article] [PubMed]
    [Google Scholar]
  18. Price TK, Lin H, Gao X, Thomas-White KJ, Hilt EE et al. Bladder bacterial diversity differs in continent and incontinent women: a cross-sectional study. Am J Obstet Gynecol 2020; 223:729 [View Article] [PubMed]
    [Google Scholar]
  19. Scillato M, Spitale A, Mongelli G, Privitera GF, Mangano K et al. Antimicrobial properties of Lactobacillus cell-free supernatants against multidrug-resistant urogenital pathogens. Microbiologyopen 2021; 10:e1173 [View Article] [PubMed]
    [Google Scholar]
  20. Komesu YM, Dinwiddie DL, Richter HE, Lukacz ES, Sung VW et al. Defining the relationship between vaginal and urinary microbiomes. Am J Obstet Gynecol 2020; 222:154 [View Article] [PubMed]
    [Google Scholar]
  21. Thomas-White K, Forster SC, Kumar N, Van Kuiken M, Putonti C et al. Culturing of female bladder bacteria reveals an interconnected urogenital microbiota. Nat Commun 2018; 9:1557 [View Article] [PubMed]
    [Google Scholar]
  22. Srivastava R, Agarwal J, Srivastava S, Mishra B. Role of special pathogenicity versus prevalence theory in pathogenesis of acute cystitis caused by Escherichia coli. J Med Microbiol 2014; 63:1038–1043 [View Article] [PubMed]
    [Google Scholar]
  23. Stamey TA, Sexton CC. The role of vaginal colonization with enterobacteriaceae in recurrent urinary infections. J Urol 1975; 113:214–217 [View Article] [PubMed]
    [Google Scholar]
  24. Lewis AL, Gilbert NM. Roles of the vagina and the vaginal microbiota in urinary tract infection: evidence from clinical correlations and experimental models. GMS Infect Dis 2020; 8:Doc02 [View Article] [PubMed]
    [Google Scholar]
  25. Harmanli OH, Cheng GY, Nyirjesy P, Chatwani A, Gaughan JP. Urinary tract infections in women with bacterial vaginosis. Obstet Gynecol 2000; 95:710–712 [View Article] [PubMed]
    [Google Scholar]
  26. Sumati AH, Saritha NK. Association of urinary tract infection in women with bacterial vaginosis. J Glob Infect Dis 2009; 1:151–152 [View Article] [PubMed]
    [Google Scholar]
  27. Amatya R, Bhattarai S, Mandal PK, Tuladhar H, Karki BMS. Urinary tract infection in vaginitis: a condition often overlooked. Nepal Med Coll J 2013; 15:65–67 [PubMed]
    [Google Scholar]
  28. Stapleton AE, Au-Yeung M, Hooton TM, Fredricks DN, Roberts PL et al. Randomized, placebo-controlled phase 2 trial of a Lactobacillus crispatus probiotic given intravaginally for prevention of recurrent urinary tract infection. Clin Infect Dis 2011; 52:1212–1217 [View Article] [PubMed]
    [Google Scholar]
  29. Sadahira T, Wada K, Araki M, Mitsuhata R, Yamamoto M et al. Efficacy of Lactobacillus vaginal suppositories for the prevention of recurrent cystitis: a phaseII clinical trial. Int J Urol 2021; 28:1026–1031 [View Article] [PubMed]
    [Google Scholar]
  30. Thomas-White K, Taege S, Limeira R, Brincat C, Joyce C et al. Vaginal estrogen therapy is associated with increased Lactobacillus in the urine of postmenopausal women with overactive bladder symptoms. Am J Obstet Gynecol 2020; 223:727 [View Article] [PubMed]
    [Google Scholar]
  31. Jung CE, Estaki M, Chopyk J, Taylor BC, Gonzalez A et al. Impact of vaginal estrogen on the urobiome in postmenopausal women with recurrent urinary tract infection. Female Pelvic Med Reconstr Surg 2022; 28:20–26 [View Article] [PubMed]
    [Google Scholar]
  32. Price TK, Dune T, Hilt EE, Thomas-White KJ, Kliethermes S et al. The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms. J Clin Microbiol 2016; 54:1216–1222 [View Article] [PubMed]
    [Google Scholar]
  33. Hilt EE, McKinley K, Pearce MM, Rosenfeld AB, Zilliox MJ et al. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol 2014; 52:871–876 [View Article] [PubMed]
    [Google Scholar]
  34. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  35. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  36. Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C et al. Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRDand ViPR. Nucleic Acids Res 2023; 51:D678–D689 [View Article] [PubMed]
    [Google Scholar]
  37. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  38. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
    [Google Scholar]
  39. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010; 5:e11147 [View Article] [PubMed]
    [Google Scholar]
  40. Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol 2021; 6:3–6 [View Article] [PubMed]
    [Google Scholar]
  41. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
    [Google Scholar]
  42. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
    [Google Scholar]
  43. Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 2018; 46:W246–W251 [View Article] [PubMed]
    [Google Scholar]
  44. Olm MR, Crits-Christoph A, Bouma-Gregson K, Firek BA, Morowitz MJ et al. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat Biotechnol 2021; 39:727–736 [View Article] [PubMed]
    [Google Scholar]
  45. Garrett SC. Pruning and tending immune memories: spacer dynamics in the CRISPR array. Front Microbiol 2021; 12:664299 [View Article] [PubMed]
    [Google Scholar]
  46. Martínez-Peña MD, Castro-Escarpulli G, Aguilera-Arreola MG. Lactobacillus species isolated from vaginal secretions of healthy and bacterial vaginosis-intermediate Mexican women: a prospective study. BMC Infect Dis 2013; 13:189 [View Article] [PubMed]
    [Google Scholar]
  47. Muok AR, Briegel A. Intermicrobial hitchhiking: how nonmotile microbes leverage communal motility. Trends Microbiol 2021; 29:542–550 [View Article] [PubMed]
    [Google Scholar]
  48. Bobay L-M, Traverse CC, Ochman H. Impermanence of bacterial clones. Proc Natl Acad Sci U S A 2015; 112:8893–8900 [View Article] [PubMed]
    [Google Scholar]
  49. Wang J, Dong X, Shao Y, Guo H, Pan L et al. Genome adaptive evolution of Lactobacillus casei under long-term antibiotic selection pressures. BMC Genom 2017; 18:320 [View Article] [PubMed]
    [Google Scholar]
  50. Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res 2017; 27:626–638 [View Article] [PubMed]
    [Google Scholar]
  51. Hawken SE, Yelin RD, Lolans K, Pirani A, Weinstein RA et al. Threshold-free genomic cluster detection to track transmission pathways in health-care settings: a genomic epidemiology analysis. Lancet Microbe 2022; 3:e652–e662 [View Article] [PubMed]
    [Google Scholar]
  52. Olm MR, Brown CT, Brooks B, Firek B, Baker R et al. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res 2017; 27:601–612 [View Article] [PubMed]
    [Google Scholar]
  53. France M, Ma B, Ravel J. Persistence and In Vivo evolution of vaginal bacterial strains over a multiyear time period. mSystems 2022; 7:e0089322 [View Article] [PubMed]
    [Google Scholar]
  54. Viver T, Conrad RE, Rodriguez-R LM, Ramírez AS, Venter SN et al. Towards estimating the number of strains that make up a natural bacterial population. Nat Commun 2024; 15:544 [View Article] [PubMed]
    [Google Scholar]
  55. Ma B, France MT, Crabtree J, Holm JB, Humphrys MS et al. A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. Nat Commun 2020; 11:940 [View Article] [PubMed]
    [Google Scholar]
  56. Tortelli BA, Lewis AL, Fay JC. The structure and diversity of strain-level variation in vaginal bacteria. Microb Genom 2021; 7:mgen000543 [View Article] [PubMed]
    [Google Scholar]
  57. Ahmed D, Wahid SUH, Sadique T, Sultana N, Islam M. Recurrent urinary tract infection due to co‐infection with extended spectrum β‐lactamase‐producer uropathogenic Escherichia coli and enteroaggregative E. coli. JMM Case Rep 2014; 1: [View Article]
    [Google Scholar]
  58. Shevchenko SG, Radey M, Tchesnokova V, Kisiela D, Sokurenko EV. Escherichia coli clonobiome: assessing the strain diversity in feces and urine by deep amplicon aequencing. Appl Environ Microbiol 2019; 85:e01866-19 [View Article] [PubMed]
    [Google Scholar]
  59. Park J, Shin E, Park AK, Kim S, Jeong HJ. Co-infection with chromosomally-located blaCTX-M-14 and plasmid-encoding blaCTX-M-15 in pathogenic Escherichia coli in the Republic of Korea. Front Microbiol 2020; 11:545591 [View Article]
    [Google Scholar]
  60. Goltsman DSA, Sun CL, Proctor DM, DiGiulio DB, Robaczewska A et al. Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. Genome Res 2018; 28:1467–1480 [View Article] [PubMed]
    [Google Scholar]
  61. Mores CR, Price TK, Wolff B, Halverson T, Limeira R et al. Genomic relatedness and clinical significance of Streptococcus mitis strains isolated from the urogenital tract of sexual partners. Microb Genom 2021; 7:mgen000535 [View Article] [PubMed]
    [Google Scholar]
  62. Thänert R, Reske KA, Hink T, Wallace MA, Wang B et al. Comparative genomics of antibiotic-resistant uropathogens implicates three routes for recurrence of urinary tract infections. mBio 2019; 10:e01977-19 [View Article] [PubMed]
    [Google Scholar]
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