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Abstract

Studies of the last decade have identified a phylogenetically diverse community of bacteria within the urinary tract of individuals with and without urinary symptoms. Mobile genetic elements (MGEs), including plasmids and phages, within this niche have only recently begun to be explored. These MGEs can expand metabolic capacity and increase virulence, as well as confer antibiotic resistance. As such, they have the potential to contribute to urinary symptoms. While plasmids for some of the bacterial taxa found within the urinary microbiota (urobiome) have been well characterized, many urinary species are under-studied with few genomes sequenced to date. Using a two-pronged bioinformatic approach, we have conducted a comprehensive investigation of the plasmid content of urinary isolates representative of 102 species. The bioinformatic tools plasmidSPAdes and Recycler were used in tandem to identify plasmid sequences from raw short-read sequence data followed by manual curation. In total, we identified 603 high-confidence plasmid sequences in 20 different genera of the urobiome. In total, 70 % of these high-confidence plasmids exhibit sequence similarity to plasmid sequences from the gut. This observation is primarily driven by plasmids from , which is found in both anatomical niches. To confirm our bioinformatic predictions, long-read sequencing was performed for 23 of the isolates in addition to two strains that were sequenced as part of a prior study. Overall, 66.95 % of these predictions were confirmed highlighting the strengths and weaknesses of current bioinformatic tools. Future studies of the urobiome, especially concerning under-studied species in the urobiome, should employ long-read sequencing to expand the catalogue of plasmids for this niche.

Funding
This study was supported by the:
  • Foundation for the National Institutes of Health (Award 1R25DK122954-01)
    • Principle Award Recipient: CatherinePutonti
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-11-30
2024-02-22
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References

  1. Pilla G, Tang CM. Going around in circles: virulence plasmids in enteric pathogens. Nat Rev Microbiol 2018; 16:484–495 [View Article] [PubMed]
    [Google Scholar]
  2. San Millan A. Evolution of plasmid-mediated antibiotic resistance in the clinical context. Trends Microbiol 2018; 26:978–985 [View Article]
    [Google Scholar]
  3. Clokie MRJ, Millard AD, Letarov AV, Heaphy S. Phages in nature. Bacteriophage 2011; 1:31–45 [View Article] [PubMed]
    [Google Scholar]
  4. Arredondo-Alonso S, Top J, McNally A, Puranen S, Pesonen M et al. Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium. mBio 2020; 11:e03284-19 [View Article]
    [Google Scholar]
  5. Montelongo Hernandez C, Putonti C, Wolfe AJ. Characterizing plasmids in bacteria species relevant to urinary health. Microbiol Spectr 2021; 9:e0094221 [View Article]
    [Google Scholar]
  6. Hughes C, Bauer E, Roberts AP. Spread of R-plasmids among Escherichia coli causing urinary tract infections. Antimicrob Agents Chemother 1981; 20:496–502 [View Article] [PubMed]
    [Google Scholar]
  7. Decano AG, Pettigrew K, Sabiiti W, Sloan DJ, Neema S et al. Pan-resistome characterization of uropathogenic Escherichia coli and Klebsiella pneumoniae strains circulating in Uganda and Kenya, isolated from 2017-2018. Antibiotics 2021; 10:1547 [View Article]
    [Google Scholar]
  8. Mitra SD, Irshad P, Anusree M, Rekha I, Shailaja S et al. Whole genome global insight of antibiotic resistance gene repertoire and virulome of high - risk multidrug-resistant Uropathogenic Escherichia coli. Microb Pathog 2021; 161:105256 [View Article]
    [Google Scholar]
  9. Di Venanzio G, Flores-Mireles AL, Calix JJ, Haurat MF, Scott NE et al. Urinary tract colonization is enhanced by a plasmid that regulates uropathogenic Acinetobacter baumannii chromosomal genes. Nat Commun 2019; 10:2763 [View Article]
    [Google Scholar]
  10. Brito IL. Examining horizontal gene transfer in microbial communities. Nat Rev Microbiol 2021; 19:442–453 [View Article] [PubMed]
    [Google Scholar]
  11. Antipov D, Raiko M, Lapidus A, Pevzner PA. Plasmid detection and assembly in genomic and metagenomic data sets. Genome Res 2019; 29:961–968 [View Article] [PubMed]
    [Google Scholar]
  12. Arredondo-Alonso S, Willems RJ, van Schaik W, Schürch AC. On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data. Microb Genom 2017; 3:e000128 [View Article]
    [Google Scholar]
  13. Laczny CC, Galata V, Plum A, Posch AE, Keller A. Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates. Brief Bioinform 2019; 20:857–865 [View Article]
    [Google Scholar]
  14. Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A et al. plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics 2016; 32:3380–3387 [View Article]
    [Google Scholar]
  15. Rozov R, Brown Kav A, Bogumil D, Shterzer N, Halperin E et al. Recycler: an algorithm for detecting plasmids from de novo assembly graphs. Bioinformatics 2017; 33:475–482 [View Article]
    [Google Scholar]
  16. Neugent ML, Hulyalkar NV, Nguyen VH, Zimmern PE, De Nisco NJ. Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection. mBio 2020; 11:e00218-20 [View Article]
    [Google Scholar]
  17. Galata V, Fehlmann T, Backes C, Keller A. PLSDB: a resource of complete bacterial plasmids. Nucleic Acids Res 2019; 47:D195–D202 [View Article]
    [Google Scholar]
  18. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
    [Google Scholar]
  19. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2020; 75:3491–3500 [View Article] [PubMed]
    [Google Scholar]
  20. Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 2019; 47:D687–D692 [View Article]
    [Google Scholar]
  21. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article]
    [Google Scholar]
  22. Lai S, Jia L, Subramanian B, Pan S, Zhang J et al. mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. Nucleic Acids Res 2021; 49:D783–D791 [View Article]
    [Google Scholar]
  23. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article]
    [Google Scholar]
  24. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  25. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article]
    [Google Scholar]
  26. Acman M, van Dorp L, Santini JM, Balloux F. Large-scale network analysis captures biological features of bacterial plasmids. Nat Commun 2020; 11:2452 [View Article]
    [Google Scholar]
  27. Zhou F, Xu Y. cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data. Bioinformatics 2010; 26:2051–2052 [View Article] [PubMed]
    [Google Scholar]
  28. Pellow D, Zorea A, Probst M, Furman O, Segal A et al. SCAPP: an algorithm for improved plasmid assembly in metagenomes. Microbiome 2021; 9:144 [View Article] [PubMed]
    [Google Scholar]
  29. Harrison E, Brockhurst MA. Plasmid-mediated horizontal gene transfer is a coevolutionary process. Trends Microbiol 2012; 20:262–267 [View Article] [PubMed]
    [Google Scholar]
  30. Goren MG, Carmeli Y, Schwaber MJ, Chmelnitsky I, Schechner V et al. Transfer of carbapenem-resistant plasmid from Klebsiella pneumoniae ST258 to Escherichia coli in patient. Emerg Infect Dis 2010; 16:1014–1017 [View Article]
    [Google Scholar]
  31. Christie PJ. The mosaic type IV secretion systems. EcoSal Plus 2016; 7: [View Article]
    [Google Scholar]
  32. Yamamoto S, Tsukamoto T, Terai A, Kurazono H, Takeda Y et al. Genetic evidence supporting the fecal-perineal-urethral hypothesis in cystitis caused by Escherichia coli. J Urol 1997; 157:1127–1129 [View Article] [PubMed]
    [Google Scholar]
  33. Hooton TM. Recurrent urinary tract infection in women. Int J Antimicrob Agents 2001; 17:259–268 [View Article] [PubMed]
    [Google Scholar]
  34. Chen SL, Wu M, Henderson JP, Hooton TM, Hibbing ME et al. Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection. Sci Transl Med 2013; 5:184ra60 [View Article]
    [Google Scholar]
  35. Nielsen KL, Dynesen P, Larsen P, Frimodt-Møller N. Faecal Escherichia coli from patients with E. coli urinary tract infection and healthy controls who have never had a urinary tract infection. J Med Microbiol 2014; 63:582–589 [View Article] [PubMed]
    [Google Scholar]
  36. 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]
    [Google Scholar]
  37. 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]
    [Google Scholar]
  38. Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol 2015; 13:269–284 [View Article] [PubMed]
    [Google Scholar]
  39. Ramirez MS, Traglia GM, Lin DL, Tran T, Tolmasky ME. Plasmid-mediated antibiotic resistance and virulence in gram-negatives: the Klebsiella pneumoniae paradigm. Microbiol Spectr 2014; 2:1–15 [View Article]
    [Google Scholar]
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