1887

Abstract

Prophages affect bacterial fitness on multiple levels. These include bacterial infectivity, toxin secretion, virulence regulation, surface modification, immune stimulation and evasion and microbiome competition. Lysogenic conversion arms bacteria with novel accessory functions thereby increasing bacterial fitness, host adaptation and persistence, and antibiotic resistance. These properties allow the bacteria to occupy a niche long term and can contribute to chronic infections and inflammation such as chronic rhinosinusitis (CRS). In this study, we aimed to identify and characterize prophages present in from patients suffering from CRS in relation to CRS disease phenotype and severity. Prophage regions were identified using PHASTER. Various tools like ResFinder and VF Analyzer were used to detect virulence genes and antibiotic resistance genes respectively. Progressive MAUVE and maximum likelihood were used for multiple sequence alignment and phylogenetics of prophages respectively. Disease severity of CRS patients was measured using computed tomography Lund–Mackay scores. Fifty-eight clinical isolates (CIs) were obtained from 28 CRS patients without nasal polyp (CRSsNP) and 30 CRS patients with nasal polyp (CRSwNP). All CIs carried at least one prophage (average=3.6) and prophages contributed up to 7.7 % of the bacterial genome. Phage integrase genes were found in 55/58 (~95 %) strains and 97/211 (~46 %) prophages. Prophages belonging to Sa3int integrase group (phiNM3, JS01, phiN315) (39/97, 40%) and Sa2int (phi2958PVL) (14/97, 14%) were the most prevalent prophages and harboured multiple virulence genes such as E/D, . Intact prophages were more frequently identified in CRSwNP than in CRSsNP (=0.0021). Intact prophages belonging to the Sa3int group were more frequent in CRSwNP than in CRSsNP (=0.0008) and intact phiNM3 were exclusively found in CRSwNP patients (=0.007). Our results expand the knowledge of prophages in isolated from CRS patients and their possible role in disease development. These findings provide a platform for future investigations into potential tripartite associations between bacteria-prophage-human immune system, evolution and CRS disease pathophysiology.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000726
2021-12-15
2022-01-29
Loading full text...

Full text loading...

/deliver/fulltext/mgen/7/12/mgen000726.html?itemId=/content/journal/mgen/10.1099/mgen.0.000726&mimeType=html&fmt=ahah

References

  1. Fokkens WJ, Lund VJ, Hopkins C, Hellings PW, Kern R et al. European position paper on Rhinosinusitis and Nasal Polyps 2020. Rhin 2020; 0:1–464 [View Article]
    [Google Scholar]
  2. Garneau J, Ramirez M, Armato SG 3rd, Sensakovic WF, Ford MK et al. Computer-assisted staging of chronic rhinosinusitis correlates with symptoms. Int Forum Allergy Rhinol 2015; 5:637–642 [View Article] [PubMed]
    [Google Scholar]
  3. Psaltis AJ, Weitzel EK, Ha KR, Wormald P-J. The effect of bacterial biofilms on post-sinus surgical outcomes. Am J Rhinol 2008; 22:1–6 [View Article] [PubMed]
    [Google Scholar]
  4. Foreman A, Psaltis AJ, Tan LW, Wormald P-J. Characterization of bacterial and fungal biofilms in chronic rhinosinusitis. Am J Rhinol Allergy 2009; 23:556–561 [View Article]
    [Google Scholar]
  5. Nayak N, Satpathy G, Prasad S, Thakar A, Chandra M et al. Clinical implications of microbial biofilms in chronic rhinosinusitis and orbital cellulitis. BMC Ophthalmol 2016; 16:165. [View Article] [PubMed]
    [Google Scholar]
  6. Copeland E, Leonard K, Carney R, Kong J, Forer M et al. Chronic rhinosinusitis: potential role of microbial dysbiosis and recommendations for sampling sites. Front Cell Infect Microbiol 2018; 8:57. [View Article] [PubMed]
    [Google Scholar]
  7. Chambers HF, Deleo FR. Waves of resistance: Staphylococcus aureus in the antibiotic era. Nat Rev Microbiol 2009; 7:629–641 [View Article] [PubMed]
    [Google Scholar]
  8. Tong SYC, Davis JS, Eichenberger E, Holland TL, Fowler VG. Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management. Clin Microbiol Rev 2015; 28:603–661 [View Article]
    [Google Scholar]
  9. Van Zele T, Gevaert P, Watelet J-B, Claeys G, Holtappels G et al. Staphylococcus aureus colonization and IgE antibody formation to enterotoxins is increased in nasal polyposis. J Allergy Clin Immunol 2004; 114:981–983 [View Article] [PubMed]
    [Google Scholar]
  10. Vickery TW, Ramakrishnan VR, Suh JD. The role of Staphylococcus aureus in patients with chronic sinusitis and nasal polyposis. Curr Allergy Asthma Rep 2019; 19:21 [View Article] [PubMed]
    [Google Scholar]
  11. Beceiro A, Tomás M, Bou G. Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world?. Clin Microbiol Rev 2013; 26:185–230 [View Article] [PubMed]
    [Google Scholar]
  12. Malachowa N, DeLeo FR. Mobile genetic elements of Staphylococcus aureus. Cell Mol Life Sci 2010; 67:3057–3071 [View Article] [PubMed]
    [Google Scholar]
  13. Hiramatsu K, Ito T, Tsubakishita S, Sasaki T, Takeuchi F et al. Genomic basis for methicillin resistance in Staphylococcus aureus. Infect Chemother 2013; 45:117–136 [View Article] [PubMed]
    [Google Scholar]
  14. Lebeurre J, Dahyot S, Diene S, Paulay A, Aubourg M et al. Comparative genome analysis of Staphylococcus lugdunensis shows clonal complex-dependent diversity of the putative virulence factor, ess/type VII locus. Front Microbiol 2019; 10:192479 [View Article] [PubMed]
    [Google Scholar]
  15. Davies EV, Winstanley C, Fothergill JL, James CE. The role of temperate bacteriophages in bacterial infection. FEMS Microbiol Lett 2016; 363:fnw015. [View Article] [PubMed]
    [Google Scholar]
  16. Calero-Cáceres W, Ye M, Balcázar JL. Bacteriophages as environmental reservoirs of antibiotic resistance. Trends Microbiol 2019; 27:570–577 [View Article] [PubMed]
    [Google Scholar]
  17. Balcázar JL. Implications of bacteriophages on the acquisition and spread of antibiotic resistance in the environment. Int Microbiol 2020; 23:475–479 [View Article] [PubMed]
    [Google Scholar]
  18. Loh B, Chen J, Manohar P, Yu Y, Hua X et al. A biological inventory of prophages in A. baumannii genomes reveal distinct distributions in classes, length, and genomic positions. Front Microbiol 2020; 11:579802 [View Article]
    [Google Scholar]
  19. Harrison E, Brockhurst MA. Ecological and evolutionary benefits of temperate phage: what does or doesn’t kill you makes you stronger. BioEssays 2017; 39:1700112 [View Article]
    [Google Scholar]
  20. Kim B, Little JW. LexA and lambda Cl repressors as enzymes: specific cleavage in an intermolecular reaction. Cell 1993; 73:1165–1173 [View Article] [PubMed]
    [Google Scholar]
  21. Shearwin KE, Brumby AM, Egan JB. The tum protein of coliphage 186 is an antirepressor. J Biol Chem 1998; 273:5708–5715 [View Article] [PubMed]
    [Google Scholar]
  22. Jin M, Liu L, Wang D-N, Yang D, Liu W-L et al. Chlorine disinfection promotes the exchange of antibiotic resistance genes across bacterial genera by natural transformation. ISME J 2020; 14:1847–1856 [View Article] [PubMed]
    [Google Scholar]
  23. Selva L, Viana D, Regev-Yochay G, Trzcinski K, Corpa JM et al. Killing niche competitors by remote-control bacteriophage induction. Proc Natl Acad Sci U S A 2009; 106:1234–1238 [View Article] [PubMed]
    [Google Scholar]
  24. de Sousa JAM, Rocha EPC. Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation. Sci Rep 2019; 9:3149 [View Article] [PubMed]
    [Google Scholar]
  25. Khan A, Wahl LM. Quantifying the forces that maintain prophages in bacterial genomes. Theoretical Population Biology 2020; 133:168–179 [View Article]
    [Google Scholar]
  26. Wahida A, Tang F, Barr JJ. Rethinking phage-bacteria-eukaryotic relationships and their influence on human health. Cell Host & Microbe 2021; 29:681–688 [View Article]
    [Google Scholar]
  27. Li L, Wang G, Li Y, Francois P, Bayer AS et al. Impact of the novel prophage ϕSA169 on persistent methicillin-resistant Staphylococcus aureus endovascular infection. mSystems 2020; 5: [View Article]
    [Google Scholar]
  28. van Wamel WJB, Rooijakkers SHM, Ruyken M, van Kessel KPM, van Strijp JAG. The innate immune modulators staphylococcal complement inhibitor and chemotaxis inhibitory protein of Staphylococcus aureus are located on beta-hemolysin-converting bacteriophages. J Bacteriol 2006; 188:1310–1315 [View Article] [PubMed]
    [Google Scholar]
  29. Deghorain M, Van Melderen L. The Staphylococci phages family: an overview. Viruses 2012; 4:3316–3335 [View Article] [PubMed]
    [Google Scholar]
  30. Shearwin KE, Truong JQ. Lysogeny. In Bamford DH, Zuckerman M. eds Encyclopedia of Virology, 4th. edn Oxford: Academic Press; 2021 pp 77–87
    [Google Scholar]
  31. Goerke C, Pantucek R, Holtfreter S, Schulte B, Zink M et al. Diversity of prophages in dominant Staphylococcus aureus clonal lineages. J Bacteriol 2009; 191:3462–3468 [View Article]
    [Google Scholar]
  32. Bardy JJ, Sarovich DS, Price EP, Steinig E, Tong S et al. Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes. BMC Ear Nose Throat Disord 2018; 18:16. [View Article] [PubMed]
    [Google Scholar]
  33. Hopkins C, Browne JP, Slack R, Lund V, Brown P. The Lund-Mackay staging system for chronic rhinosinusitis: how is it used and what does it predict?. Otolaryngol Head Neck Surg 2007; 137:555–561 [View Article] [PubMed]
    [Google Scholar]
  34. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
    [Google Scholar]
  35. 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]
  36. 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] [PubMed]
    [Google Scholar]
  37. Guy L, Kultima JR, Andersson SGE. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 2010; 26:2334–2335 [View Article] [PubMed]
    [Google Scholar]
  38. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
    [Google Scholar]
  39. 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] [PubMed]
    [Google Scholar]
  40. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  41. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018; 3:124 [View Article] [PubMed]
    [Google Scholar]
  42. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
    [Google Scholar]
  43. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
    [Google Scholar]
  44. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article] [PubMed]
    [Google Scholar]
  45. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS ONE 2010; 5:e9490 [View Article] [PubMed]
    [Google Scholar]
  46. Kahánková J, Pantůček R, Goerke C, Růžičková V, Holochová P et al. Multilocus PCR typing strategy for differentiation of Staphylococcus aureus siphoviruses reflecting their modular genome structure. Environ Microbiol 2010; 12:2527–2538 [View Article] [PubMed]
    [Google Scholar]
  47. Ene A, Miller-Ensminger T, Mores CR, Giannattasio-Ferraz S, Wolfe AJ et al. Examination of Staphylococcus aureus prophages circulating in Egypt. Viruses 2021; 13:337 [View Article] [PubMed]
    [Google Scholar]
  48. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [View Article] [PubMed]
    [Google Scholar]
  49. Tan D, Hansen MF, de Carvalho LN, Røder HL, Burmølle M et al. High cell densities favor lysogeny: induction of an H20 prophage is repressed by quorum sensing and enhances biofilm formation in Vibrio anguillarum. ISME J 2020; 14:1731–1742 [View Article] [PubMed]
    [Google Scholar]
  50. McCarthy AJ, Witney AA, Lindsay JA. Staphylococcus aureus temperate bacteriophage: carriage and horizontal gene transfer is lineage associated. Front Cell Infect Microbiol 2012; 2:6. [View Article] [PubMed]
    [Google Scholar]
  51. Ramisetty BCM, Sudhakari PA. Bacterial “Grounded” prophages: hotspots for genetic renovation and innovation. Front Genet 2019; 10:65. [View Article] [PubMed]
    [Google Scholar]
  52. Kwan T, Liu J, DuBow M, Gros P, Pelletier J. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc Natl Acad Sci U S A 2005; 102:5174–5179 [View Article] [PubMed]
    [Google Scholar]
  53. Bohlin J, Eldholm V, Pettersson JHO, Brynildsrud O, Snipen L. The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes. BMC Genomics 2017; 18:151. [View Article] [PubMed]
    [Google Scholar]
  54. Nanda AM, Thormann K, Frunzke J. Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions. J Bacteriol 2015; 197:410–419 [View Article] [PubMed]
    [Google Scholar]
  55. Canfield GS, Duerkop BA. Molecular mechanisms of enterococcal-bacteriophage interactions and implications for human health. Curr Opin Microbiol 2020; 56:38–44 [View Article] [PubMed]
    [Google Scholar]
  56. Nguyen LT, Vogel HJ. Staphylokinase has distinct modes of interaction with antimicrobial peptides, modulating its plasminogen-activation properties. Sci Rep 2016; 6:31817. [View Article] [PubMed]
    [Google Scholar]
  57. Bergmann S, Hammerschmidt S. Fibrinolysis and host response in bacterial infections. Thromb Haemost 2007; 98:512–520 [View Article] [PubMed]
    [Google Scholar]
  58. Tan NC-W, Cooksley CM, Roscioli E, Drilling AJ, Douglas R et al. Small-colony variants and phenotype switching of intracellular Staphylococcus aureus in chronic rhinosinusitis. Allergy 2014; 69:1364–1371 [View Article] [PubMed]
    [Google Scholar]
  59. Tan NC-W, Foreman A, Jardeleza C, Douglas R, Vreugde S et al. Intracellular Staphylococcus aureus: the Trojan horse of recalcitrant chronic rhinosinusitis?. Int Forum Allergy Rhinol 2013; 3:261–266 [View Article] [PubMed]
    [Google Scholar]
  60. Wise SK, Lin SY, Toskala E, Orlandi RR, Akdis CA et al. International consensus statement on allergy and rhinology: allergic rhinitis. Int Forum Allergy Rhinol 2018; 8:108–352 [View Article] [PubMed]
    [Google Scholar]
  61. Martinez FO, Helming L, Gordon S. Alternative activation of macrophages: an immunologic functional perspective. Annu Rev Immunol 2009; 27:451–483 [View Article] [PubMed]
    [Google Scholar]
  62. Tuffs SW, Haeryfar SMM, McCormick JK. Manipulation of innate and adaptive immunity by staphylococcal superantigens. Pathogens 2018; 7:E53. [View Article] [PubMed]
    [Google Scholar]
  63. Dietel A-K, Merker H, Kaltenpoth M, Kost C. Selective advantages favour high genomic AT-contents in intracellular elements; 2018
  64. Rogozin IB, Makarova KS, Natale DA, Spiridonov AN, Tatusov RL et al. Congruent evolution of different classes of non-coding DNA in prokaryotic genomes. Nucleic Acids Res 2002; 30:4264–4271 [View Article] [PubMed]
    [Google Scholar]
  65. Laumay F, Corvaglia A-R, Diene SM, Girard M, Oechslin F et al. Temperate prophages increase bacterial adhesin expression and virulence in an experimental model of endocarditis due to Staphylococcus aureus from the CC398 lineage. Front Microbiol 2019; 10:742. [View Article] [PubMed]
    [Google Scholar]
  66. Dragoš A, Andersen AJC, Lozano-Andrade CN, Kempen PJ, Kovács ÁT et al. Phages weaponize their bacteria with biosynthetic gene clusters; 2020
  67. Kondo K, Kawano M, Sugai M. Prophage elements function as reservoir for antibiotic resistance and virulence genes in nosocomial pathogens. bioRXiv 2020 [View Article]
    [Google Scholar]
  68. Popescu M, Van Belleghem JD, Khosravi A, Bollyky PL. Bacteriophages and the immune system. Annu Rev Virol 2021; 8:415–435 [View Article] [PubMed]
    [Google Scholar]
  69. Ingmer H, Gerlach D, Wolz C. Temperate phages of Staphylococcus aureus. Microbiol Spectr 2019; 7: [View Article]
    [Google Scholar]
  70. Bui LMG, Kidd SP. A full genomic characterization of the development of a stable Small Colony Variant cell-type by a clinical Staphylococcus aureus strain. Infect Genet Evol 2015; 36:345–355 [View Article] [PubMed]
    [Google Scholar]
  71. Marti E, Variatza E, Balcázar JL. Bacteriophages as a reservoir of extended-spectrum β -lactamase and fluoroquinolone resistance genes in the environment. Clin Microbiol Infect 2014; 20:456–O459 [View Article]
    [Google Scholar]
  72. Rezaei Javan R, Ramos-Sevillano E, Akter A, Brown J, Brueggemann AB. Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis. Nat Commun 2019; 10:4852. [View Article] [PubMed]
    [Google Scholar]
  73. Bobay L-M, Touchon M, Rocha EPC. Pervasive domestication of defective prophages by bacteria. Proc Natl Acad Sci U S A 2014; 111:12127–12132 [View Article] [PubMed]
    [Google Scholar]
  74. Wang G-H, Niu L-M, Ma G-C, Xiao J-H, Huang D-W. Large proportion of genes in one cryptic WO prophage genome are actively and sex-specifically transcribed in a fig wasp species. BMC Genomics 2014; 15:893 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000726
Loading
/content/journal/mgen/10.1099/mgen.0.000726
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error