1887

Abstract

Comparison of the complete genome sequence of 638R, originally isolated in the USA, was made with two previously sequenced strains isolated in the UK (NCTC 9343) and Japan (YCH46). The presence of 10 loci containing genes associated with polysaccharide (PS) biosynthesis, each including a putative Wzx flippase and Wzy polymerase, was confirmed in all three strains, despite a lack of cross-reactivity between NCTC 9343 and 638R surface PS-specific antibodies by immunolabelling and microscopy. Genomic comparisons revealed an exceptional level of PS biosynthesis locus diversity. Of the 10 divergent PS-associated loci apparent in each strain, none is similar between NCTC 9343 and 638R. YCH46 shares one locus with NCTC 9343, confirmed by mAb labelling, and a second different locus with 638R, making a total of 28 divergent PS biosynthesis loci amongst the three strains. The lack of expression of the phase-variable large capsule (LC) in strain 638R, observed in NCTC 9343, is likely to be due to a point mutation that generates a stop codon within a putative initiating glycosyltransferase, necessary for the expression of the LC in NCTC 9343. Other major sequence differences were observed to arise from different numbers and variety of inserted extra-chromosomal elements, in particular prophages. Extensive horizontal gene transfer has occurred within these strains, despite the presence of a significant number of divergent DNA restriction and modification systems that act to prevent acquisition of foreign DNA. The level of amongst-strain diversity in PS biosynthesis loci is unprecedented.

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2010-11-01
2019-11-14
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References

  1. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (editors) ( 1992; ). Current Protocols in Molecular Biology. New York. : Wiley.
    [Google Scholar]
  2. Bayley, D. P., Rocha, E. R. & Smith, C. J. ( 2000; ). Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. FEMS Microbiol Lett 193, 149–154.[CrossRef]
    [Google Scholar]
  3. Bentley, S. D., Aanensen, D. M., Mavroidi, A., Saunders, D., Rabbinowitsch, E., Collins, M., Donohoe, K., Harris, D., Murphy, L. & other authors ( 2006; ). Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet 2, e31.[CrossRef]
    [Google Scholar]
  4. Breitbart, M., Hewson, I., Felts, B., Mahaffy, J. M., Nulton, J., Salamon, P. & Rohwer, F. ( 2003; ). Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185, 6220–6223.[CrossRef]
    [Google Scholar]
  5. Campbell, E. A., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A. & Darst, S. A. ( 2001; ). Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 104, 901–912.[CrossRef]
    [Google Scholar]
  6. Campbell, E. A., Pavlova, O., Zenkin, N., Leon, F., Irschik, H., Jansen, R., Severinov, K. & Darst, S. A. ( 2005; ). Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. EMBO J 24, 674–682.[CrossRef]
    [Google Scholar]
  7. Carver, T. J., Rutherford, K. M., Berriman, M., Rajandream, M. A., Barrell, B. G. & Parkhill, J. ( 2005; ). ACT: the Artemis comparison tool. Bioinformatics 21, 3422–3423.[CrossRef]
    [Google Scholar]
  8. Cerdeño-Tárraga, A. M., Patrick, S., Crossman, L. C., Blakely, G., Abratt, V., Lennard, N., Poxton, I., Duerden, B., Harris, B. & other authors ( 2005; ). Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science 307, 1463–1465.[CrossRef]
    [Google Scholar]
  9. Chatzidaki-Livanis, M., Coyne, M. J., Roche-Hakansson, H. & Comstock, L. E. ( 2008; ). Expression of a uniquely regulated extracellular polysaccharide confers a large-capsule phenotype to Bacteroides fragilis. J Bacteriol 190, 1020–1026.[CrossRef]
    [Google Scholar]
  10. Cheng, C. W., Lin, H. S., Ye, J. J., Yang, C. C., Chiang, P. C., Wu, T. S. & Lee, M. H. ( 2009; ). Clinical significance of and outcomes for Bacteroides fragilis bacteremia. J Microbiol Immunol Infect 42, 243–250.
    [Google Scholar]
  11. Coyne, M. J., Tzianabos, A. O., Mallory, B. C., Carey, V. J., Kasper, D. L. & Comstock, L. E. ( 2001; ). Polysaccharide biosynthesis locus required for virulence of Bacteroides fragilis. Infect Immun 69, 4342–4350.[CrossRef]
    [Google Scholar]
  12. Drummelsmith, J. & Whitfield, C. ( 2000; ). Translocation of group 1 capsular polysaccharide to the surface of Escherichia coli requires a multimeric complex in the outer membrane. EMBO J 19, 57–66.[CrossRef]
    [Google Scholar]
  13. Dryden, D. T. ( 2006; ). DNA mimicry by proteins and the control of enzymatic activity on DNA. Trends Biotechnol 24, 378–382.[CrossRef]
    [Google Scholar]
  14. Fletcher, C. M., Coyne, M. J., Villa, O. F., Chatzidaki-Livanis, M. & Comstock, L. E. ( 2009; ). A general O-glycosylation system important to the physiology of a major human instestinal symbiont. Cell 137, 321–331.[CrossRef]
    [Google Scholar]
  15. Houston, S., Blakely, G. W., McDowell, A., Martin, L. & Patrick, S. ( 2010; ). Binding and degradation of fibrinogen by Bacteroides fragilis and characterization of a 54 kDa fibrinogen-binding protein. Microbiology 156, 2516–2526.[CrossRef]
    [Google Scholar]
  16. Katsandri, A., Papaparaskevas, J., Pantazatou, A., Petrikkos, G. L., Thomopoulos, G., Houhoula, D. P. & Avlamis, A. ( 2006; ). Two cases of infections due to multidrug-resistant Bacteroides fragilis group strains. J Clin Microbiol 44, 3465–3467.[CrossRef]
    [Google Scholar]
  17. Kuwahara, T., Yamashita, A., Hirakawa, H., Nakayama, H., Toh, H., Okada, N., Kuhara, S., Hattori, M., Hayashi, T. & Ohnishi, Y. ( 2004; ). Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc Natl Acad Sci U S A 101, 14919–14924.[CrossRef]
    [Google Scholar]
  18. Lutton, D. A., Patrick, S., Crockard, A. D., Stewart, L. D., Larkin, M. J., Dermott, E. & McNeill, T. A. ( 1991; ). Flow cytometric analysis of within-strain variation in polysaccharide expression by Bacteroides fragilis by use of murine monoclonal antibodies. J Med Microbiol 35, 229–237.[CrossRef]
    [Google Scholar]
  19. Mazmanian, S. K., Round, J. L. & Kasper, D. L. ( 2008; ). A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453, 620–625.[CrossRef]
    [Google Scholar]
  20. McMahon, S. A., Roberts, G. A., Johnson, K. A., Cooper, L. P., Liu, H., White, J. H., Carter, L. G., Sanghvi, B., Oke, M. & other authors ( 2009; ). Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance. Nucleic Acids Res 37, 4887–4897.[CrossRef]
    [Google Scholar]
  21. Patrick, S. ( 2002; ). Bacteroides. In Molecular Medical Microbiology, pp. 1921–1948. Edited by Sussman, M.. London. : Academic Press.
    [Google Scholar]
  22. Patrick, S. & Duerden, B. I. ( 2006; ). Gram-negative non-spore forming obligate anaerobes. In Principles and Practice of Clinical Bacteriology, 2nd edn, pp. 541–556. Edited by Gillespie, S. H. & Hawkey, P.. London. : Wiley.
    [Google Scholar]
  23. Patrick, S. & Reid, J. H. ( 1983; ). Separation of capsulate and non-capsulate Bacteroides fragilis on a discontinuous density gradient. J Med Microbiol 16, 239–241.[CrossRef]
    [Google Scholar]
  24. Patrick, S., Reid, J. H. & Coffey, A. ( 1986; ). Capsulation of in vitro and in vivo grown Bacteroides species. J Gen Microbiol 132, 1099–1109.
    [Google Scholar]
  25. Patrick, S., Stewart, L. D., Damani, N., Wilson, K. G., Lutton, D. A., Larkin, M. J., Poxton, I. & Brown, R. ( 1995; ). Immunological detection of Bacteroides fragilis in clinical samples. J Med Microbiol 43, 99–109.[CrossRef]
    [Google Scholar]
  26. Patrick, S., Gilpin, D. & Stevenson, L. ( 1999; ). Detection of intrastrain antigenic variation of Bacteroides fragilis surface polysaccharides by monoclonal antibody labelling. Infect Immun 67, 4346–4351.
    [Google Scholar]
  27. Patrick, S., Parkhill, J., McCoy, L. J., Lennard, N., Larkin, M. J., Collins, M., Sczaniecka, M. & Blakely, G. ( 2003; ). Multiple inverted DNA repeats of Bacteroides fragilis that control polysaccharide antigenic variation are similar to the hin region inverted repeats of Salmonella typhimurium. Microbiology 149, 915–924.[CrossRef]
    [Google Scholar]
  28. Patrick, S., Houston, S., Thacker, Z. & Blakely, G. W. ( 2009; ). Mutational analysis of genes implicated in LPS and capsular polysaccharide biosynthesis in the opportunistic pathogen Bacteroides fragilis. Microbiology 155, 1039–1049.[CrossRef]
    [Google Scholar]
  29. Privitera, G., Dublanchet, A. & Sebald, M. ( 1979; ). Transfer of multiple antibiotic resistance between subspecies of Bacteroides fragilis. J Infect Dis 139, 97–101.[CrossRef]
    [Google Scholar]
  30. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F. & other authors ( 2010; ). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65.[CrossRef]
    [Google Scholar]
  31. Reid, J. H. & Patrick, S. ( 1984; ). Phagocytic and serum killing of capsulate and non-capsulate Bacteroides fragilis. J Med Microbiol 17, 247–257.[CrossRef]
    [Google Scholar]
  32. Reid, J. H., Patrick, S. & Tabaqchali, S. ( 1987; ). Immunochemical characterization of a polysaccharide antigen of Bacteroides fragilis with an IgM monoclonal antibody. J Gen Microbiol 133, 171–179.
    [Google Scholar]
  33. Sakamoto, M. & Benno, Y. ( 2006; ). Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. Int J Syst Evol Microbiol 56, 1599–1605.[CrossRef]
    [Google Scholar]
  34. Samuel, G. & Reeves, P. ( 2003; ). Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly. Carbohydr Res 338, 2503–2519.[CrossRef]
    [Google Scholar]
  35. Smith, C. J. ( 1995; ). Genetic transformation of Bacteroides fragilis spp. using electroporation. In Methods in Molelcular Biology: Electroporation Protocols for Microorganisms, pp. 161–169. Edited by Nickloff, J. A.. Totowa, NJ. : Humana Press.
    [Google Scholar]
  36. Stiffler, P. W., Keller, R. & Traub, N. ( 1974; ). Isolation and characterization of several cryptic plasmids from clinical isolates of Bacteroides fragilis. J Infect Dis 130, 544–548.[CrossRef]
    [Google Scholar]
  37. Tally, F. P., Snydman, D. R., Shimell, M. J. & Malamy, M. H. ( 1982; ). Characterization of pBFTM10, a clindamycin-erythromycin resistance transfer factor from Bacteroides fragilis. J Bacteriol 151, 686–691.
    [Google Scholar]
  38. van der Woude, M. W. & Baumler, A. J. ( 2004; ). Phase and antigenic variation in bacteria. Clin Microbiol Rev 17, 581–611.[CrossRef]
    [Google Scholar]
  39. Van Tassell, R. L. & Wilkins, T. D. ( 1978; ). Isolation of auxotrophs of Bacteroides fragilis. Can J Microbiol 24, 1619–1621.[CrossRef]
    [Google Scholar]
  40. Vimr, E. R. & Steenbergen, S. M. ( 2006; ). Mobile contingency locus controlling Escherichia coli K1 polysialic acid capsule acetylation. Mol Microbiol 60, 828–837.[CrossRef]
    [Google Scholar]
  41. Wareham, D. W., Wilks, M., Ahmed, D., Brazier, J. S. & Millar, M. ( 2005; ). Anaerobic sepsis due to multidrug-resistant Bacteroides fragilis: microbiological cure and clinical response with linezolid therapy. Clin Infect Dis 40, e67–e68.[CrossRef]
    [Google Scholar]
  42. Wexler, H. M. ( 2007; ). Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev 20, 593–621.[CrossRef]
    [Google Scholar]
  43. Whitfield, C. ( 2006; ). Biosynthesis and assembly of capsular polysaccharides in Escherichia coli. Annu Rev Biochem 75, 39–68.[CrossRef]
    [Google Scholar]
  44. Xu, J., Mahowald, M. A., Ley, R. E., Lozupone, C. A., Hamady, M., Martens, E. C., Henrissat, B., Coutinho, P. M., Minx, P. & other authors ( 2007; ). Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5, e156.[CrossRef]
    [Google Scholar]
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