Genetic and Ecological Structure of Hafnia alvei in Australia

Systematic and Applied Microbiology

Volumn 26, Issue 4, 2003, Pages 585-594

  Okada, Shoko ^a   Gordon, David M ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Ecological structure; Genetic structure; Hafnia alvei; MLEE

Indexed keywords

ARTICLE; AUSTRALIA; BACTERIAL GENETICS; BACTERIUM ISOLATE; BACTERIUM ISOLATION; CONTROLLED STUDY; ECOLOGICAL NICHE; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC VARIABILITY; GEOGRAPHICAL VARIATION (SPECIES); HAFNIA ALVEI; MULTILOCUS ENZYME ELECTROPHORESIS; NONHUMAN; PRIORITY JOURNAL; TAXONOMY; WATER SAMPLING;

BACTERIA (MICROORGANISMS); HAFNIA ALVEI; NEGIBACTERIA;

EID: 0345293333     PISSN: 07232020     EISSN: None     Source Type: Journal    
DOI: 10.1078/072320203770865891     Document Type: Article

References (46)

1. Allen, D. A., Austin, B., Colwell, R. R.: Numerical taxonomy of bacterial isolates associated with a freshwater fishery. J. Gen. Microbiol. 129, 2043-2062 (1983).
2. Beltran, B., Musser, J. M., Helmuth, R., Farmer III, J. J., Frerichs, W. M., Wachsmuth, L. K., Ferris, K., McWorter, A. C., Wells, J. G., Cravioto, A., Selander, R. K.: Toward a population genetic analysis of Salmonella: Genetic diversity and relationships among strains of serotypes S. cholerasuis, S. derby, S. dublin, S. enteritidis, S. heidelberg, S. infantis, S. newport and S. typhimurium. Proc. Natl. Acad. Sci. USA 85, 7753-7757 (1988).
3. Bisercic, M., Feutrier, J. Y., Reeves, P. R.: Nucleotide sequence of the gnd genes from nine natural isolates of Escherichia coli: Evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus. J. Bacteriol. 173, 3894-3900 (1991).
4. Brenner, D. J.: Chapter 88, Introduction to the family Enterobacteriaceae, pp. 1105-1127. In: The Prokaryotes (M. P. Starr, H. Stolp, H. G. Trueper, A. Balows, H. G. Schlegel, eds.), Berlin, Springer-Verlag 1981.
5. Brown, A. D. H., Feldman, M. W., Nevo, E.: Multilocus structure of natural populations of Hordeum spontaneum. Genetics 96, 523-536 (1980).
6. Cohan, F. M.: Genetic exchange and evolutionary divergence in prokaryotes. Trends Ecol. Evol. 9, 175-180 (1994).
7. Cohan, F. M.: Bacterial species and speciation. Syst. Biol. 50, 513-524 (2001).
8. Cornuet, J. M., Pity, S., Luikart, G., Estoup, A., Solignac, M.: New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153, 1989-2000 (1999).
9. Crosa, J. H., Brenner, D. J., Ewing, W. H., Falkow, S.: Molecular relationships among the Salmonelleae. J. Bacteriol. 115, 307-315 (1973).
10. Dykhuizen, D. E., Green, L.: Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173, 7257-7268 (1991).
11. Ewing, W. H.: Edwards and Ewing's Identification of Enterobacteriaceae 4th ed., 536p., New York, Elsevier 1986.
12. Ewing, W. H., Fife, M. A.: Enterobacter hafniae (the Hafnia group). Int. J. Syst. Bacteriol. 18, 263-271 (1968).
13. Gevlev, I., Gevlev, E., Steigerwalt, A. G., Carter, G. P., Brenner, D. J.: Identification of the bacterium associated with haemorrhagic septicaemia in rainbow trout as Hafnia alvei. Res. Microbiol. 141, 573-576 (1990).
14. Gonzalez-Rodriguez, M. N., Sanz, J. J., Santos, J. A., Otero, A., Garcia-Lopez, M. L.: Bacteriological quality of aquacultured freshwater fish portions in prepacked trays stored at 3 degrees. J. Food Prot. 64, 1399-1404 (2001).
15. Gordon, D. M., FitzGibbon, E: The distribution of enteric bacteria from Australian mammals: host and geographical effects. Microbiology 145, 2663-2671 (1999).
16. Gordon, D. M., Lee, J.: The genetic structure of enteric bacteria from Australian mammals. Microbiology 145, 2673-2682 (1999).
17. Gunthard, H., Pennekamp, A.: Clinical significance of extraintestinal Hafnia alvei isolates from 61 patients and review of the literature. Clin. Infect. Dis. 22, 1040-1045 (1996).
18. Herzer, P. J., Inouye, S., Inouye, M., Whittam, T.: Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J. Bacteriol. 172, 6175-6181 (1990).
19. Janda, J. M., Abbott, S. L., Khashe, S., Probert, W.: Phenotypic and gentoypic properties of the genus Hafnia. J. Med. Microbiol. 51, 575-580 (2002).
20. Johnson, J. L.: Nucleic acids in bacterial classification, pp. 972-975. In: Bergey's manual of systematic bacteriology, vol. 2 (P. H. A. Sneath, N. S. Mair, N. E. Sharp, J. G. Holt eds.), Baltimore, Williams and Wilkins 1986.
21. Kaufmann, F.: The bacteriology of Enterobacteriaceae, 400p., Baltimore, Williams & Wilkins 1966.
22. Klapholz, A., Lessnau, K.D., Huang B., Talavera, W., Boyle, J. F.: Hafnia alvei - Respiratory tract isolates in a community hospital over a three-year period and a literature review. Chest 105, 1098-1100 (1994).
23. Lan, R., Reeves, P. R.: When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9, 419-424 (2001).
24. Leclerc, H., Mossel, D. A. A., Edberg, S. C., Struijk, C. B.: Advances in the bacteriology of the coliform group: their suitability as markers of microbial water safety. Annu. Rev. Microbiol. 55, 201-234 (2001).
25. Lindberg, A. M., Ljungh, A., Ahrne, S., Lofdahl, S., and Molin, G.: Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes. Int. J. Food Microbiol. 39, 11-17 (1998).
26. Maiden, M. C. J., Bygraves, J. A., Feil, E., Moreli, G., Russell, J. E., Urwin, R., Zhang, Q., Zurth, K., Caugant, D. A., Feavers, I.M., Achtman, M., and Spratt, B. G.: Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95, 3140-3145 (1998).
27. Maynard Smith, J., Smith, N. H., O'Rourke, M., and Spratt, B. G.: How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90, 4384-4388 (1993).
28. Mayr, E.: The growth of biological thought: diversity, evolution, and inheritance, 974p., Harvard University Press, Cambridge, Massachusetts 1982.
29. Moeller, V.: Distribution of amino acid decarboxylase in Enterobacteriaceae. Acta Pathol. Microbiol. Scand. 35, 259-277 (1954).
30. Nelson, K. and Selander, R. K.: Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria. Proc. Natl. Acad. Sci. USA 91, 10227-10231 (1994).
31. Ochman, H. and Selander, R. K.: Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157, 690-693 (1984).
32. Okada, S. and Gordon, D. M.: Host and geographical factors influence the thermal niche of enteric bacteria from native Australian mammals. Mol. Ecol. 10, 2499-2513 (2001).
33. Peakall, R. and Smouse, P. E.: GenAlEx V5: Genetic Analysis in Excel. Population genetic software for teaching and research, www.anu.edu.au/BoZo/GenAlEx/. Australian National University, Canberra, Australia 2001.
34. Pradel, N., Leroy-Setrin, S., Joly, B., and Livrelli, V.: Genomic subtraction to identify and characterize sequences of Shiga toxin-producing Escherichia coli O91:H21. Appl. Environ. Microbiol. 68, 2316-2325 (2002).
35. Ramos, A. and Damaso, D.: Extraintestinal infection due to Hafnia alvei. Eur. J. Clin. Microbiol. Infect. Dis. 19, 708-710 (2000).
36. Ridell, J., Siitonen, A., Paulin, L., Lindroos, O., Korkeala, H., and Albert, J.: Characterization of Hafnia alvei by biochemical tests, random amplified polymorphic DNA PCR, and partial sequencing of 16S rRNA gene. J. Clin. Microbiol. 33, 2372-2376 (1995).
37. Roberts, M. S. and Cohan, F. M.: The effect of DNA sequence divergence on sexual isolation in Bacillus. Genetics 134, 401-408 (1993).
38. Sherley, M., Gordon, D. M., and Collignon, P. J.: Variations in antibiotic resistance profile in Enterobacteriaceae isolated from wild Australian mammals. Environ. Microbiol. 2, 620-631 (2000).
39. Shirey, J. J. and Bisonnette, G. K.: Sheen formation and growth response of groundwater bacteria to reduced oxygen concentrations during incubation of M-Endo medium. Can. J. Microbiol. 38, 261-266 (1991).
40. Souza, V., Nguyen, T. T., Hudson, R. R., Pinero, D., and Lenski, R. E.: Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex? Proc. Natl. Acad. Sci. USA 89, 8389-8393 (1993).
41. Steigerwalt, A. G., Fanning, G. R., Fife-Asbury, M. A., and Brenner, D. J.: DNA relatedness among species of Enterobacter and Serratia. Can. J. Microbiol. 22, 121-137 (1976).
42. Tornadijo, M. E., Garcia, M. C., Fresno, J. M., and Carballo J.: Study of Enterobacteriaceae during the manufacture and ripening of San Simon cheese. Food Microbiol. 18, 499-509 (2001).
43. Van Valen, L.: Ecological species, multispecies, and oaks. Taxon 25, 233-239 (1976).
44. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K., and Swings, J.: Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60, 407-438 (1996).
45. Vulic, M., Dionisio, E, Taddei, F., and Radman, M.: Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl. Acad. Sci. USA 94, 9763-9767 (1997).
46. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E., Stackerbandt, E., et al.: Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37, 463-464 (1987).