Seasonal and genotypic changes in Escherichia coli phylogenetic groups in the Yeongsan River basin of South Korea

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Jang, Jeonghwan ^a   Di, Doris Y W ^a   Lee, Anna ^a   Unno, Tatsuya ^b   Sadowsky, Michael J ^c   Hur, Hor Gil ^a  

^a Gwangju Institute of Science and Technology (GIST)   (South Korea)

^b Jeju National University   (South Korea)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; ARTICLE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BIOCHEMICAL OXYGEN DEMAND; CONTROLLED STUDY; DNA FINGERPRINTING; ENVIRONMENTAL FACTOR; ESCHERICHIA COLI; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; MICROBIAL DIVERSITY; NONHUMAN; PHYLOGENY; PLASTICITY; RIVER BASIN; SEASONAL VARIATION; SOUTH KOREA; SPECIES DISTRIBUTION; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; RIVER; SEASON; SHIGA TOXIN PRODUCING ESCHERICHIA COLI;

DNA FINGERPRINTING; ESCHERICHIA COLI; GENOTYPE; PHYLOGENY; REPUBLIC OF KOREA; RIVERS; SEASONS; SHIGA-TOXIGENIC ESCHERICHIA COLI;

EID: 84904357447     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0100585     Document Type: Article

References (48)

1. USEPA (2006) Method 1603: Escherichia coli (E. coli) in Water by Membrane Filtration Using Modified membrane-Thermotolerant Escherichia coli Agar. U.S. Environmental Protection Agency, Washington, DC.
2. Byappanahalli MN, Fujioka RS (1998) Evidence that tropical soil environment can support the growth of Escherichia coli. Water Sci Technol 38:171-174.
3. Sadowsky MJ, Whitman RL (2010) Fecal Bacteria. ASM Press: Washington, DC.
4. Byappanahalli MN, Whitman RL, Shively DA, Sadowsky MJ, Ishii S (2006) Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed. Environ Microbiol 8:504-513.
5. Ishii S, Ksoll WB, Hicks RE, Sadowsky MJ (2006) Presence and growth of naturalized Escherichia coli in temperate soils from lake superior watersheds. Appl Environ Microbiol 72: 612-621.
6. Dombek PE, Johnson LK, Zimmerley ST, Sadowsky MJ (2000) Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl Environ Microbiol 66:2572-2577. (Pubitemid 30353967)
7. Jang J, Unno T, Lee SW, Cho KH, Sadowsky MJ, et al. (2011) Prevalence of season-specific Escherichia coli strains in the Yeongsan River Basin of South Korea. Environ Microbiol 13:3103-3113.
8. Herzer PJ, Inouye S, Inouye M, Whittam TS (1990) Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J Bacteriol 172:6175-6181. (Pubitemid 20372753)
9. Clermont O, Olier M, Hoede C, Diancourt L, Brisse S, et al. (2011) Animal and human pathogenic Escherichia coli strains share common genetic backgrounds. Infect Genet Evol 11:654-662.
10. Walk ST, Alm EW, Gordon DM, Ram JL, Toranzos GA, et al. (2009) Cryptic lineages of the genus Escherichia. Appl Environ Microbiol 75:6534-6544.
11. Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, et al. (2011) Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci USA 108:7200-7205.
12. Moissenet D, Salauze B, Clermont O, Bingen E, Arlet G, et al. (2010) Meningitis caused by Escherichia coli producing TEM-52 extended-spectrum b-lactamase within an extensive outbreak in a neonatal ward: Epidemiological investigation and characterization of the strain. J Clin Microbiol 48:2459-2463.
13. Jaureguy F, Landraud L, Passet V, Diancourt L, Frapy E, et al. (2008) Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics 9:560.
14. Tenaillon O, Skurnik D, Picard B, Denamur E (2010) The population genetics of commensal Escherichia coli. Nat Rev Microbiol 8:207-217.
15. Bergthorsson U, Ochman H (1998) Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol Biol Evol 15:6-16. (Pubitemid 28046976)
16. Gordon DM (2004) The influence of ecological factors on the distribution and genetic structure of Escherichia coli. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Neidhardt, F., et al. (eds) ASM press: Washington, DC.
17. Walk ST, Alm EW, Calhoun LM, Mladonicky JM, Whittam TS (2007) Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ Microbiol 9:2274-2288. (Pubitemid 47222119)
18. Nowrouzian FL, Adlerberth I, Wold AE (2006) Enhanced persistence in the colonic microbiota of Escherichia coli strains belonging to phylogenetic group B2: role of virulence factors and adherence to colonic cells. Microbes Infect 8:834-840.
19. Ratajczak M, Laroche E, Berthe T, Clermont O, Pawlak B, et al. (2010) Influence of hydrological conditions on the Escherichia coli population structure in the water of a creek on a rural watershed. BMC Microbiol 10:222.
20. Johnson JR, Stell AL (2000) Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise. J Infect Dis 181:261-272. (Pubitemid 30049057)
21. Le Gall T, Clermont O, Gouriou S, Picard B, Nassif X, et al. (2007) Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol 24:2373-2384. (Pubitemid 350060443)
22. Escobar-Páramo P, Grenet K, Le Menac'h A, Rode L, Salgado E, et al. (2004) Large-scale population structure of human commensal Escherichia coli isolates. Appl Environ Microbiol 70:5698-5700. (Pubitemid 39279653)
23. Picard B, Garcia JS, Gouriou S, Duriez P, Brahimi N, et al. (1999) The Link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect Immun 67:546-553. (Pubitemid 29059185)
24. Unno T, Han D, Jang J, Lee S-N, Ko G, et al. (2009) Absence of Escherichia coli phylogenetic group B2 strains in humans and domesticated animals from Jeonnam province, Republic of Korea. Appl Environ Microbiol 75:5659-5666.
25. Goullet P, Picard B (1989) Comparative electrophoretic polymorphism of esterases and other enzymes in Escherichia coli. J Gen Microbiol 135:135-143. (Pubitemid 19047349)
26. Clermont O, Bonacorsi S, Bingen E (2000) Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol 66:4555-4558.
27. Gordon DM, Clermont O, Tolley H, Denamur E (2008) Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method. Environ Microbiol 10:2484-2496.
28. Duriez P, Clermont O, Bonacorsi S, Bingen E, Chaventré A, et al. (2001) Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations. Microbiol-SGM 147:1671-1676. (Pubitemid 32544832)
29. Johnson JR, Kuskowski MA, Owens K, Gajewski A, Winokur PL (2003) Phylogenetic origin and oirulence genotype in relation to resistance to fluoroquinolones and/or extended-spectrum cephalosporins and cephamycins among Escherichia coli isolates from animals and humans. J Infect Dis 188:759-768. (Pubitemid 37115190)
30. Clermont O, Christenson JK, Denamur E, Gordon DM (2013) The clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep 5:58-65.
31. Ishii S, Sadowsky MJ (2009) Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environ Microbiol 11:733-740.
32. Johnson LK, Brown MB, Carruthers EA, Ferguson JA, Dombek PE, et al. (2004) Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Appl. Environ Microbiol 70:4478-4485. (Pubitemid 39095465)
33. Ciebin BW, Brodsky MH, Eddington R, Horsnell G, Choney A, et al. (1995) Comparative evaluation of modified m-FC and m-TEC media for membrane filter enumeration of Escherichia coli in water. Appl Environ Microbiol 61:3940-3942.
34. Sambrook J, Russell WD (2001) Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
35. Paton AW, Paton JC (1998) Detection and characterization of shiga Toxigenic Escherichia coli by using multiplex PCR assays for stx1, stx2,eaeA, Enterohemorrhagic E. coli hlyA, rfb O111, and rfb O157. J Clin Microbiol 36:598-602. (Pubitemid 28060342)
36. Park Y-S, Céréghino R, Compin A, Lek S (2003) Applications of artificial neural networks for patterning and predicting aquatic insect species richness in running waters. Ecol Model 160:265-280. (Pubitemid 36251041)
37. Park Y-S, Chang J, Lek S, Cao W, Brosse S (2003) Conservation strategies for endemic fish species threatened by the three gorges dam. Conserv Biol 17:1748-1758. (Pubitemid 37538213)
38. Tuang FN, Rademaker JLW, Alocilja EC, Louws FJ, de Bruijn FJ (1999) Identification of bacterial rep-PCR genomic fingerprints using a backpropagation neural network. FEMS Microbiol Lett 177:249-256. (Pubitemid 29352221)
39. Tudesque L, Gevrey M, Grenouillet G, Lek S (2008) Long-term changes in water physicochemistry in the Adour-Garonne hydrographic network during the last three decades. Water Res 42:732-742. (Pubitemid 351625251)
40. Weber M, Teeling H, Huang S, Waldmann J, Kassabgy M, et al. (2010) Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics. ISME J 5:918-928.
41. Gevrey M, Rimet F, Park YS, Giraudel J-L, Ector L, et al. (2004) Water quality assessment using diatom assemblages and advanced modelling techniques. Freshwater Biol 49:208-220. (Pubitemid 38162016)
42. Smilauer JLaP Multivariate Analysis of Ecological Data using CANOCO. Cambridge University Press: Cambridge, UK.
43. Boer SI, Hedtkamp SIC, van Beusekom JEE, Fuhrman JA, Boetius A, et al. (2009) Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. ISME J 3:780-791.
44. Tarr PI, Gordon CA, Chandler WL (2005) Shiga-toxin-producing Escherichia coli and haemolytic uraemic syndrome. The Lancet 365:1073-1086. (Pubitemid 40386785)
45. Nowrouzian F, Hesselmar B, Saalman R, Strannegard I-L, Aberg N, et al. (2003) Escherichia coli in infants' intestinal microflora: Colonization rate, strain turnover, and virulence gene carriage. Pediatr Res 54:8-14. (Pubitemid 36736798)
46. Gordon DM, Stern SE, Collignon PJ (2005) Influence of the age and sex of human hosts on the distribution of Escherichia coli ECOR groups and virulence traits. Microbiology-SGM 151:15-23. (Pubitemid 40207665)
47. Johnson JR, O'Bryan TT, Kuskowski M, Maslow JN (2001) Ongoing horizontal and vertical transmission of virulence genes and papA alleles among Escherichia coli blood isolates from patients with diverse-source bacteremia. Infect Immun 69:5363-5374. (Pubitemid 32786468)
48. Feng P, Lampel KA, Karch H, Whittam TS (1998) Genotypic and phenotypic changes in the emergence of Escherichia coli O157:H7. J Infect Dis 177:1750-1753.