| rpoB gene sequencing for phylogenetic analysis of avian pathogenic Escherichia coli |
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Hyuk-Joon Kwon1, Won-Jin Seong2, Tae-Eun Kim3, Yong-Jin Won4, Jae-Hong Kim5 |
1Laboratory of Poultry Clinical Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University
2Laboratory of Avian Diseases, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University
3BioPOA Co.
4Division of EcoScience, Ewha Womans University
5Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University |
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| Abstract |
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The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were identified. RST 1 was assigned to a major RST that included 34.7% (50/144) of the analyzed strains. RST 2 to RST 50 were then assigned to other strains with higher nucleotide sequence similarity to RST 1 in order. RST 1, 11, and 23 were mixed with APEC along with human commensal and pathogenic strains while RST 2, 6, 9, 13-15, 22, 24, 25, 33, 34, 36, and 41 were unique to APEC strains. Only five APEC strains grouped into RST 32 and 47, which contained human pathogenic E. coli (HPEC). Thus, most of the APEC strains had genetic backgrounds different from HPEC strains. However, the minor APEC strains similar to HPEC should be considered potential zoonotic risks. The resolution power of multi-locus sequence typing (MLST) was better than RST testing. Nevertheless, phylogenetic analysis of rpoB was simpler and more economic than MLST. |
| Key Words:
avian pathogenic Escherichia coli, rpoB, multi-locus sequence typing, phylogenetic analysis |
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