rpoB gene sequencing for phylogenetic analysis of avian pathogenic Escherichia coli.
10.14405/kjvr.2015.55.1.31
- Author:
Hyuk Joon KWON
1
;
Won Jin SEONG
;
Tae Eun KIM
;
Yong Jin WON
;
Jae Hong KIM
Author Information
1. Laboratory of Poultry Clinical Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 151-742 Korea. kwonhj01@snu.ac.kr
- Publication Type:Original Article
- Keywords:
avian pathogenic Escherichia coli;
rpoB;
multi-locus sequence typing;
phylogenetic analysis
- MeSH:
Base Sequence;
Databases, Nucleic Acid;
Escherichia coli*;
Genes, Essential;
Humans;
Shigella
- From:Korean Journal of Veterinary Research
2015;55(1):31-39
- CountryRepublic of Korea
- Language:English
-
Abstract:
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.
