Restriction Profiling of 23S Microheterogenic Ribosomal Repeats for Detection and Characterizing of E. coli and Their Clonal, Pathogenic, and Phylogroups

Table 2

Restriction site of Bfa I (C/TAG) within 23S rrlH of candidate and noncandidates and the restriction profiles with 23S P1₈₈₀.

Restriction profile within rrlH					Fragments obtained on ARDRA
F	E	Ci	K	Ea	Mic.	Fragments (amplicon size)
1.1	687	685	685	685	E	665 bp, 215 bp (880 bp)
1.2		874	874	874	C	475 bp, 214 bp, and 189 bp (878 bp)
1.3	1670	1669	1667	1670	K	475 bp, 214 bp, and 189 bp (877 bp)
1.4			2336	2339	Ea	475 bp, 214 bp, and 189 bp (876 bp)
1.5	2652	2653	2650	2654

Primers were designed against the regions flanking the bold restriction sites.
F: number of fragments; E: Escherichia coli; Ci: Citrobacter koseri; K: Klebsiella pneumoniae; Ea: Enterobacter aerogenes; Mic.: microbe.
23S P1₈₈₀-FP(+): 5′-GGCGAAAAGAACCCCGGCGA-3′ (20 nt); 23S P1₈₈₀-RP(−): 5′-AGGGGTCGACTCACCCTGCC-3′ (20 nt).
FP: forward primer; RP: reverse primer. The primer details were obtained from the results of primer blast and restriction profiling pattern was obtained from NEB V2.0. Forward and reverse primers of 23S P1₈₈₀ lie within domains I and III of 23S rRNA secondary structure, respectively, with Bfa I sites in domain II.