Fig. 2

Comparison of lacZ3-yaiO and lacZB-uidA primer sets for E. coli and coliform identification. a Agarose gels (1.5 %) electrophoresis showing representative multiplex PCR amplified products from bacterial DNA. Lanes: 1, Klebsiella pneumoniae; 2, Klebsiella oxytoca; 3,Enterobacter aerogenes; 4, Enterobacter intermedius; 5, Enterobacter cloacae; 6, Shigella sonnei; 7, Serratia marcenses; 8, Yersinia enterocolitica; 9, Salmonella typhymurium; 10, Citrobacter youngae; 11; Citrobacter freundii; 12, Hafnia alvei; M, molecular weight marker (1Kb Plus DNA ladder); 13, Escherichia coli K-12; 14, E. coli B; 15, E. coli B/r; 16, E. coli C; 17, E. coli W (Waskman); 18, E. coli W (Stoke); 19, E. coli RT1. The oligonucleotide primer pairs used are indicated on the left or below each picture. For size comparison, the locations of 100 and 200 bp bands are shown when the marker is omitted. b In vitro and in silico comparison of lacZ3-yaiO and lacZB-uidA multiplex PCR amplicons. In silico analysis (see Methods) is indicated by color shading. Cyan: positive amplification. Light red: no amplification. White: Not tested. Each PCR reaction was carried out four times. In vitro PCR products are shown by signs indicating the percentage of positive amplifications obtained. “+”; “+ − “; and “-“ represent 100 %, 50 % and 0 % positive results, respectively. No other values, (i.e., neither 75 % nor 25 % positive amplifications) were obtained. “≠“ indicates a different sized PCR product. c The 3’ end of the lacZB-R primer binds to a zone of low conservation. From top to bottom (arbitrary scale), each panel depicts the binding sites of the lacZ primers, the consensus sequence of lacZ, its coverage considering all the sequences aligned, sequence logo, and % identity