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To hasten the confirmation of suspected salmonella growth on MSRV, a PCR-based colony confirmation technique was used directly from the MSRV agar plates, which proved to be rapid, specific and sensitive.
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This became the sole method of genotyping within the established colony following confirmation that the PCR assay recapitulated results obtained by Southern blotting.
For each trial set, one salmonella colony, isolated for confirmation, was also serotyped to verify that it was the strain used for seeding that was reisolated.
Aliquot (2 μL) of the ligation was transformed into Escherichia coli 5α and subsequently plated out on Luria-Bertany (LB) agar containing ampicillin (100 μg/mL) and X-gal (40 μg/mL) for easy distinguishing of recombinant (white) colonies from non-recombinant (blue) transformant colonies with further confirmation by PCR amplification.
The plates were observed for characteristic green colonies and further confirmation was by Gram's staining and biochemical test as per IS: 13428 2005 (Annexure-D).
KAK carried out cell line studies, microarray analysis, real-time PCR confirmation and colony formation assays; she participated in study design/coordination and drafted the manuscript.
The last step consists in the selection and confirmation of colonies cured of pSLT, by first selecting colonies that were chloramphenicol sensitive followed by PCR targeting the plasmid genes spvA and repA.
Swabs of the anterior nares were streaked directly onto BBL™ CHROMagar™ MRSA plates (BD Diagnostics, Sparks, MD), which allowed positive confirmation if colonies were mauve at 24 h and presumptive identification if colonies became mauve by 48 h.
The presence of green oxidase-positive colonies was used for confirmation of P. aeruginosa systemic dissemination.
Typically, four colonies were selected for confirmation of the correct assembly of the mutation fragments and the correct sequence of the mutation cassette using primers pHA.seq.F and pHA.seq.R (see Additional file 1: Table S3).
For samples seeded with salmonella, confirmation of a suspected colony included correct colony morphology and agglutination with the specific O antigen according to the particular serotype used.
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