Variations in Serratia marcescens differentiation using different primers.

OBJECTIVES: To study primer sequences (1060, 1247, 1254, 1281, 1283, and 1290) for random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR).

METHODS: Twenty-four clinical Serratia marcescens (S. marcescens) isolates were obtained over a 6-month period from April 2002 to September 2002 from hospitals in the Fars province of Iran. Six primers were used due to S. marcescens genome properties, and RAPD-PCR was carried out. The results were subjected to unweighted pair-group method analysis using NTSYSpc 2.02. The primers were blasted with the S. marcescens genome, and the primers efficiency was estimated.

RESULTS: The results of blast primers with S. marcescens genome sequence showed that primer 1283 had the highest homology and primer 1290 had the lowest homology. Comparing the resulted dendrograms showed that the pattern of the primers to separate isolates was closely related to their sequence homology with the genome and their amount of guanine and cytosine nucleotide content.

CONCLUSIONS: There are clear differences in RAPD-PCR results when different primers are used, and it is recommended to consider genomic properties of an organism to design a primer for RAPD-PCR.