Genome sequence-based fluorescent amplified-fragment length polymorphism (FAFLP) analysis was investigated for fingerprinting and subtyping 42 multiple drug resistant (MDR) isolates of Pseudomonas aeruginosa from post-surgical endophthalmitis. The FAFLP profiles derived from EcoRI/MseI restricted fragments differentiated clinical isolates and were found to be extremely reproducible. Seventeen different amplification patterns (amplitypes) were observed for all the 42 isolates from 11 different patients. Also, we were able to genotype the isolates based on the differential amplification of a total of 31 FAFLP markers representing genomic fragments from the P. aeruginosa chromosome. This data appears to provide clues to the genetic diversity of endopthalmitis associated strains and could be converted into digitised fingerprints suitable for electronic manipulations and archiving.
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