Degenerate primed randomly amplified polymorphic DNA (DP-RAPD) fingerprinting of bacteriophages of Vibrio harveyi from shrimp hatcheries in Southern India

Vibrio harveyi is a significant pathogen of shrimp. Seventy-six bacteriophages infecting luminescent V. harveyi were isolated from a total of 194 water samples drawn from various sources of shrimp hatcheries located in South East coast and Andaman island of India. Degenerate primed randomly amplified polymorphic DNA (DP- RAPD) fingerprinting of these bacteriophages was carried out to determine their genetic relatedness. Similarity matrix based on Dice coefficient followed by construction of dendrogram by unweighted pair group method with arithmetic averages (UPGMA) revealed 12 major clusters. One phage was randomly selected from each of these major clusters for transmission electron microscopic observations. Eleven of them had an icosahedral head (46-115 nm) with a long non- contractile tail (132-329 nm), belonging to the Siphoviridae family and two phages had a short tail (15-27 nm), belonging to the family Podoviridae. The phylogenetic analysis of the phages using DP-RAPD fingerprinting correlated to some extent to the phenotypic nature of the host specifically with regard to sucrose fermentation and source of isolation. However, phages specifically infecting V. harveyi and those belonging to different families did not cluster together in the DP-PCR cluster analysis. Hence, the genetic diversity of phages infecting same host with respect to phenotypic difference was revealed by the DP-RAPD applied in this study.

Application of the Random Amplified Polymorphic DNA (RAPD) Fingerprinting to Analyze Genetic Variation in Community Associated-Methicillin Resistant Staphylococcus Aureus (CA-MRSA) Isolates in Iran

<p>The aim of this study was to apply RAPD technique to analyze the genetic variability among the Iranian CA-MRSA isolates.</p><p>The RAPD amplification was implemented on 25 strains isolated from the anterior nares of 410 healthy children using four randomly selected oligonucleotide primers from the stocks available in our laboratory, including the primers 1254, GE6, OLP6 and OLP13 from our stock. The amplified PCR products were detected on a 1.5% agarose gel and subjected to further analysis to establish the band profiles and genetic relationships using the Gel Compar® program.<strong></strong></p><p>The Iranian CA-MRSA isolates produced distinct RAPD patterns which varied based on the primer used, however, the primer 1254 revealed highly polymorphic patterns consisting 5 discernable RAPD types (RT), “RT1” (12, 48%), “RT2” (8, 32%), “RT3” (3, 12%), and “RT4 and RT5”, (a single RAPD type each, 4%). Phylogenetic analysis based on RAPD profiles divided most of the CA-MRSA isolates into 2 distinct but related RAPD clusters, a small group and two single unrelated RAPD types.</p><p>This study shows that the simple and cost-effective but rather difficult to optimize RAPD fingerprinting could be used to evaluate genetic and epidemiological relationships of CA-MRSA isolates on condition that the patterns are obtained from carefully optimized laboratory tests.</p>