The effective differentiation of Salmonella isolates using four PCR-based typing methods.

Abstract

Discrimination of Salmonella strains below the species level is very important to trace the source of outbreaks. To this end molecular typing methods can be successfully applied to routine analysis in nonspecialized laboratories due to their simplicity and speed. Here, the discriminatory ability of four molecular typing methods was investigated in 74 Salmonella enterica isolates. Salmonella strains isolated from human stool, blood, bone marrow, synovial fluid, ascites and urine sources in Iran during the years 2012 and 2013 were differentiated by random amplification of polymorphic DNA (RAPD), enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindromic (REP) and BOX repeat-based (BOXAIR) PCR methods. A total of 74 isolates were obtained, with 67 isolates belonging to eight serotypes/serogroups, while seven were nontypeable. The 74 strains produced 32 fingerprints with OPS-11 primers, 44 RAPD fingerprints using OPP-16 primers and 54 fingerprints with P1254 primers; their discriminatory index (DI) was 0·942, 0·978, and 0·984 respectively. BOXAIR fingerprinting produced 49 patterns (DI 0·985), while REP resulted in 55 patterns (DI 0·991) and ERIC in 48 fingerprints (DI 0·983). The discrimination of Salmonella isolates was improved when methods were combined. The combination of ERIC, REP and BOXAIR as well as the combination of BOXAIR with ERIC or REP could differentiate all 74 investigated Salmonella strains. The combined use of RAPD and ERIC fingerprinting offers an excellent means of differentiating Salmonella strains. The discrimination power of Salmonella molecular typing by combination of ERIC, REP and BOXAIR methods, or by combination of BOXAIR with ERIC or REP, is sufficient to determine genetic relationships for epidemiological purposes.