Effectiveness of six molecular typing methods as epidemiological tools for the study of Salmonella isolates in two Colombian regions

Abstract

Aim: The aim of this study was the genotypic characterization of the strains of Salmonella spp. isolated from broiler chickens and humans with gastroenteritis from two regions of Colombia, by BOXA1R-polymerase chain reaction (PCR) and random amplification of polymorphic DNA (RAPD)-PCR methods. Materials and Methods: Forty-nine strains of Salmonella were assessed, 15 from poultry farms in Santander region, and 34 from Tolima region isolated from poultry farms (n=24) and the stool samples of people with gastroenteritis (n=10). BOXA1R primers were selected for repetitive element-based PCR (REP-PCR) and five arbitrary primers, namely, GTG 5, OPB 15, OPP 16, OPS 11, and P 1254 were used for RAPD-PCR to generate DNA fingerprints from the isolates. Fingerprint data from each typing method were under composite analysis and the diversity of the data was analyzed by grouping (clustering). The dendrogram was generated by the unweighted group method with analysis of the arithmetic mean based on the Dice similarity coefficient. In addition, Simpson's index was evaluated to discriminate the power of the methods. Results: OPP 16 primer and composite analysis proved to be superior compared to other REP-PCR typing methods. The best discriminatory index was observed when GTG 5 (0.92) and OPP 16 (0.85) primers were used alone or combined with RAPD-PCR and BOX-PCR (0.99). Conclusion: This study indicated that OPP 16 and GTG 5 primers provide suitable molecular typing results for the discrimination of the genetic relationship among Salmonella spp. isolates and may be useful for epidemiological studies.

Molecular identification of fluoroquinolone resistance in Salmonella spp. isolated from broiler farms and human samples obtained from two regions in Colombia

“…Our research group has reported the antibiotic resistance patterns of Salmonella spp. in poultry production as well as in other sectors in Colombia, as characterized by different genotyping methods [10][11][12][13][14][15]. However, these studies did not address the molecular mechanisms associated with resistance to quinolones and fluoroquinolones.…”

Virulence Gene Properties and Phylogenetic Relationship of Salmonella Serotypes Isolated from Different Sources in North of Iran

“…RAPD-PCR has been extensively used to study the epidemiology and taxonomy of Enterobacteriaceae, including important human pathogens like Escherichia coli, Klebsiella pneumoniae, and Salmonella spp. It has also been employed to investigate the genetic diversity of these bacteria in various environmental niches, such as soil, water, and food (31)(32)(33). The results of genotyping isolates using RAPD-PCR showed that, although when calculating the performance of the genotyping method using the 1254 primer, Simpson's index shows a relatively respectable result, there was a significant relationship between RAPD genotype and Salmonella serotype, and 16 isolates (26.66%) could not be successfully genotyped using this method, which can be significant.…”

Genotyping of Salmonella enterica strains from animal and human origin using three molecular techniques

“…Noteworthily, the profiles assigned by the three genotyping methods and their combinations were able to describe a specific fingerprint for each serotype, agreeing with the previous serotyping of the isolates, and allowed us to describe intraserovar differentiations that are not perceivable with serotyping. Similarly, PCR-based genotyping methods have been previously used to differentiate Salmonella enterica strains at and below serotype level (7,25). However, our purpose is not to replace but to complement the traditional typing methods for Salmonella enterica to provide valuable data regarding the relationships within isolates, information that can be used in epidemiological surveillance.…”