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. 2019 Dec;12(12):1998-2006.
doi: 10.14202/vetworld.2019.1998-2006. Epub 2019 Dec 19.

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

Kelly Lozano-Villegas  1 , Roy Rodríguez-Hernández  2 , Iang Rondón-Barragán  1   2
Affiliations

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

Kelly Lozano-Villegas et al. Vet World. 2019 Dec.

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.

Keywords: dendrogram; serotyping; typing methods.

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Figures

Figure-1
Figure-1
Amplicon profile and phylogenetic tree from BOX-PCR of 50 Salmonella Enteritidis fingerprints showing the genetic relatedness of isolates (1-15) obtained from broiler farms in Santander (n=15), isolates (16-39) obtained from broiler farms in Tolima (n=24), and isolates (40-49) obtained from stool samples of people with gastroenteritis; clusters were obtained according to the arbitrary 90% cutoff value for grouping by genotype similarity.
Figure-2
Figure-2
Amplicon profile and phylogenetic tree from GTG 5 of 35 Salmonella Enteritidis fingerprints showing the genetic relatedness of isolates (16-39) obtained from broiler farms in Tolima (n=24) and isolates (40-49) obtained from stool samples of people with gastroenteritis; clusters were obtained according to the arbitrary 90% cutoff value for grouping by genotype similarity.
Figure-3
Figure-3
Amplicon profile and phylogenetic tree from OPB 15 of 35 Salmonella Enteritidis fingerprints showing the genetic relatedness of isolates (16-39) obtained from broiler farms in Tolima (n=24) and isolates (40-49) obtained from stool samples of people with gastroenteritis; clusters were obtained according to the arbitrary 90% cutoff value for grouping by genotype similarity.
Figure-4
Figure-4
Dendrogram of composite data set based on random amplification of polymorphic DNA and BOX primers. Thirty-five Salmonella Enteritidis fingerprints showing the genetic relatedness of isolates (16-39) obtained from broiler farms in Tolima (n=24) and isolates (40-49) obtained from stool samples of people with gastroenteritis; clusters were obtained according to the arbitrary 90% cutoff value for grouping by genotype similarity.
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