Dynamic time warping assessment and sensitive high resolution melting analysis for subtyping Salmonella isolates from the Northern Thailand

Background: Nontyphoidal Salmonella spp. transmitted through various routes are a major concern of food poisoning due to the consumption of contaminated food. Objective: To establish a molecular-based protocol for simple and rapid subtyping of Salmonella isolates from various sources. Materials and methods: Sensitive High-Resolution Melting-curve analysis (S-HRMa) and Dynamic Time Warping assessment (DTW) were applied for serotyping forty Salmonella spp. isolates from various origins and locations in seven provinces in the north of Thailand; the results were compared to those from conventional serotyping and ERIC- PCR. Results: HRM serotyping of forty Salmonella spp. initially produced fourteen melting-curves with two predominant clusters: C1 (n=18) and C2 (n=9). Applying S-HRMa and serogroups generated twenty-five sensitive clusters. Conventional serotyping revealed that cluster C1 and C2 comprised of six different Salmonella serotypes with S. Weltevradent (n=14) as the predominant one. The S-HRMa also suggested the possible subtyping in some serotypes. In addition, DTW was performed to cluster those forty Salmonella spp. into twenty-eight clusters, assigned into different four clades corresponding to S-HRMa. The two clustering methods indicated that the S. Weltevreden was the predominant subtype (DTW4-S1, n=6). Three ERIC clusters at 92% similarity index also corresponded to the results of those two clustering methods. With important and related epidemiological data, S. Derby and S. Monophasic were suggested to be related to the slaughterhouse and swine. In this study, the ERIC cluster 10 comprising two Salmonella isolates of S. Weltevraden suggested the transmission route was likely to be farm-to-farm in the same province. Conclusions: The DTW assessment and S-HRMa effectively increased the discrimatory power of clustering to the same level as that of ERIC - PCR and were a simple and rapid protocol to perform Salmonella subtyping for the epidemiological research.