Dynamic time warping assessment and sensitive high resolution melting analysis for subtyping Salmonella isolates from the Northern Thailand
Author and article information
Abstract
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.
Cite this as
2019. Dynamic time warping assessment and sensitive high resolution melting analysis for subtyping Salmonella isolates from the Northern Thailand. PeerJ Preprints 7:e27664v1 https://doi.org/10.7287/peerj.preprints.27664v1Author comment
This is a submission to PeerJ for review.
Sections
Supplemental Information
Normalized Melt Relative Fluorescent Unit (RFU) data of 40 Salmonella isolates at the Northern Thailand during February 2018 to September 2019
Normalized melt curves generated from HRM were used to construct a dendrogram of hierarchical clustering, using DTW as a distance measure.
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Nuttachat Wisittipanit performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables.
Chaiwat Pulsrikarn performed the experiments.
Saranya Wutthiosot performed the experiments.
Sitthisak Pinmongkhonkul contributed reagents/materials/analysis tools.
Kritchai Poonchareon conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Field Study Permissions
The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):
Field experiments were approved by the IACUC of University of Phayao (project number 62-02-04-001)
Data Deposition
The following information was supplied regarding data availability:
Data is available at https://drive.google.com/drive/folders/138Kmpa95g-xc4GM43sQzFRUpw5nTNRry?usp=sharing
Funding
This work was funded by the University of Phayao Grant (NO: R020058217046) provided by the Thai government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
