RAPD and ERIC-PCR coupled with HRM for species identification of non-dysenteriae Shigella species; as a potential alternative method

BMC Research Notes

Afshin Akhondzadeh Basti¹  Ali Khanjari¹  Babak Pakbin²  Wolfram Manuel Brück³  Leila Azimi⁴  Abdollah Karimi⁴ 

[1] Department of Food Hygiene and Quality of Control, Faculty of Veterinary Medicine, University of Tehran, P.O. Box 14155-6453, Tehran, Iran;Department of Food Hygiene and Quality of Control, Faculty of Veterinary Medicine, University of Tehran, P.O. Box 14155-6453, Tehran, Iran;Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Sierre, Switzerland;Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Sierre, Switzerland;Pediatric Infections Research Center, Research Institute of Children’s Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran;

关键词: PCR-HRM;    Species identification;    Shigella;    Clinical samples;   

DOI  :  10.1186/s13104-021-05759-6

来源: Springer

【 摘 要 】

ObjectiveSpecies identification of Shigella isolates are so prominent for epidemiological studies and infection prevention strategies. We developed and evaluated RAPD and ERIC-PCR coupled with HRM for differentiation of non-dysenteriae Shigella species as potential alternative methods. After isolation of eighteen Shigella strains from faecal specimens collected from children under 2 years of age with diarrhea (n = 143), the species of the isolates were identified by slide agglutination assay. Also, species were identified using developed RAPD-PCR-HRM and ERIC-PCR-HRM techniques. Differentiation of the data sets was measured by principal component analysis as a dimension reduction method. Then, sensitivity and specificity of the methods were evaluated.ResultsWe found RAPD-PCR-HRM method with high sensitivity and specificity (100 and 85% respectively) to identify non-dysenteriae Shigella species in clinical specimens. However, sensitivity and specificity of ERIC-PCR-HRM were evaluated 33 and 46% respectively and significantly lower than that of RAPD-PCR-HRM assay. Regardless of inherent poor reproducibility of DNA fingerprinting-based methods, RAPD-PCR-HRM assay can be considered as a potential alternative method to identify non-dysenteriae species of Shigella in clinical specimens. As we observed in the current study, HRM technique is more rapid, inexpensive, and sensitive than gel electrophoresis method to characterize PCR amplicons.

【 授权许可】

CC BY