In silico analysis for the design of PCR primer pairs for simultaneous identification Campylobacter jejuni and Campylobacter coli
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Author list: Rapeepat Tippayawong , Pattarapong Wenbap, Peerapon Chaisalee, Pravate Tuitemwong and Kooranee Tuitemwong
Publication year: 2022
Start page: 93
Abstract
Campylobacter jejuni/coli are the most common cause of bacterial gastroenteritis on human. The highest burden of illness caused by campylobacteriosis is seen in children under five. About 98% of broiler carcasses were contaminated with Campylobacter. Adherence is one of key virulence factors of these pathogens to invade host cells. CadF, or Campylobacter adhesion to fibronectin, gene encodes the fibronectin-binding protein. It is responsible for binding to fibronectin of the host epithelial cell for adherence. Rapid and accurate detection of this gene is important and much needed. The objective of this work was to electronically construct fibronectin-binding protein gene, cadF, highly specific for the detection of these causative agents, C. jejuni and C. coli. In this study, in silico analysis was used to identify potential PCR primers based on the cadF sequence of C. jejuni and C. coli for the species identification by PCR method. The cadF sequences were retrieved from NCBI (National Center for Biotechnology) and bioinformatics analysis was performed using several softwares including multiple sequence alignments (MSA), Uniprot, MEGA X and CLC Sequence Viewer 8 platforms. PCR simulation was conducted using Unipro UGENE to predict PCR products of each primer pairs based on cadF sequences of C. jenuni strain 2016-IZSVE-19-111250 and C. coli strain 2010D-7923. In total, 20 primer pairs specific for C. jenuni or C. coli could amplify corresponding PCR products as simulated by Unipro UGENE. It is evident that in Silico analysis technique has potential for the design of specific primers for PCR performance. Moreover, it is promising to construct effective cadF gene products before the more tedious and expensive wet laboratory testings especially when live target organisms are not available and, in many cases, in vivo and in vitro analyses are difficult or not possible.
Keywords
cadF gene, Campylobacter, In Silico Analysis