Inhibition of enteropathogenic Escherichia coli biofilm formation by DNA aptamer
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ORIGINAL ARTICLE
Inhibition of enteropathogenic Escherichia coli biofilm formation by DNA aptamer Stery Brenda Oroh1,2 · Apon Zaenal Mustopa1 · Sri Budiarti2,3 · Bugi Ratno Budiarto1 Received: 18 June 2020 / Accepted: 5 September 2020 © Springer Nature B.V. 2020
Abstract Enteropathogenic Escherichia coli (EPEC) is a bioagent that causes diarrhea through the formation of biofilm. The recalcitrant of EPEC to the current conventional antibiotic treatment has grown a big concern in a way to find effective alternative inhibitors. Aptamers have been demonstrated to show the ability to kill the pathogenic bacteria through inhibition of biofilm formation. Therefore, this study aimed to investigate antibiofilm activities of six types of aptamers against EPEC K1.1 which was isolated from patients with diarrhea. Environmental conditions such as temperatures and pH which impacted on biofilm formation of EPEC K1.1 and also biofilm inhibition of aptamer on EPEC K1.1 were performed by counting the crystal violet formation in 96-well polystyrene microplates at O D570. The motility examination combined with qPCR were applied to prove the mechanism of aptamers inhibition on biofilm by targeting essential genes that involve biofilm formation. The result showed that by applying cut off value at 0.399, aptamer SELEX 10 Colony 5 exhibited the highest biofilm inhibition against EPEC K1.1 with an absorbance value of 0.126. Further analysis showed that this aptamer also was able to reduce the motility diameter of EPEC K1.1. The effect of this aptamer on EPEC K1.1 motility was confirmed by qPCR where the mRNA level of motB, csgA and lsrA gene reduced significantly compared to the untreated group. Aptamer SELEX 10 Colony 5 was able to inhibit biofilm formation through interfering the motility ability of EPEC K1.1 and also by reducing the mRNA level of biofilm formation-related genes. This study provides evidences that aptamer is effective and promising for both antibiofilm of EPEC K1.1 and alternative treatment of diarrhea. Keywords Aptamer · Biofilm · Diarrhea · Enteropathogenic Escherichia coli K1.1
Introduction Diarrhea is an infectious disease found as the second highest cause of death in children below 5 years and ranked as eighth of top cause mortality of the total world population [1]. Health research report on Indonesian resident (Riset Kesehatan Dasar/Riskesdas) in 2018 shows that diarrhea was confirmed as one of contagious disease with highest prevalence number [2]. Enteropathogenic Escherichia coli (EPEC) is one of bacteria causing diarrhea in developing * Apon Zaenal Mustopa [email protected] 1
Research Center for Biotechnology, Indonesia Institute of Sciences (LIPI), Raya Bogor Street KM.46, Cibinong, Bogor 16911, West Java, Indonesia
2
School of Biotechnology, IPB University, Bogor, Indonesia
3
Indonesia Research Center for Bioresources and Biotechnology, IPB University, Bogor, Indonesia
countries [3]. The EPEC K1.1 was found in feces of total 55% diarrhea patients [4]. Its attachment to small intestine
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