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Inhibition of enteropathogenic Escherichia coli biofilm formation by DNA aptamer

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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 OD570. 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.

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Acknowledgements

The authors would like to thank to Nurlaili Ekawati from Research Center for Biotechnology, Indonesian Institute of Science for her assistance in manuscript preparation.

Funding

This study was fully funded and supported by Research Center for Biotechnology, Indonesian Institute of Science by Prioritas Nasional (PN) Obat 2018–2019 scheme. And also funded by Lembaga Ilmu Pengetahuan Indonesia.

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Authors and Affiliations

  1. Research Center for Biotechnology, Indonesia Institute of Sciences (LIPI), Raya Bogor Street KM.46, Cibinong, Bogor, 16911, West Java, Indonesia

    Stery Brenda Oroh, Apon Zaenal Mustopa & Bugi Ratno Budiarto

  2. School of Biotechnology, IPB University, Bogor, Indonesia

    Stery Brenda Oroh & Sri Budiarti

  3. Indonesia Research Center for Bioresources and Biotechnology, IPB University, Bogor, Indonesia

    Sri Budiarti

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  1. Stery Brenda Oroh
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  2. Apon Zaenal Mustopa
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Correspondence to Apon Zaenal Mustopa.

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Oroh, S.B., Mustopa, A.Z., Budiarti, S. et al. Inhibition of enteropathogenic Escherichia coli biofilm formation by DNA aptamer. Mol Biol Rep 47, 7567–7573 (2020). https://doi.org/10.1007/s11033-020-05822-8

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