Interview: Nanopore sequencing: the missing puzzle piece in molecular identification

Ahmed Abd El Wahed is a scientist at the Institute of Animal Hygiene, University of Leipzig, and established a mobile suitcase laboratory for the rapid detection of viruses, bacteria and parasites in low resource settings using nanopore sequencing. We caught up with Ahmed to discuss his current research interests, how he become interested in genomics and the impact long-read sequencing is having on his research.

Dr. Ahmed Abd El Wahed presented a webinar: Nanopore sequencing: the missing puzzle piece in molecular identification with Technology Networks on Tuesday 5th May.

What are your current research interests?

The necessary equipment for detection of pathogens is available only in few central laboratories, which are less accessible in low resource settings. Transport conditions of samples are poor, which can sometimes lead to unreliable results. My main research focus is to develop portable, simple, and rapid point of need detection methods, and I am also interested in mapping the immune footprint after infection or vaccination.

What first ignited your interest in genomics?

It is amazing to see that four letters can constitute unique sequences, coding for basic materials needed in all chemical reactions in our biology and define who we are. My interest in molecular biology started with the involvement in developing rapid assays using isothermal amplification technologies, which enables us to establish a mobile suitcase lab for rapid detection of emerging and neglected diseases.

Can you tell us more about how long-read sequencing technology is changing your field? How has it benefited your work?

Molecular amplification assays rely on having previous sequence knowledge of the pathogen genome. This can be avoided by implementing next generation sequencing, which can be applied to identify the pathogen responsible for the outbreak through sequencing all nucleic acids present in a sample extract. Sequencing data obtained can also potentially identify new agents or new variants of known agents. The portability of Oxford Nanopore devices facilitates sequencing in remote areas, so we are not facing the problem of sample deterioration or change in results due sample transportation over long distances. In short, the technology empowers unbiased data acquisition.

What have been the main challenges in your research and how have you approached them?

The current chemistry of sequencing is ideal, but data analysis can be an obstacle. We have overcome this by implementing offline BLAST search, which requires little bioinformatics background. Another issue is data protection because of the human genome background - of course our main interest is the genome of pathogens, but the background is a dilemma. Another issue is data storage, as nowadays we can get between 2-150 gigabyte of data per run. On one hand, this opens up an opportunity for in depth analysis and excellent coverage, but compressing the data and repository over long period of time is challenging.

What’s next for your research?

We are applying nanopore sequencing for the identification of animal species in meat. Currently, we have started two projects, one to determine the pathogen complex for diarrheal diseases in rural area and another for mapping the microbiome markers for the progress of chronic diseases.

What is your advice for someone getting started?

“Do not give up” is the main principle to achieve success. Your first sequence run might not be perfect, but the following runs will be. Johann Wolfgang von Goethe said, “We only see what we know”, but sequencing has taught us to start seeing what we did not know before, and this can only be achieved by applying various methods for analysis on the same set of sequence data. From the first moment, a definite goal must be set and collaboration between scientists from various discipline is a must.