Bacterial Genetics and Genomics book Discussion Topic: Chapter 11, question 14.
Last week I attended the Festival of Genomics in London. These are excellent events, run by Front Line Genomics and due to the support of many sponsors, they are free to attend. Going to the Festival of Genomics is an excellent opportunity to hear some outstanding talks about current research in the field, speak to vendors supporting genomic technologies, and network.
One of the most exciting things I saw was the Oxford Nanopore sequencer that fits in the palm of your hand. As described in my book, Bacterial Genetics and Genomics, nanopore sequencing can directly read the sequence of the DNA strand. This new equipment is the MinION Mk1C and combines the previous MinION, which was about the size of a big USB stick, and the computing of a standard laptop needed to run the MinION. The MinION Mk1C eliminates the need for a laptop, which means the whole sequencer can easily go in a small bag or the pocket of your cargo pants trousers. When doing field work, such as traveling to areas of outbreaks and doing real-time epidemiology, reducing the amount of extra equipment is important.
Below is a Tweet I sent out at the Festival of Genomics, which includes a video of the MinION Mk1C. As you watch the video, along the bottom of the device is the flowcell, where the sequencing is happening. The screen is showing the status of the sequencing in real-time. When the video pans to the left, you will see the standard MinION device, which holds one flowcell and via USB plugs into a laptop to run. All the computing power and software needed for sequencing and analysis is available on this one device.
In speaking to the Oxford Nanopore representatives at the Festival of Genomics, I was told that they have also miniaturized and simplified the sample preparation process with the VolTRAX system, which is about the size of the MinION and USB powered. Of course, all of the sequencing and sample preparation will require electricity, but I was told that if there aren’t any outlets available in the field location, the devices will run on powerpacks. So, truly portable, small sequencing is in the palm of our hands.
Although the MinION Mk1C has only recently become available to purchase, the technology behind it has been in the MinION and other Oxford Nanopore systems for a few years now. There are many papers that have used this technology to address bacterial epidemiology, which is Discussion Topic question 14 for Chapter 11. In addition to my general tips distributed with the book, for this question, if you are interested in application of nanopore sequencing, go to the Oxford Nanopore web site and check out their Resource Centre with its listing of papers citing their technology. I particularly like this one by Leah W. Roberts et al. from Nature Communications 2020 describing use of three types of whole genome sequencing methods to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei. It is interesting to see both what they found in the analysis of the hospital outbreak and also how they used Illumina, Pacific Biosciences, and Oxford Nanopore data together to achieve their goals.