This summer, Dr. Tim Roloff-Hansin, co-leader of the Microbial Genomics Group at the Institute for Medical Microbiology (IMM), received a compact but powerful instrument in his laboratory on the University of Zurich campus. “My first impression of this instrument was that it was quite small,” he says. “We were expecting a bigger machine with the capabilities it was supposed to be able to do.”
Roloff and his team were among the first to receive the new Illumina MiSeq i100 as part of alpha testing before the product was officially announced in October. The MiSeq i100 is Illumina’s most innovative, accessible, and sustainable benchtop sequencer to date. Easy to use and set up. The team began its first sequence run within 30 minutes of installation.
“What impressed us most about this equipment was the short uptime,” says Roloff. Before receiving the MiSeq i100, it took his team 19 hours to complete a sequencing run on the NextSeq 1000. Now you can do the same thing in 7 hours and start doing it twice a day. “This will be a real game-changer in the field of medical microbiology, as we can easily perform sequencing in one day and report results within 24 hours.”
Roloff’s lab is one of 10 at IMM that performs whole genome sequencing of bacteria and fungi. Their research primarily focuses on the mechanisms that cause antibiotic resistance and how to develop new diagnostic tests and antibiotics. They are also a diagnostic laboratory serving clinics in the Zurich metropolitan area and throughout Switzerland.
Roloff said that while bacterial genomes are small and don’t require a lot of sequencing data, microbiology research is Explain that speed is still important.
“The reduced run time will significantly speed up the process and make whole genome sequencing even more relevant for microbial questions and diagnostics,” he says. “And given that we can get up to 100 million reads from the new machine, we can do many experiments in parallel, and we can do many bacterial genomes in parallel.”
MiSeq i100 enables index-first sequencing. This means that the user has information early in the run about which samples have sufficient index representations and how much data each sample produces. Roloff’s team can begin analyzing the aligned index in about two hours, while the remaining fragments are still being processed. “This gives us completely new possibilities to design library preparation methods around it,” Roloff says. In addition to preparing the library, they can research new diagnostic tests, which “will be of great interest in our environment.” He envisions developing a test that combines screening for specific bacteria with WGS. After two hours, you can tell if the bacteria you’re looking for is present. After 7 hours, the complete dataset from the run could be filtered to analyze the specific genome associated with that bacterium to determine the presence of things like antibiotic resistance genes and virulence factors.
“The impact of this new instrument on microbial diagnostic workflows using next-generation sequencing will be significant,” he says.
Roloff and his team were excited to hear that the MiSeq i100 reagents can be shipped and stored at room temperature. This will reduce waste and eliminate the need for freezers and refrigerators. This saves storage costs. “Each sequence is actually cheaper to run.”
Roloff says he didn’t realize that storing it at room temperature would provide additional flexibility. Avoiding thaw time means you can start running right away.
“Really, the problem in the past has been turnaround time,” he says. “During the COVID-19 crisis, we found that NGS results are always delayed and can only be analyzed retrospectively, for example, to determine which lineages are present.” Roloff’s lab’s workflow allows It took about a week to report the genome sequence data. “PCR was much faster.”
The significantly reduced turnaround time essentially eliminates reliance on PCR and other methods that only look at a single element and do not provide as much information.
A final advantage the team found with the MiSeq i100 with DRAGEN software is that the data quality is as good or better than expected, and the output can be viewed immediately on screen. “We don’t need bioinformaticians waiting for data and analyzing what is generated,” Roloff says. “Even technicians can directly report the results of a sequence run.
“With this new instrument, Illumina further enhances the value of benchtop sequencing for medical microbiology. Bacteria analysis is much faster, reagent storage is cheaper and easier, and ease of use reduces the need for sequencing.” Because it actually reduces the amount of personnel, service technicians, bioinformaticians, etc. We were very excited to be involved in testing this new equipment, but in reality, all of a sudden, I was really surprised by all the possibilities.
