HiFi sequencing fast-tracks antimicrobial resistance research: 2x publications in half the time

Learn how Ibrahim Bitar, PhD, replaced fragmented assemblies with complete, circularized plasmids in a single sequencing run, accelerating antimicrobial resistance research with the Revio and Vega systems.

Story at a glance

Ibrahim Bitar, PhD, Assistant Professor at Charles University and CEO of Gene Omics, is a leading microbiology researcher in the Czech Republic. Legacy short-read sequencing bottlenecked his work on antimicrobial resistance, producing hundreds of fragments and requiring up to 6 months of manual work to resolve a single plasmid. By adopting a PacBio HiFi long-read workflow, Ibrahim eliminated this bottleneck, shrank project timelines from months to a single sequencing run, and more than doubled his annual publications

A scientist’s mission to fight antimicrobial resistance

Ibrahim Bitar, PhD, is both a frontline researcher and an entrepreneur with a clear mission. As an Assistant Professor at Charles University and the CEO of his core facility, Gene Omics, he provides the Czech and European scientific community with today’s most advanced genomic tools.

His research focuses on tracking the dissemination of antibiotic resistance genes, which are often carried on plasmids—the mobile DNA elements that allow bacteria to share threatening traits. For Ibrahim, getting a complete, unambiguous picture of these plasmids is not just an academic goal; it is a public health necessity.

The Challenge: Overcoming fragmented assemblies from short-read sequencing

For any researcher in microbial genomics, short-read sequencing data presents a familiar and frustrating puzzle. The technology’s inability to read through long, highly repetitive sections of a genome—like the mobile genetic elements that carry antibiotic resistance genes—results in shattered assemblies. For Ibrahim, this meant that a single bacterial genome could be broken into what he described as “300 contigs per assembly.” This left him with a collection of disconnected data fragments instead of the complete chromosomes and plasmids he needed.

Assembling those 300 fragments into a single, accurate answer required a grueling manual process that became a significant bottleneck. Outlined below, their lengthy journey to resolve one plasmid was a true testament to his teams persistence:

• Complex plasmid extractions and transformations.
• Time-consuming S1 nuclease PFGE to estimate plasmid size.
• Custom probe design and hybridization experiments.
• The ultimate bottleneck of manual PCR gap-closing: designing dozens of primers, running countless PCRs, and using Sanger sequencing to fill every single gap.

The frustration of this workflow was immense. “Some of the plasmids took me 3 months to close. Some of them never closed,” Ibrahim recalls. “I had to design more than 60 primers, and this is… to close only the MDR region,” not even the entire plasmid. This delay was more than an academic inconvenience; it slowed down vital insights into how deadly pathogens, like the Acinetobacter baumannii superbug he studied, were spreading in hospitals and threatening lives.

The Solution: A HiFi long-read workflow for complete genome assembly

Convinced there had to be a better way, Ibrahim transitioned his lab—and eventually founded his company—on the power of PacBio HiFi sequencing. His technology journey began with an early adoption of the Sequel system and has since progressed to the high-throughput Revio system and the accessible benchtop Vega system. The shift was fundamental, moving from a hybrid, patchwork strategy to a HiFi long-read workflow.

HiFi sequencing provided the technical breakthrough. Its long, highly accurate reads span complex regions in a single pass, providing a complete sequence from the start. This allowed him to bypass the entire ordeal of manual gap-closing that had consumed so much of his team’s time. The transition was absolute. “We don’t use short reads anymore,” he states. “It’s all with long reads.”

The Results: What was the impact of a HiFi long-read workflow?

Adopting a HiFi long-read workflow had an immediate and transformative impact, turning months of frustration into days of discovery. The fragmented “hairball” assembly graphs produced by short reads were replaced by clean, fully resolved chromosomes and circularized plasmids, often from a single sequencing run. This leap in efficiency and data quality unlocked a new level of productivity and scientific clarity for his lab.

The tangible outcomes speak for themselves:

• Productivity multiplied: Ibrahim’s annual publication output more than doubled, jumping from an average of 6–7 papers per year to 14. “With HiFi, I can now skip 4-5 months of struggling with the data because everything is there now,” he says.
• Time savings from months to days: The process of closing a complex plasmid was reduced from a 3-to-6-month manual ordeal to a single sequencing run and an automated assembly pipeline.
• Complete, unambiguous answers: Instead of fragmented drafts, his team now generates fully resolved, publication-ready genomes that provide definitive insights into plasmid structure and the spread of antimicrobial resistance. “With PacBio, you can produce these nice closed chromosomes and plasmids, which you can use as a reference,” he explains.
• Superior data quality:The exceptional accuracy of HiFi reads became critical for his epidemiological work, where even a single nucleotide polymorphism (SNP) can define a new strain in an outbreak. “It’s really important to have very accurate reads in order to differentiate between strains in an outbreak,” Ibrahim notes. “This is what the HiFi reads can bring to the table.”
• Business growth and regional leadership:The success and expertise gained from this transition fueled the launch of Gene Omics, which is now a leading service provider bringing the power of HiFi sequencing to a previously underserved market across Central and Eastern Europe.

Future plans: Empowering a scientific community

Ibrahim’s vision is to make Gene Omics the definitive sequencing partner for Central and Eastern Europe, ensuring researchers are not held back by older technology. The clarity of HiFi long-read data has already allowed him to expand into new frontiers, from single-cell bacterial sequencing to complex human genetics.

His motivation is simple: “I wanted to bring this amazing technology to the market,” he says, “so that other people can have access to this amazing machine, and they can elevate their research and their results as well.”

His experience has given him a clear message for his peers. With falling costs, he argues the small price difference for short reads no longer justifies the immense downstream work and incomplete data.

Frequently Asked Questions (FAQ)

Is switching to a long-read workflow affordable for an academic lab?

Yes. Ibrahim notes that the introduction of benchtop systems like the PacBio Vega, with physical dimensions and a price point comparable to a MiSeq, makes the technology accessible for individual research groups. When factoring in the complete elimination of downstream labor, reagents, and time associated with manual gap-closing, the total cost to get a complete, definitive answer with HiFi sequencing is highly competitive.

How does PacBio HiFi data compare to other long-read technologies like ONT?

In his own comparative experiments, Ibrahim found that other platforms produced inconsistent results, sometimes losing small plasmids entirely. He considers PacBio a mature and reliable ecosystem—including software and expert support—a critical advantage for generating trustworthy data.

Why are complete plasmids so important in microbiology research?

Plasmids are the primary vehicles that bacteria use to share genes for antibiotic resistance and virulence, often between completely different species. If a plasmid assembly is fragmented, researchers cannot accurately track how resistance is spreading during an outbreak, identify the source of dangerous genes, or fully understand how superbugs evolve. A complete, closed plasmid provides a definitive, unambiguous map for this critical public health surveillance.

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