September 1, 2022  |  Infectious disease research

Thwart food-borne contaminants with the unmatched accuracy of HiFi sequencing

Pill shaped bacterial cells

HiFi sequencing delivers the most accurate and comprehensive microbial sequence data possible to give food safety and public health professionals the clarity they need to better understand contaminants and make informed and timely decisions.

The sequencing technology of tomorrow – today

Finding causal links between specific microbial strains and food-borne illness can be a tremendous challenge for investigators when they only have access to outdated or incomplete sequence information on the suspect microbe. Due to inherent limitations in their chemistry and analysis, whole genome sequences (WGS) built with widely adopted short-read sequencing approaches can fall short in delivering the critical details needed to crack a case.

However, it does not have to be this way. The next generation of sequencing technology is already here: delivering data with a level of detail, length, and accuracy that could only be dreamed of in the past.

PacBio HiFi sequencing is that technology, and microbial genomes analyzed on the Sequel IIe system can reveal vital information on everything from the genetic mechanisms that drive virulence and pathogenicity, to those that enable an organism to persist in places like processing plants and food production facilities.

High stakes demand high accuracy

In early 2022, US national public health and food safety authorities detected a potential link between a series of Cronobacter sakazakii infections in babies and powdered infant formula (PIF) made by a major domestic producer. The suspected connection led to a shutdown of the production facility, straining already critically low stocks throughout the country.

Supply-chain disruptions created by incidents like this, and the duress and pressure that they place on families, underscores the value of complete, accurate, state-of-the art sequencing technologies like PacBio HiFi reads. Especially when phylogenetic links between isolates need to be determined with pinpoint accuracy and the resulting decisions about food safety need to be made swiftly.

C. sakazakii sequenced in extraordinary detail

To better understand food-borne contaminants like C. sakazakii and to share detailed information with the international community, Negrete et al. used HiFi microbial WGS to characterize two strains of C. sakazakii isolated from PIF manufacturing facilities in Europe that are phylogenetically similar to those found in powdered dairy production environments in the United States. In a publication describing their work, the team shared a wealth of cutting-edge data, including the chromosomal sequences for the two strains, as well as five plasmids and their associated gene annotations. Thanks to highly detailed HiFi data, the authors were able connect two plasmids with virulence and identified another as a conjugative plasmid that contained a phospholipase D gene, which is known to be a key virulence factor in multiple host-pathogen diseases.

A new standard in pathogen genomics

Studies like this beautifully demonstrate how the remarkable length and accuracy of HiFi sequencing has the potential to drive major advances in not only identifying microbial strains associated with food manufacturing (thanks to more accurate phylogenies built on more accurate sequences), but in our understanding of how adaptations like toxicity, virulence, and persistence can contribute to a microbe’s capacity to become a concerning contaminant.

HiFi sequencing delivers state-of-the-art data for generating gold-standard microbial reference genomes and solving some of the most important problems faced in food safety and public health microbiology.

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