Dr. Paul Rhodes on Why Bacterial Whole Genome Sequencing Can Transform Hospital Infection Control

Transmission detection is enabled by comparison of the whole genome sequence of bacterial infections: when two patient’s infection is connected by transmission, the sequences are almost identical.  What has prevented its use until now has been cost and throughput required for DNA sample preparation, sequencing and its bioinformatic analysis.  With the cost of sequencing itself now greatly reduced, Next Gen Diagnostics was formed by CEO Dr. Paul Rhodes to solve the last remaining bottlenecks: sample preparation and fully bioinformatic analysis.

Founded in 2017 by Dr. Paul Rhodes, NGD has built the world’s most automated bioinformatic system, capable of processing all the samples collected by a hospital, in real time, identifying infection transmission so that infection control teams have the information they need to take action. Their proprietary technology is transforming pathogen detection and outbreak investigation protocols.

“As sequencing becomes less and less costly, the superior depth of information available in whole genome sequence will inevitably increasingly become central to clinical microbiology,” says Rhodes. “This was clear 10 years ago. So we formed the company to engineer the automation of the whole process, and bring this vision to reality.”

The Evolution and Impact of WGS Technology

Unlike traditional infection control methods that are limited in their capabilities, whole genome sequencing enables rapid, accurate tracking of infectious diseases by examining a pathogen’s entire DNA sequence.

Bacterial whole genome sequencing can rapidly diagnose an infection by comparing its genetic profile to prior cases and elucidating genetic relatedness. Outbreak origin can subsequently be determined by using this method to identify transmission between patients in nearly real time, then allowing infection control teams to identify the common cause and intervene to stop further transmission and thereby prevent outbreak.

At Next Gen Diagnostics, key steps in the genomic analysis pipeline — like microfluidic specimen processing and downstream bioinformatic interpretation — are fully automated. This allows ultra-rapid sequencing and bioinformatic detection of transmission on an overnight, automated, low cost basis.

Upon completing biometrics, outbreak details including strain designation, transmission trajectory, antimicrobial resistance predictions, and associated genetic markers are displayed on the NGD dashboard for real-time infection monitoring and control.

“NGD has developed and put in use the field’s most advanced and complete bacterial [whole genome sequencing] bioinformatics suite, fully automating transmission detection, outbreak characterization, and antibiotic resistance prediction,” says Rhodes. “Our service’s rapid turnaround and uniquely low cost enable this information to be at the fingertips of infection control and infectious disease services fast enough to have a real-time impact on hospital infection control.”

Transforming Hospital Infection Control

Though hospitals furnish a critical line of defense against infectious diseases, and all hospitals have dedicated infection control teams determined to catch and prevent transmission, whole genome sequence comparison is the only way to detect that event. Now, because of its costs, it is only used to verify suspected transmission, most of which is simply missed, but with NGD’s technology it can and should be used to catch it.  The highly precise information available from bacterial whole genome sequence can then transform hospital epidemiology by delineating the genetic relatedness of antibiotic-resistant infections to trace transmission trajectories.

NGD’s automation of this genomic analysis workflow circumvents the specialized bioinformatics prowess typically needed, drastically accelerating outbreak investigation. Their streamlined systems integrate microfluidic specimen processing, sequencing, and bioinformatic interpretation to rapidly diagnose and profile bacterial infections as well as detect transmission between patients.

By comparing molecular fingerprints of nosocomial (originating in a hospital) pathogens, NGD technology enables infection prevention teams to swiftly track intra-hospital transmission events and identify reservoirs perpetuating outbreaks. Automating genotype-based mapping of transmission clusters is revolutionizing control of antibiotic resistance spread.

Case Study: Application in Clinical Settings

The efficacy of employing whole genome sequencing and Next Gen Diagnostics technology for outbreak mitigation was assessed in a 2018 pilot study at Addenbrooke’s Hospital in Cambridge, England.  The NGD team, with its collaborators, analyzed all drug resistant Staphylococcus Aureus (MRSA) samples collected, in nearly real time, providing continuous reports of detected transmission to infection control based on fully automated real-time transmission  analysis performed by the NGD platform.

The system enabled Addenbrooke’s Infection Control, to detect and then stop an ongoing outbreak unexpectedly originating in a diabetic foot ulcer treatment clinic. The outbreak detected and resulting actions by dedicated hospital staff led to a curtailment of spread, likely preventing several dozen further cases of MRSA transmission, at enormous savings of costs to the hospital and payer (by preventing extended stays required to treat MRSA infections, in addition to reduction in human suffering by already sick and in many cases elderly patients.

Thus, the NGD system delineated an outbreak that would have likely gone undetected using standard techniques. As concluded in the study, “The NGD platform provided rapid and accurate molecular data that.. supported infection control practices.”

Its automated whole genome analysis revealed transmission linkages between patients missed by conventional methods to pinpoint the events perpetuating pathogen spread. This pilot study highlights the power of sequence-driven diagnostics to curtail outbreaks within health care facilities.

Future Outlook

As whole genome sequencing continues transforming outbreak response strategies, Dr. Paul Rhodes believes NGD’s automated, economical platform will further increase the adoption of this lifesaving technology in hospitals globally.

Said Dr. Paul Rhodes, “Prospective sequencing is now, for the first time, practical as the new paradigm for the detection of transmission and prevention of outbreak in hospitals, where transmission of drug-resistant infection is a source of enormous cost, both financial, to the payers, and human, measured in needless mortality.”

With pandemic outbreaks underscoring the critical need for real-time infection tracking and response, NGD’s genomic epidemiology platform offers hope. Their sequencing analytics dashboard promises to intercept emerging hospital threats – containing tomorrow’s outbreaks before they explode into crises. Ultimately, NGD’s mission is a humane one – deploying 21st century biometrics to save lives.