NEW YORK (GenomeWeb) – A US nonprofit combatting superbugs with a database of bacterial DNA profiles has recently expanded to become a global organization and gone Hollywood to raise visibility and awareness.
The Antibiotic Resistance Monitoring, Analysis, and Diagnostics Alliance, or ARMADA, is a global expansion of a consortium launched last year, led by Seattle-based ID Genomics under the auspices of a National Institutes of Health grant. Originally, the consortium included eight medical centers and research institutes in Seattle, Los Angeles, New York City, and Minneapolis. Now, operating under the ARMADA name, the consortium has expanded to include 50 clinical and academic institutions across 20 countries.
It has also expanded in scope with aims to solicit philanthropy funds to support the gathering of bacteria samples from physician offices and hospitals worldwide and from a broader set of sample types.
It will also gather swabs from healthy citizen scientists using self-collection kits, as well as non-human samples from veterinarians and environmental scientists. "That's how we can understand what superbugs are truly circulating in communities," the group's founder, Evgeni Sokurenko, said in an interview.
Samples will be subjected to genomic "fingerprinting," a rapid and inexpensive PCR-based method developed by ID Genomics that will allow the group to identify the type bacteria. This will be added and compared with a database that contains bacterial strain resistance information coupled with location data and information about outcomes and treatments that have worked on that strain.
According to Sokurenko, the real-time database — with retrospectively collected history that can be used prospectively — will ultimately become a diagnostic tool, whereby rapid fingerprinting at the point of care can be compared to the database in order to ID a particular bacterial strain, leading to more effective treatment decisions.
The technique is called clonal diagnosis of infectious diseases, Sokurenko said. Based on a fingerprint, a doctor can pull out all the relevant information about a bacterium from the database, such as "What this particular strain or its close relatives, what we call a clonal group, have done in thousands and thousands of other patients, what kind of treatment failed, what kind of treatment worked, and what kind of complications to expect," he said.
After all, "The bug is not coming from the moon every time it appears in a patient."
Using a reconnaissance approach to continuously update a real-time database "is a very new approach in infectious diseases," said Sokurenko.
ARMADA has also partnered with actor Bill Pullman, known for his roles in "Independence Day" and "Spaceballs," to aid in outreach and mobilize potential donors of strains and funds.
Pullman said in an email that the spokesperson role entails helping to spread the word about the growing threat of antibiotic resistance.
"I felt really compelled to get involved to try to make a difference now, before the dangers begin escalating," Pullman said, adding, "It’s a very serious issue facing all of us."
ARMADA aims to create a database of the "fingerprints" of bacterial strains, both normal and antibiotic resistant, as well as geospatial mapping information.
Sokurenko, who is also a professor of microbiology at the University of Washington, explained that ARMADA's core technology uses PCR to detect SNPs in a few regions of bacterial DNA and then compares these to a database, a method that is somewhat analogous to short tandem repeat analysis in human DNA profiling.
Earlier this year the group published a study showing how the group used this fingerprinting approach to proactively identify a strain of E. coli that appeared poised to develop into a pandemic.
Specifically, the group discovered that the E. coli ST1193 strain was spreading and suggested that it has pandemic potential because it is resistant to ciprofloxacin but responds to a less frequently prescribed drug, cephalosporin. The strain was discovered after fingerprinting 11,000 bacterial strains isolated from patients at nine medical centers who had blood, urine, bladder, or kidney infections, as previously reported. After fingerprinting, response to different antibiotics was determined, and the result was then linked to the geographical and historic data.
"Using just seven SNPs for which we determined presence or absence, we showed how well [the fingerprinting technology] predicts clonal group, and how those predictions could be used for selection of the right antibiotic," Sokurenko said.
Thus, even using the early iteration of the database, Sokurenko and his colleagues were able to see that "something new had emerged," he said. "We could compare it across the country and across different years and found that this is a very fast-expanding new super clone."
The core eight consortium members have now contributed and profiled more than 30,000 bacterial strains of over 10 different bacterial species. But the global strategy involves expanding the project and continuously updating the database, so that the reconnaissance strategy can be used for real-time surveillance of the bacterial strains circulating in a given community.
For this, samples from the reservoir of bacteria carried by healthy people are also required. "One of the biggest problems, if not actually the problem, is that resistant bacteria, or superbugs, are circulating around healthy people," Sokurenko said.
For example, some of these most notorious E. coli strains that cause the majority of resistant infections are carried by 5 to 7 percent of healthy individuals, he said. The same goes for strains of methicillin-resistant Staphylococcus aureus strains.
"We are carriers of these bugs … and [resistant infections] are actually, in most cases, coming from healthy individuals," Sokurenko said.
There are projects that have a somewhat similar approach – the Global Virome Project for viruses, or the surveillance of samples from sick soldiers that is conducted at Walter Reed Army Institute of Research, for example, or even various oncology-related biobanks. But to build a bacterial database and continuously surveil the circulating microbial community for superbugs appears to be a novel approach. At this time, "No such database exists," Sokurenko said.
The spokesperson gambit
Sokurenko credits the overarching idea of bringing on a spokesperson to a conference presentation by a National Institutes of Health representative, who argued that the message that there's an epidemic of antibiotic overuse and increasing levels of resistance is not effectively getting across to the public.
"He said, to reach the public we need to have a celebrity, and we don't have one, not a single celebrity has stepped in," Sokurenko said. A celebrity can help amplify the message that people need to work on their own behavior and their expectations of antibiotics, for example, to support stewardship, he said.
Indeed, according to the website of an entertainment agent who specializes in "connecting Hollywood and healthcare" in order to form long-term spokesperson partnerships, mostly in the pharma domain, "Matching a familiar face to a health issue and brand can boost product awareness and create an emotional connection" with an audience.
In ARMADA's case, the connection with Pullman didn't go through an agent — it was more kismet than matchmaking. Sokurenko teaches microbiology at a satellite UW Medical School location in Montana, where he happened to meet Bill Pullman's brother, who is an infectious diseases specialist there.
Pullman's family also includes other healthcare professionals, so he was personally interested in the problem, and, "He has an insight that maybe most other celebrities might not have into the urgency," Sokurenko said.
Now, Pullman plans to embrace this new spokesperson role. Theoretically, when someone with celebrity status weighs in, the public tends to listen more closely, Pullman said.
"As a lay-person, I hope to help convey the bottom-line information that is shared by the team of passionate scientists and physicians ... supporting ARMADA," Pullman said. "I hope my involvement will help raise the visibility of ARMADA and the life-changing work they are doing."