SuperbugsCreating “criminal database” of drug-resistant pathogens

Using a big-data approach and a network of hospitals and clinical laboratories around the world, a new non-profit initiative aims to create a comprehensive “criminal database” of antibiotic-resistant bacterial strains that can be recognized by their genetic fingerprint.

The Antibiotic Resistance Monitoring, Analysis and Diagnostics Alliance (ARMADA) will create this global biobank of bacterial strains by collecting bacterial isolates from hospitals, doctor’s offices, clinical labs, and veterinary sources and then analyzing them to understand their resistance profiles, their genetic identity, and their epidemiological history. The idea behind ARMADA is to help researchers and clinicians understand which strains of bacteria are spreading through the healthcare system and where they are spreading, to identify which strains are drug-resistant or virulent, and to find the genetic markers that give them away.

CIDRAP reports that ARMADA, a project of the nonprofit Hopewell Fund, will use the technology and expertise of ID Genomics, a Seattle-based diagnostics company, to build the database and characterize the bacterial strains through their genetic fingerprints. ID Genomics has developed a diagnostic technology that, instead of analyzing the entire genome of a pathogen, looks for certain “barcode” genes that can be used to identify the genetic fingerprint of a bacterial strain.

According to Evgeni Sokurenko, ARMADA advisory board member and co-founder of ID Genomics, ARMADA will help researchers identify the important bacterial crime families—the clonal groups that are multidrug-resistant, spread quickly, and cause severe illness. “Just based on certain barcode genes, we’ll get an idea of which clonal group the bacteria belongs to,” Sokurenko, who’s also a professor of microbiology at the University of Washington School of Medicine, told CIDRAP News.

Combining surveillance, diagnostics
The ARMADA concept builds off proof-of-principle research, funded by the National Institutes of Health, in which Sokurenko and colleagues from clinical laboratories in four US cities are analyzing more than 20,000 clinical isolates of over 10 different bacterial species. In a recent study published in Clinical Infectious Diseases, they reported that barcode analysis of more than 6,000 Escherichia coli isolates from bloodstream and urinary tract infections revealed the rise of a new multidrug-resistant E coli clonal group, ST1193, that has seen a dramatic increase in prevalence in recent years.

“We recognized this strain by using its fingerprints, and we realized there’s been a significant shift in its prevalence,” Sokurenko said. Prior to this study, isolation of E coli ST1193 had only been reported at a few hospitals around the world. Now, researchers and health officials know that this superbug, which was found to be 100 percent resistant to ciprofloxacin, is on the rise, and may be able to do something to stop its spread.

While building a database of dangerous bacterial strains will be helpful for surveillance and for researchers working on antibiotic development, the ultimate goal of ARMADA is to translate this knowledge into clinical action, in real time, through the development of rapid diagnostic tests that can quickly identify these dangerous bacterial strains and guide appropriate antibiotic therapy. ID Genomics is currently developing its barcode technology into a rapid test targeting urinary tract infections, but Sokurenko said the ARMADA database will be open to other researchers working on rapid diagnostics.

“People could come up with even better tests,” he said.

Sokurenko also envisions that diagnostic tests will be able to feed information back into the database and keep it constantly updated.

“The idea is to combine surveillance and diagnostics,” said Sokurenko. “Surveillance works for diagnostics, and diagnostics feeds back to surveillance.”

Although ARMADA is just getting started, 50 clinical and academic institutions have agreed to join the effort. The group is currently raising money to establish the infrastructure and start strain analysis, and is seeking additional isolates from hospitals, clinical labs, doctors, and veterinarians.