This article has been updated from a previous version to include corrected and additional information from TriCore.
NEW YORK (GenomeWeb) – TriCore Reference Laboratories is developing a 16S metagenomic assay that it believes will help improve quantitative detection of bacterial pathogens in hospitals and cut down on indirect financial costs.
The New Mexico-based company currently offers the assay in its home state and hopes to eventually make it more broadly available. Despite the test's high costs, TriCore believes that clinicians will push for implementation in hospitals because of its ability to quantify bacterial species in human samples, which could help them better determine the cause of infection and improve patient treatment.
Founded in 1998, TriCore is sponsored by the University of New Mexico Health Sciences Center and Presbyterian Healthcare Service, and serves as a clinical lab for both health systems. TriCore also has a commercial arm that provides testing services for other hospitals and clinics in New Mexico. According to Shaun Yang, TriCore's director of molecular infectious disease, the laboratory provides clinical services to a large portion of New Mexico's patient population. Yang is also an assistant professor of pathology at UNM.
TriCore has designed a 16S sequencing workflow to quantify the relative abundance of all bacteria identified in patient samples. Doctors seeking detailed information about their patient's condition would send a clinical sample to TriCore's central lab in Albuquerque, where technicians would perform a series of steps, including homogenization, DNA extraction, 16S sequencing, and quantitative computation.
Yang explained that TriCore uses PCR to amplify the the 16S ribosomal RNA gene fragment that is universal for all bacteria species. Then, by applying medium-throughput sequencing,the firm is able to provide a bigger picture of the bacterial population inside the patient's body.
At the Molecular Medicine Tri-Conference earlier this month, Yang shared some specific details on the workflow.
In the first four to five hours, technicians begin sample prep and run the 16S PCR assay. Over the second and third days, the team sets up library preparation and sequences the samples using Thermo Fisher's Ion PGM. Technicians then perform cloud-based analysis on samples to determine relative abundance.
In order to analyze and quantify sequenced samples, TriCore is working with Pathogenomix, a data-analysis firm that provides cloud-based analytical software. Pathogenomix's RipSeq sequence-based analysis allows the research team to download results with speciation within five minutes.
TriCore's assay can be used on a wide variety of body fluid samples, including cerebral spinal fluid, kidney infection fluids, and bronchoalveolar lavage. In addition, the assay can be used with solid samples such as necrotic tissue and white blood cells.
In terms of clinical sensitivity, TriCore's assay is "in the range of 10-100 bacteria/ml, depending on the species, which is slightly more sensitive than PCR, which is usually in the range of 100-1000 bacteria/ml," Yang added. He declined to comment on the test's specificity.
At the Molecular Medicine Tri-Conference, however, Yang provided a few case studies demonstrating how TriCore's assay could impact patient care.
In the first case study, a one-day-old neonate was diagnosed with seizures and respiratory failure. While a MRI showed a small focus of hemorrhage in the patient's brain, CSF and blood cultures did not find any bacterial infections. TriCore's 16S test, however, revealed a Streptococcus intermedius infection, demonstrating the test's clinical utility.
In a second case study, a 54-year-old male with a brain abscess was treated initially with various antibiotics. Culture results contained S. intermedius and Aggregatibacter aphrophilus. The clinicians ran a culture update and found mixed anaerobic flora. TriCore's 16S results found four different infections, including Fusobacterium and Capnocytophaga, demonstrating the test's ability to quantify total mixed bacterial species.
In an additional case study, an elderly patient with a chronic leg ulcer wound lived in a long-term care facility. TriCore's assay detected nine bacteria species with only one non-anaerobic bacteria, highlighting the test's ability to specify and quantify a patient's complex microbiome.
While TriCore's test is promising, it has implementation issues, including a high cost of $400 to $500 per test, barriers to insurance reimbursement, and a relatively long turnaround time.
Yang admitted that cost per sample may be steep for the end user, depending on the batch size of samples. The UNM and Presbyterian Healthcare Service hospitals pay for the direct cost of the test, so reimbursement is not a issue for TriCore.
The cost issue could be a challenge for hospitals outside of the New Mexico health system, though Yang believes the same direct pay model could work.
"If you perform the budgeting, you might see that it's a tremendously expensive test, and the administration would raise questions," he noted, but added that treatment and hospitalization could be shortened by two days with cost savings of up to $10,000. TriCore noted, however, that there is currently no data to support this.
The laboratory believes, though, that by being able to detect and quantify a large amount of bacterial species, clinicians will have a clearer view of what is affecting their patients and make better judgements for patient care.
In terms of turnaround time, Yang hypothesized that if TriCore can perform the test at least twice a week, then the turnaround time for results will be potentially less than three days. If TriCore's technicians only collect enough samples to perform the test once a week however, turnaround time will require a week at minimum, which Yang admits is not ideal for infectious diseases.
Yang said that TriCore hopes to launch its clinical test more broadly by the end of this year.
"We might focus on marketing opportunities that make [the test] available to groups around the country, but we want to initially focus on inpatient situations in the hospital setting," Yang added.
TriCore may apply funding and collaborate with clinicians in orthopedics and interventional radiology in order to perform small cost-benefit pilot studies for the assay.
Yang mentioned that one other lab at the University of Washington has developed a similar 16S metagenomics assay for bacterial detection. Yang believes that TriCore's assay distinguishes itself because of its ability to provide data about the relative abundance of bacterial species in patient samples.
While TriCore's assay uses 16S ribosomal metagenomics for detecting bacteria, other researchers have used a technique called shotgun sequencing in order to detect bacterial, viral, and parasitic infections. Because it samples only a bacterial portion, Yang highlights that the TriCore's test only needs about 500,000 reads per sample, which is in contrast to the 2 million to 10 million reads per sample needed for standard shotgun metagenomics.
In addition, shotgun sequencing is best used for infections at sterile sites and identifying mysterious pathogens, while 16S RNA sequencing is a better option for polymicrobial infections and microbiome profiling.