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Molecular Genetics / January 07, 2021 / by beaconlbs

Molecular Testing for Respiratory and Gastrointestinal Infections

Molecular diagnostic testing panels now available to clinicians, have greatly improved patient care, treatment, and allowed enhanced antimicrobial stewardship.

According to the World Health Organization (WHO), lower respiratory infections caused 3 million deaths in 2016. Additionally, diarrheal diseases caused 1.4 million deaths in that same year. Healthcare providers managing patients with respiratory and gastrointestinal infections rely upon their clinical expertise supported by laboratory testing to make accurate and life-saving decisions. An accurate patient diagnosis allows for a clinician to prescribe a specific anti-viral or antibacterial medicine that is suited for the infection. The result is antimicrobial stewardship: treating the patient with the optimum drug, dose, and duration. Without access to sensitive viral antigen detection methods such as immunofluorescence or nucleic acid amplification techniques, doctors may prescribe a broad empirical antimicrobial as a precaution, even if a viral infection is suspected. Fortunately, laboratory testing for respiratory and gastrointestinal infections has improved tremendously over the last decade.

Prior to molecular diagnostic panel technology, clinical labs would use rapid antigen testing. For example, Lateral Flow ImmunoAssay (LFIA), has proven versatile in its ability to detect infectious antigens produced in response to an infection. It has a rapid turn-around time (TAT), as soon as 10-15 minutes, depending on the manufacturer. However, a limitation is the inability of LFIA to detect low concentrations of antigen in a clinical specimen, which may lead to a potential false negative result. Sometimes this methodology is supplemented with a culture test for more information. Culture tests do not have a rapid TAT, thus possibly delaying diagnosis and ultimately medical intervention.

Molecular diagnostic testing panels now available to clinicians, have greatly improved patient care, treatment, and allowed enhanced antimicrobial stewardship. These molecular panels with reduced TAT and expanded pathogen detection, have vastly improved and evolved since the first molecular test for Influenza A/B was made commercially available in 2015.  Particularly FilmArray technology has met this need, which uses multiplex PCR to test for many viruses and bacteria simultaneously. The respiratory panel includes adenovirus, common coronaviruses (excluding SARS-CoV-2/COVD-19), rhinovirus, Influenza viruses, among others, in addition to B. parapertussis (IS1001) B. pertussis (ptxP) C. pneumoniae, and M. pneumoniae. The system is automated and requires minimal training from the technician running the assay compared to other advanced laboratory techniques. TAT is approximately 45 minutes per run, which consists of a single specimen. A limitation of this technology is the inability to batch specimens, which would increase efficiency. However, labs may purchase additional instrumentation if they desire to run more than one specimen at a time. Also, for point of care (POC) management, clinicians need answers for their patients as soon as possible. While high throughput lowers cost, it may be to the detriment of the individual patient who is waiting for a rapid diagnosis.

Luminex also offers a clinical respiratory infectious disease panel. The Luminex xTAG panel tests for multiple viral and bacterial infections simultaneously and has about a 2-hour TAT. Unlike FilmArray technology, the Luminex system is high throughput, and specimens may be batched, which lowers the cost per run. However, batching specimens may not be ideal in a POC environment, as stated previously. The Luminex xTAG technology sample preparation, nucleic acid extraction, etc., is more complicated compared to FilmArray. Consequently, Luminex xTAG requires more skilled or senior-level technicians to reliably and accurately perform the test.

Molecular Testing for Respiratory and Gastrointestinal Infections

FilmArray also has a gastrointestinal panel. Testing methodology is like the respiratory panel, but it tests for bacteria, parasites, and viruses that may be present in an intestinal tract infection. The test is performed on stool samples. Studies have demonstrated FilmArray improves TAT, decreases time to start treatment, and identified more types of pathogens compared to culture. Again, the gastrointestinal FilmArray panel is not a high-throughput test and specimens cannot be batched to increase efficiency. Likewise, Luminex xTAG has a gastrointestinal infectious disease panel, with similar benefits and limitations as the xTAG respiratory panel counterpart.

Molecular diagnostic testing for POC management not only contributes to better care for patients with respiratory or gastrointestinal infections, it optimizes resource utilization. Studies have shown that molecular diagnostic testing for respiratory infections may decrease unnecessary antibiotic use and lower the need for chest radiographs, which saves healthcare dollars, and improves antimicrobial stewardship.

Infectious disease management through POC includes diagnosis and a treatment plan. This is possible through diagnostic stewardship: selecting the right test for the patient, generating clinically relevant results at the right time to improve clinical care and conserve healthcare resources. Laboratory managers and administrators are tasked with optimizing laboratory operations in support of clinicians so patients receive the best possible care. As reviewed in this article, molecular diagnostic panels for respiratory and gastrointestinal infections have been valuable tools to the clinicians caring for their patients.

As current technologies improve and new technologies become clinically available, it is important that these tests demonstrate clinical utility, which is the ability of a test to prevent or ameliorate adverse health outcomes. The literature supports the clinical utility of molecular diagnostic testing for respiratory and gastrointestinal infections. However, cost must also be considered, which may include instrumentation, reagents, supplies, labor, and potential reimbursement by payers, among other variables. Indeed, current technologies will continue to evolve, new technologies will be developed, and improved lab utilization and management, all have the aim for ideal patient care and optimal diagnostic and antimicrobial stewardship.

References:

  1. https://www.who.int/news-room/fact-sheets/detail/the-top-10-causes-of-death
  2. William Check http://www.captodayonline.com/Archives/0412/0412a_respiratory_virus.html
  3. Messacar et al. Implementation of Rapid Molecular Infectious Disease Diagnostics: The Role of Diagnostic and Antimicrobial Stewardship. PMID: 28031432. DOI:1128/JCM.02264-16
  4. Leber et al. Multicenter Evaluation of BioFire FilmArray Respiratory Panel 2 for Detection of Viruses and Bacteria in Nasopharyngeal Swab Samples. PMID: 29593057. DOI:1128/JCM.01945-17
  5. Kozel and Burnham-Marusich. Point-of-Care Testing for Infectious Diseases: Past, Present, and Future. PMID: 28539345. DOI: 10.1128/JCM.00476-17
  6. Bienvenu et al. Early diagnosis of celiac disease in IgA deficient children: contribution of a point-of-care test. PMID: 25376178. DOI: 10.1186/1471-230X-14-186.
  7. Subramony et al. Impact of Multiplex Polymerase Chain Reaction Testing for Respiratory Pathogens on Healthcare Resource Utilization for Pediatric Inpatients. PMID: 27039227. DOI: 10.1016/j.jpeds.2016.02.050
  8. Cybulski et al. Clinical Impact of a Multiplex Gastrointestinal Polymerase Chain Reaction Panel in Patients with Acute Gastroenteritis. PMID: 29697761. DOI: 10.1093/cid/ciy357
  9. Buss et al. Multicenter Evaluation of the BioFire FilmArray Gastrointestinal Panel for Etiologic Diagnosis of Infectious Gastroenteritis. PMID: 25588652. DOI: 10.1128/JCM.02674-14
  10. Grosse SD, Khoury MJ. What is the clinical utility of genetic testing? Genet Med. 2006; 8:448–450. PMID: 16845278. DOI: 10.1097/01.gim.0000227935. 26763.c6
  11. Ty Hang Et al. Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam. PMID: 29503874. doi: 10.12688/wellcomeopenres.12429.2
  12. Leva et al. Diagnostic performance of the Luminex xTAG gastrointestinal pathogens panel to detect rotavirus in Ghanaian children with and without diarrhea. PMID: 27473598. DOI: 10.1186/s12985-016-0588-1
  13. Doron and Davidson. Antimicrobial Stewardship. PMID: 22033257. doi: 10.4065/mcp.2011.0358
  14. Echavarría et al. Clinical impact of rapid molecular detection of respiratory pathogens in patients with acute respiratory infection. PMID: 30267999. DOI: 10.1016/j.jcv.2018.09.009
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