Lab Week

New test in Microbiology – Biofire Blood Culture ID

New Rapid Diagnostic Testing for Bloodstream Infections

Anna Maria Romanelli, Ph.D., Medical Director of Clinical Microbiology Laboratory

Background:

Bloodstream infections are a leading cause of morbidity and mortality in the United States [1]. The timely identification of blood borne pathogens and the selection of appropriate antimicrobial therapy can significantly improve clinical outcomes.

At the UC Davis Clinical Microbiology Laboratory, blood cultures are continuously monitored by an automated BACTEC FX blood culture instrument. Blood culture bottles are incubated for a total of 5 days and continuously checked by the instrument every 10 minutes for the growth of organisms. If growth is detected, a Gram stain will be performed from the positive blood culture and the clinician will be notified by a Clinical Laboratory Scientist of the results. Our current practice for organism identification from positive blood cultures relies on the sub-culturing of isolates followed by identification and susceptibility testing via MALDI-TOF and BD Phoenix systems, respectively. Blood culture identification by our current method is reported within in 48-72 hours or potentially longer, depending on the organism’s growth characteristics, from the initial positive Gram stain.

Laboratory Best Practice:

The UC Davis Clinical Microbiology Laboratory has completed the validation for the BioFire FilmArray Blood Culture Identification (BCID) Panel. The BCID Panel is a qualitative nucleic acid-based PCR test that can identify a panel of bacterial and fungal pathogens commonly associated with bloodstream infections, as well as detect antimicrobial resistance genes from positive blood culture samples [2]. The performance characteristics of the BCID Panel show an overall sensitivity of 98% and specificity of 99.9% [3]. The test’s high clinical sensitivity and specificity have been supported by several additional studies [4-6].

The following 27 targets will be tested by the BCID Panel:

The BCID Panel will improve our practice for blood culture identification. The test will be integrated into the current workflow at the point when new positive blood cultures are detected. After being flagged as positive by the blood culture instrument and examined on Gram stain by a Clinical Laboratory Scientist, a sample will be drawn directly from the blood culture bottle and tested with the BCID panel on a BioFire FilmArray Torch instrument. The BCID Panel will provide results within 2 hours of a new positive blood culture, in advance of confirmatory identification and susceptibility testing of sub-cultured isolates. The rapid identification of organisms and antimicrobial resistance genes by the BCID Panel will decrease turnaround time to diagnosis and allow for earlier, targeted antimicrobial therapy. Antimicrobial stewardship intervention will be built in through the laboratory’s result reporting. Reports for the BCID panel will provide comments that will aid interpretation of results for antimicrobial resistance genes if detected.

As shown in prior studies, rapid diagnosis with the BCID Panel in combination with antimicrobial stewardship has shown shorter times from blood culture collection to organism identification and shorter times to effective, narrowed therapy when compared to control groups [7, 8]. In addition, this approach has resulted in shorter times to antimicrobial de-escalation and higher rates of de-escalation. Given the demonstrated success of the test, our goal with incorporating the BCID Panel is to follow suit and improve upon bloodstream infection testing and management for our patients. By providing rapid identification and enabling earlier optimization of antimicrobial therapy, we may see benefits such as shortened hospital length of stay and lower healthcare costs overall.

However, as with all laboratory tests, the BCID Panel will carry certain limitations and a brief overview is provided in the following discussion [2]. As a test that is not all-inclusive, the BCID panel will not detect organisms outside of the BCID panel of 27 targets (see above table for test targets. Finally, a negative result does not exclude the possibility of a bloodstream infection, as it may be due to causes including sequence variation in targeted regions, the presence of inhibitors and interfering substances, organism levels below the test’s limit of detection, or an infection caused by an organism not detected by the panel. Results from this test will need to be correlated with standard identification and susceptibility testing of sub-cultured isolates in addition to the clinical history, epidemiological data, and other data available to the clinician.

Prior to its implementation, the performance characteristics of the BCID Panel must be verified to confirm the new test’s suitability for use within the UC Davis Health System. This ongoing process has entailed extensive testing of non-clinical control organisms and clinical patient specimens in comparison to reference methods. Following the completion of validation, the next steps include developing standard operating procedures and training personnel for use.

The UC Davis Clinical Microbiology Laboratory is also currently validating the BioFire FilmArray Gastrointestinal (GI) Panel, which, like the BCID panel, is run on the BioFire FilmArray Torch system and will test for 22 total targets of enteric infection including bacteria, viruses, and parasites [9]. The GI panel will similarly provide rapid identification within 2 hours and stands to offer clinical benefits such as decreased number of tests per patient, turnaround time to diagnosis, and hospital length of stay.

Bottom Line:

The BCID panel will improve upon our current practice for blood culture identification. The BCID panel will rapidly test for 27 targets within hours of detection of positive blood cultures. The test allows for decreased turnaround time to identification and susceptibility results, which, together with antimicrobial stewardship, will lead to more rapid implementation of targeted treatment for patients, shortened hospital length of stay, and lower healthcare costs overall.

The BioFire FilmArray Gastrointestinal (GI) Panel is also currently being validated by our laboratory. Like the BCID panel, the GI panel will be run on the BioFire FilmArray Torch system and will also be implemented in the near future.

References:

1. Bearman GM, Wenzel RP. Bacteremias: a leading cause of death. Arch Med Res. 2005;36:646–659.
2. FilmArray Blood Culture Identification Panel (BCID) Instruction Booklet (RFIT-PRT-0369-02). BioFire Diagnostics.
3. Aggregated Prospective Performance from the FilmArray® Blood Culture Identification Panel Clinical Trial. Data on File, BioFire Diagnostics.
4. Blaschke AJ, Heyrend C, Byington CL, Fisher MA, Barker E, Garrone NF, Thatcher SA, Pavia AT, Barney T, Alger GD, Daly JA, Ririe KM, Ota I, Poritz MA. Rapid identification of pathogens from positive blood cultures by multiplex polymerase chain reaction using the FilmArray system. Diagn Microbiol Infect Dis. 2012;74:349–355.
5. Altun O, Almuhayawi M, Ullberg M, Ozenci V. Clinical evaluation of the FilmArray blood culture identification panel in identification of bacteria and yeasts from positive blood culture bottles. J Clin Microbiol. 2013;51:4130-4136.
6. Salimnia H, Fairfax MR, Lephart PR, Schreckenberger P, DesJarlais SM, Johnson JK, Robinson G, Carroll KC, Greer A, Morgan M, Chan R, Loeffelholz M, Valencia-Shelton F, Jenkins S, Schuetz AN, Daly JA, Barney T, Hemmert A, Kanack KJ. Evaluation of the Filmarray blood culture identification panel: results of a multicenter controlled trial. J Clin Microbiol 2016;54:687–698.
7. Banerjee R, Teng CB, Cunningham SA, Ihde SM, Steckelberg JM, Moriarty JP, Shah ND, Mandrekar JN, Patel R. Randomized trial of rapid multiplex polymerase chain reaction–based blood culture identification and susceptibility testing. Clin Infect Dis 2015;61:1071–1080.
8. MacVane SH, Nolte FS. Benefits of adding a rapid PCR-based blood culture identification panel to an established antimicrobial stewardship program. J Clin Microbiol 2016;54:2455–2463.
9. FilmArray Gastrointestinal Panel (GI) Instruction Booklet (RFIT-PRT-0143-04). BioFire Diagnostics.

Partnership with ED & Lab – Public Health Screening

Laboratory Implementation of an Emergency Department HIV/HCV Screening Workflow to Minimize Re-Testing Related Visits
Nam K. Tran, Ph.D., HCLD (ABB), FACB
Scott Bainbridge, CLS
Larissa May, M.D.

Introduction: Human immunodeficiency virus (HIV) and hepatitis C virus (HCV) remains a significant public health problem in the United States. About 40,000 new cases of HIV are reported each year.¹ Similarly, an estimated 41,200 HCV infection cases are believed to occur annually.² For both infections, advancements in anti-viral therapy has provided patients with the opportunity to lead normal lives. Current treatment for HCV infection can now decrease viral load below the detection limit of modern assays – potentially “curing” them of the disease. Unfortunately, not all patients receive HIV/HCV screening due to a variety of reasons including lack of medical insurance. In 2018, as part of an Emergency Department (ED) led program³, the UC Davis Special Chemistry Laboratory Section established a modified HIV/HCV order to provide same day HIV/HCV screening and enable follow-up testing for ED patients without requiring them to return for a visit. The ultimate goal of this program is to improve patient access to care.

Overview of HIV/HCV Testing at UC Davis Health: Both HIV and HCV testing have evolved significantly over the last decade.^4,5 For HIV testing, the UC Davis Special Chemistry Laboratory employs a 4^th generation test that can detect both p24 antigen and the patient antibodies targeting HIV-1 and HIV-2. Previous 3^rd generation tests could only detect HIV-1/2 antibodies. The advantage of p24 antigen lies in its ability to detect early (~10 days earlier) infections (i.e., before the body produces antibodies against HIV). This laboratory-based 4^th generation HIV test is complemented by a rapid 4th generation test performed in the Pavilion Laboratory for cases of workplace exposure (i.e., needlestick) and emergency testing of unscreened mothers. It must be noted that the rapid test is used for emergencies only since the Special Chemistry test provides better analytical performance. For HCV testing, we utilized a high-performance antibody test on the same Special Chemistry Laboratory platform. In the end, screen positive HIV and/or HCV results prompt additional testing based on Center for Disease Control and Prevention (CDC) guidelines. In brief, a positive screening result for HIV would require confirmatory testing. If the confirmatory result is negative/indeterminant, molecular testing is required. For reactive HCV screens, following up molecular testing is also required.

New ED Workflow: Prior to this new program, HIV confirmatory negative/indeterminant results, and HCV reactive results required patients to return for a new blood draw. Unfortunately, this workflow is not compatible for ED workflow and uninsured patients may not be able to return for another visit. The joint effort by the Special Chemistry Laboratory and the Pavilion Laboratory developed a new workflow and test order to obtain two specimen samples at the same time for ED patients. This solution enabled the screening test to be performed on the same day, and if results indicated a possible infection, the second specimen could be immediately used for molecular testing.

Impact at UC Davis: The new HIV/HCV workflow has enabled the ED to identify a large cohort of patients that would not have been screened. Recent data suggest the HIV infection rates in the Sacramento area are also higher compared to other Northern California hospitals.

References

1. Centers for Disease Control and Prevention website: Accessed on April 9, 2019.
2. Centers for Disease Control and Prevention website: Accessed on April 9, 2019.
3. UC Davis Health website: Accessed on April 9, 2019.
4. Alexander TS. Human immunodeficiency virus diagnostic testing: 30 years of evolution. Clin Vaccine Immunol 2016;23:249-253.
5. Peeling RW, Boeras DI, Marinucci F, et al. The future of viral hepatitis testing: innovations in testing technologies and approaches. BMC Infect Dis 2017;17:699.

How POCT impacts hospital workflows?

The Point-of-Care Testing Team at UC Davis: Just the Tip of the Iceberg!
Nam K. Tran, Ph.D., HCLD (ABB), FACB
Shelley Gillott, CLS
Stacy Yee, CLS

Introduction: Point-of-care (POC) testing is defined as medical testing at or near the site of patient care.¹ Urine dipsticks and glucose meters are common examples of POC tests. At UC Davis Health, there are over 17 different types of POC tests used by over 3,000 operators in the emergency department (ED), operating rooms (OR), intensive care units (ICU), and various non-critical care units and clinics. Tests used at UC Davis range from simple urine dipsticks all the way to molecular pathogen detection methods with thousands of POC tests are performed on a monthly basis. In the end, the use of POC testing provides means for healthcare providers to quickly screen and manage a variety of diseases. However, healthcare providers only see the proverbial “tip of the iceberg” when it comes to POC testing. Significant infrastructure must be in place to provide safe and high quality POC testing at any institution.

Regulatory Considerations: All laboratory testing, including POC devices fall under the Centers for Medicare and Medicaid Services (CMS) Clinical Laboratory Improvement Amendment (CLIA).² This mechanism defines laboratory testing as waived or non-waived.³ Non-waived tests are further divided into moderate and highly complex devices. Point-of-care testing spans the spectrum of waived and non-waived devices, with waived testing being the most common. Waived devices are often attributed to be “simple to use” and/or “not likely to cause harm”, while more non-waived devices require additional steps and training due to the potential risk if an incorrect measurement occurs.

Laboratory Responsibility: Under CLIA, a hospital laboratory must approve and determine the performance of any type of test regardless of their waived status.^2,3 To this end, clinical laboratory scientists rigorously evaluate any new test that is considered for use. Furthermore, training, quality control, calibration, test order, result reporting requirements must be met for every device and operator.

The rationale for all these quality measures can be found in numerous reported studies and the United States Food and Drug Administration (FDA) Manufacturer and User Defined Experience (MAUDE) database.⁴ Something as simple as a waived glucose meter has been attributed to >4,000 errors and injuries from 2004-2008—making glucose meters the most frequently cited medical testing device to cause harm in healthcare!⁵ In fact, in the first 7 months of 2018 alone the MAUDE database identified 10,287 adverse events across all glucose meters. Operator competency, is thus, critical to the safe operation of any POC device (and a Federal requirement). At UC Davis Health, the POC Testing team is responsible for ensuring all operators maintain annual competency for the variety of devices used across the health system. Therefore, the importance of laboratory regulation of POC testing is critical to patient safety.

Impact of POCT at UC Davis: Since 2014, UC Davis Health has seen a significant growth in POC testing. Beginning in the Summer of 2014, the Clinical Laboratory expanded POC testing as a designated Ebola Treatment Center. In the same year, UC Davis was part of a study that helped gain FDA approval of the first (and currently the only) glucose meter that could be safety used in critically ill patients.^6,7 This study resulted in our institution to adopt these glucose meters the year after which contributed to a significant reduction in hypoglycemia rates.^8,9 In 2015, UC Davis converted from laboratory-based blood gas testing, and adopted handheld POC devices – decreasing intraoperative turnaround times from 8 to 10 minutes, down to 30 seconds. More recently in 2018, UC Davis became the largest user of POC molecular pathogen detection systems in the United States. This platform provided the ED and Primary Care Network with the ability to identify influenza A/B, Strep A, and Respiratory Syncytial Virus in 15-20 minutes using polymerase chain reaction (PCR). The adoption of POC PCR testing has now moved a definitive test to the bedside and replacing inferior screening tests for influenza A/B and Strep A.

References

1. Kost GJ and Tran NK. Effects of Point-of-Care Testing on Time, Process, Decision Making, Treatment, and Outcome. In: Kost GJ, Ed., Principles & Practice of Point-of-Care Testing. Philadelphia: Lippincott Williams and Wilkins 2002.
2. Centers for Medicare and Medicaid Services: Accessed on April 8, 2019
3. CLIA Regulations: Accessed on April 8, 2019
4. FDA MAUDE Database: Accessed on April 8, 2019
5. Krouwer JS. Reducing glucose meter adverse events by using reliability growth with the FDA MAUDE database. J Diabetes Sci Technol 2018;23 [epub ahead of print].
6. DuBois JA, Slingerland RJ, Fokkert M, Roman A, Tran NK, Clarke W, Sartori DA, Palmieri TL, Malic A, Lyon ME, Lyon AW. Does Regulatory Really Intersect Reality in Glucose Measurement in the ICU? Is the Issue Testing Method Accuracy or Specimen Type? Crit Care Med. 2017;45:e1186-e1188.
7. Dubois JA, Slingerland, RJ, Fokkert M, Roman A, Tran NK, Clarke W, Palmieri TL, Lyon ME, Lyon AW. Bedside glucose monitoring—is it safe? A new, regulatory-compliant risk assessment evaluation protocol in critically ill patient care settings. Crti Care Med 2017;45:567-574.
8. Tran NK, Godwin Z, Steele AN, et al. Clinical impact of accurate point-of-care glucose monitoring for tight glycemic control in severely burned children. Ped Crit Care Med 2016;17:3406-412.
9. Tran NK, Godwin ZR, Bockhold JC, Passerini AG, Cheng J, Ingemason M. Clinical impact of sample interference on intensive insulin therapy in severely burned patients: a pilot study. J Burn Care Res 2014;35:72-79.

Transfusion Services: The Lab Section that Never Sleeps

Sarah Barnhard M.D. FCAP FASCP
Brandon Thomas CLS

Introduction: Our mantra in Transfusion Services is “right patient, right product, right time”! At face value it seems so simple, but in practice it is infinitely complex. With 24 staff (a mixture of HLTs and CLSs), a supervisor, a technical specialist, a QA (Quality Assurance) specialist, and four pathologists, we service 24/7 all UC Davis-affiliated centers including the medical center, the surgery centers, the children’s hospital, and the infusion centers. Much of our work is hands-on, at least one of our faculty is always on call, and overnight shifts are often busier than days. We are truly ‘the section that never sleeps’. In calendar year 2018, we transfused 5,912 patients with 31,273 blood components and saw 185 transfusion reactions. We issued 139 RhIg doses to obstetric patients. The massive transfusion protocol was activated on 548 patients. We performed a total of 34,927 crossmatches and tested 38,468 type and screen samples.

Regulatory Considerations: Transfusion services is one of the most highly regulated areas in the clinical lab. The FDA’s Center for Biologics Evaluation and Research (CBER) regulates biological products for human use under applicable federal laws¹. The AABB American Association of Blood Banks) sets standards for transfusion services² and these are incorporated as state law in California³. Other organizations such as the College of American Pathology also set standards for our laboratory’s accreditation⁴. All this oversight ensures our laboratory’s processes provide accurate results. It also means at least one regulatory inspection every year, if not more.

Continuous Quality Improvement: CQI has become a daily habit. Healthcare is constantly changing, and we change right along with it working to improve the way we deliver care for our collective patients in partnership with our clinical colleagues. It is exciting to see the ripple effect of our improvements throughout the health system.

• Blood supplier transition: In October 2016, we transitioned to the American Red Cross as our blood supplier as part of the University of California’s Leveraging Scale for Value campaign led by the Office of the President. The transition took 1.5 years of planning and required a major overhaul of our ordering, stocking, communications, and disaster protocols. We experienced highly positive impacts in our platelet inventory (increased ~80%) and our O negative RBC inventory (increased ~50%). Access to rare antigen-negative RBCs has improved greatly since the Red Cross manages the Rare Donor Registry and has a nation-wide, accessible blood supply. We also felt honored to be part of UCOP’s (University of California, Office of the President) initiative to improve the way we collectively manage University of California’s taxpayer funding.

• Standing orders for blood product inventory management: The Red Cross transition brought online standing order tools to our lab. Their inventory management experts helped us set stocking targets and standard shipment times/amount per shipment. The standing orders have helped ease the burden of managing a blood supply in constant flux.

• New blood bank laboratory information system: In August 2017, we transitioned to a new LIS for Transfusion Services (Wellsky) and for the rest of the laboratory (Epic Beaker). Our transition took 2 years of planning and required extensive validation to fulfill the FDA’s blood establishment computer system requirements⁵. The most positive aspect has been the Analytics Module for Wellsky. Our reporting and monitoring capabilities greatly increased with this new system.

• Electronic Patient Information System: To ensure blood availability for patients with complex needs, we closely monitor blood product specifications, communications and orders to/from the blood supplier, infusion center and apheresis appointment scheduling, and OR cases. We compile information found in multiple systems, but recently it was a manual compilation. We developed an Electronic Blood Bank Patient Information System in VB.NET with the help of Michael Erickson IT Analyst and started using it in January 2018. It significantly improved the efficiency of managing complex patients since we no longer need extensive manual documentation.

• Ortho Vision Analyzers: In August 2017, we brought expanded automated testing to Transfusion Services. It took approximately 9 months to review available platforms, coordinate facilities installment, work on the system build including interface with new blood bank LIS, validate the testing, develop new protocols, and provide staff training. The ABO/Rh type, antibody screen, and donor unit re-typing are all automated, giving our staff more time for complex manual testing.

• Massive transfusion protocol optimization: Updating the massive transfusion packs to contain 5 RBC units and 5 plasma units instead of 6 RBC units and 4 plasma units has improved the care of our adult trauma population. The PROPPR Randomized Clinical Trial (JAMA, 2015) showed more patients resuscitated using a 1:1 ratio of RBC:Plasma units achieved hemostasis and fewer experienced death due to exsanguination by 24 hours compared to a 2:1 ratio.

• New products manufactured in-house: In-house manufacturing of specialized blood products including divided platelets, reconstituted RBCs, and volume reduced platelets has substantially decreased turn-around-time for these products (70-80% average time decrease compared to supplier-based manufacturing). These blood products are needed for diverse patients especially in the critical ED, OR and NICU settings. Divided platelets are needed by some pediatric patients, reconstituted RBCs are used for neonatal exchange transfusions, and volume reduced platelets are needed by patients at high risk of fluid overload.

• New blood components: The Red Cross has been ‘ramping up’ supply of platelets containing platelet additive solution. In these platelets, 65% of the plasma from the platelet donor is removed and replaced with a nutrient buffer solution. This small change has served to decrease our incidence of allergic transfusion reactions.

• Blood utilization: Representatives from Transfusion Services lead the Quality and Safety Department’s Transfusing Wisely Committee which works to improve the standard practices in blood transfusion health system wide. From August 2015 – December 2016, the group’s work was focused on inpatient red blood cell transfusions. For stable, hospitalized adult patients multi-unit red blood cell transfusions have been cut nearly 50% and transfusions using a hemoglobin <7 g/dL trigger increased by nearly 30%. The 2-year savings is estimated at $1.5M.

On the Horizon: It’s exciting to look backward at all we have accomplished, but even more exciting to look forward. Our goals for 2019 include delivering blood to nursing staff using the pneumatic tubes in the hospital. Our colleagues on Davis 8 and T2SICU have volunteered as beta-sites and phase I is estimated to be May ’19. We plan to bring whole blood back to UC Davis – a trend from the ‘70s! Pediatric cardiothoracic surgeons will use it to prime the cardiac bypass circuits and the trauma team may use it for resuscitation. It reduces donor exposure since the RBCs and plasma come from the same donor. We plan to bring pathogen reduced platelets in-house to reduce the risk of septic transfusion reactions. The FDA’s draft guidance is pending finalization⁶ and we are working to stay ahead of the game. We are glad to have Red Cross as a partner to help us.

Conclusion: If you see us, we would love to say hello to you and chat about blood transfusions! Hanne Jensen MD has been Transfusion Services Medical Director for over 40 years and has a host of stories to tell. Grace Monis, M.D., Ph.D., joined as faculty in 2016 and was recently appointed Apheresis Medical Director after Leonor Fernando, M.D., retired. Sarah Barnhard, M.D., joined as faculty in 2015 and started serving as Associate Medical Director of Transfusion Services in 2016. David Unold, M.D., joined as faculty in 2017 and covers Transfusion Services and Apheresis. His experience working as a physician in a donor center is invaluable. Brandon Thomas, CLS, is Transfusion Services Supervisor. Agnes Olario, CLSS, is Transfusion Services Technical Specialist, and Kasey Parker, CLS, is Transfusion Services QA Specialist.

References:

1. Information online at https://www.fda.gov/BiologicsBloodVaccines/default.htm. Accessed 4/10/19.
2. Information online at http://www.aabb.org/tm/Pages/default.aspx. Accessed 4/10/19.
3. Information online at https://www.cdph.ca.gov/Programs/OSPHLD/LFS/Pages/BloodBanksandBiologics.aspx. Accessed 4/10/19.
4. Information online at http://www.cap.org/web/home/lab/accreditation/laboratory-accreditation-program. Accessed 4/10/19.
5. Information online at https://www.fda.gov/downloads/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/Guidances/Blood/UCM078815.pdf. Accessed 4/10/19.
6. Information online at https://www.fda.gov/downloads/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/Guidances/Blood/UCM627407.pdf. Accessed 4/10/19.