Integrating rapid molecular analysis with antimicrobial stewardship in real time for Gram-negative bacteremia

Feb. 17, 2013

Recently developed rapid microbiological methods support significant clinical improvements. Rapid pathogen ID from blood cultures, early initiation of susceptibility tests, and clinical interventions supported by effective communication and interpretation of this vital data have resulted in reduced length of stay, lower mortality, and lower costs for cases of Gram-negative bacteremia at a major U.S. hospital. This article discusses the basic issues involved in rapid testing, describes the experiences of clinical laboratory professionals at that hospital (The Methodist Hospital in Houston, Texas), and suggests valid rationales for other institutions to dedicate resources to bringing rapid methods into their labs.


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Upon completion of this article, the reader will be able to:

  1. Describe how rapid testing for GN bacteremia and CVD improves quality of patient care.
  2. Describe methods for rapid GN pathogen identification.
  3. Define antimicrobial stewardship and how it applies to the MLS.
  4. Describe the application of high-sensitivity troponin assays.

Gram-negative bacteremia: the challenge of diagnostics speed

Gram-negative (GNR) bloodstream infections (BSI) are a therapy challenge due to increasing antibiotic resistance. With traditional 48-to-72 hour microbiology lab cycles from the time of blood draw, clinicians often start empiric therapy in advance of knowing the name of the pathogen or the susceptibility profile. The challenge for clinical microbiology labs is to apply available rapid methods and work collaboratively with their clinical teams to develop practical solutions. Guidelines on empiric antibiotic use in critical care patients, prepared by the Department of Surgical Education, Orlando Regional Medical Center, frame the issue succinctly:

Inappropriate empiric antibiotic therapy is widespread and associated with increased mortality in critically ill patients. Initial antibiotic selection must account for a variety of host, microbiologic, and pharmacologic factors. Institution-specific data, such as susceptibility patterns, must also be considered. Tailoring antimicrobial therapy based upon culture and sensitivity results will help to reduce costs, decrease the incidence of superinfection, and minimize the development of resistance…For patients with severe sepsis, it is recommended that intravenous antibiotic therapy be started within the first hour of recognition of severe sepsis, after appropriate cultures have been obtained.1

In a significant number of GNR cases, clinicians feel compelled to start antibiotics in absence of data. The dilemma that clinicians face, and its consequences, were described by Shorr et al in a 2011 article in Critical Care Medicine:

Initially inappropriate antibiotic therapy occurs in one-third of persons with severe sepsis and septic shock attributable to Gram-negative organisms. Beyond its impact on mortality, initially inappropriate antibiotic therapy is significantly associated with length of stay in this population. Efforts to decrease rates of initially inappropriate antibiotic therapy may serve to improve hospital resource use by leading to shorter overall hospital stays.2

Clinicians generally start with broad therapies for GNR BSI and then narrow therapies as species and reported susceptibilities are confirmed. Writing in Emergency Medicine, Dr. Lee S. Engel explains:

Patients with severe sepsis or septic shock should receive broad-spectrum antibiotics until the causative bacterium has been isolated and its susceptibility has been determined. For patients who are severely ill, combination therapy is warranted. After the susceptibilities are known, antibiotic therapy can be de-escalated to narrower-spectrum antibiotics.3 

Rapid GNR pathogen ID

The Methodist Hospital in Houston reported on a rapid GNR ID and susceptibility method that uses a new sample prep method from the blood culture bottle:

After being flagged as positive for growth by the blood culture instrument, 6 ml of broth was transferred from the blood culture bottle with a syringe to an 8.5-ml serum separator tube (Vacutainer SST Plus; BD) and centrifuged at 2,000 rpm for 15 min at room temperature. The supernatant was aspirated, using caution to not disrupt the loosely formed pellet of bacteria present at the surface of the polymeric gel. The MALDI-TOF [Matrix-Assisted Laser Desorption/Ionization-Time of Flight] mass spectrometry identification and antibiotic susceptibility panels were then prepared simultaneously.4

The Methodist Hospital later reported results of a clinical study that compared conventional microbiology and reporting methods to using MALDI-TOF just after Gram staining and directly initiating susceptibility tests. The combination of the two methods resulted in pathogen identification reports available to the clinical staff 15.3 hours sooner (P<.001), susceptibility reports delivered 23.7 hours sooner (P<.001), and therapy adjustments implemented 46 hours sooner (P=.004). 

The laboratory telephoned results of rapid pathogen identification and/or susceptibility directly to the clinical pharmacists on a 24/7 basis as data developed for each case. The pharmacists applied the IDSA recommended practice of Prospective Audit with Intervention and Feedback, a coaching method in which microbiology data is interpreted by clinical pharmacists and quality improvements for antibiotic therapy are actively recommended and implemented for the individual patient case, taking into consideration the full clinical picture. The main correction of antibiotic therapy was usually earlier de-escalation to more narrow spectrum drugs supported by susceptibility data.

The authors report outcome results of just over 101 patients in the intervention group and 100 in the control group. As a result of these interventions, hospital length of stay was 2.6 days shorter (11.9 vs. 9.3 days), hospital length of stay after BSI onset was 1.8 days shorter (9.9 vs. 8.1 days), ICU length of stay was one day shorter (7.3 vs. 6.3 days), ICU length of stay after BSI onset was 1.2 days shorter (6.1 vs. 4.9 days), and mean hospital costs for each case were $19,547 lower ($45,709 vs. $26,162). There was also a lower mortality trend in the intervention group. The authors project an annual savings of $18 million.

The authors concluded: “In an era of increasing resistance to bacterial antimicrobial agents, optimal and timely management of patients with Gram-negative BSIs is essential. Many strategies have been proposed and tried to further improve the consequences of these detrimental infections. However, our study is the first to demonstrate that integrating rapid molecular analysis by novel application of MS with antimicrobial stewardship in near real time significantly enhanced clinical care and financial outcomes.”5

Gram-negative therapy improvement—the challenge

Hospitals are coping in a critical era of rising antibiotic resistance and a very slim pipeline of new antibiotics to solve clinical problems. Broad antibiotic coverage can be effectively curtailed earlier for GNR BSI cases when labs utilize rapid methods of identification and initiate earlier susceptibility testing, and the results of these tests are interpreted by antibiotic stewardship teams supporting timely improvements in overall patient care. The Methodist Hospital team effort quality improvement example for treating Gram-negative bacteremia can support the case for investing in and implementing rapid microbiology methods in any laboratory—for both medical and financial reasons. How can you help integrate rapid methods at your institution?

Laboratories face pressure to provide results faster to improve patient care. Clinicians are aware that the value of diagnostic data from the microbiology lab decreases as it ages over 72 to 96 hours. Laboratory directors have choices of technology platforms. A growing number of FDA approved, reliable, commercially established methods include FISH, hybridization, MALDI-TOF, PCR and immunoassay-based methods that deliver species ID results in hours rather than days. These technology capabilities present a wide range of capital and operating costs, validation, training, and workflow adjustments.6

To derive the greatest sustained clinical value and permanent process changes for your hospital that will improve drug choices,  reduce mortality, reduce overhead, reduce unnecessary length of stay, and help to reverse the trends of antibiotic resistance, you need to work collaboratively with your clinical teams. We suggest this short list of considerations to help with your planning process.

Enlist the leadership of Clinical Pharmacy. When planning to add any specific rapid method, enlist your clinical pharmacists before finalizing the capital purchases and starting a validation process. Your pharmacy team may be leading new initiatives in antibiotic stewardship at your hospital. Be sure that your proposed rapid methods are included in the budgeting process and are in alignment with Stewardship Program goals. Consider a linked plan with Clinical Pharmacy as a joint presentation to hospital finance. Your goal is to propose that clinical improvements and hospital efficiencies will be better achieved with investments in more rapid diagnostics.

Learn how diagnostics apply to antibiotic management. Hospitals have unique antibiotic usage patterns and antibiotic resistance cases. Review your antibiogram with Clinical Pharmacy, and learn about the challenges of information delay regarding both species ID and susceptibility tests. Specific segments of patient needs for optimum antibiotic therapies should drive the process. Simulate with the pharmacy teams what their antibiotic administration intervention and feedback for clinicians would be if species ID and susceptibility tests were reliably available one day sooner, one shift sooner, or even several hours sooner. For every patient that is on an antibiotic regimen, there may be a more optimum path supported by rapid diagnostics. You might find it useful to quantify the incidence of Gram-positive, Gram-negative, and yeast bloodstream infections by number of annual cases. Common terms regarding antibiotic therapy are prophylaxis (prevention of infection), empiric (directed at a condition), pathogen-directed (organism identified) and susceptibility-guided (when the organism is identified and antibiotic susceptibility tests are completed).7

Get started: choose a clinical problem to solve. Based on your planning process with Clinical Pharmacy, including the antibiogram and incidence analysis, select a clinical challenge that Clinical Pharmacy agrees could have a practical impact. The solution for Gram-negatives described follows previous clinical reports that demonstrate rapid species identification and drug management improvements with significant financial impact. Published results for Gram-positive and yeast cases include earlier discontinuance or avoidance of vancomycin for cases of blood culture contamination,8 early notification in real time for S. aureus  bloodstream infections,9 better drug choice for MRSA vs. MSSA,10 and better drug choice and utilization for treatment of Enterococcus sp bloodstream infections11-12 and Candida.12-13

Measure your clinical improvement progress. Choose a pre-intervention time period of 30 to 90 days, to get a baseline of about 100 patient cases. Smaller hospitals may want to start with 25 to 50 cases. Set up a spreadsheet to track individual patient cases for Gram stain result, organism name, susceptibility, time to ID, and final result. Using Clinical Pharmacy data, track the antibiotic(s) used (track dates of switching), dosing, initiation and end, and patient admission and discharge dates, and include ICU days for each case. From the baseline cases, you can track the average and median length of stay and frequency of drug choices. Once you initiate a rapid reporting program, use the same spreadsheet to add cases with rapid ID/susceptibility interventions. Compare the drug usage and length of stay to the baseline cases. Ask for a weekly team review with your Clinical Pharmacy team; this is especially important in the early months of rapid reporting programs, so that the educational process and corrections to support clinical teams for individual cases can be understood and implemented.

Benchmark your progress. Compare your actual results with clinical literature reports. Are your clinical teams getting the ID and susceptibility data faster than they would with conventional microbiology methods? Are you initiating reporting changes that facilitate the timing of drug administration? Are you able to achieve significant changes in drug utilization, length of stay, and mortality? You can also submit your data to the hospital finance department for an analysis of cost impact. More important than matching the same number of days and dollars is demonstrating a positive trend of patient quality improvement.  Implementing rapid microbiology should not be viewed only for cost savings alone, but as a way of achieving long-term and permanent improvements in your hospital’s quality of care for bloodstream infection cases.

Philip Onigman is an independent biotechnology consultant based in the Boston area. His areas of specialization include sales management, market development, new technology introduction, infectious disease, and antibiotic and antifungal therapy. In addition to a distinguished career working for leading biomedical companies, he has lectured to university students on the role of microbiology diagnostics and its impact on antibiotic stewardship processes in U.S. hospitals.


  1. Department of Surgical Education, Orlando Regional Medical Center. Empiric antibiotic use in critical care patients. Accessed January 3, 2013.
  2. Shorr AF, Micek ST, Welch EC, Doherty BA, Reichley RM, Kollef MH.  Inappropriate antibiotic therapy in Gram-negative sepsis increases hospital length of stay. Critical Care Medicine. 2011;39(1):46-51. 
  3. Engel LS. Multidrug-resistant Gram-negative bacteria: trends, risk factors, and treatments. Emergency Medicine. 2009;41(11):18-27.
  4. Wimmer JL, Long SW, Cernoch P, et al. Strategy for rapid identification and antibiotic susceptibility testing of Gram-negative bacteria directly recovered from positive blood cultures using the Bruker MALDI Biotyper and the BD Phoenix System. J Clin Microbiol. 2012;50(7):2452-2454.
  5. Perez KK, Olsen RJ, Musick WL, et al. Integrating rapid pathogen identification and antimicrobial stewardship significantly decreases hospital costs. Arch Pathol Lab Med. 2012;Dec 6:1-8.
  6. Goff D, Jankowski C, Tenover FC. Using rapid diagnostic tests to optimize antimicrobial selection in antimicrobial stewardship programs. Pharmacotherapy. 2012;32(8):677-687.
  7. Rybak MJ, Cooperative Antimicrobial Stewardship: partnering with the microbiology laboratory. Medscape. 2012; July 25. Accessed January 3, 2013.
  8. Forrest GN, Mehta S, Weekes E, Lincalis DP, Johnson JK, Venezia RA. Impact of rapid in situ hybridization testing on coagulase negative staphylococci positive blood cultures. J Antimicrob Chemother. 2006;58(1):154-158.
  9. Ly T,  Gulia J, Pyrgos V, Waga M, Shoham S. Impact upon clinical outcomes of translation of PNA FISH-generated laboratory data from the clinical microbiology bench to bedside in real time. Ther Clin Risk Manag. 2008;4(3):637-640.
  10. Bauer KA, West JE, Balada-Llasat JM, Pancholi P, Stevenson KB, Goff DA. An Antimicrobial Stewardship Program’s impact with rapid polymerase chain reaction methicillin-resistant Staphylococcus aureus/S. aureus blood culture test in patients with S. aureus bacteremia. CID. 2010;51(9):1074-1080.
  11. Forrest GN, Roghmann MC, Toombs LS, et al. Peptide nucleic acid fluorescent in situ hybridization for hospital-acquired enterococcal bacteremia: delivering earlier effective antimicrobial therapy. Antimicrob Agents Chemother. 2008;52(10):3558-3563.
  12. Gamage DC, Olson DP, Stickell LH, et al. Significant decreases in mortality and hospital costs after laboratory testing with PNA FISH. ICAAC 2011 poster D-01302b.
  13. Heil EL, Daniels LM, Long DM, Rodino KG, Weber DJ, Miller MB. Impact of a rapid peptide nucleic acid fluorescence in situ hybridization assay on treatment of Candida infections. Am J Health Syst Pharm. 2012;69(21):1910-1914.