Ways to move quickly on bloodstream infection

William Check, PhD

October 2013—Since 1942, when penicillin was first used to treat infections caused by gram-positive bacteria, many improved and potent beta-lactam antimicrobials have been developed. Yet today, if a patient in an intensive care unit develops a bloodstream infection with Staphylococcus aureus, that person has a one in three chance of dying. High mortality rates apply to many other pathogens that cause bloodstream infections in ICU patients—from one in five for coagulase-negative staphylococci and Escherichia coli to almost 40 percent for Pseudomonas aeruginosa and Candida spp. Enterobacter spp and Enterococcus spp have intermediate mortality rates: one in four and one in three, respectively. Even among patients on a non-ICU ward, bloodstream infections are associated with mortality rates between 20 percent and 30 percent.

At this year’s annual meeting of the American Society for Microbiology, Christine C. Ginocchio, PhD, MT(ASCP), senior medical director and chief of the Division of Infectious Disease Diagnostics at North Shore-LIJ Laboratories, gave the Division C Lecture on the clinical and infection control implications of rapid detection and identification of bloodstream pathogens. Recently introduced molecular technologies can significantly shorten time to identification. Technologies in development now may shorten that time even more.

In her ASM lecture, which was the BD Award for Research in Clinical Microbiology presentation, Dr. Ginocchio showed that, at an incidence of 377 per 100,000 population, sepsis is more common than stroke (223), cancer (332), or heart disease (208) (Hall MJ, et al. NCHS data brief, No. 62. Hyattsville, Md. National Center for Health Statistics, 2011).

Moreover, the NCHS document says the rate of sepsis is increasing. Septicemia or sepsis as a first-listed diagnosis more than doubled between 2000 and 2010, from 11.6 per 10,000 population to 26.5, says Dr. Ginocchio, who is professor in the Departments of Pathology and Laboratory Medicine and of Molecular Medicine in the Feinstein Institute for Medical Research, Hofstra North Shore-LIJ School of Medicine, New York. Hospitalizations did not increase during that period.

Among patients hospitalized for sepsis, length of stay rises from 4.8 to 8.4 days. Particularly affected are those under age 65, whose LOS rises from 4.3 to 9.1 days when sepsis is present, according to the NCHS.

In addition to the toll it takes on patients, sepsis is costly. “Patients can get sepsis as a result of nosocomial infection, which is no longer reimbursable,” Dr. Ginocchio points out.

Time to organism identification and antimicrobial susceptibility testing is critical to improving survival, as demonstrated by data showing a strong inverse relationship between time to effective antibiotic therapy and survival. In one patient analysis, by four hours half of patients had received effective antibiotic therapy. Yet even with this early treatment only half survived (Kumar A, et al. Crit Care Med. 2006;34: 1589–1596).

Dr. Ginocchio discussed currently available rapid molecular methods for directly detecting organisms from positive blood cultures.

One, AdvanDx PNA FISH, is a technology in which fluorescence-tagged peptide nucleic acid (PNA) probes detect 16S rRNA directly from positive blood cultures. “One of the problems with the old version of these assays was that it took many steps and many hours,” Dr. Ginocchio said in an interview. QuickFISH is the streamlined version; it has a turnaround time of 20 minutes once the blood culture turns positive, she says. Four kits are available: S. aureus versus coagulase-negative staphylococci; E. faecalis versus non-faecalis enterococci (E. faecium); E. coli versus K. pneumoniae versus P. aeruginosa; and C. albicans versus C. parapsilosis versus C. glabrata. Speciation of Candida helps decide whether to treat with fluconazole.

Dr. Ginocchio showed several published studies demonstrating shorter time to identification with PNA FISH. One retrospective analysis found a potential savings of 60 to 80 hours relative to standard culture methods for identifying a range of organisms that cause bloodstream infection (Harris DM, Hata DJ. Ann Clin Microbiol Antimicrob. 2013;12:2). Accuracy was 99 percent.

A second study, using PNA FISH to distinguish S. aureus from coagulase-negative staphylococci in blood cultures, demonstrated reduced length of stay (from six to four days) with PNA FISH (Forrest GN, et al. J Antimicrob Chemother. 2006;58:154–158). No significant effect on vancomycin usage was found.

In a third bloodstream infection study, comparing PNA FISH to the C. albicans screen test for differentiating C. albicans from non-albicans Candida species, potential cost savings were identified (Alexander BD, et al. Diagn Microbiol Infect Dis. 2006;54:277–282). Savings were realized through a decrease in antifungal drug costs, particularly caspofungin, the authors wrote. They noted that their interpretation assumed “physician notification of yeast identity concurrent with blood culture positivity.”

Turning to amplification methods, Dr. Ginocchio listed four: BD-GeneOhm’s StaphSR, Cepheid’s Xpert MRSA/SA (methicillin-resistant and -sensitive S. aureus), Nanosphere’s Verigene system for gram-negative and -positive organisms, and BioFire’s assay for bloodstream infection. All work on samples from a positive blood culture bottle. “There are no FDA-cleared tests that can be done directly from blood,” she says.

BD-GeneOhm’s StaphSR yields results within two hours. Results are reported as negative or positive for S. aureus or MRSA or both.

Cepheid’s GeneXpert MRSA/SA was approved in August. In one study, outcomes during the four-month period after the assay was adopted were compared with the four months before its adoption. Results of the assay were communicated to an infectious disease pharmacist for possible regimen change. Investigators concluded that it “allows rapid differentiation of S. aureus bacteremia, enabling timely, effective therapy and is associated with decreased length of stay and health care costs” (Bauer KA, et al. Clin Infect Dis. 2010;51:1074–1080). Its impact was more pronounced on MSSA isolates, increasing the number of switches to non-vancomycin therapy and shortening the time to switching.

BioFire’s amplification assay for bloodstream infection was also recently approved, in this case for a range of gram-positive and -negative organisms and Candida species.

Nanosphere’s Verigene system performs multiplex analysis using one cartridge per specimen. It can also detect three genetic resistance determinants. Results from each test are available in about 1.5 hours. The Verigene BC-GP is FDA cleared for detection of 12 gram-positive bloodstream pathogens. In a report that appeared online in July, Dr. Ginocchio and other investigators conducted a five-center study to evaluate the diagnostic accuracy of the Verigene BC-GP directly from positive blood culture broths containing gram-positive bacteria (Buchan BW, et al. PLoS Med. 2013; Jul;10: e1001478).

They found:

• Sensitivity was 94.8 percent to 100 percent, except for E. faecium, 92.6 percent.
• Specificity was 98.9 percent to 100 percent.
• Sensitivity for mecA and vanA genes was 98.6 percent and 100 percent, respectively.
• Identification was achieved an average of 42 to 47 hours sooner using the BC-GP test compared with routine culture methods; for the Strep viridans group, it was 70 hours sooner.
• Retrospective analysis of 107 separate blood cultures demonstrated that identification of methicillin-resistant S. aureus and vancomycin-resistant Enterococcus spp was completed an average of 41.8 to 42.4 hours earlier compared with routine culture methods.

One drawback: About 7.5 percent of single-organism cultures contained gram-positive bacteria not present on the BC-GP test panel.

A version of the Verigene BC-GP for gram-negative bloodstream infection is in development.

Dr. Ginocchio was part of a group that evaluated a detection method based on RNA-dependent nucleic acid sequence-based amplification and molecular beacon (NASBA-MB) that uses pan-gram-negative, pan-gram-positive, pan-fungal, pan-Candida, and pan-Aspergillus probes and primers (Zhao Y, et al. J Clin Microbiol. 2009;47:2067–2078). In a clinical study of 570 blood culture samples, the candidate assay produced “excellent” results, Dr. Ginocchio says. However, on further evaluation, it did not have adequate sensitivity to detect pathogens directly from patient samples. “We could get a faster result if we sampled blood culture bottles every few hours,” Dr. Ginocchio says, “but this is not practical.”

Radically different from molecular methods is Matrix-assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry. In MALDI-TOF MS, microbes are identified by matching the protein profiles of sample organisms generated via the procedure to profiles contained in a proprietary database. Like molecular methods, MALDI-TOF MS is used on positive blood culture bottles. However, since it does not require an amplification step, it is even more rapid, returning results for each sample in minutes.

Dr. Ginocchio characterizes MALDI-TOF MS as fast, accurate, comprehensive, and inexpensive. “It is no more expensive than the instruments we use for traditional identification,” she says. Vitek, Phoenix, and MicroScan automated identification instruments cost about $150,000; a mass spectrometer can be purchased for under $200,000. More significant, reagents for conventional machines cost about $5 to $8 and for molecular assays about $75 to $125 per test, while per-test cost for a mass spectrometer is less than $1.