By Renee DiIulio

 The TIGRIS DTS System by Gen-Probe delivers first results in 3.5 hours.

In December 2004, physicians at the Aaron Diamond AIDS Research Center (ADARC of New York City) diagnosed a male New York City resident in his mid-40s with HIV using ELISA (enzyme-linked immunosorbent assay) and Western Blot tests—not an event for alarm. By January 2005, phenotypic testing revealed that the patient was infected with a strain known as 3-drug-class-resistant HIV-1 (3DCR HIV), meaning it exhibited resistance to three of the four most commonly prescribed treatments: nucleoside or nucleotide reverse transcriptase inhibitors (NRTI), nonnucleoside reverse transcriptase inhibitors (NNRTI), and protease inhibitors (PI). Resistance to any of these drugs isn’t uncommon either, but resistance against all three before treatment has even begun is unusual. So was the rapid onset of AIDS. The patient had progressed to the disease stage much more rapidly than normal, somewhere between 2 and 20 months compared to a more typical 10 years.

Fearing a public health crisis, the New York City Department of Health and Mental Hygiene put out a public alert. Some scientists, who felt more data was needed, suggested the alert had come too soon; for instance, it was possible that the early onset of AIDS was related to the particular patient rather than the particular virus. Various organizations, such as the Community HIV/AIDS Mobilization Project (New York City), agreed that the alert could unnecessarily create a public backlash against the gay and/or HIV-infected community and that further research should have been completed before sounding an alarm. Two cases of 3DCR HIV had been previously seen in Vancouver with no resulting public health crisis, though the patients had not been as ill as the New York City male.

Whether an outbreak results or not, the case encapsulates the many issues microbiology labs are facing today, not the least of which is the unknown. Diseases thought to be under control can change to once again pose a serious threat — this HIV case is only one example. Labs will be required to run these tests more frequently; in the New York City case, doctors were asked to screen all recently HIV-diagnosed patients for the particular strain.

At the same time, medical institutions must be on the lookout for new diseases that can suddenly appear, such as SARS (Severe Acute Respiratory Syndrome), which spread rapidly to great alarm after emerging in 2003 but has not been seen since its last diagnosis in 2004. West Nile virus (WNV), on the other hand, spread slowly after entering the country in 1999 and has become more entrenched with each passing year.

Emerging resistance poses as big a challenge as emerging viruses—drug-resistant tuberculosis (TB) and nosocomial infections being two prime examples—and microbiology labs need to focus on susceptibility testing as much as detection. Further demands are placed on the lab as the nation’s population ages; elderly patients tend to require more lab services than the average patient. Faced with a dwindling labor pool in addition to test limitations, throughput in the microbiology lab becomes an issue.

The past decade has seen developments in testing technologies that have helped to ease some of these responsibilities. The advances have come in both large and small steps and have resulted in shorter turnaround times, fewer labor requirements, and greater workflow efficiency. Automation has entered the microbiology lab along with new technologies. Companies are even turning an eye to traditional media, finding ways to improve growth cultures that save time, labor, and money.

The improvements have not been entirely focused on testing technology, though—information management has also played a role. In addition to providing physicians with information rather than results, labs may be required to track data that can identify nosocomial trends and predict outbreaks. “Delivering the right information to the right person at the right time is key,” says George Goedesky, senior director of clinical marketing, bioMérieux Inc (Durham, NC). He cites a key precept of his company: “Results need to be right, rapid, and relevant.”

Cracking the Code
According to the National Institute of Allergy and Infectious Diseases (NIAID of Bethesda, MD), at the turn of the century, infectious diseases were the leading cause of death worldwide. The World Health Organization (WHO of Geneva, Switzerland) found that of the 53.9 million deaths in 1998, 13.3 million of them, or 25%, were caused by infectious disease.

NIAID estimates the annual cost of infectious diseases at more than $120 billion. The WHO reported that in 1998, the top six infectious disease killers were acute respiratory infections (including pneumonia and influenza), AIDS, diarrhoeal diseases, TB, malaria, and measles. Emerging infections and bioterrorist threats are also causes for concern. The microbiology lab is charged with identifying them all, and determining drug susceptibility so that a successful course of treatment can be prescribed.

Technology is helping to do this. Tests have become increasingly more sophisticated, and quicker turnaround times have resulted in improved patient care with shorter hospital stays, fewer services used, and better patient outcomes.

Molecular diagnostics, in particular, is a burgeoning field. The demand to shorten time to result has driven the development of this technology. “A culture takes time. Nucleic acid amplification dramatically shortens turnaround time and increases the quality of the result,” says Michael Watts, senior director of investor relations and corporate communications at Gen-Probe Inc (San Diego).

Molecular testing saves time becomes it does not require waiting for growth. Turnaround time for Gen-Probe’s TIGRIS DTS System is 3.5 hours to first results. The fully automated nucleic acid amplification instrument can detect chlamydia, gonorrhea, HIV, and HCV, according to Craig Hill, manager of science affairs with Gen-Probe. “The technologist puts the specimen in one end and gets the result out of the other—the process is entirely automated,” he says.

 Gen-Probe’s APTIMA assays are second-generation nucleic acid amplification probe tests that use target capture, TMA, and DKA technologies.

The system works with Gen-Probe’s APTIMA assays, second-generation nucleic acid amplification tests that utilize target capture to streamline processing, transcription-mediated amplification (TMA) to amplify target rRNA, and dual kinetic assay (DKA) technologies to detect amplification. “The new technology builds upon the first generation to provide higher clinical sensitivity, a low false-negative rate, and the ability to test various forms of media, including urine and vaginal swabs,” says Hill.

Nucleic acid amplification technology is more sensitive because the amplification technique increases the organism’s DNA millions of times so that it is more easily detected. Other molecular diagnostic technologies perform analysis using other parameters.

TREK Diagnostics Systems’ (Cleveland, Ohio) VersaTREK detects changes in the headspace pressure of specimens, based on the consumption and production of gas promoted by company-unique media. “VersaTREK performs comprehensive detection testing by looking at all gases, not just CO2,” says Les Stutzman, director of global marketing for TREK.

 Cellestis’ Quantiferon-TB Gold tests cell-mediated immune response to two TB proteins.

Cellestis’ Quantiferon-TB Gold tests cell-mediated immune response to two TB proteins made by Mycobacterium tuberculosis, the bacterium that causes TB. The test offers more speed, convenience, sensitivity, and specificity than the traditional skin test. It requires only one patient visit, and provides a clear positive or negative result; the traditional skin test is read subjectively.

Giant Leaps and Baby Steps
These molecular diagnostic tests, many now in second generations, have allowed microbiology labs to take huge steps forward, particularly in shortening turnaround times, but Stutzman suggests that improvements are now being made in incremental steps.

For instance, the VersaTREK was able to increase time to result by a small amount by employing a magnetized motor and stir bar to improve the oxygenation of aerobic bottles. As a result of consistent stirring, organisms in the sample grow faster.

bioMérieux’s NucliSens miniMag uses proprietary technology to extract DNA or RNA, performing 12 extractions in 45 minutes. “The first step in detecting the pathogen from its nucleic acid is to extract the nucleic acid,” says Goedesky.

BD Diagnostics (Sparks, MD) has recently taken molecular automation to the next level, employing advanced robotics as used in the aerospace and silicon-chip manufacturing industry to automate molecular testing on the BD Viper system. “To date, traditional automated lab equipment has still relied on 60-year-old technology involving syringe pumps, vacuum tubing, and the like. The BD Viper system uses robotics to do the work, resulting in reduced labor requirements, high throughput, improved pipetting accuracy, and increased reliability,” says Tom Polen, BD’s worldwide director of marketing.

Fast and Accurate
Polen notes that molecular technologies are easier to automate and will increase. Much of today’s automation within the microbiology lab is focused on identification of organisms and susceptibility. Screening has become a regular part of health care. Government regulations require every patient be tested for TB. Blood donations are screened for a panel of infectious diseases. Some hospitals are even screening patients before surgery.

“Many hospitals screen their patients before surgery to determine if they carry organisms such as MRSA. Protocols differ depending on the answer. A patient with a communicable disease may be isolated or treated with specific drugs. The sooner the health care team has this information, the sooner the protocol can be initiated,” says Polen.

Stutzman poses a new variation on the chicken/egg question. “Is it more important to identify the organism or determine its susceptibility?” he asks. Today, companies provide systems that do both.

bioMérieux’s Vitek 2 line features rapid, automated identification and antibiotic susceptibility testing (ID/AST). The newest product is the Vitek 2 Compact, designed for small to midsized laboratories. The Vitek 2 60 and 120 are intended for larger labs with high throughput. The instruments use photometric technology to read color changes in advanced colorimetric cards within a short amount of time. The Vitek 2 Compact delivers results for 90% of patients within 6–8 hours.

Rapid testing has advantages beyond patient care. It also saves the hospital money. Patients with improved care and faster treatment onset generally have shorter stays and use fewer services. “Rapid results have been shown to save $1,700 per patient,” says Goedesky.

Using both colorimetric and fluorometric technology, the BD Phoenix Automated Microbiology System can identify more than 300 organisms and more than 175 trillion different biotypes, according to Polen. It can run up to 100 specimens simultaneously and do so more quickly than traditional methods. For instance, BD Phoenix can accurately and rapidly detect critical resistance markers, including VRE and ESBLs, in less than 6 hours so that infection-control strategies can improve patient outcomes.

Not all systems can readily detect vancomycin-resistant Staphylococcus aureus (VRSA), says Stutzman. The Centers for Disease Control and Prevention (CDC of Atlanta, Ga) found that two out of three VRSA isolates were not reliably detected by automated testing systems. “All systems must now have an insert for backup methodologies,” notes Stutzman. The CDC recommends that laboratories using automated methods or disk diffusion incorporate a vancomycin screen plate for enhanced detection of VRSA; it also suggests incorporating vancomycin screen agar plates for all Staphylococcus aureus testing.

“The market wants rapid and customized testing, but it also wants it to be 100% accurate. Rapid testing may have reached the limits of in vitro testing — you can push detection time only so far. To some extent, it is dependent on the organism’s duplication rate. E. coli will duplicate in 20 minutes, while other organisms will require 24 hours,” says Stutzman.

Traditions Die Hard
As a result, the technology of the blood culture has not been altered much. “The technology of automated growth-dependent systems has been around for roughly 15 years, much greater longevity than expected,” says Stutzman, comparing this to the typical 5–7 year life span for products of this nature.

    Polen agrees. “The traditional blood plate used today is similar to that used more than 80 years ago,” he says. But companies are beginning to look at ways to refine this process as well. BD launched a new line of chromagenic media last year. Proprietary synthetic chromagenic substrates are added to primary selective and nonselective media. When the colorless substrates are cleaved by specific enzymes and oxidized, they produce a specific, characteristic color. Depending on the media type and organism, identification can thus be accomplished without the need for confirmatory testing, subculturing, or supplemental biochemical or latex testing.

BBL CHROMagar MRSA can be used to detect methicillin-resistant Staphylococcus aureus (MRSA). “Traditionally, the sample was streaked onto a plate, incubated for 24 hours, and then subcultured for an additional 24 hours to isolate MRSA, for a total 48-hour turnaround time. With the new BD chromagenic plate, the sample is streaked onto just the one plate and read 24 hours later. If the color is pink, than the test is positive for MRSA,” says Polen, pointing out that dealing with one plate read in 24 hours is more cost-efficient, particularly as it allows the hospital to take preventive measures to avoid an outbreak. The cost to treat a new MRSA infection has been estimated to be as high as $35,000.

WHO found that at any time, more than 1.4 million people worldwide suffer from nosocomial infections; an average of 8.7% of hospital patients were affected. The CDC estimated that in 1995, nosocomial infections cost the nation $4.5 billion and contributed to more than 88,000 deaths. “Nosocomial infections have been found to average $14,000 per episode per patient,” says Goedesky.

Providing Information Rather Than Data
With such high costs, hospitals are creating surveillance programs based in microbiology to discern patterns. Which organisms does the hospital support? Are patients bringing latent organisms in? Can outbreaks be predicted and prevented?

Microbiology labs very often can perform the tests to create the data needed to deliver answers to these questions, but analyzing it to discern trends can be time and labor consuming. Informatics allows labs to process the large amounts of data generated quickly and efficiently.

BD’s new EpiCenter system is a microbiology data-management system that monitors results of BD instruments to generate epidemiological trends within the hospital. It will identify and proactively alert health-care providers to patient- and hospital-specific infectious disease events and trends. A Windows-based application, it can go on any desktop where access might be needed, such as the pharmacy, infection control, or physician’s workstation, and its audible alarms can be customized for the user. “Health care has not made maximum use of information technology, but products such as Epicenter can be used to improve patient outcome,” says Polen, suggesting advisories regarding treatment as just one way.

Data management can also assist with identifying unusual resistance patterns. TREK’s SWIN and ARIS 2X, which together provide an automated ID/AST system, were designed to combat growing antimicrobial resistance concerns. They feature an intelligent and customizable Expert System that can identify the appropriate intervention in a timely fashion. “Its rules are based on National Committee for Clinical Laboratory Standards (NCCLS) guidelines as well as standard rules from other providers. Individual users can modify them to fit their own standards. When an organism is identified, it helps the technologist remember the rules,” says Stutzman.

bioMérieux has built advanced expert capabilities into the Vitek 2 line. And its STELLARA family accepts input from bioMérieux instruments, such as Vitek, to assist with tasks such as patient and antimicrobial monitoring. The Antibiotic Assistant identifies syndromes, confirms demographics, notes allergies, establishes clinical classification and treatment location, and gathers unknown organism/empiric therapy information to add known susceptibilities and include mitigating factors. It displays a recommended therapy as well as decision logic and alternative therapies.

“These tools have been proven to meet targets regarding improved patient outcomes and lower costs,” says Goedesky. Hospitals are coming under increasing pressure to meet these goals. “Institutions have squeezed their supply and personnel budgets as much as possible and are now looking at processes. With pilot programs under way that study pay-per-performance reimbursement, hospitals will come under even more pressure to improve processes, both to save money and, by proving improved patient outcomes, make money,” says Goedesky.

To contribute to this process, labs need to deliver information that is intelligent and interpreted, notes Goedesky. “You are not just providing data but information, and developing a better process for turnaround time and exact delivery,” he says.

“Data management is intended to provide the lab with the means to handle large volumes of information efficiently, but they must have the core principles and a foundation of good testing technology behind these systems,” says Stutzman.

It was a traditional foundation of good technology, the ELISA and Western Blot tests, that identified the unusual HIV strain in New York City. It was fear of an outbreak that prompted city officials to put out an alert. Being able to identify trends can better assist officials with making the decisions that can save lives and avoid unnecessary panic, but there will still be surprises. Microbiology deals with living organisms that can change in a generation; only a crystal ball can accurately predict when that will happen—for now.

Renee DiIulio is a contributing writer for Clinical Lab Products.