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'GreeneChip' — New diagnostic tool that rapidly and accurately identifies multiple pathogens

December 06, 2006

Researchers in the Greene Infectious Disease Laboratory at Columbia University Mailman School of Public Health and their colleagues in the WHO Global Laboratory Network have developed a new tool for pathogen surveillance and discovery-the GreeneChip System. The GreeneChip is the first tool to provide comprehensive, differential diagnosis of infectious diseases, including those caused by viruses, bacteria, fungi, or parasites. In addition, it is the first tool that can be used on a wide variety of samples, including tissue, blood, urine, and stool, allowing for the rapid identification of pathogens in a variety of laboratory and clinical settings.

The GreeneChip system and its application in an outbreak investigation when other methods failed to implicate a microorganism in a fatal hemorrhagic fever case is described in the January 2007 issue of the CDC's Emerging Infectious Diseases (online December 6 at www.cdc.gov/EID/13/1/06-0837.htm).

Globalization of travel and trade brings new infectious agents into new contexts. It is increasingly important to be prepared for the unexpected. "Because clinical syndromes are rarely specific for single pathogens, methods that simultaneously screen for multiple agents are important, particularly when early accurate diagnosis can alter treatment or assist in containment of an outbreak," stated W. Ian Lipkin, MD, director of the Greene Infectious Disease Laboratory at the Mailman School's Department of Epidemiology. He added, "To address the challenges of emerging infectious diseases and biodefense, public health practioners and diagnosticians need a comprehensive set of tools for pathogen surveillance and detection."

GreeneChip features include a comprehensive microbial sequence database that integrates previously distinct reserves of information about pathogens-for every entry of a pathogen and its properties, the GreeneChip contains a correlate of its genetic makeup.

GreeneChip performance was initially tested by using samples obtained from patients with respiratory disease, hemorrhagic fever, tuberculosis, and urinary tract infections. In all cases, GreeneChip analysis detected an agent that was consistent with the diagnosis obtained by more traditional and slower methods, such as culture or polymerase chain reaction (PCR).

In addition, the GreeneChip was used in the analysis of an unknown sample from a patient with a viral hemorrhagic fever (VHF)-like syndrome. Within six to eight days of infection, Marburg virus causes an acute febrile illness that frequently progresses to liver failure, delirium, shock, and hemorrhage. From October 2004 through July 2005, a Marburg outbreak in Angola resulted in 252 cases of hemorrhagic fever, with 90% of the cases fatal. Although most of the cases were confirmed through PCR as caused by Marburg virus, some were not.

During this outbreak, a healthcare worker from a nongovernmental organization had acute fever and liver failure that culminated in death within one week. PCR assays of RNA extracted from blood showed no evidence of Marburg infection. The same RNA was processed for panviral analysis with the GreeneChip. Still nothing was detected. The RNA was then tested with the GreeneChip for parasites. Analysis identified a Plasmodium (the species of parasite that causes human malaria). Chart review showed that the patient had recently arrived in Angola from a country where malaria was not endemic and that he had not taken malaria prophylaxis. Had the GreeneChip been available in the field to confirm the correct pathogen, the patient could have been treated for malaria.

Differential diagnosis of hemorrhagic fevers poses challenges for clinical medicine and public health. Syndromes associated with agents are not distinctive, particularly early in the course of disease. In some instances, including the case presented above, more than one agent may be endemic in the region with an outbreak. Outbreaks caused by different agents may also overlap in time and geography.

"We are very excited to work with the WHO to make an impact in managing disease outbreaks globally-especially in regions of the world where resources are scarce," stated Thomas Briese, PhD, associate director of the Greene Laboratory.

Implicit in globalization is the risk of known or new agents that appear in novel contexts. In 1996 a presumptive diagnosis of Ebola viral hemorrhagic fever in two children who had recently returned to New York City from West Africa resulted in closing a hospital emergency room. For example, one of the children died of cardiac failure caused by plasmodium falciparum (malaria). Therapeutic options for treatment of VHF are limited; however, rapid isolation if infected persons is critical to curb contagion. In contrast, human-to-human transmission is not a primary concern with malaria and early, specific therapy can have a profound effect on illness and death. The GreeneChip provides unprecedented opportunities for unbiased pathogen discovery and reduction of illness and death caused by infectious disease.

Columbia University's Mailman School of Public Health