Massively multiplexed microbial identification using resequencing DNA microarrays for outbreak investigation. T. A. Leski *1 , R. Ansumana 2 , D. H. Jimmy 2 , U. Bangura 2 , A. P. Malanoski 1 , B. Lin 1 , D. A. Stenger 1 1 Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington DC 20375; 2 Njala University/Mercy Hospital Research Laboratory, Kulanda Town, Bo City, Sierra Leone ABSTRACT Multiplexed microbial diagnostic assays are a promising method for detection and identification of pathogens causing syndromes characterized by nonspecific symptoms in which traditional differential diagnosis is difficult. Also such assays can play an important role in outbreak investigations and environmental screening for intentional or accidental release of biothreat agents, which requires simultaneous testing for hundreds of potential pathogens. The resequencing pathogen microarray (RPM) is an emerging technological platform, relying on a combination of massively multiplex PCR and high-density DNA microarrays for rapid detection and high-resolution identification of hundreds of infectious agents simultaneously. The RPM diagnostic system was deployed in Sierra Leone, West Africa in collaboration with Njala University and Mercy Hospital Research Laboratory located in Bo. We used the RPM-Flu microarray designed for broad-range detection of human respiratory pathogens, to investigate a suspected outbreak of avian influenza in a number of poultry farms in which significant mortality of chickens was observed. The microarray results were additionally confirmed by influenza specific real-time PCR. The results of the study excluded the possibility that the outbreak was caused by influenza, but implicated Klebsiella pneumoniae as a possible pathogen. The outcome of this feasibility study confirms that application of broad-spectrum detection platforms for outbreak investigation in low-resource locations is possible and allows for rapid discovery of the responsible agents, even in cases when different agents are suspected. This strategy enables quick and cost effective detection of low probability events such as outbreak of a rare disease or intentional release of a biothreat agent. Keywords: outbreak investigation, influenza, resequencing microarray, broad range pathogen detection, poultry infections 1. INTRODUCTION Identification of the etiologic agent causing an outbreak is not a trivial task as many infectious syndromes are characterized by almost undistinguishable symptoms, especially in the initial phases of infection. This refers equally to epidemic and zoonotic diseases. In many situations, quick identification of the pathogen causing an outbreak is essential, especially when natural outbreak or deliberate release of an agent has potentially significant public health consequences. This includes most of the pathogens classified as category A priority pathogens as defined by Centers for Disease Control and Prevention (CDC) 1 . For some of these pathogens, outbreaks in the human population may be preceded by or be concomitant with zoonotic outbreaks (some examples include influenza A 2 , Nipah virus 3 and Ebola * tomasz.leski@nrl.navy.mil; phone: 202 767-0140; fax: 202 767-9594. Sensing Technologies for Global Health, Military Medicine, Disaster Response, and Environmental Monitoring; and Biometric Technology for Human Identification VIII, eds. Vijaya Kumar, Prabhakar, Ross, Montgomery, Southern, Taylor, Weigl, Proc. of SPIE Vol. 8029, 802904 · © 2011 SPIE · CCC code: 0277-786X/11/$18 · doi: 10.1117/12.884782 Proc. of SPIE Vol. 8029 802904-1 Downloaded from SPIE Digital Library on 16 May 2011 to 132.250.22.10. Terms of Use: http://spiedl.org/terms