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Companion Diagnostic Platform for Rapid Assessment of Bacteriophage Susceptibility in Antibiotic-Resistant Bacterial Pathogens



OBJECTIVE: Develop state-of-the-art diagnostic technology for rapid detection of antimicrobial susceptibility in pathogens from infected wounds that can be used to guide clinical decisions for use of non-traditional antimicrobials.

DESCRIPTION: U.S. military service members who are medically evacuated from theatre due to combat-related injuries have sustained high impact insults such as explosions, gunshot wounds and motor vehicle accidents, leading to significant skin and soft tissue injuries that may be frequently contaminated. A large proportion of these service members are at increased risk for infectious complications of their traumatic injuries, and the most common infections involve skin and soft tissue, wound infections, and osteomyelitis and sepsis if not treated in a timely manner. Acinetobacter baumannii has been identified as one of the most frequently associated organisms with skin and soft tissue infections among wounded warriors, occurring in 35% of wound infections. Within this 35%, up to 90% of the culture isolates were assessed to be antimicrobial resistant (AMR) [1]. Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is a well-recognized cause of skin and soft tissue infections (SSTI) in US military hospitals with a reported prevalence of 68% to 70% in selected military hospital emergency rooms [2]. High rates of MRSA skin and soft tissue infections have been observed among soldiers in training [3]. In addition to skin and soft tissue infection, MRSA is the most frequently isolated organism late in infection in traumatically injured service members [2]. Late infection in this population often results in limb salvaging amputation. Pseudomonas aeruginosa and Klebsiella pneumoniae are responsible for significant morbidity and mortality among both civilian and military populations, often colonizing mucosal surfaces, wounds, and foreign devices such as catheters and endotracheal tubes with biofilms that are highly resistant to antibiotic penetration and clearance by the immune system. In civilian and veteran populations these same types of infections frequently occur in individuals that have skin and soft tissue and prosthetic joint infections [4]. In a patient infected with multi-drug resistant organisms, the treatment choices often become limited due to waning approvals of new antibiotics. Frequently, these patients are hospitalized for prolonged periods of time and subsequently experience multiple episodes of hospital readmissions related to infectious complications of their wound or orthopedic implants. In addition to increased patient morbidity, provision of medical care for service members with infected traumatic wounds can be very costly and lead to intense resource utilization.Furthermore, the prolonged systemic administration of broad spectrum antibiotics to soldiers and sailors escalates the risk of selecting for bacterial organisms with increased antibiotic resistance profiles. The dwindling arsenal of antibiotics active against multidrug-resistant organisms urgently necessitates novel therapeutics such as phage to decrease the rates of mortality and morbidity associated with MDR infections and maintain current standards of medical practice in the future. However, the clinical utility of novel antimicrobials, such as bacteriophage [5], will be limited by the inability to monitor the bacterial susceptibility in real time to guide clinical decisions and therapeutic use. Current antibiotic susceptibility testing systems are closed both from hardware and reagents to the software analytic pieces that prevent evaluation of alternative antimicrobials such as phage. This topic seeks an open standards system (easily expandable or modified for evaluation of different antimicrobial types) that can monitor individual bacterial susceptibility to bacteriophage and eventually other non-traditional antimicrobial agents to support preclinical development and evaluation of therapeutic candidates and for future use as a companion diagnostic in the clinics to guide treatment decisions.

PHASE I: Selected performer determines the feasibility of the concept by developing a prototype diagnostic susceptibility-based assay that has the potential to meet the broad needs discussed in this topic description. Currently there are no FDA-cleared, field-capable assays that can be used to rapidly identify the most common bacterial pathogens causing wound and sepsis infections as described in references 1-6 (to include but not limited to the ESKAPE group of pathogens: Enterococcus spp., Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp, and Escherichia coli), as well as an ability to determine the respective susceptibility of the detected pathogen to bacteriophage. Development of an assay for that can rapidly determine the susceptibility of AMR bacteria to bacteriophage is therefore a high priority for development and eventual clinical use of these promising therapeutics. Assay run time should be congruent with or more rapid (less than or equal to overnight culture; 16-18h) than current automated antibiotic susceptibility testing systems in order to provide results within a clinically relevant timeframe to guide therapeutic use.

PHASE II: Based on the results from Phase I, the selected performer provides up to 3 initial lots of at least 50 prototype assays (tests or plates) each to the COR. These initial lots will be evaluated for sensitivity and specificity using a diversity set of bacterial strains and cognate bacteriophage for evaluation in vitro. Can coordinate with WRAIR/NMRC for materials and assistance with preclinical evaluation if needed. Feedback regarding the sensitivity/specificity of each lot of prototype assays will be provided to the performer. This data will then be used to optimize each subsequent lot of assays. The goal in Phase II is the development of a prototype assay that provides 85% sensitivity and 85% specificity when compared to phage plaque assays. Once sensitivity and specificity requirements have been met in preclinical tests, the selected performer will confirm the performance characteristics of the assay (sensitivity, specificity, positive and negative predictive value, accuracy and reliability) using preclinical or clinical specimens. The elected performer will require a Federal-Wide Assurance of Compliance before government funds can be provided for any effort that requires human testing or uses of clinical samples. The selected performer will also conduct stability testing of the prototype device in Phase II. Stability testing will follow both real-time and accelerated (attempt to force the product to fail under a broad range of temperature and humidity conditions and extremes) testing in accordance with FDA requirements. The data package plan required for application to the U.S. Food and Drug Administration will be prepared at the end of phase II.

PHASE III: During this phase the performance of the assay should be evaluated in field studies or clinical trials that will conclusively demonstrate that the assay meets the requirements of this topic. The performer may coordinate with WRAIR/NMRC for this objective. Military applications: AMR bacterial infections occur worldwide. The diagnosis of these wound infections and sepsis cases are often delayed, because the currently available tests, mostly reliant on bacterial culture or high-complexity nucleic acid amplification, are not field-capable, not rapid, and can vary considerably among different laboratories even when using the same procedure or method. With the availability of an easy and rapid assay developed under this topic, wounded and ill soldiers can be treated with more effective antimicrobials such as bacteriophage, alongside traditional antibiotics, in a timely manner in any military medical organization (such as a Battalion Aid Station, a Combat Support Hospital, Forward operation base, or a fixed medical facility). The performer should coordinate with WRAIR/NMRC to establish a National Stock Number (NSN) for potential inclusion in into appropriate "Sets, Kits and Outfits" that are used by deployed medical forces. Civilian applications: MDR bacterial infections occur in communities and hospitals, in wounds, skin and soft tissue infections, pneumonia, and blood stream infections. We envision that the performer that develops the rapid diagnostic assay and will be able to sell and/or market this assay to a variety of civilian medical organizations, and that this market will be adequate to sustain the continued production of this device.

KEYWORDS: Wound Infections, ESKAPE, AMR, MDR, Diagnostic, Bacteriophage, Phage therapy, antimicrobial, susceptibility testing


1. Davis, K.A., et al., Multidrug-resistant Acinetobacter extremity infections in soldiers. Emerg Infect Dis, 2005. 11(8): p. 1218-24. 2. Morrison-Rodriguez, S.M., et al., Community-associated methicillin-resistant Staphylococcus aureus infections at an Army training installation. Epidemiol Infect, 2010. 138(5): p. 721-9. 3. Burns, T.C., et al., Microbiology and injury characteristics in severe open tibia fractures from combat. J Trauma Acute Care Surg, 2012. 72(4): p. 1062-7. 4. Hospenthal, D.R., et al., Guidelines for the prevention of infections associated with combat-related injuries: 2011 update: endorsed by the Infectious Diseases Society of America and the Surgical Infection Society. J Trauma, 2011. 71(2 Suppl 2): p. S210-34. 5. Kutter, E., et al., Phage therapy in clinical practice: treatment of human infections. Curr Pharm Biotechnol, 2010. 11(1): p. 69-86.

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