Rapid multiplex method for direct phenotypic ID/AST of bacterial pathogens

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Urinary tract infections (UTI) are diseases of the kidneys, ureters, bladder or urethra and are caused by microbes that live in the bowel. They afflict millions of people every year and are the second most common type of bacterial infection encountered by humans throughout their life span. Approximately 150 million UTI occur worldwide annually, accounting for $6 billion in healthcare costs. In the U.S.A., UTI are responsible for 8 million annual visits to healthcare providers. Some infections can lead to serious kidney complications and septicemia, with 13,000 deaths annually being attributed to nosocomial UTI. Although different microorganisms (e.g. bacteria, viruses, fungi) can cause these infections, Gram-negative bacteria are the most prevalent. The standard methods for species diagnosis are culture-based protocols that take up to 48 h. As a result, UTI are one of the most frequent reasons for antimicrobial prescriptions in healthcare facilities without a confirmed diagnosis. Therefore, modern rapid diagnostic methods that promote antimicrobial stewardship are crucial. Moreover, as patient outcomes are directly correlated to length of time to diagnosis and administration of appropriate therapy, the development of novel diagnostics that can rapidly identify (ID) the pathogen directly in clinical specimens, and simultaneously provide antibiotic susceptibility testing (AST) is a critical factor for UTI management. The goal of this project is to develop a product called multIDAST UTI that is superior to microbiological culture-based methods used for ID/AST of UTI. MultIDAST UTI will be developed as a qualitative in vitro diagnostic (IVD) test for rapid (<3 h) multiplexed identification of Gram-negative pathogens of uncomplicated UTI directly from urine and simultaneous characterization of their phenotypic responses to commonly prescribed antimicrobials. The product thereby bypasses the need for bacterial amplification and isolation and thus overcomes the major time-limiting step of current diagnostics. This will be achieved by uniquely combining species-specific phages, which have been engineered to produce a signature molecule upon bacterial infection, and isothermal helicase dependent amplification (HDA), which amplifies the signal ∼108-fold. The ensuing phenotypic signal is directly correlated to cell fitness; thus, we can rapidly generate information related to the pathogens sensitivity or resistance to a particular drug by incubation in the absence or presence of antimicrobials. Signal responses will be measured using Solana, a fluorometer currently used in multiple FDA- cleared HDA diagnostic assays. The practical purpose of this contemporary system is to identify the pathogen and determine the antibiotic suitable to cure an infection, thereby promoting antimicrobial stewardship. It will support the fight against antibiotic resistance by addressing the emergence of carbapenem-resistant Enterobacteriaceae (CRE), classified by the Centers for Disease Control as one of the nation's 'urgent' antibiotic-resistant threats.