Discovering antimicrobials acting against MDR pathogens

Abstract We are experiencing an antimicrobial resistance crisis (AMR), a direct result of a decline in antibiotic discovery. The WHO designated a list of priority pathogens, and of these, MDR Gram- negative Enterobacteriaceae (E. coli, S. typhimurium, Klebsiella pneumoniae, Enterobacter), Pseudomonas aeruginosa, and Acinetobacter baumannii) are of "critical priority". These pathogens are the focus of the present proposal aimed at developing a platform for efficient discovery of novel antimicrobials. The field once enjoyed a golden era of discovery, fueled mainly by screening of soil actinomycetes. All major classes of broad-spectrum antibiotics active against Gram-negative pathogens were discovered by the 1960s. Overmining of actinomycetes resulted in the collapse of the discovery platform. Novel antibiotics discovered since then only act against Gram-positive species. We developed methods to access a broader range of bacteria, with a focus on uncultured species that make up 99% of total biodiversity. A number of novel compounds came from this source, including teixobactin, representing a new class of cell- wall acting compounds without detectable resistance (Ling et al., 2015). Teixobactin is undergoing IND-enabling studies; it is also a narrow-spectrum compound. We propose to develop a platform for efficient discovery of novel antimicrobials. The main problem is the enormous background of toxic, and to a lesser extent, known compounds. We hypothesize that the bottleneck of dereplication can be resolved by differential screening that detects the presence of a promising compound prior to dereplication. Using this approach, we recently discovered darobactins that have a novel scaffold and target the essential outer membrane protein BamA (Imai et al., 2019), and several additional novel compounds. In the proposed project, we will develop an ultra-high throughput screen based on encapsulating producing bacteria together with different fluorescently labeled reporters in microdroplets created in a microfluidics device. Our preliminary data show that sorting droplets can be performed at a rate of 106 a day, and leads to detection of producers of desirable antimicrobials. We will evaluate several modalities of this screen, aimed at discovering selective as well as broad-spectrum compounds acting against Gram-negative bacteria; and anti-persister compounds. The platform is likely to be of use to the field of antibiotic discovery. Leads that come out of this screen will be evaluated in vitro and in animal models of infection. Novel leads that come out of this project will be ready to enter IND-enabling studies.