Heteroresistance Interdisciplinary Research Unit

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ABSTRACT Antibiotic resistance is one of the most serious medical challenges of our time. This crisis puts patients at risk of untreatable bacterial infections and threatens major advances of modern medicine that rely on antibiotics (transplants, chemotherapy, etc). There are at least 2.8 million antibiotic resistant infections each year in the US, leading to over 35,000 deaths [1]. Without significant action, worldwide annual mortality due to these infections is predicted to reach 10 million by 2050, surpassing that predicted for cancer [2]. Understanding resistance mechanisms is critical to designing novel approaches and therapeutics to combat resistant bacteria. Heteroresistance (HR) is an enigmatic form of antibiotic resistance in which a bacterial isolate harbors a resistant subpopulation that can rapidly replicate in the presence of an antibiotic, while a susceptible subpopulation is killed [3, 4]. Not only do many species of bacteria exhibit this form of phenotypic resistance, but it has been reported against nearly all classes of antibiotics [3, 5, 6]. Unfortunately, our understanding of HR is extremely limited and its relevance during infection has been unclear. We recently demonstrated that HR to diverse antibiotics, including the last-line antibiotic colistin, can cause treatment failure in an in vivo model [4, 5, 7]. Furthermore, when the frequency of the resistant subpopulation is very low (<1 in 10,000 cells) HR is misclassified as susceptible by clinical diagnostic tests, yet is still able to mediate treatment failure [4]. Our surveillance data reveal that HR to diverse classes of antibiotics is widespread even among highly resistant carbapenem-resistant Enterobacteriaceae (CRE) and Acinetobacter baumannii (CRAB). Further, we recently discovered that targeting pan-resistant bacteria with two antibiotics to which a strain exhibits HR reliably leads to effective combination therapy, highlighting that knowledge of HR can be used to guide effective therapies [5]. Taken together, these data highlight a largely unappreciated and undetected epidemic of HR in the clinic that may cause unexplained antibiotic treatment failure but can also be exploited therapeutically. The Heteroresistance Interdisciplinary Research Unit (HR-IRU) brings together an interdisciplinary team of experts in an unprecedented effort to understand the mechanisms, dynamics, and prevalence of HR. The proposed projects, supported by Clinical Isolate and Single-Cell Analysis Cores, will use a combination of genetics, single cell microscopy, dynamic flow and in vivo infection studies, modeling, and epidemiological analyses to make foundational insights into HR. At a basic level, this work will significantly broaden our understanding of how traits exhibited by subpopulations of cells can impact bacterial physiology. At a translational level, this effort will be a critical step in our fight against antibiotic resistant bacteria and lay the foundation for the discovery of novel therapeutics, diagnostics, and approaches to alleviate human suffering.