Chemical-genetic profiling reveals cross-resistance and collateral sensitivity between antimicrobial peptides

Abstract

27Antimicrobial peptides (AMPs) are key effectors of the innate immune system and promising ther-28 apeutic agents. Yet, knowledge on how to design AMPs with minimal cross-resistance to human 29 host-defense peptides remains limited. Here, with a chemical-genetic approach, we systemati-30 cally assessed the resistance determinants of Escherichia coli against 15 different AMPs. Alt-31 hough generalizations about AMP resistance are common in the literature, we found that AMPs 32 with different physicochemical properties and cellular targets vary considerably in their resistance 33 determinants. As a consequence, collateral sensitivity effects were common: numerous genes 34 decreased susceptibility to one AMP while simultaneously sensitized to others. Finally, the chem- 35ical-genetic map predicted the cross-resistance spectrum of laboratory-evolved human-B-defen-36 sin-3 resistant lineages. Our work substantially broadens the scope of known resistance-modu-37 lating genes and explores the pleiotropic effects of AMP resistance. In the future, the chemical-38 genetic map could inform efforts to minimize cross-resistance between therapeutic and human 39 host AMPs. 40 41 Introduction 42 Antimicrobial peptides (AMPs) play a crucial role in general defense mechanisms against micro-43 bial pathogens in all classes of life. Although there is a considerable diversity in their amino acid 44 content, length, and structure, AMPs are typically positively charged and amphipathic mole-45 cules 1,2 . These properties allow them to adsorb onto the bacterial cell surface and penetrate 46 through the membrane to exert their diverse antibacterial actions 3 . As AMPs have a broad spec-47 trum of activity, considerable efforts have been allocated to the research and development of 48 novel anti-infective compounds originating from AMPs 4,5 . However, the clinical development of 49AMP therapies, has also raised concerns that these approaches may drive bacterial evolution of 50 resistance to human host-defense peptides 6,7 . As well, therapeutic AMPs are required to be active 51 against pathogenic bacteria, many of which have already evolved resistance against human host 52 AMPs 8 . Therefore, ideally, resistance mechanisms against therapeutic and host AMPs should not 53 overlap. 54Accumulating evidence suggest that AMPs differ considerably in their mode of actions, 55 which may influence the specific microbial resistance mechanisms against them 1,9 . First, there 56 are substantial differences in the electrostatic interactions and transport processes that lead to 57 the cellular uptake of AMPs 3,10 . Second, the cellular targets of AMPs are also diverse in nature. 58For instance, apart from their membrane-disruptive activities, AMPs inhibit intracellular processes 59 3 such as bacterial DNA and RNA synthesis, translation, cell wall synthesis, and diverse metabolic 60 pathways 1,11 . However, the extent to which the genetic determinants of resistance differ across 61 AMPs remains unclear, because most of our knowledge comes from case stud...

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“…AMPs comprise a potentially promising toolkit combatting MDR because antibioticresistant bacteria perform a high frequency of collateral sensitivity to antimicrobial peptides, [13], [16][17]. X. budapestensis (EMA) and X. szentirmaii (EMC) are abundant sources of NR-AMP molecules of large target spectra and strong anti-pathogen potential, [35].…”

“…The AMPs are of great perspectives to combat MDR prokaryotes because antibiotic-resistant bacteria perform a high frequency of collateral sensitivity to antimicrobial peptides, [16]. Furthermore, the mobility patterns of AMP-resistance genes differ from those of the antibiotics-resistance genes [17]. .…”