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Witzany C, Rolff J, Regoes RR, Igler C. The pharmacokinetic-pharmacodynamic modelling framework as a tool to predict drug resistance evolution. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001368. [PMID: 37522891 PMCID: PMC10433423 DOI: 10.1099/mic.0.001368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Pharmacokinetic-pharmacodynamic (PKPD) models, which describe how drug concentrations change over time and how that affects pathogen growth, have proven highly valuable in designing optimal drug treatments aimed at bacterial eradication. However, the fast rise of antimicrobial resistance calls for increased focus on an additional treatment optimization criterion: avoidance of resistance evolution. We demonstrate here how coupling PKPD and population genetics models can be used to determine treatment regimens that minimize the potential for antimicrobial resistance evolution. Importantly, the resulting modelling framework enables the assessment of resistance evolution in response to dynamic selection pressures, including changes in antimicrobial concentration and the emergence of adaptive phenotypes. Using antibiotics and antimicrobial peptides as an example, we discuss the empirical evidence and intuition behind individual model parameters. We further suggest several extensions of this framework that allow a more comprehensive and realistic prediction of bacterial escape from antimicrobials through various phenotypic and genetic mechanisms.
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Affiliation(s)
| | - Jens Rolff
- Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Roland R. Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Claudia Igler
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- School of Biological Sciences, University of Manchester, Manchester, UK
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2
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Jangir PK, Ogunlana L, Szili P, Czikkely M, Shaw LP, Stevens EJ, Yu Y, Yang Q, Wang Y, Pál C, Walsh TR, MacLean CR. The evolution of colistin resistance increases bacterial resistance to host antimicrobial peptides and virulence. eLife 2023; 12:e84395. [PMID: 37094804 PMCID: PMC10129329 DOI: 10.7554/elife.84395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 04/05/2023] [Indexed: 04/26/2023] Open
Abstract
Antimicrobial peptides (AMPs) offer a promising solution to the antibiotic resistance crisis. However, an unresolved serious concern is that the evolution of resistance to therapeutic AMPs may generate cross-resistance to host AMPs, compromising a cornerstone of the innate immune response. We systematically tested this hypothesis using globally disseminated mobile colistin resistance (MCR) that has been selected by the use of colistin in agriculture and medicine. Here, we show that MCR provides a selective advantage to Escherichia coli in the presence of key AMPs from humans and agricultural animals by increasing AMP resistance. Moreover, MCR promotes bacterial growth in human serum and increases virulence in a Galleria mellonella infection model. Our study shows how the anthropogenic use of AMPs can drive the accidental evolution of resistance to the innate immune system of humans and animals. These findings have major implications for the design and use of therapeutic AMPs and suggest that MCR may be difficult to eradicate, even if colistin use is withdrawn.
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Affiliation(s)
- Pramod K Jangir
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Lois Ogunlana
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Petra Szili
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research NetworkSzegedHungary
- Doctoral School of Multidisciplinary Medical Sciences, University of SzegedSzegedHungary
| | - Marton Czikkely
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research NetworkSzegedHungary
| | - Liam P Shaw
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Emily J Stevens
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhouChina
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and RegulaWon, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Yang Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural UniversityBeijingChina
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research NetworkSzegedHungary
| | - Timothy R Walsh
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Craig R MacLean
- Department of Biology, University of OxfordOxfordUnited Kingdom
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3
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Rodríguez-Rojas A, Rolff J. Antimicrobial activity of cationic antimicrobial peptides against stationary phase bacteria. Front Microbiol 2022; 13:1029084. [PMID: 36386690 PMCID: PMC9641054 DOI: 10.3389/fmicb.2022.1029084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/10/2022] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial peptides (AMPs) are ancient antimicrobial weapons used by multicellular organisms as components of their innate immune defenses. Because of the antibiotic crisis, AMPs have also become candidates for developing new drugs. Here, we show that five different AMPs of different classes are effective against non-dividing Escherichia coli and Staphylococcus aureus. By comparison, three conventional antibiotics from the main three classes of antibiotics poorly kill non-dividing bacteria at clinically relevant doses. The killing of fast-growing bacteria by AMPs is faster than that of slow-dividing bacteria and, in some cases, without any difference. Still, non-dividing bacteria are effectively killed over time. Our results point to a general property of AMPs, which might explain why selection has favored AMPs in the evolution of metazoan immune systems. The ability to kill non-dividing cells is another reason that makes AMPs exciting candidates for drug development.
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Affiliation(s)
- Alexandro Rodríguez-Rojas
- Evolutionary Biology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Department for Small Animal Internal Medicine, Clinic for Small Animals, University of Veterinary Medicine, Vienna, Austria
| | - Jens Rolff
- Evolutionary Biology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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4
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Hu LI, Stohl EA, Seifert HS. The Neisseria gonorrhoeae type IV pilus promotes resistance to hydrogen peroxide- and LL-37-mediated killing by modulating the availability of intracellular, labile iron. PLoS Pathog 2022; 18:e1010561. [PMID: 35714158 PMCID: PMC9246397 DOI: 10.1371/journal.ppat.1010561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 06/30/2022] [Accepted: 04/29/2022] [Indexed: 11/20/2022] Open
Abstract
The Neisseria gonorrhoeae Type IV pilus is a multifunctional, dynamic fiber involved in host cell attachment, DNA transformation, and twitching motility. We previously reported that the N. gonorrhoeae pilus is also required for resistance against hydrogen peroxide-, antimicrobial peptide LL-37-, and non-oxidative, neutrophil-mediated killing. We tested whether the hydrogen peroxide, LL-37, and neutrophil hypersensitivity phenotypes in non-piliated N. gonorrhoeae could be due to elevated iron levels. Iron chelation in the growth medium rescued a nonpiliated pilE mutant from both hydrogen peroxide- and antimicrobial peptide LL-37-mediated killing, suggesting these phenotypes are related to iron availability. We used the antibiotic streptonigrin, which depends on free cytoplasmic iron and oxidation to kill bacteria, to determine whether piliation affected intracellular iron levels. Several non-piliated, loss-of-function mutants were more sensitive to streptonigrin killing than the piliated parental strain. Consistent with the idea that higher available iron levels in the under- and non-piliated strains were responsible for the higher streptonigrin sensitivity, iron limitation by desferal chelation restored resistance to streptonigrin in these strains and the addition of iron restored the sensitivity to streptonigrin killing. The antioxidants tiron and dimethylthiourea rescued the pilE mutant from streptonigrin-mediated killing, suggesting that the elevated labile iron pool in non-piliated bacteria leads to streptonigrin-dependent reactive oxygen species production. These antioxidants did not affect LL-37-mediated killing. We confirmed that the pilE mutant is not more sensitive to other antibiotics showing that the streptonigrin phenotypes are not due to general bacterial envelope disruption. The total iron content of the cell was unaltered by piliation when measured using ICP-MS suggesting that only the labile iron pool is affected by piliation. These results support the hypothesis that piliation state affects N. gonorrhoeae iron homeostasis and influences sensitivity to various host-derived antimicrobial agents. Neisseria gonorrhoeae is a bacterium that causes the sexually transmitted infection, gonorrhea. The bacteria express a fiber on their surface called a pilus that mediates many interactions of the bacterial cell with host cells and tissues. The ability to resist killing by white cells is one important ability that N. gonorrhoeae uses to allow infection of otherwise healthy people. We show here that the pilus help resist white cell killing by modulating the levels of iron within the bacterial cell.
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Affiliation(s)
- Linda I. Hu
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Elizabeth A. Stohl
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - H Steven Seifert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- * E-mail:
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5
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Yoo YJ, Chung IY, Jalde SS, Choi HK, Cho YH. An iron-chelating sulfonamide identified from Drosophila-based screening for antipathogenic discovery. Virulence 2022; 13:833-843. [PMID: 35521696 PMCID: PMC9090290 DOI: 10.1080/21505594.2022.2069325] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
We exploited bacterial infection assays using the fruit fly Drosophila melanogaster to identify anti-infective compounds that abrogate the pathological consequences in the infected hosts. Here, we demonstrated that a pyridine-3-N-sulfonylpiperidine derivative (4a) protects Drosophila from the acute infections caused by bacterial pathogens including Pseudomonas aeruginosa. 4a did not inhibit the growth of P. aeruginosa in vitro, but inhibited the production of secreted toxins such as pyocyanin and hydrogen cyanide, while enhancing the production of pyoverdine and pyochelin, indicative of iron deprivation. Based on its catechol moiety, 4a displayed iron-chelating activity in vitro toward both iron (II) and iron (III), more efficiently than the approved iron-chelating drugs such as deferoxamine and deferiprone, concomitant with more potent antibacterial efficacy in Drosophila infections and unique transcriptome profile. Taken together, these results delineate a Drosophila-based strategy to screen for antipathogenic compounds, which interfere with iron uptake crucial for bacterial virulence and survival in host tissues.
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Affiliation(s)
- Yeon-Ji Yoo
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam, Korea
| | - In-Young Chung
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam, Korea
| | | | | | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam, Korea
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6
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Li C, Sutherland D, Hammond SA, Yang C, Taho F, Bergman L, Houston S, Warren RL, Wong T, Hoang LMN, Cameron CE, Helbing CC, Birol I. AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens. BMC Genomics 2022; 23:77. [PMID: 35078402 PMCID: PMC8788131 DOI: 10.1186/s12864-022-08310-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/12/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Antibiotic resistance is a growing global health concern prompting researchers to seek alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are attracting attention again as therapeutic agents with promising utility in this domain, and using in silico methods to discover novel AMPs is a strategy that is gaining interest. Such methods can sift through large volumes of candidate sequences and reduce lab screening costs. RESULTS Here we introduce AMPlify, an attentive deep learning model for AMP prediction, and demonstrate its utility in prioritizing peptide sequences derived from the Rana [Lithobates] catesbeiana (bullfrog) genome. We tested the bioactivity of our predicted peptides against a panel of bacterial species, including representatives from the World Health Organization's priority pathogens list. Four of our novel AMPs were active against multiple species of bacteria, including a multi-drug resistant isolate of carbapenemase-producing Escherichia coli. CONCLUSIONS We demonstrate the utility of deep learning based tools like AMPlify in our fight against antibiotic resistance. We expect such tools to play a significant role in discovering novel candidates of peptide-based alternatives to classical antibiotics.
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Affiliation(s)
- Chenkai Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Darcy Sutherland
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC, V5Z 4R4, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Figali Taho
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Lauren Bergman
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C3, Canada
| | - Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C3, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Titus Wong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Medical Microbiology Laboratory, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - Linda M N Hoang
- Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC, V5Z 4R4, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C3, Canada
- Division of Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Caren C Helbing
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C3, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
- Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC, V5Z 4R4, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.
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7
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Escobar‐Salom M, Torrens G, Jordana‐Lluch E, Oliver A, Juan C. Mammals' humoral immune proteins and peptides targeting the bacterial envelope: from natural protection to therapeutic applications against multidrug‐resistant
Gram
‐negatives. Biol Rev Camb Philos Soc 2022; 97:1005-1037. [PMID: 35043558 PMCID: PMC9304279 DOI: 10.1111/brv.12830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
Abstract
Mammalian innate immunity employs several humoral ‘weapons’ that target the bacterial envelope. The threats posed by the multidrug‐resistant ‘ESKAPE’ Gram‐negative pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are forcing researchers to explore new therapeutic options, including the use of these immune elements. Here we review bacterial envelope‐targeting (peptidoglycan and/or membrane‐targeting) proteins/peptides of the mammalian immune system that are most likely to have therapeutic applications. Firstly we discuss their general features and protective activity against ESKAPE Gram‐negatives in the host. We then gather, integrate, and discuss recent research on experimental therapeutics harnessing their bactericidal power, based on their exogenous administration and also on the discovery of bacterial and/or host targets that improve the performance of this endogenous immunity, as a novel therapeutic concept. We identify weak points and knowledge gaps in current research in this field and suggest areas for future work to obtain successful envelope‐targeting therapeutic options to tackle the challenge of antimicrobial resistance.
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Affiliation(s)
- María Escobar‐Salom
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
| | - Gabriel Torrens
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
| | - Elena Jordana‐Lluch
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
| | - Antonio Oliver
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
| | - Carlos Juan
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
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8
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Multidrug resistance crisis during COVID-19 pandemic: Role of anti-microbial peptides as next-generation therapeutics. Colloids Surf B Biointerfaces 2021; 211:112303. [PMID: 34952285 PMCID: PMC8685351 DOI: 10.1016/j.colsurfb.2021.112303] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/03/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023]
Abstract
The decreasing effectiveness of conventional drugs due to multidrug-resistance is a major challenge for the scientific community, necessitating development of novel antimicrobial agents. In the present era of coronavirus 2 (COVID-19) pandemic, patients are being widely exposed to antimicrobial drugs and hence the problem of multidrug-resistance shall be aggravated in the days to come. Consequently, revisiting the phenomena of multidrug resistance leading to formulation of effective antimicrobial agents is the need of the hour. As a result, this review sheds light on the looming crisis of multidrug resistance in wake of the COVID-19 pandemic. It highlights the problem, significance and approaches for tackling microbial resistance with special emphasis on anti-microbial peptides as next-generation therapeutics against multidrug resistance associated diseases. Antimicrobial peptides exhibit exceptional mechanism of action enabling rapid killing of microbes at low concentration, antibiofilm activity, immunomodulatory properties along with a low tendency for resistance development providing them an edge over conventional antibiotics. The review is unique as it discusses the mode of action, pharmacodynamic properties and application of antimicrobial peptides in areas ranging from therapeutics to agriculture.
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9
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Nunes LGP, Reichert T, Machini MT. His-Rich Peptides, Gly- and His-Rich Peptides: Functionally Versatile Compounds with Potential Multi-Purpose Applications. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10302-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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Ridyard KE, Overhage J. The Potential of Human Peptide LL-37 as an Antimicrobial and Anti-Biofilm Agent. Antibiotics (Basel) 2021; 10:antibiotics10060650. [PMID: 34072318 PMCID: PMC8227053 DOI: 10.3390/antibiotics10060650] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
The rise in antimicrobial resistant bacteria threatens the current methods utilized to treat bacterial infections. The development of novel therapeutic agents is crucial in avoiding a post-antibiotic era and the associated deaths from antibiotic resistant pathogens. The human antimicrobial peptide LL-37 has been considered as a potential alternative to conventional antibiotics as it displays broad spectrum antibacterial and anti-biofilm activities as well as immunomodulatory functions. While LL-37 has shown promising results, it has yet to receive regulatory approval as a peptide antibiotic. Despite the strong antimicrobial properties, LL-37 has several limitations including high cost, lower activity in physiological environments, susceptibility to proteolytic degradation, and high toxicity to human cells. This review will discuss the challenges associated with making LL-37 into a viable antibiotic treatment option, with a focus on antimicrobial resistance and cross-resistance as well as adaptive responses to sub-inhibitory concentrations of the peptide. The possible methods to overcome these challenges, including immobilization techniques, LL-37 delivery systems, the development of LL-37 derivatives, and synergistic combinations will also be considered. Herein, we describe how combination therapy and structural modifications to the sequence, helicity, hydrophobicity, charge, and configuration of LL-37 could optimize the antimicrobial and anti-biofilm activities of LL-37 for future clinical use.
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11
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Nakahara H, Mori K, Mori T, Matsuzoe N. Induction of spontaneous phenotype conversion in Ralstonia solanacearum by addition of iron compounds in liquid medium. J Microbiol Methods 2021; 186:106233. [PMID: 33965508 DOI: 10.1016/j.mimet.2021.106233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 11/19/2022]
Abstract
Ralstonia solanacearum is a soil-borne pathogen that causes bacterial wilt in plants. The wild-type strain of R. solanacearum undergoes spontaneous phenotype conversion (PC), from a fluidal to non-fluidal colony morphology. PC mutants are non-pathogenic due to reduced virulence factors, and can control wilt diseases as biological control agents. The induction factors of PC in R. solanacearum are currently unclear. Here, we investigated the effect of iron treatment on bacterial growth of wild-type strain and PC mutant, and PC of the wild-type strain in liquid medium. Interestingly, PC was frequently induced in the single cultured wild-type strain by iron treatment; however, PC was not induced in the co-culture. In a co-culture of both strains, the PC mutant showed increased growth compared to the wild-type strain by iron treatment. Furthermore, we investigated the effects of iron treatment on the bacterial growth and PC of the wild-type strain under different culture conditions of medium type (MM broth, BG broth, and water medium), iron compounds, and pH. In BG broth, PC occurred frequently regardless of iron treatment. In MM broth, the optimal conditions for high frequency induction of PC by iron treatments were treatment of iron (III) EDTA, and under pH 7-8. Conversely, PC was not induced by iron treatment in water medium and in MM broth under pH 5 conditions. Common to the culture conditions wherein PC was not induced by iron treatment, the bacterial density of the wild-type strain was as low as 106 CFU mL-1 or less. Finally, we investigated the effects on bacterial growth and PC of the wild-type strain by the iron treatment and addition of culture filtrate after cultivation of the wild-type strain at high concentration. In medium containing only the culture filtrate, PC did not occur. However, in medium containing the culture filtrate and iron, PC occurred frequently. Our results thus suggest that high-density growth of the wild-type strain as well as the presence of iron are involved in inducing PC in R. solanacearum.
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Affiliation(s)
- Hiroki Nakahara
- Arid Land Research Center, Tottori University, Hamasaka 1390, Tottori 680-0001, Japan.
| | - Kento Mori
- Graduate School of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Tsukide 3-1-100, Higashi-ku, Kumamoto 862-8502, Japan
| | - Taro Mori
- Faculty of Education, Shiga University, Hiratsu 2-5-1, Otsu, Shiga 520-0862, Japan
| | - Naotaka Matsuzoe
- Graduate School of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Tsukide 3-1-100, Higashi-ku, Kumamoto 862-8502, Japan
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12
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UPR modulation of host immunity by Pseudomonas aeruginosa in cystic fibrosis. Clin Sci (Lond) 2020; 134:1911-1934. [PMID: 32537652 DOI: 10.1042/cs20200066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/11/2022]
Abstract
Cystic fibrosis (CF) is a progressive multiorgan autosomal recessive disease with devastating impact on the lungs caused by derangements of the CF transmembrane conductance regulator (CFTR) gene. Morbidity and mortality are caused by the triad of impaired mucociliary clearance, microbial infections and chronic inflammation. Pseudomonas aeruginosa is the main respiratory pathogen in individuals with CF infecting most patients in later stages. Despite its recognized clinical impact, molecular mechanisms that underlie P. aeruginosa pathogenesis and the host response to P. aeruginosa infection remain incompletely understood. The nuclear hormone receptor peroxisome proliferator-activated receptor (PPAR) γ (PPARγ), has shown to be reduced in CF airways. In the present study, we sought to investigate the upstream mechanisms repressing PPARγ expression and its impact on airway epithelial host defense. Endoplasmic reticulum-stress (ER-stress) triggered unfolded protein response (UPR) activated by misfolded CFTR and P. aeruginosa infection contributed to attenuated expression of PPARγ. Specifically, the protein kinase RNA (PKR)-like ER kinase (PERK) signaling pathway led to the enhanced expression of the CCAAT-enhancer-binding-protein homologous protein (CHOP). CHOP induction led to the repression of PPARγ expression. Mechanistically, we showed that CHOP induction mediated PPARγ attenuation, impacted the innate immune function of normal and ∆F508 primary airway epithelial cells by reducing expression of antimicrobial peptide (AMP) and paraoxanse-2 (PON-2), as well as enhancing IL-8 expression. Furthermore, mitochondrial reactive oxygen species production (mt-ROS) and ER-stress positive feedforward loop also dysregulated mitochondrial bioenergetics. Additionally, our findings implicate that PPARγ agonist pioglitazone (PIO) has beneficial effect on the host at the multicellular level ranging from host defense to mitochondrial re-energization.
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13
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Rodríguez-Rojas A, Nath A, El Shazely B, Santi G, Kim JJ, Weise C, Kuropka B, Rolff J. Antimicrobial Peptide Induced-Stress Renders Staphylococcus aureus Susceptible to Toxic Nucleoside Analogs. Front Immunol 2020; 11:1686. [PMID: 33133056 PMCID: PMC7550632 DOI: 10.3389/fimmu.2020.01686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
Cationic antimicrobial peptides (AMPs) are active immune effectors of multicellular organisms and are also considered as new antimicrobial drug candidates. One of the problems encountered when developing AMPs as drugs is the difficulty of reaching sufficient killing concentrations under physiological conditions. Here, using pexiganan, a cationic peptide derived from a host defense peptide of the African clawed frog and the first AMP developed into an antibacterial drug, we studied whether sub-lethal effects of AMPs can be harnessed to devise treatment combinations. We studied the pexiganan stress response of Staphylococcus aureus at sub-lethal concentrations using quantitative proteomics. Several proteins involved in nucleotide metabolism were elevated, suggesting a metabolic demand. We then show that Staphylococcus aureus is highly susceptible to antimetabolite nucleoside analogs when exposed to pexiganan, even at sub-inhibitory concentrations. These findings could be used to enhance pexiganan potency while decreasing the risk of resistance emergence, and our findings can likely be extended to other antimicrobial peptides.
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Affiliation(s)
| | - Arpita Nath
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Baydaa El Shazely
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
- Zoology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Greta Santi
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Joshua Jay Kim
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jens Rolff
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
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14
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Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress. PLoS Genet 2020; 16:e1008649. [PMID: 32163413 PMCID: PMC7093028 DOI: 10.1371/journal.pgen.1008649] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 03/24/2020] [Accepted: 02/04/2020] [Indexed: 11/19/2022] Open
Abstract
Unicellular organisms have the prevalent challenge to survive under oxidative stress of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). ROS are present as by-products of photosynthesis and aerobic respiration. These reactive species are even employed by multicellular organisms as potent weapons against microbes. Although bacterial defences against lethal and sub-lethal oxidative stress have been studied in model bacteria, the role of fluctuating H2O2 concentrations remains unexplored. It is known that sub-lethal exposure of Escherichia coli to H2O2 results in enhanced survival upon subsequent exposure. Here we investigate the priming response to H2O2 at physiological concentrations. The basis and the duration of the response (memory) were also determined by time-lapse quantitative proteomics. We found that a low level of H2O2 induced several scavenging enzymes showing a long half-life, subsequently protecting cells from future exposure. We then asked if the phenotypic resistance against H2O2 alters the evolution of resistance against oxygen stress. Experimental evolution of H2O2 resistance revealed faster evolution and higher levels of resistance in primed cells. Several mutations were found to be associated with resistance in evolved populations affecting different loci but, counterintuitively, none of them was directly associated with scavenging systems. Our results have important implications for host colonisation and infections where microbes often encounter reactive oxygen species in gradients. Throughout evolution, bacteria were exposed to reactive oxygen species and evolved the ability to scavenge toxic oxygen radicals. Furthermore, multicellular organisms evolved the ability to produce such oxygen species directed against pathogens. Recent studies also suggest that ROS such as H2O2 play an important role during host gut colonisation by its microbiota. Traditionally, experiments with different antimicrobials have been carried out using fixed concentrations while in nature, including in intra-host environments, microbes are more likely to experience this type of stress in steps or gradients. Here we show that bacteria treated with sub-lethal concentrations of H2O2 (priming) survive far better than non-treated cells when they subsequently encounter a higher concentration. We also found that the 'priming' response has a protective role from lethal mutagenesis. This protection is provided by long-lived proteins that, upon priming, remain at a high level for several generations as determined by time-lapse LC-mass spectrometry. Bacteria that were primed evolved H2O2 resistance faster and to a higher level. Moreover, mutations that increase resistance to H2O2, as determined by whole-genome sequencing (WGS), do not occur in known scavenger encoding genes but in loci coding for other functions, at least in E. coli.
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15
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Malhotra S, Hayes D, Wozniak DJ. Cystic Fibrosis and Pseudomonas aeruginosa: the Host-Microbe Interface. Clin Microbiol Rev 2019; 32:e00138-18. [PMID: 31142499 PMCID: PMC6589863 DOI: 10.1128/cmr.00138-18] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In human pathophysiology, the clash between microbial infection and host immunity contributes to multiple diseases. Cystic fibrosis (CF) is a classical example of this phenomenon, wherein a dysfunctional, hyperinflammatory immune response combined with chronic pulmonary infections wreak havoc upon the airway, leading to a disease course of substantial morbidity and shortened life span. Pseudomonas aeruginosa is an opportunistic pathogen that commonly infects the CF lung, promoting an accelerated decline of pulmonary function. Importantly, P. aeruginosa exhibits significant resistance to innate immune effectors and to antibiotics, in part, by expressing specific virulence factors (e.g., antioxidants and exopolysaccharides) and by acquiring adaptive mutations during chronic infection. In an effort to review our current understanding of the host-pathogen interface driving CF pulmonary disease, we discuss (i) the progression of disease within the primitive CF lung, specifically focusing on the role of host versus bacterial factors; (ii) critical, neutrophil-derived innate immune effectors that are implicated in CF pulmonary disease, including reactive oxygen species (ROS) and antimicrobial peptides (e.g., LL-37); (iii) P. aeruginosa virulence factors and adaptive mutations that enable evasion of the host response; and (iv) ongoing work examining the distribution and colocalization of host and bacterial factors within distinct anatomical niches of the CF lung.
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Affiliation(s)
- Sankalp Malhotra
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Don Hayes
- The Ohio State University College of Medicine, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Section of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Daniel J Wozniak
- The Ohio State University College of Medicine, Columbus, Ohio, USA
- Section of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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16
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Yu G, Baeder DY, Regoes RR, Rolff J. Predicting drug resistance evolution: insights from antimicrobial peptides and antibiotics. Proc Biol Sci 2019. [PMID: 29540517 DOI: 10.1098/rspb.2017.2687] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antibiotic resistance constitutes one of the most pressing public health concerns. Antimicrobial peptides (AMPs) of multicellular organisms are considered part of a solution to this problem, and AMPs produced by bacteria such as colistin are last-resort drugs. Importantly, AMPs differ from many antibiotics in their pharmacodynamic characteristics. Here we implement these differences within a theoretical framework to predict the evolution of resistance against AMPs and compare it to antibiotic resistance. Our analysis of resistance evolution finds that pharmacodynamic differences all combine to produce a much lower probability that resistance will evolve against AMPs. The finding can be generalized to all drugs with pharmacodynamics similar to AMPs. Pharmacodynamic concepts are familiar to most practitioners of medical microbiology, and data can be easily obtained for any drug or drug combination. Our theoretical and conceptual framework is, therefore, widely applicable and can help avoid resistance evolution if implemented in antibiotic stewardship schemes or the rational choice of new drug candidates.
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Affiliation(s)
- Guozhi Yu
- Evolutionary Biology, Institut für Biologie, Freie Universität Berlin, Koenigin-Luise Strasse 1-3, 14195 Berlin, Germany
| | - Desiree Y Baeder
- Institute of Integrative Biology, Universitätsstrasse 16 ETH Zurich, 8092 Zurich, Switzerland
| | - Roland R Regoes
- Institute of Integrative Biology, Universitätsstrasse 16 ETH Zurich, 8092 Zurich, Switzerland
| | - Jens Rolff
- Evolutionary Biology, Institut für Biologie, Freie Universität Berlin, Koenigin-Luise Strasse 1-3, 14195 Berlin, Germany .,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
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17
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Tzeng YL, Berman Z, Toh E, Bazan JA, Turner AN, Retchless AC, Wang X, Nelson DE, Stephens DS. Heteroresistance to the model antimicrobial peptide polymyxin B in the emerging Neisseria meningitidis lineage 11.2 urethritis clade: mutations in the pilMNOPQ operon. Mol Microbiol 2018; 111:254-268. [PMID: 30338585 DOI: 10.1111/mmi.14153] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2018] [Indexed: 02/02/2023]
Abstract
Clusters of Neisseria meningitidis (Nm) urethritis among primarily heterosexual males in multiple US cities have been attributed to a unique non-encapsulated meningococcal clade (the US Nm urethritis clade, US_NmUC) within the hypervirulent clonal complex 11. Resistance to antimicrobial peptides (AMPs) is a key feature of urogenital pathogenesis of the closely related species, Neisseria gonorrhoeae. The US_NmUC isolates were found to be highly resistant to the model AMP, polymyxin B (PmB, MICs 64-256 µg ml-1 ). The isolates also demonstrated stable subpopulations of heteroresistant colonies that showed near total resistant to PmB (MICs 384-1024 µg ml-1 ) and colistin (MIC 256 µg ml-1 ) as well as enhanced LL-37 resistance. This is the first observation of heteroresistance in N. meningitidis. Consistent with previous findings, overall PmB resistance in US_NmUC isolates was due to active Mtr efflux and LptA-mediated lipid A modification. However, whole genome sequencing, variant analyses and directed mutagenesis revealed that the heteroresistance phenotypes and very high-level AMP resistance were the result of point mutations and IS1655 element movement in the pilMNOPQ operon, encoding the type IV pilin biogenesis apparatus. Cross-resistance to other classes of antibiotics was also observed in the heteroresistant colonies. High-level resistance to AMPs may contribute to the pathogenesis of US_NmUC.
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Affiliation(s)
- Yih-Ling Tzeng
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zachary Berman
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Evelyn Toh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jose A Bazan
- Division of Infectious Diseases, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, OH, 43210, USA.,Sexual Health Clinic, Columbus Public Health, Columbus, OH, 43210, USA
| | - Abigail Norris Turner
- Division of Infectious Diseases, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Adam C Retchless
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Xin Wang
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - David E Nelson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David S Stephens
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, 30322, USA
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18
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Mixed Communities of Mucoid and Nonmucoid Pseudomonas aeruginosa Exhibit Enhanced Resistance to Host Antimicrobials. mBio 2018; 9:mBio.00275-18. [PMID: 29588399 PMCID: PMC5874919 DOI: 10.1128/mbio.00275-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa causes chronic pulmonary infections in patients with cystic fibrosis (CF). P. aeruginosa mucoid conversion, defined by overproduction of the exopolysaccharide alginate, correlates with accelerated decline in CF patient lung function. Recalcitrance of the mucoid phenotype to clearance by antibiotics and the immune response is well documented. However, despite advantages conferred by mucoidy, mucoid variants often revert to a nonmucoid phenotype both in vitro and in vivo Mixed populations of mucoid isolates and nonmucoid revertants are recovered from CF lungs, suggesting a selective benefit for coexistence of these variants. In this study, cocultures of mucoid and nonmucoid variants exhibited enhanced resistance to two host antimicrobials: LL-37, a cationic antimicrobial peptide, and hydrogen peroxide (H2O2). Alginate production by mucoid isolates protected nonmucoid variants in consortia from LL-37, as addition of alginate exogenously to nonmucoid variants abrogated LL-37 killing. Conversely, nonmucoid revertants shielded mucoid variants from H2O2 stress via catalase (KatA) production, which was transcriptionally repressed by AlgT and AlgR, central regulators of alginate biosynthesis. Furthermore, extracellular release of KatA by nonmucoid revertants was dependent on lys, encoding an endolysin implicated in autolysis and extracellular DNA (eDNA) release. Overall, these data provide a rationale to study interactions of P. aeruginosa mucoid and nonmucoid variants as contributors to evasion of innate immunity and persistence within the CF lung.IMPORTANCEP. aeruginosa mucoid conversion within lungs of cystic fibrosis (CF) patients is a hallmark of chronic infection and predictive of poor prognosis. The selective benefit of mixed populations of mucoid and nonmucoid variants, often isolated from chronically infected CF patients, has not been explored. Here, we show that mixed-variant communities of P. aeruginosa demonstrate advantages in evasion of innate antimicrobials via production of shared goods: alginate and catalase. These data argue for therapeutically targeting multiple constituents (both mucoid and nonmucoid variants) within diversified P. aeruginosa communities in vivo, as these variants can differentially shield one another from components of the host response.
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19
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Gunn JS, Bakaletz LO, Wozniak DJ. What's on the Outside Matters: The Role of the Extracellular Polymeric Substance of Gram-negative Biofilms in Evading Host Immunity and as a Target for Therapeutic Intervention. J Biol Chem 2016; 291:12538-12546. [PMID: 27129225 DOI: 10.1074/jbc.r115.707547] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Biofilms are organized multicellular communities encased in an extracellular polymeric substance (EPS). Biofilm-resident bacteria resist immunity and antimicrobials. The EPS provides structural stability and presents a barrier; however, a complete understanding of how EPS structure relates to biological function is lacking. This review focuses on the EPS of three Gram-negative pathogens: Pseudomonas aeruginosa, nontypeable Haemophilus influenzae, and Salmonella enterica serovar Typhi/Typhimurium. Although EPS proteins and polysaccharides are diverse, common constituents include extracellular DNA, DNABII (DNA binding and bending) proteins, pili, flagella, and outer membrane vesicles. The EPS biochemistry promotes recalcitrance and informs the design of therapies to reduce or eliminate biofilm burden.
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Affiliation(s)
- John S Gunn
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, Ohio 43210; Center for Microbial Interface Biology, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205
| | - Lauren O Bakaletz
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, Ohio 43210; Center for Microbial Interface Biology, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205; Departments of Pediatrics and Otolaryngology, The Research Institute at Nationwide Children's Hospital and Ohio State University, Columbus, Ohio 43210
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, Ohio 43210; Center for Microbial Interface Biology, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205; Department of Microbiology, Ohio State University, Columbus, Ohio 43210.
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