1
|
Ghosh C, Popella L, Dhamodharan V, Jung J, Dietzsch J, Barquist L, Höbartner C, Vogel J. A comparative analysis of peptide-delivered antisense antibiotics using diverse nucleotide mimics. RNA (NEW YORK, N.Y.) 2024; 30:624-643. [PMID: 38413166 PMCID: PMC11098465 DOI: 10.1261/rna.079969.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes have great potential for counteracting antimicrobial resistance and for precision microbiome editing. To date, the development of such antisense antibiotics has primarily focused on using phosphorodiamidate morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based human therapy. Here, we directly compare the activities of seven chemically distinct 10mer ASOs, all designed to target the essential gene acpP upon delivery with a KFF-peptide carrier into Salmonella. Our systematic analysis of PNA, PMO, phosphorothioate (PTO)-modified DNA, 2'-methylated RNA (RNA-OMe), 2'-methoxyethylated RNA (RNA-MOE), 2'-fluorinated RNA (RNA-F), and 2'-4'-locked RNA (LNA) is based on a variety of in vitro and in vivo methods to evaluate ASO uptake, target pairing and inhibition of bacterial growth. Our data show that only PNA and PMO are efficiently delivered by the KFF peptide into Salmonella to inhibit bacterial growth. Nevertheless, the strong target binding affinity and in vitro translational repression activity of LNA and RNA-MOE make them promising modalities for antisense antibiotics that will require the identification of an effective carrier.
Collapse
Affiliation(s)
- Chandradhish Ghosh
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), Munich, Germany
| | - V Dhamodharan
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Julia Dietzsch
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), Munich, Germany
- Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
| |
Collapse
|
2
|
Zheng S, Tang X, Yang Q, Zhou X, Li Y, Wu Z. Aeromonas veronii tolC modulates its virulence and the immune response of freshwater pearl mussels, Hyriopsis cumingii. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 153:105137. [PMID: 38224762 DOI: 10.1016/j.dci.2024.105137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/17/2024]
Abstract
Aeromonas veronii is an opportunistic pathogen that causes diseases in aquatic animals, but its key virulence factors remain unclear. We screened the gene tolC with significantly different expression levels in the two isolates, A. veronii GL2 (higher virulence) and A. veronii FO1 (lower virulence). Therefore, we constructed mutant strain ΔtolC and analyzed its immunological properties. ΔtolC exhibited the reduced ability of biofilms formation, inhibited envelope stress response mediated by several antibiotics except cefuroxime, implying the ability to evade host immunity might be restrained. Challenge tests showed that the LD50 of ΔtolC was 10.89-fold than that of GL2. Enzymatic activities of ΔtolC group were significantly lower and peak time was delayed to 12 h, as demonstrated by qRT-PCR results. Histopathological examination displayed that the degree of tissue damage in ΔtolC group was alleviated. The results show that tolC is an important virulence factor of A. veronii, which provides references for live-attenuated vaccine.
Collapse
Affiliation(s)
- Sichun Zheng
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Xiaoqi Tang
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Qinglin Yang
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Xicheng Zhou
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Yanhong Li
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Zhengli Wu
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
3
|
Zhang L, Tian X, Sun L, Mi K, Wang R, Gong F, Huang L. Bacterial Efflux Pump Inhibitors Reduce Antibiotic Resistance. Pharmaceutics 2024; 16:170. [PMID: 38399231 PMCID: PMC10892612 DOI: 10.3390/pharmaceutics16020170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Bacterial resistance is a growing problem worldwide, and the number of deaths due to drug resistance is increasing every year. We must pay great attention to bacterial resistance. Otherwise, we may go back to the pre-antibiotic era and have no drugs on which to rely. Bacterial resistance is the result of several causes, with efflux mechanisms widely recognised as a significant factor in the development of resistance to a variety of chemotherapeutic and antimicrobial medications. Efflux pump inhibitors, small molecules capable of restoring the effectiveness of existing antibiotics, are considered potential solutions to antibiotic resistance and have been an active area of research in recent years. This article provides a review of the efflux mechanisms of common clinical pathogenic bacteria and their efflux pump inhibitors and describes the effects of efflux pump inhibitors on biofilm formation, bacterial virulence, the formation of bacterial persister cells, the transfer of drug resistance among bacteria, and mismatch repair. Numerous efforts have been made in the past 20 years to find novel efflux pump inhibitors which are known to increase the effectiveness of medicines against multidrug-resistant strains. Therefore, the application of efflux pump inhibitors has excellent potential to address and reduce bacterial resistance.
Collapse
Affiliation(s)
- Lan Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyuan Tian
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Sun
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Kun Mi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Ru Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengying Gong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingli Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
4
|
Aksomaitiene J, Novoslavskij A, Malakauskas M. Whole-Genome Sequencing-Based Profiling of Antimicrobial Resistance Genes and Core-Genome Multilocus Sequence Typing of Campylobacter jejuni from Different Sources in Lithuania. Int J Mol Sci 2023; 24:16017. [PMID: 37958998 PMCID: PMC10648690 DOI: 10.3390/ijms242116017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Campylobacter jejuni is known as one of the main causative agents of gastroenteritis in humans worldwide, and the rise of antimicrobial resistance (AMR) in Campylobacter is a growing public health challenge of special concern. Whole-genome sequencing (WGS) was used to characterize genetic determinants of AMR in 53 C. jejuni isolates from dairy cattle, broiler products, wild birds, and humans in Lithuania. The WGS-based study revealed 26 C. jejuni AMR markers that conferred resistance to various antimicrobials. Genetic markers associated with resistance to beta-lactamases, tetracycline, and aminoglycosides were found in 79.3%, 28.3%, and 9.4% of C. jejuni isolates, respectively. Additionally, genetic markers associated with multidrug resistance (MDR) were found in 90.6% of C. jejuni isolates. The WGS data analysis revealed that a common mutation in the quinolone resistance-determining region (QRDR) was R285K (854G > A) at 86.8%, followed by A312T (934G > A) at 83% and T86I (257C > T) at 71.7%. The phenotypic resistance analysis performed with the agar dilution method revealed that ciprofloxacin (CIP) (90.6%), ceftriaxone (CRO) (67.9%), and tetracycline (TET) (45.3%) were the predominant AMR patterns. MDR was detected in 41.5% (22/53) of the isolates tested. Fifty-seven virulence genes were identified in all C. jejuni isolates; most of these genes were associated with motility (n = 28) and chemotaxis (n = 10). Additionally, all C. jejuni isolates harbored virulence genes related to adhesion, invasion, LOS, LPS, CPS, transportation, and CDT. In total, 16 sequence types (STs) and 11 clonal complexes (CC) were identified based on core-genome MLST (cgMLST) analysis. The data analysis revealed distinct diversity depending on phenotypic and genotypic antimicrobial resistance of C. jejuni.
Collapse
Affiliation(s)
- Jurgita Aksomaitiene
- Department of Food Safety and Quality, Faculty of Veterinary Medicine, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania; (A.N.); (M.M.)
| | | | | |
Collapse
|
5
|
Mongès A, Yaakoub H, Bidon B, Glévarec G, Héricourt F, Carpin S, Chauderon L, Drašarová L, Spíchal L, Binder BM, Papon N, Rochange S. Are Histidine Kinases of Arbuscular Mycorrhizal Fungi Involved in the Response to Ethylene and Cytokinins? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:656-665. [PMID: 37851914 DOI: 10.1094/mpmi-05-23-0056-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Signals are exchanged at all stages of the arbuscular mycorrhizal (AM) symbiosis between fungi and their host plants. Root-exuded strigolactones are well-known early symbiotic cues, but the role of other phytohormones as interkingdom signals has seldom been investigated. Here we focus on ethylene and cytokinins, for which candidate receptors have been identified in the genome of the AM fungus Rhizophagus irregularis. Ethylene is known from the literature to affect asymbiotic development of AM fungi, and in the present study, we found that three cytokinin forms could stimulate spore germination in R. irregularis. Heterologous complementation of a Saccharomyces cerevisiae mutant strain with the candidate ethylene receptor RiHHK6 suggested that this protein can sense and transduce an ethylene signal. Accordingly, its N-terminal domain expressed in Pichia pastoris displayed saturable binding to radiolabeled ethylene. Thus, RiHHK6 displays the expected characteristics of an ethylene receptor. In contrast, the candidate cytokinin receptor RiHHK7 did not complement the S. cerevisiae mutant strain or Medicago truncatula cytokinin receptor mutants and seemed unable to bind cytokinins, suggesting that another receptor is involved in the perception of these phytohormones. Taken together, our results support the hypothesis that AM fungi respond to a range of phytohormones and that these compounds bear multiple functions in the rhizosphere beyond their known roles as internal plant developmental regulators. Our analysis of two phytohormone receptor candidates also sheds new light on the possible perception mechanisms in AM fungi. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Ayla Mongès
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, INP Toulouse, 31326 Castanet-Tolosan, France
| | - Hajar Yaakoub
- UNIV Angers, IRF, SFR 4208 ICAT, F-49000 Angers, France
| | | | - Gaëlle Glévarec
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - François Héricourt
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
| | - Sabine Carpin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
| | - Lucie Chauderon
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, INP Toulouse, 31326 Castanet-Tolosan, France
| | - Lenka Drašarová
- Isotope Laboratory, Institute of Experimental Botany, The Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Lukáš Spíchal
- Czech Advanced Technology and Research Institute, Šlechtitelů 27, Olomouc CZ-783 71, Palacký University, Olomouc, Czech Republic
| | - Brad M Binder
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, U.S.A
| | - Nicolas Papon
- UNIV Angers, IRF, SFR 4208 ICAT, F-49000 Angers, France
| | - Soizic Rochange
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, INP Toulouse, 31326 Castanet-Tolosan, France
| |
Collapse
|
6
|
Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 218] [Impact Index Per Article: 218.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
Collapse
Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
| |
Collapse
|
7
|
Comparison of Phenotype and Genotype Virulence and Antimicrobial Factors of Salmonella Typhimurium Isolated from Human Milk. Int J Mol Sci 2023; 24:ijms24065135. [PMID: 36982209 PMCID: PMC10048834 DOI: 10.3390/ijms24065135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
Salmonella is a common foodborne infection. Many serovars belonging to Salmonella enterica subsp. enterica are present in the gut of various animal species. They can cause infection in human infants via breast milk or cross-contamination with powdered milk. In the present study, Salmonella BO was isolated from human milk in accordance with ISO 6579-1:2017 standards and sequenced using whole-genome sequencing (WGS), followed by serosequencing and genotyping. The results also allowed its pathogenicity to be predicted. The WGS results were compared with the bacterial phenotype. The isolated strain was found to be Salmonella enterica subsp. enterica serovar Typhimurium 4:i:1,2_69M (S. Typhimurium 69M); it showed a very close similarity to S. enterica subsp. enterica serovar Typhimurium LT2. Bioinformatics sequence analysis detected eleven SPIs (SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14, C63PI, CS54_island). Significant changes in gene sequences were noted, causing frameshift mutations in yeiG, rfbP, fumA, yeaL, ybeU (insertion) and lpfD, avrA, ratB, yacH (deletion). The sequences of several proteins were significantly different from those coded in the reference genome; their three-dimensional structure was predicted and compared with reference proteins. Our findings indicate the presence of a number of antimicrobial resistance genes that do not directly imply an antibiotic resistance phenotype.
Collapse
|
8
|
Amarnani R, Revdekar A, Salvi B, Shende P. Potential of nanocarriers using ABC transporters for antimicrobial resistance. Drug Discov Today 2023; 28:103570. [PMID: 36990146 DOI: 10.1016/j.drudis.2023.103570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/08/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Some existing therapies such as antimicrobial regimens, drug combinations, among others, are employed for the treatment of infections that are a threat to the healthcare industry owing to low drug efficacy, increasing dosage regimes, mutation in bacteria and poor pharmacokinetics/pharmacodynamics properties of drugs. Overuse of antibiotics is fostering the emergence and spread of inherent microorganisms that confer temporary and permanent resistance. Nanocarriers accompanying the ABC transporter efflux mechanism are considered 'magic bullets' (i.e., effective antibacterial agents) and can traverse the multidrug-resistant obstacle owing to their multifunctional capabilities (e.g., nanostructure, variability in in vivo functions, etc.) by interfering with normal cell activity. This review focuses on novel applications of the ABC transporter pump by nanocarriers to overcome the resistance caused by the various organs of the body. Teaser: Nanocarriers, the ABC transporter and overcoming multidrug resistance.
Collapse
Affiliation(s)
- Ragini Amarnani
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India
| | - Amey Revdekar
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India
| | - Bhagyashree Salvi
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India
| | - Pravin Shende
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India.
| |
Collapse
|
9
|
RND Pump-Mediated Efflux of Amotosalen, a Compound Used in Pathogen Inactivation Technology to Enhance Safety of Blood Transfusion Products, May Compromise Its Gram-Negative Anti-Bacterial Activity. mSphere 2023; 8:e0067322. [PMID: 36853056 PMCID: PMC10117049 DOI: 10.1128/msphere.00673-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Pathogen inactivation is a strategy to improve the safety of transfusion products. The only pathogen reduction technology for blood products currently approved in the US utilizes a psoralen compound, called amotosalen, in combination with UVA light to inactivate bacteria, viruses, and protozoa. Psoralens have structural similarity to bacterial multidrug efflux pump substrates. As these efflux pumps are often overexpressed in multidrug-resistant pathogens, we tested whether contemporary drug-resistant pathogens might show resistance to amotosalen and other psoralens based on multidrug efflux mechanisms through genetic, biophysical, and molecular modeling analysis. The main efflux systems in Enterobacterales, Acinetobacter baumannii, and Pseudomonas aeruginosa are tripartite resistance-nodulation-cell division (RND) systems, which span the inner and outer membranes of Gram-negative pathogens, and expel antibiotics from the bacterial cytoplasm into the extracellular space. We provide evidence that amotosalen is an efflux substrate for the E. coli AcrAB, Acinetobacter baumannii AdeABC, and P. aeruginosa MexXY RND efflux pumps. Furthermore, we show that the MICs for contemporary Gram-negative bacterial isolates for these species and others in vitro approached and exceeded the concentration of amotosalen used in the approved platelet and plasma inactivation procedures. These findings suggest that otherwise safe and effective inactivation methods should be further studied to identify possible gaps in their ability to inactivate contemporary, multidrug-resistant bacterial pathogens. IMPORTANCE Pathogen inactivation is a strategy to enhance the safety of transfused blood products. We identify the compound, amotosalen, widely used for pathogen inactivation, as a bacterial multidrug efflux substrate. Specifically, experiments suggest that amotosalen is pumped out of bacteria by major efflux pumps in E. coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. Such efflux pumps are often overexpressed in multidrug-resistant pathogens. Importantly, the MICs for contemporary multidrug-resistant Enterobacterales, Acinetobacter baumannii, Pseudomonas aeruginosa, Burkholderia spp., and Stenotrophomonas maltophilia isolates approached or exceeded the amotosalen concentration used in approved platelet and plasma inactivation procedures, potentially as a result of efflux pump activity. Although there are important differences in methodology between our experiments and blood product pathogen inactivation, these findings suggest that otherwise safe and effective inactivation methods should be further studied to identify possible gaps in their ability to inactivate contemporary, multidrug-resistant bacterial pathogens.
Collapse
|
10
|
Cetin E, Atilgan AR, Atilgan C. DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies. J Chem Inf Model 2022; 62:6715-6726. [PMID: 35984987 PMCID: PMC9795552 DOI: 10.1021/acs.jcim.2c00507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Antibiotic resistance is a global health problem in which mutations occurring in functional proteins render drugs ineffective. The working mechanisms of the arising mutants are seldom apparent; a methodology to decipher these mechanisms systematically would render devising therapies to control the arising mutational pathways possible. Here we utilize Cα-Cβ bond vector relaxations obtained from moderate length MD trajectories to determine conduits for functionality of the resistance conferring mutants of Escherichia coli dihydrofolate reductase. We find that the whole enzyme is synchronized to the motions of the substrate, irrespective of the mutation introducing gain-of-function or loss-of function. The total coordination of the motions suggests changes in the hydrogen bond dynamics with respect to the wild type as a possible route to determine and classify the mode-of-action of individual mutants. As a result, nine trimethoprim-resistant point mutations arising frequently in evolution experiments are categorized. One group of mutants that display the largest occurrence (L28R, W30G) work directly by modifying the dihydrofolate binding region. Conversely, W30R works indirectly by the formation of the E139-R30 salt bridge which releases energy resulting from tight binding by distorting the binding cavity. A third group (D27E, F153S, I94L) arising as single, resistance invoking mutants in evolution experiment trajectories allosterically and dynamically affects a hydrogen bonding motif formed at residues 59-69-71 which in turn modifies the binding site dynamics. The final group (I5F, A26T, R98P) consists of those mutants that have properties most similar to the wild type; these only appear after one of the other mutants is fixed on the protein structure and therefore display clear epistasis. Thus, we show that the binding event is governed by the entire enzyme dynamics while the binding site residues play gating roles. The adjustments made in the total enzyme in response to point mutations are what make quantifying and pinpointing their effect a hard problem. Here, we show that hydrogen bond dynamics recorded on sub-μs time scales provide the necessary fingerprints to decipher the various mechanisms at play.
Collapse
|
11
|
Barkowsky G, Abt C, Pöhner I, Bieda A, Hammerschmidt S, Jacob A, Kreikemeyer B, Patenge N. Antimicrobial Activity of Peptide-Coupled Antisense Peptide Nucleic Acids in Streptococcus pneumoniae. Microbiol Spectr 2022; 10:e0049722. [PMID: 36321914 PMCID: PMC9784828 DOI: 10.1128/spectrum.00497-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pneumoniae is the most common cause of community-acquired pneumonia and is responsible for multiple other infectious diseases, such as meningitis and otitis media, in children. Resistance to penicillins, macrolides, and fluoroquinolones is increasing and, since the introduction of pneumococcal conjugate vaccines (PCVs), vaccine serotypes have been replaced by non-vaccine serotypes. Antisense peptide nucleic acids (PNAs) have been shown to reduce the growth of several pathogenic bacteria in various infection models. PNAs are frequently coupled to cell-penetrating peptides (CPPs) to improve spontaneous cellular PNA uptake. In this study, different CPPs were investigated for their capability to support translocation of antisense PNAs into S. pneumoniae. HIV-1 TAT- and (RXR)4XB-coupled antisense PNAs efficiently reduced the viability of S. pneumoniae strains TIGR4 and D39 in vitro. Two essential genes, gyrA and rpoB, were used as targets for antisense PNAs. Overall, the antimicrobial activity of anti-gyrA PNAs was higher than that of anti-rpoB PNAs. Target gene transcription levels in S. pneumoniae were reduced following antisense PNA treatment. The effect of HIV-1 TAT- and (RXR)4XB-anti-gyrA PNAs on pneumococcal survival was also studied in vivo using an insect infection model. Treatment increased the survival of infected Galleria mellonella larvae. Our results represent a proof of principle and may provide a basis for the development of efficient antisense molecules for treatment of S. pneumoniae infections. IMPORTANCE Streptococcus pneumoniae is the most common cause of community-acquired pneumonia and is responsible for the deaths of up to 2 million children each year. Antibiotic resistance and strain replacement by non-vaccine serotypes are growing problems. For this reason, S. pneumoniae has been added to the WHO "global priority list" of antibiotic-resistant bacteria for which novel antimicrobials are most urgently needed. In this study, we investigated whether CPP-coupled antisense PNAs show antibacterial activity in S. pneumoniae. We demonstrated that HIV-1 TAT- and (RXR)4XB-coupled antisense PNAs were able to kill S. pneumoniae in vitro. The specificity of the antimicrobial effect was verified by reduced target gene transcription levels in S. pneumoniae. Moreover, CPP-antisense PNA treatment increased the survival rate of infected Galleria mellonella larvae in vivo. Based on these results, we believe that efficient antisense PNAs can be developed for the treatment of S. pneumoniae infections.
Collapse
Affiliation(s)
- Gina Barkowsky
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Corina Abt
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Irina Pöhner
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Adam Bieda
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Anette Jacob
- Peps4LS GmbH, Heidelberg, Germany
- Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| |
Collapse
|
12
|
Sequence-Specific Gene Silencing of acrA in the Multi-drug Efflux System AcrAB Induces Sensitivity in Drug-Resistant Klebsiella pneumoniae. Mol Biotechnol 2022; 65:953-960. [DOI: 10.1007/s12033-022-00585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
|
13
|
Konwar AN, Hazarika SN, Bharadwaj P, Thakur D. Emerging Non-Traditional Approaches to Combat Antibiotic Resistance. Curr Microbiol 2022; 79:330. [PMID: 36155858 PMCID: PMC9510247 DOI: 10.1007/s00284-022-03029-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022]
Abstract
An increasing number of bacterial pathogens are acquiring resistance to the commonly used antibiotics. This has spurred a global threat leading to a resistance era and has penetrated the consciousness of the common people and the clinicians alike. The delay in discovering new antibiotics has exacerbated the resistance problem, forcing researchers to focus on unconventional antimicrobial therapeutics that differ from conventional antibiotics. Alternative therapies have emerged in recent years, including antimicrobial peptides, phage therapy, efflux pump inhibitors, antibodies, and immunomodulatory agents, which have produced impressive results in both laboratory and in clinical trials. Additionally, ultra-narrow-spectrum therapeutics such as CRISPR-Cas system and peptide nucleic acids aided in the development of sequence-specific antimicrobials. Moreover, combinatorial therapies that combine these new approaches have been efficient enough to get approval for clinical use and have accelerated the discovery of novel combination approaches that enhance the performance of already in-use antibiotics. In this review, we provide an overview of these approaches along with studies that focus on the uncharted microbial territories that have been able to deliver some of the important new antibiotics of recent times. It is hoped that the information gathered in this article will provide an update on the current antibiotic resistance threat and encourage profound research.
Collapse
Affiliation(s)
- Aditya Narayan Konwar
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam, 781035, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shabiha Nudrat Hazarika
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam, 781035, India
- Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam, 781001, India
| | - Pranami Bharadwaj
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam, 781035, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debajit Thakur
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam, 781035, India.
| |
Collapse
|
14
|
Köbel T, Melo Palhares R, Fromm C, Szymanski W, Angelidou G, Glatter T, Georg J, Berghoff BA, Schindler D. An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria. ACS Synth Biol 2022; 11:2989-3003. [PMID: 36044590 PMCID: PMC9486967 DOI: 10.1021/acssynbio.2c00164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic biology approaches life from the perspective of an engineer. Standardized and de novo design of genetic parts to subsequently build reproducible and controllable modules, for example, for circuit design, is a key element. To achieve this, natural systems and elements often serve as a blueprint for researchers. Regulation of protein abundance is controlled at DNA, mRNA, and protein levels. Many tools for the activation or repression of transcription or the destabilization of proteins are available, but easy-to-handle minimal regulatory elements on the mRNA level are preferable when translation needs to be modulated. Regulatory RNAs contribute considerably to regulatory networks in all domains of life. In particular, bacteria use small regulatory RNAs (sRNAs) to regulate mRNA translation. Slowly, sRNAs are attracting the interest of using them for broad applications in synthetic biology. Here, we promote a "plug and play" plasmid toolset to quickly and efficiently create synthetic sRNAs to study sRNA biology or their application in bacteria. We propose a simple benchmarking assay by targeting the acrA gene of Escherichia coli and rendering cells sensitive toward the β-lactam antibiotic oxacillin. We further highlight that it may be necessary to test multiple seed regions and sRNA scaffolds to achieve the desired regulatory effect. The described plasmid toolset allows quick construction and testing of various synthetic sRNAs based on the user's needs.
Collapse
Affiliation(s)
- Tania
S. Köbel
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,MaxGENESYS
Biofoundry, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany
| | - Rafael Melo Palhares
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christin Fromm
- Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Witold Szymanski
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Georgia Angelidou
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Timo Glatter
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Jens Georg
- Institut
für Biologie III, Albert-Ludwigs-Universität
Freiburg, Schänzlestraße
1, 79104 Freiburg, Germany
| | - Bork A. Berghoff
- Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany,
| | - Daniel Schindler
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,MaxGENESYS
Biofoundry, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,
| |
Collapse
|
15
|
Yamamoto K, Yamamoto N, Ayukawa S, Yasutake Y, Ishiya K, Nakashima N. Scaffold size-dependent effect on the enhanced uptake of antibiotics and other compounds by Escherichia coli and Pseudomonas aeruginosa. Sci Rep 2022; 12:5609. [PMID: 35379875 PMCID: PMC8980104 DOI: 10.1038/s41598-022-09635-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/24/2022] [Indexed: 11/29/2022] Open
Abstract
The outer membrane of Gram-negative bacteria functions as an impermeable barrier to foreign compounds. Thus, modulating membrane transport can contribute to improving susceptibility to antibiotics and efficiency of bioproduction reactions. In this study, the cellular uptake of hydrophobic and large-scaffold antibiotics and other compounds in Gram-negative bacteria was investigated by modulating the homolog expression of bamB encoding an outer membrane lipoprotein and tolC encoding an outer membrane efflux protein via gene deletion and gene silencing. The potential of deletion mutants for biotechnological applications, such as drug screening and bioproduction, was also demonstrated. Instead of being subjected to gene deletion, wild-type bacterial cells were treated with cell-penetrating peptide conjugates of a peptide nucleic acid (CPP-PNA) against bamB and tolC homologs as antisense agents. Results revealed that the single deletion of bamB and tolC in Escherichia coli increased the uptake of large- and small-scaffold hydrophobic compounds, respectively. A bamB-and-tolC double deletion mutant had a higher uptake efficiency for certain antibiotics and other compounds with high hydrophobicity than each single deletion mutant. The CPP-PNA treated E. coli and Pseudomonas aeruginosa cells showed high sensitivity to various antibiotics. Therefore, these gene deletion and silencing approaches can be utilized in therapeutic and biotechnological fields.
Collapse
Affiliation(s)
- Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan
| | - Nao Yamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Shotaro Ayukawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan
| | - Yoshiaki Yasutake
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, 169-8555, Japan
| | - Koji Ishiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan
| | - Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| |
Collapse
|
16
|
Peng Z, Maciel-Guerra A, Baker M, Zhang X, Hu Y, Wang W, Rong J, Zhang J, Xue N, Barrow P, Renney D, Stekel D, Williams P, Liu L, Chen J, Li F, Dottorini T. Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming. PLoS Comput Biol 2022; 18:e1010018. [PMID: 35333870 PMCID: PMC8986120 DOI: 10.1371/journal.pcbi.1010018] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/06/2022] [Accepted: 03/14/2022] [Indexed: 01/26/2023] Open
Abstract
Anthropogenic environments such as those created by intensive farming of livestock, have been proposed to provide ideal selection pressure for the emergence of antimicrobial-resistant Escherichia coli bacteria and antimicrobial resistance genes (ARGs) and spread to humans. Here, we performed a longitudinal study in a large-scale commercial poultry farm in China, collecting E. coli isolates from both farm and slaughterhouse; targeting animals, carcasses, workers and their households and environment. By using whole-genome phylogenetic analysis and network analysis based on single nucleotide polymorphisms (SNPs), we found highly interrelated non-pathogenic and pathogenic E. coli strains with phylogenetic intermixing, and a high prevalence of shared multidrug resistance profiles amongst livestock, human and environment. Through an original data processing pipeline which combines omics, machine learning, gene sharing network and mobile genetic elements analysis, we investigated the resistance to 26 different antimicrobials and identified 361 genes associated to antimicrobial resistance (AMR) phenotypes; 58 of these were known AMR-associated genes and 35 were associated to multidrug resistance. We uncovered an extensive network of genes, correlated to AMR phenotypes, shared among livestock, humans, farm and slaughterhouse environments. We also found several human, livestock and environmental isolates sharing closely related mobile genetic elements carrying ARGs across host species and environments. In a scenario where no consensus exists on how antibiotic use in the livestock may affect antibiotic resistance in the human population, our findings provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming. Moreover, our original data analysis method has the potential to uncover AMR transmission pathways when applied to the study of other pathogens active in other anthropogenic environments characterised by complex interconnections between host species. Livestock have been suggested as an important source of antimicrobial-resistant (AMR) Escherichia coli, capable of infecting humans and carrying resistance to drugs used in human medicine. China has a large intensive livestock farming industry, poultry being the second most important source of meat in the country, and is the largest user of antibiotics for food production in the world. Here we studied antimicrobial resistance gene overlap between E. coli isolates collected from humans, livestock and their shared environments in a large-scale Chinese poultry farm and associated slaughterhouse. By using a computational approach that integrates machine learning, whole-genome sequencing, gene sharing network and mobile genetic elements analysis we characterized the E. coli community structure, antimicrobial resistance phenotypes and the genetic relatedness of non-pathogenic and pathogenic E. coli strains. We uncovered the network of genes, associated with AMR, shared across host species (animals and workers) and environments (farm and slaughterhouse). Our approach opens up new avenues for the development of a fast, affordable and effective computational solutions that provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming.
Collapse
Affiliation(s)
- Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Xibin Zhang
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Jia Rong
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Jing Zhang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Ning Xue
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Paul Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - David Renney
- Nimrod Veterinary Products Limited, Moreton-in-Marsh, United Kingdom
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
| | - Paul Williams
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Longhai Liu
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
- * E-mail: (FL); (TD)
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- * E-mail: (FL); (TD)
| |
Collapse
|
17
|
Chigan JZ, Hu Z, Liu L, Xu YS, Ding HH, Yang KW. Quinolinyl sulfonamides and sulphonyl esters exhibit inhibitory efficacy against New Delhi metallo-β-lactamase-1 (NDM-1). Bioorg Chem 2022; 120:105654. [DOI: 10.1016/j.bioorg.2022.105654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/14/2022] [Accepted: 02/01/2022] [Indexed: 11/27/2022]
|
18
|
Stasiak M, Maćkiw E, Kowalska J, Kucharek K, Postupolski J. Silent Genes: Antimicrobial Resistance and Antibiotic Production. Pol J Microbiol 2022; 70:421-429. [PMID: 35003274 PMCID: PMC8702603 DOI: 10.33073/pjm-2021-040] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/15/2021] [Indexed: 11/05/2022] Open
Abstract
Silent genes are DNA sequences that are generally not expressed or expressed at a very low level. These genes become active as a result of mutation, recombination, or insertion. Silent genes can also be activated in laboratory conditions using pleiotropic, targeted genome-wide, or biosynthetic gene cluster approaches. Like every other gene, silent genes can spread through horizontal gene transfer. Most studies have focused on strains with phenotypic resistance, which is the most common subject. However, to fully understand the mechanism behind the spreading of antibiotic resistance, it is reasonable to study the whole resistome, including silent genes.
Collapse
Affiliation(s)
- Monika Stasiak
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Elżbieta Maćkiw
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Joanna Kowalska
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Katarzyna Kucharek
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Jacek Postupolski
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| |
Collapse
|
19
|
Potentiating antibiotic efficacy via perturbation of non-essential gene expression. Commun Biol 2021; 4:1267. [PMID: 34741116 PMCID: PMC8571399 DOI: 10.1038/s42003-021-02783-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/21/2021] [Indexed: 02/06/2023] Open
Abstract
Proliferation of multidrug-resistant (MDR) bacteria poses a threat to human health, requiring new strategies. Here we propose using fitness neutral gene expression perturbations to potentiate antibiotics. We systematically explored 270 gene knockout-antibiotic combinations in Escherichia coli, identifying 90 synergistic interactions. Identified gene targets were subsequently tested for antibiotic synergy on the transcriptomic level via multiplexed CRISPR-dCas9 and showed successful sensitization of E. coli without a separate fitness cost. These fitness neutral gene perturbations worked as co-therapies in reducing a Salmonella enterica intracellular infection in HeLa. Finally, these results informed the design of four antisense peptide nucleic acid (PNA) co-therapies, csgD, fnr, recA and acrA, against four MDR, clinically isolated bacteria. PNA combined with sub-minimal inhibitory concentrations of trimethoprim against two isolates of Klebsiella pneumoniae and E. coli showed three cases of re-sensitization with minimal fitness impacts. Our results highlight a promising approach for extending the utility of current antibiotics.
Collapse
|
20
|
In-Vitro Characterization of Growth Inhibition against the Gut Pathogen of Potentially Probiotic Lactic Acid Bacteria Strains Isolated from Fermented Products. Microorganisms 2021; 9:microorganisms9102141. [PMID: 34683462 PMCID: PMC8537437 DOI: 10.3390/microorganisms9102141] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 12/19/2022] Open
Abstract
Lactic acid bacteria (LAB) are probiotic candidates that may restore the balance of microbiota populations in intestinal microbial ecosystems by controlling pathogens and thereby promoting host health. The goal of this study was to isolate potential probiotic LAB strains and characterize their antimicrobial abilities against pathogens in intestinal microbiota. Among 54 LAB strains isolated from fermented products, five LAB strains (NSMJ15, NSMJ16, NSMJ23, NSMJ42, and NFFJ04) were selected as potential probiotic candidates based on in vitro assays of acid and bile salt tolerance, cell surface hydrophobicity, adhesion to the intestinal epithelium, and antagonistic activity. Phylogenetic analysis based on 16S rRNA genes showed that they have high similarities of 99.58-100% to Lacticaseibacillus paracasei strains NSMJ15 and NFFJ04, Lentilactobacillus parabuchneri NSMJ16, Levilactobacillus brevis NSMJ23, and Schleiferilactobacillus harbinensis NSMJ42. To characterize their antimicrobial abilities against pathogens in intestinal microbiota, the impact of cell-free supernatant (CFS) treatment in 10% (v/v) fecal suspensions prepared using pooled cattle feces was investigated using in vitro batch cultures. Bacterial community analysis using rRNA amplicon sequencing for control and CFS-treated fecal samples at 8 and 16 h incubation showed the compositional change after CFS treatment for all five LAB strains. The changed compositions were similar among them, but there were few variable increases or decreases in some bacterial groups. Interestingly, as major genera that could exhibit pathogenicity and antibiotic resistance, the members of Bacillus, Escherichia, Leclercia, Morganella, and Vagococcus were decreased at 16 h in all CFS-treated samples. Species-level classification suggested that the five LAB strains are antagonistic to gut pathogens. This study showed the probiotic potential of the five selected LAB strains; in particular, their antimicrobial properties against pathogens present in the intestinal microbiota. These strains would therefore seem to play an important role in modulating the intestinal microbiome of the host.
Collapse
|
21
|
Andersson J, Fuller M, Ashenden A, Holt SA, Köper I. Increasing Antibiotic Susceptibility: The Use of Cationic Gold Nanoparticles in Gram-Negative Bacterial Membrane Models. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9735-9743. [PMID: 34347499 DOI: 10.1021/acs.langmuir.1c01150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance will be one of the most prominent challenges to health-care systems in the coming decades, with the OECD predicting that up to 2.4 million deaths will be caused between 2015 and 2050 by drug-resistant bacterial infections in first-world countries alone, with infections costing health-care systems billions of dollars each year. Developing new methods to increase bacterial susceptibility toward drugs is an important step in treating resistant infections. Here, the synergistic effects of gold nanoparticles and the antibiotic drug colistin sulfate have been examined. A tethered lipid bilayer membrane was used to mimic a Gram-negative bacterial cell membrane. Exposing the membrane to gold nanoparticles prior to adding the antibiotic significantly increased the effect of the antibiotic on the membrane. Cationic gold nanoparticles could thus be used to enhance bacterial susceptibility to antibiotics, leading to a more potent treatment.
Collapse
Affiliation(s)
- Jakob Andersson
- Flinders Institute for Nanoscale Science and Technology, Flinders University, Bedford Park 5042, South Australia
- Australian Centre for Neutron Scattering, Australian Nuclear Science Technology Institute, Lucas Heights 2234, New South Wales, Australia
- Austrian Institute of Technology GmbH, Giefinggase 4, 1210 Vienna, Austria
| | - Melanie Fuller
- Flinders Institute for Nanoscale Science and Technology, Flinders University, Bedford Park 5042, South Australia
- Australian Centre for Neutron Scattering, Australian Nuclear Science Technology Institute, Lucas Heights 2234, New South Wales, Australia
| | - Alex Ashenden
- Flinders Institute for Nanoscale Science and Technology, Flinders University, Bedford Park 5042, South Australia
| | - Stephen A Holt
- Australian Centre for Neutron Scattering, Australian Nuclear Science Technology Institute, Lucas Heights 2234, New South Wales, Australia
| | - Ingo Köper
- Flinders Institute for Nanoscale Science and Technology, Flinders University, Bedford Park 5042, South Australia
| |
Collapse
|
22
|
Specific and Global RNA Regulators in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22168632. [PMID: 34445336 PMCID: PMC8395346 DOI: 10.3390/ijms22168632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 01/20/2023] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.
Collapse
|
23
|
Tamer YT, Gaszek I, Rodrigues M, Coskun FS, Farid M, Koh AY, Russ W, Toprak E. The antibiotic efflux protein TolC is a highly evolvable target under colicin E1 or TLS phage selection. Mol Biol Evol 2021; 38:4493-4504. [PMID: 34175926 PMCID: PMC8476145 DOI: 10.1093/molbev/msab190] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages and bacterial toxins are promising antibacterial agents to treat infections caused by multidrug-resistant (MDR) bacteria. In fact, bacteriophages have recently been successfully used to treat life-threatening infections caused by MDR bacteria (Schooley RT, Biswas B, Gill JJ, Hernandez-Morales A, Lancaster J, Lessor L, Barr JJ, Reed SL, Rohwer F, Benler S, et al. 2017. Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrob Agents Chemother. 61(10); Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. 2018. Phage treatment of an aortic graft infected with Pseudomonas aeruginosa. Evol Med Public Health. 2018(1):60–66; Petrovic Fabijan A, Lin RCY, Ho J, Maddocks S, Ben Zakour NL, Iredell JR, Westmead Bacteriophage Therapy Team. 2020. Safety of bacteriophage therapy in severe Staphylococcus aureus infection. Nat Microbiol. 5(3):465–472). One potential problem with using these antibacterial agents is the evolution of resistance against them in the long term. Here, we studied the fitness landscape of the Escherichia coli TolC protein, an outer membrane efflux protein that is exploited by a pore forming toxin called colicin E1 and by TLS phage (Pagie L, Hogeweg P. 1999. Colicin diversity: a result of eco-evolutionary dynamics. J Theor Biol. 196(2):251–261; Andersen C, Hughes C, Koronakis V. 2000. Chunnel vision. Export and efflux through bacterial channel-tunnels. EMBO Rep. 1(4):313–318; Koronakis V, Andersen C, Hughes C. 2001. Channel-tunnels. Curr Opin Struct Biol. 11(4):403–407; Czaran TL, Hoekstra RF, Pagie L. 2002. Chemical warfare between microbes promotes biodiversity. Proc Natl Acad Sci U S A. 99(2):786–790; Cascales E, Buchanan SK, Duché D, Kleanthous C, Lloubès R, Postle K, Riley M, Slatin S, Cavard D. 2007. Colicin biology. Microbiol Mol Biol Rev. 71(1):158–229). By systematically assessing the distribution of fitness effects of ∼9,000 single amino acid replacements in TolC using either positive (antibiotics and bile salts) or negative (colicin E1 and TLS phage) selection pressures, we quantified evolvability of the TolC. We demonstrated that the TolC is highly optimized for the efflux of antibiotics and bile salts. In contrast, under colicin E1 and TLS phage selection, TolC sequence is very sensitive to mutations. Finally, we have identified a large set of mutations in TolC that increase resistance of E. coli against colicin E1 or TLS phage without changing antibiotic susceptibility of bacterial cells. Our findings suggest that TolC is a highly evolvable target under negative selection which may limit the potential clinical use of bacteriophages and bacterial toxins if evolutionary aspects are not taken into account.
Collapse
Affiliation(s)
- Yusuf Talha Tamer
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ilona Gaszek
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Marinelle Rodrigues
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Fatma Sevde Coskun
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michael Farid
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Andrew Y Koh
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - William Russ
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Erdal Toprak
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
24
|
Wang X, Wang Y, Ling Z, Zhang C, Fu M, Wang Y, Wang S, Zhang S, Shen Z. Peptide nucleic acid restores colistin susceptibility through modulation of MCR-1 expression in Escherichia coli. J Antimicrob Chemother 2021; 75:2059-2065. [PMID: 32417908 DOI: 10.1093/jac/dkaa140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Plasmid-mediated mechanisms of drug resistance accelerate the spread of polymyxin resistance, leaving clinicians with few or no antibacterial options for the treatment of infections caused by MDR bacteria, especially carbapenemase-producing strains. OBJECTIVES To evaluate the associations among promoter sequence variation, mcr-1 expression, host factors and levels of colistin resistance and to propose antisense agents such as peptide nucleic acids (PNAs) targeting mcr-1 as a tool to restore colistin susceptibility through modulation of MCR-1 expression in Escherichia coli. METHODS A β-galactosidase assay was performed to study mcr-1 promoter activity. Quantitative real-time PCR and western blot assays were used to identify the expression level of MCR-1 in WT strains and transformants. Three PNAs targeting different regions of mcr-1 were designed and synthesized to determine whether they can effectively inhibit MCR-1 expression. MIC was measured to test colistin susceptibility in the presence or absence of PNA-1 in mcr-1-carrying E. coli. RESULTS Variation in the mcr-1 promoter sequence and host species affect promoter activity, MCR-1 expression levels and colistin MICs. One PNA targeting the ribosome-binding site fully inhibited the expression of mcr-1 at a concentration of 4 μM, resulting in significantly increased susceptibility to colistin. The MIC90 of colistin decreased from 8 to 2 mg/L (P < 0.05) in the presence of 4 μM PNA. CONCLUSIONS These findings suggest that the antisense approach is a possible strategy to combat mcr-1-mediated resistance as well as other causes of emerging global resistance.
Collapse
Affiliation(s)
- Xiaoming Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yao Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Zhuoren Ling
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chaoyang Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Mingming Fu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shaolin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Suxia Zhang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| |
Collapse
|
25
|
Popella L, Jung J, Popova K, Ðurica-Mitić S, Barquist L, Vogel J. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics. Nucleic Acids Res 2021; 49:4705-4724. [PMID: 33849070 PMCID: PMC8096218 DOI: 10.1093/nar/gkab242] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.
Collapse
Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Kristina Popova
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Svetlana Ðurica-Mitić
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| |
Collapse
|
26
|
Schafer ME, Browne H, Goldberg JB, Greenberg DE. Peptides and Antibiotic Therapy: Advances in Design and Delivery. Acc Chem Res 2021; 54:2377-2385. [PMID: 33881843 DOI: 10.1021/acs.accounts.1c00040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibiotic resistance (AMR) is an increasing public health crisis worldwide. This threatens our ability to adequately care for patients with infections due to multi-drug-resistant (MDR) pathogens. As such, there is an urgent need to develop new classes of antimicrobials that are not based on currently utilized antibiotic scaffolds. One promising avenue of antimicrobial research that deserves renewed examination involves the use of peptides. Although antimicrobial peptides (AMPs) have been studied for a number of years, innovations in peptide design and their applications are increasingly making this approach a viable alternative to traditional small-molecule antibiotics. This review will provide updates on two ways in which peptides are being explored as antibiotics. The first topic will focus on novel types of peptides and conjugation methods that are being exploited to act as antibiotics themselves. These direct-acting modified peptides could serve as potentially useful drugs while mitigating many of the known liabilities of AMPs. The second topic relates to the use of peptides as delivery vehicles for other active compounds with antimicrobial activity. Cell-penetrating peptides (CPPs) are peptides designed to carry compounds across cell membranes and are a promising method for delivering a variety of antimicrobial compounds. When conjugated to other compounds, CPPs have been shown to be effective at increasing the uptake of both small- and large-molecular-weight compounds. This includes conjugation to antisense molecules and traditional antibiotics, resulting in increased effectiveness of these antimicrobials. One particular approach utilizes CPPs conjugated to phosphorodiamidate morpholino oligomers (PMOs). PMOs are designed to target particular pathogens in a gene-specific way. They target mRNA and block protein translation. Peptide-conjugated PMOs (PPMOs) allow for efficient delivery into the Gram-negative cytoplasm, and recent updates to their in vitro and in vivo activity are reviewed. This includes recent data to suggest that PPMOs maintain activity in the setting of multi-drug-resistant (MDR) strains, an important finding as it relates to the further development of this therapeutic approach. Other topics include the ability to have activity in the biofilm setting, a finding that likely relates to the peptide portion of the conjugate. Finally, what is known and anticipated related to the development of resistance to these peptides will be discussed.
Collapse
Affiliation(s)
- Morgan E. Schafer
- Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics and Center for Cystic Fibrosis and Airway Diseases Research, Children’s Healthcare of Atlanta, Emory University School of Medicine, 1510 Clifton Road NE, Suite 3009, Atlanta, Georgia 30322, United States
| | | | - Joanna B. Goldberg
- Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics and Center for Cystic Fibrosis and Airway Diseases Research, Children’s Healthcare of Atlanta, Emory University School of Medicine, 1510 Clifton Road NE, Suite 3009, Atlanta, Georgia 30322, United States
| | | |
Collapse
|
27
|
Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
Collapse
Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
| |
Collapse
|
28
|
Faulkner V, Cox AA, Goh S, van Bohemen A, Gibson AJ, Liebster O, Wren BW, Willcocks S, Kendall SL. Re-sensitization of Mycobacterium smegmatis to Rifampicin Using CRISPR Interference Demonstrates Its Utility for the Study of Non-essential Drug Resistance Traits. Front Microbiol 2021; 11:619427. [PMID: 33597931 PMCID: PMC7882622 DOI: 10.3389/fmicb.2020.619427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022] Open
Abstract
A greater understanding of the genes involved in antibiotic resistance in Mycobacterium tuberculosis (Mtb) is necessary for the design of improved therapies. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been previously utilized in mycobacteria to identify novel drug targets by the demonstration of gene essentiality. The work presented here shows that it can also be usefully applied to the study of non-essential genes involved in antibiotic resistance. The expression of an ADP-ribosyltransferase (Arr) involved in rifampicin resistance in Mycobacterium smegmatis was silenced using CRISPRi and the impact on rifampicin susceptibility was measured. Gene silencing resulted in a decrease in the minimum inhibitory concentration (MIC) similar to that previously reported in an arr deletion mutant. There is contradictory evidence for the toxicity of Streptococcus pyogenes dCas9 (dCas9Spy) in the literature. In this study the expression of dCas9Spy in M. smegmatis showed no impact on viability. Silencing was achieved with concentrations of the aTc inducer lower than previously described and with shorter induction times. Finally, designing small guide RNAs (sgRNAs) that target transcription initiation, or the early stages of elongation had the most impact on rifampicin susceptibility. This study demonstrates that CRISPRi based gene silencing can be as impactful as gene deletion for the study of non-essential genes and further contributes to the knowledge on the design and induction of sgRNAs for CRISPRi. This approach can be applied to other non-essential antimicrobial resistance genes such as drug efflux pumps.
Collapse
Affiliation(s)
- Valwynne Faulkner
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Adrienne Adele Cox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Shan Goh
- Department of Clinical, Pharmaceutical & Biological Science, School of Life & Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Annelies van Bohemen
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Amanda J. Gibson
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
- Centre of Excellence for Bovine TB, Aberystwyth University, Aberystwyth, United Kingdom
| | - Oliver Liebster
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Brendan W. Wren
- Department of Infection Biology, The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sam Willcocks
- Department of Infection Biology, The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sharon L. Kendall
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| |
Collapse
|
29
|
Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers Retain Activity against Multidrug-Resistant Pseudomonas aeruginosa In Vitro and In Vivo. mBio 2021; 12:mBio.02411-20. [PMID: 33436433 PMCID: PMC7844538 DOI: 10.1128/mbio.02411-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Numerous Gram-negative bacteria are becoming increasingly resistant to multiple, if not all, classes of existing antibiotics. Multidrug-resistant Pseudomonas aeruginosa bacteria are a major cause of health care-associated infections in a variety of clinical settings, endangering patients who are immunocompromised or those who suffer from chronic infections, such as people with cystic fibrosis (CF). Most antimicrobials currently in the clinical pipeline are modifications of existing classes of antibiotics and are considered short-term solutions due to the emergence of resistance. Pseudomonas aeruginosa represents a major challenge for new antimicrobial drug discovery due to its versatile lifestyle, ability to develop resistance to most antibiotic classes, and capacity to form robust biofilms on surfaces and in certain hosts such as those living with cystic fibrosis (CF). A precision antibiotic approach to treating Pseudomonas could be achieved with an antisense method, specifically by using peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs). Here, we demonstrate that PPMOs targeting acpP (acyl carrier protein), lpxC (UDP-(3-O-acyl)-N-acetylglucosamine deacetylase), and rpsJ (30S ribosomal protein S10) inhibited the in vitro growth of several multidrug-resistant clinical P. aeruginosa isolates at levels equivalent to those that were effective against sensitive strains. Lead PPMOs reduced established pseudomonal biofilms alone or in combination with tobramycin or piperacillin-tazobactam. Lead PPMO dosing alone or combined with tobramycin in an acute pneumonia model reduced lung bacterial burden in treated mice at 24 h and reduced morbidity up to 5 days postinfection. PPMOs reduced bacterial burden of extensively drug-resistant P. aeruginosa in the same model and resulted in superior survival compared to conventional antibiotics. These data suggest that lead PPMOs alone or in combination with clinically relevant antibiotics represent a promising therapeutic approach for combating P. aeruginosa infections.
Collapse
|
30
|
AlMatar M, Albarri O, Makky EA, Köksal F. Efflux pump inhibitors: new updates. Pharmacol Rep 2020; 73:1-16. [PMID: 32946075 DOI: 10.1007/s43440-020-00160-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/17/2022]
Abstract
The discovery of antibiotics ought to have ended the issue of bacterial infections, but this was not the case as it has led to the evolution of various mechanisms of bacterial resistance against various antibiotics. The efflux pump remains one of the mechanisms through which organisms develop resistance against antibiotics; this is because organisms can extrude most of the clinically relevant antibiotics from the interior cell environment to the exterior environment via the efflux pumps. Efflux pumps are thought to contribute significantly to biofilm formation as highlighted by various studies. Therefore, the inhibition of these efflux pumps can be a potential way of improving the activity of antibiotics, particularly now that the discovery of novel antibiotics is becoming tedious. Efflux pump inhibitors (EPIs) are molecules that can inhibit efflux pumps; they have been considered potential therapeutic agents for rejuvenating the activity of antibiotics that have already lost their activity against bacteria. However, studies are yet to determine the specific substrates for such pumps; the effect of altered efflux activity of these pumps on biofilm formation is still being investigated. A clear knowledge of the involvement of efflux pumps in biofilm development could aid in developing new agents that can interfere with their function and help to prevent biofilms formation; thereby, improving the outcome of treatment strategies. This review focuses on the novel update of EPIs and discusses the evidence of the roles of efflux pumps in biofilm formation; the potential approaches towards overcoming the increasing problem of biofilm-based infections are also discussed.
Collapse
Affiliation(s)
- Manaf AlMatar
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang (UMP), 26300, Gambang, Kuantan, Malaysia.
| | - Osman Albarri
- Department of Biotechnology, Institute of Natural and Applied Sciences (Fen Bilimleri Enstitüsü), Çukurova University, Adana, Turkey
| | - Essam A Makky
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang (UMP), 26300, Gambang, Kuantan, Malaysia.
| | - Fatih Köksal
- Department of Medical Microbiology, Faculty of Medicine, Çukurova University, Adana, Turkey
| |
Collapse
|
31
|
Pifer R, Greenberg DE. Antisense antibacterial compounds. Transl Res 2020; 223:89-106. [PMID: 32522669 DOI: 10.1016/j.trsl.2020.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 02/08/2023]
Abstract
Extensive antibiotic use combined with poor historical drug stewardship practices have created a medical crisis in which once treatable bacterial infections are now increasingly unmanageable. To combat this, new antibiotics will need to be developed and safeguarded. An emerging class of antibiotics based upon nuclease-stable antisense technologies has proven valuable in preclinical testing against a variety of bacterial pathogens. This review describes the current state of development of antisense-based antibiotics, the mechanisms thus far employed by these compounds, and possible future avenues of research.
Collapse
Affiliation(s)
- Reed Pifer
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - David E Greenberg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas.
| |
Collapse
|
32
|
Ma KC, Mortimer TD, Hicks AL, Wheeler NE, Sánchez-Busó L, Golparian D, Taiaroa G, Rubin DHF, Wang Y, Williamson DA, Unemo M, Harris SR, Grad YH. Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae. Nat Commun 2020; 11:4126. [PMID: 32807804 PMCID: PMC7431566 DOI: 10.1038/s41467-020-17980-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 07/24/2020] [Indexed: 01/01/2023] Open
Abstract
Neisseria gonorrhoeae is an urgent public health threat due to rapidly increasing incidence and antibiotic resistance. In contrast with the trend of increasing resistance, clinical isolates that have reverted to susceptibility regularly appear, prompting questions about which pressures compete with antibiotics to shape gonococcal evolution. Here, we used genome-wide association to identify loss-of-function (LOF) mutations in the efflux pump mtrCDE operon as a mechanism of increased antibiotic susceptibility and demonstrate that these mutations are overrepresented in cervical relative to urethral isolates. This enrichment holds true for LOF mutations in another efflux pump, farAB, and in urogenitally-adapted versus typical N. meningitidis, providing evidence for a model in which expression of these pumps in the female urogenital tract incurs a fitness cost for pathogenic Neisseria. Overall, our findings highlight the impact of integrating microbial population genomics with host metadata and demonstrate how host environmental pressures can lead to increased antibiotic susceptibility.
Collapse
Affiliation(s)
- Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Allison L Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nicole E Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other STIs, Swedish Reference Laboratory for STIs, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - George Taiaroa
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Daniel H F Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yi Wang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, Swedish Reference Laboratory for STIs, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simon R Harris
- Microbiotica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
33
|
Ahmed E, El-Gendy AO, Moniem Radi NA, Mohamed T. The bactericidal efficacy of femtosecond laser-based therapy on the most common infectious bacterial pathogens in chronic wounds: an in vitro study. Lasers Med Sci 2020; 36:641-647. [PMID: 32725427 DOI: 10.1007/s10103-020-03104-0] [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: 04/23/2020] [Accepted: 07/22/2020] [Indexed: 12/29/2022]
Abstract
We investigated the influence of femtosecond laser irradiation on the growth of the two most common infectious bacterial pathogens in wounds; Staphylococcus aureus and Pseudomonas aeruginosa as an attempt to validate optimum parameters for a laser-based bactericidal modality to be used clinically. Bacterial cultures were exposed to femtosecond laser irradiation at different wavelengths, exposure times, and laser powers. The source of femtosecond laser was INSPIRE HF100 laser system, Spectra-Physics, which is pumped by a mode-locked femtosecond Ti: sapphire laser MAI TAI HP, Spectra-Physics. After irradiation, bacterial cells' survival was monitored by observing the clear zones of inhibition in cultured agar plates. Results for all strains indicated that the exposure to femtosecond laser irradiation with a wavelength ranging from ultraviolet (λ > 350 nm) to blue laser light (λ < 480 nm), for a period above 20 min and with a power density of ≈ 0.063 W/cm2, was enough to inhibit both bacterial pathogens with the results maintained for 1 week following irradiation.
Collapse
Affiliation(s)
- Esraa Ahmed
- Laser Institute for Research and Applications LIRA, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Ahmed O El-Gendy
- Laser Institute for Research and Applications LIRA, Beni-Suef University, Beni-Suef, 62511, Egypt.,Faculty of Pharmacy, Department of Microbiology and Immunology, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Naglaa A Moniem Radi
- Faculty of Medicine, Department of Microbiology and Immunology, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Tarek Mohamed
- Laser Institute for Research and Applications LIRA, Beni-Suef University, Beni-Suef, 62511, Egypt.
| |
Collapse
|
34
|
Zhang D, Hu Y, Zhu Q, Huang J, Chen Y. Proteomic interrogation of antibiotic resistance and persistence in Escherichia coli - progress and potential for medical research. Expert Rev Proteomics 2020; 17:393-409. [PMID: 32567419 DOI: 10.1080/14789450.2020.1784731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction Escherichia coli strains possess two survival strategies to endure lethal antibiotic exposure including antibiotic resistance and persistence, in which persistence can contribute to the emergence of antibiotic resistance and increasing the risk of multidrug resistance. Using high-throughput proteomics for the comprehensive understanding of mechanisms of antibiotic resistance and persistence is an effective strategy for development of target-based anti-bacterial therapies. Areas covered In this review, we summarize a comprehensive proteomic perspective of antibiotic resistance and persistence in E. coli, and overview of anti-antibiotic resistance and anti-persister molecules and strategies for the development of potential therapies. Expert opinion Proteomics allows us to globally identify the critical proteins and pathways involved in antibiotic resistance and persistence. Advancements in methodologies of proteomics and multi-omic strategies are required to overcome the limitations of proteomics and better understand mechanisms of antibiotic resistance and persistence in E. coli, and to open the possibility for identification of new targets for alternative strategies in therapeutics.
Collapse
Affiliation(s)
- Danfeng Zhang
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Yuanqing Hu
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Qiuqiang Zhu
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Jiafu Huang
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China.,Engineering Technological Center of Mushroom Industry , Zhangzhou, China
| | - Yiyun Chen
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| |
Collapse
|
35
|
Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nat Commun 2020; 11:3105. [PMID: 32561723 PMCID: PMC7305214 DOI: 10.1038/s41467-020-16932-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics. The antibiotic resistance crisis calls for new ways of restricting the ability of bacteria to evolve resistance. Here, Lukačišinová et al. perform highly controlled evolution experiments in E. coli strains to identify genetic perturbations that strongly limit the evolution of antibiotic resistance through epistasis.
Collapse
|
36
|
Moshafi MH, Ghasemshirazi S, Abiri A. The art of suicidal molecular seduction for targeting drug resistance. Med Hypotheses 2020; 140:109676. [PMID: 32203818 DOI: 10.1016/j.mehy.2020.109676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/29/2020] [Accepted: 03/14/2020] [Indexed: 12/11/2022]
Abstract
The development of drug resistance is one of the most significant challenges of the current century in the pharmaceutical industry. Superinfections, cancer chemoresistance, and resistance observed in many non-infectious diseases are nullifying the efforts and monetary supplies, put in the advent of new drug molecules. Millions of people die because of this drug resistance developed gradually through extensive use of the drugs. Inherently, some drugs are less prone to become ineffective by drug resistance than others. Covalent inhibitors bind to their targets via a biologically permanent bound with their cognate receptor and therefore display more potent inhibiting characteristics. Suicide inhibitors or mechanism-based inhibitors are one of the covalent inhibitors, which require a pre-activation step by their targeting enzyme. This step accrues their selectivity and specificity with respect to other covalent inhibitors. After that pre-activation step, they produce an analogue of the transition state of the catalytic enzyme, which is practically incapable of dissociating from the enzyme. Suicide inhibitors, due to their high intrinsic affinity toward the related enzyme, are resistant to many mechanisms involved in the development of drug resistance and can be regarded as one of the enemies of this scientific hurdle. These inhibitors compete even with monoclonal antibodies in terms of their cost-effectiveness and efficacy.
Collapse
Affiliation(s)
- Mohammad Hassan Moshafi
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Saeid Ghasemshirazi
- Department of Computer Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
| |
Collapse
|
37
|
McNeil HE, Alav I, Torres RC, Rossiter AE, Laycock E, Legood S, Kaur I, Davies M, Wand M, Webber MA, Bavro VN, Blair JMA. Identification of binding residues between periplasmic adapter protein (PAP) and RND efflux pumps explains PAP-pump promiscuity and roles in antimicrobial resistance. PLoS Pathog 2019; 15:e1008101. [PMID: 31877175 PMCID: PMC6975555 DOI: 10.1371/journal.ppat.1008101] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/22/2020] [Accepted: 09/20/2019] [Indexed: 11/19/2022] Open
Abstract
Active efflux due to tripartite RND efflux pumps is an important mechanism of clinically relevant antibiotic resistance in Gram-negative bacteria. These pumps are also essential for Gram-negative pathogens to cause infection and form biofilms. They consist of an inner membrane RND transporter; a periplasmic adaptor protein (PAP), and an outer membrane channel. The role of PAPs in assembly, and the identities of specific residues involved in PAP-RND binding, remain poorly understood. Using recent high-resolution structures, four 3D sites involved in PAP-RND binding within each PAP protomer were defined that correspond to nine discrete linear binding sequences or "binding boxes" within the PAP sequence. In the important human pathogen Salmonella enterica, these binding boxes are conserved within phylogenetically-related PAPs, such as AcrA and AcrE, while differing considerably between divergent PAPs such as MdsA and MdtA, despite overall conservation of the PAP structure. By analysing these binding sequences we created a predictive model of PAP-RND interaction, which suggested the determinants that may allow promiscuity between certain PAPs, but discrimination of others. We corroborated these predictions using direct phenotypic data, confirming that only AcrA and AcrE, but not MdtA or MsdA, can function with the major RND pump AcrB. Furthermore, we provide functional validation of the involvement of the binding boxes by disruptive site-directed mutagenesis. These results directly link sequence conservation within identified PAP binding sites with functional data providing mechanistic explanation for assembly of clinically relevant RND-pumps and explain how Salmonella and other pathogens maintain a degree of redundancy in efflux mediated resistance. Overall, our study provides a novel understanding of the molecular determinants driving the RND-PAP recognition by bridging the available structural information with experimental functional validation thus providing the scientific community with a predictive model of pump-contacts that could be exploited in the future for the development of targeted therapeutics and efflux pump inhibitors.
Collapse
Affiliation(s)
- Helen E. McNeil
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Ilyas Alav
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | | - Amanda E. Rossiter
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Eve Laycock
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Simon Legood
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Inderpreet Kaur
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Matthew Davies
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Matthew Wand
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Vassiliy N. Bavro
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- * E-mail: (VNB); (JMAB)
| | - Jessica M. A. Blair
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail: (VNB); (JMAB)
| |
Collapse
|
38
|
Sturge CR, Felder-Scott CF, Pifer R, Pybus C, Jain R, Geller BL, Greenberg DE. AcrAB-TolC Inhibition by Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers Restores Antibiotic Activity in Vitro and in Vivo. ACS Infect Dis 2019; 5:1446-1455. [PMID: 31119935 DOI: 10.1021/acsinfecdis.9b00123] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Overexpression of bacterial efflux pumps is a driver of increasing antibiotic resistance in Gram-negative pathogens. The AcrAB-TolC efflux pump has been implicated in resistance to a number of important antibiotic classes including fluoroquinolones, macrolides, and β-lactams. Antisense technology, such as peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs), can be utilized to inhibit expression of efflux pumps and restore susceptibility to antibiotics. Targeting of the AcrAB-TolC components with PPMOs revealed a sequence for acrA, which was the most effective at reducing antibiotic efflux. This acrA-PPMO enhances the antimicrobial effects of the levofloxacin and azithromycin in a panel of clinical Enterobacteriaceae strains. Additionally, acrA-PPMO enhanced azithromycin in vivo in a K. pneumoniae septicemia model. PPMOs targeting the homologous resistance-nodulation-division (RND)-efflux system in P. aeruginosa, MexAB-OprM, also enhanced potency to several classes of antibiotics in a panel of strains and in a cell culture infection model. These data suggest that PPMOs can be used as an adjuvant in antibiotic therapy to increase the efficacy or extend the spectrum of useful antibiotics against a variety of Gram-negative infections.
Collapse
Affiliation(s)
- Carolyn R. Sturge
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Christina F. Felder-Scott
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Reed Pifer
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Christine Pybus
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Raksha Jain
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Bruce L. Geller
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, United States
| | - David E. Greenberg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| |
Collapse
|
39
|
Elsayed HYA, Borroto ET, Pliego AB, Dibarrat JA, Ramirez FR, Chagoyán JCV, Salas NP, Diaz-Albiter H. Sperm Quality in Mouse After Exposure to Low Doses of TCDD. Curr Top Med Chem 2019; 19:931-943. [DOI: 10.2174/1568026619666190520090132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/05/2018] [Accepted: 03/27/2019] [Indexed: 02/07/2023]
Abstract
Background:
In the last decade, the harmful use of dioxin has been demonstrated in human
health and in the whole environment. It is well known among scientists that 2, 3, 7, 8-tetrachloro
dibenzo-p-dioxin (TCDD) is an environmental pollutant that causes endocrine disruption, which causes
male reproductive toxicity.
Objective:
The objective of the present study was to evaluate the toxicity effect of low doses of TCDD
in male CD1 mice.
Materials and Methods:
Three concentrations of TCDD (0.375, 0.75, 1.5 mg / kg) were analyzed and
the effects on spermatozoa were evaluated 10 days after oral administration of the product. As
bioindicators of TCDD toxicity, an exhaustive analysis of several spermatic parameters including
motility, vitality, count, morphology and viability, flow cytometry was used to determine the affected
sperm population by cytotoxicity and apoptosis. In addition, a morphometric analysis of testicles was
performed.
Results:
The results show that the body weight of the treated animals was reduced in medium and high
doses (0.75, 1.5 mg / kg) with respect to the control groups. In the groups treated with TCDD, the
abnormal head of the sperm increased by 52.5% more than the control group. Significant differences in
apoptosis were observed between the negative control and vehicle control, including the median dose
(0.75 mg / kg).
Conclusion:
It is concluded that at these low doses there was an impact on the quality of the mouse
sperm, adding an effect on apoptosis and cytotoxicity of sperm exposed to these doses of TCDD.
Collapse
Affiliation(s)
- Heba Yehia Anwar Elsayed
- Centro de Investigacion y Estudios Avanzados de Salud Animal, Facultad de Medicina Veterinaria y Zootecnia Universidad Autonoma del Estado de Mexico, Toluca, Mexico
| | - Esvieta Tenorio Borroto
- Centro de Investigacion y Estudios Avanzados de Salud Animal, Facultad de Medicina Veterinaria y Zootecnia Universidad Autonoma del Estado de Mexico, Toluca, Mexico
| | - Alberto Barbabosa Pliego
- Centro de Investigacion y Estudios Avanzados de Salud Animal, Facultad de Medicina Veterinaria y Zootecnia Universidad Autonoma del Estado de Mexico, Toluca, Mexico
| | - Jorge Acosta Dibarrat
- Centro de Investigacion y Estudios Avanzados de Salud Animal, Facultad de Medicina Veterinaria y Zootecnia Universidad Autonoma del Estado de Mexico, Toluca, Mexico
| | | | - Juan Carlos Vázquez Chagoyán
- Centro de Investigacion y Estudios Avanzados de Salud Animal, Facultad de Medicina Veterinaria y Zootecnia Universidad Autonoma del Estado de Mexico, Toluca, Mexico
| | - Nazario Pescador Salas
- Centro de Investigacion y Estudios Avanzados de Salud Animal, Facultad de Medicina Veterinaria y Zootecnia Universidad Autonoma del Estado de Mexico, Toluca, Mexico
| | - Hector Diaz-Albiter
- Universidad Tecnologica del Valla de Toluca, Estado de Mexico, Toluca, Mexico
| |
Collapse
|
40
|
Tamer YT, Gaszek IK, Abdizadeh H, Batur TA, Reynolds KA, Atilgan AR, Atilgan C, Toprak E. High-Order Epistasis in Catalytic Power of Dihydrofolate Reductase Gives Rise to a Rugged Fitness Landscape in the Presence of Trimethoprim Selection. Mol Biol Evol 2019; 36:1533-1550. [PMID: 30982891 PMCID: PMC6573477 DOI: 10.1093/molbev/msz086] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Evolutionary fitness landscapes of several antibiotic target proteins have been comprehensively mapped showing strong high-order epistasis between mutations, but understanding these effects at the biochemical and structural levels remained open. Here, we carried out an extensive experimental and computational study to quantitatively understand the evolutionary dynamics of Escherichia coli dihydrofolate reductase (DHFR) enzyme in the presence of trimethoprim-induced selection. To facilitate this, we developed a new in vitro assay for rapidly characterizing DHFR steady-state kinetics. Biochemical and structural characterization of resistance-conferring mutations targeting a total of ten residues spanning the substrate binding pocket of DHFR revealed distinct changes in the catalytic efficiencies of mutated DHFR enzymes. Next, we measured biochemical parameters (Km, Ki, and kcat) for a mutant library carrying all possible combinations of six resistance-conferring DHFR mutations and quantified epistatic interactions between them. We found that the high-order epistasis in catalytic power of DHFR (kcat and Km) creates a rugged fitness landscape under trimethoprim selection. Taken together, our data provide a concrete illustration of how epistatic coupling at the level of biochemical parameters can give rise to complex fitness landscapes, and suggest new strategies for developing mutant specific inhibitors.
Collapse
Affiliation(s)
- Yusuf Talha Tamer
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ilona K Gaszek
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Haleh Abdizadeh
- Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | | | - Kimberly A Reynolds
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ali Rana Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Erdal Toprak
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX
| |
Collapse
|
41
|
Soler-Bistué A, Zorreguieta A, Tolmasky ME. Bridged Nucleic Acids Reloaded. Molecules 2019; 24:E2297. [PMID: 31234313 PMCID: PMC6630285 DOI: 10.3390/molecules24122297] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022] Open
Abstract
Oligonucleotides are key compounds widely used for research, diagnostics, and therapeutics. The rapid increase in oligonucleotide-based applications, together with the progress in nucleic acids research, has led to the design of nucleotide analogs that, when part of these oligomers, enhance their efficiency, bioavailability, or stability. One of the most useful nucleotide analogs is the first-generation bridged nucleic acids (BNA), also known as locked nucleic acids (LNA), which were used in combination with ribonucleotides, deoxyribonucleotides, or other analogs to construct oligomers with diverse applications. However, there is still room to improve their efficiency, bioavailability, stability, and, importantly, toxicity. A second-generation BNA, BNANC (2'-O,4'-aminoethylene bridged nucleic acid), has been recently made available. Oligomers containing these analogs not only showed less toxicity when compared to LNA-containing compounds but, in some cases, also exhibited higher specificity. Although there are still few applications where BNANC-containing compounds have been researched, the promising results warrant more effort in incorporating these analogs for other applications. Furthermore, newer BNA compounds will be introduced in the near future, offering great hope to oligonucleotide-based fields of research and applications.
Collapse
Affiliation(s)
- Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús, CONICET, Universidad Nacional de San Martín, San Martín 1650, Argentina.
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires C1405BWE, Argentina.
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92834-6850, USA.
| |
Collapse
|
42
|
Weldrick PJ, Iveson S, Hardman MJ, Paunov VN. Breathing new life into old antibiotics: overcoming antibacterial resistance by antibiotic-loaded nanogel carriers with cationic surface functionality. NANOSCALE 2019; 11:10472-10485. [PMID: 31112150 DOI: 10.1039/c8nr10022e] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Multidrug-resistant pathogens are prevalent in chronic wounds. There is an urgent need to develop novel antimicrobials and formulation strategies that can overcome antibiotic resistance and provide a safe alternative to traditional antibiotics. This work aimed to develop a novel nanocarrier for two cationic antibiotics, tetracycline hydrochloride and lincomycin hydrochloride which can potentially overcome antibiotic resistance. In this study, we report the use of surface functionalised polyacrylic copolymer nanogels as carriers for cationic antibiotics. These nanogels can encapsulate small cationic antimicrobial molecules and act as a drug delivery system. They were further functionalised with a biocompatible cationic polyelectrolyte, bPEI, to increase their affinity towards the negatively charged bacterial cell walls. These bPEI-coated nanocarrier-encapsulated antibiotics were assessed against a range of wound isolated pathogens, which had been shown through antimicrobial susceptibility testing (AST) to be resistant to tetracycline and lincomycin. Our data reveal that bPEI-coated nanogels with encapsulated tetracycline or lincomycin displayed increased antimicrobial performance against selected wound-derived bacteria, including strains highly resistant to the free antibiotic in solution. Additionally, our nanocarrier-based antibiotics showed no detectable cytotoxic effect against human keratinocytes. We attribute the increase in the antimicrobial activity of the cationically functionalised antibiotic-loaded nanogel carriers to specific electrostatic adhesion to the microbial cell wall delivering a higher local antibiotic concentration, confirmed by scanning electron microscopy. Such a nanotechnology based approach may enhance the effectiveness of a wide variety of existing antibiotics, offering a potentially new mechanism to overcome antibiotic resistance.
Collapse
Affiliation(s)
- Paul J Weldrick
- Department of Chemistry and Biochemistry, University of Hull, Hull, HU6 7RX, UK.
| | | | | | | |
Collapse
|
43
|
Liu Y, Li R, Xiao X, Wang Z. Antibiotic adjuvants: an alternative approach to overcome multi-drug resistant Gram-negative bacteria. Crit Rev Microbiol 2019; 45:301-314. [PMID: 30985240 DOI: 10.1080/1040841x.2019.1599813] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Antibiotic resistance in Gram-negative pathogens has emerged and constituted a global crisis, thereby novel antibiotics and other anti-infective strategies are urgently needed. However, the growing gap between clinical need and drug innovation, coupled with the membrane permeability barrier in Gram-negative bacteria restricts the discovery of Gram-negative antibiotics. Antibiotic adjuvants approach provides an alternative and complementary strategy for new antibiotic discovery. These compounds restore or potentiate the activity of commonly used antibiotics against multi-drug resistant (MDR) Gram-negative bacteria by targeting resistance or enhancing action of antibiotics. In this review, we first provide a brief overview of antibiotic resistance mechanism in Gram-negative bacteria, which can be used to guide the development of new antibiotic adjuvants. Additionally, we summarize the recent achievements in the search for antibiotic adjuvants based on their modes of action. Lastly, we discuss our perspectives in developing next-generation adjuvants such as broad-spectrum adjuvants and hybridization approach, which would contribute to enrich our arsenal against MDR Gram-negative bacteria.
Collapse
Affiliation(s)
- Yuan Liu
- a College of Veterinary Medicine, Yangzhou University , Yangzhou , Jiangsu , China.,b Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou , Jiangsu , China.,c Institute of Comparative Medicine, Yangzhou University , Yangzhou , Jiangsu , China
| | - Ruichao Li
- a College of Veterinary Medicine, Yangzhou University , Yangzhou , Jiangsu , China.,b Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou , Jiangsu , China
| | - Xia Xiao
- a College of Veterinary Medicine, Yangzhou University , Yangzhou , Jiangsu , China.,b Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou , Jiangsu , China
| | - Zhiqiang Wang
- a College of Veterinary Medicine, Yangzhou University , Yangzhou , Jiangsu , China.,b Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou , Jiangsu , China
| |
Collapse
|
44
|
Ghosh C, Sarkar P, Issa R, Haldar J. Alternatives to Conventional Antibiotics in the Era of Antimicrobial Resistance. Trends Microbiol 2019; 27:323-338. [PMID: 30683453 DOI: 10.1016/j.tim.2018.12.010] [Citation(s) in RCA: 352] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 11/30/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023]
Abstract
As more antibiotics are rendered ineffective by drug-resistant bacteria, focus must be shifted towards alternative therapies for treating infections. Although several alternatives already exist in nature, the challenge is to implement them in clinical use. Advancements within biotechnology, genetic engineering, and synthetic chemistry have opened up new avenues towards the search for therapies that can substitute for antibiotics. This review provides an introduction to the various promising approaches that have been adopted in this regard. Whilst the use of bacteriophages and antibodies has been partly implemented, other promising strategies, such as probiotics, lysins, and antimicrobial peptides, are in various stages of development. Propitious concepts such as genetically modified phages, antibacterial oligonucleotides, and CRISPR-Cas9 are also discussed.
Collapse
Affiliation(s)
- Chandradhish Ghosh
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Paramita Sarkar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Rahaf Issa
- Department of Infection, Immunity and Cardiovascular Diseases, The University of Sheffield, Sheffield, UK
| | - Jayanta Haldar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India.
| |
Collapse
|
45
|
Pasupureddy R, Atul, Seshadri S, Pande V, Dixit R, Pandey KC. Current scenario and future strategies to fight artemisinin resistance. Parasitol Res 2018; 118:29-42. [PMID: 30478733 DOI: 10.1007/s00436-018-6126-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/19/2018] [Indexed: 02/05/2023]
Abstract
Despite several setbacks in the fight against malaria such as insecticide and drug resistance as well as low efficacy of available vaccines, considerable success in reducing malaria burden has been achieved in the past decade. Artemisinins (ARTs and their combination therapies, ACTs), the current frontline drugs against uncomplicated malaria, rapidly kill plasmodial parasites and are non-toxic at short exposures. Though the exact mode of action remains unclear, the endoperoxide bridge, indispensable for ART activity, is thought to react with heme released from hemoglobin hydrolysis and generate free radicals that alkylate multiple protein targets, thereby disrupting proteostasis pathways. However, rapid development of ART resistance in recent years with no potential alternatives on the horizon threaten the elimination efforts. The Greater Mekong Subregion in South-East Asia continues to churn out mutants resistant to multiple ACTs and detected in increasingly expanding geographies. Extensive research on ART-resistant strains have identified a potential candidate Kelch13, crucial for mediating ART resistance. Parasites with mutations in the propeller domains of Plasmodium falciparum Kelch13 protein were shown to have enhanced phosphatidylinositol 3-kinase levels that were concomitant with delayed parasite clearance. Current research focused on understanding the mechanism of Kelch13-mediated ART resistance could provide better insights into Plasmodium resistome. This review covers the current proposed mechanisms of ART activity, resistance strategies adopted by the parasite in response to ACTs and possible future approaches to mitigate the spread of resistance from South-East Asia.
Collapse
Affiliation(s)
- Rahul Pasupureddy
- National Institute of Malaria Research, Dwarka Sector 8, New Delhi, 110077, India.,Institute of Science, Nirma University, SG Highway, Ahmedabad, Gujarat, 382481, India
| | - Atul
- National Institute of Malaria Research, Dwarka Sector 8, New Delhi, 110077, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, 263001, India
| | - Sriram Seshadri
- Institute of Science, Nirma University, SG Highway, Ahmedabad, Gujarat, 382481, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, 263001, India
| | - Rajnikant Dixit
- National Institute of Malaria Research, Dwarka Sector 8, New Delhi, 110077, India
| | - Kailash C Pandey
- National Institute of Malaria Research, Dwarka Sector 8, New Delhi, 110077, India. .,Department of Biochemistry, Indian Council of Medical Research, National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, 462001, India.
| |
Collapse
|
46
|
Somboro AM, Osei Sekyere J, Amoako DG, Kumalo HM, Khan R, Bester LA, Essack SY. In vitro potentiation of carbapenems with tannic acid against carbapenemase-producing enterobacteriaceae: exploring natural products as potential carbapenemase inhibitors. J Appl Microbiol 2018; 126:452-467. [PMID: 30365206 DOI: 10.1111/jam.14141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 02/03/2023]
Abstract
AIMS We hypothesized and confirmed that tannic acid (TA) reverses carbapenem resistance by inhibiting carbapenemases in class A and B carbapenemase-producing Enterobacteriaceae. METHODS AND RESULTS Minimum inhibitory concentrations of carbapenems in the presence and absence of TA and other efflux pump inhibitors, TA-carbapenemases inhibition assays and computational studies showed that TA had the greatest effect on metallo-β-lactamases (MBLs) followed by class A serine-β-lactamases (SBLs). TA completely reversed the MICs of MBL producers from between 32 and ≥512 mg l-1 to susceptible values (<4 mg l-1 ) while substantially reducing the MICs of SBLs from between 16 and >512 mg l-1 to <4 to 16 mg l-1 . Tolerable cytotoxic effect was observed for the concentrations tested (8-1024 mg l-1 ). TA inhibited enzymes with a marked difference of ≈50% inhibition (IC50 ) for NDM-1 (270 μmol l-1 ) and KPC-2 (15 μmol l-1 ). CONCLUSION TA inhibited both MBLs and SBLs by targeting their hydrophobic sites. Moreover, TA had a stronger binding affinity for MBLs than SBLs as the MBLs, specifically VIM-1 (-43·7220 ± 0·4513 kcal mol-1 ) and NDM-1(-44·2329 ± 0·3806 kcal mol-1 ), interact with a larger number of their catalytic active-site residues than that of OXA-48 (-22·5275 ± 0·1300 kcal mol-1 ) and KPC-2 (-22·1164 ± 0·0111 kcal mol-1 ). SIGNIFICANCE AND IMPACT OF THE STUDY Tannic acid or its analogues could be developed into carbapenemase-inhibiting adjuvants to restore carbapenem activity in CRE infections, save many lives and reduce healthcare associated costs.
Collapse
Affiliation(s)
- A M Somboro
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - J Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - D G Amoako
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - H M Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - R Khan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - L A Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - S Y Essack
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
47
|
Blanco P, Sanz-García F, Hernando-Amado S, Martínez JL, Alcalde-Rico M. The development of efflux pump inhibitors to treat Gram-negative infections. Expert Opin Drug Discov 2018; 13:919-931. [PMID: 30198793 DOI: 10.1080/17460441.2018.1514386] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION One of the possibilities for reducing the emergence and spread of antibiotic resistance is the use of anti-resistance compounds capable of resensitizing resistant microorganisms to current antimicrobials. For this purpose, multidrug efflux pumps, whose inhibition may increase bacterial susceptibility to several antibiotics, including macrolides to which Gram-negatives are considered intrinsically resistant, have emerged as suitable targets. Areas covered: In the current review, the authors discuss different mechanisms that can be exploited for inhibiting multidrug efflux pumps and describe the properties and the potential therapeutic value of already studied efflux pumps inhibitors. Although efforts have already been made to develop these inhibitors, there are currently no good candidates for treating infectious diseases. Consequently, the authors also discuss potential approaches for their development. Expert opinion: Classical anti-resistance drugs such as beta-lactamases inhibitors, while useful, are only purposeful for treating infections caused by beta-lactamase producers. However, inhibitors of multidrug efflux pumps, which are present on all organisms, can sensitize both susceptible and resistant bacteria to antibiotics belonging to several different structural families. Since some efflux pumps are involved in bacterial infections, their inhibition may also reduce the infectivity of Gram-negative bacterial pathogens.
Collapse
Affiliation(s)
- Paula Blanco
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología. CSIC , Madrid , Spain
| | - Fernando Sanz-García
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología. CSIC , Madrid , Spain
| | - Sara Hernando-Amado
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología. CSIC , Madrid , Spain
| | - José Luis Martínez
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología. CSIC , Madrid , Spain
| | - Manuel Alcalde-Rico
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología. CSIC , Madrid , Spain
| |
Collapse
|
48
|
Sharma AK, Krzeminski J, Weissig V, Hegarty JP, Stewart DB. Cationic amphiphilic bolaamphiphile-based delivery of antisense oligonucleotides provides a potentially microbiome sparing treatment for C. difficile. J Antibiot (Tokyo) 2018; 71:713-721. [PMID: 29674636 PMCID: PMC6063762 DOI: 10.1038/s41429-018-0056-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/22/2022]
Abstract
Conventional antibiotics for C. difficile infection (CDI) have mechanisms of action without organismal specificity, potentially perpetuating the dysbiosis contributing to CDI, making antisense approaches an attractive alternative. Here, three (APDE-8, CODE-9, and CYDE-21) novel cationic amphiphilic bolaamphiphiles (CABs) were synthesized and tested for their ability to form nano-sized vesicles or vesicle-like aggregates (CABVs), which were characterized based on their physiochemical properties, their antibacterial activities, and their toxicity toward colonocyte (Caco-2) cell cultures. The antibacterial activity of empty CABVs was tested against cultures of E. coli, B. fragilis, and E. faecalis, and against C. difficile by "loading" CABVs with 25-mer antisense oligonucleotides (ASO) targeting dnaE. Our results demonstrate that empty CABVs have minimal colonocyte toxicity until concentrations of 71 µM, with CODE-9 demonstrating the least toxicity. Empty CABVs had little effect on C. difficile growth in culture (MIC90 ≥ 160 µM). While APDE-8 and CODE-9 nanocomplexes demonstrated high MIC90 against C. difficile cultures (>300 µM), CYDE-21 nanocomplexes demonstrated MIC90 at CABV concentrations of 19 µM. Empty CABVs formed from APDE-8 and CODE-9 had virtually no effect on E. coli, B. fragilis, and E. faecalis across all tested concentrations, while empty CYDE-21 demonstrated MIC90 of >160 µM against E. coli and >40 µM against B. fragilisand E. faecalis. Empty CABVs have limited antibacterial activity and they can deliver an amount of ASO effective against C. difficile at CABV concentrations associated with limited colonocyte toxicity, while sparing other bacteria. With further refinement, antisense therapies for CDI may become a viable alternative to conventional antibiotic treatment.
Collapse
Affiliation(s)
- Arun K Sharma
- Department of Pharmacology, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA
| | - Jacek Krzeminski
- Department of Pharmacology, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA
| | - Volkmar Weissig
- Department of Pharmaceutical Sciences, Nanomedicine Center of Excellence, College of Pharmacy Midwestern University, Glendale, AZ, 85308, USA
| | - John P Hegarty
- Department of Medicine, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA
| | - David B Stewart
- Department of Surgery, University of Arizona - Banner University Medical Center, Tucson, AZ, 85724, USA.
| |
Collapse
|
49
|
Durão P, Balbontín R, Gordo I. Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance. Trends Microbiol 2018; 26:677-691. [DOI: 10.1016/j.tim.2018.01.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/05/2018] [Accepted: 01/24/2018] [Indexed: 01/10/2023]
|
50
|
Daly SM, Sturge CR, Marshall-Batty KR, Felder-Scott CF, Jain R, Geller BL, Greenberg DE. Antisense Inhibitors Retain Activity in Pulmonary Models of Burkholderia Infection. ACS Infect Dis 2018; 4:806-814. [PMID: 29461800 DOI: 10.1021/acsinfecdis.7b00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Burkholderia cepacia complex is a group of Gram-negative bacteria that are opportunistic pathogens in immunocompromised individuals, such as those with cystic fibrosis (CF) or chronic granulomatous disease (CGD). Burkholderia are intrinsically resistant to many antibiotics and the lack of antibiotic development necessitates novel therapeutics. Peptide-conjugated phosphorodiamidate morpholino oligomers are antisense molecules that inhibit bacterial mRNA translation. Targeting of PPMOs to the gene acpP, which is essential for membrane synthesis, lead to defects in the membrane and ultimately bactericidal activity. Exploration of additional PPMO sequences identified the ATG and Shine-Dalgarno sites as the most efficacious for targeting acpP. The CF lung is a complex microenvironment, but PPMO inhibition was still efficacious in an artificial model of CF sputum. PPMOs had low toxicity in human CF cells at doses that were antibacterial. PPMOs also reduced the bacterial burden in the lungs of immunocompromised CyBB mice, a model of CGD. Finally, the use of multiple PPMOs was efficacious in inhibiting the growth of both Burkholderia and Pseudomonas in an in vitro model of coinfection. Due to the intrinsic resistance of Burkholderia to traditional antibiotics, PPMOs represent a novel and viable approach to the treatment of Burkholderia infections.
Collapse
Affiliation(s)
- Seth M. Daly
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Carolyn R. Sturge
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Kimberly R. Marshall-Batty
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Christina F. Felder-Scott
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Raksha Jain
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
- Department of Microbiology, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Bruce L. Geller
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, Oregon 97331, United States
| | - David E. Greenberg
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
- Department of Microbiology, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| |
Collapse
|