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Liu JH, Liu YY, Shen YB, Yang J, Walsh TR, Wang Y, Shen J. Plasmid-mediated colistin-resistance genes: mcr. Trends Microbiol 2024; 32:365-378. [PMID: 38008597 DOI: 10.1016/j.tim.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/28/2023]
Abstract
Colistin is regarded as a last-line drug against serious infections caused by multidrug-resistant Gram-negative bacterial pathogens. Therefore, the emergence of mobile colistin resistance (mcr) genes has attracted global concern and led to policy changes for the use of colistin in food animals across many countries. Currently, the distribution, function, mechanism of action, transmission vehicles, origin of mcr, and new treatment strategies against MCR-producing pathogens have been extensively studied. Here we review the prevalence, structure and function of mcr, the fitness cost and persistence of mcr-carrying plasmids, the impact of MCR on host immune response, as well as the control strategies to combat mcr-mediated colistin resistance.
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Affiliation(s)
- Jian-Hua Liu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou 510642, China.
| | - Yi-Yun Liu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou 510642, China
| | - Ying-Bo Shen
- National Key Laboratory of Veterinary Public Health Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou 510642, China
| | | | - Yang Wang
- National Key Laboratory of Veterinary Public Health Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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2
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Materon IC, Palzkill T. Structural biology of MCR-1-mediated resistance to polymyxin antibiotics. Curr Opin Struct Biol 2023; 82:102647. [PMID: 37399693 PMCID: PMC10527939 DOI: 10.1016/j.sbi.2023.102647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 07/05/2023]
Abstract
Polymyxins, a last resort antibiotic, target the outer membrane of pathogens and are used to address the increasing prevalence of multidrug-resistant Gram-negative bacteria. The plasmid-encoded enzyme MCR-1 confers polymyxin resistance to bacteria by modifying the outer membrane. Transferable resistance to polymyxins is a major concern; therefore, MCR-1 is an important drug target. In this review, we discuss recent structural and mechanistic aspects of MCR-1 function, its variants and homologs, and how they are relevant to polymyxin resistance. Specifically, we discuss work on polymyxin-mediated disruption of the outer and inner membranes, computational studies on the catalytic mechanism of MCR-1, mutagenesis and structural analysis concerning residues important for substrate binding in MCR-1, and finally, advancements in inhibitors targeting MCR-1.
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Affiliation(s)
- Isabel Cristina Materon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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3
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Hanpaibool C, Ounjai P, Yotphan S, Mulholland AJ, Spencer J, Ngamwongsatit N, Rungrotmongkol T. Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation. J Comput Aided Mol Des 2023; 37:479-489. [PMID: 37488458 DOI: 10.1007/s10822-023-00519-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
Owing to the emergence of antibiotic resistance, the polymyxin colistin has been recently revived to treat acute, multidrug-resistant Gram-negative bacterial infections. Positively charged colistin binds to negatively charged lipids and damages the outer membrane of Gram-negative bacteria. However, the MCR-1 protein, encoded by the mobile colistin resistance (mcr) gene, is involved in bacterial colistin resistance by catalysing phosphoethanolamine (PEA) transfer onto lipid A, neutralising its negative charge, and thereby reducing its interaction with colistin. Our preliminary results showed that treatment with a reference pyrazolone compound significantly reduced colistin minimal inhibitory concentrations in Escherichia coli expressing mcr-1 mediated colistin resistance (Hanpaibool et al. in ACS Omega, 2023). A docking-MD combination was used in an ensemble-based docking approach to identify further pyrazolone compounds as candidate MCR-1 inhibitors. Docking simulations revealed that 13/28 of the pyrazolone compounds tested are predicted to have lower binding free energies than the reference compound. Four of these were chosen for in vitro testing, with the results demonstrating that all the compounds tested could lower colistin MICs in an E. coli strain carrying the mcr-1 gene. Docking of pyrazolones into the MCR-1 active site reveals residues that are implicated in ligand-protein interactions, particularly E246, T285, H395, H466, and H478, which are located in the MCR-1 active site and which participate in interactions with MCR-1 in ≥ 8/10 of the lowest energy complexes. This study establishes pyrazolone-induced colistin susceptibility in E. coli carrying the mcr-1 gene, providing a method for the development of novel treatments against colistin-resistant bacteria.
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Affiliation(s)
- Chonnikan Hanpaibool
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Center of Excellence On Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok, 10400, Thailand
| | - Sirilata Yotphan
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Department of Chemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Natharin Ngamwongsatit
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand.
- Laboratory of Bacteria, Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand.
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.
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Rogga V, Kosalec I. Untying the anchor for the lipopolysaccharide: lipid A structural modification systems offer diagnostic and therapeutic options to tackle polymyxin resistance. Arh Hig Rada Toksikol 2023; 74:145-166. [PMID: 37791675 PMCID: PMC10549895 DOI: 10.2478/aiht-2023-74-3717] [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: 01/01/2023] [Revised: 01/01/2023] [Accepted: 07/01/2023] [Indexed: 10/05/2023] Open
Abstract
Polymyxin antibiotics are the last resort for treating patients in intensive care units infected with multiple-resistant Gram-negative bacteria. Due to their polycationic structure, their mode of action is based on an ionic interaction with the negatively charged lipid A portion of the lipopolysaccharide (LPS). The most prevalent polymyxin resistance mechanisms involve covalent modifications of lipid A: addition of the cationic sugar 4-amino-L-arabinose (L-Ara4N) and/or phosphoethanolamine (pEtN). The modified structure of lipid A has a lower net negative charge, leading to the repulsion of polymyxins and bacterial resistance to membrane disruption. Genes encoding the enzymatic systems involved in these modifications can be transferred either through chromosomes or mobile genetic elements. Therefore, new approaches to resistance diagnostics have been developed. On another note, interfering with these enzymatic systems might offer new therapeutic targets for drug discovery. This literature review focuses on diagnostic approaches based on structural changes in lipid A and on the therapeutic potential of molecules interfering with these changes.
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Affiliation(s)
- Vanessa Rogga
- University of Zagreb Faculty of Pharmacy and Biochemistry, Department of Microbiology, Zagreb, Croatia
| | - Ivan Kosalec
- University of Zagreb Faculty of Pharmacy and Biochemistry, Department of Microbiology, Zagreb, Croatia
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Thai VC, Stubbs KA, Sarkar-Tyson M, Kahler CM. Phosphoethanolamine Transferases as Drug Discovery Targets for Therapeutic Treatment of Multi-Drug Resistant Pathogenic Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:1382. [PMID: 37760679 PMCID: PMC10525099 DOI: 10.3390/antibiotics12091382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic resistance caused by multidrug-resistant (MDR) bacteria is a major challenge to global public health. Polymyxins are increasingly being used as last-in-line antibiotics to treat MDR Gram-negative bacterial infections, but resistance development renders them ineffective for empirical therapy. The main mechanism that bacteria use to defend against polymyxins is to modify the lipid A headgroups of the outer membrane by adding phosphoethanolamine (PEA) moieties. In addition to lipid A modifying PEA transferases, Gram-negative bacteria possess PEA transferases that decorate proteins and glycans. This review provides a comprehensive overview of the function, structure, and mechanism of action of PEA transferases identified in pathogenic Gram-negative bacteria. It also summarizes the current drug development progress targeting this enzyme family, which could reverse antibiotic resistance to polymyxins to restore their utility in empiric therapy.
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Affiliation(s)
- Van C. Thai
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (V.C.T.); (M.S.-T.)
| | - Keith A. Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia;
| | - Mitali Sarkar-Tyson
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (V.C.T.); (M.S.-T.)
| | - Charlene M. Kahler
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (V.C.T.); (M.S.-T.)
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Jia Y, Liu J, Yang Q, Zhang W, Efferth T, Liu S, Hua X. Cajanin stilbene acid: A direct inhibitor of colistin resistance protein MCR-1 that restores the efficacy of polymyxin B against resistant Gram-negative bacteria. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 114:154803. [PMID: 37058946 DOI: 10.1016/j.phymed.2023.154803] [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: 01/02/2023] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The resistance of Gram-negative bacteria to polymyxin B, caused by the plasmid-mediated colistin resistance gene mcr-1, which encodes a phosphoethanolamine transferase (MCR-1), is a serious threat to global public health. Therefore, it is urgent to find new drugs that can effectively alleviate polymyxin B resistance. Through the screening of 78 natural compounds, we found that cajanin stilbene acid (CSA) can significantly restore the susceptibility of polymyxin B to mcr-1 positive Escherichia coli (E. coli). PURPOSE In this study, we tried to evaluate the ability of CSA to restore the susceptibility of polymyxin B towards the E. coli, and explore the mechanism of sensitivity recovery. STUDY DESIGN AND METHODS Checkerboard MICs, time-killing curves, scanning electron microscope, lethal and semi-lethal models of infection in mice were used to assess the ability of CSA to restore the susceptibility of polymyxyn to E. coli. The interaction between CSA and MCR-1 was evaluated using surface plasmon resonance (SPR), and molecular docking experiments. RESULTS Here, we find that CSA, a potential direct inhibitor of MCR-1, effectively restores the sensitivity of E. coli to polymyxin B. CSA can restore the sensitivity of polymyxin B to drug-resistant E. coli, and the MIC value can be reduced to 1 μg/ml. The time killing curve and scanning electron microscopy results also showed that CSA can effectively restore polymyxin B sensitivity. In vivo experiments showed that the simultaneous use of CSA and polymyxin B can effectively reduce the infection of drug-resistant E. coli in mice. SPR and molecular docking experiments confirmed that CSA strongly bound to MCR-1. The 17-carbonyl oxygen and 12- and 18‑hydroxyl oxygens of CSA were the key sites binding to MCR-1. CONCLUSION CSA is able to significantly restore the sensitivity of polymyxin B to E. coli in vivo and in vitro. CSA inhibits the enzymatic activity of the MCR-1 protein by binding to key amino acids at the active center of the MCR-1 protein.
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Affiliation(s)
- Yue Jia
- Division of Bacterial Diseases, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Juzhao Liu
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qin Yang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Wanjiang Zhang
- Division of Bacterial Diseases, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz 55128, Germany.
| | - Siguo Liu
- Division of Bacterial Diseases, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China.
| | - Xin Hua
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education Harbin, China; College of Life Science, Northeast Forestry University Harbin, China.
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Huang Y, Wang Z, Liu Z, Huan Q, Liu Y, Li R, Wang M, Xiao X. Gigantol restores the sensitivity of mcr carrying multidrug-resistant bacteria to colistin. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 117:154886. [PMID: 37269755 DOI: 10.1016/j.phymed.2023.154886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/27/2023] [Accepted: 05/15/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND The emergence and wide spread of plasmid-mediated colistin resistance gene (mcr-1) and its mutants have immensely limited the efficacy of colistin in treating multidrug-resistant (MDR) Gram-negative bacterial infections. The development of synergistic combinations of antibiotics with a natural product that coped with the resistance of MDR bacteria was an economic strategy to restore antibiotics activity. Herein, we investigated gigantol, a bibenzyl phytocompound, for restoring in vitro and in vivo, the sensitivity of mcr-positive bacteria to colistin. METHODS The synergistic activity of gigantol and colistin against multidrug-resistant Enterobacterales was studied via checkerboard assay and time-killing curve. Subsequently, the transcription and protein expression levels of mcr-1 gene were determined by RT-PCR and Western blots. The interaction of gigantol and MCR-1 was simulated via molecular docking and verified via site-directed mutagenesis of MCR-1. Hemolytic activity and cytotoxicity assay were used to evaluate the safety of gigantol. Finally, the in vivo synergistic effect was evaluated via two animal infection models. RESULTS Gigantol restored the activity of colistin against mcr-positive bacteria E.coli B2 (MIC from 4 μg/ml to 0.25 μg/ml), Salmonella 15E343 (MIC from 8 μg/ml to 1 μg/ml), K. pneumoniae 19-2-1 (MIC from 32 μg/ml to 2 μg/ml) carrying mcr-1, mcr-3, mcr-8, respectively. Mechanistic studies revealed that gigantol down-regulated the expression of genes involved in LPS-modification, reduced the MCR-1 products and inhibited the activity of MCR-1 by binding to amino acid residues Tyr287 and Pro481 in its D-glucose-binding pocket. Safety evaluation showed that the addition of gigantol relieves the hemolysis caused by colistin. Compared with monotherapy, the combination of gigantol and colistin significantly improved the survival rate of Gallgallella mellonella larvae and mice infected by E.coli B2. Moreover, there was a considerable decrease in the bacterial load present in the viscera of mice. CONCLUSION Our results confirmed that gigantol was a potential colistin adjuvant, and could be used to tackle multi-drug resistant Gram-negative pathogen infections combined with colistin.
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Affiliation(s)
- Yanhu Huang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Ziyi Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Quanmin Huan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Xia Xiao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
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Hanpaibool C, Ngamwongsatit N, Ounjai P, Yotphan S, Wolschann P, Mulholland AJ, Spencer J, Rungrotmongkol T. Pyrazolones Potentiate Colistin Activity against MCR-1-Producing Resistant Bacteria: Computational and Microbiological Study. ACS OMEGA 2023; 8:8366-8376. [PMID: 36910942 PMCID: PMC9996792 DOI: 10.1021/acsomega.2c07165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The polymyxin colistin is a last line antibiotic for extensively resistant Gram-negative bacteria. Colistin binding to lipid A disrupts the Gram-negative outer membrane, but mobile colistin resistance (mcr) gene family members confer resistance by catalyzing phosphoethanolamine (PEA) transfer onto lipid A, neutralizing its negative charge to reduce colistin interactions. Multiple mcr isoforms have been identified in clinical and environmental isolates, with mcr-1 being the most widespread and mcr-3 being common in South and East Asia. Preliminary screening revealed that treatment with pyrazolones significantly reduced mcr-1, but not mcr-3, mediated colistin resistance. Molecular dynamics (MD) simulations of the catalytic domains of MCR-1 and a homology model of MCR-3, in different protonation states of active site residues H395/H380 and H478/H463, indicate that the MCR-1 active site has greater water accessibility than MCR-3, but that this is less influenced by changes in protonation. MD-optimized structures of MCR-1 and MCR-3 were used in virtual screening of 20 pyrazolone derivatives. Docking of these into the MCR-1/MCR-3 active sites identifies common residues likely to be involved in protein-ligand interactions, specifically the catalytic threonine (MCR-1 T285, MCR-3 T277) site of PEA addition, as well as differential interactions with adjacent amino acids. Minimal inhibitory concentration assays showed that the pyrazolone with the lowest predicted binding energy (ST3f) restores colistin susceptibility of mcr-1, but not mcr-3, expressing Escherichia coli. Thus, simulations indicate differences in the active site structure between MCR-1 and MCR-3 that may give rise to differences in pyrazolone binding and so relate to differential effects upon producer E. coli. This work identifies pyrazolones as able to restore colistin susceptibility of mcr-1-producing bacteria, laying the foundation for further investigations of their activity as phosphoethanolamine transferase inhibitors as well as of their differential activity toward mcr isoforms.
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Affiliation(s)
- Chonnikan Hanpaibool
- Center
of Excellence in Biocatalyst and Sustainable Biotechnology, Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Natharin Ngamwongsatit
- Department
of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
- Laboratory
of Bacteria, Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Puey Ounjai
- Department
of Biology, Faculty of Science, Mahidol
University, Bangkok 10400, Thailand
- Center
of Excellence on Environmental Health and Toxicology, Office of Higher
Education Commission, Ministry of Education, Bangkok 10400, Thailand
| | - Sirilata Yotphan
- Center of
Excellence for Innovation in Chemistry (PERCH-CIC), Department of
Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Peter Wolschann
- Institute
of Theoretical Chemistry, University of
Vienna, Vienna 1090, Austria
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - James Spencer
- School
of Cellular and Molecular Medicine, University
of Bristol, Bristol BS8 1TD, U.K.
| | - Thanyada Rungrotmongkol
- Center
of Excellence in Biocatalyst and Sustainable Biotechnology, Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10400, Thailand
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Qiao H, Yu J, Wang X, Nie T, Hu X, Yang X, Li C, You X. Effect of Different Tolerable Levels of Constitutive mcr-1 Expression on Escherichia coli. Microbiol Spectr 2022; 10:e0174822. [PMID: 35980194 PMCID: PMC9603290 DOI: 10.1128/spectrum.01748-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/28/2022] [Indexed: 12/31/2022] Open
Abstract
To study the effect of different tolerable levels of constitutive mcr-1 expression on Escherichia coli, and to provide direct evidence for moderate resistance mediated by mcr-1, construction of E. coli strains carrying mcr-1 on the chromosome with promoters of different strengths was conducted using λ-red recombination. Our results demonstrated that over-high expression of mcr-1 cannot be tolerated, and seven constructs with more than 200-fold mcr-1 transcriptional expression differences were obtained. The colistin MICs of the seven strains increased with the increase of MCR-1 levels, and the highest MIC was 8 μg/mL. Lower expression of mcr-1 didn't demonstrate many effects on bacteria, while higher tolerable expression of mcr-1 tended to show fitness costs in growth rate, competitive ability, and cell structures, but no obvious change of virulence was observed in mice. Bacteria demonstrated colistin MICs of 4-8 μg/mL at mcr-1 expression levels similar to clinical isolates, which were the mcr-1 expression levels with relatively lower fitness costs. IMPORTANCE The effects of relatively lower tolerable levels of mcr-1 were not evaluated thoroughly, and direct evidence for moderate resistance mediated by mcr-1 was lacking. In the present study, we made constructs carrying mcr-1 on the E. coli K12 chromosome under the control of serial constitutive promoters of different strengths and studied the effects of different tolerable levels of mcr-1 expression in vitro and in vivo. The results demonstrated that generally, except QH0007 (the construct with the highest mcr-1 expression that showed some extent of cell death), the fitness costs of tolerable mcr-1 expression on bacteria were not apparent or low. Bacteria demonstrated colistin MICs of 4-8 μg/mL at mcr-1 expression levels similar to clinical isolates, which corresponded to the lower levels of mcr-1 expression that can lead to colistin resistance, indicating the cleverness of bacteria to balance the benefit and cost of MCR-1-mediated colistin resistance.
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Affiliation(s)
- Han Qiao
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Institutes for Food and Drug Control, Beijing, China
| | - Jie Yu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiukun Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tongying Nie
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinxin Hu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinyi Yang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Congran Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuefu You
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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10
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Mmatli M, Mbelle NM, Osei Sekyere J. Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update. Front Cell Infect Microbiol 2022; 12:941358. [PMID: 36093193 PMCID: PMC9462459 DOI: 10.3389/fcimb.2022.941358] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/01/2022] [Indexed: 12/28/2022] Open
Abstract
Background Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane. Results and discussion Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI2 conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins. Conclusion The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, United States
- Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
- *Correspondence: John Osei Sekyere, ;
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11
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Deep Mutational Scanning Reveals the Active-Site Sequence Requirements for the Colistin Antibiotic Resistance Enzyme MCR-1. mBio 2021; 12:e0277621. [PMID: 34781730 PMCID: PMC8593676 DOI: 10.1128/mbio.02776-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Colistin (polymyxin E) and polymyxin B have been used as last-resort agents for treating infections caused by multidrug-resistant Gram-negative bacteria. However, their efficacy has been challenged by the emergence of the mobile colistin resistance gene mcr-1, which encodes a transmembrane phosphoethanolamine (PEA) transferase enzyme, MCR-1. The enzyme catalyzes the transfer of the cationic PEA moiety of phosphatidylethanolamine (PE) to lipid A, thereby neutralizing the negative charge of lipid A and blocking the binding of positively charged polymyxins. This study aims to facilitate understanding of the mechanism of the MCR-1 enzyme by investigating its active-site sequence requirements. For this purpose, 23 active-site residues of MCR-1 protein were randomized by constructing single-codon randomization libraries. The libraries were individually selected for supporting Escherichia coli cell growth in the presence of colistin or polymyxin B. Deep sequencing of the polymyxin-resistant clones revealed that wild-type residues predominates at 17 active-site residue positions, indicating these residues play critical roles in MCR-1 function. These residues include Zn2+-chelating residues as well as residues that may form a hydrogen bond network with the PEA moiety or make hydrophobic interactions with the acyl chains of PE. Any mutations at these residues significantly decrease polymyxin resistance levels and the PEA transferase activity of the MCR-1 enzyme. Therefore, deep sequencing of the randomization libraries of MCR-1 enzyme identifies active-site residues that are essential for its polymyxin resistance function. Thus, these residues may be utilized as targets to develop inhibitors to circumvent MCR-1-mediated polymyxin resistance.
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12
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Gogry FA, Siddiqui MT, Sultan I, Haq QMR. Current Update on Intrinsic and Acquired Colistin Resistance Mechanisms in Bacteria. Front Med (Lausanne) 2021; 8:677720. [PMID: 34476235 PMCID: PMC8406936 DOI: 10.3389/fmed.2021.677720] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/09/2021] [Indexed: 01/07/2023] Open
Abstract
Colistin regained global interest as a consequence of the rising prevalence of multidrug-resistant Gram-negative Enterobacteriaceae. In parallel, colistin-resistant bacteria emerged in response to the unregulated use of this antibiotic. However, some Gram-negative species are intrinsically resistant to colistin activity, such as Neisseria meningitides, Burkholderia species, and Proteus mirabilis. Most identified colistin resistance usually involves modulation of lipid A that decreases or removes early charge-based interaction with colistin through up-regulation of multistep capsular polysaccharide expression. The membrane modifications occur by the addition of cationic phosphoethanolamine (pEtN) or 4-amino-l-arabinose on lipid A that results in decrease in the negative charge on the bacterial surface. Therefore, electrostatic interaction between polycationic colistin and lipopolysaccharide (LPS) is halted. It has been reported that these modifications on the bacterial surface occur due to overexpression of chromosomally mediated two-component system genes (PmrAB and PhoPQ) and mutation in lipid A biosynthesis genes that result in loss of the ability to produce lipid A and consequently LPS chain, thereafter recently identified variants of plasmid-borne genes (mcr-1 to mcr-10). It was hypothesized that mcr genes derived from intrinsically resistant environmental bacteria that carried chromosomal pmrC gene, a part of the pmrCAB operon, code three proteins viz. pEtN response regulator PmrA, sensor kinase protein PmrAB, and phosphotransferase PmrC. These plasmid-borne mcr genes become a serious concern as they assist in the dissemination of colistin resistance to other pathogenic bacteria. This review presents the progress of multiple strategies of colistin resistance mechanisms in bacteria, mainly focusing on surface changes of the outer membrane LPS structure and other resistance genetic determinants. New handier and versatile methods have been discussed for rapid detection of colistin resistance determinants and the latest approaches to revert colistin resistance that include the use of new drugs, drug combinations and inhibitors. Indeed, more investigations are required to identify the exact role of different colistin resistance determinants that will aid in developing new less toxic and potent drugs to treat bacterial infections. Therefore, colistin resistance should be considered a severe medical issue requiring multisectoral research with proper surveillance and suitable monitoring systems to report the dissemination rate of these resistant genes.
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Affiliation(s)
| | | | - Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
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13
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The MCR-3 inside linker appears as a facilitator of colistin resistance. Cell Rep 2021; 35:109135. [PMID: 34010644 DOI: 10.1016/j.celrep.2021.109135] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/23/2020] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
An evolving family of mobile colistin resistance (MCR) enzymes is threatening public health. However, the molecular mechanism by which the MCR enzyme as a rare member of lipid A-phosphoethanolamine (PEA) transferases gains the ability to confer phenotypic colistin resistance remains enigmatic. Here, we report an unusual example that genetic duplication and amplification produce a functional variant (Ah762) of MCR-3 in certain Aeromonas species. The lipid A-binding cavity of Ah762 is functionally defined. Intriguingly, we locate a hinge linker of Ah762 (termed Linker 59) that determines the MCR. Genetic and biochemical characterization reveals that Linker 59 behaves as a facilitator to render inactive MCR variants to regain the ability of colistin resistance. Along with molecular dynamics (MD) simulation, isothermal titration calorimetry (ITC) suggests that this facilitator guarantees the formation of substrate phosphatidylethanolamine (PE)-accessible pocket within MCR-3-like enzymes. Therefore, our finding defines an MCR-3 inside facilitator for colistin resistance.
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14
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Gabale U, Peña Palomino PA, Kim H, Chen W, Ressl S. The essential inner membrane protein YejM is a metalloenzyme. Sci Rep 2020; 10:17794. [PMID: 33082366 PMCID: PMC7576196 DOI: 10.1038/s41598-020-73660-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/18/2020] [Indexed: 12/27/2022] Open
Abstract
Recent recurrent outbreaks of Gram-negative bacteria show the critical need to target essential bacterial mechanisms to fight the increase of antibiotic resistance. Pathogenic Gram-negative bacteria have developed several strategies to protect themselves against the host immune response and antibiotics. One such strategy is to remodel the outer membrane where several genes are involved. yejM was discovered as an essential gene in E. coli and S. typhimurium that plays a critical role in their virulence by changing the outer membrane permeability. How the inner membrane protein YejM with its periplasmic domain changes membrane properties remains unknown. Despite overwhelming structural similarity between the periplasmic domains of two YejM homologues with hydrolases like arylsulfatases, no enzymatic activity has been previously reported for YejM. Our studies reveal an intact active site with bound metal ions in the structure of YejM periplasmic domain. Furthermore, we show that YejM has a phosphatase activity that is dependent on the presence of magnesium ions and is linked to its function of regulating outer membrane properties. Understanding the molecular mechanism by which YejM is involved in outer membrane remodeling will help to identify a new drug target in the fight against the increased antibiotic resistance.
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Affiliation(s)
- Uma Gabale
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA.
| | - Perla Arianna Peña Palomino
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA
| | - HyunAh Kim
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA
| | - Wenya Chen
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA
| | - Susanne Ressl
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA.
- Department of Neuroscience, The University of Texas At Austin, 100 E. 24th St., NHB 2.504, Austin, TX, 78712, USA.
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15
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Resensitizing carbapenem- and colistin-resistant bacteria to antibiotics using auranofin. Nat Commun 2020; 11:5263. [PMID: 33067430 PMCID: PMC7568570 DOI: 10.1038/s41467-020-18939-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/17/2020] [Indexed: 12/19/2022] Open
Abstract
Global emergence of Gram-negative bacteria carrying the plasmid-borne resistance genes, blaMBL and mcr, raises a significant challenge to the treatment of life-threatening infections by the antibiotics, carbapenem and colistin (COL). Here, we identify an antirheumatic drug, auranofin (AUR) as a dual inhibitor of metallo-β-lactamases (MBLs) and mobilized colistin resistance (MCRs), two resistance enzymes that have distinct structures and substrates. We demonstrate that AUR irreversibly abrogates both enzyme activity via the displacement of Zn(II) cofactors from their active sites. We further show that AUR synergizes with antibiotics on killing a broad spectrum of carbapenem and/or COL resistant bacterial strains, and slows down the development of β-lactam and COL resistance. Combination of AUR and COL rescues all mice infected by Escherichia coli co-expressing MCR-1 and New Delhi metallo-β-lactamase 5 (NDM-5). Our findings provide potential therapeutic strategy to combine AUR with antibiotics for combating superbugs co-producing MBLs and MCRs. Multi-drug resistant pathogens remain a serious public health threat. Here, Sun and colleagues identify a role for auranofin, which is normally used as a drug for rheumatoid arthritis, for reversing antibiotic resistance to carbapenem and colistin.
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16
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Ullah S, Ji K, Li J, Xu Y, Jiang C, Zhang H, Huang M, Feng Y. Characterization of NMCR-2, a new non-mobile colistin resistance enzyme: implications for an MCR-8 ancestor. Environ Microbiol 2020; 23:844-860. [PMID: 32686285 DOI: 10.1111/1462-2920.15171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/07/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022]
Abstract
MCR-4 and MCR-8 are two recently identified members of an ongoing MCR family of colistin resistance. Although that aquatic reservoir for MCR-4 is proposed, the origin and mechanism of MCR-8 is poorly understood. Here we report a previously unrecognized non-mobile colistin resistance enzyme, termed NMCR-2, originating from the plant pathogen Kosakonia pseudosacchari. NMCR-2 (551aa) gives 67.3% identity to MCR-8 (565aa). NMCR-2 is placed as a progenitor/ancestor for MCR-8 in phylogeny of MCR members. Genetic study reveals that nmcr-2 is comparable to mcr-8 in the ability of producing phenotypic colistin resistance. Biochemical analyses determine that these two enzymes catalyse the transfer of PEA from the donor PE lipid substrate to the recipient lipid A molecule by a putative 'ping-pong' trade-off. Further experiment of protein engineering demonstrates that the two motifs (TM region and catalytic domain) of NMCR-2 are functionally exchangeable with that of MCR-8, rather than MCR-1. Physiological impacts of nmcr-2 and/or mcr-8 are detected in Escherichia coli, featuring with fitness cost. Evidently, the action and mechanism of NMCR-2 is analogous to that of MCR-8. Therefore, our finding underlines that NMCR-2 might be a possible progenitor of MCR-8.
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Affiliation(s)
- Saif Ullah
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China
| | - Kai Ji
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China.,Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Guangxi, China
| | - Jun Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Zhejiang, Hangzhou, China
| | - Yongchang Xu
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China.,Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, 610500, China
| | - Chengjian Jiang
- Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Guangxi, China
| | - Huimin Zhang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Man Huang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310058, China.,Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Guangxi, China.,Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, 610500, China.,College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
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17
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Samantha A, Vrielink A. Lipid A Phosphoethanolamine Transferase: Regulation, Structure and Immune Response. J Mol Biol 2020; 432:5184-5196. [PMID: 32353363 DOI: 10.1016/j.jmb.2020.04.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 01/23/2023]
Abstract
A wide variety of antibiotics are targeted to the bacterial membrane due to its unique arrangement and composition relative to the host mammalian membranes. By modification of their membranes, some gram-negative pathogens resist the action of antibiotics. Lipid A phosphoethanolamine transferase (EptA) is an intramembrane enzyme that modifies the lipid A portion of lipopolysaccharide/lipooligosaccharide by the addition of phosphoethanolamine. This modification reduces the overall net-negative charge of the outer membrane of some gram-negative bacteria, conferring resistance to polymyxin. This resistance mechanism has resulted in a global public health issue due to the increased use of polymyxin as last-resort antibiotic treatments against multi-drug-resistant pathogens. Studies show that, without EptA, pathogenic bacteria become more sensitive to polymyxin and to clearance by the host immune system, suggesting the importance of this target enzyme for the development of novel therapeutic agents. In this review, EptA will be discussed comprehensively. Specifically, this review will cover the regulation of eptA expression by the two component systems PmrA/PmrB and PhoP/PhoQ, the site of modification on lipid A, the structure and catalytic mechanism of EptA in comparison to MCR-1 and Escherichia coli alkaline phosphatase, and the host immune system's response to lipid A modification by EptA. The overarching aim of this review is to provide a comprehensive overview of polymyxin resistance mediated by EptA.
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Affiliation(s)
- Ariela Samantha
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia.
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18
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Guo Y, Lv X, Wang Y, Zhou Y, Lu N, Deng X, Wang J. Honokiol Restores Polymyxin Susceptibility to MCR-1-Positive Pathogens both In Vitro and In Vivo. Appl Environ Microbiol 2020; 86:e02346-19. [PMID: 31862719 PMCID: PMC7028959 DOI: 10.1128/aem.02346-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/17/2019] [Indexed: 01/15/2023] Open
Abstract
The emergence of the plasmid-mediated colistin resistance gene mcr-1 has led to serious multidrug-resistant (MDR) Enterobacteriaceae infections, which are a great threat to the clinic. This study aims to find an inhibitor of MCR-1 to reestablish the use of polymyxins against MDR Enterobacteriaceae infections. Here, we determined that the natural compound honokiol could enhance the efficacy of polymyxins against MDR Enterobacteriaceae infections by a checkerboard MIC assay, a time-kill assay, a combined disk test, Western blotting, molecular simulation dynamics, and mouse infection models. The MIC results indicated that honokiol can recover the sensitivity of polymyxins against MCR-1-positive Klebsiella pneumoniae and Escherichia coli (with a fractional inhibitory concentration index ranging from 0.09 ± 0.00 to 0.27 ± 0.06). Based on time-kill curve analysis, all of the tested bacteria were killed within 1 h following the combined therapy with honokiol and polymyxins. Molecular simulation dynamics results suggested that honokiol directly binds to the MCR-1 active region, reducing the biological activity of MCR-1. The combination of honokiol and polymyxins could increase the 40% protection rate and reduce the bacterial load on the thigh muscles of mice. Our study indicates that honokiol is a predominant natural compound whose combination therapy with polymyxins is very promising in future treatment options for MCR-1-positive Enterobacteriaceae infections.IMPORTANCE In the present study, honokiol could effectively inhibit the activity of MCR-1 and showed almost no cytotoxicity to MH-S cells. According to our results, the combination of honokiol and polymyxin had a clear synergistic effect against MCR-1-positive Enterobacteriaceae in vitro Combination therapy also showed a powerful therapeutic effect in vivo, which can significantly improve mouse livability, reduced the load of bacteria, and reduced pathological change. This combined therapy of small molecule compounds and antibiotics may not continue to induce new bacterial resistance, due to the fact that MCR-1 targeted by honokiol is not indispensable for the bacterial viability; on the other hand, it can reduce the dosage of combined antibiotics, and it is also a promising alternative therapy for the treatment of drug-resistant infections in the future.
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Affiliation(s)
- Yan Guo
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiaohong Lv
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Yanling Wang
- Qingdao Vland Biological Limited Co., Ltd., Qingdao, China
| | - Yonglin Zhou
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Na Lu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuming Deng
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jianfeng Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
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19
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Recent progress on elucidating the molecular mechanism of plasmid-mediated colistin resistance and drug design. Int Microbiol 2019; 23:355-366. [PMID: 31872322 PMCID: PMC7347692 DOI: 10.1007/s10123-019-00112-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/29/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022]
Abstract
Antibiotic resistance is a growing global challenge to public health. Polymyxin is considered to be the last-resort antibiotic against most gram-negative bacteria. Recently, discoveries of a plasmid-mediated, transferable mobilized polymyxin resistance gene (mcr-1) in many countries have heralded the increased threat of the imminent emergence of pan-drug-resistant super bacteria. MCR-1 is an inner membrane protein that enables bacteria to develop resistance to polymyxin by transferring phosphoethanolamine to lipid A. However, the mechanism associated with polymyxin resistance has yet to be elucidated, and few drugs exist to address this issue. Here, we review our current understanding regarding MCR-1 and small molecule inhibitors to provide a detailed enzymatic mechanism of MCR-1 and the associated implications for drug design.
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20
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Lan XJ, Yan HT, Lin F, Hou S, Li CC, Wang GS, Sun W, Xiao JH, Li S. Design, Synthesis and Biological Evaluation of 1-Phenyl-2-(phenylamino) Ethanone Derivatives as Novel MCR-1 Inhibitors. Molecules 2019; 24:molecules24152719. [PMID: 31357453 PMCID: PMC6696459 DOI: 10.3390/molecules24152719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 01/25/2023] Open
Abstract
Polymyxins are considered to be the last-line antibiotics that are used to treat infections caused by multidrug-resistant (MDR) gram-negative bacteria; however, the plasmid-mediated transferable colistin resistance gene (mcr-1) has rendered polymyxins ineffective. Therefore, the protein encoded by mcr-1, MCR-1, could be a target for structure-based design of inhibitors to tackle polymyxins resistance. Here, we identified racemic compound 3 as a potential MCR-1 inhibitor by virtual screening, and 26 compound 3 derivatives were synthesized and evaluated in vitro. In the cell-based assay, compound 6g, 6h, 6i, 6n, 6p, 6q, and 6r displayed more potent activity than compound 3. Notably, 25 μΜ of compound 6p or 6q combined with 2 μg·mL-1 colistin could completely inhibit the growth of BL21(DE3) expressing mcr-1, which exhibited the most potent activity. In the enzymatic assay, we elucidate that 6p and 6q could target the MCR-1 to inhibit the activity of the protein. Additionally, a molecular docking study showed that 6p and 6q could interact with Glu246 and Thr285 via hydrogen bonds and occupy well the cavity of the MCR-1 protein. These results may provide a potential avenue to overcome colistin resistance, and provide some valuable information for further investigation on MCR-1 inhibitors.
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Affiliation(s)
- Xiu-Juan Lan
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Hai-Tao Yan
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Feng Lin
- School of Life Sciences, Jilin University, Changchun 130021, China
| | - Shi Hou
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Chen-Chen Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Guang-Shu Wang
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China.
| | - Wei Sun
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China.
| | - Jun-Hai Xiao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Song Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
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21
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Zhang H, Wei W, Huang M, Umar Z, Feng Y. Definition of a Family of Nonmobile Colistin Resistance (NMCR-1) Determinants Suggests Aquatic Reservoirs for MCR-4. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900038. [PMID: 31179218 PMCID: PMC6548957 DOI: 10.1002/advs.201900038] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Polymyxins, a family of cationic antimicrobial peptides, are recognized as a last-resort clinical option used in the treatment of lethal infections with carbapenem-resistant pathogens. A growing body of mobile colistin resistance (MCR) determinants renders colistin ineffective in the clinical and human sectors, posing a challenge to human health and food security. However, the origin and reservoir of the MCR family enzymes is poorly understood. Herein, a new family of nonmobile colistin resistance (from nmcr-1 to nmcr-1.8) from the aquatic bacterium Shewanella is reported. NMCR-1 (541aa) displays 62.78% identity to MCR-4. Genetic and structural analyses reveal that NMCR-1 shares a similar catalytic mechanism and functional motifs, both of which are required for MCR action and its resultant phenotypic resistance to polymyxin. Phylogeny and domain-swapping demonstrate that NMCR-1 is a progenitor of MCR-4 rather than MCR-1/2. Additionally, the experiment of bacterial growth and viability reveals that NMCR-1 promotes fitness cost as MCR-1/4 does in the recipient Escherichia coli. In summary, the finding suggests that the aquatic bacterium Shewanella (and even its associated aquaculture) is a reservoir for MCR-4 mobile colistin resistance.
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Affiliation(s)
- Huimin Zhang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Wenhui Wei
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Man Huang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Zeeshan Umar
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
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22
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MCR-1: a promising target for structure-based design of inhibitors to tackle polymyxin resistance. Drug Discov Today 2019; 24:206-216. [DOI: 10.1016/j.drudis.2018.07.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/10/2018] [Accepted: 07/16/2018] [Indexed: 11/18/2022]
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23
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Zhao Y, Meng Q, Lai Y, Wang L, Zhou D, Dou C, Gu Y, Nie C, Wei Y, Cheng W. Structural and mechanistic insights into polymyxin resistance mediated by EptC originating from Escherichia coli. FEBS J 2018; 286:750-764. [PMID: 30537137 DOI: 10.1111/febs.14719] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/08/2018] [Accepted: 12/03/2018] [Indexed: 02/05/2023]
Abstract
Gram-negative bacteria defend against the toxicity of polymyxins by modifying their outer membrane lipopolysaccharide (LPS). This modification mainly occurs through the addition of cationic molecules such as phosphoethanolamine (PEA). EcEptC is a PEA transferase from Escherichia coli (E. coli). However, unlike its homologs CjEptC (Campylobacter jejuni) and MCR-1, EcEptC is unable to mediate polymyxin resistance when overexpressed in E. coli. Here, we report crystal structures of the C-terminal putative catalytic domain (EcEptCΔN, 205-577 aa) of EcEptC in apo and Zn2+ -bound states at 2.10 and 2.60 Å, respectively. EcEptCΔN is arranged into an α-β-α fold and equipped with the zinc ion in a conserved mode. Coupled with isothermal titration calorimetry (ITC) data, we provide insights into the mechanism by which EcEptC recognizes Zn2+ . Furthermore, structure comparison analysis indicated that disulfide bonds, which play a key role in polymyxin resistance, were absent in EcEptCΔN. Supported by structural and biochemical evidence, we reveal mechanistic implications for disulfide bonds in PEA transferase-mediated polymyxin resistance. Significantly, because the structural effects exhibited by disulfide bonds are absent in EcEptC, it is impossible for this protein to participate in polymyxin resistance in E. coli. DATABASE: Structural data are available in the PDB under the accession numbers 6A82 and 6A83. ENZYME: EC 2.7.8.43.
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Affiliation(s)
- Yanqun Zhao
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Qiang Meng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yujie Lai
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Li Wang
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Dan Zhou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Chao Dou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yijun Gu
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Pudong District, Shanghai, China
| | - Chunlai Nie
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yuquan Wei
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.,Department of Pathophysiology, the Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, China
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24
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Dortet L, Bonnin RA, Pennisi I, Gauthier L, Jousset AB, Dabos L, Furniss RCD, Mavridou DAI, Bogaerts P, Glupczynski Y, Potron A, Plesiat P, Beyrouthy R, Robin F, Bonnet R, Naas T, Filloux A, Larrouy-Maumus G. Rapid detection and discrimination of chromosome- and MCR-plasmid-mediated resistance to polymyxins by MALDI-TOF MS in Escherichia coli: the MALDIxin test. J Antimicrob Chemother 2018; 73:3359-3367. [PMID: 30184212 DOI: 10.1093/jac/dky330] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
Background Polymyxins are currently considered a last-resort treatment for infections caused by MDR Gram-negative bacteria. Recently, the emergence of carbapenemase-producing Enterobacteriaceae has accelerated the use of polymyxins in the clinic, resulting in an increase in polymyxin-resistant bacteria. Polymyxin resistance arises through modification of lipid A, such as the addition of phosphoethanolamine (pETN). The underlying mechanisms involve numerous chromosome-encoded genes or, more worryingly, a plasmid-encoded pETN transferase named MCR. Currently, detection of polymyxin resistance is difficult and time consuming. Objectives To develop a rapid diagnostic test that can identify polymyxin resistance and at the same time differentiate between chromosome- and plasmid-encoded resistances. Methods We developed a MALDI-TOF MS-based method, named the MALDIxin test, which allows the detection of polymyxin resistance-related modifications to lipid A (i.e. pETN addition), on intact bacteria, in <15 min. Results Using a characterized collection of polymyxin-susceptible and -resistant Escherichia coli, we demonstrated that our method is able to identify polymyxin-resistant isolates in 15 min whilst simultaneously discriminating between chromosome- and plasmid-encoded resistance. We validated the MALDIxin test on different media, using fresh and aged colonies and show that it successfully detects all MCR-1 producers in a blindly analysed set of carbapenemase-producing E. coli strains. Conclusions The MALDIxin test is an accurate, rapid, cost-effective and scalable method that represents a major advance in the diagnosis of polymyxin resistance by directly assessing lipid A modifications in intact bacteria.
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Affiliation(s)
- Laurent Dortet
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.,Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Remy A Bonnin
- EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Ivana Pennisi
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Lauraine Gauthier
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Agnès B Jousset
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Laura Dabos
- EA7361 'Structure, dynamic, function and expression of broad spectrum ß-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - R Christopher D Furniss
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Despoina A I Mavridou
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Pierre Bogaerts
- Laboratory of Clinical Microbiology, Belgian National Reference Center for Monitoring Antimicrobial Resistance in Gram-negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Youri Glupczynski
- Laboratory of Clinical Microbiology, Belgian National Reference Center for Monitoring Antimicrobial Resistance in Gram-negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Anais Potron
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Besançon, Besançon, France
| | - Patrick Plesiat
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Besançon, Besançon, France
| | - Racha Beyrouthy
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Frédéric Robin
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Richard Bonnet
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
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25
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Ding S, Han X, Li J, Gao W, Chen Z, Feng Y. Discovery of multi-drug resistant, MCR-1 and ESBL-coproducing ST117 Escherichia coli from diseased chickens in northeast China. Sci Bull (Beijing) 2018; 63:1059-1066. [PMID: 36755458 DOI: 10.1016/j.scib.2018.07.017] [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: 05/11/2018] [Revised: 06/11/2018] [Accepted: 06/22/2018] [Indexed: 11/26/2022]
Abstract
An endemic multi-drug resistant ST117 E. coli isolate coproducing MCR-1 and 3 ESBL loci was, for the first time, detected from diseased chicken, Liaoning Province, in Northeast China, from 2011 to 2012. Whole-genome sequencing revealed 5 unique plasmids, namely pHXH-1, pHXH-2, pHXH-3, pHXH-4 and pHXH-5). Among them, pHXH1 and pHXH4 encode ESBL, and pHXH-5 mediates MCR-1 colistin resistance. The results indicate that the potentially-national dissemination of MCR-1-positive pathogens with pan-drug resistance proceeds via food chains.
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Affiliation(s)
- Sijia Ding
- School of Stomatology, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiaohu Han
- Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, China
| | - Jun Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Weifan Gao
- Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, China
| | - Zeliang Chen
- Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, China.
| | - Youjun Feng
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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26
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Molecular Insights into Functional Differences between mcr-3- and mcr-1-Mediated Colistin Resistance. Antimicrob Agents Chemother 2018; 62:AAC.00366-18. [PMID: 29987148 DOI: 10.1128/aac.00366-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/27/2018] [Indexed: 11/20/2022] Open
Abstract
The global emergence of plasmid-mediated colistin resistance genes mcr-1 and mcr-3 has threatened the role of the "last-resort" drug colistin in the defense against infections caused by multidrug-resistant Gram-negative bacteria. However, functional differences between these two genes in mediating colistin resistance remain poorly understood. Protein sequence alignment of MCR-3 and MCR-1 was therefore conducted in Clustal Omega to identify sequence divergence. The molecular recognition of lipid A head group phosphatidylethanolamine and MCR-3 enzyme was studied by homology modeling and molecular docking, with the catalytic mechanism of MCR-3 also being explored. Thr277 in MCR-3 was validated as the key amino acid residue responsible for the catalytic reaction using site-directed mutagenesis and was shown to act as a nucleophile. Lipid A modification induced by the MCR-3 and MCR-1 enzymes was confirmed by electrospray ionization-time of flight mass spectrometry. Far-UV circular dichroism spectra of the MCR-3 and MCR-1 enzymes suggested that MCR-3 was more thermostable than MCR-1, with a melting temperature of 66.19°C compared with 61.14°C for MCR-1. These data provided molecular insight into the functional differences between mcr-3 and mcr-1 in conferring colistin resistance.
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27
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Wei W, Srinivas S, Lin J, Tang Z, Wang S, Ullah S, Kota VG, Feng Y. Defining ICR-Mo, an intrinsic colistin resistance determinant from Moraxella osloensis. PLoS Genet 2018; 14:e1007389. [PMID: 29758020 PMCID: PMC5983563 DOI: 10.1371/journal.pgen.1007389] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/01/2018] [Accepted: 05/02/2018] [Indexed: 11/19/2022] Open
Abstract
Polymyxin is the last line of defense against severe infections caused by carbapenem-resistant gram-negative pathogens. The emergence of transferable MCR-1/2 polymyxin resistance greatly challenges the renewed interest in colistin (polymyxin E) for clinical treatments. Recent studies have suggested that Moraxella species are a putative reservoir for MCR-1/2 genetic determinants. Here, we report the functional definition of ICR-Mo from M. osloensis, a chromosomally encoded determinant of colistin resistance, in close relation to current MCR-1/2 family. ICR-Mo transmembrane protein was prepared and purified to homogeneity. Taken along with an in vitro enzymatic detection, MALDI-TOF mass spectrometry of bacterial lipid A pools determined that the ICR-Mo enzyme might exploit a possible "ping-pong" mechanism to accept the phosphoethanolamine (PEA) moiety from its donor phosphatidylethanolamine (PE) and then transfer it to the 1(or 4')-phosphate position of lipid A via an ICR-Mo-bound PEA adduct. Structural decoration of LPS-lipid A by ICR-Mo renders the recipient strain of E. coli resistant to polymyxin. Domain swapping assays indicate that the two domains of ICR-Mo cannot be functionally-exchanged with its counterparts in MCR-1/2 and EptA, validating its phylogenetic position in a distinct set of MCR-like genes. Structure-guided functional mapping of ICR-Mo reveals a PE lipid substrate recognizing cavity having a role in enzymatic catalysis and the resultant conference of antibiotic resistance. Expression of icr-Mo in E. coli significantly prevents the formation of reactive oxygen species (ROS) induced by colistin. Taken together, our results define a member of a group of intrinsic colistin resistance genes phylogenetically close to the MCR-1/2 family, highlighting the evolution of transferable colistin resistance.
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Affiliation(s)
- Wenhui Wei
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, United States of America
| | - Jingxia Lin
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zichen Tang
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shihua Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Saif Ullah
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Vishnu Goutham Kota
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Youjun Feng
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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28
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Crystal Structure of the Catalytic Domain of MCR-1 (cMCR-1) in Complex with d-Xylose. CRYSTALS 2018. [DOI: 10.3390/cryst8040172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Xu Y, Wei W, Lei S, Lin J, Srinivas S, Feng Y. An Evolutionarily Conserved Mechanism for Intrinsic and Transferable Polymyxin Resistance. mBio 2018; 9:e02317-17. [PMID: 29636432 PMCID: PMC5893884 DOI: 10.1128/mbio.02317-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/08/2018] [Indexed: 12/30/2022] Open
Abstract
Polymyxins, a family of cationic antimicrobial cyclic peptides, act as a last line of defense against severe infections by Gram-negative pathogens with carbapenem resistance. In addition to the intrinsic resistance to polymyxin E (colistin) conferred by Neisseria eptA, the plasmid-borne mobilized colistin resistance gene mcr-1 has been disseminated globally since the first discovery in Southern China, in late 2015. However, the molecular mechanisms for both intrinsic and transferable resistance to colistin remain largely unknown. Here, we aim to address this gap in the knowledge of these proteins. Structural and functional analyses of EptA and MCR-1 and -2 have defined a conserved 12-residue cavity that is required for the entry of the lipid substrate, phosphatidylethanolamine (PE). The in vitro and in vivo data together have allowed us to visualize the similarities in catalytic activity shared by EptA and MCR-1 and -2. The expression of either EptA or MCR-1 or -2 is shown to remodel the surface of enteric bacteria (e.g., Escherichia coli, Salmonella enterica, Klebsiella pneumoniae, etc.), rendering them resistant to colistin. The parallels in the PE substrate-binding cavities among EptA, MCR-1, and MCR-2 provide a comprehensive understanding of both intrinsic and transferable colistin resistance. Domain swapping between EptA and MCR-1 and -2 reveals that the two domains (transmembrane [TM] region and phosphoethanolamine [PEA] transferase) are not functionally exchangeable. Taken together, the results represent a common mechanism for intrinsic and transferable PEA resistance to polymyxin, a last-resort antibiotic against multidrug-resistant pathogens.IMPORTANCE EptA and MCR-1 and -2 remodel the outer membrane, rendering bacteria resistant to colistin, a final resort against carbapenem-resistant pathogens. Structural and functional analyses of EptA and MCR-1 and -2 reveal parallel PE lipid substrate-recognizing cavities, which explains intrinsic and transferable colistin resistance in gut bacteria. A similar mechanism is proposed for the catalytic activities of EptA and MCR-1 and -2. Together, they constitute a common mechanism for intrinsic and transferable polymyxin resistance.
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Affiliation(s)
- Yongchang Xu
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wenhui Wei
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Sheng Lei
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jingxia Lin
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Youjun Feng
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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30
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Xu Y, Lin J, Cui T, Srinivas S, Feng Y. Mechanistic insights into transferable polymyxin resistance among gut bacteria. J Biol Chem 2018; 293:4350-4365. [PMID: 29462787 DOI: 10.1074/jbc.ra117.000924] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/05/2018] [Indexed: 12/15/2022] Open
Abstract
Polymyxins such as colistin are antibiotics used as a final line of defense in the management of infections with multidrug-resistant Gram-negative bacteria. Although natural resistance to polymyxins is rare, the discovery of a mobilized colistin resistance gene (mcr-1) in gut bacteria has raised significant concern. As an intramembrane enzyme, MCR-1 catalyzes the transfer of phosphoethanolamine (PEA) to the 1 (or 4')-phosphate group of the lipid A moiety of lipopolysaccharide, thereby conferring colistin resistance. However, the structural and biochemical mechanisms used by this integral membrane enzyme remain poorly understood. Here, we report the modeled structure of the full-length MCR-1 membrane protein. Together with molecular docking, our structural and functional dissection of the complex of MCR-1 with its phosphatidylethanolamine (PE) substrate suggested the presence of a 12 residue-containing cavity for substrate entry, which is critical for both enzymatic activity and its resultant phenotypic resistance to colistin. More importantly, two periplasm-facing helices (PH2 and PH2') of the trans-membrane domain were essential for MCR-1 activity. MALDI-TOF MS and thin-layer chromatography assays provide both in vivo and in vitro evidence that MCR-1 catalyzes the transfer of PEA from the PE donor substrate to its recipient substrate lipid A. Also, the chemical modification of lipid A species was detected in clinical species of bacteria carrying mcr-1 Our results provide mechanistic insights into transferable MCR-1 polymyxin resistance, raising the prospect of rational design of small molecules that reverse bacterial polymyxin resistance, as a last-resort clinical option to combat pathogens with carbapenem resistance.
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Affiliation(s)
- Yongchang Xu
- From the Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingxia Lin
- From the Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Tao Cui
- the School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China, and
| | - Swaminath Srinivas
- the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Youjun Feng
- From the Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China, .,the College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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