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Brem J, Panduwawala T, Hansen JU, Hewitt J, Liepins E, Donets P, Espina L, Farley AJM, Shubin K, Campillos GG, Kiuru P, Shishodia S, Krahn D, Leśniak RK, Schmidt Adrian J, Calvopiña K, Turrientes MC, Kavanagh ME, Lubriks D, Hinchliffe P, Langley GW, Aboklaish AF, Eneroth A, Backlund M, Baran AG, Nielsen EI, Speake M, Kuka J, Robinson J, Grinberga S, Robinson L, McDonough MA, Rydzik AM, Leissing TM, Jimenez-Castellanos JC, Avison MB, Da Silva Pinto S, Pannifer AD, Martjuga M, Widlake E, Priede M, Hopkins Navratilova I, Gniadkowski M, Belfrage AK, Brandt P, Yli-Kauhaluoma J, Bacque E, Page MGP, Björkling F, Tyrrell JM, Spencer J, Lang PA, Baranczewski P, Cantón R, McElroy SP, Jones PS, Baquero F, Suna E, Morrison A, Walsh TR, Schofield CJ. Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors. Nat Chem 2022; 14:15-24. [PMID: 34903857 DOI: 10.1038/s41557-021-00831-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 09/30/2021] [Indexed: 11/08/2022]
Abstract
Carbapenems are vital antibiotics, but their efficacy is increasingly compromised by metallo-β-lactamases (MBLs). Here we report the discovery and optimization of potent broad-spectrum MBL inhibitors. A high-throughput screen for NDM-1 inhibitors identified indole-2-carboxylates (InCs) as potential β-lactamase stable β-lactam mimics. Subsequent structure-activity relationship studies revealed InCs as a new class of potent MBL inhibitor, active against all MBL classes of major clinical relevance. Crystallographic studies revealed a binding mode of the InCs to MBLs that, in some regards, mimics that predicted for intact carbapenems, including with respect to maintenance of the Zn(II)-bound hydroxyl, and in other regards mimics binding observed in MBL-carbapenem product complexes. InCs restore carbapenem activity against multiple drug-resistant Gram-negative bacteria and have a low frequency of resistance. InCs also have a good in vivo safety profile, and when combined with meropenem show a strong in vivo efficacy in peritonitis and thigh mouse infection models.
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Affiliation(s)
- Jürgen Brem
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK.
| | - Tharindi Panduwawala
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | | | - Joanne Hewitt
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
| | | | - Pawel Donets
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Laura Espina
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | - Alistair J M Farley
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Kirill Shubin
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Gonzalo Gomez Campillos
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Paula Kiuru
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Shifali Shishodia
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Daniel Krahn
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Robert K Leśniak
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Juliane Schmidt Adrian
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Karina Calvopiña
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - María-Carmen Turrientes
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Madeline E Kavanagh
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Gareth W Langley
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Charles River Laboratories, Saffron Walden, UK
| | - Ali F Aboklaish
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | - Anders Eneroth
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Uppsala University, Uppsala, Sweden
| | - Maria Backlund
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Uppsala University, Uppsala, Sweden
| | | | | | - Michael Speake
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Janis Kuka
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - John Robinson
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | | | - Lindsay Robinson
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Michael A McDonough
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Anna M Rydzik
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Research and Early Development, Respiratory & Immunology, AstraZeneca, Mölndal, Sweden
| | - Thomas M Leissing
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Juan Carlos Jimenez-Castellanos
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Chemical Biology of Antibiotics, Centre for Infection & Immunity (CIIL), Pasteur Institute, INSERM U1019 - CNRS UMR 9017, Lille, France
| | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Solange Da Silva Pinto
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Andrew D Pannifer
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
| | | | - Emma Widlake
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | | | | | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Anna Karin Belfrage
- Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
- Beactica Therapeutics AB, Uppsala, Sweden
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Eric Bacque
- Evotec Infectious Diseases Lyon, Marcy l'Etoile, France
| | | | - Fredrik Björkling
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan M Tyrrell
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Pauline A Lang
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Pawel Baranczewski
- Department of Pharmacy, SciLifeLab Drug Discovery and Development Platform, ADME of Therapeutics Facility, Uppsala University, Uppsala, Sweden
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Stuart P McElroy
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Philip S Jones
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Edgars Suna
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Angus Morrison
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Timothy R Walsh
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK.
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2
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Juhas M, Widlake E, Teo J, Huseby DL, Tyrrell JM, Polikanov YS, Ercan O, Petersson A, Cao S, Aboklaish AF, Rominski A, Crich D, Böttger EC, Walsh TR, Hughes D, Hobbie SN. In vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii. J Antimicrob Chemother 2020; 74:944-952. [PMID: 30629184 PMCID: PMC6419615 DOI: 10.1093/jac/dky546] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/17/2018] [Accepted: 11/29/2018] [Indexed: 02/01/2023] Open
Abstract
Objectives Widespread antimicrobial resistance often limits the availability of therapeutic options to only a few last-resort drugs that are themselves challenged by emerging resistance and adverse side effects. Apramycin, an aminoglycoside antibiotic, has a unique chemical structure that evades almost all resistance mechanisms including the RNA methyltransferases frequently encountered in carbapenemase-producing clinical isolates. This study evaluates the in vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii, and provides a rationale for its superior antibacterial activity in the presence of aminoglycoside resistance determinants. Methods A thorough antibacterial assessment of apramycin with 1232 clinical isolates from Europe, Asia, Africa and South America was performed by standard CLSI broth microdilution testing. WGS and susceptibility testing with an engineered panel of aminoglycoside resistance-conferring determinants were used to provide a mechanistic rationale for the breadth of apramycin activity. Results MIC distributions and MIC90 values demonstrated broad antibacterial activity of apramycin against Escherichia coli, Klebsiella pneumoniae, Enterobacter spp., Morganella morganii, Citrobacter freundii, Providencia spp., Proteus mirabilis, Serratia marcescens and A. baumannii. Genotypic analysis revealed the variety of aminoglycoside-modifying enzymes and rRNA methyltransferases that rendered a remarkable proportion of clinical isolates resistant to standard-of-care aminoglycosides, but not to apramycin. Screening a panel of engineered strains each with a single well-defined resistance mechanism further demonstrated a lack of cross-resistance to gentamicin, amikacin, tobramycin and plazomicin. Conclusions Its superior breadth of activity renders apramycin a promising drug candidate for the treatment of systemic Gram-negative infections that are resistant to treatment with other aminoglycoside antibiotics.
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Affiliation(s)
- Mario Juhas
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, Zürich, Switzerland
| | - Emma Widlake
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Jeanette Teo
- Department of Laboratory Medicine, National University Hospital, 5 Lower Kent Ridge Road, Singapore, Singapore
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Jonathan M Tyrrell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Yury S Polikanov
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, 900 South Ashland Avenue, MBRB 4170, Chicago, IL, USA
| | - Onur Ercan
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Anna Petersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Ali F Aboklaish
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Anna Rominski
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, Zürich, Switzerland
| | - David Crich
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, USA
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, Zürich, Switzerland
| | - Timothy R Walsh
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, Zürich, Switzerland
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3
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Tselepis L, Langley GW, Aboklaish AF, Widlake E, Jackson DE, Walsh TR, Schofield CJ, Brem J, Tyrrell JM. In vitro efficacy of imipenem-relebactam and cefepime-AAI101 against a global collection of ESBL-positive and carbapenemase-producing Enterobacteriaceae. Int J Antimicrob Agents 2020; 56:105925. [PMID: 32084512 DOI: 10.1016/j.ijantimicag.2020.105925] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 01/03/2020] [Accepted: 02/11/2020] [Indexed: 01/04/2023]
Abstract
OBJECTIVES To evaluate the potential clinical in vitro efficacy of novel β-lactam/β-lactamase-inhibitor combinations - including imipenem-relebactam (IPM-REL) and cefepime-AAI101 (enmetazobactam) (FEP-AAI) - against contemporary multidrug-resistant (MDR) Enterobacteriaceae. METHODS Agar-based MIC screening against MDR Enterobacteriaceae (n = 264) was used to evaluate the in vitro efficacy of IPM-REL and FEP-AAI, to compare the results with established combinations, and to investigate alternative β-lactam partners for relebactam (REL) and enmetazobactam (AAI). The inhibition activities of REL, AAI and the comparators avibactam (AVI) and tazobactam, against isolated recombinant β-lactamases covering representatives from all four Ambler classes of β-lactamases, were tested using a fluorescence-based assay. RESULTS Using recombinant proteins, all four inhibitors were highly active against the tested class A serine β-lactamases (SBLs). REL and AVI showed moderate activity against the Class C AmpC from Pseudomonas aeruginosa and the Class D OXA-10/-48 SBLs, but outperformed tazobactam and AAI. All tested inhibitors lacked activity against Class B metallo-β-lactamases (MBLs). In the presence of REL and IPM, but not AAI, susceptibility increased against Klebsiella pnuemoniae carbapenemase (KPC)-positive and OXA-48-positive isolates. Both aztreonam-AVI and ceftolozane-tazobactam were more effective than IPM-REL. In all the tested combinations, AAI was a more effective inhibitor of class A β-lactamases (ESBLs) than the established inhibitors. CONCLUSION The results lead to the proposal of alternative combination therapies involving REL and AAI to potentiate the use of β-lactams against clinical Gram-negative isolates expressing a variety of lactamases. They highlight the potential of novel combinations for combating strains not covered by existing therapies.
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Affiliation(s)
- Lucas Tselepis
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Gareth W Langley
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom; Charles River Laboratories, Chesterford Research Park, Saffron Walden, United Kingdom
| | - Ali F Aboklaish
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Emma Widlake
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Dana E Jackson
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Chris J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom.
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom; School of Cellular & Molecular Medicine, Biomedical Sciences Building, University Walk, Bristol, United Kingdom.
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4
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Yu Y, Walsh TR, Yang RS, Zheng M, Wei MC, Tyrrell JM, Wang Y, Liao XP, Sun J, Liu YH. Novel partners with colistin to increase its in vivo therapeutic effectiveness and prevent the occurrence of colistin resistance in NDM- and MCR-co-producing Escherichia coli in a murine infection model. J Antimicrob Chemother 2020; 74:87-95. [PMID: 30346547 DOI: 10.1093/jac/dky413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/13/2018] [Indexed: 12/23/2022] Open
Abstract
Objectives The emergence of NDM- and MCR-1-co-producing Escherichia coli has compromised the use of carbapenems and colistin, which are critically important in clinical therapy, and represents a severe threat to public health worldwide. Here, we demonstrate synergism of colistin combined with existing antibiotics as a potential strategy to overcome XDR E. coli co-harbouring NDM and MCR-1 genes. Methods To comprehensively evaluate their combined activity, antibiotic combinations were tested against 34 different E. coli strains carrying both NDM and MCR-1 genes. Antibiotic resistance profiles and molecular characteristics were investigated by susceptibility testing, PCR, MLST, S1-PFGE and WGS. Antibiotic synergistic efficacy was evaluated through in vitro chequerboard experiments and dose-response assays. A mouse model was used to confirm active combination therapies. Additionally, combinations were tested for their ability to prevent high-level colistin-resistant mutants (HLCRMs). Results Combinations of colistin with rifampicin, rifabutin and minocycline showed synergistic activity against 34 XDR NDM- and MCR-1-co-producing E. coli strains, restoring, in part, susceptibility to both colistin and the partnering antibiotics. The therapeutic effectiveness of colistin combined with rifampicin or minocycline was demonstrated in a mouse model. Furthermore, colistin plus rifampicin showed significant activity in preventing the occurrence of HLCRMs. Conclusions The synergism of colistin in combinations with rifampicin, rifabutin or minocycline offers viable therapeutic alternatives against XDR NDM- and MCR-positive E. coli.
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Affiliation(s)
- Yang Yu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China.,Department of Medical Microbiology and Infectious Disease, Institute of Infection & Immunity, Heath Park Hospital, Cardiff, UK
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Institute of Infection & Immunity, Heath Park Hospital, Cardiff, UK
| | - Run-Shi Yang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
| | - Mei Zheng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Meng-Chao Wei
- College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
| | - Jonathan M Tyrrell
- Department of Medical Microbiology and Infectious Disease, Institute of Infection & Immunity, Heath Park Hospital, Cardiff, UK
| | - Yang Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
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5
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Krajnc A, Brem J, Hinchliffe P, Calvopiña K, Panduwawala TD, Lang PA, Kamps JJAG, Tyrrell JM, Widlake E, Saward BG, Walsh TR, Spencer J, Schofield CJ. Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-β-Lactamases. J Med Chem 2019; 62:8544-8556. [PMID: 31454231 PMCID: PMC6767355 DOI: 10.1021/acs.jmedchem.9b00911] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
bicyclic boronate VNRX-5133 (taniborbactam) is a new type of
β-lactamase inhibitor in clinical development. We report that
VNRX-5133 inhibits serine-β-lactamases (SBLs) and some clinically
important metallo-β-lactamases (MBLs), including NDM-1 and VIM-1/2.
VNRX-5133 activity against IMP-1 and tested B2/B3 MBLs was lower/not
observed. Crystallography reveals how VNRX-5133 binds to the class
D SBL OXA-10 and MBL NDM-1. The crystallographic results highlight
the ability of bicyclic boronates to inhibit SBLs and MBLs via binding
of a tetrahedral (sp3) boron species. The structures imply
conserved binding of the bicyclic core with SBLs/MBLs. With NDM-1,
by crystallography, we observed an unanticipated VNRX-5133 binding
mode involving cyclization of its acylamino oxygen onto the boron
of the bicyclic core. Different side-chain binding modes for bicyclic
boronates for SBLs and MBLs imply scope for side-chain optimization.
The results further support the “high-energy-intermediate”
analogue approach for broad-spectrum β-lactamase inhibitor development
and highlight the ability of boron inhibitors to interchange between
different hybridization states/binding modes.
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Affiliation(s)
- Alen Krajnc
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk , University of Bristol , Bristol BS8 1TD , United Kingdom
| | - Karina Calvopiña
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Tharindi D Panduwawala
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Pauline A Lang
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Jos J A G Kamps
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - Emma Widlake
- Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - Benjamin G Saward
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk , University of Bristol , Bristol BS8 1TD , United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
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6
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Qamar MU, Walsh TR, Toleman MA, Tyrrell JM, Saleem S, Aboklaish A, Jahan S. Dissemination of genetically diverse NDM-1, -5, -7 producing-Gram-negative pathogens isolated from pediatric patients in Pakistan. Future Microbiol 2019; 14:691-704. [PMID: 31148474 DOI: 10.2217/fmb-2019-0012] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aim: To determine the prevalence of New Delhi metallo-β-lactamase (NDM)-producing Gram-negative pathogens isolated from children's samples. Materials & methods: Carbapenem-resistant clinical isolates (n = 117) were confirmed by VITEK® 2 compact system, matrix-assisted laser desorption ionization-time of flight and multilocus sequence typing. MIC (μg/ml) of various antibiotics was determined by VITEK 2 compact system. Molecular characterization of the isolates was performed by PCR, DNA sequencing, PFGE and DNA hybridization. Results: Out of 117 carbapenemase producers, 37 (31.6%) and 29 (24.7%) were Klebsiella pneumoniae and Acinetobacter baumannii, respectively. 72 (61.5%) isolates were NDM positive and among these 60, 9 and 3 were NDM-1, -5 and -7, respectively. Majority of the NDM-producing K. pneumoniae belonged to ST11 and ST273 while most of the Escherichia coli belonged to ST405 and ST101. blaNDM were mainly located on 150kb plasmids. MIC displayed high resistance against β-lactams drugs including carbapenems, and the most sensitive drugs were tigecycline and colistin. Conclusion: Dissemination of blaNDM-producing pathogens, particularly in children clinical settings, is a matter of great public health concern.
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Affiliation(s)
- Muhammad Usman Qamar
- Department of Microbiology, University of Health Sciences, Punjab, Pakistan.,Department of Microbiology, Faculty of Life Sciences, Government College University, Punjab, Pakistan.,Department of Medical Microbiology & Infectious Diseases, Institute of Infection & Immunity, School of Medicine, Cardiff University, Wales, UK
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Diseases, Institute of Infection & Immunity, School of Medicine, Cardiff University, Wales, UK
| | - Mark A Toleman
- Department of Medical Microbiology & Infectious Diseases, Institute of Infection & Immunity, School of Medicine, Cardiff University, Wales, UK
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Diseases, Institute of Infection & Immunity, School of Medicine, Cardiff University, Wales, UK
| | - Sidrah Saleem
- Department of Microbiology, University of Health Sciences, Punjab, Pakistan
| | - Ali Aboklaish
- Department of Medical Microbiology & Infectious Diseases, Institute of Infection & Immunity, School of Medicine, Cardiff University, Wales, UK
| | - Shah Jahan
- Department of Immunology, University of Health Sciences, Punjab, Pakistan
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7
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Langley GW, Cain R, Tyrrell JM, Hinchliffe P, Calvopiña K, Tooke CL, Widlake E, Dowson CG, Spencer J, Walsh TR, Schofield CJ, Brem J. Profiling interactions of vaborbactam with metallo-β-lactamases. Bioorg Med Chem Lett 2019; 29:1981-1984. [PMID: 31171422 PMCID: PMC6593178 DOI: 10.1016/j.bmcl.2019.05.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 11/20/2022]
Abstract
β-Lactams are the most successful antibacterials, yet their use is threatened by resistance, importantly as caused by β-lactamases. β-Lactamases fall into two mechanistic groups: the serine β-lactamases that utilise a covalent acyl-enzyme mechanism and the metallo β-lactamases that utilise a zinc-bound water nucleophile. Achieving simultaneous inhibition of both β-lactamase classes remains a challenge in the field. Vaborbactam is a boronate-based inhibitor that reacts with serine-β-lactamases to form covalent complexes that mimic tetrahedral intermediates in catalysis. Vaborbactam has recently been approved for clinical use in combination with the carbapenem meropenem. Here we show that vaborbactam moderately inhibits metallo-β-lactamases from all 3 subclasses (B1, B2 and B3), with a potency of around 20-100 fold below that by which it inhibits its current clinical targets, the Class A serine β-lactamases. This result contrasts with recent investigations of bicyclic boronate inhibitors, which potently inhibit subclass B1 MBLs but which presently lack activity against B2 and B3 enzymes. These findings indicate that cyclic boronate scaffolds have the potential to inhibit the full range of β-lactamases and justify further work on the development of boronates as broad-spectrum β-lactamase inhibitors.
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Affiliation(s)
- Gareth W Langley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom; Current address: Charles River Laboratories, Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Ricky Cain
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Karina Calvopiña
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Catherine L Tooke
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Emma Widlake
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Christopher G Dowson
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
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8
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Cahill ST, Tyrrell JM, Navratilova IH, Calvopiña K, Robinson SW, Lohans CT, McDonough MA, Cain R, Fishwick CWG, Avison MB, Walsh TR, Schofield CJ, Brem J. Studies on the inhibition of AmpC and other β-lactamases by cyclic boronates. Biochim Biophys Acta Gen Subj 2019; 1863:742-748. [PMID: 30738906 DOI: 10.1016/j.bbagen.2019.02.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/23/2019] [Accepted: 02/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The β-lactam antibiotics represent the most successful drug class for treatment of bacterial infections. Resistance to them, importantly via production of β-lactamases, which collectively are able to hydrolyse all classes of β-lactams, threatens their continued widespread use. Bicyclic boronates show potential as broad spectrum inhibitors of the mechanistically distinct serine- (SBL) and metallo- (MBL) β-lactamase families. METHODS Using biophysical methods, including crystallographic analysis, we have investigated the binding mode of bicyclic boronates to clinically important β-lactamases. Induction experiments and agar-based MIC screening against MDR-Enterobacteriaceae (n = 132) were used to evaluate induction properties and the in vitro efficacy of a bicyclic boronate in combination with meropenem. RESULTS Crystallographic analysis of a bicyclic boronate in complex with AmpC from Pseudomonas aeruginosa reveals it binds to form a tetrahedral boronate species. Microbiological studies on the clinical coverage (in combination with meropenem) and induction of β-lactamases by bicyclic boronates further support the promise of such compounds as broad spectrum β-lactamase inhibitors. CONCLUSIONS Together with reported studies on the structural basis of their inhibition of class A, B and D β-lactamases, biophysical studies, including crystallographic analysis, support the proposal that bicyclic boronates mimic tetrahedral intermediates common to SBL and MBL catalysis. GENERAL SIGNIFICANCE Bicyclic boronates are a new generation of broad spectrum inhibitors of both SBLs and MBLs.
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Affiliation(s)
- Samuel T Cahill
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Iva Hopkins Navratilova
- University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom; Research Complex at Harwell, Rutherford Appleton Lab, Harwell, Oxford OX11 0FA, United Kingdom
| | - Karina Calvopiña
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, United Kingdom
| | - Sean W Robinson
- Kinetic Discovery Ltd, Rutherford Appleton Laboratory, Oxford, Didcot OX11 0FA, United Kingdom
| | - Christopher T Lohans
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ricky Cain
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | | | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
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Tyrrell JM, Aboklaish AF, Walsh TR, Vaara T, Vaara M. The polymyxin derivative NAB739 is synergistic with several antibiotics against polymyxin-resistant strains of Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. Peptides 2019; 112:149-153. [PMID: 30586602 DOI: 10.1016/j.peptides.2018.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/11/2022]
Abstract
The antibiotic crisis has reinstated polymyxins, once abandoned because of their toxicity. Now, preclinical studies have revealed better tolerated and more effective derivatives of polymyxins such as NAB739. Simultaneously, polymyxin-resistant (PMR) strains such as the mcr-1 strains have received lots of justified publicity, even though they are still very rare. Here we show that NAB739 sensitizes the PMR strains to rifampin, a classic "anti-Gram-positive" antibiotic excluded by the intact outer membrane (OM) permeability barrier, as well as to retapamulin, the surrogate of lefamulin, an antibiotic under development against Gram-positive bacteria. Polymyxin B was used as a comparator. The combination of NAB739 and rifampin was synergistic against ten out of eleven PMR strains of Escherichia coli (Fractional Synergy Indices, FICs, 0.14-0.19) and that of NAB739 and retapamulin against all the tested eleven strains (FICs 0.19-0.25). Against PMR Klebsiella pneumoniae (n = 7), the FICs were 0.13-0.27 for NAB739 + rifampin and 0.14-0.28 for NAB739+retapamulin. Against Acinetobacter baumannii (n = 2), the combination of NAB739 and rifampin had the FIC of 0.09-0.19. Furthermore, NAB739 and meropenem were synergistic (FICs 0.25-0.50) against four out of five PMR strains that were simultaneously resistant to meropenem.
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Affiliation(s)
- Jonathan M Tyrrell
- Department of Medical Microbiology and Infectious Disease, Cardiff University Medical School, Cardiff, Wales, United Kingdom
| | - Ali F Aboklaish
- Department of Medical Microbiology and Infectious Disease, Cardiff University Medical School, Cardiff, Wales, United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Cardiff University Medical School, Cardiff, Wales, United Kingdom
| | - Timo Vaara
- Northern Antibiotics Ltd, FI-02150, Espoo, Finland
| | - Martti Vaara
- Northern Antibiotics Ltd, FI-02150, Espoo, Finland; Department of Bacteriology and Immunology, Helsinki University Medical School, FI-00014, Helsinki, Finland.
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10
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Salimraj R, Hinchliffe P, Kosmopoulou M, Tyrrell JM, Brem J, van Berkel SS, Verma A, Owens RJ, McDonough MA, Walsh TR, Schofield CJ, Spencer J. Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-β-lactamases. FEBS J 2019; 286:169-183. [PMID: 30430727 PMCID: PMC6326847 DOI: 10.1111/febs.14695] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/06/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022]
Abstract
Metallo-β-Lactamases (MBLs) protect bacteria from almost all β-lactam antibiotics. Verona integron-encoded MBL (VIM) enzymes are among the most clinically important MBLs, with VIM-1 increasing in carbapenem-resistant Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae) that are among the hardest bacterial pathogens to treat. VIM enzymes display sequence variation at residues (224 and 228) that in related MBLs are conserved and participate in substrate binding. How they accommodate this variability, while retaining catalytic efficiency against a broad substrate range, has remained unclear. Here, we present crystal structures of VIM-1 and its complexes with a substrate-mimicking thioenolate inhibitor, ML302F, that restores meropenem activity against a range of VIM-1 producing clinical strains, and the hydrolysed product of the carbapenem meropenem. Comparison of these two structures identifies a water-mediated hydrogen bond, between the carboxylate group of substrate/inhibitor and the backbone carbonyl of the active site zinc ligand Cys221, that is common to both complexes. Structural comparisons show that the responsible Cys221-bound water is observed in all known VIM structures, participates in carboxylate binding with other inhibitor classes, and thus effectively replicates the role of the conserved Lys224 in analogous complexes with other MBLs. These results provide a mechanism for substrate binding that permits the variation at positions 224 and 228 that is a hallmark of VIM MBLs. ENZYMES: EC 3.5.2.6 DATABASES: Co-ordinates and structure factors for protein structures described in this manuscript have been deposited in the Protein Data Bank (www.rcsb.org/pdb) with accession codes 5N5G (VIM-1), 5N5H (VIM-1:ML302F complex) and 5N5I (VIM-1-hydrolysed meropenem complex).
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Affiliation(s)
- Ramya Salimraj
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | | | | | | | - Jürgen Brem
- Department of ChemistryUniversity of OxfordUK
| | | | - Anil Verma
- Oxford Protein Production Facility UKRutherford Appleton LaboratoryOxfordshireUK
| | - Raymond J. Owens
- Oxford Protein Production Facility UKRutherford Appleton LaboratoryOxfordshireUK
| | | | | | | | - James Spencer
- School of Cellular and Molecular MedicineUniversity of BristolUK
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11
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Vaara M, Vaara T, Tyrrell JM. Structure-activity studies on polymyxin derivatives carrying three positive charges only reveal a new class of compounds with strong antibacterial activity. Peptides 2017; 91:8-12. [PMID: 28300674 DOI: 10.1016/j.peptides.2017.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 11/23/2022]
Abstract
Recent years have brought in an increased interest to develop improved polymyxins. The currently used polymyxins, i.e. polymyxin B and colistin (polymyxin E) are pentacationic lipopeptides that possess a cyclic heptapeptide part with three positive charges, a linear "panhandle" part with two positive charges, and a fatty acyl tail. Unfortunately, their clinical use is shadowed by their notable nephrotoxicity. We have previously developed a polymyxin derivative NAB739 which lacks the positive charges in the linear part. This derivative is better tolerated than polymyxin B in cynomolgus monkeys and is, in contrast to polymyxin B, excreted into urine in monkeys and rats. Here we have conducted further structure-activity relationship (SAR) studies on 17 derivatives with three positive charges only. We discovered a remarkably antibacterial class, as exemplified by NAB815, that carries two positive charges only in the cyclic part.
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Affiliation(s)
- Martti Vaara
- Northern Antibiotics Ltd., FI-02150 Espoo, Finland; Division of Clinical Microbiology, Helsinki University Hospital, FI-00029 Helsinki, Finland; Department of Bacteriology and Immunology, Helsinki University Medical School, FI-00014 Helsinki, Finland.
| | - Timo Vaara
- Northern Antibiotics Ltd., FI-02150 Espoo, Finland
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UGW Main Building, Heath Park Campus, Cardiff, Wales, UK
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12
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Wang Y, Zhang R, Li J, Wu Z, Yin W, Schwarz S, Tyrrell JM, Zheng Y, Wang S, Shen Z, Liu Z, Liu J, Lei L, Li M, Zhang Q, Wu C, Zhang Q, Wu Y, Walsh TR, Shen J. Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production. Nat Microbiol 2017; 2:16260. [PMID: 28165472 DOI: 10.1038/nmicrobiol.2016.260] [Citation(s) in RCA: 295] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/29/2016] [Indexed: 12/20/2022]
Abstract
By 2030, the global population will be 8.5 billion, placing pressure on international poultry production, of which China is a key producer1. From April 2017, China will implement the withdrawal of colistin as a growth promoter, removing over 8,000 tonnes per year from the Chinese farming sector2. To understand the impact of banning colistin and the epidemiology of multi-drug-resistant (MDR) Escherichia coli (using blaNDM and mcr-1 as marker genes), we sampled poultry, dogs, sewage, wild birds and flies. Here, we show that mcr-1, but not blaNDM, is prevalent in hatcheries, but blaNDM quickly contaminates flocks through dogs, flies and wild birds. We also screened samples directly for resistance genes to understand the true breadth and depth of the environmental and animal resistome. Direct sample testing for blaNDM and mcr-1 in hatcheries, commercial farms, a slaughterhouse and supermarkets revealed considerably higher levels of positive samples than the blaNDM- and mcr-1-positive E. coli, indicating a substantial segment of unseen resistome-a phenomenon we have termed the 'phantom resistome'. Whole-genome sequencing identified common blaNDM-positive E. coli shared among farms, flies, dogs and farmers, providing direct evidence of carbapenem-resistant E. coli transmission and environmental contamination.
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Affiliation(s)
- Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Rongmin Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jiyun Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zuowei Wu
- College of Veterinary Medicine, Iowa State University, Ames, Iowa 50011-1134, USA
| | - Wenjuan Yin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535 Neustadt-Mariensee, Germany
| | - Jonathan M Tyrrell
- Department of Medical Microbiology and Infectious Disease, Institute of Infection &Immunity, UHW Main Building, Heath Park Hospital, Cardiff CF14 4XN, UK
| | - Yongjun Zheng
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Shaolin Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhihai Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing 100193, China
| | - Jianye Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing 100193, China
| | - Lei Lei
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing 100193, China
| | - Mei Li
- Department of Medical Microbiology and Infectious Disease, Institute of Infection &Immunity, UHW Main Building, Heath Park Hospital, Cardiff CF14 4XN, UK
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing 100193, China
| | - Qidi Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Congming Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qijing Zhang
- College of Veterinary Medicine, Iowa State University, Ames, Iowa 50011-1134, USA
| | - Yongning Wu
- The Key Laboratory of Food Safety Risk Assessment, Ministry of Health and China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Institute of Infection &Immunity, UHW Main Building, Heath Park Hospital, Cardiff CF14 4XN, UK
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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13
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Wang Y, Tian GB, Zhang R, Shen Y, Tyrrell JM, Huang X, Zhou H, Lei L, Li HY, Doi Y, Fang Y, Ren H, Zhong LL, Shen Z, Zeng KJ, Wang S, Liu JH, Wu C, Walsh TR, Shen J. Prevalence, risk factors, outcomes, and molecular epidemiology of mcr-1-positive Enterobacteriaceae in patients and healthy adults from China: an epidemiological and clinical study. Lancet Infect Dis 2017; 17:390-399. [PMID: 28139431 DOI: 10.1016/s1473-3099(16)30527-8] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 11/07/2016] [Accepted: 11/11/2016] [Indexed: 11/16/2022]
Abstract
BACKGROUND The mcr-1 gene confers transferable colistin resistance. mcr-1-positive Enterobacteriaceae (MCRPE) have attracted substantial medical, media, and political attention; however, so far studies have not addressed their clinical impact. Herein, we report the prevalence of MCRPE in human infections and carriage, clinical associations of mcr-1-positive Escherichia coli (MCRPEC) infection, and risk factors for MCRPEC carriage. METHODS We undertook this study at two hospitals in Zhejiang and Guangdong, China. We did a retrospective cross-sectional assessment of prevalence of MCRPE infection from isolates of Gram-negative bacteria collected at the hospitals from 2007 to 2015 (prevalence study). We did a retrospective case-control study of risk factors for infection and mortality after infection, using all MCRPEC from infection isolates and a random sample of mcr-1-negative E coli infections from the retrospective collection between 2012 and 2015 (infection study). We also did a prospective case-control study to assess risk factors for carriage of MCRPEC in rectal swabs from inpatients with MCRPEC and mcr-1 negative at the hospitals and collected between May and December, 2015, compared with mcr-1-negative isolates from rectal swabs of inpatients (colonisation study). Strains were analysed for antibiotic resistance, plasmid typing, and transfer analysis, and strain relatedness. FINDINGS We identified 21 621 non-duplicate isolates of Enterobacteriaceae, Acinetobacter spp, and Pseudomonas aeruginosa from 18 698 inpatients and 2923 healthy volunteers. Of 17 498 isolates associated with infection, mcr-1 was detected in 76 (1%) of 5332 E coli isolates, 13 (<1%) of 348 Klebsiella pneumoniae, one (<1%) of 890 Enterobacter cloacae, and one (1%) of 162 Enterobacter aerogenes. For the infection study, we included 76 mcr-1-positive clinical E coli isolates and 508 mcr-1-negative isolates. Overall, MCRPEC infection was associated with male sex (209 [41%] vs 47 [63%], adjusted p=0·011), immunosuppression (30 [6%] vs 11 [15%], adjusted p=0·011), and antibiotic use, particularly carbapenems (45 [9%] vs 18 [24%], adjusted p=0·002) and fluoroquinolones (95 [19%] vs 23 [30%], adjusted p=0·017), before hospital admission. For the colonisation study, we screened 2923 rectal swabs from healthy volunteers, of which 19 were MCRPEC, and 1200 rectal swabs from patients, of which 35 were MCRPEC. Antibiotic use before hospital admission (p<0·0001) was associated with MCRPEC carriage in 35 patients compared with 378 patients with mcr-1-negative E coli colonisation, whereas living next to a farm was associated with mcr-1-negative E coli colonisation (p=0·03, univariate test). mcr-1 could be transferred between bacteria at high frequencies (10-1 to 10-3), and plasmid types and MCRPEC multi-locus sequence types (MLSTs) were more variable in Guangdong than in Zhejiang and included the human pathogen ST131. MCRPEC also included 17 unreported ST clades. INTERPRETATION In 2017, colistin will be formally banned from animal feeds in China and switched to human therapy. Infection with MRCPEC is associated with sex, immunosuppression, and previous antibiotic exposure, while colonisation is also associated with antibiotic exposure. MLST and plasmid analysis shows that MCRPEC are diversely spread throughout China and pervasive in Chinese communities. FUNDING National Key Basic Research Program of China, National Natural Science Foundation of China/Zhejiang, National Key Research and Development Program, and MRC, UK.
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Affiliation(s)
- Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guo-Bao Tian
- Key Laboratory of Tropical Diseases Control (Ministry of Education), Program of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Yingbo Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jonathan M Tyrrell
- Department of Medical Microbiology and Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park Hospital, Cardiff, UK
| | - Xi Huang
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhu, China
| | - Hongwei Zhou
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Lei Lei
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hong-Yu Li
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh Medical Center, PA, USA
| | - Ying Fang
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Hongwei Ren
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lan-Lan Zhong
- Key Laboratory of Tropical Diseases Control (Ministry of Education), Program of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kun-Jiao Zeng
- Key Laboratory of Tropical Diseases Control (Ministry of Education), Program of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shaolin Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jian-Hua Liu
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou, China
| | - Congming Wu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park Hospital, Cardiff, UK.
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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14
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Tyrrell JM, Wootton M, Toleman MA, Howe RA, Woodward M, Walsh TR. Genetic & virulence profiling of ESBL-positive E. coli from nosocomial & veterinary sources. Vet Microbiol 2016; 186:37-43. [PMID: 27016755 DOI: 10.1016/j.vetmic.2016.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 12/08/2015] [Accepted: 02/11/2016] [Indexed: 11/25/2022]
Abstract
CTX-M genes are the most prevalent ESBL globally, infiltrating nosocomial, community and environmental settings. Wild and domesticated animals may act as effective vectors for the dissemination of CTX-producing Enterobacteriaceae. This study aimed to contextualise blaCTX-M-14-positive, cephalosporin-resistant Enterobacteriaceae human infections and compared resistance and pathogenicity markers with veterinary isolates. Epidemiologically related human (n=18) and veterinary (n=4) blaCTX-M-14-positive E. coli were fully characterised. All were typed by XbaI pulsed field gel electrophoresis and ST. Chromosomal/plasmidic locations of blaCTX-M-14 were deduced by S1-nuclease digestion, and association with ISEcp1 was investigated by sequencing. Conjugation experiments assessed transmissibility of plasmids carrying blaCTX-M-14. Presence of virulence determinants was screened by PCR assay and pathogenicity potential was determined by in vitro Galleria mellonella infection models. 84% of clinical E. coli originated from community patients. blaCTX-M-14 was found ubiquitously downstream of ISEcp1 upon conjugative plasmids (25-150 kb). blaCTX-M-14 was also found upon the chromosome of eight E. coli isolates. CTX-M-14-producing E. coli were found at multiple hospital sites. Clonal commonality between patient, hospitals and livestock microbial populations was found. In vivo model survival rates from clinical isolates (30%) and veterinary isolates (0%) were significantly different (p<0.05). Co-transfer of blaCTX-M-14 and virulence determinants was demonstrated. There is evidence of clonal spread of blaCTX-M-14-positive E. coli involving community patients and farm livestock. blaCTX-M-14 positive human clinical isolates carry a lower intrinsic pathogenic potential than veterinary E. coli highlighting the need for greater veterinary practices in preventing dissemination of MDR E. coli among livestock.
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Affiliation(s)
- J M Tyrrell
- Department of Medical Microbiology & Infectious Disease, Heath Hospital, Cardiff CF14 4XW, UK.
| | - M Wootton
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
| | - M A Toleman
- Department of Medical Microbiology & Infectious Disease, Heath Hospital, Cardiff CF14 4XW, UK
| | - R A Howe
- Department of Medical Microbiology & Infectious Disease, Heath Hospital, Cardiff CF14 4XW, UK
| | - M Woodward
- Department of Food & Nutritional Studies, University of Reading, RG6 6AP, UK
| | - T R Walsh
- Department of Medical Microbiology & Infectious Disease, Heath Hospital, Cardiff CF14 4XW, UK
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