1
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Carascal MB, Destura RV, Rivera WL. Colorimetric Loop-Mediated Isothermal Amplification Assays Accurately Detect blaOXA-23-like and ISAba1 Genes from Acinetobacter baumannii in Pure Cultures and Spiked Human Sera. Microb Drug Resist 2024. [PMID: 39193641 DOI: 10.1089/mdr.2024.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024] Open
Abstract
Carbapenem resistance in Acinetobacter baumannii is a critical global health threat attributed to transferrable carbapenemase genes. Carbapenemase genotyping using polymerase chain reaction (PCR) presents a challenge in resource-limited settings because of its technical requirements. This study designed new loop-mediated isothermal amplification (LAMP) primers using multiple sequence alignment-based workflows, validated the primer performance against multiple target variants in silico, and developed novel LAMP assays (LAntRN-OXA23 and LAntRN-ISAba1) to detect the transferable blaOXA-23-like carbapenemase genes and ISAba1 elements in pure cultures and A. baumannii-spiked serum samples. The designed LAMP primers bind to the conserved regions of their highly polymorphic targets, with their in silico performance comparable with other published primers. The in vitro LAMP assays (using 30 PCR-profiled A. baumannii and 10 standard multidrug-resistant gram-negative isolates) have 100% concordance with the PCR-positive clinical samples, limits of detection as low as 1 pg/µL (200 copies/µL), and specificities of 57.89-100%. Both assays produced positive results when testing DNA samples (extracted using a commercial kit) from blaOXA-23-like and ISAba1-blaOXA-51-like PCR-positive A. baumannii-spiked normal human sera (five set-ups per target). In summary, the LAMP assays accurately detected the target genes and have applications in infection management, control, and point-of-care testing in resource-limited healthcare settings.
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Affiliation(s)
- Mark B Carascal
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
| | - Raul V Destura
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
- National Training Center for Biosafety and Biosecurity, National Institutes of Health, University of the Philippines, Manila, Philippines
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
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2
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Klamer ZL, June CM, Wawrzak Z, Taracila MA, Grey JA, Benn AMI, Russell CP, Bonomo RA, Powers RA, Leonard DA, Szarecka A. Structural and Dynamic Features of Acinetobacter baumannii OXA-66 β-Lactamase Explain Its Stability and Evolution of Novel Variants. J Mol Biol 2024; 436:168603. [PMID: 38729259 PMCID: PMC11198252 DOI: 10.1016/j.jmb.2024.168603] [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: 03/07/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
OXA-66 is a member of the OXA-51 subfamily of class D β-lactamases native to the Acinetobacter genus that includes Acinetobacter baumannii, one of the ESKAPE pathogens and a major cause of drug-resistant nosocomial infections. Although both wild type OXA-66 and OXA-51 have low catalytic activity, they are ubiquitous in the Acinetobacter genomes. OXA-51 is also remarkably thermostable. In addition, newly emerging, single and double amino acid variants show increased activity against carbapenems, indicating that the OXA-51 subfamily is growing and gaining clinical significance. In this study, we used molecular dynamics simulations, X-ray crystallography, and thermal denaturation data to examine and compare the dynamics of OXA-66 wt and its gain-of-function variants: I129L (OXA-83), L167V (OXA-82), P130Q (OXA-109), P130A, and W222L (OXA-234). Our data indicate that OXA-66 wt also has a high melting temperature, and its remarkable stability is due to an extensive and rigid hydrophobic bridge formed by a number of residues around the active site and harbored by the three loops, P, Ω, and β5-β6. Compared to the WT enzyme, the mutants exhibit higher flexibility only in the loop regions, and are more stable than other robust carbapenemases, such as OXA-23 and OXA-24/40. All the mutants show increased rotational flexibility of residues I129 and W222, which allows carbapenems to bind. Overall, our data support the hypothesis that structural features in OXA-51 and OXA-66 promote evolution of multiple highly stable variants with increased clinical relevance in A. baumannii.
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Affiliation(s)
- Zachary L Klamer
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA
| | - Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA
| | - Zdzislaw Wawrzak
- Life Sciences Collaborative Access Team, Synchrotron Research Center, Northwestern University, Argonne, IL, USA
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Joshua A Grey
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA
| | - Alyssa M I Benn
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA
| | | | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Departments of Pharmacology, Biochemistry, and Molecular Biology and Microbiology, and Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA.
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA.
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA.
| | - Agnieszka Szarecka
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA.
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3
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Arrigoni R, Ballini A, Santacroce L, Palese LL. The Dynamics of OXA-23 β-Lactamase from Acinetobacter baumannii. Int J Mol Sci 2023; 24:17527. [PMID: 38139363 PMCID: PMC10743560 DOI: 10.3390/ijms242417527] [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: 11/09/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Antibiotic resistance is a pressing topic, which also affects β-lactam antibiotic molecules. Until a few years ago, it was considered no more than an interesting species from an academic point of view, Acinetobacter baumanii is today one of the most serious threats to public health, so much so that it has been declared one of the species for which the search for new antibiotics, or new ways to avoid its resistance, is an absolute priority according to WHO. Although there are several molecular mechanisms that are responsible for the extreme resistance of A. baumanii to antibiotics, a class D β-lactamase is the main cause for the clinical concern of this bacterial species. In this work, we analyzed the A. baumanii OXA-23 protein via molecular dynamics. The results obtained show that this protein is able to assume different conformations, especially in some regions around the active site. Part of the OXA-23 protein has considerable conformational motility, while the rest is less mobile. The importance of these observations for understanding the functioning mechanism of the enzyme as well as for designing new effective molecules for the treatment of A. baumanii is discussed.
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Affiliation(s)
- Roberto Arrigoni
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy;
| | - Andrea Ballini
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Luigi Santacroce
- Interdisciplinary Department of Medicine (DIM), University of Bari ‘Aldo Moro’, 70124 Bari, Italy;
| | - Luigi Leonardo Palese
- Department of Translational Biomedicine and Neurosciences—(DiBraiN), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
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4
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Moussa SH, Shapiro AB, McLeod SM, Iyer R, Carter NM, Tsai YK, Siu LK, Miller AA. Molecular drivers of resistance to sulbactam-durlobactam in contemporary clinical isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 2023; 67:e0066523. [PMID: 37843305 PMCID: PMC10648852 DOI: 10.1128/aac.00665-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/07/2023] [Indexed: 10/17/2023] Open
Abstract
Acinetobacter baumannii-calcoaceticus complex (ABC) causes severe infections that are difficult to treat due to pre-existing antibiotic resistance. Sulbactam-durlobactam (SUL-DUR) is a targeted β-lactam/β-lactamase inhibitor combination antibiotic designed to treat serious infections caused by Acinetobacter, including multidrug- and carbapenem-resistant strains. In a recent global surveillance study of 5,032 ABC clinical isolates collected from 2016 to 2021, less than 2% of ABC isolates had SUL-DUR MIC values >4 µg/mL. Molecular characterization of these isolates confirmed the primary drivers of resistance are metallo-β-lactamases or penicillin-binding protein 3 (PBP3) mutations, as previously described. In addition, this study shows that certain common PBP3 variants, such as A515V, are insufficient to confer sulbactam resistance and that the efflux of durlobactam by AdeIJK is likely to play a role in a subset of strains.
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Affiliation(s)
- Samir H. Moussa
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Adam B. Shapiro
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Sarah M. McLeod
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Ramkumar Iyer
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Nicole M. Carter
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Yu-Kuo Tsai
- Kemyth Biotech Co., Ltd., Taipei City, Taiwan
| | | | - Alita A. Miller
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
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5
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Vuillemin X, Da Silva M, Bour M, Landon C, Plésiat P, Jeannot K. Cefiderocol activity is compromised by acquired extended-spectrum oxacillinases in Pseudomonas aeruginosa. Int J Antimicrob Agents 2023; 62:106917. [PMID: 37429451 DOI: 10.1016/j.ijantimicag.2023.106917] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/16/2023] [Accepted: 07/04/2023] [Indexed: 07/12/2023]
Abstract
OBJECTIVES Cefiderocol has an excellent in vitro activity on clinical strains of Pseudomonas aeruginosa (P. aeruginosa). However, the resistance of some isolates has been associated with the production of some β-lactamases. Whether some acquired extended-spectrum oxacillinases (ES-OXA) common in this species may compromise the susceptibility of P. aeruginosa to cefiderocol has not been evaluated so far. METHODS Eighteen genes encoding OXA belonging to the major subgroups identified in P. aeruginosa OXA-1 (n = 3); - 2 (n = 5); - 10 (n = 8), and - 46 (n = 2) were cloned into pUCP24 shuttle vector and transferred into reference strain PAO1. RESULTS Although production of the OXA-1 subgroup enzymes did not alter cefiderocol MICs, the β-lactamases of OXA-2, OXA-46, and four variants of the OXA-10 subgroup resulted in an 8-fold to 32-fold decrease in susceptibility in the PAO1 background. Interestingly, point mutations Ala149Pro and Asp150Gly in OXA-2 subgroup, Trp154Cys and Gly157Asp in OXA-10 subgroup (all located in the Ω loop), and the duplication of a Thr206 and a Gly207 in the β5-β6 loop of OXA-10 subgroup were related to decreased susceptibility to cefiderocol. We also showed that some ES-OXA, including the most frequent ES-OXA in P. aeruginosa strains, OXA-19 (derived from OXA-10 subgroup), significantly compromised activity of cefiderocol in addition to ceftazidime, ceftolozane/tazobactam, and ceftazidime/avibactam in clinical strains. CONCLUSION This work shows that several ES-OXA have a significant effect on cefiderocol susceptibility. Of concern are the Trp154Cys and Gly157Asp mutations that occur in some of these β-lactamases, as they are associated with a decreased activity of the most recent cephalosporins introduced to combat P. aeruginosa infections.
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Affiliation(s)
- Xavier Vuillemin
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, Besançon, France; Laboratoire Associé au Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France; Chrono-environnement, Université Bourgogne-Franche Comté, Besançon, France
| | - Maëlle Da Silva
- Laboratoire Associé au Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Maxime Bour
- Laboratoire Associé au Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | | | - Patrick Plésiat
- Chrono-environnement, Université Bourgogne-Franche Comté, Besançon, France
| | - Katy Jeannot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, Besançon, France; Laboratoire Associé au Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France; Chrono-environnement, Université Bourgogne-Franche Comté, Besançon, France.
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6
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Jain D, Verma J, Ajith T, Bhattacharjee A, Ghosh AS. Two non-active site residues W165 and L166 prominently influence the beta-lactam hydrolytic ability of OXA-23 beta-lactamase. J Antibiot (Tokyo) 2023; 76:489-498. [PMID: 37095236 DOI: 10.1038/s41429-023-00624-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 04/26/2023]
Abstract
Dissemination of class D OXA-type carbapenemases is one of the significant causes of beta-lactam resistance in Gram-negative bacteria. The amino acid residues present near the active site are involved in hydrolytic mechanism of class D carbapenemases, though it is not identified in OXA-23. Here, with the help of site-directed mutagenesis, we aimed to explicate the importance of the residues W165, L166 and V167 of the possible omega loop and residue D222 in the short β5-β6 loop on the activity of OXA-23. All the residues were substituted with alanine. The resultant proteins were assayed for the changes in activity in E. coli cells and purified for in vitro activity, and stability assessment. E. coli cells harboring OXA-23_W165A and OXA-23_L166A, individually, exhibited a significant decrease in resistance towards beta-lactam antibiotics as compared to OXA-23. Further, purified OXA-23_W165A and OXA-23_L166A imparted about >4-fold decrease in catalytic efficiency and displayed reduced thermal stability as compared to OXA-23. Bocillin-FL binding assay revealed that W165A substitution results in improper N-carboxylation of K82, leading to deacylation deficient OXA-23. Therefore, we infer that the residue W165 maintains the integrity of N-carboxylated lysine (K82) of OXA-23 and the residue L166 might be responsible for properly orientating the antibiotic molecules.
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Affiliation(s)
- Diamond Jain
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | - Jyoti Verma
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | - Tejavath Ajith
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | | | - Anindya Sundar Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
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7
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Introvigne ML, Beardsley TJ, Fernando MC, Leonard DA, Wallar BJ, Rudin SD, Taracila MA, Rather PN, Colquhoun JM, Song S, Fini F, Hujer KM, Hujer AM, Prati F, Powers RA, Bonomo RA, Caselli E. Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat Resistance in Acinetobacter baumannii. Antibiotics (Basel) 2023; 12:antibiotics12040644. [PMID: 37107006 PMCID: PMC10135033 DOI: 10.3390/antibiotics12040644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 04/29/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative organism listed as an urgent threat pathogen by the World Health Organization (WHO). Carbapenem-resistant A. baumannii (CRAB), especially, present therapeutic challenges due to complex mechanisms of resistance to β-lactams. One of the most important mechanisms is the production of β-lactamase enzymes capable of hydrolyzing β-lactam antibiotics. Co-expression of multiple classes of β-lactamases is present in CRAB; therefore, the design and synthesis of "cross-class" inhibitors is an important strategy to preserve the efficacy of currently available antibiotics. To identify new, nonclassical β-lactamase inhibitors, we previously identified a sulfonamidomethaneboronic acid CR167 active against Acinetobacter-derived class C β-lactamases (ADC-7). The compound demonstrated affinity for ADC-7 with a Ki = 160 nM and proved to be able to decrease MIC values of ceftazidime and cefotaxime in different bacterial strains. Herein, we describe the activity of CR167 against other β-lactamases in A. baumannii: the cefepime-hydrolysing class C extended-spectrum β-lactamase (ESAC) ADC-33 and the carbapenem-hydrolyzing OXA-24/40 (class D). These investigations demonstrate CR167 as a valuable cross-class (C and D) inhibitor, and the paper describes our attempts to further improve its activity. Five chiral analogues of CR167 were rationally designed and synthesized. The structures of OXA-24/40 and ADC-33 in complex with CR167 and select chiral analogues were obtained. The structure activity relationships (SARs) are highlighted, offering insights into the main determinants for cross-class C/D inhibitors and impetus for novel drug design.
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Affiliation(s)
- Maria Luisa Introvigne
- Department of Life Sciences, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Trevor J Beardsley
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Micah C Fernando
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Bradley J Wallar
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Susan D Rudin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Philip N Rather
- Research Service, Atlanta Veterans Medical Center, Decatur, GA 30033, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30307, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Jennifer M Colquhoun
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Shaina Song
- Research Service, Atlanta Veterans Medical Center, Decatur, GA 30033, USA
| | - Francesco Fini
- Department of Life Sciences, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Fabio Prati
- Department of Life Sciences, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH 44106, USA
| | - Emilia Caselli
- Department of Life Sciences, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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8
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Rahimzadeh G, Rezai MS, Farshidi F. Genotypic Patterns of Multidrug-Resistant Acinetobacter baumannii: A Systematic Review. Adv Biomed Res 2023; 12:56. [PMID: 37200758 PMCID: PMC10186031 DOI: 10.4103/abr.abr_434_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 05/20/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is one of the most common bacteria in nosocomial infections. Inappropriate usage of antibiotics has led to expanding emergence resistance to A. baumannii as a multidrug-resistant (MDR) strain. Empirical antibiotic therapy is necessary to evaluate the resistant gene pattern of MDR A. baumannii. For this purpose, the present study evaluated the resistance genes pattern of MDR A. baumannii collected from hospitalized patients using a genotypic diagnostic technique. To find evidence related to the study objectives, databases were searched such as Google Scholar, Web of Science, Science Direct, PubMed, and Scopus from 2000 to 2022, with specified keywords in the title and text of the articles. Articles were included based on inclusion and exclusion criteria. The mentioned database displayed 284 articles. After screening, 65 eligible articles were included. The results showed that various b-lactamases genes, aminoglycoside-modifying enzymes (AMEs) genes, and pump-expressing genes are resistance gene patterns in MDR A. baumannii isolates. MDR A. baumannii has significantly become resistant to b-lactams, carbapenems, and aminoglycosides.
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Affiliation(s)
- Golnar Rahimzadeh
- Pediatric Infectious Diseases Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad S. Rezai
- Pediatric Infectious Diseases Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
- Address for correspondence: Prof. Mohammad S. Rezai, Pediatric Infectious Diseases Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari - 4815838477, Iran. E-mail:
| | - Fereshteh Farshidi
- Pediatric Infectious Diseases Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
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9
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Avci FG, Tastekil I, Jaisi A, Ozbek Sarica P, Sariyar Akbulut B. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens. Pathog Glob Health 2022; 117:219-234. [PMID: 35758005 PMCID: PMC10081068 DOI: 10.1080/20477724.2022.2088496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Turkey
| | - Ilgaz Tastekil
- Bioengineering Department, Marmara University, Kadikoy, 34722, Turkey
| | - Amit Jaisi
- Drug and Cosmetics Excellence Center, School of Pharmacy, Walailak University, 80160, Nakhon Si Thammarat, Thailand
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10
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OXA-23-producing Acinetobacter baumannii isolates in L. Pasteur University Hospital in Slovakia from September 2021 to December 2021. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01119-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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11
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Mitchell JM, June CM, Baggett VL, Lowe BC, Ruble JF, Bonomo RA, Leonard DA, Powers RA. Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40. J Biol Chem 2022; 298:102127. [PMID: 35709986 PMCID: PMC9293634 DOI: 10.1016/j.jbc.2022.102127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
The evolution of multidrug resistance in Acinetobacter spp. increases the risk of our best antibiotics losing their efficacy. From a clinical perspective, the carbapenem-hydrolyzing class D β-lactamase subfamily present in Acinetobacter spp. is particularly concerning because of its ability to confer resistance to carbapenems. The kinetic profiles of class D β-lactamases exhibit variability in carbapenem hydrolysis, suggesting functional differences. To better understand the structure–function relationship between the carbapenem-hydrolyzing class D β-lactamase OXA-24/40 found in Acinetobacter baumannii and carbapenem substrates, we analyzed steady-state kinetics with the carbapenem antibiotics meropenem and ertapenem and determined the structures of complexes of OXA-24/40 bound to imipenem, meropenem, doripenem, and ertapenem, as well as the expanded-spectrum cephalosporin cefotaxime, using X-ray crystallography. We show that OXA-24/40 exhibits a preference for ertapenem compared with meropenem, imipenem, and doripenem, with an increase in catalytic efficiency of up to fourfold. We suggest that superposition of the nine OXA-24/40 complexes will better inform future inhibitor design efforts by providing insight into the complicated and varying ways in which carbapenems are selected and bound by class D β-lactamases.
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Affiliation(s)
- Joshua M Mitchell
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Vincent L Baggett
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Beth C Lowe
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - James F Ruble
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH; Departments of Medicine, Biochemistry, Molecular Biology and Microbiology, Pharmacology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH.
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI.
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12
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Ayoub Moubareck C, Hammoudi Halat D. The Collateral Effects of COVID-19 Pandemic on the Status of Carbapenemase-Producing Pathogens. Front Cell Infect Microbiol 2022; 12:823626. [PMID: 35372126 PMCID: PMC8968076 DOI: 10.3389/fcimb.2022.823626] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
The serious challenge of antimicrobial resistance continues to threaten public health and lingers in the era of the coronavirus disease 2019 (COVID-19), declared pandemic by the World Health Organization. While the pandemic has triggered the importance of infection control practices and preventive measures such as physical distancing, hand hygiene, travel reduction and quarantine, the ongoing alarm of antimicrobial resistance seems to accompany the pandemic too. Antimicrobial resistance has been fostered during COVID-19, possibly due to high rate of empirical antibiotic utilization in COVID-19 patients, increased use of biocides, and the disruption of proper healthcare for other conditions. Specifically, carbapenemase-producing Gram-negative bacteria have shown to cause secondary bacterial infections in patients hospitalized for COVID-19. Clinical and microbiological evidence of such infections is accumulating in different parts of the world. With the resilient nature of carbapenemases, their association with mortality, and the limited treatment options available, concerns regarding this group of antibiotic-hydrolyzing enzymes during the pandemic are expected to upsurge. While the additional burden carbapenemases exert on healthcare is worrisome, it remains hidden or abandoned among the various health consequences of the pandemic. The purpose of this minireview is to shed a light on carbapenemase-associated infections during such unprecedented time of COVID-19. A focused insight shall be made into carbapenemases, their implications for COVID-19 patients, and the features and consequences of co-infection, with a review of available evidence from pertinent literature. The importance of increased surveillance for carbapenemase-producers and optimizing their management in relation to the pandemic, shall be addressed as well.
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Affiliation(s)
| | - Dalal Hammoudi Halat
- Department of Pharmaceutical Sciences, School of Pharmacy, Lebanese International University, Bekaa, Lebanon
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13
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Selim S, Faried OA, Almuhayawi MS, Mohammed OA, Saleh FM, Warrad M. Dynamic Gene Clusters Mediating Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates. Antibiotics (Basel) 2022; 11:antibiotics11020168. [PMID: 35203771 PMCID: PMC8868416 DOI: 10.3390/antibiotics11020168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Acinetobacter baumanni (A. baumannii), a nonfermenting Gram-negative bacterium, has recently been associated with a broad range of nosocomial infections. To gain more meaningful insight into the problem of nosocomial illnesses caused by the multidrug-resistant (MDR) A. baumannii, as well as the factors that increase the risk of catching these infections, this investigation included a total of 86 clinical A. baumannii infections. Repetitive extragenic palindromic (REP)-PCR was used to investigate imipenem-resistant A. baumannii isolates for dynamic gene clusters causing carbapenem resistance. Four distinct A. baumannii lineages were found in the REP-PCR-DNA fingerprints of all isolates, with 95% of the samples coming from two dominant lineages. Imipenem, amikacin, and ciprofloxacin were less effective against genotype (A) isolates because of enhanced antibiotic tolerance. Lastly, to gain more insight into the mode of action of imipenem, we explored the binding affinity of imipenem toward different Acinetobacter baumannii OXA beta-lactamase class enzymes.
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Affiliation(s)
- Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72341, Saudi Arabia
- Correspondence:
| | - Osama Ahmed Faried
- Medical Microbiology and Immunology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef 62513, Egypt;
| | - Mohamed S. Almuhayawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Osama A. Mohammed
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt;
- Department of Clinical Pharmacology, Faculty of Medicine, Bisha University, Bisha 61922, Saudi Arabia
| | - Fayez M. Saleh
- Department of Medical Microbiology, Faculty of Medicine, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Mona Warrad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Quriat, Jouf University, Al-Quriat 77454, Saudi Arabia;
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14
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Gontijo AVL, Pereira SL, de Lacerda Bonfante H. Can Drug Repurposing be Effective Against Carbapenem-Resistant Acinetobacter baumannii? Curr Microbiol 2021; 79:13. [PMID: 34905109 PMCID: PMC8669236 DOI: 10.1007/s00284-021-02693-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 09/09/2021] [Indexed: 11/25/2022]
Abstract
Carbapenem-resistant Acinetobacter baumannii has been classified as a top priority for the development of new therapies due to its resistance to most antibiotics. Drug repurposing may be a fast and inexpensive strategy for treating this pathogen. This review aims to critically evaluate repurposed drugs for the treatment of infections caused by carbapenem-resistant A. baumannii, correlating their antimicrobial activity with data available for toxicity and side effects. Some drugs have been suggested as promising candidates for repurposing; however, in some cases, high toxicity and low plasma concentrations reduce applicability in clinical practice. The most favorable applicability is offered by fusidic acid and colistin, possibly combined with a third agent, promising to be well tolerated and achieving satisfactory plasma concentrations.
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Affiliation(s)
- Aline Vidal Lacerda Gontijo
- Department of Pharmacology, Institute of Biological Sciences, Federal University of Juiz de Fora (UFJF), Rua José Lourenço Kelmer, s/n, São Pedro, Juiz de Fora, Minas Gerais, 36036-900, Brazil.
| | - Sharlene Lopes Pereira
- Department of Pharmacology, Institute of Biological Sciences, Federal University of Juiz de Fora (UFJF), Rua José Lourenço Kelmer, s/n, São Pedro, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Herval de Lacerda Bonfante
- Department of Pharmacology, Institute of Biological Sciences, Federal University of Juiz de Fora (UFJF), Rua José Lourenço Kelmer, s/n, São Pedro, Juiz de Fora, Minas Gerais, 36036-900, Brazil
- Division of Rheumatology, Hospital Santa Casa de Misericórdia de Juiz de Fora (SCMJF), Juiz de Fora, Minas Gerais, Brazil
- Department of Internal Medicine, School of Medical Sciences, Health of Juiz de Fora (SUPREMA), Juiz de Fora, Minas Gerais, Brazil
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15
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Extended Spectrum Beta-Lactamase (ESBL) Produced by Gram-Negative Bacteria in Trinidad and Tobago. Int J Microbiol 2021; 2021:5582755. [PMID: 34475957 PMCID: PMC8408010 DOI: 10.1155/2021/5582755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
Gram-negative bacterial infections are a global health problem. The production of beta-lactamase is still the most vital factor leading to beta-lactam resistance. In Trinidad and Tobago, extended spectrum beta-lactamase (ESBL) production has been detected and reported mainly in the isolates of Klebsiella pneumoniae and Escherichia coli and constitutes a public health emergency that causes high morbidity and mortality in some patients. In this literature review, the authors cover vast information on ESBL frequency and laboratory detection using both conventional and molecular methods from clinical data. The aim is to make the reader reflect on how the actual knowledge can be used for rapid detection and understanding of the spread of antimicrobial resistance problems stemming from ESBL production among common Gram-negative organisms in the health care system.
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16
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VanPelt J, Stoffel S, Staude MW, Dempster K, Rose HA, Graney S, Graney E, Braynard S, Kovrigina E, Leonard DA, Peng JW. Arginine Modulates Carbapenem Deactivation by OXA-24/40 in Acinetobacter baumannii. J Mol Biol 2021; 433:167150. [PMID: 34271009 DOI: 10.1016/j.jmb.2021.167150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022]
Abstract
The resistance of Gram-negative bacteria to β-lactam antibiotics stems mainly from β-lactamase proteins that hydrolytically deactivate the β-lactams. Of particular concern are the β-lactamases that can deactivate a class of β-lactams known as carbapenems. Carbapenems are among the few anti-infectives that can treat multi-drug resistant bacterial infections. Revealing the mechanisms of their deactivation by β-lactamases is a necessary step for preserving their therapeutic value. Here, we present NMR investigations of OXA-24/40, a carbapenem-hydrolyzing Class D β-lactamase (CHDL) expressed in the gram-negative pathogen, Acinetobacter baumannii. Using rapid data acquisition methods, we were able to study the "real-time" deactivation of the carbapenem known as doripenem by OXA-24/40. Our results indicate that OXA-24/40 has two deactivation mechanisms: canonical hydrolytic cleavage, and a distinct mechanism that produces a β-lactone product that has weak affinity for the OXA-24/40 active site. The mechanisms issue from distinct active site environments poised either for hydrolysis or β-lactone formation. Mutagenesis reveals that R261, a conserved active site arginine, stabilizes the active site environment enabling β-lactone formation. Our results have implications not only for OXA-24/40, but the larger family of CHDLs now challenging clinical settings on a global scale.
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Affiliation(s)
- Jamie VanPelt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shannon Stoffel
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael W Staude
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Kayla Dempster
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Heath A Rose
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sarah Graney
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Erin Graney
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sara Braynard
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Elizaveta Kovrigina
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Jeffrey W Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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17
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Abstract
Class D β-lactamases are composed of 14 families and the majority of the member enzymes are included in the OXA family. The genes for class D β-lactamases are frequently identified in the chromosome as an intrinsic resistance determinant in environmental bacteria and a few of these are found in mobile genetic elements carried by clinically significant pathogens. The most dominant OXA family among class D β-lactamases is superheterogeneous and the family needs to have an updated scheme for grouping OXA subfamilies through phylogenetic analysis. The OXA enzymes, even the members within a subfamily, have a diverse spectrum of resistance. Such varied activity could be derived from their active sites, which are distinct from those of the other serine β-lactamases. Their substrate profile is determined according to the size and position of the P-, Ω- and β5-β6 loops, assembling the active-site channel, which is very hydrophobic. Also, amino acid substitutions occurring in critical structures may alter the range of hydrolysed substrates and one subfamily could include members belonging to several functional groups. This review aims to describe the current class D β-lactamases including the functional groups, occurrence types (intrinsic or acquired) and substrate spectra and, focusing on the major OXA family, a new model for subfamily grouping will be presented.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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18
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Mlynarcik P, Chudobova H, Zdarska V, Kolar M. In Silico Analysis of Extended-Spectrum β-Lactamases in Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10070812. [PMID: 34356733 PMCID: PMC8300632 DOI: 10.3390/antibiotics10070812] [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] [Received: 06/16/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
The growing bacterial resistance to available β-lactam antibiotics is a very serious public health problem, especially due to the production of a wide range of β-lactamases. At present, clinically important bacteria are increasingly acquiring new elements of resistance to carbapenems and polymyxins, including extended-spectrum β-lactamases (ESBLs), carbapenemases and phosphoethanolamine transferases of the MCR type. These bacterial enzymes limit therapeutic options in human and veterinary medicine. It must be emphasized that there is a real risk of losing the ability to treat serious and life-threatening infections. The present study aimed to design specific oligonucleotides for rapid PCR detection of ESBL-encoding genes and in silico analysis of selected ESBL enzymes. A total of 58 primers were designed to detect 49 types of different ESBL genes. After comparing the amino acid sequences of ESBLs (CTX-M, SHV and TEM), phylogenetic trees were created based on the presence of conserved amino acids and homologous motifs. This study indicates that the proposed primers should be able to specifically detect more than 99.8% of all described ESBL enzymes. The results suggest that the in silico tested primers could be used for PCR to detect the presence of ESBL genes in various bacteria, as well as to monitor their spread.
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Affiliation(s)
- Patrik Mlynarcik
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 77515 Olomouc, Czech Republic; (V.Z.); (M.K.)
- Correspondence:
| | - Hana Chudobova
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacky University, Šlechtitelů 27, 78371 Olomouc, Czech Republic;
| | - Veronika Zdarska
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 77515 Olomouc, Czech Republic; (V.Z.); (M.K.)
| | - Milan Kolar
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 77515 Olomouc, Czech Republic; (V.Z.); (M.K.)
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 5, 77900 Olomouc, Czech Republic
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19
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Antimicrobial Resistance Conferred by OXA-48 β-Lactamases: Towards a Detailed Mechanistic Understanding. Antimicrob Agents Chemother 2021; 65:AAC.00184-21. [PMID: 33753332 DOI: 10.1128/aac.00184-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OXA-48-type β-lactamases are now routinely encountered in bacterial infections caused by carbapenem-resistant Enterobacterales These enzymes are of high and growing clinical significance due to the importance of carbapenems in treatment of health care-associated infections by Gram-negative bacteria, the wide and increasing dissemination of OXA-48 enzymes on plasmids, and the challenges posed by their detection. OXA-48 confers resistance to penicillin (which is efficiently hydrolyzed) and carbapenem antibiotics (which is more slowly broken down). In addition to the parent enzyme, a growing array of variants of OXA-48 is now emerging. The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins. The growth in importance and diversity of the OXA-48 group has motivated increasing numbers of studies that aim to elucidate the relationship between structure and specificity and establish the mechanistic basis for β-lactam turnover in this enzyme family. In this review, we collate recently published structural, kinetic, and mechanistic information on the interactions between clinically relevant β-lactam antibiotics and inhibitors and OXA-48 β-lactamases. Collectively, these studies are starting to form a detailed picture of the underlying bases for the differences in β-lactam specificity between OXA-48 variants and the consequent differences in resistance phenotype. We focus specifically on aspects of carbapenemase and cephalosporinase activities of OXA-48 β-lactamases and discuss β-lactamase inhibitor development in this context. Throughout the review, we also outline key open research questions for future investigation.
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20
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Lence E, González‐Bello C. Bicyclic Boronate β‐Lactamase Inhibitors: The Present Hope against Deadly Bacterial Pathogens. ADVANCED THERAPEUTICS 2021. [DOI: 10.1002/adtp.202000246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica Universidade de Santiago de Compostela calle Jenaro de la Fuente s/n Santiago de Compostela 15782 Spain
| | - Concepción González‐Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica Universidade de Santiago de Compostela calle Jenaro de la Fuente s/n Santiago de Compostela 15782 Spain
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21
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Cefoperazone/sulbactam: New composites against multiresistant gram negative bacteria? INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 88:104707. [PMID: 33418147 DOI: 10.1016/j.meegid.2021.104707] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/27/2020] [Accepted: 12/31/2020] [Indexed: 01/29/2023]
Abstract
Sulbactam, a class A β-lactamase inhibitor, added to cefoperazone either at a fixed 8 mg/L level of sulbactam or at a level of fixed cefoperazone: sulbactam ratio (2:1) would constitute a combination form of cefoperazone/sulbactam, which has better activities against Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii than cefoperazone alone. Cefoperazone/sulbactam (1:1 or 1:2) has greater in-vitro activity against most multidrug-resistant organisms (ESBL- and AmpC-producing Enterobacteriaceae and carbapenem-resistant A. baumannii except for carbapenem-resistant P. aeruginosa) than a 2:1 ratio. However, increased sulbactam concentration may induce AmpC production. Besides, sulbactam concentration might not be readily achievable in serum if the susceptibility rates were defined by the breakpoints of higher sulbactam composites, such as ≤16/16 (1:1) or 16/32 (1:2) mg/L. Carbapenemases (KPC-, OXA-type enzymes and metallo-β-lactamases) can't be inhibited by sulbactam. Some in-vitro studies showed that increasing sulbactam composites of cefoperazone/sulbactam had no effect on carbapenem-resistant P. aeruginosa, suggesting the presence of carbapenemases or AmpC overproduction that could not be overcome by increasing sulbactam levels to recover cefoperazone activity. Sulbactam alone has good intrinsic activity against carbapenem-resistant Acinetobacter strains sometimes even in the presence of carbapenemase genes, suggesting unsteady levels of carbapenemases. In conclusion, appropriate composites of cefoperazone and β-lactamase inhibitor sulbactam may expand the clinical use if the pharmacokinetic optimization could be achieved in the human serum.
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22
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Can We Exploit β-Lactamases Intrinsic Dynamics for Designing More Effective Inhibitors? Antibiotics (Basel) 2020; 9:antibiotics9110833. [PMID: 33233339 PMCID: PMC7700307 DOI: 10.3390/antibiotics9110833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022] Open
Abstract
β-lactamases (BLs) represent the most frequent cause of antimicrobial resistance in Gram-negative bacteria. Despite the continuous efforts in the development of BL inhibitors (BLIs), new BLs able to hydrolyze the last developed antibiotics rapidly emerge. Moreover, the insurgence rate of effective mutations is far higher than the release of BLIs able to counteract them. This results in a shortage of antibiotics that is menacing the effective treating of infectious diseases. The situation is made even worse by the co-expression in bacteria of BLs with different mechanisms and hydrolysis spectra, and by the lack of inhibitors able to hit them all. Differently from other targets, BL flexibility has not been deeply exploited for drug design, possibly because of the small protein size, for their apparent rigidity and their high fold conservation. In this mini-review, we discuss the evidence for BL binding site dynamics being crucial for catalytic efficiency, mutation effect, and for the design of new inhibitors. Then, we report on identified allosteric sites in BLs and on possible allosteric inhibitors, as a strategy to overcome the frequent occurrence of mutations in BLs and the difficulty of competing efficaciously with substrates. Nevertheless, allosteric inhibitors could work synergistically with traditional inhibitors, increasing the chances of restoring bacterial susceptibility towards available antibiotics.
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23
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Yang Z, Wang P, Song P, Li X. Carbapenemase OXA-423: A Novel OXA-23 Variant in Acinetobacter baumannii. Infect Drug Resist 2020; 13:4069-4075. [PMID: 33204124 PMCID: PMC7666985 DOI: 10.2147/idr.s277364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/26/2020] [Indexed: 11/23/2022] Open
Abstract
Purpose A novel variant of OXA-23, named OXA-423, was identified in an Acinetobacter baumannii clinical isolate. The aim of this study was to analyse the resistance phenotype of OXA-423. Methods The A. baumannii strain WY-0713 was isolated from an intensive care unit patient. PCR was used to detect the blaOXA-23-like genes. Amplifying, cloning and sequencing were performed for the complete blaOXA-23-like. The novel blaOXA-423 and its ancestor blaOXA-23 were cloned into the expression vector pET-28b(+), and transformed into E. coli Rosetta (DE3) for antibiotic susceptibility testing. SDS-PAGE, modified Hodge test and CarbaNP test were used for detecting the expression of OXA-423 and OXA-23. Results PCR screening of A. baumannii WY-0713 was positive for blaOXA-23-like genes. Sequencing of the PCR product identified a novel blaOXA-23-like, named blaOXA-423 which encoding OXA-423. OXA-423 differed from OXA-23 by a crucial amino acid substitution (Val128Ala). The V128A substitution was located at the conserved active-site motifs SAV of OXA-23. Antibiotic susceptibility testing performed using isogenic E. coli showed that the MICs of E. coli Rosetta (pET-OXA-423) for penicillins and carbapenems were lower (reduced MICs 4-fold to 16-fold) than that of E. coli Rosetta (pET-OXA-23). The MICs of cefotaxime, ceftazidime and aztreonam for both transformants remained the same as the acceptor strain. Moreover, OXA-423 was slightly inhibited by sulbactam, clavulanic acid and tazobactam. SDS-PAGE analysis showed that OXA-423 and OXA-23 were conspicuously expressed. Modified Hodge test and CarbaNP test were positive demonstrated both of them were functional. Conclusion OXA-423, the first report of an amino acid substitution located at conserved active-site motifs of OXA-23, conferred lower MIC values of penicillins and carbapenems as compared with OXA-23, while without affecting the resistance profiles of expanded-spectrum cephalosporins and aztreonam.
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Affiliation(s)
- Zhenghai Yang
- Department of Clinical Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Peng Wang
- College of Life Sciences, Anhui Normal University, Wuhu, People's Republic of China
| | - Ping Song
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, People's Republic of China
| | - Xiaoning Li
- Department of Clinical Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, People's Republic of China
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24
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Hujer AM, Hujer KM, Leonard DA, Powers RA, Wallar BJ, Mack AR, Taracila MA, Rather PN, Higgins PG, Prati F, Caselli E, Marshall SH, Clarke T, Greco C, Venepally P, Brinkac L, Kreiswirth BN, Fouts DE, Bonomo RA. A comprehensive and contemporary "snapshot" of β-lactamases in carbapenem resistant Acinetobacter baumannii. Diagn Microbiol Infect Dis 2020; 99:115242. [PMID: 33248392 PMCID: PMC7562987 DOI: 10.1016/j.diagmicrobio.2020.115242] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/23/2020] [Accepted: 10/10/2020] [Indexed: 10/30/2022]
Abstract
Successful treatment of Acinetobacter baumannii infections require early and appropriate antimicrobial therapy. One of the first steps in this process is understanding which β-lactamase (bla) alleles are present and in what combinations. Thus, we performed WGS on 98 carbapenem-resistant A. baumannii (CR Ab). In most isolates, an acquired blaOXA carbapenemase was found in addition to the intrinsic blaOXA allele. The most commonly found allele was blaOXA-23 (n = 78/98). In some isolates, blaOXA-23 was found in addition to other carbapenemase alleles: blaOXA-82 (n = 12/78), blaOXA-72 (n = 2/78) and blaOXA-24/40 (n = 1/78). Surprisingly, 20% of isolates carried carbapenemases not routinely assayed for by rapid molecular diagnostic platforms, i.e., blaOXA-82 and blaOXA-172; all had ISAba1 elements. In 8 CR Ab, blaOXA-82 or blaOXA-172 was the only carbapenemase. Both blaOXA-24/40 and its variant blaOXA-72 were each found in 6/98 isolates. The most prevalent ADC variants were blaADC-30 (21%), blaADC-162 (21%), and blaADC-212 (26%). Complete combinations are reported.
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Affiliation(s)
- Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA
| | - Bradley J Wallar
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA
| | - Andrew R Mack
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Philip N Rather
- Research Service, Atlanta Veterans Medical Center, Decatur, GA, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA; Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany
| | - Fabio Prati
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Emilia Caselli
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Steven H Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | | | | | | | | | - Barry N Kreiswirth
- Hackensack Meridian Health, Center for Discovery and Innovation, Nutley, NJ, USA
| | | | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Departments of Biochemistry, Pharmacology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA.
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Antibiotic Resistance Profiles, Molecular Mechanisms and Innovative Treatment Strategies of Acinetobacter baumannii. Microorganisms 2020; 8:microorganisms8060935. [PMID: 32575913 PMCID: PMC7355832 DOI: 10.3390/microorganisms8060935] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic resistance is one of the biggest challenges for the clinical sector and industry, environment and societal development. One of the most important pathogens responsible for severe nosocomial infections is Acinetobacter baumannii, a Gram-negative bacterium from the Moraxellaceae family, due to its various resistance mechanisms, such as the β-lactamases production, efflux pumps, decreased membrane permeability and altered target site of the antibiotic. The enormous adaptive capacity of A. baumannii and the acquisition and transfer of antibiotic resistance determinants contribute to the ineffectiveness of most current therapeutic strategies, including last-line or combined antibiotic therapy. In this review, we will present an update of the antibiotic resistance profiles and underlying mechanisms in A. baumannii and the current progress in developing innovative strategies for combating multidrug-resistant A. baumannii (MDRAB) infections.
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Ramirez MS, Bonomo RA, Tolmasky ME. Carbapenemases: Transforming Acinetobacter baumannii into a Yet More Dangerous Menace. Biomolecules 2020; 10:biom10050720. [PMID: 32384624 PMCID: PMC7277208 DOI: 10.3390/biom10050720] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Acinetobacter baumannii is a common cause of serious nosocomial infections. Although community-acquired infections are observed, the vast majority occur in people with preexisting comorbidities. A. baumannii emerged as a problematic pathogen in the 1980s when an increase in virulence, difficulty in treatment due to drug resistance, and opportunities for infection turned it into one of the most important threats to human health. Some of the clinical manifestations of A. baumannii nosocomial infection are pneumonia; bloodstream infections; lower respiratory tract, urinary tract, and wound infections; burn infections; skin and soft tissue infections (including necrotizing fasciitis); meningitis; osteomyelitis; and endocarditis. A. baumannii has an extraordinary genetic plasticity that results in a high capacity to acquire antimicrobial resistance traits. In particular, acquisition of resistance to carbapenems, which are among the antimicrobials of last resort for treatment of multidrug infections, is increasing among A. baumannii strains compounding the problem of nosocomial infections caused by this pathogen. It is not uncommon to find multidrug-resistant (MDR, resistance to at least three classes of antimicrobials), extensively drug-resistant (XDR, MDR plus resistance to carbapenems), and pan-drug-resistant (PDR, XDR plus resistance to polymyxins) nosocomial isolates that are hard to treat with the currently available drugs. In this article we review the acquired resistance to carbapenems by A. baumannii. We describe the enzymes within the OXA, NDM, VIM, IMP, and KPC groups of carbapenemases and the coding genes found in A. baumannii clinical isolates.
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Affiliation(s)
- Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
| | - Robert A. Bonomo
- Medical Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA;
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics; Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- WRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH 44106, USA
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
- Correspondence: ; Tel.: +657-278-5263
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Gupta D, Singh A, Somvanshi P, Singh A, Khan AU. Structure-Based Screening of Non-β-Lactam Inhibitors against Class D β-Lactamases: An Approach of Docking and Molecular Dynamics. ACS OMEGA 2020; 5:9356-9365. [PMID: 32363287 PMCID: PMC7191842 DOI: 10.1021/acsomega.0c00356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
Abstract
The manifestation of class D β-lactamases in the community raises significant concern as they can hydrolyze carbapenem antibiotics. Hence, it is exceptionally alluring to design novel inhibitors. Structure-based virtual screening using docking programs and molecular dynamics simulations was employed to identify two novel non-β-lactam compounds that possess the ability to block different OXA variants. Furthermore, the presence of a nonpolar aliphatic amino acid, valine, near the active site serine, was identified in all OXA variants that can be accounted to block the catalytic activity of OXA enzymes.
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Affiliation(s)
- Divya Gupta
- Interdisciplinary
Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India
- Department of Life Sciences, Uttarakhand
Technical University, Dehradun 248007 Uttarakhand, India
| | - Aditi Singh
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi 110070, India
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi 110070, India
| | - Ajeet Singh
- Department of Biotechnology, G. B. Pant Engineering College, Pauri 246194, India
| | - Asad U. Khan
- Interdisciplinary
Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Malaysia
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The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:antibiotics9040186. [PMID: 32316342 PMCID: PMC7235769 DOI: 10.3390/antibiotics9040186] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 11/16/2022] Open
Abstract
Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and can be encoded by both chromosomal and plasmid-mediated genes. These enzymes represent the most potent β-lactamases, which hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemase production are clinical due to compromising the activity of the last resort antibiotics used for treating serious infections, and epidemiological due to their dissemination into various bacteria across almost all geographic regions. Carbapenemase-producing Enterobacteriaceae have received more attention upon their first report in the early 1990s. Currently, there is increased awareness of the impact of nonfermenting bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa, as well as other Gram-negative bacteria that are carbapenemase-producers. Outside the scope of clinical importance, carbapenemases are also detected in bacteria from environmental and zoonotic niches, which raises greater concerns over their prevalence, and the need for public health measures to control consequences of their propagation. The aims of the current review are to define and categorize the different families of carbapenemases, and to overview the main lines of their spread across different bacterial groups.
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Rodríguez D, Maneiro M, Vázquez-Ucha JC, Beceiro A, González-Bello C. 6-Arylmethylidene Penicillin-Based Sulfone Inhibitors for Repurposing Antibiotic Efficiency in Priority Pathogens. J Med Chem 2020; 63:3737-3755. [PMID: 32196336 DOI: 10.1021/acs.jmedchem.0c00127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The ability of 6-(aryl)methylidene penicillin-based sulfones 1-7 to repurpose β-lactam antibiotics activity with bacterial species that carry carbapenem-hydrolyzing class D β-lactamases (OXA-23, OXA-24/40 and OXA-48), as well as with class A (TEM-1, CTX-M-2) and class C (CMY-2, DHA-1) enzymes, is reported. The combinations imipenem/3 and imipenem/4 restored almost completely the antibiotic efficacy in OXA-23 and OXA-24/40 carbapenemase-producing A. baumannii strains (1 μg mL-1) and also provided good results for OXA-48 carbapenemase-producing K. pneumoniae strains (4 μg mL-1). Compounds 2-6 in combinations with ceftazidime and ampicillin were also efficient in restoring antibiotic efficacy in E. coli strains carrying class C (CMY-2 and DHA-1) and class A (TEM-1 and CTX-M-2) β-lactamase enzymes, respectively. Kinetic and inhibition studies with the OXA-24/40 enzyme, protein mass spectrometry analysis and docking studies allowed us to gain an insight into the inhibition mechanism and the experimentally observed differences between the ligands.
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Affiliation(s)
- Diana Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Juan C Vázquez-Ucha
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Xubias de Arriba, 84, 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Xubias de Arriba, 84, 15006 A Coruña, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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Interactions between Avibactam and Ceftazidime-Hydrolyzing Class D β-Lactamases. Biomolecules 2020; 10:biom10030483. [PMID: 32209976 PMCID: PMC7175300 DOI: 10.3390/biom10030483] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/10/2020] [Accepted: 03/15/2020] [Indexed: 12/15/2022] Open
Abstract
Class D β-lactamases exhibit very heterogeneous hydrolysis activity spectra against the various types of clinically useful β-lactams. Similarly, and according to the available data, their sensitivities to inactivation by avibactam can vary by a factor of more than 100. In this paper, we performed a detailed kinetic study of the interactions between two ceftazidime-hydrolyzing OXA enzymes and showed that they were significantly more susceptible to avibactam than several other class D enzymes that do not hydrolyze ceftazidime. From a clinical point of view, this result is rather interesting if one considers that avibactam is often administered in combination with ceftazidime.
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Therapeutic Efficacy of LN-1-255 in Combination with Imipenem in Severe Infection Caused by Carbapenem-Resistant Acinetobacter baumannii. Antimicrob Agents Chemother 2019; 63:AAC.01092-19. [PMID: 31383666 DOI: 10.1128/aac.01092-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022] Open
Abstract
The carbapenem-hydrolyzing class D β-lactamases (CHDLs) are the main mechanism of carbapenem resistance in Acinetobacter baumannii CHDLs are not effectively inactivated by clinically available β-lactam-type inhibitors. We have previously described the in vitro efficacy of the inhibitor LN-1-255 in combination with carbapenems. The aim of this study was to compare the efficacy of LN-1-255 with that of imipenem in murine pneumonia using A. baumannii strains carrying their most extended carbapenemases, OXA-23 and OXA-24/40. The bla OXA-23 and bla OXA-24/40 genes were cloned into the carbapenem-susceptible A. baumannii ATCC 17978 strain. Clinical isolates Ab1 and JC12/04, producing the enzymes OXA-23 and OXA-24/40, respectively, were used in the study. Pharmacokinetic (PK) parameters were determined. An experimental pneumonia model was used to evaluate the efficacy of the combined imipenem-LN-1-255 therapy. MICs of imipenem decreased between 32- and 128-fold in the presence of LN-1-255. Intramuscular treatment with imipenem-LN-1-255 (30/50 mg/kg) decreased the bacterial burden by (i) 4 and 1.7 log10 CFU/g lung in the infection with the ATCC 17978-OXA-23 and Ab1 strains, respectively, and by (ii) 2.5 and 4.5 log10 CFU/g lung in the infection produced by the ATCC 17978-OXA-24/40 and the JC12/04 strains, respectively. In all assays, combined therapy offered higher protection against pneumonia than that provided by monotherapy. No toxicity was observed in treated mice. Imipenem treatment combined with LN-1-255 treatment significantly reduced the severity of infection by carbapenem-resistant A. baumannii strains carrying CHDLs. Preclinical assays demonstrated the potential of LN-1-255 and imipenem therapy as a new antibacterial treatment.
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32
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Antunes VU, Llontop EE, Vasconcelos FNDC, López de Los Santos Y, Oliveira RJ, Lincopan N, Farah CS, Doucet N, Mittermaier A, Favaro DC. Importance of the β5-β6 Loop for the Structure, Catalytic Efficiency, and Stability of Carbapenem-Hydrolyzing Class D β-Lactamase Subfamily OXA-143. Biochemistry 2019; 58:3604-3616. [PMID: 31355630 DOI: 10.1021/acs.biochem.9b00365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The class D β-lactamase OXA-143 has been described as an efficient penicillinase, oxacillinase, and carbapenemase. The D224A variant, known as OXA-231, was described in 2012 as exhibiting less activity toward imipenem and increased oxacillinase activity. Additionally, the P227S mutation was reported as a case of convergent evolution for homologous enzymes. To investigate the impact of both mutations (D224A and P227S), we describe in this paper a deep investigation of the enzymatic activities of these three homologues. OXA-143(P227S) presented enhanced catalytic activity against ampicillin, oxacillins, aztreonam, and carbapenems. In addition, OXA-143(P227S) was the only member capable of hydrolyzing ceftazidime. These enhanced activities were due to a combination of a higher affinity (lower Km) and a higher turnover number (higher kcat). We also determined the crystal structure of apo OXA-231. As expected, the structure of this variant is very similar to the published OXA-143 structure, except for the two M223 conformations and the absence of electron density for three solvent-exposed loop segments. Molecular dynamics calculations showed that both mutants experience higher flexibility compared to that of the wild-type form. Therefore, our results illustrate that D224A and P227S act as deleterious and positive mutations, respectively, within the evolutionary path of the OXA-143 subfamily toward a more efficient carbapenemase.
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Affiliation(s)
- Víctor U Antunes
- Department of Organic Chemistry , State University of Campinas , São Paulo , SP 13083-970 , Brazil
| | - Edgar E Llontop
- Department of Biochemistry, Institute of Chemistry , University of Sao Paulo , Av. Prof. Lineu Prestes 748 , São Paulo , SP 05508-000 , Brazil
| | | | - Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , Laval , QC H7V 1B7 , Canada
| | - Ronaldo J Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , 38064-200 Uberaba , MG , Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences , University of Sao Paulo , São Paulo , SP 05508-900 , Brazil
| | - Chuck S Farah
- Department of Biochemistry, Institute of Chemistry , University of Sao Paulo , Av. Prof. Lineu Prestes 748 , São Paulo , SP 05508-000 , Brazil
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , Laval , QC H7V 1B7 , Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications , Université Laval , Québec , QC G1V 0A6 , Canada
| | - Anthony Mittermaier
- Department of Chemistry , McGill University , Montreal , QC H3A 0G4 , Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications , Université Laval , Québec , QC G1V 0A6 , Canada
| | - Denize C Favaro
- Department of Organic Chemistry , State University of Campinas , São Paulo , SP 13083-970 , Brazil.,Department of Chemistry , McGill University , Montreal , QC H3A 0G4 , Canada
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Qin J, Maixnerová M, Nemec M, Feng Y, Zhang X, Nemec A, Zong Z. Acinetobacter cumulans sp. nov., isolated from hospital sewage and capable of acquisition of multiple antibiotic resistance genes. Syst Appl Microbiol 2019; 42:319-325. [PMID: 30808586 DOI: 10.1016/j.syapm.2019.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/03/2019] [Accepted: 02/08/2019] [Indexed: 02/05/2023]
Abstract
We studied the taxonomic position of six phenetically related strains of the genus Acinetobacter, which were recovered from hospital sewage in China and showed different patterns of resistance to clinically important antibiotics. Whole-genome sequencing of these strains and genus-wide phylogeny reconstruction based on a set of 107 Acinetobacter core genes indicated that they formed a separate and internally cohesive clade within the genus. The average nucleotide identity based on BLAST and digital DNA-DNA hybridization values between the six new genomes were 97.25-98.67% and 79.2-89.3%, respectively, whereas those between them and the genomes of the known species were ≤78.57% and ≤28.5%, respectively. The distinctness of the strains at the species level was also supported by the results of the cluster analysis of the whole-cell protein fingerprints generated by MALDI-TOF MS. Moreover, the strains displayed a catabolically unique profile and could be differentiated from the phylogenetically closest species at least by their inability to grow on d,l-lactate. A total of 18 different genes were found in the six genome sequences which encode resistance to seven classes of antimicrobial agents, including clinically important carbapenems, oxyimino-cephalosporins, or aminoglycosides. These genes occurred in five different combinations, with three to 10 different genes per strain. We conclude that the six strains represent a novel Acinetobacter species, for which we propose the name Acinetobacter cumulans sp. nov. to reflect its ability to acquire and cumulate diverse resistance determinants. The type strain is WCHAc060092T (ANC 5797T=CCTCC AB 2018119T=GDMCC 1.1380T=KCTC 62576T).
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Affiliation(s)
- Jiayuan Qin
- Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Center for Pathogen Research, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China
| | - Martina Maixnerová
- Laboratory of Bacterial Genetics, Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
| | - Matěj Nemec
- Laboratory of Bacterial Genetics, Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Center for Pathogen Research, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China
| | - Xinzhuo Zhang
- School of International Education, Southwest Medical University, No. 1 Xianglin Road, Luzhou 646000, Sichuan, China; Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, No. 1 Xianglin Road, Luzhou 646000, Sichuan, China
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic; Department of Laboratory Medicine, Third Faculty of Medicine, Charles University, Šrobárova 50, 100 34 Prague 10, Czech Republic.
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Center for Pathogen Research, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China.
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OXA-23 Is a Prevalent Mechanism Contributing to Sulbactam Resistance in Diverse Acinetobacter baumannii Clinical Strains. Antimicrob Agents Chemother 2018; 63:AAC.01676-18. [PMID: 30348663 DOI: 10.1128/aac.01676-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Toth M, Stewart NK, Smith C, Vakulenko SB. Intrinsic Class D β-Lactamases of Clostridium difficile. mBio 2018; 9:e01803-18. [PMID: 30563905 PMCID: PMC6299217 DOI: 10.1128/mbio.01803-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
Clostridium difficile is the causative agent of the deadly C. difficile infection. Resistance of the pathogen to β-lactam antibiotics plays a major role in the development of the disease, but the mechanism of resistance is currently unknown. We discovered that C. difficile encodes class D β-lactamases, i.e., CDDs, which are intrinsic to this species. We studied two CDD enzymes, CDD-1 and CDD-2, and showed that they display broad-spectrum, high catalytic efficiency against various β-lactam antibiotics, including penicillins and expanded-spectrum cephalosporins. We demonstrated that the cdd genes are poorly expressed under the control of their own promoters and contribute only partially to the observed resistance to β-lactams. However, when the cdd1 gene was expressed under the control of efficient promoters in the antibiotic-sensitive Clostridium cochlearium strain, it produced high-level resistance to β-lactams. Taken together, the results determined in this work demonstrate the existence in C. difficile of intrinsic class D β-lactamases which constitute a reservoir of highly potent enzymes capable of conferring broad-spectrum, clinically relevant levels of resistance to β-lactam antibiotics. This discovery is a significant contribution to elucidation of the mechanism(s) of resistance of the clinically important pathogen C. difficile to β-lactam antibiotics.IMPORTANCEC. difficile is a spore-forming anaerobic bacterium which causes infection of the large intestine with high mortality rates. The C. difficile infection is difficult to prevent and treat, as the pathogen is resistant to many antimicrobial agents. Prolonged use of β-lactam antibiotics for treatment of various infectious diseases triggers the infection, as these drugs suppress the abundance of protective gut bacteria, allowing the resistant C. difficile bacteria to multiply. While resistance of C. difficile to β-lactam antibiotics plays the major role in the development of the disease, the mechanism of resistance is unknown. The significance of our research is in the discovery in C. difficile of β-lactamases, enzymes that destroy β-lactam antibiotics. These findings ultimately can help to combat deadly C. difficile infections.
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Affiliation(s)
- Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nichole K Stewart
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Clyde Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California, USA
| | - Sergei B Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Phillips-Jones MK, Harding SE. Antimicrobial resistance (AMR) nanomachines-mechanisms for fluoroquinolone and glycopeptide recognition, efflux and/or deactivation. Biophys Rev 2018; 10:347-362. [PMID: 29525835 PMCID: PMC5899746 DOI: 10.1007/s12551-018-0404-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/05/2018] [Indexed: 12/11/2022] Open
Abstract
In this review, we discuss mechanisms of resistance identified in bacterial agents Staphylococcus aureus and the enterococci towards two priority classes of antibiotics-the fluoroquinolones and the glycopeptides. Members of both classes interact with a number of components in the cells of these bacteria, so the cellular targets are also considered. Fluoroquinolone resistance mechanisms include efflux pumps (MepA, NorA, NorB, NorC, MdeA, LmrS or SdrM in S. aureus and EfmA or EfrAB in the enterococci) for removal of fluoroquinolone from the intracellular environment of bacterial cells and/or protection of the gyrase and topoisomerase IV target sites in Enterococcus faecalis by Qnr-like proteins. Expression of efflux systems is regulated by GntR-like (S. aureus NorG), MarR-like (MgrA, MepR) regulators or a two-component signal transduction system (TCS) (S. aureus ArlSR). Resistance to the glycopeptide antibiotic teicoplanin occurs via efflux regulated by the TcaR regulator in S. aureus. Resistance to vancomycin occurs through modification of the D-Ala-D-Ala target in the cell wall peptidoglycan and removal of high affinity precursors, or by target protection via cell wall thickening. Of the six Van resistance types (VanA-E, VanG), the VanA resistance type is considered in this review, including its regulation by the VanSR TCS. We describe the recent application of biophysical approaches such as the hydrodynamic technique of analytical ultracentrifugation and circular dichroism spectroscopy to identify the possible molecular effector of the VanS receptor that activates expression of the Van resistance genes; both approaches demonstrated that vancomycin interacts with VanS, suggesting that vancomycin itself (or vancomycin with an accessory factor) may be an effector of vancomycin resistance. With 16 and 19 proteins or protein complexes involved in fluoroquinolone and glycopeptide resistances, respectively, and the complexities of bacterial sensing mechanisms that trigger and regulate a wide variety of possible resistance mechanisms, we propose that these antimicrobial resistance mechanisms might be considered complex 'nanomachines' that drive survival of bacterial cells in antibiotic environments.
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Affiliation(s)
- Mary K Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, Loughborough, Leicestershire, UK.
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, Loughborough, Leicestershire, UK
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Multiple substitutions lead to increased loop flexibility and expanded specificity in Acinetobacter baumannii carbapenemase OXA-239. Biochem J 2018; 475:273-288. [PMID: 29229762 DOI: 10.1042/bcj20170702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/07/2017] [Accepted: 12/11/2017] [Indexed: 11/17/2022]
Abstract
OXA-239 is a class D carbapenemase isolated from an Acinetobacter baumannii strain found in Mexico. This enzyme is a variant of OXA-23 with three amino acid substitutions in or near the active site. These substitutions cause OXA-239 to hydrolyze late-generation cephalosporins and the monobactam aztreonam with greater efficiency than OXA-23. OXA-239 activity against the carbapenems doripenem and imipenem is reduced ∼3-fold and 20-fold, respectively. Further analysis demonstrated that two of the substitutions (P225S and D222N) are largely responsible for the observed alteration of kinetic parameters, while the third (S109L) may serve to stabilize the protein. Structures of OXA-239 with cefotaxime, doripenem and imipenem bound as acyl-intermediates were determined. These structures reveal that OXA-239 has increased flexibility in a loop that contains P225S and D222N. When carbapenems are bound, the conformation of this loop is essentially identical with that observed previously for OXA-23, with a narrow active site that makes extensive contacts to the ligand. When cefotaxime is bound, the loop can adopt a different conformation that widens the active site to allow binding of that bulky drug. This alternate conformation is made possible by P225S and further stabilized by D222N. Taken together, these results suggest that the three substitutions were selected to expand the substrate specificity profile of OXA-23 to cephalosporins and monobactams. The loss of activity against imipenem, however, suggests that there may be limits to the plasticity of class D enzymes with regard to evolving active sites that can effectively bind multiple classes of β-lactam drugs.
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38
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Optimization of novel monobactams with activity against carbapenem-resistant Enterobacteriaceae - Identification of LYS228. Bioorg Med Chem Lett 2018; 28:748-755. [PMID: 29336873 DOI: 10.1016/j.bmcl.2018.01.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 11/23/2022]
Abstract
Metallo-β-lactamases (MBLs), such as New Delhi metallo-β-lactamase (NDM-1) have spread world-wide and present a serious threat. Expression of MBLs confers resistance in Gram-negative bacteria to all classes of β-lactam antibiotics, with the exception of monobactams, which are intrinsically stable to MBLs. However, existing first generation monobactam drugs like aztreonam have limited clinical utility against MBL-expressing strains because they are impacted by serine β-lactamases (SBLs), which are often co-expressed in clinical isolates. Here, we optimized novel monobactams for stability against SBLs, which led to the identification of LYS228 (compound 31). LYS228 is potent in the presence of all classes of β-lactamases and shows potent activity against carbapenem-resistant isolates of Enterobacteriaceae (CRE).
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Rouhi S, Ramazanzadeh R. Prevalence of bla Oxacillinase-23and bla Oxacillinase-24/40-type Carbapenemases in Pseudomonas aeruginosa Species Isolated From Patients With Nosocomial and Non-nosocomial Infections in the West of Iran. IRANIAN JOURNAL OF PATHOLOGY 2018; 13:348-356. [PMID: 30636958 PMCID: PMC6322529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/10/2018] [Indexed: 12/03/2022]
Abstract
BACKGROUND AND OBJECTIVE Pseudomonas aeruginosa (P. aeruginosa) cause serious nosocomial and non-nosocomial infections. The bla Oxacillinases (OXA)-23 and bla OXA24/40 induce resistance to carbapenems. The current study aimed at detecting blaOXA-23 and blaOXA-24/40 in P. aeruginosa strains isolated from patients with nosocomial and non-nosocomial infections. carbapenems. The current study aimed at detecting blaOXA-23 and blaOXA-24/40 in P. aeruginosa strains isolated from patients with nosocomial and non-nosocomial infections. METHODS The current descriptive cross sectional study was conducted in Sanandaj, Iran (Kurdistan Province) from December 2015 to August 2017, on 146 strains of Pseudomonas spp. isolated from patients' specimens. Microbiological methods and polymerase chain reaction (PCR) for gyrB were applied to detect P. aeruginosa. Imipenem (IMP)-disk diffusion method and OXA-23-/OXA-24/40-multiplex PCR were used to identify resistant strains. Stata 12 using Fisher exact test and logistic regression were employed to analyze the data (P ≤0.05). RESULTS The gyrB-PCR results showed that 91.78% of isolates were P. aeruginosa. Nosocomial infection caused by P. aeruginosa was observed in 41.79% of the studied patients; however, 27.61% of P. aeruginosa strains were resistant to IMP; bla OXA-23 and bla OXA24/40 were detected in 11.19% and 2.24% of the strains, respectively; a co-existence of bla OXA-23 and bla OXA24/40 was also observed in 2.23% of P. aeruginosa strains. There were no significant relationships between antibiotic resistance and harboring resistance genes; in addition, between IMP resistance and age, gender, place of residence, inpatient/outpatient, and type of specimen no association was found (P≥ 0.05). CONCLUSION Resistance to IMP and the detection of resistant genes in the current study were observed in the clinical samples. Antibiotics should be prescribed more cautiously in order to prevent antibiotic resistance in pathogens.
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Affiliation(s)
- Samaneh Rouhi
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran,Cellular and Molecular Research Center, Health Development Research Institute, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Rashid Ramazanzadeh
- Cellular and Molecular Research Center, Health Development Research Institute, Kurdistan University of Medical Sciences, Sanandaj, Iran,Microbiology Dept, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran,Rashid Ramazanzadeh, Cellular and Molecular Research Center, Health Development Research Institute, Kurdistan University of Medical Sciences, Sanandaj, Iran
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40
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Cecchini T, Yoon EJ, Charretier Y, Bardet C, Beaulieu C, Lacoux X, Docquier JD, Lemoine J, Courvalin P, Grillot-Courvalin C, Charrier JP. Deciphering Multifactorial Resistance Phenotypes in Acinetobacter baumannii by Genomics and Targeted Label-free Proteomics. Mol Cell Proteomics 2017; 17:442-456. [PMID: 29259044 DOI: 10.1074/mcp.ra117.000107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/22/2017] [Indexed: 12/19/2022] Open
Abstract
Resistance to β-lactams in Acinetobacter baumannii involves various mechanisms. To decipher them, whole genome sequencing (WGS) and real-time quantitative polymerase chain reaction (RT-qPCR) were complemented by mass spectrometry (MS) in selected reaction monitoring mode (SRM) in 39 clinical isolates. The targeted label-free proteomic approach enabled, in one hour and using a single method, the quantitative detection of 16 proteins associated with antibiotic resistance: eight acquired β-lactamases (i.e. GES, NDM-1, OXA-23, OXA-24, OXA-58, PER, TEM-1, and VEB), two resident β-lactamases (i.e. ADC and OXA-51-like) and six components of the two major efflux systems (i.e. AdeABC and AdeIJK). Results were normalized using "bacterial quantotypic peptides," i.e. peptide markers of the bacterial quantity, to obtain precise protein quantitation (on average 8.93% coefficient of variation for three biological replicates). This allowed to correlate the levels of resistance to β-lactam with those of the production of acquired as well as resident β-lactamases or of efflux systems. SRM detected enhanced ADC or OXA-51-like production and absence or increased efflux pump production. Precise protein quantitation was particularly valuable to detect resistance mechanisms mediated by regulated genes or by overexpression of chromosomal genes. Combination of WGS and MS, two orthogonal and complementary techniques, allows thereby interpretation of the resistance phenotypes at the molecular level.
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Affiliation(s)
- Tiphaine Cecchini
- From the ‡Technology Research Department, Innovation Unit, bioMérieux SA, Marcy l'Etoile, France.,§UMR 5280, Institut des Sciences Analytiques, Université de Lyon, Lyon 1, Villeurbanne, France
| | - Eun-Jeong Yoon
- ¶Institut Pasteur, Unité des Agents Antibactériens, Paris, France
| | - Yannick Charretier
- From the ‡Technology Research Department, Innovation Unit, bioMérieux SA, Marcy l'Etoile, France.,§UMR 5280, Institut des Sciences Analytiques, Université de Lyon, Lyon 1, Villeurbanne, France
| | - Chloé Bardet
- From the ‡Technology Research Department, Innovation Unit, bioMérieux SA, Marcy l'Etoile, France.,§UMR 5280, Institut des Sciences Analytiques, Université de Lyon, Lyon 1, Villeurbanne, France
| | - Corinne Beaulieu
- From the ‡Technology Research Department, Innovation Unit, bioMérieux SA, Marcy l'Etoile, France
| | - Xavier Lacoux
- ‖R&D ImmunoAssays, bioMérieux SA, Marcy l'Etoile, France
| | | | - Jerome Lemoine
- §UMR 5280, Institut des Sciences Analytiques, Université de Lyon, Lyon 1, Villeurbanne, France
| | | | | | - Jean-Philippe Charrier
- From the ‡Technology Research Department, Innovation Unit, bioMérieux SA, Marcy l'Etoile, France;
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41
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Identification and Isolation of Insertion Sequences, in Carbapenem Resistant Clinical Isolates of Acinetobacter baumannii from Tehran Hospitals. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.58251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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42
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Activity of the β-Lactamase Inhibitor LN-1-255 against Carbapenem-Hydrolyzing Class D β-Lactamases from Acinetobacter baumannii. Antimicrob Agents Chemother 2017; 61:AAC.01172-17. [PMID: 28807908 DOI: 10.1128/aac.01172-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/02/2017] [Indexed: 12/21/2022] Open
Abstract
The number of infections caused by Gram-negative pathogens carrying carbapenemases is increasing, and the group of carbapenem-hydrolyzing class D β-lactamases (CHDLs) is especially problematic. Several clinically important CHDLs have been identified in Acinetobacter baumannii, including OXA-23, OXA-24/40, OXA-58, OXA-143, OXA-235, and the chromosomally encoded OXA-51. The selection and dissemination of carbapenem-resistant A. baumannii strains constitutes a serious global threat. Carbapenems have been successfully utilized as last-resort antibiotics for the treatment of multidrug-resistant A. baumannii infections. However, the spread of OXA carbapenemases is compromising the continued use of these antimicrobials. In response to this clinical issue, it is necessary and urgent to design and develop new specific inhibitors with efficacy against these enzymes. The aim of this work was to characterize the inhibitory activity of LN-1-255 (a 6-alkylidene-2-substituted penicillin sulfone) and compare it to that of two established inhibitors (avibactam and tazobactam) against the most relevant enzymes of each group of class D carbapenemases in A. baumannii The β-lactamase inhibitor LN-1-255 demonstrated excellent microbiological synergy and inhibition kinetics parameters against all tested CHDLs and a significantly higher activity than tazobactam and avibactam. A combination of carbapenems and LN-1-255 was effective against A. baumannii class D carbapenemases. Docking assays confirmed the affinity of LN-1-255 for the active site of these enzymes. LN-1-255 represents a potential new β-lactamase inhibitor that may have a significant role in eradicating infections caused by A. baumannii isolates carrying CHDLs.
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43
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González-Bello C. Antibiotic adjuvants - A strategy to unlock bacterial resistance to antibiotics. Bioorg Med Chem Lett 2017; 27:4221-4228. [PMID: 28827113 DOI: 10.1016/j.bmcl.2017.08.027] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/08/2017] [Accepted: 08/13/2017] [Indexed: 12/11/2022]
Abstract
Resistance to available antibiotics in pathogenic bacteria is currently a global challenge since the number of strains that are resistant to multiple types of antibiotics has increased dramatically each year and has spread worldwide. To unlock this problem, the use of an 'antibiotic adjuvant' in combination with an antibiotic is now being exploited. This approach enables us to prolong the lifespan of these life-saving drugs. This digests review provides an overview of the main types of antibiotic adjuvants, the basis of their operation and the remaining issues to be tackled in this field. Particular emphasis is placed on those compounds that are already in clinical development, namely β-lactamase inhibitors.
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Affiliation(s)
- Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
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44
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Werner JP, Mitchell JM, Taracila MA, Bonomo RA, Powers RA. Exploring the potential of boronic acids as inhibitors of OXA-24/40 β-lactamase. Protein Sci 2017; 26:515-526. [PMID: 27997706 DOI: 10.1002/pro.3100] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/08/2016] [Accepted: 12/08/2016] [Indexed: 01/01/2023]
Abstract
β-lactam antibiotics are crucial to the management of bacterial infections in the medical community. Due to overuse and misuse, clinically significant bacteria are now resistant to many commercially available antibiotics. The most widespread resistance mechanism to β-lactams is the expression of β-lactamase enzymes. To overcome β-lactamase mediated resistance, inhibitors were designed to inactivate these enzymes. However, current inhibitors (clavulanic acid, tazobactam, and sulbactam) for β-lactamases also contain the characteristic β-lactam ring, making them susceptible to resistance mechanisms employed by bacteria. This presents a critical need for novel, non-β-lactam inhibitors that can circumvent these resistance mechanisms. The carbapenem-hydrolyzing class D β-lactamases (CHDLs) are of particular concern, given that they efficiently hydrolyze potent carbapenem antibiotics. Unfortunately, these enzymes are not inhibited by clinically available β-lactamase inhibitors, nor are they effectively inhibited by the newest, non-β-lactam inhibitor, avibactam. Boronic acids are known transition state analog inhibitors of class A and C β-lactamases, and are not extensively characterized as inhibitors of class D β-lactamases. Importantly, boronic acids provide a novel way to potentially inhibit class D β-lactamases. Sixteen boronic acids were selected and tested for inhibition of the CHDL OXA-24/40. Several compounds were identified as effective inhibitors of OXA-24/40, with Ki values as low as 5 μM. The X-ray crystal structures of OXA-24/40 in complex with BA3, BA4, BA8, and BA16 were determined and revealed the importance of interactions with hydrophobic residues Tyr112 and Trp115. These boronic acids serve as progenitors in optimization efforts of a novel series of inhibitors for class D β-lactamases.
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Affiliation(s)
- Josephine P Werner
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Joshua M Mitchell
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Magdalena A Taracila
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, 44106.,Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, 44106
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, 44106.,Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, 44106
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
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45
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Staude MW, Leonard DA, Peng JW. Expanded Substrate Activity of OXA-24/40 in Carbapenem-Resistant Acinetobacter baumannii Involves Enhanced Binding Loop Flexibility. Biochemistry 2016; 55:6535-6544. [DOI: 10.1021/acs.biochem.6b00806] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Michael W. Staude
- Department
of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - David A. Leonard
- Department
of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
| | - Jeffrey W. Peng
- Department
of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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46
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Simakov N, Leonard DA, Smith JC, Wymore T, Szarecka A. A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω Loop. J Phys Chem B 2016; 121:3285-3296. [PMID: 27668669 DOI: 10.1021/acs.jpcb.6b07884] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Widespread antibiotic resistance, particularly when mediated by broad-spectrum β-lactamases, has major implications for public health. Substitutions in the active site often allow broad-spectrum enzymes to accommodate diverse types of β-lactams. Substitutions observed outside the active site are thought to compensate for the loss of thermal stability. The OXA-1 clade of class D β-lactamases contains a pair of conserved cysteines located outside the active site that forms a disulfide bond in the periplasm. Here, the effect of the distal disulfide bond on the structure and dynamics of OXA-1 was investigated via 4 μs molecular dynamics simulations. The results reveal that the disulfide promotes the preorganized orientation of the catalytic residues and affects the conformation of the functionally important Ω loop. Furthermore, principal component analysis reveals differences in the global dynamics between the oxidized and reduced forms, especially in the motions involving the Ω loop. A dynamical network analysis indicates that, in the oxidized form, in addition to its role in ligand binding, the KTG family motif is a central hub of the global dynamics. As activity of OXA-1 has been measured only in the reduced form, we suggest that accurate assessment of its functional profile would require oxidative conditions mimicking periplasm.
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Affiliation(s)
- Nikolay Simakov
- Carnegie Mellon University , Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213, United States.,Center for Computational Research, SUNY at Buffalo , New York 14203, United States
| | | | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Troy Wymore
- Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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47
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June CM, Muckenthaler TJ, Schroder EC, Klamer ZL, Wawrzak Z, Powers RA, Szarecka A, Leonard DA. The structure of a doripenem-bound OXA-51 class D β-lactamase variant with enhanced carbapenemase activity. Protein Sci 2016; 25:2152-2163. [PMID: 27636561 DOI: 10.1002/pro.3040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/09/2016] [Accepted: 09/09/2016] [Indexed: 11/10/2022]
Abstract
OXA-51 is a class D β-lactamase that is thought to be the native carbapenemase of Acinetobacter baumannii. Many variants of OXA-51 containing active site substitutions have been identified from A. baumannii isolates, and some of these substitutions increase hydrolytic activity toward carbapenem antibiotics. We have determined the high-resolution structures of apo OXA-51 and OXA-51 with one such substitution (I129L) with the carbapenem doripenem trapped in the active site as an acyl-intermediate. The structure shows that acyl-doripenem adopts an orientation very similar to carbapenem ligands observed in the active site of OXA-24/40 (doripenem) and OXA-23 (meropenem). In the OXA-51 variant/doripenem complex, the indole ring of W222 is oriented away from the doripenem binding site, thereby eliminating a clash that is predicted to occur in wildtype OXA-51. Similarly, in the OXA-51 variant complex, L129 adopts a different rotamer compared to I129 in wildtype OXA-51. This alternative position moves its side chain away from the hydroxyethyl moiety of doripenem and relieves another potential clash between the enzyme and carbapenem substrates. Molecular dynamics simulations of OXA-51 and OXA-51 I129L demonstrate that compared to isoleucine, a leucine at this position greatly favors a rotamer that accommodates the ligand. These results provide a molecular justification for how this substitution generates enhanced binding affinity for carbapenems, and therefore helps explain the prevalence of this substitution in clinical OXA-51 variants.
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Affiliation(s)
- Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | | | - Emma C Schroder
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Zachary L Klamer
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, Michigan, 49401
| | - Zdzislaw Wawrzak
- Life Sciences Collaborative Access Team, Synchrotron Research Center, Northwestern University, Argonne, Illinois, 60439
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Agnieszka Szarecka
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, Michigan, 49401
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
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48
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Clinical Variants of the Native Class D β-Lactamase of Acinetobacter baumannii Pose an Emerging Threat through Increased Hydrolytic Activity against Carbapenems. Antimicrob Agents Chemother 2016; 60:6155-64. [PMID: 27480863 DOI: 10.1128/aac.01277-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/26/2016] [Indexed: 11/20/2022] Open
Abstract
The threat posed by the chromosomally encoded class D β-lactamase of Acinetobacter baumannii (OXA-51/66) has been unclear, in part because of its relatively low affinity and turnover rate for carbapenems. Several hundred clinical variants of OXA-51/66 have been reported, many with substitutions of active-site residues. We determined the kinetic properties of OXA-66 and five clinical variants with respect to a wide variety of β-lactam substrates. The five variants displayed enhanced activity against carbapenems and in some cases against penicillins, late-generation cephalosporins, and the monobactam aztreonam. Molecular dynamics simulations show that in OXA-66, P130 inhibits the side-chain rotation of I129 and thereby prevents doripenem binding because of steric clash. A single amino acid substitution at this position (P130Q) in the variant OXA-109 greatly enhances the mobility of both I129 and a key active-site tryptophan (W222), thereby facilitating carbapenem binding. This expansion of substrate specificity represents a very worrisome development for the efficacy of β-lactams against this troublesome pathogen.
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49
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Sgrignani J, Grazioso G, De Amici M. Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations. Biochemistry 2016; 55:5191-200. [PMID: 27534275 DOI: 10.1021/acs.biochem.6b00461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem-OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path.
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Affiliation(s)
- Jacopo Sgrignani
- Istituto di Chimica del Riconoscimento Molecolare, CNR , Via Mario Bianco 9, 20131 Milan, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marco De Amici
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
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50
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Na JH, Cha SS. Structural basis for the extended substrate spectrum of AmpC BER and structure-guided discovery of the inhibition activity of citrate against the class C β-lactamases AmpC BER and CMY-10. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:976-85. [PMID: 27487828 DOI: 10.1107/s2059798316011311] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/11/2016] [Indexed: 11/10/2022]
Abstract
AmpC BER is an extended substrate spectrum class C β-lactamase with a two-amino-acid insertion in the R2 loop compared with AmpC EC2. The crystal structures of AmpC BER (S64A mutant) and AmpC EC2 were determined. Structural comparison of the two proteins revealed that the insertion increases the conformational flexibility of the R2 loop. Two citrate molecules originating from the crystallization solution were observed in the active site of the S64A mutant. One citrate molecule makes extensive interactions with active-site residues that are highly conserved among class C β-lactamases, whereas the other one is weakly bound. Based on this structural observation, it is demonstrated that citrate, a primary metabolite that is widely used as a food additive, is a competitive inhibitor of two class C β-lactamases (AmpC BER and CMY-10). Consequently, the data indicate enhancement of the flexibility of the R2 loop as an operative strategy for molecular evolution of extended-spectrum class C β-lactamases, and also suggest that the citrate scaffold is recognized by the active sites of class C β-lactamases.
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Affiliation(s)
- Jung Hyun Na
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun Shin Cha
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
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