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Azman AA, Leow ATC, Noor NDM, Noor SAM, Latip W, Ali MSM. Worldwide trend discovery of structural and functional relationship of metallo-β-lactamase for structure-based drug design: A bibliometric evaluation and patent analysis. Int J Biol Macromol 2024; 256:128230. [PMID: 38013072 DOI: 10.1016/j.ijbiomac.2023.128230] [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: 05/25/2023] [Revised: 10/11/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Metallo-β-lactamase (MBL) is an enzyme produced by clinically important bacteria that can inactivate many commonly used antibiotics, making them a significant concern in treating bacterial infections and the risk of having high antibiotic resistance issues among the community. This review presents a bibliometric and patent analysis of MBL worldwide research trend based on the Scopus and World Intellectual Property Organization databases in 2013-2022. Based on the keywords related to MBL in the article title, abstract, and keywords, 592 research articles were retrieved for further analysis using various tools such as Microsoft Excel to determine the frequency analysis, VOSviewer for bibliometric networks visualization, and Harzing's Publish or Perish for citation metrics analysis. Standard bibliometric parameters were analysed to evaluate the field's research trend, such as the growth of publications, topographical distribution, top subject area, most relevant journal, top cited documents, most relevant authors, and keyword trend analysis. Within 10 years, MBL discovery has shown a steady and continuous growth of interest among the community of researchers. United States of America, China, and the United Kingdom are the top 3 countries contribute high productivity to the field. The patent analysis also shows several impactful filed patents, indicating the significance of development research on the structural and functional relationship of MBL for an effective structure-based drug design (SBDD). Developing new MBL inhibitors using SBDD could help address the research gap and provide new successful therapeutic options for treating MBL-producing bacterial infections.
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Affiliation(s)
- Ameera Aisyah Azman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Siti Aminah Mohd Noor
- Center for Defence Foundation Studies, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur 57000, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
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Piccirilli A, Di Marcantonio S, Costantino V, Simonetti O, Busetti M, Luzzati R, Principe L, Di Domenico M, Rinaldi A, Cammà C, Perilli M. Identification of IncA Plasmid, Harboring blaVIM-1 Gene, in S. enterica Goldcoast ST358 and C. freundii ST62 Isolated in a Hospitalized Patient. Antibiotics (Basel) 2023; 12:1659. [PMID: 38136693 PMCID: PMC10741216 DOI: 10.3390/antibiotics12121659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
In the present study, we analyzed the genome of two S. enterica strains TS1 and TS2 from stool and blood cultures, respectively, and one strain of C. freundii TS3, isolated from a single hospitalized patient with acute myeloid leukemia. The S. enterica Goldcoast ST358 (O:8 (C2-C3) serogroup), sequenced by the MiSeq Illumina system, showed the presence of β-lactamase genes (blaVIM-1, blaSHV-12 and blaOXA-10), aadA1, ant(2″)-Ia, aac(6')-Iaa, aac(6')-Ib3, aac(6')-Ib-cr, qnrVC6, parC(T57S), and several incompatibility plasmids. A wide variety of insertion sequences (ISs) and transposon elements were identified. In C. freundii TS3, these were the blaVIM-1, blaCMY-150, and blaSHV-12, aadA1, aac(6')-Ib3, aac(6')-Ib-cr, mph(A), sul1, dfrA14, ARR-2, qnrVC6, and qnrB38. IncA plasmid isolated from E.coli/K12 transconjugant and C. freundii exhibited a sequence identity >99.9%. The transfer of IncA plasmid was evaluated by conjugation experiments.
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Affiliation(s)
- Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (S.D.M.); (M.P.)
| | - Sascia Di Marcantonio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (S.D.M.); (M.P.)
| | - Venera Costantino
- Microbiology Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (V.C.); (M.B.)
| | - Omar Simonetti
- Infectious Diseases Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (O.S.); (R.L.)
| | - Marina Busetti
- Microbiology Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (V.C.); (M.B.)
| | - Roberto Luzzati
- Infectious Diseases Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (O.S.); (R.L.)
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, “S. Giovanni di Dio” Hospital, 88900 Crotone, Italy;
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (A.R.); (C.C.)
| | - Antonio Rinaldi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (A.R.); (C.C.)
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (A.R.); (C.C.)
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (S.D.M.); (M.P.)
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Ruggiero M, Brunetti F, Dabos L, Girlich D, Muñoz JIB, Conza JD, Power P, Gutkind G, Naas T. Diversity of genetic platforms harboring the bla PER-2 gene in Enterobacterales and insights into the role of ISPa12 in its mobilization and dissemination. Int J Antimicrob Agents 2023:106850. [PMID: 37178777 DOI: 10.1016/j.ijantimicag.2023.106850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/22/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
The production of PER-like extended-spectrum β-lactamases has recently been associated with reduced susceptibility to the last resort drugs aztreonam/avibactam and cefiderocol. PER-2 have been mainly confined to Argentina and neighboring countries. Until now, only three plasmids harboring blaPER-2 genes have been characterized but very little is known about the involvement of different plasmid groups in its dissemination. This study analyzed the diversity of genetic platforms associated with blaPER-2 genes from a collection of PER-producing Enterobacterales by describing both the close environment as well as the plasmid backbones. Full sequences of eleven plasmids were obtained by short (Illumina) and long read (Oxford Nanopore or PacBio) sequencing technologies. De novo assemblies, annotation and sequence analysis were performed by Unicycler, Prokka and BLAST. Plasmids analysis revealed that blaPER-2 gene is encoded on plasmids of different incompatibility groups (A, C, FIB, HI1B, N2) suggesting that this gene may have been disseminated through a variety of plasmids. Analysis and comparison with the few public available nucleotide sequences describing blaPER-2 genetic environment, including those from the environmental species Pararheinheimera spp. (considered as the progenitor of blaPER genes), suggests a role of ISPa12 in blaPER-2 gene mobilization from the chromosome of Pararheinheimera spp. Also, the blaPER-2 gene was carried by a novel ISPa12-composite transposon Tn7390. In addition, its association with ISKox2-like elements in the close genetic environment in all analyzed plasmids suggests a role of this IS in further dissemination of blaPER-2 genes.
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Affiliation(s)
- Melina Ruggiero
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Florencia Brunetti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Laura Dabos
- Team RESIST, UMR1184, INSERM, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, Le Kremlin-Bicêtre, France; Polytechnic University of Madrid, Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), Evolutionary systems genetics of microbes Laboratory, Spain
| | - Delphine Girlich
- Team RESIST, UMR1184, INSERM, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, Le Kremlin-Bicêtre, France
| | - Jackson Ivan Briceño Muñoz
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - José Di Conza
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pablo Power
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Thierry Naas
- Team RESIST, UMR1184, INSERM, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance "Carbapenemase-producing Enterobacterales"
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To Be or Not to Be an OXA-48 Carbapenemase. Microorganisms 2022; 10:microorganisms10020258. [PMID: 35208713 PMCID: PMC8875484 DOI: 10.3390/microorganisms10020258] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 12/03/2022] Open
Abstract
Since the first description of OXA-48, more than forty variants have been recovered from Enterobacterales isolates. Whereas some OXA-48-related enzymes have been reported as conferring similar resistance patterns, namely, the hydrolysis of carbapenems and penicillins with very weak or almost no activity against expanded-spectrum cephalosporins, some have reduced carbapenem and temocillin hydrolysis, and others hydrolyze expanded-spectrum cephalosporins and carbapenems only marginally. With such drastic differences in the hydrolytic profile, especially of carbapenems, it becomes urgent to establish hydrolytic cutoffs in order to determine when an OXA-48-like enzyme may be considered as a carbapenemase or not. With this aim, the coefficient of activity for imipenem (kcat/Km) was determined for a total of 30 enzymes, including OXA-48, OXA-48-like natural variants, and OXA-48 synthetic mutants. In addition, six different methods for the detection of carbapenemase-producers were performed. The coefficients of activity for imipenem for all the different enzymes went from 550 mM−1·s−1 to 0.02 mM−1·s−1. In order to match the coefficient of activity results with the biochemical confirmatory tests, we suggest the value of 0.27 mM−1·s−1 as the cutoff above which an OXA-48 variant may be considered a carbapenem-hydrolyzing enzyme.
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Identification of qnrE3 and qnrE4, New Transferable Quinolone Resistance qnrE Family Genes Originating from Enterobacter mori and Enterobacter asburiae, Respectively. Antimicrob Agents Chemother 2021; 65:e0045621. [PMID: 34097486 DOI: 10.1128/aac.00456-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The qnrE family was designated in 2017. To date, two qnrE alleles have been discovered that are carried by plasmids. Here, we identified a new quinolone resistance gene, qnrE3, in the chromosome of Enterobacter mori clinical isolate 08-091 in China. qnrE3 conferred decreased susceptibility to fluoroquinolones, similar to qnrE1 and qnrE2. To investigate the precise origin of qnrE1, qnrE2, and qnrE3, 79 qnrE-bearing strains producing 30 qnrE variants were retrieved from the NCBI database. Phylogenetic analysis illustrated two major clusters, QnrEEmo and QnrEEas, produced mainly by the E. mori and E. asburiae strains, respectively. Comparison of the genetic context of qnrE alleles demonstrated that qnrE3 and qnrEEas2 alleles presumably were captured by ISEcp1 and mobilized from the E. mori and E. asburiae strains to the E. xiangfangensis and Escherichia coli strains, respectively. qnrEEas2 was proposed to be named qnrE4, since it has spread to another genus. All the qnrE alleles were harbored by the Enterobacter species, except those captured by ISEcp1 and mobilized into other species of Enterobacterales. E. mori is probably the source of qnrE1 to qnrE3 alleles, and E. asburiae is the reservoir of qnrE4.
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Practical agar-based disk-diffusion tests using sulfamoyl heteroarylcarboxylic acids for identification of subclass B1 metallo-β-lactamase-producing Enterobacterales. J Clin Microbiol 2021; 59:e0076121. [PMID: 34260275 DOI: 10.1128/jcm.00761-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The worldwide distribution of carbapenemase-producing Enterobacterales (CPE) is a serious public health concern as they exhibit carbapenem resistance, thus limiting the choice of antimicrobials for treating CPE infections. The combination treatment with a β-lactam and one of the newly approved β-lactamase inhibitors, such as avibactam, relebactam, or vaborbactam, provides a valuable tool to cope with CPE; however, these inhibitors are active only against serine-type carbapenemases, and not against metallo-β-lactamases (MβLs). Therefore, it is important to readily differentiate carbapenemases produced by CPE by using simple and reliable methods in order to choose an appropriate treatment. Here, we developed three practical agar-based disk-diffusion tests (double-disk synergy test [DDST], disk potentiation test, and modified carbapenem inactivation method [mCIM]) to discriminate the production of subclass B1 MβLs, such as IMP-, NDM-, and VIM-type MβLs, from the other carbapenemases, especially serine-type carbapenemases. This was accomplished using B1 MβL-specific sulfamoyl heteroarylcarboxylic acid inhibitors, 2,5-dimethyl-4-sulfamoylfuran-3-carboxylic acid (SFC) and 2,5-diethyl-1-methyl-4-sulfamoylpyrrole-3-carboxylic acid (SPC), originally developed by us. The DDST and mCIM using SFC and SPC revealed high sensitivity (95.3%) and specificity (100%) in detecting B1 MβL-producing Enterobacterales. In disk potentiation test, the sensitivities using SFC and SPC were 89.1% and 93.8%, respectively, whereas the specificities for both were 100%. These methods are simple and inexpensive, and have a high accuracy rate. These methods would, therefore, be of immense assistance in the specific detection and discrimination of B1 MβL-producing Enterobacterales in clinical microbiology laboratories, and would lead to better prevention against infection with such multidrug-resistant bacteria in clinical settings.
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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Berglund F, Johnning A, Larsson DGJ, Kristiansson E. An updated phylogeny of the metallo-β-lactamases. J Antimicrob Chemother 2021; 76:117-123. [PMID: 33005957 DOI: 10.1093/jac/dkaa392] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/15/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Metallo-β-lactamases (MBLs) are enzymes that use zinc-dependent hydrolysis to confer resistance to almost all available β-lactam antibiotics. They are hypothesized to originate from commensal and environmental bacteria, from where some have mobilized and transferred horizontally to pathogens. The current phylogeny of MBLs, however, is biased as it is founded largely on genes encountered in pathogenic bacteria. This incompleteness is emphasized by recent findings of environmental MBLs with new forms of zinc binding sites and atypical functional profiles. OBJECTIVES To expand the phylogeny of MBLs to provide a more accurate view of their evolutionary history. METHODS We searched more than 16 terabases of genomic and metagenomic data for MBLs of the three subclasses B1, B2 and B3 using the validated fARGene method. Predicted genes, together with the previously known ones, were used to infer phylogenetic trees. RESULTS We identified 2290 unique MBL genes forming 817 gene families, of which 741 were previously uncharacterized. MBLs from subclasses B1 and B3 separated into distinct monophyletic groups, in agreement with their taxonomic and functional properties. We present evidence that clinically associated MBLs were mobilized from Proteobacteria. Additionally, we identified three new variants of the zinc binding sites, indicating that the functional repertoire is broader than previously reported. CONCLUSIONS Based on our results, we recommend that the nomenclature of MBLs is refined into the phylogenetic groups B1.1-B1.5 and B3.1-B3.4 that more accurately describe their molecular and functional characteristics. Our results will also facilitate the annotation of novel MBLs, reflecting their taxonomic organization and evolutionary origin.
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Affiliation(s)
- Fanny Berglund
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Department of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Chalmers Science Park, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
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Muntean MM, Muntean AA, Guerin F, Cattoir V, Creton E, Cotellon G, Oueslati S, Popa MI, Girlich D, Iorga BI, Bonnin RA, Naas T. Optimization of the rapid carbapenem inactivation method for use with AmpC hyperproducers. J Antimicrob Chemother 2021; 76:2294-2301. [PMID: 34143889 DOI: 10.1093/jac/dkab170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Detection of carbapenemase-producing Enterobacterales (CPEs) is sometimes difficult with AmpC-hyperproducing Enterobacterales (AHEs), as they may falsely be classified as CPEs. Here, we present a rapid Carbapenem Inactivation Method (rCIM) optimized for AmpC producers (rCIM-A) that allows rapid and easy discrimination between AHEs and CPEs. METHODS Enterobacterales (n = 249), including natural AmpC producers, AHEs, CPEs and non-carbapenemase-producing carbapenem-resistant control strains were evaluated, using Carba NP, rCIM and rCIM-A. The rCIM-A differs from the rCIM by the addition of cloxacillin (400 μg/mL) to the initial antibiotic incubation step. RESULTS The rCIM-A yielded a sensitivity and specificity of 84.26% (95% CI: 76.00%-90.55%) and 99.29% (95% CI: 96.11%-99.98%), respectively, while those of the rCIM were 86.11% (95% CI: 78.13%-92.01%) and 80.85% (95% CI: 73.38%-86.99%), respectively; those of Carba NP were lower at 84.04% (95% CI: 75.05%-90.78%) and 91.37% (95% CI: 85.41%-95.46%), respectively, due to indeterminate results. The rCIM-A was capable of discriminating between AHEs and true CPEs, but still failed to identify OXA-23-producing Proteus mirabilis isolates and remained only partially reliable for identifying IMI-like producers and a few MBL (2 NDM-1, 1 LMB-1, 1 TMB-1 and 1 IMP-13) producers. One chromosomally encoded AmpC variant, MIR-10, gave repeatedly positive results using all three tests and was thus considered a false positive. CONCLUSIONS Specificity for AHEs greatly improved with the rCIM-A without altering the test performance for the other resistance mechanisms. It may replace the rCIM as a cheap, easy, rapid and accurate CPE detection test.
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Affiliation(s)
- Mădălina Maria Muntean
- TeamRESIST, INSERM U1184, School of Medicine, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France.,The "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania.,The "Cantacuzino" National Medico-Military Institute for Research and Development, Bucharest, Romania
| | - Andrei-Alexandru Muntean
- TeamRESIST, INSERM U1184, School of Medicine, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France.,The "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania.,The "Cantacuzino" National Medico-Military Institute for Research and Development, Bucharest, Romania
| | - François Guerin
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques ("laboratoire associé Entérocoques"), Rennes, France
| | - Vincent Cattoir
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques ("laboratoire associé Entérocoques"), Rennes, France.,Université de Rennes 1, Inserm U1230, Rennes, France
| | - Elodie Creton
- TeamRESIST, INSERM U1184, School of Medicine, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance: Carbapenem-resistant Enterobacterales, Le Kremlin-Bicêtre, France.,Joint research Unit EERA "Evolution and Ecology of Resistance to Antibiotics", Institut Pasteur-APHP-Université Paris Sud, Paris, France
| | - Garance Cotellon
- TeamRESIST, INSERM U1184, School of Medicine, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance: Carbapenem-resistant Enterobacterales, Le Kremlin-Bicêtre, France.,Joint research Unit EERA "Evolution and Ecology of Resistance to Antibiotics", Institut Pasteur-APHP-Université Paris Sud, Paris, France
| | - Saoussen Oueslati
- TeamRESIST, INSERM U1184, School of Medicine, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance: Carbapenem-resistant Enterobacterales, Le Kremlin-Bicêtre, France.,Joint research Unit EERA "Evolution and Ecology of Resistance to Antibiotics", Institut Pasteur-APHP-Université Paris Sud, Paris, France
| | - Mircea Ioan Popa
- The "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania.,The "Cantacuzino" National Medico-Military Institute for Research and Development, Bucharest, Romania
| | - Delphine Girlich
- TeamRESIST, INSERM U1184, School of Medicine, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance: Carbapenem-resistant Enterobacterales, Le Kremlin-Bicêtre, France.,Joint research Unit EERA "Evolution and Ecology of Resistance to Antibiotics", Institut Pasteur-APHP-Université Paris Sud, Paris, France
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Rémy A Bonnin
- TeamRESIST, INSERM U1184, School of Medicine, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance: Carbapenem-resistant Enterobacterales, Le Kremlin-Bicêtre, France.,Joint research Unit EERA "Evolution and Ecology of Resistance to Antibiotics", Institut Pasteur-APHP-Université Paris Sud, Paris, France
| | - Thierry Naas
- TeamRESIST, INSERM U1184, School of Medicine, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance: Carbapenem-resistant Enterobacterales, Le Kremlin-Bicêtre, France.,Joint research Unit EERA "Evolution and Ecology of Resistance to Antibiotics", Institut Pasteur-APHP-Université Paris Sud, Paris, France
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10
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Bonnin RA, Jousset AB, Emeraud C, Oueslati S, Dortet L, Naas T. Genetic Diversity, Biochemical Properties, and Detection Methods of Minor Carbapenemases in Enterobacterales. Front Med (Lausanne) 2021; 7:616490. [PMID: 33553210 PMCID: PMC7855592 DOI: 10.3389/fmed.2020.616490] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/09/2020] [Indexed: 01/05/2023] Open
Abstract
Gram-negative bacteria, especially Enterobacterales, have emerged as major players in antimicrobial resistance worldwide. Resistance may affect all major classes of anti-gram-negative agents, becoming multidrug resistant or even pan-drug resistant. Currently, β-lactamase-mediated resistance does not spare even the most powerful β-lactams (carbapenems), whose activity is challenged by carbapenemases. The dissemination of carbapenemases-encoding genes among Enterobacterales is a matter of concern, given the importance of carbapenems to treat nosocomial infections. Based on their amino acid sequences, carbapenemases are grouped into three major classes. Classes A and D use an active-site serine to catalyze hydrolysis, while class B (MBLs) require one or two zinc ions for their activity. The most important and clinically relevant carbapenemases are KPC, IMP/VIM/NDM, and OXA-48. However, several carbapenemases belonging to the different classes are less frequently detected. They correspond to class A (SME-, Nmc-A/IMI-, SFC-, GES-, BIC-like…), to class B (GIM, TMB, LMB…), class C (CMY-10 and ACT-28), and to class D (OXA-372). This review will address the genetic diversity, biochemical properties, and detection methods of minor acquired carbapenemases in Enterobacterales.
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Affiliation(s)
- Rémy A Bonnin
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France
| | - Agnès B Jousset
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Cécile Emeraud
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Saoussen Oueslati
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France
| | - Laurent Dortet
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
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11
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Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae: a Systematic Review of Current Reports. mSystems 2020; 5:5/6/e00783-20. [PMID: 33323413 PMCID: PMC7771540 DOI: 10.1128/msystems.00783-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. A systematic review of all studies published in PubMed database between 2015 to October 2020 was performed. Journal articles evaluating carbapenem and polymyxin resistance mechanisms, respectively, were included. The search identified 171 journal articles for inclusion. Different New Delhi metallo-β-lactamase (NDM) carbapenemase variants had different transcriptional and affinity responses to different carbapenems. Mutations within the Klebsiella pneumoniae carbapenemase (KPC) mobile transposon, Tn4401, affect its promoter activity and expression levels, increasing carbapenem resistance. Insertion of IS26 in ardK increased imipenemase expression 53-fold. ompCF porin downregulation (mediated by envZ and ompR mutations), micCF small RNA hyperexpression, efflux upregulation (mediated by acrA, acrR, araC, marA, soxS, ramA, etc.), and mutations in acrAB-tolC mediated clinical carbapenem resistance when coupled with β-lactamase activity in a species-specific manner but not when acting without β-lactamases. Mutations in pmrAB, phoPQ, crrAB, and mgrB affect phosphorylation of lipid A of the lipopolysaccharide through the pmrHFIJKLM (arnBCDATEF or pbgP) cluster, leading to polymyxin resistance; mgrB inactivation also affected capsule structure. Mobile and induced mcr, efflux hyperexpression and porin downregulation, and Ecr transmembrane protein also conferred polymyxin resistance and heteroresistance. Carbapenem and polymyxin resistance is thus mediated by a diverse range of genetic and transcriptional mechanisms that are easily activated in an inducing environment. The molecular understanding of these emerging mechanisms can aid in developing new therapeutics for multidrug-resistant Enterobacteriaceae isolates.
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12
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Metallo-β-Lactamases: Structure, Function, Epidemiology, Treatment Options, and the Development Pipeline. Antimicrob Agents Chemother 2020; 64:AAC.00397-20. [PMID: 32690645 DOI: 10.1128/aac.00397-20] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Modern medicine is threatened by the global rise of antibiotic resistance, especially among Gram-negative bacteria. Metallo-β-lactamase (MBL) enzymes are a particular concern and are increasingly disseminated worldwide, though particularly in Asia. Many MBL producers have multiple further drug resistances, leaving few obvious treatment options. Nonetheless, and more encouragingly, MBLs may be less effective agents of carbapenem resistance in vivo, under zinc limitation, than in vitro Owing to their unique structure and function and their diversity, MBLs pose a particular challenge for drug development. They evade all recently licensed β-lactam-β-lactamase inhibitor combinations, although several stable agents and inhibitor combinations are at various stages in the development pipeline. These potential therapies, along with the epidemiology of producers and current treatment options, are the focus of this review.
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13
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García-Betancur JC, Appel TM, Esparza G, Gales AC, Levy-Hara G, Cornistein W, Vega S, Nuñez D, Cuellar L, Bavestrello L, Castañeda-Méndez PF, Villalobos-Vindas JM, Villegas MV. Update on the epidemiology of carbapenemases in Latin America and the Caribbean. Expert Rev Anti Infect Ther 2020; 19:197-213. [PMID: 32813566 DOI: 10.1080/14787210.2020.1813023] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Carbapenemases are β-lactamases able to hydrolyze a wide range of β-lactam antibiotics, including carbapenems. Carbapenemase production in Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter spp., with and without the co-expression of other β-lactamases is a serious public health threat. Carbapenemases belong to three main classes according to the Ambler classification: class A, class B, and class D. AREAS COVERED Carbapenemase-bearing pathogens are endemic in Latin America. In this review, we update the status of carbapenemases in Latin America and the Caribbean. EXPERT OPINION Understanding the current epidemiology of carbapenemases in Latin America and the Caribbean is of critical importance to improve infection control policies limiting the dissemination of multi-drug-resistant pathogens and in implementing appropriate antimicrobial therapy.
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Affiliation(s)
| | - Tobias Manuel Appel
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque . Bogotá, Colombia
| | - German Esparza
- Programa de Aseguramiento de Calidad. PROASECAL SAS, Bogotá, Colombia
| | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP , São Paulo, Brazil
| | | | | | - Silvio Vega
- Complejo Hospitalario Metropolitano , Ciudad de Panamá, Panama
| | - Duilio Nuñez
- Infectious Diseases División, IPS Hospital Central , Asunción, Paraguay
| | - Luis Cuellar
- Servicio de Infectologia, Instituto Nacional de Enfermedades Neoplasicas , Lima, Peru
| | | | - Paulo F Castañeda-Méndez
- Department of Infectious Diseases, Hospital San Angel Inn Universidad , Ciudad de México, Mexico
| | | | - María Virginia Villegas
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque . Bogotá, Colombia.,Centro Médico Imbanaco . Cali, Colombia
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