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Raro OHF, Le Terrier C, Nordmann P, Poirel L. Impact of extended-spectrum chromosomal AmpC (ESAC) of Escherichia coli on susceptibility to cefiderocol. Microbiol Spectr 2024; 12:e0070424. [PMID: 38860818 PMCID: PMC11218523 DOI: 10.1128/spectrum.00704-24] [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: 03/25/2024] [Accepted: 04/24/2024] [Indexed: 06/12/2024] Open
Abstract
The impact of chromosomally encoded wild-type or extended-spectrum (ESAC) AmpC β-lactamases of Escherichia coli on susceptibility to ceftazidime, cefepime, and cefiderocol was evaluated in different genetic backgrounds, including wild-type, PBP3-modified, and porin-deficient E. coli strains. Recombinant E. coli strains possessing the different backgrounds and producing variable ESACs were evaluated. Although ESAC enzymes conferred resistance to ceftazidime and decreased susceptibility to cefepime as expected, we showed here that cefiderocol was also a substrate of ESAC enzymes. IMPORTANCE We showed here that chromosomally encoded intrinsic extended-spectrum cephalosporinases of Escherichia coli may impact susceptibility not only to ceftazidime and cefepime but also to cefiderocol.
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Affiliation(s)
- Otávio Hallal Ferreira Raro
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Christophe Le Terrier
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Division of Intensive Care Unit, University hospitals of Geneva, Geneva, Switzerland
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
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Abstract
Class C β-lactamases or cephalosporinases can be classified into two functional groups (1, 1e) with considerable molecular variability (≤20% sequence identity). These enzymes are mostly encoded by chromosomal and inducible genes and are widespread among bacteria, including Proteobacteria in particular. Molecular identification is based principally on three catalytic motifs (64SXSK, 150YXN, 315KTG), but more than 70 conserved amino-acid residues (≥90%) have been identified, many close to these catalytic motifs. Nevertheless, the identification of a tiny, phylogenetically distant cluster (including enzymes from the genera Legionella, Bradyrhizobium, and Parachlamydia) has raised questions about the possible existence of a C2 subclass of β-lactamases, previously identified as serine hydrolases. In a context of the clinical emergence of extended-spectrum AmpC β-lactamases (ESACs), the genetic modifications observed in vivo and in vitro (point mutations, insertions, or deletions) during the evolution of these enzymes have mostly involved the Ω- and H-10/R2-loops, which vary considerably between genera, and, in some cases, the conserved triplet 150YXN. Furthermore, the conserved deletion of several amino-acid residues in opportunistic pathogenic species of Acinetobacter, such as A. baumannii, A. calcoaceticus, A. pittii and A. nosocomialis (deletion of residues 304-306), and in Hafnia alvei and H. paralvei (deletion of residues 289-290), provides support for the notion of natural ESACs. The emergence of higher levels of resistance to β-lactams, including carbapenems, and to inhibitors such as avibactam is a reality, as the enzymes responsible are subject to complex regulation encompassing several other genes (ampR, ampD, ampG, etc.). Combinations of resistance mechanisms may therefore be at work, including overproduction or change in permeability, with the loss of porins and/or activation of efflux systems.
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Zavala A, Retailleau P, Elisée E, Iorga BI, Naas T. Genetic, Biochemical, and Structural Characterization of CMY-136 β-Lactamase, a Peculiar CMY-2 Variant. ACS Infect Dis 2019; 5:528-538. [PMID: 30788955 DOI: 10.1021/acsinfecdis.8b00240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the widespread use and abuse of antibiotics for the past decades, antimicrobial resistance poses a serious threat to public health nowadays. β-Lactams are the most used antibiotics, and β-lactamases are the most widespread resistance mechanism. Class C β-lactamases, also known as cephalosporinases, usually do not hydrolyze the latest and most potent β-lactams, expanded spectrum cephalosporins and carbapenems. However, the recent emergence of extended-spectrum AmpC cephalosporinases, their resistance to inhibition by classic β-lactamase inhibitors, and the fact that they can contribute to carbapenem resistance when paired with impermeability mechanisms, means that these enzymes may still prove worrisome in the future. Here we report and characterize the CMY-136 β-lactamase, a Y221H point mutant derivative of CMY-2. CMY-136 confers an increased level of resistance to ticarcillin, cefuroxime, cefotaxime, and ceftolozane/tazobactam. It is also capable of hydrolyzing ticarcillin and cloxacillin, which act as inhibitors of CMY-2. X-ray crystallography and modeling experiments suggest that the hydrolytic profile alterations seem to be the result of an increased flexibility and altered conformation of the Ω-loop, caused by the Y221H mutation.
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Affiliation(s)
- Agustin Zavala
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, Bât. 27, 91198 Gif-sur-Yvette, France
- EA7361 “Structure, dynamic, function and expression of broad spectrum β-lactamases”, Université Paris Sud, Université Paris Saclay, LabEx LERMIT, Faculty of Medicine, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, Bât. 27, 91198 Gif-sur-Yvette, France
| | - Eddy Elisée
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, Bât. 27, 91198 Gif-sur-Yvette, France
| | - Bogdan I. Iorga
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, Bât. 27, 91198 Gif-sur-Yvette, France
| | - Thierry Naas
- EA7361 “Structure, dynamic, function and expression of broad spectrum β-lactamases”, Université Paris Sud, Université Paris Saclay, LabEx LERMIT, Faculty of Medicine, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
- Carbapenemase-producing Enterobacteriaceae, Associated French National Reference Center for Antibiotic Resistance, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
- Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur, APHP, Université Paris Sud, 25-28 Rue du Dr Roux, 75015 Paris, France
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4
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Pérez-Llarena FJ, Vázquez-Ucha JC, Kerff F, Zamorano L, Miró E, Cabral MP, Fleites A, Lantero M, Martínez-Martínez L, Oliver A, Galleni M, Navarro F, Beceiro A, Bou G. Increased Antimicrobial Resistance in a Novel CMY-54 AmpC-Type Enzyme with a GluLeu217–218 Insertion in the Ω-Loop. Microb Drug Resist 2018; 24:527-533. [DOI: 10.1089/mdr.2017.0017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Frédéric Kerff
- Centre d'Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Laura Zamorano
- Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Elisenda Miró
- Servicio de Microbiología, Hospital de la Santa Creu i Sant Pau/IIB-Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María Póvoa Cabral
- Servicio de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Ana Fleites
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Marta Lantero
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Luis Martínez-Martínez
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla-IDIVAL, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Moreno Galleni
- Centre d'Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Ferrán Navarro
- Servicio de Microbiología, Hospital de la Santa Creu i Sant Pau/IIB-Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña, A Coruña, Spain
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Porres-Osante N, Sáenz Y, Somalo S, Torres C. Characterization of Beta-lactamases in Faecal Enterobacteriaceae Recovered from Healthy Humans in Spain: Focusing on AmpC Polymorphisms. MICROBIAL ECOLOGY 2015; 70:132-40. [PMID: 25501887 DOI: 10.1007/s00248-014-0544-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/26/2014] [Indexed: 05/21/2023]
Abstract
The intestinal tract is a huge reservoir of Enterobacteriaceae, some of which are opportunist pathogens. Several genera of these bacteria harbour intrinsic antibiotic resistance genes, such as ampC genes in species of Citrobacter, Enterobacter or Escherichia genera. In this work, beta-lactamases and other resistance mechanisms have been characterized in Enterobacteriaceae isolates recovered from healthy human faecal samples, focusing on the ampC beta-lactamase genes. Fifty human faecal samples were obtained, and 70 Enterobacteriaceae bacteria were isolated: 44 Escherichia coli, 4 Citrobacter braakii, 9 Citrobacter freundii, 8 Enterobacter cloacae, 1 Proteus mirabilis, 1 Proteus vulgaris, 1 Klebsiella oxytoca, 1 Serratia sp. and 1 Cronobacter sp. A high percentage of resistance to ampicillin was detected (57%), observing the AmpC phenotype in 22 isolates (31%) and the ESBL phenotype in 3 isolates. AmpC molecular characterization showed high diversity into bla CMY and bla ACT genes from Citrobacter and Enterobacter species, respectively, and the pulsed-field gel electrophoresis (PFGE) analysis demonstrated low clonality among them. The prevalence of people colonized by strains carrying plasmid-mediated ampC genes obtained in this study was 2%. The unique plasmid-mediated bla AmpC identified in this study was the bla CMY-2 gene, detected in an E. coli isolate ascribed to the sequence type ST405 which belonged to phylogenetic group D. The hybridization and conjugation experiments demonstrated that the ISEcp1-bla CMY-2-blc structure was carried by a ~78-kb self-transferable IncK plasmid. This study shows a high polymorphism among beta-lactamase genes in Enterobacteriaceae from healthy people microbiota. Extensive AmpC-carrier studies would provide important information and could allow the anticipation of future global health problems.
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Affiliation(s)
- Nerea Porres-Osante
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
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Characterization of a novel AmpC β-lactamase produced by a carbapenem-resistant Cedecea davisae clinical isolate. Antimicrob Agents Chemother 2014; 58:6942-5. [PMID: 25136020 DOI: 10.1128/aac.03237-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Cedecea davisae isolate, which was intermediate or resistant to third-generation cephalosporins and carbapenems, was recovered from a urine sample. Susceptibility testing, isoelectric focusing, and analysis of outer membrane proteins showed that AmpC β-lactamase expression combined with porin deficiency accounted for the carbapenem resistance. A cloning experiment followed by phenotypic and enzymatic characterization identified a novel class C enzyme that was phylogenetically and biochemically close to the chromosome-borne β-lactamases of the genera Enterobacter and Citrobacter.
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N152G, -S, and -T substitutions in CMY-2 β-lactamase increase catalytic efficiency for cefoxitin and inactivation rates for tazobactam. Antimicrob Agents Chemother 2013; 57:1596-602. [PMID: 23318801 DOI: 10.1128/aac.01334-12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Class C cephalosporinases are a growing threat, and clinical inhibitors of these enzymes are currently unavailable. Previous studies have explored the role of Asn152 in the Escherichia coli AmpC and P99 enzymes and have suggested that interactions between C-6' or C-7' substituents on penicillins or cephalosporins and Asn152 are important in determining substrate specificity and enzymatic stability. We sought to characterize the role of Asn152 in the clinically important CMY-2 cephalosporinase with substrates and inhibitors. Mutagenesis of CMY-2 at position 152 yields functional mutants (N152G, -S, and -T) that exhibit improved penicillinase activity and retain cephamycinase activity. We also tested whether the position 152 substitutions would affect the inactivation kinetics of tazobactam, a class A β-lactamase inhibitor with in vitro activity against CMY-2. Using standard assays, we showed that the N152G, -S, and -T variants possessed increased catalytic activity against cefoxitin compared to the wild type. The 50% inhibitory concentration (IC50) for tazobactam improved dramatically, with an 18-fold reduction for the N152S mutant due to higher rates of enzyme inactivation. Modeling studies have shown active-site expansion due to interactions between Y150 and S152 in the apoenzyme and the Michaelis-Menten complex with tazobactam. Substitutions at N152 might become clinically important as new class C β-lactamase inhibitors are developed.
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Interactions of oximino-substituted boronic acids and β-lactams with the CMY-2-derived extended-spectrum cephalosporinases CMY-30 and CMY-42. Antimicrob Agents Chemother 2012; 57:968-76. [PMID: 23229484 DOI: 10.1128/aac.01620-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
CMY-30 and CMY-42 are extended-spectrum (ES) derivatives of CMY-2. ES characteristics are due to substitutions of Gly (CMY-30) and Ser (CMY-42) for Val211 in the Ω-loop. To characterize the effects of 211 substitutions, we studied the interactions of CMY-2, -30, and -42 with boronic acid transition state inhibitors (BATSIs) resembling ceftazidime and cefotaxime, assessed thermal stability of the enzymes in their free forms and in complexes with BATSIs and oximino-β-lactams, and simulated, using molecular dynamics (MD), the CMY-42 apoenzyme and the CMY-42 complexes with ceftazidime and the ceftazidime-like BATSI. Inhibition constants showed that affinities between CMY-30 and CMY-42 and the R1 groups of BATSIs were lower than those of CMY-2. ES variants also exhibited decreased thermal stability either as apoenzymes or in covalent complexes with oximino compounds. MD simulations further supported destabilization of the ES variants. Val211Ser increased thermal factors of the Ω-loop backbone atoms, as previously observed for CMY-30. The similar effects of the two substitutions seemed to be due to a less-constrained Tyr221 likely inducing concerted movement of elements at the edges of the active site (Ω-loop-Q120 loop-R2 loop/H10 helix). This inner-protein movement, along with the wider R1 binding cleft, enabled intense vibrations of the covalently bound ceftazidime and ceftazidime-like BATSIs. Increased flexibility of the ES enzymes may assist the productive adaptation of the active site to the various geometries of the oximino substrates during the reaction (higher frequency of near-attack conformations).
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