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Zhu Y, Gu J, Zhao Z, Chan AWE, Mojica MF, Hujer AM, Bonomo RA, Haider S. Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning. J Chem Inf Model 2024; 64:3706-3717. [PMID: 38687957 PMCID: PMC11094718 DOI: 10.1021/acs.jcim.4c00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
L2 β-lactamases, serine-based class A β-lactamases expressed by Stenotrophomonas maltophilia, play a pivotal role in antimicrobial resistance (AMR). However, limited studies have been conducted on these important enzymes. To understand the coevolutionary dynamics of L2 β-lactamase, innovative computational methodologies, including adaptive sampling molecular dynamics simulations, and deep learning methods (convolutional variational autoencoders and BindSiteS-CNN) explored conformational changes and correlations within the L2 β-lactamase family together with other representative class A enzymes including SME-1 and KPC-2. This work also investigated the potential role of hydrophobic nodes and binding site residues in facilitating the functional mechanisms. The convergence of analytical approaches utilized in this effort yielded comprehensive insights into the dynamic behavior of the β-lactamases, specifically from an evolutionary standpoint. In addition, this analysis presents a promising approach for understanding how the class A β-lactamases evolve in response to environmental pressure and establishes a theoretical foundation for forthcoming endeavors in drug development aimed at combating AMR.
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Affiliation(s)
- Yu Zhu
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
| | - Jing Gu
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
| | - Zhuoran Zhao
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
| | - A. W. Edith Chan
- Division
of Medicine, UCL School of Pharmacy, London WC1E 6BT, U.K.
| | - Maria F. Mojica
- Department
of Molecular Biology and Microbiology, Case
Western Reserve University School of Medicine, Cleveland, Ohio 44106-5029, United
States
- Research
Service, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- CWRU-Cleveland
VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA
CARES), Cleveland, Ohio 44106-5029, United States
| | - Andrea M. Hujer
- Research
Service, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- Department
of Medicine, Case Western Reserve University
School of Medicine, Cleveland, Ohio 44106-5029, United States
| | - Robert A. Bonomo
- Research
Service, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- CWRU-Cleveland
VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA
CARES), Cleveland, Ohio 44106-5029, United States
- Clinician
Scientist Investigator, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- Departments
of Pharmacology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-5029, United
States
- Departments
of Molecular Biology and Microbiology, Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-5029, United
States
| | - Shozeb Haider
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
- UCL
Centre for Advanced Research in Computing, University College London, London WC1H 9RL, U.K.
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Ruggiero M, Briceño Muñoz I, Gutkind G, Hujer AM, Bonomo RA, Power P. Insights into the activity of cefiderocol against PER-2 producing Enterobacterales. Antimicrob Agents Chemother 2024:e0172023. [PMID: 38690895 DOI: 10.1128/aac.01720-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/30/2024] [Indexed: 05/03/2024] Open
Abstract
The PER-2 β-lactamase is a unique class A enzyme conferring broad spectrum cephalosporin resistance. In this study, we explored the stability of cefiderocol (FDC) against PER-2 β-lactamase to gain insights into structure activity relationships (SAR) of this synthetic siderophore-conjugated antibiotic. Herein, we show that the MICs of FDC for PER-2 producing isolates and transformants ranged between 0.125 and 64 µg/mL; diazabicyclooctanes (DBOs) reduced the MIC values. In PER-2 mutants, MIC values decreased up to 10-12 dilutions in agreement with previous observations especially in the case of Arg220 substitutions. Catalytic efficiency for PER-2 was 0.072 µM-1 s-1, comparable with PER-1 (0.046 µM-1 s-1) and NDM-1 (0.067 µM-1 s-1). In silico models revealed that FDC within the active site of PER-2 demonstrates unique interactions as a result of the inverted Ω loop fold and extension of the β3-β4 connecting loop.
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Affiliation(s)
- Melina Ruggiero
- Universidad de Buenos Aires, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ivan Briceño Muñoz
- Universidad de Buenos Aires, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Departments of Molecular Biology and Microbiology, Pharmacology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Pablo Power
- Universidad de Buenos Aires, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Doganay MT, Roman E, Hujer AM, Bonomo RA, Deeks SG, Kuritzkes DR, Draz MS. AMPLON: Amplifying DNA with Multiarm Priming and Looping Optimization of Nucleic Acid. Adv Mater 2024:e2311634. [PMID: 38657970 DOI: 10.1002/adma.202311634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/22/2024] [Indexed: 04/26/2024]
Abstract
Nucleic acid amplification, the bedrock of biotechnology and molecular diagnostics, surges in applications-especially isothermal approaches-heightening the demand for advanced and precisely engineered methods. Here, a novel approach for amplifying DNA with multiarm priming and looping optimization of nucleic acid (AMPLON) is presented. AMPLON relies on a novel polymeric material with unique set of multiarm polyethylene glycol-DNA primers for efficient DNA amplification under isothermal conditions. Each arm carries single-stranded DNA complementing the sense or antisense sequence of the target DNA. The amplification reaction begins with antisense arms binding to the target DNA, forming a template for sense-carrying arms to direct multiarm large DNA amplicon synthesis through successive DNA looping and unlooping steps. Using human immunodeficiency virus type 1 (HIV-1) as a model clinical target, AMPLON exhibits high sensitivity, detecting target concentrations as low as 100 copies mL-1. Compared to a quantitative real-time polymerase chain reaction assay using sensitive primers, AMPLON reliably identifies HIV-1 RNA in plasma samples (n = 20) with a significant agreement rate of 95%. With its ability to achieve highly specific and sensitive target amplification within 30 min, AMPLON holds immense potential to transform the field of nucleic acid research and unleashing new possibilities in medicine and biotechnology.
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Affiliation(s)
- Mert Tunca Doganay
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ethan Roman
- Department of Medicine, Case Western Reserve University School of Medicine, 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
| | - 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
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA, 94110, USA
| | - Daniel R Kuritzkes
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02139, USA
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH, 44106, USA
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Parwana D, Gu J, Chen S, Bethel CR, Marshall E, Hujer AM, Bonomo RA, Haider S. The Structural Role of N170 in Substrate-Assisted Deacylation in KPC-2 β-Lactamase. Angew Chem Int Ed Engl 2024; 63:e202317315. [PMID: 38227422 DOI: 10.1002/anie.202317315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
The amino acid substitutions in Klebsiella pneumoniae carbapenemase 2 (KPC-2) that have arisen in the clinic are observed to lead to the development of resistance to ceftazidime-avibactam, a preferred treatment for KPC bearing Gram-negative bacteria. Specific substitutions in the omega loop (R164-D179) result in changes in the structure and function of the enzyme, leading to alterations in substrate specificity, decreased stability, and more recently observed, increased resistance to ceftazidime/avibactam. Using accelerated rare-event sampling well-tempered metadynamics simulations, we explored in detail the structural role of R164 and D179 variants that are described to confer ceftazidime/avibactam resistance. The buried conformation of D179 substitutions produce a pronounced structural disorder in the omega loop - more than R164 mutants, where the crystallographic omega loop structure remains mostly intact. Our findings also reveal that the conformation of N170 plays an underappreciated role impacting drug binding and restricting deacylation. The results further support the hypothesis that KPC-2 D179 variants employ substrate-assisted catalysis for ceftazidime hydrolysis, involving the ring amine of the aminothiazole group to promote deacylation and catalytic turnover. Moreover, the shift in the WT conformation of N170 contributes to reduced deacylation and an altered spectrum of enzymatic activity.
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Affiliation(s)
| | - Jing Gu
- UCL School of Pharmacy, London, UK
| | | | - Christopher R Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Emma Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Department of Molecular Biology and Microbiology, Pharmacology, Biochemistry, 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
| | - Shozeb Haider
- UCL School of Pharmacy, London, UK
- UCL Centre for Advanced Research Computing, London, UK
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5
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Chen S, Mack AR, Hujer AM, Bethel CR, Bonomo RA, Haider S. Ω-Loop mutations control the dynamics of the active site by modulating a network of hydrogen bonds in PDC-3 β-lactamase. bioRxiv 2024:2024.02.04.578824. [PMID: 38370743 PMCID: PMC10871217 DOI: 10.1101/2024.02.04.578824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The expression of antibiotic-inactivating enzymes, such as Pseudomonas-derived cephalosporinase-3 (PDC-3), is a major mechanism of intrinsic resistance in bacteria. To explore the relationships between structural dynamics and altered substrate specificity as a result of amino acid substitutions in PDC-3, innovative computational methods like machine learning driven adaptive bandit molecular dynamics simulations and markov state modeling of the wild-type PDC-3 and nine clinically identified variants were conducted. Our analysis reveals that structural changes in the Ω loop controls the dynamics of the active site. The E219K and Y221A substitutions have the most pronounced effects. The modulation of three key hydrogen bonds K67(sc)-G220(bb), Y150(bb)-A292(bb) and N287(sc)-N314(sc) were found to result in an expansion of the active site, which could have implications for the binding and inactivation of cephalosporins. Overall, the findings highlight the importance of understanding the structural dynamics of PDC-3 in the development of new treatments for antibiotic-resistant infections.
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Affiliation(s)
| | - Andrew R Mack
- Research Service, 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
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Christopher R Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Robert A Bonomo
- Research Service, 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
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Departments of Pharmacology, Biochemistry, 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
| | - Shozeb Haider
- UCL School of Pharmacy, London UK
- UCL Centre for Advanced Research Computing, London UK
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6
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Bonomo RA, Perez F, Hujer AM, Hujer KM, Vila AJ. The Real Crisis in Antimicrobial Resistance: Failure to Anticipate and Respond. Clin Infect Dis 2024:ciad758. [PMID: 38289748 DOI: 10.1093/cid/ciad758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Indexed: 02/01/2024] Open
Affiliation(s)
- Robert A Bonomo
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center (VAMC), Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Case Western Reserve University (CWRU)-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Federico Perez
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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7
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Mack AR, Kumar V, Taracila MA, Mojica MF, O'Shea M, Schinabeck W, Silver G, Hujer AM, Papp-Wallace KM, Chen S, Haider S, Caselli E, Prati F, van den Akker F, Bonomo RA. Natural protein engineering in the Ω-loop: the role of Y221 in ceftazidime and ceftolozane resistance in Pseudomonas-derived cephalosporinase. Antimicrob Agents Chemother 2023; 67:e0079123. [PMID: 37850746 PMCID: PMC10648885 DOI: 10.1128/aac.00791-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/07/2023] [Indexed: 10/19/2023] Open
Abstract
A wide variety of clinically observed single amino acid substitutions in the Ω-loop region have been associated with increased minimum inhibitory concentrations and resistance to ceftazidime (CAZ) and ceftolozane (TOL) in Pseudomonas-derived cephalosporinase and other class C β-lactamases. Herein, we demonstrate the naturally occurring tyrosine to histidine substitution of amino acid 221 (Y221H) in Pseudomonas-derived cephalosporinase (PDC) enables CAZ and TOL hydrolysis, leading to similar kinetic profiles (k cat = 2.3 ± 0.2 µM and 2.6 ± 0.1 µM, respectively). Mass spectrometry of PDC-3 establishes the formation of stable adducts consistent with the formation of an acyl enzyme complex, while spectra of E219K (a well-characterized, CAZ- and TOL-resistant comparator) and Y221H are consistent with more rapid turnover. Thermal denaturation experiments reveal decreased stability of the variants. Importantly, PDC-3, E219K, and Y221H are all inhibited by avibactam and the boronic acid transition state inhibitors (BATSIs) LP06 and S02030 with nanomolar IC50 values and the BATSIs stabilize all three enzymes. Crystal structures of PDC-3 and Y221H as apo enzymes and complexed with LP06 and S02030 (1.35-2.10 Å resolution) demonstrate ligand-induced conformational changes, including a significant shift in the position of the sidechain of residue 221 in Y221H (as predicted by enhanced sampling well-tempered metadynamics simulations) and extensive hydrogen bonding between the enzymes and BATSIs. The shift of residue 221 leads to the expansion of the active site pocket, and molecular docking suggests substrates orientate differently and make different intermolecular interactions in the enlarged active site compared to the wild-type enzyme.
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Affiliation(s)
- Andrew R. Mack
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Vijay Kumar
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Magdalena A. Taracila
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Maria F. Mojica
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Margaret O'Shea
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - William Schinabeck
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Galen Silver
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Andrea M. Hujer
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Krisztina M. Papp-Wallace
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Shuang Chen
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, England, United Kingdom
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, England, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London, England, United Kingdom
| | - Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Robert A. Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
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Thomas CA, Cheng Z, Bethel CR, Hujer AM, Sturgill AM, Onuoha K, Page RC, Bonomo RA, Crowder MW. The directed evolution of NDM-1. Antimicrob Agents Chemother 2023; 67:e0071423. [PMID: 37874296 PMCID: PMC10649027 DOI: 10.1128/aac.00714-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/10/2023] [Indexed: 10/25/2023] Open
Abstract
β-Lactam antibiotics are among the most frequently prescribed therapeutic agents. A common mechanism of resistance toward β-lactam antibiotics is the production of β-lactamases. These enzymes are capable of hydrolyzing the β-lactam bond, rendering the drug inactive. Among the four described classes, the metallo- β-lactamases (MBLs, class B) employ one or two zinc ions in the active site for catalysis. One of the three most clinically relevant MBLs is New Delhi Metallo- β-Lactamase (NDM-1). The current study sought to investigate the in vitro protein evolution of NDM-1 β-lactamase using error-prone polymerase chain reaction. Evaluation revealed that variants were not found to confer higher levels of resistance toward meropenem based on amino acid substitutions. Thus, we postulate that increases in transcription or changes in zinc transport may be clinically more relevant to meropenem resistance than amino acid substitutions.
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Affiliation(s)
- Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Aidan M. Sturgill
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Kelechi Onuoha
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Richard C. Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Clinician Scientist Investigator, Ohio, Cleveland, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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Yasmin M, Nutman A, Wang L, Marshall S, Chen K, Wang J, Yahav D, Lupinsky L, Hujer AM, Bhimraj A, van Duin D, Li J, Bonomo RA. Utilizing Ceftazidime/Avibactam Therapeutic Drug Monitoring in the Treatment of Neurosurgical Meningitis Caused by Difficult-to-Treat Resistant Pseudomonas aeruginosa and KPC-Producing Enterobacterales. Open Forum Infect Dis 2023; 10:ofad507. [PMID: 38023540 PMCID: PMC10661062 DOI: 10.1093/ofid/ofad507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Background Central nervous system (CNS) infections caused by Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacterales and difficult-to-treat resistant (DTR) Pseudomonas aeruginosa represent a formidable clinical challenge. Antimicrobial regimens that efficiently penetrate the cerebrospinal fluid (CSF) and achieve sufficient concentrations associated with microbiologic and clinical cure are limited. We evaluated therapy with ceftazidime-avibactam (CAZ-AVI) in order to guide precise dosing in the treatment of CNS infections. Methods Therapeutic drug monitoring (TDM) was performed in 3 patients with health care-associated ventriculitis and meningitis (HAVM) using CAZ-AVI 2.5 g infused intravenously every 8 hours as standard and extended infusion. Simultaneous CSF and plasma samples were obtained throughout the dosing interval in each patient. Concentrations of CAZ and AVI were determined by liquid chromatography/mass spectrometry. Results Bacterial identification revealed KPC-producing Klebsiella pneumoniae (KPC-Kp), DTR Pseudomonas aeruginosa, and KPC-producing Enterobacter cloacae (KPC-Ent.c). All isolates were resistant to carbapenems. The minimum inhibitory concentrations (MICs) of CAZ-AVI were 0.25/4, 4/4, and 0.25/4 μg/mL, respectively. CAZ and AVI concentrations were determined in CSF samples ranging from 29.0 to 15.0 µg/mL (CAZ component) and 4.20 to 0.92 µg/mL (AVI component), respectively. AVI achieved concentrations ≥1 µg/mL in 11 out of 12 CSF samples collected throughout the dosing interval. Clinical and microbiologic cure were attained in all patients. Conclusions Postinfusion concentrations of CAZ-AVI were measured in plasma and CSF samples obtained from 3 patients with complicated CNS infections caused by antimicrobial-resistant isolates. The measured concentrations revealed that standard CAZ and AVI exposures sufficiently attained values correlating to 50% fT > MIC, which are associated with efficient bacterial killing.
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Affiliation(s)
- Mohamad Yasmin
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Amir Nutman
- Infectious Diseases Unit, Rabin Medical Center, Beilinson Campus, Petah Tiqva and Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Lu Wang
- Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Steven Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Ke Chen
- Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Jiping Wang
- Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Dafna Yahav
- Infectious Diseases Unit, Rabin Medical Center, Beilinson Campus, Petah Tiqva and Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Liad Lupinsky
- Neurosurgical Department, Rabin Medical Center, Beilinson Campus, Petah Tiqva, Israel
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Adarsh Bhimraj
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
| | - David van Duin
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jian Li
- Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- Departments of Proteomics and Bioinformatics, Pharmacology, and Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Hujer AM, Marshall SH, Mack AR, Hujer KM, Bakthavatchalam YD, Umarkar K, Palwe SR, Takalkar S, Joshi PR, Shrivastava R, Periasamy H, Bhagwat SS, Patel MV, Veeraraghavan B, Bonomo RA. Transcending the challenge of evolving resistance mechanisms in Pseudomonas aeruginosa through β-lactam-enhancer-mechanism-based cefepime/zidebactam. mBio 2023; 14:e0111823. [PMID: 37889005 PMCID: PMC10746216 DOI: 10.1128/mbio.01118-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/14/2023] [Indexed: 10/28/2023] Open
Abstract
Multi-drug resistant (MDR) Pseudomonas aeruginosa harbor a complex array of β-lactamases and non-enzymatic resistance mechanisms. In this study, the activity of a β-lactam/β-lactam-enhancer, cefepime/zidebactam, and novel β-lactam/β-lactamase inhibitor combinations was determined against an MDR phenotype-enriched, challenge panel of P. aeruginosa (n = 108). Isolates were multi-clonal as they belonged to at least 29 distinct sequence types (STs) and harbored metallo-β-lactamases, serine β-lactamases, penicillin binding protein (PBP) mutations, and other non-enzymatic resistance mechanisms. Ceftazidime/avibactam, ceftolozane/tazobactam, imipenem/relebactam, and cefepime/taniborbactam demonstrated MIC90s of >128 mg/L, while cefepime/zidebactam MIC90 was 16 mg/L. In a neutropenic-murine lung infection model, a cefepime/zidebactam human epithelial-lining fluid-simulated regimen achieved or exceeded a translational end point of 1-log10 kill for the isolates with elevated cefepime/zidebactam MICs (16-32 mg/L), harboring VIM-2 or KPC-2 and alterations in PBP2 and PBP3. In the same model, to assess the impact of zidebactam on the pharmacodynamic (PD) requirement of cefepime, dose-fractionation studies were undertaken employing cefepime-susceptible P. aeruginosa isolates. Administered alone, cefepime required 47%-68% fT >MIC for stasis to ~1 log10 kill effect, while cefepime in the presence of zidebactam required just 8%-16% for >2 log10 kill effect, thus, providing the pharmacokinetic/PD basis for in vivo efficacy of cefepime/zidebactam against isolates with MICs up to 32 mg/L. Unlike β-lactam/β-lactamase inhibitors, β-lactam enhancer mechanism-based cefepime/zidebactam shows a potential to transcend the challenge of ever-evolving resistance mechanisms by targeting multiple PBPs and overcoming diverse β-lactamases including carbapenemases in P. aeruginosa.IMPORTANCECompared to other genera of Gram-negative pathogens, Pseudomonas is adept in acquiring complex non-enzymatic and enzymatic resistance mechanisms thus remaining a challenge to even novel antibiotics including recently developed β-lactam and β-lactamase inhibitor combinations. This study shows that the novel β-lactam enhancer approach enables cefepime/zidebactam to overcome both non-enzymatic and enzymatic resistance mechanisms associated with a challenging panel of P. aeruginosa. This study highlights that the β-lactam enhancer mechanism is a promising alternative to the conventional β-lactam/β-lactamase inhibitor approach in combating ever-evolving MDR P. aeruginosa.
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Affiliation(s)
- Andrea M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Steven H. Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
| | - Andrew R. Mack
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Kristine M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | - Kushal Umarkar
- Wockhardt Research Centre, Aurangabad, Maharashtra, India
| | | | | | | | | | | | | | | | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Pharmacology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
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11
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Logan LK, Coy LR, Pitstick CE, Marshall SH, Medernach RL, Domitrovic TN, Konda S, Qureshi NK, Hujer AM, Zheng X, Rudin SD, Weinstein RA, Bonomo RA. The role of the plasmid-mediated fluoroquinolone resistance genes as resistance mechanisms in pediatric infections due to Enterobacterales. Front Cell Infect Microbiol 2023; 13:1249505. [PMID: 37900312 PMCID: PMC10613066 DOI: 10.3389/fcimb.2023.1249505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/30/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Fluoroquinolones (FQs) are not commonly prescribed in children, yet the increasing incidence of multidrug-resistant (MDR) Enterobacterales (Ent) infections in this population often reveals FQ resistance. We sought to define the role of FQ resistance in the epidemiology of MDR Ent in children, with an overall goal to devise treatment and prevention strategies. Methods A case-control study of children (0-18 years) at three Chicago hospitals was performed. Cases had infections by FQ-susceptible, β-lactamase-producing (bla) Ent harboring a non- or low-level expression of PMFQR genes (PMFQS Ent). Controls had FQR infections due to bla Ent with expressed PMFQR genes (PMFQR Ent). We sought bla genes by PCR or DNA (BD Max Check-Points assay®) and PMFQR genes by PCR. We performed rep-PCR, MLST, and E. coli phylogenetic grouping. Whole genome sequencing was additionally performed on PMFQS Ent positive isolates. Demographics, comorbidities, and device, antibiotic, and healthcare exposures were evaluated. Predictors of infection were assessed. Results Of 170 β-lactamase-producing Ent isolates, 85 (50%) were FQS; 23 (27%) had PMFQR genes (PMFQS cases). Eighty-five (50%) were FQR; 53 (62%) had PMFQR genes (PMFQR controls). The median age for children with PMFQS Ent and PMFQR Ent was 4.3 and 6.2 years, respectively (p = NS). Of 23 PMFQS Ent, 56% were Klebsiella spp., and of 53 PMFQR Ent, 76% were E. coli. The most common bla and PMFQR genes detected in PMFQS Ent were bla SHV ESBL (44%) and oqxAB (57%), and the corresponding genes detected in PMFQR Ent were bla CTX-M-1-group ESBL (79%) and aac(6')-Ib-cr (83%). Whole genome sequencing of PMFQS Ent revealed the additional presence of mcr-9, a transferable polymyxin resistance gene, in 47% of isolates, along with multiple plasmids and mobile genetic elements propagating drug resistance. Multivariable regression analysis showed that children with PMFQS Ent infections were more likely to have hospital onset infection (OR 5.7, 95% CI 1.6-22) and isolates containing multiple bla genes (OR 3.8, 95% CI 1.1-14.5). The presence of invasive devices mediated the effects of healthcare setting in the final model. Differences in demographics, comorbidities, or antibiotic use were not found. Conclusions Paradoxically, PMFQS Ent infections were often hospital onset and PMFQR Ent infections were community onset. PMFQS Ent commonly co-harbored multiple bla and PMFQR genes, and additional silent, yet transferrable antibiotic resistance genes such as mcr-9, affecting therapeutic options and suggesting the need to address infection prevention strategies to control spread. Control of PMFQS Ent infections will require validating community and healthcare-based sources and risk factors associated with acquisition.
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Affiliation(s)
- Latania K. Logan
- Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Department of Pediatrics, Children’s Healthcare of Atlanta, Atlanta, GA, United States
- Pediatrics, Rush University Medical Center, Chicago, IL, United States
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States
| | - Laura Rojas Coy
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States
- Molecular Biology, and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | | | - Steven H. Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States
| | - Rachel L. Medernach
- Pediatrics, Rush University Medical Center, Chicago, IL, United States
- Medicine, Rush University Medical Center, Chicago, IL, United States
| | - T. Nicholas Domitrovic
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States
| | - Sreenivas Konda
- Biostatistics, University of Illinois at Chicago, Chicago, IL, United States
| | - Nadia K. Qureshi
- Pediatrics, Loyola University Medical Center, Maywood, IL, United States
| | - Andrea M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States
- Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Xiaotian Zheng
- Microbiology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
- Pathology, Northwestern Feinberg School of Medicine, Chicago, IL, United States
| | - Susan D. Rudin
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States
| | - Robert A. Weinstein
- Medicine, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Cook County Health, Chicago, IL, United States
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States
- Molecular Biology, and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Biochemistry, Pharmacology, Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Case Western Reserve University (CWRU)-Cleveland VA Medical Center (VAMC) Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, United States
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12
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Kumar I, Sagar A, Dhiman K, Bethel CR, Hujer AM, Carifi J, Ashish, Bonomo RA. Insights into dynamic changes in ADC-7 and P99 cephalosporinases using small angle x-ray scattering (SAXS). J Biomol Struct Dyn 2023:1-13. [PMID: 37578017 DOI: 10.1080/07391102.2023.2240427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023]
Abstract
To counter the emergence of β-lactamase (BL) mediated resistance, design of new β-lactamase inhibitors (BLIs) is critical. Many high-resolution crystallographic structures of BL complexed with BLIs are available. However, their impact on BLI design is struggling to keep pace with novel and emerging variants. Small angle x-ray scattering (SAXS) in combination with molecular modeling is a useful tool to determine dynamic structures of macromolecules in solution. An important application of SAXS is to determine the conformational changes that occur when BLI bind to BL. To probe if conformational dynamics occur in class C cephalosporinases, we studied SAXS profiles of two clinically relevant class C β-lactamases, Acinetobacter baumannii ADC-7 and Enterobacter cloacae P99 in apo format complexed with BLIs. Importantly, SAXS data analysis demonstrated that in solution, these representative class C enzymes remain monomeric and did not show the associated assemblies that were seen in various crystal structures. SAXS data acquired for ADC-7 and P99, in apo and inhibitor bound states, clearly showed that these enzymes undergo detectable conformational changes, and these class C β-lactamases also close upon binding inhibitors as does BlaC. Further analysis revealed that addition of inhibitor led to the compacting of a range of residues around the active site, indicating that the conformational changes that both P99 and ADC-7 undergo are central to inhibitor recognition and efficacy. Our findings support the importance of exploring conformational changes using SAXS analysis in the design of future BLIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ish Kumar
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, Teaneck, NJ, USA
| | - Amin Sagar
- Centre de Biochimie Structurale (CBS), Montpellier, France
| | - Kanika Dhiman
- GNR Advanced Protein Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Christopher R Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Justin Carifi
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, Teaneck, NJ, USA
| | - Ashish
- GNR Advanced Protein Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Departments of Biochemistry, Pharmacology, Molecular Biology and Microbiology, 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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13
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Doganay MT, Chelliah CJ, Tozluyurt A, Hujer AM, Obaro SK, Gurkan U, Patel R, Bonomo RA, Draz M. 3D Printed Materials for Combating Antimicrobial Resistance. Mater Today (Kidlington) 2023; 67:371-398. [PMID: 37790286 PMCID: PMC10545363 DOI: 10.1016/j.mattod.2023.05.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Three-dimensional (3D) printing is a rapidly growing technology with a significant capacity for translational applications in both biology and medicine. 3D-printed living and non-living materials are being widely tested as a potential replacement for conventional solutions for testing and combating antimicrobial resistance (AMR). The precise control of cells and their microenvironment, while simulating the complexity and dynamics of an in vivo environment, provides an excellent opportunity to advance the modeling and treatment of challenging infections and other health conditions. 3D-printing models the complicated niches of microbes and host-pathogen interactions, and most importantly, how microbes develop resistance to antibiotics. In addition, 3D-printed materials can be applied to testing and delivering antibiotics. Here, we provide an overview of 3D printed materials and biosystems and their biomedical applications, focusing on ever increasing AMR. Recent applications of 3D printing to alleviate the impact of AMR, including developed bioprinted systems, targeted bacterial infections, and tested antibiotics are presented.
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Affiliation(s)
- Mert Tunca Doganay
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Cyril John Chelliah
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Abdullah Tozluyurt
- Department of Medicine, Case Western Reserve University School of Medicine, 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, USA
| | | | - Umut Gurkan
- Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology and Division of Public Health, Infectious Diseases, and Occupational medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, 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, USA
- Molecular Biology and Microbiology, 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
| | - Mohamed Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH 44106, USA
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14
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Powers RA, June CM, Fernando MC, Fish ER, Maurer OL, Baumann RM, Beardsley TJ, Taracila MA, Rudin SD, Hujer KM, Hujer AM, Santi N, Villamil V, Introvigne ML, Prati F, Caselli E, Bonomo RA, Wallar BJ. Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter-Derived Cephalosporinase Variants with an Expanded-Substrate Spectrum. J Med Chem 2023. [PMID: 37358467 DOI: 10.1021/acs.jmedchem.3c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Class C Acinetobacter-derived cephalosporinases (ADCs) represent an important target for inhibition in the multidrug-resistant pathogen Acinetobacter baumannii. Many ADC variants have emerged, and characterization of their structural and functional differences is essential. Equally as important is the development of compounds that inhibit all prevalent ADCs despite these differences. The boronic acid transition state inhibitor, MB076, a novel heterocyclic triazole with improved plasma stability, was synthesized and inhibits seven different ADC β-lactamase variants with Ki values <1 μM. MB076 acted synergistically in combination with multiple cephalosporins to restore susceptibility. ADC variants containing an alanine duplication in the Ω-loop, specifically ADC-33, exhibited increased activity for larger cephalosporins, such as ceftazidime, cefiderocol, and ceftolozane. X-ray crystal structures of ADC variants in this study provide a structural context for substrate profile differences and show that the inhibitor adopts a similar conformation in all ADC variants, despite small changes near their active sites.
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Affiliation(s)
- Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
| | - Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
| | - Micah C Fernando
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
| | - Erin R Fish
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
| | - Olivia L Maurer
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
| | - Rachelle M Baumann
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
| | - Trevor J Beardsley
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Susan D Rudin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Nicolò Santi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Valentina Villamil
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Maria Luisa Introvigne
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
- Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio 44106, United States
| | - Bradley J Wallar
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Yasmin M, Rojas LJ, Marshall SH, Hujer AM, Cmolik A, Marshall E, Boucher HW, Vila AJ, Soldevila M, Diene SM, Rolain JM, Bonomo RA. Characterization of a Novel Pathogen in Immunocompromised Patients: Elizabethkingia anophelis-Exploring the Scope of Resistance to Contemporary Antimicrobial Agents and β-lactamase Inhibitors. Open Forum Infect Dis 2023; 10:ofad014. [PMID: 36820316 PMCID: PMC9938519 DOI: 10.1093/ofid/ofad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Indexed: 02/04/2023] Open
Abstract
Background Elizabethkingia anophelis is an emerging Gram-negative nonlactose fermenter in the health care setting, where it causes life-threatening infections in immunocompromised patients. We aimed to characterize the molecular mechanisms of antimicrobial resistance and evaluate the utility of contemporary antibiotics with the intent to offer targeted therapy against an uncommonly encountered pathogen. Methods Whole-genome sequencing (WGS) was conducted to accurately identify isolate species and elucidate the determinants of β-lactam resistance. Antimicrobial susceptibility testing was performed using broth microdilution and disk diffusion assays. To assess the functional contribution of the major metallo-β-lactamase (MBL) encoding genes to the resistance profile, bla BlaB was cloned into pBCSK(-) phagemid vector and transformed into Escherichia coli DH10B. Results WGS identified the organism as E. anophelis. MBL genes bla BlaB-1 and bla GOB-26 were identified, in addition to bla CME-2, which encodes for an extended-spectrum β-lactamase (ESBL). Plasmids were not detected. The isolate was nonsusceptible to all commonly available β-lactams, carbapenems, newer β-lactam β-lactamase inhibitor combinations, and to the combination of aztreonam (ATM) with ceftazidime-avibactam (CAZ-AVI). Susceptibility to the novel siderophore cephalosporin cefiderocol was determined. A BlaB-1 transformant E. coli DH10B isolate was obtained and demonstrated increased minimum inhibitory concentrations to cephalosporins, carbapenems, and CAZ-AVI, but not ATM. Conclusions Using WGS, we accurately identified and characterized an extensively drug-resistant E. anophelis in an immunocompromised patient. Rapid evaluation of the genetic background can guide accurate susceptibility testing to better inform antimicrobial therapy selection.
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Affiliation(s)
- Mohamad Yasmin
- Correspondence: Robert A. Bonomo, MD, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH 44106 (); or Mohamad Yasmin, MD, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH 44106 ()
| | - Laura J Rojas
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA,Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Steven H Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Anna Cmolik
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Emma Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | | | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
| | - Maxime Soldevila
- MEPHI, IRD, APHM, IHU-Méditerranée Infection, Faculté de Pharmacie, Aix Marseille Université, Marseille, France
| | - Seydina M Diene
- MEPHI, IRD, APHM, IHU-Méditerranée Infection, Faculté de Pharmacie, Aix Marseille Université, Marseille, France,IHU-Méditerranée Infection, Aix Marseille Université, Marseille, France
| | - Jean-Marc Rolain
- MEPHI, IRD, APHM, IHU-Méditerranée Infection, Faculté de Pharmacie, Aix Marseille Université, Marseille, France,IHU-Méditerranée Infection, Aix Marseille Université, Marseille, France
| | - Robert A Bonomo
- Correspondence: Robert A. Bonomo, MD, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH 44106 (); or Mohamad Yasmin, MD, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH 44106 ()
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17
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Yasmin M, Chen L, Marshall S, Rhoads DD, Jacobs MR, Rojas LJ, Perez F, Hujer AM, Kreiswirth BN, Bonomo RA. 142. Evaluation of Meropenem-Vaborbactam Susceptibility and Underlying Resistance Mechanisms among Clinical KPC-producing Klebsiella pneumoniae. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
Meropenem-vaborbactam (MV) is the first carbapenem/β-lactamase inhibitor combination developed to restore meropenem susceptibility against KPC-producing carbapenem-resistant Enterobacterales(CRE). Vaborbactam (VAB) potently inhibits Ambler class A and C β-lactamases by reversible covalent binding of boronate to serine side chains of β-lactamases. Resistance to MV in non-metallo-β-lactamase (MBL) producing Klebsiella pneumoniae (KP) isolates has been described but remains rare. We sought to identify the major molecular mechanisms associated with MV resistance in KPC-producing KP (KPC-KP) isolates.
Methods
Clinical isolates with elevated MV MICs were identified by the consult service. Additional clinical isolates with mutations in ompK35 or ompK36 genes were selected from a historic database. Isolates with MBL or OXA-48-like genes were excluded. Controls were comprised of MV susceptible KPC-KP isolates. MICs determination was done using Sensititre automated broth microdilution (BMD) according to CLSI. VAB and avibactam concentrations were held at 8 µg/ml and 4 µg/ml, respectively. Whole genome sequencing (WGS) was performed on all isolates. Genome libraries were prepared using Illumina Nextera XT and sequencing was performed on MiSeq and MinION.
Results
A total 119 KPC-KP isolates were included in the study. All isolates were resistant to meropenem. Twenty-one KPC-KP with elevated MV MICs were identified. All MV resistant isolates harbored mutations in ompK36 genes. Glycine/aspartate (GD 134-135) insertion, premature stop codon in ompK36 genes, and concomitantly elevated blaKPC copy number were predominant among MV resistant isolates. No insertion elements in ompK36 gene promoter region were found. Two MV resistant isolates exhibited unique mutations in blaKPC and envZ genes. See table for WGS and MIC results. Table 1.Whole genome sequencing and MICs of MV resistant KPC-KP isolatesα: Truncated at nodes 14 and 76, partial genotype consistent with blaSHV-12WT: Wild type*: Premature stop codonGD: Duplication of Glycine (G134) and Aspartate (D135)FS: Frameshift mutationins: insertionMEM: meropenemMVB: meropenem-vaborbactamCZA: ceftazidime-avibactamCFD: cefiderocolN/A: not availableTable 2.Whole genome sequencing and MICs of MV susceptible KPC-KP isolates
Conclusion
MV resistant KPC-KP isolates were reliably analyzed using WGS to reveal the contribution of omp gene mutations and blaKPC copy number to this phenotype. Elevated MV MICs were additionally recognized among clinical isolates from a historic database preceding MV availability. In the absence of MBL production, caution remains warranted with the use of MV empirically against KPC-KP due to non-β-lactamase mediated resistance mechanisms.
Disclosures
Daniel D. Rhoads, M.D. PhD, Luminex: Advisor/Consultant|Talis Biomedical: Advisor/Consultant|Thermo Fisher: Advisor/Consultant Federico Perez, M.D., Accelerate: Grant/Research Support|Merck: Grant/Research Support|Pfizer: Grant/Research Support Robert A. Bonomo, MD, NIH VA: Grant/Research Support|VenatoRx Merck Wockhardt Cystic Fibrosis Foundation: Grant/Research Support.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Barry N Kreiswirth
- Center for Discovery and Innovation , Hakensack Meridian Health, Nutley, New Jersey
| | - Robert A Bonomo
- Case Western Reserve University/ Louis Stokes Cleveland VA Medical Center , Cleveland, OH
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Tierney BT, Singh NK, Simpson AC, Hujer AM, Bonomo RA, Mason CE, Venkateswaran K. Multidrug-resistant Acinetobacter pittii is adapting to and exhibiting potential succession aboard the International Space Station. Microbiome 2022; 10:210. [PMID: 36503581 PMCID: PMC9743659 DOI: 10.1186/s40168-022-01358-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/11/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND Monitoring the adaptation of microorganisms to the extreme environment of the International Space Station (ISS) is crucial to understanding microbial evolution and infection prevention. Acinetobacter pittii is an opportunistic nosocomial pathogen, primarily impacting immunocompromised patients, that was recently isolated from two missions aboard the ISS. RESULTS Here, we report how ISS-associated A. pittii (n = 20 genomes) has formed its own genetically and functionally discrete clade distinct from most Earth-bound isolates (n = 291 genomes). The antimicrobial susceptibility testing of ISS strains and two related clinical isolates demonstrated that ISS strains acquired more resistance, specifically with regard to expanded-spectrum cephalosporins, despite no prediction of increased resistance based on genomic analysis of resistance genes. By investigating 402 longitudinal environmental and host-associated ISS metagenomes, we observed that viable A. pittii is increasing in relative abundance and therefore potentially exhibiting succession, being identified in >2X more metagenomic samples in back-to-back missions. ISS strains additionally contain functions that enable them to survive in harsh environments, including the transcriptional regulator LexA. Via a genome-wide association study, we identified a high level of mutational burden in methionine sulfoxide reductase genes relative to the most closely related Earth strains. CONCLUSIONS Overall, these results indicated a step forward in understanding how microorganisms might evolve and alter their antibiotic resistance phenotype in extreme, resource-limited, human-built environments. Video Abstract.
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Affiliation(s)
- Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Anna C Simpson
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, 44106, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, 44106, USA
- Departments of Biochemistry, Pharmacology, Molecular Biology and Microbiology, and 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
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA.
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19
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Pitstick CE, Marshall S, Konda S, Medernach RL, Domitrovic TN, Hujer AM, Qureshi NK, Rudin SD, Zheng X, Weinstein RA, Bonomo RA, Logan LK. 1145. The Role of the Plasmid-Mediated Fluoroquinolone-Resistance (PMFQR) Genes As Resistance Mechanisms in Pediatric Infections due to Enterobacterales (Ent). Open Forum Infect Dis 2021. [PMCID: PMC8644197 DOI: 10.1093/ofid/ofab466.1338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Fluoroquinolones (FQs) are not commonly prescribed in children, yet the increasing incidence of multidrug resistant (MDR) Ent infections in this population often reveals FQ resistance. We sought to define the role of FQ resistance in the epidemiology of MDR Ent in children, with an overall goal to devise treatment and prevention strategies. Methods A case-control study of children (0-18 years) at 3 Chicago hospitals was performed. Cases had infections by FQ susceptible, 3rd generation cephalosporin-resistant (3GCR) and/or carbapenem-resistant (CR) Ent harboring a non or low level expressed PMFQR gene (PMFQS Ent). Controls had FQR infections due to 3GCR and/or CR Ent with expressed PMFQR genes (PMFQR Ent). We sought bla genes by PCR or DNA (BD Max Check-Points assay®) and PMFQR genes by PCR. We performed Rep-PCR, MLST, and E. coli phylogenetic grouping. Demographics; comorbidities; and device, antibiotic, and healthcare exposures were evaluated. Predictors of infection were assessed. Results Of 170 G3CR and/or CR Ent isolates, 85 (50%) were FQS; 23 (27%) had PMFQR genes (PMFQS cases). 85 (50%) were FQR; 53 (62%) had PMFQR genes (PMFQR controls). The median age for children with PMFQS Ent and PMFQR Ent were 4.3 and 6.2 years, respectively (p=NS). Of 23 PMFQS Ent, 53% were Klebsiella and of 53 PMFQR Ent, 76% were E. coli. The most common bla and PMFQR genes in PMFQS Ent were blaSHV ESBL (44%); oqxB (57%) and aac-6’1b-cr (52%) and in PMFQR Ent were blaCTX-M-1 group (76%); aac-6’1b-cr (91%) and oqxA (17%). Multivariable regression analysis showed children with PMFQS Ent infections were more likely to have hospital onset infection (OR 5.7, 95% CI 1.6-22) and isolates with multiple bla genes (OR 3.8, 95% CI 1.1-14.5). The presence of invasive devices mediated the effects of healthcare setting in the final model. Differences in demographics, comorbidities, or antibiotic use were not found. Conclusion Paradoxically, PMFQS Ent infections were often hospital onset and PMFQR Ent infections were community onset. PMFQS Ent commonly co-harbored multiple bla and PMFQR genes, affecting therapeutic options and suggesting need for contact precautions. Control of PMFQS Ent infections in children will require validating sources and risk factors. Disclosures Robert A. Bonomo, MD, entasis (Research Grant or Support)Merck (Grant/Research Support)NIH (Grant/Research Support)VA Merit Award (Grant/Research Support)VenatoRx (Grant/Research Support)
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiaotian Zheng
- Northwestern University Feinberg School of Medicine; Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL
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20
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Mills JP, Rojas LJ, Marshall SH, Rudin SD, Hujer AM, Nayak L, Bachman MA, Bonomo RA, Kaye KS. Risk Factors for and Mechanisms of COlistin Resistance Among Enterobacterales: Getting at the CORE of the Issue. Open Forum Infect Dis 2021; 8:ofab145. [PMID: 34285928 PMCID: PMC8286092 DOI: 10.1093/ofid/ofab145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/31/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Despite the recent emergence of plasmid-mediated colistin resistance, the epidemiology and mechanisms of colistin-resistant Enterobacterales (CORE) infections remain poorly understood. METHODS A case-case-control study was conducted utilizing routine clinical isolates obtained at a single tertiary health system in Ann Arbor, Michigan. Patients with CORE isolates from January 1, 2016, to March 31, 2017, were matched 1:1 with patients with colistin-susceptible Enterobacterales (COSE) and uninfected controls. Multivariable logistic regression was used to compare clinical and microbiologic features of patients with CORE and COSE to controls. A subset of available CORE isolates underwent whole-genome sequencing to identify putative colistin resistance genes. RESULTS Of 16 373 tested clinical isolates, 166 (0.99%) were colistin-resistant, representing 103 unique patients. Among 103 CORE isolates, 103 COSE isolates, and 102 uninfected controls, antibiotic exposure in the antecedent 90 days and age >55 years were predictors of both CORE and COSE. Of 33 isolates that underwent whole-genome sequencing, a large variety of mutations associated with colistin resistance were identified, including 4 mcr-1/mcr-1.1 genes and 4 pmrA/B mutations among 9 Escherichia coli isolates and 5 mgrB and 3 PmrA mutations among 8 Klebsiella pneumoniae isolates. Genetic mutations found in Enterobacter species were not associated with known phenotypic colistin resistance. CONCLUSIONS Increased age and prior antibiotic receipt were associated with increased risk for patients with CORE and for patients with COSE. Mcr-1, pmrA/B, and mgrB were the predominant colistin resistance-associated mutations identified among E. coli and K. pneumoniae, respectively. Mechanisms of colistin resistance among Enterobacter species could not be determined.
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Affiliation(s)
- John P Mills
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura J Rojas
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Steve H Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Susan D Rudin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Luke Nayak
- Division of Hospital Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Bachman
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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21
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Yasmin M, Fouts DE, Jacobs MR, Haydar H, Marshall SH, White R, D'Souza R, Lodise TP, Rhoads DD, Hujer AM, Rojas LJ, Hoyen C, Perez F, Edwards A, Bonomo RA. Monitoring Ceftazidime-Avibactam and Aztreonam Concentrations in the Treatment of a Bloodstream Infection Caused by a Multidrug-Resistant Enterobacter sp. Carrying Both Klebsiella pneumoniae Carbapenemase-4 and New Delhi Metallo-β-Lactamase-1. Clin Infect Dis 2021; 71:1095-1098. [PMID: 31802119 DOI: 10.1093/cid/ciz1155] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 12/04/2019] [Indexed: 12/29/2022] Open
Abstract
In an infection with an Enterobacter sp. isolate producing Klebsiella pneumoniae Carbapenemase-4 and New Delhi Metallo-β-Lactamase-1 in the United States, recognition of the molecular basis of carbapenem resistance allowed for successful treatment by combining ceftazidime-avibactam and aztreonam. Antimicrobial synergy testing and therapeutic drug monitoring assessed treatment adequacy.
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Affiliation(s)
- Mohamad Yasmin
- Division of Infectious Diseases, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA.,Geriatric Research, Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | | | - Michael R Jacobs
- Division of Clinical Microbiology, Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Hanan Haydar
- Division of Pediatric Infectious Diseases, Rainbow Babies and Children's Hospital, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Steven H Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | | | | | - Thomas P Lodise
- Department of Pharmacy Practice, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Daniel D Rhoads
- Division of Clinical Microbiology, Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Laura J Rojas
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Claudia Hoyen
- Division of Pediatric Infectious Diseases, Rainbow Babies and Children's Hospital, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Federico Perez
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA.,Geriatric Research, Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Amy Edwards
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Division of Pediatric Infectious Diseases, Rainbow Babies and Children's Hospital, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA.,Geriatric Research, Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA.,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Molecular Biology & Microbiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, Ohio, USA.,CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
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22
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Logan LK, Rispens JR, Medernach RL, Domitrovic TN, Hujer AM, Marshall SH, Rudin SD, Qureshi NK, Zheng X, Hayden MK, Weinstein RA, Bonomo RA. A Multicentered Study of the Clinical and Molecular Epidemiology of TEM- and SHV-type Extended-Spectrum Beta-Lactamase Producing Enterobacterales Infections in Children. Pediatr Infect Dis J 2021; 40:39-43. [PMID: 33021591 PMCID: PMC7721995 DOI: 10.1097/inf.0000000000002916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales-(Ent) infections are increasing in pediatrics. Before CTX-M ESBL emerged, the most common infection-associated ESBL genes were TEM and SHV-type ESBLs. We sought to define the current epidemiology of Ent infections in children due to blaTEM and blaSHV (TEM-SHV-Ent). METHODS A retrospective case-control analysis of children with TEM-SHV-Ent infections at 3 Chicago-area hospitals was performed. Cases had extended-spectrum-cephalosporin (ESC)-resistant infections due to blaTEM or blaSHV. DNA analysis assessed β-lactamase (bla) genes, multilocus sequence types, and E. coli phylogenetic grouping. Controls had ESC-susceptible Ent infections, matched 3:1 to cases by age, source, and hospital. Clinical-epidemiologic infection predictors were assessed. RESULTS Of 356 ESC-R-Ent isolates from children (median 4.3 years), 38 (10.7%) were positive solely for blaTEM-ESBL (26%) or blaSHV-ESBL genes (74%). Predominant organisms were Klebsiella (34.2%) and E. coli (31.6%); 67% of E. coli were phylogroup B2. Multilocus sequence types revealed multiple strains, 58% resistant to ≥3 antibiotic classes. On multivariable analysis, children with TEM-SHV-Ent infections more often had recent inpatient care (OR, 8.2), yet were diagnosed mostly as outpatients (OR, 25.6) and less in Neonatal Intensive Care Units (OR, 0.036) than controls. TEM-SHV-Ent patients had more gastrointestinal (OR, 23.7) and renal comorbidities (OR, 4.2). Differences in demographics, antibiotic exposure, and foreign bodies were not found. CONCLUSION TEM-SHV-Ent are commonly linked to inpatient exposures in children with chronic conditions but most often present in outpatient settings. Clinicians should be aware of the potential increased risk for TEM-SHV-Ent infections in outpatients with gastrointestinal and renal comorbidities and histories of prolonged hospital stays.
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Affiliation(s)
- Latania K. Logan
- Pediatrics, Rush University Medical Center, Chicago, Illinois, United States
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Jared R. Rispens
- Pediatrics, Rush University Medical Center, Chicago, Illinois, United States
- Medicine, Rush University Medical Center, Chicago, Illinois, United States
| | - Rachel L. Medernach
- Pediatrics, Rush University Medical Center, Chicago, Illinois, United States
- Medicine, Rush University Medical Center, Chicago, Illinois, United States
| | - T. Nicholas Domitrovic
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
- Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio
| | - Andrea M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
- Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio
| | - Steven H. Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Susan D. Rudin
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
- Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio
| | - Nadia K. Qureshi
- Pediatrics, Loyola University Medical Center, Maywood, Illinois, United States
| | - Xiaotian Zheng
- Microbiology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States
- Pathology, Northwestern Feinberg School of Medicine, Chicago, Illinois, United States
| | - Mary K. Hayden
- Medicine, Rush University Medical Center, Chicago, Illinois, United States
| | - Robert A. Weinstein
- Medicine, Rush University Medical Center, Chicago, Illinois, United States
- Cook County Health and Hospital Systems, Chicago, Illinois, United States
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
- Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio
- Pharmacology, Molecular Biology, and Microbiology, Case Western Reserve School of Medicine, Cleveland, Ohio
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Goldberg J, Bethel C, Hujer AM, Marshall S, Taracila MA, Papp-Wallce KM, Kumar V, van den Akker F, Plummer M, Bonomo RA. 1256. In Vivo Activity and Structural Characterization of a New Generation γ-Lactam Siderophore Antibiotic Against Multidrug-Resistant Gram-Negative Bacteria and Acinetobacter spp. Open Forum Infect Dis 2020. [PMCID: PMC7776719 DOI: 10.1093/ofid/ofaa439.1440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Multidrug-resistant (MDR) A. baumannii presents a critical need for innovative antibacterial development. We have identified a new series of γ-lactam (oxopyrazole) antibiotics that target penicillin binding proteins (PBPs) and incorporate a siderophore moiety to facilitate periplasmic uptake. YU253911, an advanced iteration of this class shows potent in vitro activity against clinically relevant Gram-negative organisms including Acinetobacter spp.
Methods
Minimum inhibitory concentrations (MICs) for YU253911 were determined using broth microdilution against a 198-member panel of clinical isolates of Acinetobacter spp. Resistant strains were further evaluated for susceptibility to YU253911 in combination with sulbactam. The antibiotic’s target protein was evaluated by binding studies with Bocillin™, a fluorescent penicillin analogue, and modeled in the PBP active site. YU253911 was evaluated in vivo in a mouse soft tissue infection model.
Results
MIC testing for YU253911 revealed an MIC50 of 0.5 μg/mL and an MIC90 of 16 μg/mL, which compared favorably to all tested β-lactam antibiotics including penicillins, cephalosporins, monobactams and carbapenems (MIC50 = 2 to > 16 μg/mL). Combination with sulbactam augmented the activity of the agent. There was no apparent correlation between YU253911-resistance and the presence of specific β-lactamase genes, and incubation with representative β-lactamase proteins (KPC-2, OXA-23, OXA-24, PER-2, PDC-3, NDM-1, VIM-2, and IMP-1) showed negligible hydrolysis of the agent. YU253911 showed promising preclinical pharmacokinetics in mice with a 15 h half-life from intravenous administration and demonstrated a dose-dependent reduction in colony forming units from 50 and 100 mg/kg q6h dosing in a mouse thigh infection model using P. aeruginosa.
Conclusion
YU253911, a new generation γ-lactam antibiotic effective against MDR A. baumannii demonstrated promising in in vitro potency and favorable pharmacokinetics which correlated with in vivo efficacy.
Disclosures
Krisztina M. Papp-Wallce, PhD, Entasis (Grant/Research Support)Merck (Grant/Research Support)Venatorx (Grant/Research Support) Robert A. Bonomo, MD, Entasis, Merck, Venatorx (Research Grant or Support)
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Affiliation(s)
| | | | | | | | - Magdalena A Taracila
- Case Western Reserve University & Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio
| | | | - Vijay Kumar
- Case Western Reserve University, Cleveland, Ohio
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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Sid Ahmed MA, Abdel Hadi H, Hassan AAI, Abu Jarir S, Al-Maslamani MA, Eltai NO, Dousa KM, Hujer AM, Sultan AA, Soderquist B, Bonomo RA, Ibrahim EB, Jass J, Omrani AS. Evaluation of in vitro activity of ceftazidime/avibactam and ceftolozane/tazobactam against MDR Pseudomonas aeruginosa isolates from Qatar. J Antimicrob Chemother 2020; 74:3497-3504. [PMID: 31504587 DOI: 10.1093/jac/dkz379] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/16/2019] [Accepted: 08/02/2019] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES To investigate the in vitro activity of ceftazidime/avibactam and ceftolozane/tazobactam against clinical isolates of MDR Pseudomonas aeruginosa from Qatar, as well as the mechanisms of resistance. METHODS MDR P. aeruginosa isolated between October 2014 and September 2015 from all public hospitals in Qatar were included. The BD PhoenixTM system was used for identification and initial antimicrobial susceptibility testing, while Liofilchem MIC Test Strips (Liofilchem, Roseto degli Abruzzi, Italy) were used for confirmation of ceftazidime/avibactam and ceftolozane/tazobactam susceptibility. Ten ceftazidime/avibactam- and/or ceftolozane/tazobactam-resistant isolates were randomly selected for WGS. RESULTS A total of 205 MDR P. aeruginosa isolates were included. Of these, 141 (68.8%) were susceptible to ceftazidime/avibactam, 129 (62.9%) were susceptible to ceftolozane/tazobactam, 121 (59.0%) were susceptible to both and 56 (27.3%) were susceptible to neither. Twenty (9.8%) isolates were susceptible to ceftazidime/avibactam but not to ceftolozane/tazobactam and only 8 (3.9%) were susceptible to ceftolozane/tazobactam but not to ceftazidime/avibactam. Less than 50% of XDR isolates were susceptible to ceftazidime/avibactam or ceftolozane/tazobactam. The 10 sequenced isolates belonged to six different STs and all produced AmpC and OXA enzymes; 5 (50%) produced ESBL and 4 (40%) produced VIM enzymes. CONCLUSIONS MDR P. aeruginosa susceptibility rates to ceftazidime/avibactam and ceftolozane/tazobactam were higher than those to all existing antipseudomonal agents, except colistin, but were less than 50% in extremely resistant isolates. Non-susceptibility to ceftazidime/avibactam and ceftolozane/tazobactam was largely due to the production of ESBL and VIM enzymes. Ceftazidime/avibactam and ceftolozane/tazobactam are possible options for some patients with MDR P. aeruginosa in Qatar.
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Affiliation(s)
- Mazen A Sid Ahmed
- Microbiology Division, Hamad Medical Corporation, Doha, Qatar.,The Life Science Centre, School of Science and Technology, Örebro University, Örebro, Sweden
| | - Hamad Abdel Hadi
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
| | | | | | | | | | - Khalid M Dousa
- University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - 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
| | - Ali A Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Bo Soderquist
- The Life Science Centre, School of Science and Technology, Örebro University, Örebro, Sweden
| | - 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.,Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,The CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
| | | | - Jana Jass
- The Life Science Centre, School of Science and Technology, Örebro University, Örebro, Sweden
| | - Ali S Omrani
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
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26
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Evans SR, Tran TTT, Hujer AM, Hill CB, Hujer KM, Mediavilla JR, Manca C, Domitrovic TN, Perez F, Farmer M, Pitzer KM, Wilson BM, Kreiswirth BN, Patel R, Jacobs MR, Chen L, Fowler VG, Chambers HF, Bonomo RA. Rapid Molecular Diagnostics to Inform Empiric Use of Ceftazidime/Avibactam and Ceftolozane/Tazobactam Against Pseudomonas aeruginosa: PRIMERS IV. Clin Infect Dis 2020; 68:1823-1830. [PMID: 30239599 DOI: 10.1093/cid/ciy801] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/18/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Overcoming β-lactam resistance in pathogens such as Pseudomonas aeruginosa is a major clinical challenge. Rapid molecular diagnostics (RMDs) have the potential to inform selection of empiric therapy in patients infected by P. aeruginosa. METHODS In this study, we used a heterogeneous collection of 197 P. aeruginosa that included multidrug-resistant isolates to determine whether 2 representative RMDs (Acuitas Resistome test and VERIGENE gram-negative blood culture test) could identify susceptibility to 2 newer β-lactam/β-lactamase inhibitor (BL-BLI) combinations, ceftazidime/avibactam (CZA) and ceftolozane/tazobactam (TOL/TAZO). RESULTS We found that the studied RMD platforms were able to correctly identify BL-BLI susceptibility (susceptibility sensitivity, 100%; 95% confidence interval [CI], 97%, 100%) for both BLs-BLIs. However, their ability to detect resistance to these BLs-BLIs was lower (resistance sensitivity, 66%; 95% CI, 52%, 78% for TOL/TAZO and 33%; 95% CI, 20%, 49% for CZA). CONCLUSIONS The diagnostic platforms studied showed the most potential in scenarios where a resistance gene was detected or in scenarios where a resistance gene was not detected and the prevalence of resistance to TOL/TAZO or CZA is known to be low. Clinicians need to be mindful of the benefits and risks that result from empiric treatment decisions that are based on resistance gene detection in P. aeruginosa, acknowledging that such decisions are impacted by the prevalence of resistance, which varies temporally and geographically.
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Affiliation(s)
- Scott R Evans
- The Biostatistics Center and the Department of Epidemiology and Biostatistics, George Washington University, Rockville, Maryland
| | - Thuy Tien T Tran
- The Biostatistics Center and the Department of Epidemiology and Biostatistics, George Washington University, Rockville, Maryland
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Carol B Hill
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Jose R Mediavilla
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Claudia Manca
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - T Nicholas Domitrovic
- Department of Medicine, Case Western Reserve University School of Medicine.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Federico Perez
- Department of Medicine, Case Western Reserve University School of Medicine.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | | | | | - Brigid M Wilson
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Barry N Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Michael R Jacobs
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Liang Chen
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Vance G Fowler
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina.,Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | | | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine.,Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio.,Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine.,CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Ohio
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27
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Hujer AM, Long SW, Olsen RJ, Taracila MA, Rojas LJ, Musser JM, Bonomo RA. Predicting β-lactam resistance using whole genome sequencing in Klebsiella pneumoniae: the challenge of β-lactamase inhibitors. Diagn Microbiol Infect Dis 2020; 98:115149. [PMID: 32858260 DOI: 10.1016/j.diagmicrobio.2020.115149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 06/01/2020] [Accepted: 07/18/2020] [Indexed: 11/25/2022]
Abstract
Although multiple antimicrobial resistance (AMR) determinants can confer the same in vitro antimicrobial susceptibility testing (AST) phenotype, their differing effect on optimal therapeutic choices is uncertain. Using a large population-based collection of clinical strains spanning a 3.5-year period, we applied WGS to detect inhibitor resistant (IR), extended-spectrum β-lactamase (ESBL), and carbapenem resistant (CR) β-lactamase (bla) genes and compared the genotype to the AST phenotype in select isolates. All blaNDM-1 (9/9) and the majority of blaNDM-1/OXA-48 (3/4) containing isolates were resistant to CAZ/AVI as predicted by WGS. The combination of ATM and CAZ/AVI restored susceptibility by disk diffusion assay. Unexpectedly, clinical Kp isolates bearing blaKPC-8 (V240G) and blaKPC-14 (G242 and T243 deletion) did not test fully resistant to CAZ/AVI. Lastly, despite the complexity of the β-lactamase background, CAZ/AVI retained potency. Presumed phenotypes conferred by AMR determinants need to be tested if therapeutic decisions are being guided by their presence or absence.
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Affiliation(s)
- Andrea M Hujer
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - Laura J Rojas
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH; Department of Molecular Biology and Microbiology, Pharmacology, Biochemistry, and the Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH; CWRU-Cleveland VAMC, Center, for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH.
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28
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Goldberg JA, Nguyen H, Kumar V, Spencer EJ, Hoyer D, Marshall EK, Cmolik A, O'Shea M, Marshall SH, Hujer AM, Hujer KM, Rudin SD, Domitrovic TN, Bethel CR, Papp-Wallace KM, Logan LK, Perez F, Jacobs MR, van Duin D, Kreiswirth BM, Bonomo RA, Plummer MS, van den Akker F. A γ-Lactam Siderophore Antibiotic Effective against Multidrug-Resistant Gram-Negative Bacilli. J Med Chem 2020; 63:5990-6002. [PMID: 32420736 DOI: 10.1021/acs.jmedchem.0c00255] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Treatment of multidrug-resistant Gram-negative bacterial pathogens represents a critical clinical need. Here, we report a novel γ-lactam pyrazolidinone that targets penicillin-binding proteins (PBPs) and incorporates a siderophore moiety to facilitate uptake into the periplasm. The MIC values of γ-lactam YU253434, 1, are reported along with the finding that 1 is resistant to hydrolysis by all four classes of β-lactamases. The druglike characteristics and mouse PK data are described along with the X-ray crystal structure of 1 binding to its target PBP3.
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Affiliation(s)
- Joel A Goldberg
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Ha Nguyen
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Vijay Kumar
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Elizabeth J Spencer
- Yale Center for Molecular Discovery, West Haven, Connecticut 06516, United States
| | - Denton Hoyer
- Yale Center for Molecular Discovery, West Haven, Connecticut 06516, United States
| | - Emma K Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Anna Cmolik
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Margaret O'Shea
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Steven H Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Kristine M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Susan D Rudin
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - T Nicholas Domitrovic
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Christopher R Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Latania K Logan
- Department of Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, Illinois 60612, United States.,Cook County Health and Hospital Systems, Chicago, Illinois 60612, United States
| | - Federico Perez
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Geriatric Research, Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Michael R Jacobs
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Department of Pathology, University Hospitals Cleveland Medical Center, Division of Clinical Microbiology, Cleveland, Ohio 44106, United States
| | - David van Duin
- University of North Carolina School of Medicine, Chapel Hill, North Carolina 27514, United States
| | - Barry M Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07601, United States
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Geriatric Research, Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Departments of Pharmacology, Molecular Biology & Microbiology, and Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106, United States.,CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio 44106, United States
| | - Mark S Plummer
- Yale Center for Molecular Discovery, West Haven, Connecticut 06516, United States
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
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29
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van Duin D, Arias CA, Komarow L, Chen L, Hanson BM, Weston G, Cober E, Garner OB, Jacob JT, Satlin MJ, Fries BC, Garcia-Diaz J, Doi Y, Dhar S, Kaye KS, Earley M, Hujer AM, Hujer KM, Domitrovic TN, Shropshire WC, Dinh A, Manca C, Luterbach CL, Wang M, Paterson DL, Banerjee R, Patel R, Evans S, Hill C, Arias R, Chambers HF, Fowler VG, Kreiswirth BN, Bonomo RA. Molecular and clinical epidemiology of carbapenem-resistant Enterobacterales in the USA (CRACKLE-2): a prospective cohort study. Lancet Infect Dis 2020; 20:731-741. [PMID: 32151332 DOI: 10.1016/s1473-3099(19)30755-8] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/04/2019] [Accepted: 12/20/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Carbapenem-resistant Enterobacterales (CRE) are a global threat. We aimed to describe the clinical and molecular characteristics of Centers for Disease Control and Prevention (CDC)-defined CRE in the USA. METHODS CRACKLE-2 is a prospective, multicentre, cohort study. Patients hospitalised in 49 US hospitals, with clinical cultures positive for CDC-defined CRE between April 30, 2016, and Aug 31, 2017, were included. There was no age exclusion. The primary outcome was desirability of outcome ranking (DOOR) at 30 days after index culture. Clinical data and bacteria were collected, and whole genome sequencing was done. This trial is registered with ClinicalTrials.gov, number NCT03646227. FINDINGS 1040 patients with unique isolates were included, 449 (43%) with infection and 591 (57%) with colonisation. The CDC-defined CRE admission rate was 57 per 100 000 admissions (95% CI 45-71). Three subsets of CDC-defined CRE were identified: carbapenemase-producing Enterobacterales (618 [59%] of 1040), non-carbapenemase-producing Enterobacterales (194 [19%]), and unconfirmed CRE (228 [22%]; initially reported as CRE, but susceptible to carbapenems in two central laboratories). Klebsiella pneumoniae carbapenemase-producing clonal group 258 K pneumoniae was the most common carbapenemase-producing Enterobacterales. In 449 patients with CDC-defined CRE infections, DOOR outcomes were not significantly different in patients with carbapenemase-producing Enterobacterales, non-carbapenemase-producing Enterobacterales, and unconfirmed CRE. At 30 days 107 (24%, 95% CI 20-28) of these patients had died. INTERPRETATION Among patients with CDC-defined CRE, similar outcomes were observed among three subgroups, including the novel unconfirmed CRE group. CDC-defined CRE represent diverse bacteria, whose spread might not respond to interventions directed to carbapenemase-producing Enterobacterales. FUNDING National Institutes of Health.
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Affiliation(s)
- David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA.
| | - Cesar A Arias
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, Houston, TX, USA; Center for Infectious Diseases, UTHealth, Houston, TX, USA; Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Lauren Komarow
- The Biostatistics Center, The George Washington University, Rockville, MD, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Blake M Hanson
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, Houston, TX, USA; Center for Infectious Diseases, UTHealth, Houston, TX, USA
| | - Gregory Weston
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eric Cober
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, OH, USA
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
| | - Jesse T Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Bettina C Fries
- Department of Medicine, Division of Infectious Diseases, Stony Brook University, Stony Brook, NY, USA
| | - Julia Garcia-Diaz
- Department of Infectious Diseases, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
| | - Sorabh Dhar
- Division of Infectious Diseases, Detroit Medical Center, Wayne State University, Detroit, MI, USA
| | - Keith S Kaye
- Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Michelle Earley
- The Biostatistics Center, The George Washington University, Rockville, MD, USA
| | - Andrea M Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kristine M Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - T Nicholas Domitrovic
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - William C Shropshire
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, Houston, TX, USA
| | - An Dinh
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, Houston, TX, USA
| | - Claudia Manca
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Courtney L Luterbach
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - David L Paterson
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital Campus, QL, Australia
| | - Ritu Banerjee
- Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Scott Evans
- The Biostatistics Center, The George Washington University, Rockville, MD, USA
| | - Carol Hill
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA
| | - Rebekka Arias
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA
| | - Henry F Chambers
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Vance G Fowler
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University, Durham, NC, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, OH, USA
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Fida M, Cunningham SA, Murphy MP, Bonomo RA, Hujer KM, Hujer AM, Kreiswirth BN, Chia N, Jeraldo PR, Nelson H, Zinsmaster NM, Toraskar N, Chang W, Patel R. Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow. Diagn Microbiol Infect Dis 2020; 97:114996. [PMID: 32098688 DOI: 10.1016/j.diagmicrobio.2020.114996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
Abstract
Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates of K. pneumoniae which are part of the Antimicrobial Resistance Leadership Group (ARLG) isolate collection, alongside 10 Mayo Clinic K. pneumoniae isolates, comparing results to those of pulsed-field gel electrophoresis (PFGE). Additionally, we used the WGS data to predict phenotypic antimicrobial susceptibility (AST). Thirty-one of 40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside 3 isolates of different PFGE types, formed a large cluster by cgMLST. PFGE and cgMLST were completely concordant for the 10 Mayo Clinic K. pneumoniae isolates. For AST prediction, the overall agreement between phenotypic AST and genotypic prediction was 95.6%.
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Affiliation(s)
- Madiha Fida
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN.
| | | | | | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veteran Affairs Medical Center, Cleveland, OH; Department of Medicine, Case Western Reserve University, Cleveland, OH; Departments of Pharmacology, Biochemistry, Molecular Biology and Microbiology, and the Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH
| | - Kristine M Hujer
- Louis Stokes Cleveland Department of Veteran Affairs Medical Center, Cleveland, OH; Department of Medicine, Case Western Reserve University, Cleveland, OH
| | - Andrea M Hujer
- Louis Stokes Cleveland Department of Veteran Affairs Medical Center, Cleveland, OH; Department of Medicine, Case Western Reserve University, Cleveland, OH
| | | | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Department of Surgery, Mayo Clinic, Rochester, MN
| | - Patricio R Jeraldo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Department of Surgery, Mayo Clinic, Rochester, MN
| | - Heidi Nelson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Department of Surgery, Mayo Clinic, Rochester, MN
| | | | | | | | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN; Division of Clinical Microbiology, Mayo Clinic, Rochester, MN
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Goldberg J, Bethel C, Hujer AM, Hujer K, Marshall S, Papp-Wallace KM, Perez F, Spencer E, Hoyer D, Plummer M, Bonomo RA. 698. In vitro Activity of a New Generation Oxopyrazole Antibiotic Against Multidrug-Resistant Gram-Negative Bacilli. Open Forum Infect Dis 2019. [PMCID: PMC6811137 DOI: 10.1093/ofid/ofz360.766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Multidrug-resistant Gram-negative bacilli (MDRGNB) are emerging as a challenging cause of hospital-acquired infections and represent a critical need for innovative antibacterial development. New oxopyrazole agents targeting penicillin-binding proteins (PBPs) based on a non-β-lactam core and incorporating a siderophore moiety (Figure 1) which facilitates transport to the periplasm are being developed that show promise against Gram-negative organisms including multidrug-resistant strains of E. coli, K. pneumoniae and P. aeruginosa.
Methods
YU253434, an example of this new class of antibacterials, was investigated in vitro. Minimum inhibitory concentrations (MICs) were determined by broth microdilution against a representative panel comprising 15 strains each of E. coli, K. pneumoniae and P. aeruginosa, which contain extended-spectrum β-lactamase (ESBL) and/or carbapenemases genes.All studies were performed according to current Clinical & Laboratory Standards Institute (CLSI) guidelines using iron-depleted media. Ceftazidime breakpoints were arbitrability chosen as a reference for YU253434 (susceptibilities ≤4 μg/mL for Enterobacteriaceae and ≤8 μg/mL for P. aeruginosa).
Results
MIC testing (Figures 2–4) against E. coli showed 11 strains were YU253434 susceptible (compared with 6 for ceftazidime, and 3 for imipenem); against K. pneumoniae 13 strains were YU253434 susceptible (compared with 2 for ceftazidime and 6 for imipenem); against P. aeruginosa 10 strains were YU253434 susceptible (compared with 0 for both ceftazidime and imipenem). There appeared to be no correlation between YU253434 resistance and the presence of specific lactamase genes.
Conclusion
YU253434, a new generation oxopyrazole antibiotic, demonstrated promising in vitro potency against a panel of E. coli, K. pneumonia, and P. aeruginosa strains which contain ESBL and/or carbapenemases genes.
Disclosures
All authors: No reported disclosures.
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Goldberg J, Bethel C, Hujer AM, Hujer K, Marshall S, Papp-Wallace KM, Perez F, Spencer E, Hoyer D, Plummer M, Bonomo RA. 687. In vitro Activity of a New Generation Oxopyrazole Antibiotic Against Acinetobacter spp. Open Forum Infect Dis 2019. [PMCID: PMC6810957 DOI: 10.1093/ofid/ofz360.755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Acinetobacter spp. resistant to common antibiotics have become a worrying cause of hospital-acquired infections and represent a critical need for innovative antibacterial development. New oxopyrazole agents targeting penicillin-binding proteins (PBPs) based on a non-β-lactam core and incorporating a siderophore moiety (figure) which facilitates transport to the periplasm are being developed which show promise against Gram-negative organisms including Acinetobacter spp. Methods YU253911, an example of this new class of antibacterials, was characterized in vitro. Minimum inhibitory concentrations (MICs) were determined by broth microdilution against a collection of 200 previously described (whole-genome sequencing) Acinetobacter isolates including 98 carbapenem-resistant A. baumannii strains. YU253911’s antimicrobial activity was also evaluated in combination with complementary PBP agents and β-lactamase inhibitors by MIC and disc diffusion testing. All studies were performed according to current Clinical and Laboratory Standards Institute (CLSI) guidelines using iron-depleted media. Breakpoints for ceftazidime were arbitrarily chosen as reference. Results Using ceftazidime (breakpoint ≤8 μg/mL) as a comparator, 175 of the 200 Acinetobacter isolates were susceptible to YU253911, which possessed an MIC50 of 0.5 μg/mL and an MIC90 of 16 μg/mL. This compared favorably to all previously tested β-lactams including penicillins, cephalosporins, monobactams and carbapenems (MIC50s 2 to >16 μg/mL). Against the subset of carbapenem-resistant A. baumannii isolates, YU253911’s potency was similar with an MIC50 of 1 μg/mL. Genetic analysis showed β-lactamase genes, including OXA-23 and other carbapenemases, were common in both YU253911-resistant and susceptible strains. Conclusion YU253911 demonstrates promising in vitro potency against a collection of Acinetobacter isolates and compares favorably to β-lactam antibiotics. Understanding interactions with PBP agents and β lactamase inhibitors is being explored as well as further studies on the mechanism of resistance. ![]()
Disclosures All authors: No reported disclosures.
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Affiliation(s)
| | | | | | | | | | - Krisztina M Papp-Wallace
- Case Western Reserve University, Cleveland, Ohio
- Louis Sokes Cleveland VA Medical Center, Cleveland, Ohio
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McClure E, Newman J, Krishnan N, Rutter J, Hujer AM, Adams MD, Scott J, Bonomo RA. 609. Differing Genotypic Contexts Between E. coli and A. baumannii Modulate the Role of blaADC-7 in the Development of Antibiotic Collateral Sensitivity. Open Forum Infect Dis 2019. [PMCID: PMC6810876 DOI: 10.1093/ofid/ofz360.678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Antibiotic resistance is a global health crisis. While persistent drug discovery of novel antibiotics has previously been relied upon to thwart resistance, evolution inevitably perseveres. While genes conferring antibiotic resistance have previously been characterized, it is unclear how varying genetic contexts can change the antibiotic resistance phenotype a given gene confers.
Methods
The DH10B strain of E. coli was transformed with a blaADC-7 plasmid. In 12 evolutionary replicates, the modified E. coli strain and a clinical strain of A. baumannii containing the same resistance gene were passaged daily for 10 days on cefepime gradient agar plates with gradually increasing concentrations of cefepime. MICs of cefepime and a diverse set of 15 other drugs were determined for the parental strains and after the final passage passage. MIC of cefepime after intermediary passages were determined for select replicates. Lastly the blaADC-7 gene after the final passage was sequenced.
Results
At the end of 10 passages, collateral sensitivity in A. baumannii was observed to tigecycline and fosfomycin in 5 and 6 replicates respectively, out of 12 total. 4 out of 12 E. coli replicates displayed collateral sensitivity to minocycline (Figure 1). In the third E. coli replicate, Sanger sequencing revealed a novel S286R mutation in blaADC-7 appearing in passage seven which preceded a several log fold increase in the MIC of cefepime (Figures 2 and 3). No additional mutations were found in the other evolutionary replicates.
Conclusion
Patterns of resistance varied among antibiotics of the same class, (e.g., tetracyclines, fourth-generation cephalosporins) in both E. coli and A. baumannii; however, A. baumannii expressed less widespread collateral resistance than E. coli. A previously undiscovered S286R mutation in blaADC-7 coincided with a pronounced increased in resistance to cefepime. Further studies are required to determine whether this mutation gives rise to a structural change in the protein product. Given that no other mutations were found, resistance to cefepime and subsequent collateral resistance to other antibiotics may have developed due to epigenetic changes or mutations outside the blaADC-7 genes. Indeed, future experiments with whole-genome sequencing may reveal such changes.
Disclosures
All authors: No reported disclosures.
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Affiliation(s)
- Erin McClure
- Cleveland Clinic Foundation, Cleveland Heights, Ohio
| | | | - Nikhil Krishnan
- Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Joseph Rutter
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio
| | | | - Mark D Adams
- The Jackson Laboratory for Genomic Medicine, Bar Harbor, Maine
| | - Jacob Scott
- Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
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Rosa R, Rudin SD, Rojas LJ, Perez-Cardona A, Aragon L, Nicolau DP, Perez F, Hujer AM, Tekin A, Martinez O, Camargo JF, Bonomo RA, Abbo LM. Application of "Precision Medicine" Through the Molecular Characterization of Extensively Drug-Resistant Klebsiella pneumoniae in a Multivisceral Transplant Patient. Clin Infect Dis 2019; 65:701-702. [PMID: 29017264 DOI: 10.1093/cid/cix387] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Rossana Rosa
- Department of Medicine, Jackson Memorial Hospital.,Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida
| | - Susan D Rudin
- Louis Stokes Cleveland Veterans Affairs Medical Center.,Medicine
| | - Laura J Rojas
- Louis Stokes Cleveland Veterans Affairs Medical Center.,Microbiology and Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | - Laura Aragon
- Pharmacy, Jackson Memorial Hospital, Miami, Florida
| | - David P Nicolau
- Center for Anti-Infective Research and Development, Hartford, Connecticut
| | | | - Andrea M Hujer
- Louis Stokes Cleveland Veterans Affairs Medical Center.,Medicine
| | | | - Octavio Martinez
- Pathology, University of Miami Miller School of Medicine, Florida
| | - Jose F Camargo
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida
| | - Robert A Bonomo
- Louis Stokes Cleveland Veterans Affairs Medical Center.,Medicine.,Microbiology and Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Pharmacology.,Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Lilian M Abbo
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida
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35
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Logan LK, Medernach RL, Domitrovic TN, Rispens JR, Hujer AM, Qureshi NK, Marshall SH, Nguyen DC, Rudin SD, Zheng X, Konda S, Weinstein RA, Bonomo RA. The Clinical and Molecular Epidemiology of CTX-M-9 Group Producing Enterobacteriaceae Infections in Children. Infect Dis Ther 2019; 8:243-254. [PMID: 30772921 PMCID: PMC6522575 DOI: 10.1007/s40121-019-0237-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 01/13/2023] Open
Abstract
Introduction The pandemic of extended-spectrum beta-lactamase-(ESBL)-producing Enterobacteriaceae (Ent) is strongly linked to the dissemination of CTX-M-type-ESBL-Ent. We sought to define the epidemiology of infections in children due to an emerging resistance type, CTX-M-9-group-producing-Ent (CTX-M-9-grp-Ent). Methods A retrospective matched case-control analysis of children with CTX-M-9-grp-Ent infections who received medical care at three Chicago area hospitals was performed. Cases were defined as children possessing extended-spectrum cephalosporin-resistant (ESC-R) infections due to blaCTX-M-9. PCR and DNA analysis assessed beta-lactamase (bla) genes, multi-locus sequence types (MLST) and phylogenetic grouping of E. coli. Controls were children with ESC-susceptible (ESC-S)-Ent infections matched one case to three controls by age, source, and hospital. The clinical-epidemiologic predictors of CTX-M-9-grp-Ent infection were assessed. Results Of 356 ESC-R-Ent isolates from children (median age 4.1 years), the CTX-M-9-group was the solely detected bla gene in 44 (12.4%). The predominant species was E. coli (91%) of virulent phylogroups D (60%) and B2 (40%). MLST revealed multiple strain types. On multivariable analysis, CTX-M-9-grp-Ent occurred more often in E. coli than other Ent genera (OR 7.4, 95% CI 2.4, 27.2), children of non-Black-White-Hispanic race (OR 7.4, 95% CI 2.4, 28.2), and outpatients (OR 4.5, 95% CI 1.7, 12.3), which was a very unexpected finding for infections due to antibiotic-resistant bacteria. Residents of South Chicago had a 6.7 times higher odds of having CTX-M-9-grp-Ent infections than those in the reference region (West), while residence in Northwestern Chicago was associated with an 81% decreased odds of infection. Other demographic, comorbidity, invasive-device, and antibiotic use differences were not found. Conclusion CTX-M-9-grp-Ent infection may be associated with patient residence and is occurring in children without traditional in-patient exposure risk factors. This suggests that among children, the community environment may be a key contributor in the spread of these resistant pathogens.
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Affiliation(s)
- Latania K Logan
- Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, IL, USA. .,Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA. .,Cook County Health and Hospital Systems, Chicago, IL, USA.
| | - Rachel L Medernach
- Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, IL, USA.,Medicine, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - T Nicholas Domitrovic
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.,Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Jared R Rispens
- Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, IL, USA.,Medicine, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.,Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Nadia K Qureshi
- Pediatrics, Loyola University Medical Center, Maywood, IL, USA
| | - Steven H Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - David C Nguyen
- Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, IL, USA.,Case Western Reserve School of Medicine, Cleveland, OH, USA.,Medicine, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Susan D Rudin
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Xiaotian Zheng
- Microbiology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sreenivas Konda
- Epidemiology and Biostatistics, University of Illinois at Chicago, Chicago, IL, USA
| | - Robert A Weinstein
- Medicine, Rush University Medical Center, Rush Medical College, Chicago, IL, USA.,Cook County Health and Hospital Systems, Chicago, IL, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.,Case Western Reserve School of Medicine, Cleveland, OH, USA.,Pharmacology, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.,Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.,Biochemistry, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.,Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
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Jacobs MR, Abdelhamed AM, Good CE, Rhoads DD, Hujer KM, Hujer AM, Domitrovic TN, Rudin SD, Richter SS, van Duin D, Kreiswirth BN, Greco C, Fouts DE, Bonomo RA. ARGONAUT-I: Activity of Cefiderocol (S-649266), a Siderophore Cephalosporin, against Gram-Negative Bacteria, Including Carbapenem-Resistant Nonfermenters and Enterobacteriaceae with Defined Extended-Spectrum β-Lactamases and Carbapenemases. Antimicrob Agents Chemother 2019; 63:e01801-18. [PMID: 30323050 PMCID: PMC6325197 DOI: 10.1128/aac.01801-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/06/2018] [Indexed: 01/06/2023] Open
Abstract
The activity of the siderophore cephalosporin cefiderocol is targeted against carbapenem-resistant Gram-negative bacteria. In this study, the activity of cefiderocol against characterized carbapenem-resistant Acinetobacter baumannii complex, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Enterobacteriaceae strains was determined by microdilution in iron-depleted Mueller-Hinton broth. The MIC90s against A. baumannii, S. maltophilia, and P. aeruginosa were 1, 0.25, and 0.5 mg/liter, respectively. Against Enterobacteriaceae, the MIC90 was 1 mg/liter for the group harboring OXA-48-like, 2 mg/liter for the group harboring KPC-3, and 8 mg/liter for the group harboring TEM/SHV ESBL, NDM, and KPC-2.
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Affiliation(s)
- Michael R Jacobs
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Ayman M Abdelhamed
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Caryn E Good
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Daniel D Rhoads
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - T Nicholas Domitrovic
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Susan D Rudin
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Sandra S Richter
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - David van Duin
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Barry N Kreiswirth
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Chris Greco
- J. Craig Venter Institute, Rockville, Maryland, USA
| | | | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case Virginia, USA CARES), Cleveland, Ohio, USA
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37
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Luterbach CL, Boshe A, Henderson HI, Cober E, Richter SS, Salata RA, Kalayjian RC, Watkins RR, Hujer AM, Hujer KM, Rudin SD, Domitrovic TN, Doi Y, Kaye KS, Evans S, Fowler VG, Bonomo RA, van Duin D. The Role of Trimethoprim/Sulfamethoxazole in the Treatment of Infections Caused by Carbapenem-Resistant Enterobacteriaceae. Open Forum Infect Dis 2018; 6:ofy351. [PMID: 30631796 PMCID: PMC6324543 DOI: 10.1093/ofid/ofy351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/13/2018] [Indexed: 02/05/2023] Open
Abstract
In the Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae (CRACKLE), trimethoprim-sulfamethoxazole (TMP-SMX) had a limited role in the treatment of less severe carbapenem-resistant Enterobacteriaceae (CRE) infections, especially urinary tract infections. Of tested CRE, only 29% were susceptible to TMP-SMX. Development of resistance further limits the use of TMP-SMX in CRE infections.
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Affiliation(s)
- Courtney L Luterbach
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Ashley Boshe
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Heather I Henderson
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Eric Cober
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, Ohio
| | - Sandra S Richter
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Robert A Salata
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | - Richard R Watkins
- Department of Internal Medicine, Northeast Ohio Medical University, Rootstown, Ohio.,Division of Infectious Diseases, Akron General Medical Center, Akron, Ohio
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Susan D Rudin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - T Nicholas Domitrovic
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Keith S Kaye
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Scott Evans
- The Biostatistics Center, The George Washington University, Rockville, Maryland
| | - Vance G Fowler
- Division of Infectious Diseases, Duke University, Durham, North Carolina.,Duke Clinical Research Institute, Duke University, Durham, North Carolina
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio.,Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio.,CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio
| | - David van Duin
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina.,Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
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Jacobs MR, Abdelhamed AM, Good CE, Rhoads DD, Hujer KM, Hujer AM, Domitrovic TN, Rudin SD, Richter SS, Van Duin D, Kreiswirth BN, Bonomo RA. 1351. In vitro Activity of Cefiderocol (S-649266), a Siderophore Cephalosporin, Against Enterobacteriaceae With Defined Extended-Spectrum Β-Lactamases and Carbapenemases. Open Forum Infect Dis 2018. [PMCID: PMC6253113 DOI: 10.1093/ofid/ofy210.1182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Cefiderocol is a novel siderophore cephalosporin targeted for activity against carbapenem and multidrug-resistant Gram-negative species, including extended-spectrum β-lactamase (ESBL) and carbapenemase-producing strains. The Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae (CRACKLE) is a federally funded, prospective multi-center consortium of 20 hospitals from nine US healthcare systems to track carbapenem-resistant Enterobacteriaceae.
Methods
Minimum inhibitory concentrations (MICs) of cefiderocol and meropenem were determined by broth microdilution according to current CLSI guidelines. Cefiderocol was tested in iron-depleted cation-adjusted Mueller–Hinton (MH) broth, meropenem was tested in cation-adjusted MH broth. Cefiderocol MICs were read as the first drug well in which the growth was significantly reduced (i.e., a button of <1 mm or light/faint turbidity) relative to the growth observed in the growth control well containing the same medium. Trailing endpoints were disregarded. Isolates tested included 35 Escherichia coli, five Enterobacter/Citrobacter group, and 794 Klebsiella pneumoniae. Isolates had characterized β-lactamases including TEM, SHV, and CTX-M ESBLs and KPC, NDM, and OXA carbapenemases.
Results
Cefiderocol MICs ranged from ≤0.03 to >64 mg/L, with overall MIC50 of 0.5 mg/L and MIC90 of 4 mg/L (table). MIC90 value (≤0.03 mg/L) was lowest against isolates with no ESBLs or carbapenemases. MIC90 was 1 mg/L for OXA and TEM/SHV groups, 2–4 mg/L for KPC-3 groups and 8 mg/L for NDM and KPC-2 groups.
Conclusion
Compared with isolates without ESBLs and carbapenemases, cefiderocol shows higher MICs against isolates with ESBLs, including TEM, SHV, and CTX-M and carbapenemases including KPC, NDM, and OXA. The clinical utility of cefiderocol against ESBL and carbapenemase-producing Enterobacteriaceae is dependent on the pharmacokinetic and pharmacodynamic properties of cefiderocol.
Disclosures
M. R. Jacobs, Achaogen: Investigator, Research grant. Shionogi: Investigator, Research grant. S. S. Richter, bioMerieux: Grant Investigator, Research grant. BD Diagnostics: Grant Investigator, Research grant. Roche: Grant Investigator, Research grant. Hologic: Grant Investigator, Research grant. Diasorin: Grant Investigator, Research grant. Accelerate: Grant Investigator, Research grant. Biofire: Grant Investigator, Research grant. D. Van Duin, Shionogi: Scientific Advisor, Consulting fee. achaogen: Scientific Advisor, Consulting fee. Allergan: Scientific Advisor, Consulting fee. Astellas: Scientific Advisor, Consulting fee. Neumedicine: Consultant, Consulting fee. T2 Biosystems: Scientific Advisor, Consulting fee. Roche: Scientific Advisor, Consulting fee.
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Affiliation(s)
- Michael R Jacobs
- Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Ayman M Abdelhamed
- Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Caryn E Good
- Pathology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Daniel D Rhoads
- Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Kristine M Hujer
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Case Western Reserve University, Cleveland, Ohio
| | - Andrea M Hujer
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Case Western Reserve University, Cleveland, Ohio
| | - T Nicholas Domitrovic
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Case Western Reserve University, Cleveland, Ohio
| | - Susan D Rudin
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Case Western Reserve University, Cleveland, Ohio
| | - Sandra S Richter
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - David Van Duin
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Barry N Kreiswirth
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Robert A Bonomo
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Case Western Reserve University, Cleveland, Ohio
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Jacobs MR, Good CE, Abdelhamed AM, Rhoads DD, Hujer KM, Hujer AM, Rudin SD, Domitrovic TN, Connolly L, Krause KM, Richter SS, Van Duin D, Kreiswirth BN, Bonomo RA. 1348. In vitro Activity of Plazomicin, a Next-Generation Aminoglycoside, Against Carbapenemase-Producing Klebsiella pneumoniae. Open Forum Infect Dis 2018. [PMCID: PMC6254231 DOI: 10.1093/ofid/ofy210.1179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
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Affiliation(s)
- Michael R Jacobs
- Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Caryn E Good
- Pathology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Ayman M Abdelhamed
- Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Daniel D Rhoads
- Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Kristine M Hujer
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio,Case Western Reserve University, Cleveland, Ohio
| | - Andrea M Hujer
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio,Case Western Reserve University, Cleveland, Ohio
| | - Susan D Rudin
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio,Case Western Reserve University, Cleveland, Ohio
| | - T Nicholas Domitrovic
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio,Case Western Reserve University, Cleveland, Ohio
| | | | | | - Sandra S Richter
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - David Van Duin
- Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Barry N Kreiswirth
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Robert A Bonomo
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio,Case Western Reserve University, Cleveland, Ohio
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Medernach RL, Domitrovic TN, Rispens JR, Hujer AM, Qureshi NK, Marshall SH, Nguyen DC, Rudin SD, Zheng X, Weinstein RA, Bonomo RA, Logan LK. 2336. Resistance Mechanisms and Factors Associated With CTX-M-9 Group Extended-Spectrum β-Lactamase (ESBL)-Producing Enterobacteriaceae Infections in Children. Open Forum Infect Dis 2018. [PMCID: PMC6254941 DOI: 10.1093/ofid/ofy210.1989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background There is an increasing incidence of extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae infections in children. However, most studies focus only on CTX-M-1 group (CTX-M-15). We sought to define the epidemiology of the CTX-M-9 group (CTX-M-9) producing Enterobacteriaceae infections in children to devise more effective treatment and prevention strategies. Methods A case–control study of children (0–21 y), cared for by 3 Chicago area hospitals during 2011–16, was performed. Cases were 44 children diagnosed with third-generation cephalosporin (3GC) resistant and/or carbapenem-resistant (CR) Enterobacteriaceae infections who had CTX-M-9 genes accounting for β-lactam resistance. PCR amplification, DNA sequencing, and DNA microarray analysis (Check-Points®) assessed for bla genes. MLST, rep-PCR and phylogenetic analysis were also performed. Controls were 135 children with 3GC and carbapenem susceptible Enterobacteriaceae infections matched by age range and hospital. Demographics; comorbidities; device, antibiotic, and healthcare exposures; and the impact of location of patient residence were evaluated. Race categories were white, black, Hispanic, and other. Stratified analysis and multivariable logistic regression were used to explore associations between predictors and CTX-M-9 infection. Data were analyzed in SAS 9.4. Results The median age of cases was 4.1 years. The predominant organism (39/44, 89%) was E. coli of virulent phylogroups B2 (41%) and D (59%). MLST analysis revealed that this collection of strains was polyclonal. On multivariable analysis, children with CTX-M-9 Enterobacteriaceae infections were more likely to be diagnosed in an outpatient clinic (OR 4.5), have E. coli infection (OR 7.0), and be of race “other” (OR 7.6) vs. controls. Residents of South Chicago were 6.7 times more likely to have a CTX-M-9 Enterobacteriaceae infection than controls; while residence in Northwest Chicago was associated with a 81% decreased risk. Significant differences in other demographics, comorbidities, invasive devices, antibiotic use, or recent healthcare were not found. Conclusion We observed striking regional differences in occurrence of CTX-M-9 producing Enterobacteriaceae, suggesting that environmental influences and plasmid transfer may contribute to acquisition. It is worrisome that a large number of ESBL Enterobacteriaceae strains bearing CTX-M ESBLs circulate in the community among children. Disclosures All authors: No reported disclosures.
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Affiliation(s)
| | | | - Jared R Rispens
- Internal Medicine and Pediatrics, Rush University Medical Center, Chicago, Illinois
| | - Andrea M Hujer
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio
| | - Nadia K Qureshi
- Pediatrics, Loyola University Medical Center, Maywood, Illinois
| | - Steven H Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - David C Nguyen
- Departments of Internal Medicine and Pediatrics, Rush University Medical Center, Chicago, Illinois
| | - Susan D Rudin
- Research Service, VA Cleveland Medical Center, Cleveland, Ohio
| | | | - Robert A Weinstein
- Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
| | - Robert A Bonomo
- Research, Louis Stokes Cleveland Veteran’s Affairs Medical Center, Cleveland, Ohio
- Case Western Reserve University, Cleveland, Ohio
| | - Latania K Logan
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Pediatrics, Rush University Medical Center, Chicago, Illinois
- Rush Medical College, Chicago, Illinois
- John Stroger Hospital of Cook County, Chicago, Illinois
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41
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Kanwar A, Marshall SH, Perez F, Tomas M, Jacobs MR, Hujer AM, Domitrovic TN, Rudin SD, Rojas LJ, Kreiswirth BN, Chen L, Quinones-Mateu M, van Duin D, Bonomo RA. Emergence of Resistance to Colistin During the Treatment of Bloodstream Infection Caused by Klebsiella pneumoniae Carbapenemase-Producing Klebsiella pneumoniae. Open Forum Infect Dis 2018; 5:ofy054. [PMID: 30014001 DOI: 10.1093/ofid/ofy054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/18/2018] [Indexed: 11/14/2022] Open
Abstract
We report the emergence of colistin resistance in Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae after 8 days of colistin-based therapy, resulting in relapse of bloodstream infection and death. Disruption of the mgrB gene by insertion of a mobile genetic element was found to be the mechanism, which was replicated in vitro after exposure to subinhibitory concentrations of colistin and meropenem.
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Affiliation(s)
- Anubhav Kanwar
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | | | - Federico Perez
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Research Service.,Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Myreen Tomas
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Michael R Jacobs
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Andrea M Hujer
- Research Service.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - T Nicholas Domitrovic
- Research Service.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Susan D Rudin
- Research Service.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Laura J Rojas
- Research Service.,Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Barry N Kreiswirth
- Public Health Research Institute Center New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, New Jersey
| | - Liang Chen
- Public Health Research Institute Center New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, New Jersey
| | - Miguel Quinones-Mateu
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Robert A Bonomo
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Research Service.,Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio
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42
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Rosa R, Rudin SD, Rojas LJ, Hujer AM, Perez-Cardona A, Perez F, Bonomo RA, Martinez O, Abbo LM, Camargo JF. "Double carbapenem" and oral fosfomycin for the treatment of complicated urinary tract infections caused by bla NDM -harboring Enterobacteriaceae in kidney transplantation. Transpl Infect Dis 2018; 20:10.1111/tid.12795. [PMID: 29064133 PMCID: PMC5809302 DOI: 10.1111/tid.12795] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/18/2017] [Accepted: 06/30/2017] [Indexed: 12/31/2022]
Abstract
Infections with carbapenemase-producing carbapenem-resistant Enterobacteriaceae represent an emergent problem worldwide. Treatment of infections caused by New Delhi metallo-beta-lactamase (NDM)-harboring Enterobacteriaceae is particularly challenging as it frequently involves the use of nephrotoxic agents, which is problematic in kidney transplant recipients and non-renal transplant patients with marginal kidney function. We present two cases of urinary tract infections caused by NDM-harboring Enterobacteriaceae successfully treated with a combination of "double carbapenem" and oral fosfomycin.
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Affiliation(s)
- Rossana Rosa
- Department of Medicine, Jackson Memorial Hospital, Miami, FL USA
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL USA
| | - Susan D. Rudin
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH USA
| | - Laura J. Rojas
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
- Microbiology and Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, OH USA
| | - Andrea M. Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH USA
| | | | - Federico Perez
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - Robert A. Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH USA
- Microbiology and Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, OH USA
- Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH USA
- Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH USA
- Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH USA
| | - Octavio Martinez
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL
| | - Lilian M. Abbo
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL USA
| | - Jose F. Camargo
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL USA
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Richter SS, Karichu J, Otiso J, Van Heule H, Keller G, Cober E, Rojas LJ, Hujer AM, Hujer KM, Marshall S, Perez F, Rudin SD, Domitrovic TN, Kaye KS, Salata R, van Duin D, Bonomo RA. Evaluation of Sensititre Broth Microdilution Plate for determining the susceptibility of carbapenem-resistant Klebsiella pneumoniae to polymyxins. Diagn Microbiol Infect Dis 2018; 91:89-92. [PMID: 29456071 DOI: 10.1016/j.diagmicrobio.2018.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 12/20/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
Abstract
Colistin and polymyxin B MICs were determined for 106 carbapenem-resistant Klebsiella pneumoniae (CR-Kp) isolates using Sensititre Research Use Only GNX2F plates (Thermo Fisher) and compared to CLSI broth macrodilution (BMD) as the reference method. For colistin, EUCAST breakpoints were applied and testing of isolates with very major (VM) errors was repeated in duplicate by both methods to determine a majority result. Essential agreement (MIC ± one dilution) of GNX2F with the reference method was 97.1% for polymyxin B and 92.5% for colistin (7 VM errors, 22.6%). After discrepancy testing, there were 28 colistin resistant isolates by BMD and essential agreement was 94.3% with 4 VM errors (14.3%). Colistin and polymyxin B GNX2F results showed acceptable essential agreement with BMD for MICS without interpretation. Colistin VM errors with EUCAST breakpoints were due to MIC variability in the 2 to 4 μg/mL range that could be addressed by establishing an intermediate category.
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Affiliation(s)
| | | | | | | | | | | | - Laura J Rojas
- Department of Veteran Affairs Medical Center, Cleveland, OH,; Department of Molecular Biology and Microbiology, Case Western Reserve Univ. School of Medicine, Cleveland, OH
| | - Andrea M Hujer
- Department of Veteran Affairs Medical Center, Cleveland, OH,; Case-VA CARES, Case Western Reserve Univ., Cleveland, OH
| | - Kristine M Hujer
- Department of Veteran Affairs Medical Center, Cleveland, OH,; Department of Medicine, Case Western Reserve Univ. School of Medicine, Cleveland, OH
| | - Steve Marshall
- Department of Veteran Affairs Medical Center, Cleveland, OH
| | - Frederico Perez
- Department of Veteran Affairs Medical Center, Cleveland, OH,; Case-VA CARES, Case Western Reserve Univ., Cleveland, OH,; Department of Medicine, Case Western Reserve Univ. School of Medicine, Cleveland, OH
| | - Susan D Rudin
- Department of Veteran Affairs Medical Center, Cleveland, OH,; Department of Medicine, Case Western Reserve Univ. School of Medicine, Cleveland, OH
| | - T Nicholas Domitrovic
- Department of Veteran Affairs Medical Center, Cleveland, OH,; Department of Medicine, Case Western Reserve Univ. School of Medicine, Cleveland, OH
| | | | - Robert Salata
- Case-VA CARES, Case Western Reserve Univ., Cleveland, OH
| | | | - Robert A Bonomo
- Department of Veteran Affairs Medical Center, Cleveland, OH,; Case-VA CARES, Case Western Reserve Univ., Cleveland, OH,; Department of Medicine, Case Western Reserve Univ. School of Medicine, Cleveland, OH; Department of Molecular Biology and Microbiology, Case Western Reserve Univ. School of Medicine, Cleveland, OH; Department of Biochemistry, Case Western Reserve Univ. School of Medicine, Cleveland, OH; Department of Pharmacology, Case Western Reserve Univ. School of Medicine, Cleveland, OH; Department of Proteomics and Bioinformatics, Case Western Reserve Univ. School of Medicine, Cleveland, OH
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Henig O, Cober E, Richter SS, Perez F, Salata RA, Kalayjian RC, Watkins RR, Marshall S, Rudin SD, Domitrovic TN, Hujer AM, Hujer KM, Doi Y, Evans S, Fowler VG, Bonomo RA, van Duin D, Kaye KS. A Prospective Observational Study of the Epidemiology, Management, and Outcomes of Skin and Soft Tissue Infections Due to Carbapenem-Resistant Enterobacteriaceae. Open Forum Infect Dis 2017; 4:ofx157. [PMID: 29026866 PMCID: PMC5629814 DOI: 10.1093/ofid/ofx157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/26/2017] [Indexed: 01/21/2023] Open
Abstract
Background This study was performed to characterize the epidemiology, management, and outcomes of skin and soft tissue infection (SSTI) and colonization due to carbapenem-resistant Enterobacteriaceae (CRE). Methods Patients from the Consortium on Resistance Against Carbapenem in Klebsiella and Other Enterobacteriaceae (CRACKLE-1) from December 24, 2011 to October 1, 2014 with wound cultures positive for CRE were included in the study. Predictors of surgical intervention were analyzed. Molecular typing of isolates was performed using repetitive extragenic palindromic polymerase chain reaction (PCR). Carbapenemase genes were detected using PCR. Results One hundred forty-two patients were included: 62 had SSTI (44%) and 56% were colonized. Mean age was 61 years, and 48% were male: median Charlson score was 3 (interquartile range, 1–5). Forty-eight percent of patients were admitted from long-term care facilities (LTCFs), and 31% were from the community. Two strain types (ST258A and ST258B) were identified (73% of 45 tested). Carbapenemase genes were detected in 40 of 45 isolates (blaKPC-3 [47%], blaKPC-2 [42%]). Sixty-eight patients (48%) underwent surgical intervention, 63% of whom had SSTI. Patients admitted from LTCFs were less likely to undergo surgical intervention (odds ratio [OR], 0.36; 95% confidence interval [CI], 0.18–0.71). In multivariable analysis, among patients with SSTI, those admitted from LTCFs were less likely to undergo debridement (OR, 0.18; 95% CI, 0.04–0.93). Conclusions Patients admitted from LTCFs with CRE SSTI were less likely to undergo surgical intervention. Sixteen percent of the patients died, and approximately 50% of survivors required more intensive care upon discharge. These findings suggest a unique, impactful syndrome within the CRE infection spectrum. Further studies are needed to assess the role of surgical debridement in management of CRE-SSTI, particularly among LTCF residents.
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Affiliation(s)
- Oryan Henig
- Department of Medicine, University of Michigan, Ann Arbor; Departments of
| | | | | | - Federico Perez
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Ohio.,Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Robert A Salata
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | - Richard R Watkins
- Department of Internal Medicine, Northeast Ohio Medical University, Rootstown.,Division of Infectious Diseases, Akron General Medical Center, Ohio; Departments of
| | - Steve Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Ohio
| | - Susan D Rudin
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Ohio.,Medicine
| | - T Nicholas Domitrovic
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Ohio.,Medicine
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Ohio.,Medicine
| | - Kristine M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Ohio.,Medicine
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
| | - Scott Evans
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Vance G Fowler
- Division of Infectious Diseases and.,Duke Clinical Research Institute, Duke University, Durham, North Carolina
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Ohio.,Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Medicine.,Pharmacology.,Molecular Biology and Microbiology.,Biochemistry, and.,Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill
| | - Keith S Kaye
- Department of Medicine, University of Michigan, Ann Arbor; Departments of
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Manca C, Hill C, Hujer AM, Patel R, Evans SR, Bonomo RA, Kreiswirth BN. Leading Antibacterial Laboratory Research by Integrating Conventional and Innovative Approaches: The Laboratory Center of the Antibacterial Resistance Leadership Group. Clin Infect Dis 2017; 64:S13-S17. [PMID: 28350898 PMCID: PMC5848373 DOI: 10.1093/cid/ciw826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Antibacterial Resistance Leadership Group (ARLG) Laboratory Center (LC) leads the evaluation, development, and implementation of laboratory-based research by providing scientific leadership and supporting standard/specialized laboratory services. The LC has developed a physical biorepository and a virtual biorepository. The physical biorepository contains bacterial isolates from ARLG-funded studies located in a centralized laboratory and they are available to ARLG investigators. The Web-based virtual biorepository strain catalogue includes well-characterized gram-positive and gram-negative bacterial strains published by ARLG investigators. The LC, in collaboration with the ARLG Leadership and Operations Center, developed procedures for review and approval of strain requests, guidance during the selection process, and for shipping strains from the distributing laboratories to the requesting investigators. ARLG strains and scientific and/or technical guidance have been provided to basic research laboratories and diagnostic companies for research and development, facilitating collaboration between diagnostic companies and the ARLG Master Protocol for Evaluating Multiple Infection Diagnostics (MASTERMIND) initiative for evaluation of multiple diagnostic devices from a single patient sampling event. In addition, the LC has completed several laboratory-based studies designed to help evaluate new rapid molecular diagnostics by developing, testing, and applying a MASTERMIND approach using purified bacterial strains. In collaboration with the ARLG's Statistical and Data Management Center (SDMC), the LC has developed novel analytical strategies that integrate microbiologic and genetic data for improved and accurate identification of antimicrobial resistance. These novel approaches will aid in the design of future ARLG studies and help correlate pathogenic markers with clinical outcomes. The LC's accomplishments are the result of a successful collaboration with the ARLG's Leadership and Operations Center, Diagnostics and Devices Committee, and SDMC. This interactive approach has been pivotal for the success of LC projects.
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Affiliation(s)
- Claudia Manca
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Carol Hill
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina
| | - Andrea M Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, and
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota ; and
| | - Scott R Evans
- Center for Biostatistics in AIDS Research and the Department of Biostatistics, Harvard University, Boston, Massachusetts
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, and
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Barry N Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
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Rojas LJ, Salim M, Cober E, Richter SS, Perez F, Salata RA, Kalayjian RC, Watkins RR, Marshall S, Rudin SD, Domitrovic TN, Hujer AM, Hujer KM, Doi Y, Kaye KS, Evans S, Fowler VG, Bonomo RA, van Duin D. Colistin Resistance in Carbapenem-Resistant Klebsiella pneumoniae: Laboratory Detection and Impact on Mortality. Clin Infect Dis 2017; 64:711-718. [PMID: 27940944 PMCID: PMC5850634 DOI: 10.1093/cid/ciw805] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/11/2017] [Accepted: 11/29/2017] [Indexed: 11/12/2022] Open
Abstract
Background Polymyxins including colistin are an important "last-line" treatment for infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKp). Increasing use of colistin has led to resistance to this cationic antimicrobial peptide. Methods A cohort nested within the Consortium on Resistance against Carbapenems in Klebsiella pneumoniae (CRACKLE) was constructed of patients with infection, or colonization with CRKp isolates tested for colistin susceptibility during the study period of December, 2011 to October, 2014. Reference colistin resistance determination as performed by broth macrodilution was compared to results from clinical microbiology laboratories (Etest) and to polymyxin resistance testing. Each patient was included once, at the time of their first colistin-tested CRKp positive culture. Time to 30-day in-hospital all-cause mortality was evaluated by Kaplan-Meier curves and Cox proportional hazard modeling. Results In 246 patients with CRKp, 13% possessed ColR CRKp. ColR was underestimated by Etest (very major error rate = 35%, major error rate = 0.4%). A variety of rep-PCR strain types were encountered in both the ColS and the ColR groups. Carbapenem resistance was mediated primarily by blaKPC-2 (46%) and blaKPC-3 (50%). ColR was associated with increased hazard for in-hospital mortality (aHR 3.48; 95% confidence interval, 1.73-6.57; P < .001). The plasmid-associated ColR genes, mcr-1 and mcr-2 were not detected in any of the ColR CRKp. Conclusions In this cohort, 13% of patients with CRKp presented with ColR CRKp. The apparent polyclonal nature of the isolates suggests de novo emergence of ColR in this cohort as the primary factor driving ColR. Importantly, mortality was increased in patients with ColR isolates.
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Affiliation(s)
- Laura J Rojas
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Madiha Salim
- Division of Infectious Diseases, Detroit Medical Center, Wayne State University, Michigan, USA
| | - Eric Cober
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sandra S Richter
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Federico Perez
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Robert A Salata
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Robert C Kalayjian
- Department of Medicine, MetroHealth Medical Center, Cleveland, Ohio, USA
| | - Richard R Watkins
- Department of Internal Medicine, Northeast Ohio Medical University, Rootstown, OH , USA
- Division of Infectious Diseases, Cleveland Clinic Akron General Medical Center , Akron , OH , USA
| | - Steve Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Susan D Rudin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - T Nicholas Domitrovic
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Detroit Medical Center, Wayne State University, Michigan, USA
| | - Scott Evans
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, USA
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Iovleva A, Perez F, Marshall SH, Hujer AM, Jacobs MR, Stiefel U, Ray A, Bonomo RA. Ceftazidime/Avibactam and Ceftolozane/Tazobactam in Treatment of Pulmonary Infections by Imipenem Resistant Pseudomonas aeruginosa. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw172.1551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alina Iovleva
- Internal Medicine, University Hospitals Case Medical Center, Cleveland, Ohio; Internal Medicine, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio
| | - Federico Perez
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
| | - Steve H. Marshall
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
| | | | - Michael R. Jacobs
- Case Western Reserve University/University Hospitals of Cleveland, Cleveland, Ohio
| | - Usha Stiefel
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Amy Ray
- Infectious Diseases, University Hospitals Case Medical Center, Cleveland, Ohio
| | - Robert A. Bonomo
- Pharmacology, Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio
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Logan LK, Hujer AM, Marshall SH, Domitrovic TN, Rudin SD, Scaggs FA, Zheng X, Qureshi NK, Hayden MK, Karadkhele A, Hayani KC, Jacobs NM, Bonomo RA. Multi-Center Study of the Molecular Epidemiology of Beta-Lactam Resistance in Enterobacteriaceae From Chicago Area Children: A Continuing Update. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw194.95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Latania K. Logan
- Pediatrics, Rush University Medical Center, Chicago, Illinois
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Rush Medical College, Chicago, Illinois
| | - Andrea M. Hujer
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Case Western Reserve University, Cleveland, Ohio
| | - Steve H. Marshall
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
| | | | | | | | - Xiaotian Zheng
- Microbiology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
- Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | - Mary K. Hayden
- Rush Medical College, Chicago, Illinois
- Internal Medicine (Infectious Diseases) and Pathology, Rush University Medical Center, Chicago, Illinois
| | | | - Karen C. Hayani
- Pediatrics, University of Illinois at Chicago, Chicago, Illinois
| | - Norman M. Jacobs
- Pediatrics, Cook County Health and Hospital Systems, Chicago, Illinois
| | - Robert A. Bonomo
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Pharmacology, Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio
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Domitrovic TN, Hujer AM, Perez F, Marshall SH, Hujer KM, Woc-Colburn LE, Parta M, Bonomo RA. Multidrug Resistant Pseudomonas aeruginosa Causing Prosthetic Valve Endocarditis: A Genetic-Based Chronicle of Evolving Antibiotic Resistance. Open Forum Infect Dis 2016; 3:ofw188. [PMID: 29057280 PMCID: PMC5091635 DOI: 10.1093/ofid/ofw188] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/30/2016] [Indexed: 11/12/2022] Open
Abstract
A rare case of MDR P. aeruginosa causing PVE is analyzed at the genetic level with the goal of understanding acquired resistance mechanisms. The molecular basis of evolving antibiotic resistance gives clinicians insight into the nature of persistent P. aeruginosa infections. Background. Successful treatment of infections caused by multidrug-resistant (MDR) Pseudomonas aeruginosa is thwarted by the emergence of antibiotic resistance and biofilm formation on prosthetic devices. Our aims were to decipher the molecular basis of resistance in a unique case of prosthetic valve endocarditis (PVE) caused by MDR P. aeruginosa. Methods. Five sequential MDR P. aeruginosa blood isolates collected during a 7-month period were recovered from a patient suffering from PVE previously exposed to β-lactam antibiotics. Minimum inhibitory concentrations (MICs) of several classes of antibiotics were used to indicate clinical resistance characteristics; relatedness of the isolates was determined using multilocus sequence typing and repetitive sequence-based polymerase chain reaction. Amplification and sequencing of regulatory and resistance genes was performed. Results. All isolates belonged to ST 298, possessed blaPDC-16, and were resistant to fluoroquinolones and carbapenems. In the course of therapy, we observed a >2-fold increase in cephalosporin resistance (4 µg/mL to >16 µg/mL). Sequencing of the AmpC regulator, ampR, revealed a D135N point mutation in cephalosporin-resistant isolates. Common carbapenemase genes were not identified. All isolates demonstrated a premature stop codon at amino acid 79 of the outer membrane protein OprD and mutations in the quinolone resistance-determining regions of gyrA and parC. Point mutations in nalC, an efflux pump regulator, were also observed. Conclusions. In this analysis, we chart the molecular evolution of β-lactam resistance in a case of PVE. We show that mutations in regulatory genes controlling efflux and cephalosporinase production contributed to the MDR phenotype.
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Affiliation(s)
- T Nicholas Domitrovic
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Andrea M Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Federico Perez
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Steven H Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center
| | - Kristine M Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | - Mark Parta
- Baylor College of Medicine, Houston, Texas
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio
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Evans S, Kreiswirth B, Fowler V, Chambers H, Patel R, Hujer AM, Perez F, Bonomo RA. Reply to Lesho and Clifford. Clin Infect Dis 2016; 63:571-2. [PMID: 27225238 DOI: 10.1093/cid/ciw336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/08/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Scott Evans
- Center for Biostatistics in AIDS Research and the Department of Biostatistics, Harvard University, Boston, Massachusetts
| | - Barry Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Vance Fowler
- Duke Clinical Research Institute, Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Henry Chambers
- University of California, San Francisco General Hospital
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine Louis Stokes Cleveland Department of Veterans Affairs Medical Center
| | - Federico Perez
- Department of Medicine, Case Western Reserve University School of Medicine Louis Stokes Cleveland Department of Veterans Affairs Medical Center
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine Louis Stokes Cleveland Department of Veterans Affairs Medical Center Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio
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