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Mukomena PN, Simuunza M, Munsaka S, Kwenda G, Bumbangi F, Yamba K, Kabwe J, Kayembe JM, Muma JB. Antimicrobial resistance profiles of and associated risk factors for Pseudomonas aeruginosa nosocomial infection among patients at two tertiary healthcare facilities in Lusaka and Copperbelt Provinces, Zambia. JAC Antimicrob Resist 2024; 6:dlae139. [PMID: 39286817 PMCID: PMC11403203 DOI: 10.1093/jacamr/dlae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/28/2024] [Indexed: 09/19/2024] Open
Abstract
Background Antimicrobial resistance (AMR) of pathogens such as Pseudomonas aeruginosa is among the top 10 threats to global health. However, clinical and molecular data are scarce in Zambia. We, therefore, evaluated the AMR profiles of P. aeruginosa nosocomial infections (NIs). Methods A year-long hospital-based cross-sectional study was conducted at two large tertiary-level hospitals in Zambia. Patients with current or previous hospital contact were screened for NIs. The current study focused on patients diagnosed with P. aeruginosa NIs. Clinical specimens were collected for bacteriological culture, and PCR amplification of 16S rRNA gene fragments was performed on pure isolates. Hospital or NIs were defined as infections that arise during hospitalization, occurring at least 48 h after admission. The Kirby-Bauer's disk diffusion method was used to evaluate antibiotic resistance patterns. The association between AMR and risk factors was analysed using the χ2 test. Results Eight hundred and forty-one patients were screened, and clinical specimens were collected and analysed. Of them, 116 (13.7%) were diagnosed with P. aeruginosa NIs. The participants' ages ranged from 15 to 98 years, with a mean of 51 (SD ± 18). Catheter-associated urinary tract infections (57%) were the most common, followed by pressure sores (38.7%). P. aeruginosa isolates were primarily susceptible to amikacin, which had the highest resistance to FEP. We observed a high prevalence of multidrug resistance (73.6%). The AMR was associated with carbapenem-hydrolysing β-lactamase gene blaOXA-51 and surgical care. Conclusions This study has demonstrated that multidrug-resistant P. aeruginosa is prevalent in hospitals in Zambia's Lusaka and Ndola districts and possibly countrywide.
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Affiliation(s)
- Patrice Ntanda Mukomena
- Department of Medicine, School of Medicine, Eden University, Lusaka, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Martin Simuunza
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Flavien Bumbangi
- Department of Medicine, School of Medicine, Eden University, Lusaka, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Kaunda Yamba
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Josephine Kabwe
- Department of Medicine, School of Medicine, Eden University, Lusaka, Zambia
| | - Jean-Marie Kayembe
- Department of Medicine, School of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - John Bwalya Muma
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
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2
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Singh A, Tanwar M, Singh TP, Sharma S, Sharma P. An escape from ESKAPE pathogens: A comprehensive review on current and emerging therapeutics against antibiotic resistance. Int J Biol Macromol 2024; 279:135253. [PMID: 39244118 DOI: 10.1016/j.ijbiomac.2024.135253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024]
Abstract
The rise of antimicrobial resistance has positioned ESKAPE pathogens as a serious global health threat, primarily due to the limitations and frequent failures of current treatment options. This growing risk has spurred the scientific community to seek innovative antibiotic therapies and improved oversight strategies. This review aims to provide a comprehensive overview of the origins and resistance mechanisms of ESKAPE pathogens, while also exploring next-generation treatment strategies for these infections. In addition, it will address both traditional and novel approaches to combating antibiotic resistance, offering insights into potential new therapeutic avenues. Emerging research underscores the urgency of developing new antimicrobial agents and strategies to overcome resistance, highlighting the need for novel drug classes and combination therapies. Advances in genomic technologies and a deeper understanding of microbial pathogenesis are crucial in identifying effective treatments. Integrating precision medicine and personalized approaches could enhance therapeutic efficacy. The review also emphasizes the importance of global collaboration in surveillance and stewardship, as well as policy reforms, enhanced diagnostic tools, and public awareness initiatives, to address resistance on a worldwide scale.
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Affiliation(s)
- Anamika Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mansi Tanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - T P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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3
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Chopra A, Bhuvanagiri G, Natu K, Chopra A. Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review. Mol Oral Microbiol 2024. [PMID: 39224035 DOI: 10.1111/omi.12483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/05/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences capable of editing a host genome sequence. CRISPR and its specific CRISPR-associated (Cas) protein complexes have been adapted for various applications. These include activating or inhibiting specific genetic sequences or acting as molecular scissors to cut and modify the host DNA precisely. CRISPR-Cas systems are also naturally present in many oral bacteria, where they aid in nutrition, biofilm formation, inter- and intraspecies communication (quorum sensing), horizontal gene transfer, virulence, inflammation modulation, coinfection, and immune response evasion. It even functions as an adaptive immune system, defending microbes against invading viruses and foreign genetic elements from other bacteria by targeting and degrading their DNA. Recently, CRISPR-Cas systems have been tested as molecular editing tools to manipulate specific genes linked with periodontal disease (such as periodontitis) and as novel methods of delivering antimicrobial agents to overcome antimicrobial resistance. With the rapidly increasing role of CRISPR in treating inflammatory diseases, its application in periodontal disease is also becoming popular. Therefore, this review aims to discuss the different types of CRISPR-Cas in oral microbes and their role in periodontal disease pathogenesis and precision periodontal therapy.
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Affiliation(s)
- Aditi Chopra
- Department of Periodontology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Geeta Bhuvanagiri
- Department of Periodontology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kshitija Natu
- School of Dentistry, University of California, Los Angeles, California, USA
| | - Avneesh Chopra
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité-University Medicine Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
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4
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Ghiglione B, Rodríguez MM, Penzotti P, Bethel CR, Gutkind G, Bonomo RA, Klinke S, Power P. Crystal structure of the class A extended-spectrum β-lactamase CTX-M-96 in complex with relebactam at 1.03 Angstrom resolution. Antimicrob Agents Chemother 2024; 68:e0172123. [PMID: 38990013 PMCID: PMC11304709 DOI: 10.1128/aac.01721-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/30/2024] [Indexed: 07/12/2024] Open
Abstract
The use of β-lactam/β-lactamase inhibitors constitutes an important strategy to counteract β-lactamases in multidrug-resistant (MDR) Gram-negative bacteria. Recent reports have described ceftazidime-/avibactam-resistant isolates producing CTX-M variants with different amino acid substitutions (e.g., P167S, L169Q, and S130G). Relebactam (REL) combined with imipenem has proved very effective against Enterobacterales producing ESBLs, serine-carbapenemases, and AmpCs. Herein, we evaluated the inhibitory efficacy of REL against CTX-M-96, a CTX-M-15-type variant. The CTX-M-96 structure was obtained in complex with REL at 1.03 Å resolution (PDB 8EHH). REL was covalently bound to the S70-Oγ atom upon cleavage of the C7-N6 bond. Compared with apo CTX-M-96, binding of REL forces a slight displacement of the deacylating water inwards the active site (0.81 Å), making the E166 and N170 side chains shift to create a proper hydrogen bonding network. Binding of REL also disturbs the hydrophobic patch formed by Y105, P107, and Y129, likely due to the piperidine ring of REL that creates clashes with these residues. Also, a remarkable change in the positioning of the N104 sidechain is also affected by the piperidine ring. Therefore, differences in the kinetic behavior of REL against class A β-lactamases seem to rely, at least in part, on differences in the residues being involved in the association and stabilization of the inhibitor before hydrolysis. Our data provide the biochemical and structural basis for REL effectiveness against CTX-M-producing Gram-negative pathogens and essential details for further DBO design. Imipenem/REL remains an important choice for dealing with isolates co-producing CTX-M with other β-lactamases.
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Affiliation(s)
- Barbara Ghiglione
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Margarita Rodríguez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pedro Penzotti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Departments of Pharmacology, Biochemistry, Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Sebastián Klinke
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentin
| | - Pablo Power
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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5
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Chaves AC, Boa Ventura PDV, Pereira MS, da Silva BF, de Carvalho FJN, Costa RA, Lima BP, Maciel WC, Carneiro VA. Preliminary snapshot reveals a relationship between multidrug-resistance and biofilm production among enterobacteriaceae isolated from fecal samples of farm-raised poultry in ceará, Brazil. Microb Pathog 2024; 193:106778. [PMID: 38972366 DOI: 10.1016/j.micpath.2024.106778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 07/09/2024]
Abstract
Antimicrobial resistance and biofilm formation by microbial pathogens pose a significant challenge to poultry production systems due to the persistent risk of dissemination and compromise of bird health and productivity. In this context, the study aimed to investigate the occurrence of different multiresistance phenotypes and the biofilm-forming ability of Enterobacteriaceae isolated from broiler chicken excreta in poultry production units in Ceará, Brazil. Samples were collected from three distinct broiler breeding facilities and subjected to isolation, identification, antibiotic susceptibility testing, phenotypic screening for β-lactamases enzymes, and biofilm formation evaluation. Seventy-one strains were identified, being Escherichia coli (37 %) and Proteus mirabilis (32 %), followed by Klebsiella pneumoniae (11 %), Providencia stuartii (9 %), Klebsiella aerogenes (6 %), Alcaligenes faecalis (4 %), and Salmonella sp. (1 %). A significant proportion (87 %) of multiresistant strains were detected. For the phenotypic evaluation of β-lactamases production, strains with resistance to second and third-generation cephalosporins and carbapenems were tested. About 4 of 6 and 10 of 26 were positive for inducible chromosomal AmpC β-lactamase and extended-spectrum β-lactamase (ESBL), respectively. Regarding biofilm formation, it was observed that all MDR strains were capable of forming biofilm. In this sense the potential of these MDR bacteria to develop biofilms becomes a significant concern, representing a real threat to both human and animal health, as biofilms offer stability, antimicrobial protection, and facilitate genetic transfer.
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Affiliation(s)
- Andrey Carvalho Chaves
- Center for Bioprospecting and Applied Molecular Experimentation (NUBEM), University Center INTA - UNINTA, Sobral, 62.050-100, Brazil; Laboratory for Avian Pathological Studies (LABEO), Faculty of Veterinary Medicine, State University of Ceará - UECE, Fortaleza, 60.714.903, Brazil
| | - Priscila de Vasconcelos Boa Ventura
- Center for Bioprospecting and Applied Molecular Experimentation (NUBEM), University Center INTA - UNINTA, Sobral, 62.050-100, Brazil; Laboratory for Avian Pathological Studies (LABEO), Faculty of Veterinary Medicine, State University of Ceará - UECE, Fortaleza, 60.714.903, Brazil
| | - Mainara Saraiva Pereira
- Center for Bioprospecting and Applied Molecular Experimentation (NUBEM), University Center INTA - UNINTA, Sobral, 62.050-100, Brazil
| | - Benise Ferreira da Silva
- Center for Bioprospecting and Applied Molecular Experimentation (NUBEM), University Center INTA - UNINTA, Sobral, 62.050-100, Brazil; Northeast Network of Biotechnology Program (RENORBIO), State University of Ceará, Campus Itaperi, Fortaleza, 60714-903, Brazil
| | - Felipe José Negreiros de Carvalho
- Center for Bioprospecting and Applied Molecular Experimentation (NUBEM), University Center INTA - UNINTA, Sobral, 62.050-100, Brazil
| | - Renata Albuquerque Costa
- Center for Bioprospecting and Applied Molecular Experimentation (NUBEM), University Center INTA - UNINTA, Sobral, 62.050-100, Brazil
| | - Bruno Pessoa Lima
- Laboratory for Avian Pathological Studies (LABEO), Faculty of Veterinary Medicine, State University of Ceará - UECE, Fortaleza, 60.714.903, Brazil
| | - William Cardoso Maciel
- Laboratory for Avian Pathological Studies (LABEO), Faculty of Veterinary Medicine, State University of Ceará - UECE, Fortaleza, 60.714.903, Brazil
| | - Victor Alves Carneiro
- Center for Bioprospecting and Applied Molecular Experimentation (NUBEM), University Center INTA - UNINTA, Sobral, 62.050-100, Brazil.
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6
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Grigorenko VG, Krivitskaya AV, Khrenova MG, Rubtsova MY, Presnova GV, Andreeva IP, Serova OV, Egorov AM. Saturation Mutagenesis and Molecular Modeling: The Impact of Methionine 182 Substitutions on the Stability of β-Lactamase TEM-1. Int J Mol Sci 2024; 25:7691. [PMID: 39062934 PMCID: PMC11276661 DOI: 10.3390/ijms25147691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Serine β-lactamase TEM-1 is the first β-lactamase discovered and is still common in Gram-negative pathogens resistant to β-lactam antibiotics. It hydrolyzes penicillins and cephalosporins of early generations. Some of the emerging TEM-1 variants with one or several amino acid substitutions have even broader substrate specificity and resistance to known covalent inhibitors. Key amino acid substitutions affect catalytic properties of the enzyme, and secondary mutations accompany them. The occurrence of the secondary mutation M182T, called a "global suppressor", has almost doubled over the last decade. Therefore, we performed saturating mutagenesis at position 182 of TEM-1 to determine the influence of this single amino acid substitution on the catalytic properties, thermal stability, and ability for thermoreactivation. Steady-state parameters for penicillin, cephalothin, and ceftazidime are similar for all TEM-1 M182X variants, whereas melting temperature and ability to reactivate after incubation at a higher temperature vary significantly. The effects are multidirectional and depend on the particular amino acid at position 182. The M182E variant of β-lactamase TEM-1 demonstrates the highest residual enzymatic activity, which is 1.5 times higher than for the wild-type enzyme. The 3D structure of the side chain of residue 182 is of particular importance as observed from the comparison of the M182I and M182L variants of TEM-1. Both of these amino acid residues have hydrophobic side chains of similar size, but their residual activity differs by three-fold. Molecular dynamic simulations add a mechanistic explanation for this phenomenon. The important structural element is the V159-R65-E177 triad that exists due to both electrostatic and hydrophobic interactions. Amino acid substitutions that disturb this triad lead to a decrease in the ability of the β-lactamase to be reactivated.
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Affiliation(s)
- Vitaly G. Grigorenko
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.G.G.); (M.Y.R.); (G.V.P.); (I.P.A.); (A.M.E.)
| | - Alexandra V. Krivitskaya
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Maria G. Khrenova
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.G.G.); (M.Y.R.); (G.V.P.); (I.P.A.); (A.M.E.)
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Maya Yu. Rubtsova
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.G.G.); (M.Y.R.); (G.V.P.); (I.P.A.); (A.M.E.)
| | - Galina V. Presnova
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.G.G.); (M.Y.R.); (G.V.P.); (I.P.A.); (A.M.E.)
| | - Irina P. Andreeva
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.G.G.); (M.Y.R.); (G.V.P.); (I.P.A.); (A.M.E.)
| | - Oxana V. Serova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia;
| | - Alexey M. Egorov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.G.G.); (M.Y.R.); (G.V.P.); (I.P.A.); (A.M.E.)
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7
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Ma Z, Liu R, Wang J, Yu T, Zou Y, Chen F, Cui C, Yang H, Xie H. Rapid Detection of Bacterial Resistance to β-Lactam Antibiotics with a Relay-Response Chemiluminescence Assay. ACS Infect Dis 2024; 10:1970-1979. [PMID: 38819944 DOI: 10.1021/acsinfecdis.3c00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Bacterial resistance caused by β-lactamases has been a major threat to public health around the world, seriously weakening the efficacy of β-lactam antibiotics, the most widely used therapeutic agents against infectious diseases. To detect the bacterial resistance to β-lactam antibiotics, particularly specific type of β-lactam antibiotics, in a rapid manner, we report herein a relay-response chemiluminescence assay. This assay mainly consists of two reagents: a β-lactam-caged thiophenol and a thiophenol-sensitive chemiluminescence reporter, both of which are synthetically feasible. The selective hydrolysis of β-lactam by β-lactamase leads to the releasing of free thiophenol, which then triggers the emission of a chemiluminescence signal in a relay manner. Three thiophenol-caged β-lactams, structural analogues of cephalothin, cefotaxime, and meropenem, respectively, have been synthesized. And the application of this assay with these analogues of β-lactam antibiotics allows fast detection of β-lactamase-expressing resistant bacteria and, more impressively, provides detailed information on the resistant scope of bacteria.
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Affiliation(s)
- Zheng Ma
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Runqiu Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jie Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Tao Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yingqiu Zou
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Fangfang Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Cui Cui
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Huixin Yang
- Clinical Laboratory, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian 362000, China
| | - Hexin Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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8
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Kang SJ, Kim DH, Lee BJ. Metallo-β-lactamase inhibitors: A continuing challenge for combating antibiotic resistance. Biophys Chem 2024; 309:107228. [PMID: 38552402 DOI: 10.1016/j.bpc.2024.107228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/18/2024] [Accepted: 03/23/2024] [Indexed: 04/22/2024]
Abstract
β-lactam antibiotics are the most successful and commonly used antibacterial agents, but the emergence of resistance to these drugs has become a global health threat. The expression of β-lactamase enzymes produced by pathogens, which hydrolyze the amide bond of the β-lactam ring, is the major mechanism for bacterial resistance to β-lactams. In particular, among class A, B, C and D β-lactamases, metallo-β-lactamases (MBLs, class B β-lactamases) are considered crucial contributors to resistance in gram-negative bacteria. To combat β-lactamase-mediated resistance, great efforts have been made to develop β-lactamase inhibitors that restore the activity of β-lactams. Some β-lactamase inhibitors, such as diazabicyclooctanes (DBOs) and boronic acid derivatives, have also been approved by the FDA. Inhibitors used in the clinic can inactivate mostly serine-β-lactamases (SBLs, class A, C, and D β-lactamases) but have not been effective against MBLs until now. In order to develop new inhibitors particularly for MBLs, various attempts have been suggested. Based on structural and mechanical studies of MBL enzymes, several MBL inhibitor candidates, including taniborbactam in phase 3 and xeruborbactam in phase 1, have been introduced in recent years. However, designing potent inhibitors that are effective against all subclasses of MBLs is still extremely challenging. This review summarizes not only the types of β-lactamase and mechanisms by which β-lactam antibiotics are inactivated, but also the research finding on β-lactamase inhibitors targeting these enzymes. These detailed information on β-lactamases and their inhibitors could give valuable information for novel β-lactamase inhibitors design.
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Affiliation(s)
- Su-Jin Kang
- College of Pharmacy, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Do-Hee Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea; Mastermeditech Ltd., Seoul 07793, Republic of Korea.
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9
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Jeong BG, Kim MY, Jeong CS, Do H, Hwang J, Lee JH, Cha SS. Characterization of the extended substrate spectrum of the class A β-lactamase CESS-1 from Stenotrophomonas sp. and structure-based investigation into its substrate preference. Int J Antimicrob Agents 2024; 63:107171. [PMID: 38588869 DOI: 10.1016/j.ijantimicag.2024.107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 03/10/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES Stenotrophomonas spp. intrinsically resistant to many β-lactam antibiotics are found throughout the environment. CESS-1 identified in Stenotrophomonas sp. KCTC 12332 is an uncharacterized class A β-lactamase. The goal of this study was to reveal biochemical and structural characteristics of CESS-1. METHODS The hydrolytic activities of CESS-1 towards penicillins (penicillin G and ampicillin), cephalosporins (cephalexin, cefaclor, and cefotaxime), and carbapenems (imipenem and meropenem) was spectrophotometrically monitored. Structural information on E166Q mutants of CESS-1 acylated by cefaclor, cephalexin, or ampicillin were determined by X-ray crystallography. RESULTS CESS-1 displayed hydrolytic activities toward penicillins and cephalosporins, with negligible activity toward carbapenems. Although cefaclor, cephalexin, and ampicillin have similar structures with identical R1 side chains, the catalytic parameters of CESS-1 toward them were distinct. The kcat values for cefaclor, cephalexin, and ampicillin were 1249.6 s-1, 204.3 s-1, and 69.8 s-1, respectively, with the accompanying KM values of 287.6 μM, 236.7 μM, and 28.8 μM, respectively. CONCLUSIONS CESS-1 was able to discriminate between cefaclor and cephalexin with a single structural difference at C3 position: -Cl (cefaclor) and -CH3 (cephalexin). Structural comparisons among three E166Q mutants of CESS-1 acylated by cefaclor, cephalexin, or ampicillin, revealed that cooperative positional changes in the R1 side chain of substrates and their interaction with the β5-β6 loop affect the distance between Asn170 and the deacylating water at the acyl-enzyme intermediate state. This is directly associated with the differential hydrolytic activities of CESS-1 toward the three structurally similar β-lactam antibiotics.
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Affiliation(s)
- Bo-Gyeong Jeong
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Myeong-Yeon Kim
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Chang-Sook Jeong
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Hackwon Do
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Jisub Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Jun Hyuck Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea.
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea.
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10
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Benin BM, Hillyer T, Aguirre N, Sham YY, Willard B, Shin WS. Carbapenem-induced β-lactamase-isoform expression trends in Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596663. [PMID: 38853951 PMCID: PMC11160735 DOI: 10.1101/2024.05.30.596663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAb) is an urgent bacterial threat to public health, with only a few treatment options and a >50% fatality rate. Although several resistance mechanisms are understood, the appearance of these mutations is generally considered stochastic. Recent reports have, however, begun to challenge this assumption. Here, we demonstrate that independent samples of Ab, exposed to different carbapenems with escalating concentrations, show concentration- and carbapenem-dependent trends in β-lactamase-isoform expression. This result, based on the isoforms identified through label-free-quantification LC-MS/MS measurements of cell-free, gel-separated β-lactamases, suggests that the appearance of antibiotic resistance may be somewhat non-stochastic. Specifically, several minor AmpC/ADC β-lactamase-isoforms were found to exhibit both dose- and carbapenem-dependent expression, suggesting the possibility of non-stochastic mutations. Additionally, these also have high sequence similarity to major expressed isoforms, indicating a potential path over which resistance occurred in independent samples. Antibiotic resistance maybe somewhat antibiotic-directed by a hitherto unknown mechanism and further investigation may lead to new strategies for mitigating antibiotic resistance. Teaser The emergence of antibiotic-resistant β-lactamase proteins from mutations may exhibit patterns based on specific antibiotics.
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11
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Baral R, Tuladhar R, Manandhar S, Singh A, Sherchan S. Detection of bla KPC gene among carbapenemase producing Klebsiella pneumoniae isolated from different clinical specimens at tertiary care hospital of Nepal. BMC Microbiol 2024; 24:144. [PMID: 38664608 PMCID: PMC11044503 DOI: 10.1186/s12866-024-03301-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae infections have become a major cause of hospital acquired infection worldwide with the increased rate of acquisition of resistance to antibiotics. Carbapenem resistance mainly among Gram negative is an ongoing problem which causes serious outbreaks dramatically limiting treatment options. This prospective cross-sectional study was designed to detect blaKPC gene from carbapenem resistant K. pneumoniae. MATERIALS AND METHODS A totally of 1118 different clinical specimens were screened and confirmed for KPC producing K. pneumoniae phenotypically using Meropenem (10 μg) disc. The blaKPC gene was amplified from the isolates of K. pneumoniae to detect the presence of this gene. RESULT Of the total samples processed, 18.6% (n = 36) were K. pneumoniae and among 36 K. pneumoniae, 61.1% (n = 22/36) were meropenem resistant. This study demonstrated the higher level of MDR 91.7% (n = 33) and KPC production 47.2% (n = 17) among K. pneumoniae isolates. The blaKPC gene was detected in 8.3% (n = 3) of meropenem resistant isolates. CONCLUSION Since the study demonstrates the higher level of MDR and KPC producing K. pneumoniae isolates that has challenged the use of antimicrobial agents, continuous microbiology, and molecular surveillance to assist early detection and minimize the further dissemination of blaKPC should be initiated. We anticipate that the findings of this study will be useful in understanding the prevalence of KPC-producing K. pneumoniae in Nepal.
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Affiliation(s)
- Rakshya Baral
- Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal.
- Department of Biology, Morgan State University, Baltimore, USA.
| | - Reshma Tuladhar
- Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal
| | - Sarita Manandhar
- Department of Microbiology, Tri-Chandra Multiple Campus, Tribhuvan University, Kathmandu, Nepal
| | - Anjana Singh
- Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal
| | - Samendra Sherchan
- Department of Biology, Morgan State University, Baltimore, USA
- Department of Environmental Health Sciences, Tulane University, New Orleans, USA
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12
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Wen Z, Chen Y, Liu T, Han J, Jiang Y, Zhang K. Predicting Antibiotic Tolerance in hvKP and cKP Respiratory Infections Through Biofilm Formation Analysis and Its Resistance Implications. Infect Drug Resist 2024; 17:1529-1537. [PMID: 38650753 PMCID: PMC11033731 DOI: 10.2147/idr.s449712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Introduction Respiratory infections are a major global health concern, with Klebsiella pneumoniae standing out due to its evolving antibiotic resistance. This study compares the resistance profiles of hypervirulent Klebsiella pneumoniae (hvKP) and classical Klebsiella pneumoniae (cKP), aiming to shed light on their clinical implications. Methods We analyzed 86 cases, comprising 42 hvKP and 44 cKP strains, using comprehensive antimicrobial susceptibility testing and clinical data evaluation to assess antibiotic tolerance and resistance mechanisms. Results Our findings reveal distinct resistance patterns between hvKP and cKP, highlighting the role of chromosomal mutations and plasmid-mediated gene transfer in conferring antibiotic resistance. Notably, hvKP strains exhibited unique resistance trends, including the production of extended-spectrum β-lactamases (ESBLs) and carbapenemases, differing from those of cKP. Discussion This research underscores the importance of continuous surveillance and the development of targeted therapies against antibiotic-resistant Klebsiella pneumoniae. It emphasizes the critical need for judicious antibiotic use and novel therapeutic approaches to combat respiratory infections caused by these increasingly resistant pathogens.
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Affiliation(s)
- Zhongwei Wen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Yiqiang Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Tangjuan Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Jiahui Han
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Yuting Jiang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Ke Zhang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
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13
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Miranda CD, Concha C, Hurtado L, Urtubia R, Rojas R, Romero J. Occurrence of Antimicrobial-Resistant Bacteria in Intestinal Contents of Wild Marine Fish in Chile. Antibiotics (Basel) 2024; 13:332. [PMID: 38667008 PMCID: PMC11047320 DOI: 10.3390/antibiotics13040332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024] Open
Abstract
Antimicrobial-resistant bacteria (ARB) from the intestinal contents of wild fish may have a relevant ecological significance and could be used as indicators of antimicrobial-resistance dissemination in natural bacterial populations in water bodies impacted by urban contamination. Thus, the occurrence of ARB in the intestinal contents of pelagic and demersal wild fishes captured in anthropogenic-impacted Coquimbo Bay in Chile was studied. Culturable counts of total and antimicrobial-resistant bacteria were determined by a spread plate method using Trypticase soy agar and R2A media, both alone and supplemented with the antimicrobials amoxicillin, streptomycin, florfenicol, oxytetracycline and ciprofloxacin, respectively. Heterotrophic plate counts of pelagic and demersal fishes ranged from 1.72 × 106 CFU g-1 to 3.62 × 109 CFU g-1, showing variable proportions of antimicrobial resistance. Representative antimicrobial-resistant isolates were identified by 16S rRNA gene sequencing, and isolates (74) from pelagic fishes mainly belonged to Pseudomonas (50.0%) and Shewanella (17.6%) genera, whereas isolates (68) from demersal fishes mainly belonged to Vibrio (33.8%) and Pseudomonas (26.5%) genera. Antimicrobial-resistant isolates were tested for susceptibility to 12 antimicrobials by an agar disk diffusion method, showing highest resistance to streptomycin (85.2%) and amoxicillin (64.8%), and lowest resistance to oxytetracycline (23.2%) and ciprofloxacin (0.7%). Only furazolidone and trimethoprim/sulfamethoxazole were statistically different (p < 0.05) in comparisons between isolates from pelagic and demersal wild fishes. Furthermore, an important number of these isolates carried plasmids (53.5%) and produced Extended-Spectrum-β-lactamases (ESBL) (16.9%), whereas the detection of Metallo-β-Lactamases and class 1-integron was rare. This study provides evidence that wild fish are important reservoirs and spreading-vehicles of ARB, carrying plasmids and producing ESBLs in Chilean marine environments.
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Affiliation(s)
- Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Christopher Concha
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Luz Hurtado
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Rocío Urtubia
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Jaime Romero
- Laboratorio de Biotecnología de los Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7830417, Chile;
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14
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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] [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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15
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Bakhtiyari N, Farajnia S, Ghasemali S, Farajnia S, Pormohammad A, Saeidvafa S. Strategies to Overcome Antimicrobial Resistance in Nosocomial Infections, A Review and Update. Infect Disord Drug Targets 2024; 24:e260124226226. [PMID: 38284691 DOI: 10.2174/0118715265276529231214105423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 01/30/2024]
Abstract
Nosocomial infections, also known as healthcare-associated infections, are a significant global concern due to their strong association with high mortality and morbidity in both developed and developing countries. These infections are caused by a variety of pathogens, particularly the ESKAPE group of bacteria, which includes the six pathogens Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These bacteria have demonstrated noteworthy resistance to different antibiotics. Antimicrobial resistance mechanisms can manifest in various forms, including restricting drug uptake, modifying drug targets, inactivating drugs, active drug efflux, and biofilm formation. Accordingly, various strategies have been developed to combat antibiotic-resistant bacteria. These strategies encompass the development of new antibiotics, the utilization of bacteriophages that specifically target these bacteria, antimicrobial combination therapy and the use of peptides or enzymes that target the genomes or essential proteins of resistant bacteria. Among promising approaches to overcome antibiotic resistance, the CRISPR/Cas system stands out and offers many advantages. This system enables precise and efficient editing of genetic material at specific locations in the genome. Functioning as a bacterial "adaptive immune system," the CRISPR/Cas system recognizes, degrades, and remembers foreign DNA sequences through the use of spacer DNA segments that are transcribed into CRISPR RNAs (crRNA). This paper has focused on nosocomial infections, specifically the pathogens involved in hospital infections, the mechanisms underlying bacterial resistance, and the strategies currently employed to address this issue. Special emphasis has been placed on the application of CRISPR/Cas technology for overcoming antimicrobial resistance.
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Affiliation(s)
- Nasim Bakhtiyari
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Samaneh Ghasemali
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sahar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Pormohammad
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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16
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Carvajal-Garcia J, Bracey H, Johnson AE, Hernandez Viera AJ, Egli M, Simsek EN, Jaremba EA, Kim K, Merrikh H. A small molecule that inhibits the evolution of antibiotic resistance. NAR MOLECULAR MEDICINE 2024; 1:ugae001. [PMID: 38911259 PMCID: PMC11188740 DOI: 10.1093/narmme/ugae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 06/25/2024]
Abstract
Antibiotic resistance rapidly develops against almost all available therapeutics. Therefore, searching for new antibiotics to overcome the problem of antibiotic resistance alone is insufficient. Given that antibiotic resistance can be driven by mutagenesis, an avenue for preventing it is the inhibition of mutagenic processes. We previously showed that the DNA translocase Mfd is mutagenic and accelerates antibiotic resistance development. Here, we present our discovery of a small molecule that inhibits Mfd-dependent mutagenesis, ARM-1 (anti-resistance molecule 1). We found ARM-1 using a high-throughput, small molecule, in vivo screen. Using biochemical assays, we characterized the mechanism by which ARM-1 inhibits Mfd. Critically, we found that ARM-1 reduces mutagenesis and significantly delays antibiotic resistance development across highly divergent bacterial pathogens. These results demonstrate that the mutagenic proteins accelerating evolution can be directly inhibited. Furthermore, our findings suggest that Mfd inhibition, alongside antibiotics, is a potentially effective approach for prevention of antibiotic resistance development during treatment of infections.
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Affiliation(s)
| | - Harrison Bracey
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Anna E Johnson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Esra N Simsek
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Emily A Jaremba
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Kwangho Kim
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Houra Merrikh
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
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17
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Enany S, Tartor YH, Kishk RM, Gadallah AM, Ahmed E, Magdeldin S. Proteomics and metabolomics analyses of Streptococcus agalactiae isolates from human and animal sources. Sci Rep 2023; 13:20980. [PMID: 38017083 PMCID: PMC10684508 DOI: 10.1038/s41598-023-47976-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023] Open
Abstract
Streptococcus agalactiae (S. agalactiae), group B Streptococcus (GBS), a major cause of infection in a wide variety of diseases, have been compared in different human and animal sources. We aimed to compare the bacterial proteome and metabolome profiles of human and animal S. agalactiae strains to delineate biological interactions relevant to infection. With the innovative advancement in mass spectrometry, a comparative result between both strains provided a solid impression of different responses to the host. For instance, stress-related proteins (Asp23/Gls24 family envelope stress response protein and heat shock protein 70), which play a role in the survival of GBS under extreme environmental conditions or during treatment, are highly expressed in human and animal strains. One human strain contains ꞵ-lactamase (serine hydrolase) and biofilm regulatory protein (lytR), which are important virulence regulators and potential targets for the design of novel antimicrobials. Another human strain contains the aminoglycosides-resistance bifunctional AAC/APH (A0A0U2QMQ5) protein, which confers resistance to almost all clinically used aminoglycosides. Fifteen different metabolites were annotated between the two groups. L-aspartic acid, ureidopropionic acid, adenosine monophosphate, L-tryptophan, and guanosine monophosphate were annotated at higher levels in human strains. Butyric acid, fumaric acid, isoleucine, leucine, and hippuric acid have been found in both human and animal strains. Certain metabolites were uniquely expressed in animal strains, with fold changes greater than 2. For example, putrescine modulates biofilm formation. Overall, this study provides biological insights into the substantial possible bacterial response reflected in its macromolecular production, either at the proteomic or metabolomic level.
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Affiliation(s)
- Shymaa Enany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, 41522, Egypt.
- Biomedical Research Department, Armed Force College of Medicine, Cairo, Egypt.
| | - Yasmine H Tartor
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, 44511, Egypt
| | - Rania M Kishk
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Ahmed M Gadallah
- Department of Obstetrics and Gynecology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Eman Ahmed
- Proteomics and Metabolomics Unit, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, 11441, Egypt
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Sameh Magdeldin
- Proteomics and Metabolomics Unit, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, 11441, Egypt
- Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
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18
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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] [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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19
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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] [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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20
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Darrah K, Albright S, Kumbhare R, Tsang M, Chen JK, Deiters A. Antisense Oligonucleotide Activation via Enzymatic Antibiotic Resistance Mechanism. ACS Chem Biol 2023; 18:2176-2182. [PMID: 37326511 PMCID: PMC10592181 DOI: 10.1021/acschembio.3c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
The structure and mechanism of the bacterial enzyme β-lactamase have been well-studied due to its clinical role in antibiotic resistance. β-Lactamase is known to hydrolyze the β-lactam ring of the cephalosporin scaffold, allowing a spontaneous self-immolation to occur. Previously, cephalosporin-based sensors have been developed to evaluate β-lactamase expression in both mammalian cells and zebrafish embryos. Here, we present a circular caged morpholino oligonucleotide (cMO) activated by β-lactamase-mediated cleavage of a cephalosporin motif capable of silencing the expression of T-box transcription factor Ta (tbxta), also referred to as no tail a (ntla), eliciting a distinct, observable phenotype. We explore the use of β-lactamase to elicit a biological response in aquatic embryos for the first time and expand the utility of cephalosporin as a cleavable linker beyond targeting antibiotic-resistant bacteria. The addition of β-lactamase to the current suite of enzymatic triggers presents unique opportunities for robust, orthogonal control over endogenous gene expression in a spatially resolved manner.
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Affiliation(s)
- Kristie
E. Darrah
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Savannah Albright
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rohan Kumbhare
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department
of Developmental Biology, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - James K. Chen
- Department
of Chemical and Systems Biology, Stanford
University School of Medicine, Stanford, California 94305, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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21
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Materon IC, Palzkill T. Structural biology of MCR-1-mediated resistance to polymyxin antibiotics. Curr Opin Struct Biol 2023; 82:102647. [PMID: 37399693 PMCID: PMC10527939 DOI: 10.1016/j.sbi.2023.102647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 07/05/2023]
Abstract
Polymyxins, a last resort antibiotic, target the outer membrane of pathogens and are used to address the increasing prevalence of multidrug-resistant Gram-negative bacteria. The plasmid-encoded enzyme MCR-1 confers polymyxin resistance to bacteria by modifying the outer membrane. Transferable resistance to polymyxins is a major concern; therefore, MCR-1 is an important drug target. In this review, we discuss recent structural and mechanistic aspects of MCR-1 function, its variants and homologs, and how they are relevant to polymyxin resistance. Specifically, we discuss work on polymyxin-mediated disruption of the outer and inner membranes, computational studies on the catalytic mechanism of MCR-1, mutagenesis and structural analysis concerning residues important for substrate binding in MCR-1, and finally, advancements in inhibitors targeting MCR-1.
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Affiliation(s)
- Isabel Cristina Materon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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22
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Thakur M, Khushboo, Kumar Y, Yadav V, Pramanik A, Dubey KK. Understanding resistance acquisition by Pseudomonas aeruginosa and possible pharmacological approaches in palliating its pathogenesis. Biochem Pharmacol 2023; 215:115689. [PMID: 37481132 DOI: 10.1016/j.bcp.2023.115689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/03/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Pseudomonas aeruginosa can utilize various virulence factors necessary for host infection and persistence. These virulence factors include pyocyanin, proteases, exotoxins, 2-heptyl-4-hydroxyquinoline N-oxide (HQNO), phospholipases, and siderophores that enable the bacteria to cause severe infections in immunocompromised individuals. P. aeruginosa falls into the category of nosocomial pathogens that are typically resistant to available antibiotics and therapeutic approaches. P. aeruginosa bio-film formation is a major concern in hospitals because it can cause chronic infection and increase the risk of mortality. Therefore, the development of new strategies to disrupt biofilm formation and improve antibiotic efficacy for the treatment of P. aeruginosa infections is crucial. Anti-biofilm and anti-quorum sensing (QS) activity can be viewed as an anti-virulence approach to control the infectious nature of P. aeruginosa. Inhibition of QS and biofilm formation can be achieved through pharmacological approaches such as phytochemicals and essential oils, which have shown promising results in laboratory studies. A regulatory protein called LasR plays a key role in QS signaling to coordinate gene expression. Designing an antagonist molecule that mimics the natural autoinducer might be the best approach for LasR inhibition. Here we reviewed the mechanism behind antibiotic resistance and alternative approaches to combat the pathogenicity of P. aeruginosa.
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Affiliation(s)
- Mony Thakur
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Khushboo
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Yatin Kumar
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Avijit Pramanik
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Kashyap Kumar Dubey
- Biomanufacturing and Process Development Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi-67, India.
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23
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Mayorga-Ramos A, Zúñiga-Miranda J, Carrera-Pacheco SE, Barba-Ostria C, Guamán LP. CRISPR-Cas-Based Antimicrobials: Design, Challenges, and Bacterial Mechanisms of Resistance. ACS Infect Dis 2023; 9:1283-1302. [PMID: 37347230 PMCID: PMC10353011 DOI: 10.1021/acsinfecdis.2c00649] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Indexed: 06/23/2023]
Abstract
The emergence of antibiotic-resistant bacterial strains is a source of public health concern across the globe. As the discovery of new conventional antibiotics has stalled significantly over the past decade, there is an urgency to develop novel approaches to address drug resistance in infectious diseases. The use of a CRISPR-Cas-based system for the precise elimination of targeted bacterial populations holds promise as an innovative approach for new antimicrobial agent design. The CRISPR-Cas targeting system is celebrated for its high versatility and specificity, offering an excellent opportunity to fight antibiotic resistance in pathogens by selectively inactivating genes involved in antibiotic resistance, biofilm formation, pathogenicity, virulence, or bacterial viability. The CRISPR-Cas strategy can enact antimicrobial effects by two approaches: inactivation of chromosomal genes or curing of plasmids encoding antibiotic resistance. In this Review, we provide an overview of the main CRISPR-Cas systems utilized for the creation of these antimicrobials, as well as highlighting promising studies in the field. We also offer a detailed discussion about the most commonly used mechanisms for CRISPR-Cas delivery: bacteriophages, nanoparticles, and conjugative plasmids. Lastly, we address possible mechanisms of interference that should be considered during the intelligent design of these novel approaches.
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Affiliation(s)
- Arianna Mayorga-Ramos
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Johana Zúñiga-Miranda
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Saskya E. Carrera-Pacheco
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Carlos Barba-Ostria
- Escuela
de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170902, Ecuador
| | - Linda P. Guamán
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
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24
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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. MATERIALS TODAY (KIDLINGTON, ENGLAND) 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] [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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25
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Ashraf MV, Pant S, Khan MAH, Shah AA, Siddiqui S, Jeridi M, Alhamdi HWS, Ahmad S. Phytochemicals as Antimicrobials: Prospecting Himalayan Medicinal Plants as Source of Alternate Medicine to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:881. [PMID: 37375828 DOI: 10.3390/ph16060881] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Among all available antimicrobials, antibiotics hold a prime position in the treatment of infectious diseases. However, the emergence of antimicrobial resistance (AMR) has posed a serious threat to the effectiveness of antibiotics, resulting in increased morbidity, mortality, and escalation in healthcare costs causing a global health crisis. The overuse and misuse of antibiotics in global healthcare setups have accelerated the development and spread of AMR, leading to the emergence of multidrug-resistant (MDR) pathogens, which further limits treatment options. This creates a critical need to explore alternative approaches to combat bacterial infections. Phytochemicals have gained attention as a potential source of alternative medicine to address the challenge of AMR. Phytochemicals are structurally and functionally diverse and have multitarget antimicrobial effects, disrupting essential cellular activities. Given the promising results of plant-based antimicrobials, coupled with the slow discovery of novel antibiotics, it has become highly imperative to explore the vast repository of phytocompounds to overcome the looming catastrophe of AMR. This review summarizes the emergence of AMR towards existing antibiotics and potent phytochemicals having antimicrobial activities, along with a comprehensive overview of 123 Himalayan medicinal plants reported to possess antimicrobial phytocompounds, thus compiling the existing information that will help researchers in the exploration of phytochemicals to combat AMR.
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Affiliation(s)
- Mohammad Vikas Ashraf
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Shreekar Pant
- Centre for Biodiversity Studies, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - M A Hannan Khan
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Ali Asghar Shah
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Sazada Siddiqui
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | - Mouna Jeridi
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | | | - Shoeb Ahmad
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
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26
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Qi Z, Jin S, Guo X, Tong H, Ren N, You S. Distribution and transmission of β-lactamase resistance genes in meal-to-milk chain on dairy farm. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 331:121831. [PMID: 37209898 DOI: 10.1016/j.envpol.2023.121831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 05/22/2023]
Abstract
Antibiotics have been widely used in animal husbandry, which leads to high risk of food-borne transfer of antibiotic resistance genes (ARGs). The present study investigated the distribution of β-lactamase resistance genes (β-RGs) on dairy farm in the Songnen Plain of western Heilongjiang Province, China, to provide mechanistic insights into food-borne transmission of β-RGs through "meal-to-milk" chain under practically relevant circumstances. The results demonstrated that the abundance of β-RGs (91%) was much higher than that of other ARGs in the livestock farms. The blaTEM exhibited the content as high as 94.55% among all ARGs, and higher than 98% blaTEM was detected in meal, water and milk sample. The metagenomic taxonomy analysis indicated that the blaTEM should be carried by tnpA-04 (7.04%) and tnpA-03 (1.48%) hosted in Pseudomonas genus (15.36%) and Pantoea (29.02%) genus. Both tnpA-04 and tnpA-03 in the milk sample were identified to be the key mobile genetic elements (MGEs) responsible for transferring blaTEM along the "meal-manure-soil-surface water-milk" chain. The ARGs transfer across ecological boundaries underscored the need to evaluate potential dissemination of high-risk Proteobacteria and Bacteroidetes carried by humans and animals. They were capable of producing expanded-spectrum β-lactamases (ESBLs) and destroying commonly used antibiotics, leading to possible risk of food-borne horizontal transmission of ARGs. This study not only has important environmental implications for identifying the pathway for ARGs transfer, but also highlights the demand for appropriate policy toward safe regulation of dairy farm and husbandry products.
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Affiliation(s)
- Zheng Qi
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China
| | - Shuhan Jin
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China
| | - Xiaorui Guo
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China
| | - Hailong Tong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Shijie You
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China.
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27
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Smith CA, Stewart NK, Toth M, Quan P, Buynak JD, Vakulenko SB. The C5α-Methyl-Substituted Carbapenem NA-1-157 Exhibits Potent Activity against Klebsiella spp. Isolates Producing OXA-48-Type Carbapenemases. ACS Infect Dis 2023; 9:1123-1136. [PMID: 37130087 PMCID: PMC10722881 DOI: 10.1021/acsinfecdis.3c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The wide spread of carbapenem-hydrolyzing β-lactamases in Gram-negative bacteria has diminished the utility of the last-resort carbapenem antibiotics, significantly narrowing the available therapeutic options. In the Enterobacteriaceae family, which includes many important clinical pathogens such as Klebsiella pneumoniae and Escherichia coli, production of class D β-lactamases from the OXA-48-type family constitutes the major mechanism of resistance to carbapenems. To address the public health threat posed by these enzymes, novel, effective therapeutics are urgently needed. Here, we report evaluation of a novel, C5α-methyl-substituted carbapenem, NA-1-157, and show that its MICs against bacteria producing OXA-48-type enzymes were reduced by 4- to 32-fold when compared to meropenem. When combined with commercial carbapenems, the potency of NA-1-157 was further enhanced, resulting in target potentiation concentrations ranging from 0.125 to 2 μg/mL. Kinetic studies demonstrated that the compound is poorly hydrolyzed by OXA-48, with a catalytic efficiency 30- to 50-fold lower than those of imipenem and meropenem. Acylation of OXA-48 by NA-1-157 was severely impaired, with a rate 10,000- to 36,000-fold slower when compared to the commercial carbapenems. Docking, molecular dynamics, and structural studies demonstrated that the presence of the C5α-methyl group in NA-1-157 creates steric clashes within the active site, leading to differences in the position and the hydrogen-bonding pattern of the compound, which are incompatible with efficient acylation. This study demonstrates that NA-1-157 is a promising novel carbapenem for treatment of infections caused by OXA-48-producing bacterial pathogens.
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Affiliation(s)
- Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California 94025, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Nichole K Stewart
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Pojun Quan
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - John D Buynak
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Sergei B Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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28
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Bognanni N, Brisdelli F, Piccirilli A, Basile L, La Piana L, Di Bella S, Principe L, Vecchio G, Perilli M. New polyimidazole ligands against subclass B1 metallo-β-lactamases: Kinetic, microbiological, docking analysis. J Inorg Biochem 2023; 242:112163. [PMID: 36842244 DOI: 10.1016/j.jinorgbio.2023.112163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/10/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023]
Abstract
Beta-lactam antibiotics are one of the most commonly used drug classes in managing bacterial infections. However, their use is threatened by the alarming phenomenon of antimicrobial resistance, which represents a worldwide health concern. Given the continuous spread of metallo-β-lactamases (MBLs) producing pathogens, the need to discover broad-spectrum β-lactamase inhibitors is increasingly growing. A series of zinc chelators have been synthesized and investigated for their ability to hamper the Zn-ion network of interactions in the active site of MBLs. We assessed the inhibitory activity of new polyimidazole ligands N,N'-bis((imidazol-4-yl)methyl)-ethylenediamine, N,N,N'-tris((imidazol-4-yl)methyl)-ethylenediamine, N,N,N,N'-tetra((imidazol-4-yl-methyl)-ethylenediamine toward three different subclasses B1 MBLs: VIM-1, NDM-1 and IMP-1 by in vitro assays. The activity of known zinc chelators such as 1,4,7,10,13-Pentaazacyclopentadecane, 1,4,8,11-Tetraazacyclotetradecane and 1,4,7,10-Tetraazacyclododecane-1,4,7,10-tetraacetic acid was also assessed. Moreover, a molecular docking study was carried to gain insight into the interaction mode of the most active ligands.
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Affiliation(s)
- Noemi Bognanni
- Dipartimento di Scienze Chimiche, University of Catania, V.le A. Doria 6, 95122 Catania, Italy
| | - Fabrizia Brisdelli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Livia Basile
- Dipartimento di Scienze Chimiche, University of Catania, V.le A. Doria 6, 95122 Catania, Italy
| | - Luana La Piana
- Dipartimento di Scienze Chimiche, University of Catania, V.le A. Doria 6, 95122 Catania, Italy
| | - Stefano Di Bella
- Clinical Department of Medical, Surgical and Health Sciences, University of Trieste, 34129 Trieste, Italy
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, "S. Giovanni di Dio" Hospital, 88900 Crotone, Italy
| | - Graziella Vecchio
- Dipartimento di Scienze Chimiche, University of Catania, V.le A. Doria 6, 95122 Catania, Italy.
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
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Baran A, Kwiatkowska A, Potocki L. Antibiotics and Bacterial Resistance-A Short Story of an Endless Arms Race. Int J Mol Sci 2023; 24:ijms24065777. [PMID: 36982857 PMCID: PMC10056106 DOI: 10.3390/ijms24065777] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Despite the undisputed development of medicine, antibiotics still serve as first-choice drugs for patients with infectious disorders. The widespread use of antibiotics results from a wide spectrum of their actions encompassing mechanisms responsible for: the inhibition of bacterial cell wall biosynthesis, the disruption of cell membrane integrity, the suppression of nucleic acids and/or proteins synthesis, as well as disturbances of metabolic processes. However, the widespread availability of antibiotics, accompanied by their overprescription, acts as a double-edged sword, since the overuse and/or misuse of antibiotics leads to a growing number of multidrug-resistant microbes. This, in turn, has recently emerged as a global public health challenge facing both clinicians and their patients. In addition to intrinsic resistance, bacteria can acquire resistance to particular antimicrobial agents through the transfer of genetic material conferring resistance. Amongst the most common bacterial resistance strategies are: drug target site changes, increased cell wall permeability to antibiotics, antibiotic inactivation, and efflux pumps. A better understanding of the interplay between the mechanisms of antibiotic actions and bacterial defense strategies against particular antimicrobial agents is crucial for developing new drugs or drug combinations. Herein, we provide a brief overview of the current nanomedicine-based strategies that aim to improve the efficacy of antibiotics.
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Affiliation(s)
- Aleksandra Baran
- Department of Biotechnology, College of Natural Sciences, University of Rzeszów, Pigonia 1, 35-310 Rzeszow, Poland
| | - Aleksandra Kwiatkowska
- Institute of Physical Culture Studies, College of Medical Sciences, University of Rzeszów, ul. Towarnickiego 3, 35-959 Rzeszów, Poland
| | - Leszek Potocki
- Department of Biotechnology, College of Natural Sciences, University of Rzeszów, Pigonia 1, 35-310 Rzeszow, Poland
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30
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Colistin Resistance in Acinetobacter baumannii: Molecular Mechanisms and Epidemiology. Antibiotics (Basel) 2023; 12:antibiotics12030516. [PMID: 36978383 PMCID: PMC10044110 DOI: 10.3390/antibiotics12030516] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Acinetobacter baumannii is recognized as a clinically significant pathogen causing a wide spectrum of nosocomial infections. Colistin was considered a last-resort antibiotic for the treatment of infections caused by multidrug-resistant A. baumannii. Since the reintroduction of colistin, a number of mechanisms of colistin resistance in A. baumannii have been reported, including complete loss of LPS by inactivation of the biosynthetic pathway, modifications of target LPS driven by the addition of phosphoethanolamine (PEtN) moieties to lipid A mediated by the chromosomal pmrCAB operon and eptA gene-encoded enzymes or plasmid-encoded mcr genes and efflux of colistin from the cell. In addition to resistance to colistin, widespread heteroresistance is another feature of A. baumannii that leads to colistin treatment failure. This review aims to present a critical assessment of relevant published (>50 experimental papers) up-to-date knowledge on the molecular mechanisms of colistin resistance in A. baumannii with a detailed review of implicated mutations and the global distribution of colistin-resistant strains.
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31
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Li Y, Fang C, Wang X, Liu Q, Qiu Y, Dai X, Zhang L. A new class A beta-lactamase gene bla CAE-1 coexists with bla AFM-1 in a novel untypable plasmid in Comamonas aquatica. Sci Rep 2023; 13:3634. [PMID: 36869066 PMCID: PMC9984417 DOI: 10.1038/s41598-023-28312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/17/2023] [Indexed: 03/05/2023] Open
Abstract
Antimicrobial resistance, especially carbapenem resistance, poses a serious threat to global public health. Here, a carbapenem-resistant Comamonas aquatica isolate SCLZS63 was recovered from hospital sewage. Whole-genome sequencing showed that SCLZS63 has a 4,048,791-bp circular chromosome and three plasmids. The carbapenemase gene blaAFM-1 is located on the 143,067-bp untypable plasmid p1_SCLZS63, which is a novel type of plasmid with two multidrug-resistant (MDR) regions. Notably, a novel class A serine β-lactamase gene, blaCAE-1, coexists with blaAFM-1 in the mosaic MDR2 region. Cloning assay showed that CAE-1 confers resistance to ampicillin, piperacillin, cefazolin, cefuroxime, and ceftriaxone, and elevates the MIC of ampicillin-sulbactam two-fold in Escherichia coli DH5α, suggesting that CAE-1 functions as a broad-spectrum β-lactamase. Amino acid sequences analysis suggested that blaCAE-1 may originate from Comamonadaceae. The blaAFM-1 in p1_SCLZS63 is located in a conserved structure of ISCR29-ΔgroL-blaAFM-1-ble-ΔtrpF-ΔISCR27-msrB-msrA-yfcG-corA. Comprehensive analysis of the blaAFM-bearing sequences revealed important roles of ISCR29 and ΔISCR27 in the mobilization and truncation of the core module of blaAFM alleles, respectively. The diverse passenger contents of class 1 integrons flanking the blaAFM core module make the complexity of genetic contexts for blaAFM. In conclusion, this study reveals that Comamonas may act as an important reservoir for antibiotics-resistance genes and plasmids in the environment. Continuous monitoring for the environmental emergence of antimicrobial-resistant bacteria is needed to control the spread of antimicrobial resistance.
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Affiliation(s)
- Ying Li
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Science, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Chengju Fang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Xu Wang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Qian Liu
- Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Yichuan Qiu
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Xiaoyi Dai
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China.
| | - Luhua Zhang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China.
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32
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Structural and Biochemical Features of OXA-517: a Carbapenem and Expanded-Spectrum Cephalosporin Hydrolyzing OXA-48 Variant. Antimicrob Agents Chemother 2023; 67:e0109522. [PMID: 36648230 PMCID: PMC9933634 DOI: 10.1128/aac.01095-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
OXA-48-producing Enterobacterales have now widely disseminated throughout the world. Several variants have now been reported, differing by just a few amino-acid substitutions or deletions, mostly in the region of the loop β5-β6. As OXA-48 hydrolyzes carbapenems but lacks significant expanded-spectrum cephalosporin (ESC) hydrolytic activity, ESCs were suggested as a therapeutic option. Here, we have characterized OXA-517, a natural variant of OXA-48- with an Arg214Lys substitution and a deletion of Ile215 and Glu216 in the β5-β6 loop, capable of hydrolyzing at the same time ESC and carbapenems. MICs values of E. coli expressing blaOXA-517 gene revealed reduced susceptibility to carbapenems (similarly to OXA-48) and resistance to ESCs. Steady-state kinetic parameters revealed high catalytic efficiencies for ESCs and carbapenems. The blaOXA-517 gene was located on a ca. 31-kb plasmid identical to the prototypical IncL blaOXA-48-carrying plasmid except for an IS1R-mediated deletion of 30.7-kb in the tra operon. The crystal structure of OXA-517, determined to 1.86 Å resolution, revealed an expanded active site compared to that of OXA-48, which allows for accommodation of the bulky ceftazidime substrate. Our work illustrates the remarkable propensity of OXA-48-like carbapenemases to evolve through mutation/deletion in the β5-β6 loop to extend its hydrolysis profile to encompass most β-lactam substrates.
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Bonardi S, Cabassi CS, Fiaccadori E, Cavirani S, Parisi A, Bacci C, Lamperti L, Rega M, Conter M, Marra F, Crippa C, Gambi L, Spadini C, Iannarelli M, Paladini C, Filippin N, Pasquali F. Detection of carbapenemase- and ESBL-producing Klebsiella pneumoniae from bovine bulk milk and comparison with clinical human isolates in Italy. Int J Food Microbiol 2023; 387:110049. [PMID: 36521239 DOI: 10.1016/j.ijfoodmicro.2022.110049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Klebsiella pneumoniae is the most common Klebsiella species infecting animals and is one of the causing agents of mastitis in cows. The rise of antimicrobial resistance in K. pneumoniae, particularly in strains producing extended-spectrum β-lactamases (ESBLs) and/or carbapenemases, is of concern worldwide. Recently (Regulation UE No 2022/1255), carbapenems and cephalosporins in combination with β-lactamase inhibitors have been reserved only to human treatments in the European Union. The aim of this study was to investigate the role of cattle as carrier of human pathogenic carbapenem-resistant (CR) and ESBL-producing K. pneumoniae. On this purpose, a study involving 150 dairy farms in Parma province (Northern Italy) and 14 non replicate K. pneumoniae isolates from patients admitted at Parma University-Hospital was planned. Four multidrug resistant (MDR) K. pneumoniae strains were detected from 258 milk filters collected between 2019 and 2021. One carbapenemase KPC-3-positive K. pneumoniae ST307 (0.4 %; 95 % CI - 0.07 - 2.2) was detected in milk filters. The isolate also harboured OXA-9, CTX-M-15 and SHV-106 determinants, together with genes conferring resistance to aminoglycosides (aac(3')-IIa, aph (3″)-Ib, aph (6)-Id), fluoroquinolones (oqxA, oqxB, qnrB1), phosphonic acids (fosA6), sulphonamides (sul2), tetracyclines (tet(A)6) and trimethoprim (dfrA14). One KPC-3-producing K. pneumoniae ST307 was identified also among the human isolates, thus suggesting a possible circulation of pathogens out of the clinical settings. The remaining three bovine isolates were MDR ESBL-producing K. pneumoniae characterized by different genomic profiles: CTX-M-15, TEM-1B and SHV-187 genes (ST513); CTX-M-15 and SHV-145 (ST307); SHV-187 and DHA-1 (ST307). Occurrence of ESBL-producing K. pneumoniae in milk filters was 1.2 % (95 % CI 0.4-3.4). All the isolates showed resistance to aminoglycosides, 3rd-generation cephalosporins, and fluoroquinolones. Among the human isolates, two multidrug resistant ESBL-producing K. pneumoniae ST307 were found, thus confirming the circulation of this high-risk lineage between humans and cattle. Our findings suggest that food-producing animals can carry human pathogenic microorganisms harboring resistance genes against carbapenems and 3rd-generation cephalosporins, even if not treated with such antimicrobials. Moreover, on the MDR K. pneumoniae farms, the antimicrobial use was much higher than the Italian median value, thus highlighting the importance of a more prudent use of antibiotics in animal productions.
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Affiliation(s)
- S Bonardi
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy.
| | - C S Cabassi
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - E Fiaccadori
- Nephrology Unit, Parma University-Hospital, Department of Medicine and Surgery, Parma University, Via Gramsci 24, 43126 Parma, Italy
| | - S Cavirani
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - A Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Chiancolla, 1, 70017 Putignano, BA, Italy
| | - C Bacci
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - L Lamperti
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - M Rega
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - M Conter
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - F Marra
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - C Crippa
- Food Safety Unit, Department of Agricultural and Food Sciences Alma Mater Studiorum, University of Bologna, Via del Florio, 2, 40064 Ozzano dell'Emilia, BO, Italy
| | - L Gambi
- Food Safety Unit, Department of Agricultural and Food Sciences Alma Mater Studiorum, University of Bologna, Via del Florio, 2, 40064 Ozzano dell'Emilia, BO, Italy
| | - C Spadini
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - M Iannarelli
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - C Paladini
- National Veterinary Service, Via Vasari 13/A, 43126 Parma, Italy
| | - N Filippin
- National Veterinary Service, Via Vasari 13/A, 43126 Parma, Italy
| | - F Pasquali
- Food Safety Unit, Department of Agricultural and Food Sciences Alma Mater Studiorum, University of Bologna, Via del Florio, 2, 40064 Ozzano dell'Emilia, BO, Italy
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34
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Jing X, Hu Y, Wu T, Zhang X, Luo S, Wang W, Min X, Sun R, Zeng J. A rapid method for detecting and distinguishing metallo-β-lactamase-and serine carbapenemase-producing Enterobacteriales using MALDI-TOF MS. Front Microbiol 2023; 13:1096987. [PMID: 36713184 PMCID: PMC9880429 DOI: 10.3389/fmicb.2022.1096987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction Carbapenemase-producing Enterobacteriales (CPE) are a major health threat worldwide, and therefore the development of rapid detection methods is needed. Here, we established a method to distinguish metallo-β-lactamase and serine carbapenemases using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with ethylenediaminetetraacetic acid (EDTA) and phenylboronic acid (PB). Methods To assess the specificity and sensitivity of the method, 110 carbapenemase-producing and 72 carbapenemase-negative Enterobacteriales isolates were collected, among which 51 strains produced only metallo-β-lactamase, 55 strains only serine carbapenemases, and four strains both metallo-β-lactamase and serine carbapenemases. In the proposed MALDI-TOF MS method, imipenem (IPM) and the bacterial strains to be tested were mixed, EDTA and/or PB was added, and the mixture was incubated for 4 h. The carbapenemase type was confirmed by the IPM waveform spectrum before and after incubation. Results Based on the presence, absence, and recovery of the IPM-cyano-4-hydroxy-cinnamic acid-specific waveform peak near 479 m/z, the detection sensitivity and specificity of the method were 98.2 and 100%, respectively. Discussion Although CPE detection by MALDI-TOF MS has been studied previously, our method distinguishes between metallo-β-lactamase and serine carbapenemases, which will be very helpful for the clinical selection of antibiotics.
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Affiliation(s)
- Xiaopeng Jing
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Yanyan Hu
- Clinical Microbiology Laboratory, School of Medicine, 2nd Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Tingting Wu
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Xing Zhang
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Shaofeng Luo
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Wei Wang
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Xiaochun Min
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Ruiling Sun
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Ji Zeng
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China,*Correspondence: Ji Zeng,
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35
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Yamaguchi Y, Kato K, Ichimaru Y, Uenosono Y, Tawara S, Ito R, Matsuse N, Wachino JI, Toma-Fukai S, Jin W, Arakawa Y, Otsuka M, Fujita M, Fukuishi N, Sugiura K, Imai M, Kurosaki H. Difference in the Inhibitory Effect of Thiol Compounds and Demetallation Rates from the Zn(II) Active Site of Metallo-β-lactamases (IMP-1 and IMP-6) Associated with a Single Amino Acid Substitution. ACS Infect Dis 2023; 9:65-78. [PMID: 36519431 DOI: 10.1021/acsinfecdis.2c00395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria producing metallo-β-lactamases (MBLs) have become a considerable threat to public health. MBLs including the IMP, VIM, and NDM types are Zn(II) enzymes that hydrolyze the β-lactam ring present in a broad range of antibiotics, such as N-benzylpenicillin, meropenem, and imipenem. Among IMPs, IMP-1 and IMP-6 differ in a single amino acid substitution at position 262, where serine in IMP-1 is replaced by glycine in IMP-6, conferring a change in substrate specificity. To investigate how this mutation influences enzyme function, we examined lactamase inhibition by thiol compounds. Ethyl 3-mercaptopropionate acted as a competitive inhibitor of IMP-1, but a noncompetitive inhibitor of IMP-6. A comparison of the crystal structures previously reported for IMP-1 (PDB code: 5EV6) and IMP-6 (PDB code: 6LVJ) revealed a hydrogen bond between the side chain of Ser262 and Cys221 in IMP-1 but the absence of hydrogen bond in IMP-6, which affects the Zn2 coordination sphere in its active site. We investigated the demetallation rates of IMP-1 and IMP-6 in the presence of chelating agent ethylenediaminetetraacetic acid (EDTA) and found that the demetallation reactions had fast and slow phases with a first-order rate constant (kfast = 1.76 h-1, kslow = 0.108 h-1 for IMP-1, and kfast = 14.0 h-1 and kslow = 1.66 h-1 for IMP-6). The difference in the flexibility of the Zn2 coordination sphere between IMP-1 and IMP-6 may influence the demetallation rate, the catalytic efficiency against β-lactam antibiotics, and the inhibitory effect of thiol compounds.
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Affiliation(s)
- Yoshihiro Yamaguchi
- Environmental Safety Center, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto860-8555, Japan.,Graduate School of Science and Technology, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto860-8555, Japan.,Faculty of Engineering, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto860-8555, Japan
| | - Koichi Kato
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi463-8521, Japan.,Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi468-8503, Japan.,Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences, 16-48, Kamishinano, Totsuka-ku, Yokohama, Kanagawa244-0806, Japan
| | - Yoshimi Ichimaru
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi463-8521, Japan.,Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences, 16-48, Kamishinano, Totsuka-ku, Yokohama, Kanagawa244-0806, Japan
| | - Yuya Uenosono
- Graduate School of Science and Technology, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto860-8555, Japan
| | - Sakiko Tawara
- Graduate School of Science and Technology, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto860-8555, Japan
| | - Rio Ito
- Graduate School of Science and Technology, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto860-8555, Japan
| | - Natsuki Matsuse
- Faculty of Engineering, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto860-8555, Japan
| | - Jun-Ichi Wachino
- Department of Medical Technology, Faculty of Medical Sciences, Shubun University, 6 Nikko-cho, Ichinomiya, Aichi491-0938, Japan
| | - Sachiko Toma-Fukai
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara630-0192, Japan
| | - Wanchun Jin
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi463-8521, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi466-8550, Japan
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto862-0973, Japan.,Department of Drug Discovery, Science Farm Ltd., 1-7-30 Kuhonji, Chuo-ku, Kumamoto862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto862-0973, Japan
| | - Nobuyuki Fukuishi
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi463-8521, Japan
| | - Kirara Sugiura
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi463-8521, Japan
| | - Masanori Imai
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi463-8521, Japan
| | - Hiromasa Kurosaki
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi463-8521, Japan
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36
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Vallianou NG, Skourtis A, Kounatidis D, Margellou E, Panagopoulos F, Geladari E, Evangelopoulos A, Jahaj E. The Role of the Respiratory Microbiome in the Pathogenesis of Aspiration Pneumonia: Implications for Diagnosis and Potential Therapeutic Choices. Antibiotics (Basel) 2023; 12:antibiotics12010140. [PMID: 36671341 PMCID: PMC9855160 DOI: 10.3390/antibiotics12010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
Although the lungs were considered to be sterile until recently, the advent of molecular biology techniques, such as polymerase chain reaction, 16 S rRNA sequencing and metagenomics has led to our expanding knowledge of the lung microbiome. These methods may be particularly useful for the identification of the causative agent(s) in cases of aspiration pneumonia, in which there is usually prior administration of antibiotics. The most common empirical treatment of aspiration pneumonia is the administration of broad-spectrum antibiotics; however, this may result in negative cultures from specimens taken from the respiratory tract. Therefore, in such cases, polymerase chain reaction or metagenomic next-generation sequencing may be life-saving. Moreover, these modern molecular methods may assist with antimicrobial stewardship. Based upon factors such as age, altered mental consciousness and recent hospitalization, there is a shift towards the predominance of aerobes, especially Gram-negative bacteria, over anaerobes in aspiration pneumonia. Thus, the therapeutic choices should be expanded to cover multi-drug resistant Gram-negative bacteria in selected cases of aspiration pneumonia.
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Zhang M, Ma Y, Xu H, Wang M, Li L. Surfaces of gymnastic equipment as reservoirs of microbial pathogens with potential for transmission of bacterial infection and antimicrobial resistance. Front Microbiol 2023; 14:1182594. [PMID: 37152727 PMCID: PMC10157288 DOI: 10.3389/fmicb.2023.1182594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Gymnastic equipment surfaces are shared by many people, and could mediate the transfer of bacterial pathogens. To better understand this detrimental potential, investigations on the reservoirs of bacterial pathogens and antimicrobial resistance on the surfaces of gymnastic equipment were performed by analyzing the bacterial community structures, prevalence of viable bacteria, and presence of antimicrobial resistance on both indoor and outdoor gymnastic facilities. The results of high-throughput 16S rDNA amplicon sequencing showed that Gram-positive bacteria on the surfaces of indoor gymnastic equipment significantly enriched, including the opportunistic pathogen Staphylococcus strains, while Enterobacteriaceae significantly enriched on surfaces of outdoor gymnastic equipment. The analysis of α-diversities showed a higher richness and diversity for bacterial communities on the surfaces of gymnastic equipment than the environment. Analysis of β-diversities showed that the bacterial communities on the surfaces of gymnastic equipment differ significantly from environmental bacterial communities, while the bacterial communities on indoor and outdoor equipment are also significantly different. Thirty-four bacterial isolates were obtained from the surfaces of gymnastic equipment, including three multidrug Staphylococcus and one multidrug resistant Pantoea. In particular, Staphylococcus hemolyticus 5-6, isolated from the dumbbell surface, is a multidrug resistant, hemolytic, high- risk pathogen. The results of quantitative PCR targeting antibiotic resistance related genes (intI1, sul1 and bla TEM) showed that the abundances of sul1 and bla TEM genes on the surfaces of gymnastic equipment are higher than the environment, while the abundances of sul1 gene on indoor equipment are higher than outdoor equipment. These results lead to the conclusion that the surfaces of gymnastic equipment are potential dissemination pathways for highly dangerous pathogens as well as antimicrobial resistance, and the risks of indoor equipment are higher than outdoor equipment.
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Mohamed HMA, Abd-Elhafeez HH, Al-Jabr OA, El-Zamkan MA. Characterization of Acinetobacter baumannii Isolated from Raw Milk. BIOLOGY 2022; 11:biology11121845. [PMID: 36552354 PMCID: PMC9775129 DOI: 10.3390/biology11121845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Acinetobacter baumannii (A. baumannii) is an opportunistic pathogen associated with nosocomial infections. In this study, 100 raw milk samples were collected from Qena, Egypt, and subjected to conventional and molecular assays to determine the presence of A. baumannii and investigate their antimicrobial resistance and biofilm formation. Our findings revealed that, among the 100 samples, Acinetobacter spp. were found in 13 samples based on CHROM agar results. We further characterized them using rpoB and 16S-23SrRNA sequencing and gyrB multiplex PCR analysis and confirmed that 9 out of the 13 Acinetobacter spp. isolates were A. baumannii and 4 were other species. The A. baumannii isolates were resistant to β-lactam drugs, including cefotaxime (44%), ampicillin-sulbactam and levofloxacin (33.3% for each), imipenem, meropenem and aztreonam (22.2% for each). We observed different antimicrobial resistance patterns, with a multi-antibiotic resistant (MAR) index ranging from 0.2 to 0.3. According to the PCR results, blaOXA-51 and blaOXA-23 genes were amplified in 100% and 55.5% of the A. baumannii isolates, respectively, while the blaOXA-58 gene was not amplified. Furthermore, the metallo-β-lactamases (MBL) genes blaIMP and blaNDM were found in 11.1% and 22.2% of isolates, respectively, while blaVIM was not amplified. Additionally, eight A. baumannii isolates (88.8%) produced black-colored colonies on Congo red agar, demonstrating their biofilm production capacity. These results showed that, besides other foodborne pathogens, raw milk should also be examined for A. baumannii, which could be a public health concern.
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Affiliation(s)
- Hams M. A. Mohamed
- Department of Microbiology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Hanan H. Abd-Elhafeez
- Department of Cells and Tissues, Faculty of Veterinary Medicine, Assiut University, Assiut 71526, Egypt
- Correspondence:
| | - Omar A. Al-Jabr
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Mona A. El-Zamkan
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
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Kong WP, Chen YW, Wong KY. The crystal structure of the H116Q mutant of NDM-1: An enzyme devoid of zinc ions. J Struct Biol 2022; 214:107922. [PMID: 36375744 DOI: 10.1016/j.jsb.2022.107922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
New Delhi metallo-β-lactamase 1 (NDM-1) is an important causative factor of antimicrobial resistance due to its efficient hydrolysis of a broad range of β-lactam compounds. The two zinc ions at the active site play essential roles in the NDM-1 catalytic activities. In a previous work, H116, one of the three ligands at the Zn1 site, was mutated in order to investigate the nature of zinc ion chelation. We report here the crystal structure of the NDM-1 H116Q mutant, that was designed to convert a B1 di-zinc enzyme into a B3 type, which either still binds two zinc ions or binds only one at the Zn2 site. The effect of mutation on the overall structure is minimal. Unexpectedly, no zinc ion was observed in the crystal structure. The Zn2-site ligating residue C221 forms a covalent bond with the nearby K121, a residue important in maintaining the active-site structure. The largest conformational changes were found at main-chain and side-chain atoms at residues 232-236 (loop 10), the proper configuration of which is known to be essential for substrate binding. The catalytic-site mutation caused little local changes, yet the effects were amplified and propagated to the substrate binding residues. There were big changes in the ψ angles of residues G232 and L234, which resulted in the side chain of N233 being displaced away from the substrate-binding site. In summary, we failed in turning a B1 enzyme into a B3 enzyme, yet we produced a zinc-less NDM-1 with residual activities.
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Affiliation(s)
- Wai-Po Kong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Yu Wai Chen
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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How does electron exchange correlation influences reactivity of metallo-β-lactamase L1 against cephalosporin antibiotics. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Waśko I, Kozińska A, Kotlarska E, Baraniak A. Clinically Relevant β-Lactam Resistance Genes in Wastewater Treatment Plants. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192113829. [PMID: 36360709 PMCID: PMC9657204 DOI: 10.3390/ijerph192113829] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 05/17/2023]
Abstract
Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in multiple areas, which is consistent with One Health's concept of close interconnections between people, animals, plants, and their shared environments. Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) circulate constantly in various niches, sediments, water sources, soil, and wastes of the animal and plant sectors, and is linked to human activities. Sewage of different origins gets to the wastewater treatment plants (WWTPs), where ARB and ARG removal efficiency is still insufficient, leading to their transmission to discharge points and further dissemination. Thus, WWTPs are believed to be reservoirs of ARGs and the source of spreading AMR. According to a World Health Organization report, the most critical pathogens for public health include Gram-negative bacteria resistant to third-generation cephalosporins and carbapenems (last-choice drugs), which represent β-lactams, the most widely used antibiotics. Therefore, this paper aimed to present the available research data for ARGs in WWTPs that confer resistance to β-lactam antibiotics, with a particular emphasis on clinically important life-threatening mechanisms of resistance, including extended-spectrum β-lactamases (ESBLs) and carbapenemases (KPC, NDM).
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Affiliation(s)
- Izabela Waśko
- Department of Biomedical Research, National Medicines Institute, Chelmska 30/34, 00-725 Warsaw, Poland
- Correspondence: ; Tel.: +48-228-410-623
| | - Aleksandra Kozińska
- Department of Biomedical Research, National Medicines Institute, Chelmska 30/34, 00-725 Warsaw, Poland
| | - Ewa Kotlarska
- Genetics and Marine Biotechnology Department, Institute of Oceanology of the Polish Academy of Sciences, Powstancow Warszawy 55, 81-712 Sopot, Poland
| | - Anna Baraniak
- Department of Biomedical Research, National Medicines Institute, Chelmska 30/34, 00-725 Warsaw, Poland
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Molecular and Kinetic Characterization of MOX-9, a Plasmid-Mediated Enzyme Representative of a Novel Sublineage of MOX-Type Class C β-Lactamases. Antimicrob Agents Chemother 2022; 66:e0059522. [PMID: 36040170 PMCID: PMC9487596 DOI: 10.1128/aac.00595-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The MOX lineage of β-lactamases includes a group of molecular class C enzymes (AmpCs) encoded by genes mobilized from the chromosomes of Aeromonas spp. to plasmids. MOX-9, previously identified as a plasmid-encoded enzyme from a Citrobacter freundii isolate, belongs to a novel sublineage of MOX enzymes, derived from the resident Aeromonas media AmpC. The blaMOX-9 gene was found to be carried on a transposon, named Tn7469, likely responsible for its mobilization to plasmidic context. MOX-9 was overexpressed in Escherichia coli, purified, and subjected to biochemical characterization. Kinetic analysis showed a relatively narrow-spectrum profile with strong preference for cephalosporin substrates, with some differences compared with MOX-1 and MOX-2. MOX-9 was not inhibited by clavulanate and sulbactam, while both tazobactam and avibactam acted as inhibitors in the micromolar range.
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Castanheira M, Deshpande LM, Mendes RE, Doyle TB, Sader HS. Prevalence of carbapenemase genes among carbapenem-nonsusceptible Enterobacterales collected in US hospitals in a five-year period and activity of ceftazidime/avibactam and comparator agents. JAC Antimicrob Resist 2022; 4:dlac098. [PMID: 36196444 PMCID: PMC9524567 DOI: 10.1093/jacamr/dlac098] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives To evaluate the prevalence of acquired β-lactamase genes and susceptibility profiles of carbapenem-nonsusceptible Enterobacterales (CNSE) clinical isolates collected in US hospitals during a 5-year period. Methods Isolates were susceptibility tested by reference broth microdilution methods. Results were interpreted using CLSI breakpoints. Isolates displaying nonsusceptible MICs for imipenem or meropenem were categorized as CNSE. CNSE isolates were screened for β-lactamase-encoding genes using whole-genome sequencing. New genes were cloned, expressed in an Escherichia coli background and susceptibility tested. Results A total of 450 (1.3%) isolates were CNSE. Klebsiella pneumoniae serine carbapenemase (KPC) production was the most common resistance mechanism among CNSE isolates: 281/450 (62.4%) carried blaKPC, including three new variants. OXA-48-like and metallo-β-lactamase (MBL) encoding genes were detected among seven and 12 isolates, respectively. Among MBL genes, blaNDM-1 was the most common, but blaNDM-5, blaVIM-1 and blaIMP-27 were also identified. 169 (37.6% of the CNSE) isolates did not produce carbapenemases. Ceftazidime/avibactam was the most active agent (95.0% to 100.0% susceptible) against CNSE isolates from all carbapenemase groups except MBL-producing isolates. Ceftazidime/avibactam, meropenem/vaborbactam and imipenem/relebactam inhibited 100.0%, 97.6% and 92.3% of the non-carbapenemase CNSE isolates, respectively. Among the three new blaKPC variants, one conferred resistance to ceftazidime/avibactam and low meropenem MIC results while the other two had profiles similar to blaKPC-2 or blaKPC-3. Conclusions A decline in carbapenemase production was noticed in US hospitals in the 5-year period analysed in this study. New β-lactam/β-lactamase inhibitor combinations tested had good activity against CNSE isolates.
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Affiliation(s)
- Mariana Castanheira
- JMI Laboratories , 345 Beaver Kreek Centre, Suite A, North Liberty, IA 52317 , USA
| | | | - Rodrigo E Mendes
- JMI Laboratories , 345 Beaver Kreek Centre, Suite A, North Liberty, IA 52317 , USA
| | - Timothy B Doyle
- JMI Laboratories , 345 Beaver Kreek Centre, Suite A, North Liberty, IA 52317 , USA
| | - Helio S Sader
- JMI Laboratories , 345 Beaver Kreek Centre, Suite A, North Liberty, IA 52317 , USA
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Sinner EK, Li R, Marous DR, Townsend CA. ThnL, a B12-dependent radical S-adenosylmethionine enzyme, catalyzes thioether bond formation in carbapenem biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2206494119. [PMID: 35969793 PMCID: PMC9407657 DOI: 10.1073/pnas.2206494119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Complex carbapenems are important clinical antibiotics used to treat recalcitrant infections. Their biosynthetic gene clusters contain three essential B12-dependent radical S-adenosylmethionine (rSAM) enzymes. The majority of characterized enzymes in this subfamily catalyze methyl transfer, but only one is required to sequentially install all methionine-derived carbons in complex carbapenems. Therefore, it is probable that the other two rSAM enzymes have noncanonical functions. Through a series of fermentation and in vitro experiments, we show that ThnL uses radical SAM chemistry to catalyze thioether bond formation between C2 of a carbapenam precursor and pantetheine, uniting initial bicycle assembly common to all carbapenems with later tailoring events unique to complex carbapenems. ThnL also catalyzes reversible thiol/disulfide redox on pantetheine. Neither of these functions has been observed previously in a B12-dependent radical SAM enzyme. ThnL expands the known activity of this subclass of enzymes beyond carbon-carbon bond formation or rearrangement. It is also the only radical SAM enzyme currently known to catalyze carbon-sulfur bond formation with only an rSAM Fe-S cluster and no additional auxiliary clusters.
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Affiliation(s)
- Erica K. Sinner
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Daniel R. Marous
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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Resistance mechanisms in Gram-negative bacteria. Med Intensiva 2022; 46:392-402. [PMID: 35660283 DOI: 10.1016/j.medine.2022.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/13/2022] [Indexed: 12/24/2022]
Abstract
Enterobacterales resistant to carbapenems or producing extended-spectrum β-lactamases (ESBL) and non-fermenters resistant to carbapenems present resistance to many of the antimicrobials commonly used in clinical practice, and have been recognized by the World Health Organization as a critical priority for the development of new antimicrobials. In this review, the main mechanisms of resistance of Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia to β-lactams, quinolones, aminoglycosides and polymyxins will be addressed. Updated information will be presented on the importance in resistance of antimicrobial modification mechanisms (including class C or extended-spectrum β-lactamases, carbapenemases and aminoglycoside-modifying enzymes), permeability alterations due to porin or lipopolysaccharide expression disorders, production of active efflux pumps, target alterations or protection, and expression of two-component systems.
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Sultan I, Siddiqui MT, Gogry FA, Haq QMR. Molecular characterization of resistance determinants and mobile genetic elements of ESBL producing multidrug-resistant bacteria from freshwater lakes in Kashmir, India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154221. [PMID: 35245551 DOI: 10.1016/j.scitotenv.2022.154221] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Antibiotic resistance conceded as a global concern is a phenomenon that emerged from the bacterial response to the extensive utilization of antimicrobials. The expansion of resistance determinants through horizontal transfer is linked with mobile genetic elements (MGEs) like transposons, insertion sequences, and integrons. Heavy metals also create consequential health hazards. Metal resistance gene in alliance with antibiotic resistance genes (ARGs) and MGEs is assisting bacteria to attain exalted quantity of resistance. METHODOLOGY The present work was carried out to study ARGs blaCTX-M, AmpC, qnrS, MGEs like ISecp1, TN3, TN21, and Int I by performing PCR and sequencing from Wular and Dal lakes of Kashmir; India. The genetic environment analysis of blaCTX-M-15 was carried out using PCR amplification, and sequencing approach followed by in-silico docking and mutational studies. Co-occurrence of ARGs and HMRGs was determined. Plasmid typing was done using PCR-based replicon typing (PBRT) and conjugation assay was also performed. RESULTS Out of 201 isolates attained from 16 locations, 33 were ESBLs producers. 30 ESBL displaying isolates were perceived positive for CTX-M gene, followed by AmpC (17), qnrS (13), ISecp1 (15), TN3 (11), TN21 (11), Int I (18), and SulI (14). The genetic environment of blaCTX-M-15 was observed as (ISEcp1-blaCTX-M-15-orf477), classical promoter-10 TACAAT and -35 TTGAA was found at the 3' region. The 3D structure of CTX-M-15 and ISEcp1 was generated and CTX-M-15-ISEcp1 (R299L) docking and mutation showed a reduction in hydrogen bonds. Co-occurrence of antibiotics and HMRGs (mer, sil, and ars) was found in 18, 14, and 8 isolates. PBRT analysis showed the presence of Inc. groups- B/O, F, I1, HI1, FIA, HI2, N, FIB, L/M. Molecular analysis of transconjugants showed the successful transfer of ARGs, MGEs, and HMRGs in the E. coli J53 AZR strain. CONCLUSION This study highlights the occurrence of ESBL producing bacteria in the aquatic environment of Kashmir India that can serve as a reservoir of ARGs. It also discussed the molecular mechanisms of MGEs which can help in containing the spread of antibiotic resistance.
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Affiliation(s)
- Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
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Tiwari A, Paakkanen J, Österblad M, Kirveskari J, Hendriksen RS, Heikinheimo A. Wastewater Surveillance Detected Carbapenemase Enzymes in Clinically Relevant Gram-Negative Bacteria in Helsinki, Finland; 2011-2012. Front Microbiol 2022; 13:887888. [PMID: 35722284 PMCID: PMC9201422 DOI: 10.3389/fmicb.2022.887888] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance profiling of pathogens helps to identify the emergence of rare or new resistance threats and prioritize possible actions to be taken against them. The analysis of wastewater (WW) can reveal the circulation of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARG) among the catchment communities. Here, we analyzed WW influent samples to determine the prevalence of carbapenemase genes-carrying Gram-negative bacteria (Carba-GNB) in Helsinki, Finland. This study set important historical reference points from the very early stage of the carbapenemase era, during the period 2011-2012. A total of 405 bacterial isolates grown on CHROMagarKPC (n = 195) and CHROMagarESBL (n = 210) from WW influent samples were collected between October 2011 and August 2012 and were analyzed. The bacterial DNA from the isolates was extracted, and the prevalence of carbapenemases genes bla KPC, bla NDM, bla GES, bla OXA-48, bla IMP, bla IMI, and bla VIM were screened with multiplexed PCR. All carbapenemase-positive isolates were identified taxonomically to species or genus level with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The nucleic acid extraction was successful for 399 isolates, of which 59 (14.8%) were found to carry carbapenemase genes. A total of 89.8% of the carbapenemase positive isolates (53 out of 59) were obtained from CHROMagarKPC plates and only 10.2% (six out of 59) were obtained from CHROMagar ESBL plates. Among the Carba-GNB isolates, 86.4% were bla GES (51 out of 59), 10.2% were bla KPC (six out of 59), and 3.4% were bla VIM (two out of 59). The most common carba-gene, bla GES, was carried by 10 different bacterial species, including Aeromonas spp., Enterobacter spp., and Kluyvera spp.; the bla KPC gene was carried by Escherichia coli, Klebsiella pneumoniae, and Kluyvera cryocescens; and the bla VIM gene was carried by Aeromonas hydrophila/caviae and Citrobacter amalonaticus. This study emphasizes that wastewater surveillance (WWS) can be an additional tool for monitoring antimicrobial resistance (AMR) at the population level.
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Affiliation(s)
- Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | | | - Monica Österblad
- Antimicrobial Resistance Unit, Finnish Institute for Health and Welfare, Turku, Finland
| | | | - Rene S. Hendriksen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics, Kongens Lyngby, Denmark
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority, Seinajöki, Finland
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Assefa M. Multi-drug resistant gram-negative bacterial pneumonia: etiology, risk factors, and drug resistance patterns. Pneumonia (Nathan) 2022; 14:4. [PMID: 35509063 PMCID: PMC9069761 DOI: 10.1186/s41479-022-00096-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/11/2022] [Indexed: 12/27/2022] Open
Abstract
Bacterial pneumonia is one of the most serious public health issues owing to its medical and economic costs, which result in increased morbidity and mortality in people of all ages around the world. Furthermore, antimicrobial resistance has risen over time, and the advent of multi-drug resistance in GNB complicates therapy and has a detrimental impact on patient outcomes. The current review aimed to summarize bacterial pneumonia with an emphasis on gram-negative etiology, pathogenesis, risk factors, resistance mechanisms, treatment updates, and vaccine concerns to tackle the problem before it causes a serious consequence. In conclusion, the global prevalence of GNB in CAP was reported 49.7% to 83.1%, whereas in VAP patients ranged between 76.13% to 95.3%. The most commonly reported MDR-GNB causes of pneumonia were A. baumannii, K. pneumoniae, and P. aeruginosa, with A. baumannii isolated particularly in VAP patients and the elderly. In most studies, ampicillin, tetracyclines, amoxicillin-clavulanic acid, cephalosporins, and carbapenems were shown to be highly resistant. Prior MDR-GNB infection, older age, previous use of broad-spectrum antibiotics, high frequency of local antibiotic resistance, prolonged hospital stays, ICU admission, mechanical ventilation, and immunosuppression are associated with the MDR-GNB colonization. S. maltophilia was reported as a severe cause of HAP/VAP in patients with mechanically ventilated and having hematologic malignancy due to its ability of biofilm formation, site adhesion in respiratory devices, and its intrinsic and acquired drug resistance mechanisms. Effective combination therapies targeting PDR strains and drug-resistant genes, antibiofilm agents, gene-based vaccinations, and pathogen-specific lymphocytes should be developed in the future.
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Affiliation(s)
- Muluneh Assefa
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, P.O. Box 196, Gondar, Ethiopia.
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Metagenomic insights into the microbial community structure and resistomes of a tropical agricultural soil persistently inundated with pesticide and animal manure use. Folia Microbiol (Praha) 2022; 67:707-719. [PMID: 35415828 DOI: 10.1007/s12223-022-00970-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/05/2022] [Indexed: 11/04/2022]
Abstract
Persistent use of pesticides and animal manure in agricultural soils inadvertently introduced heavy metals and antibiotic/antibiotic resistance genes (ARGs) into the soil with deleterious consequences. The microbiome and heavy metal and antibiotic resistome of a pesticide and animal manure inundated agricultural soil (SL6) obtained from a vegetable farm at Otte, Eiyenkorin, Kwara State, Nigeria, was deciphered via shotgun metagenomics and functional annotation of putative ORFs (open reading frames). Structural metagenomics of SL6 microbiome revealed 29 phyla, 49 classes, 94 orders, 183 families, 366 genera, 424 species, and 260 strains with the preponderance of the phyla Proteobacteria (40%) and Actinobacteria (36%), classes Actinobacteria (36%), Alphaproteobacteria (18%), and Gammaproteobacteria (17%), and genera Kocuria (16%), Sphingobacterium (11%), and Brevundimonas (10%), respectively. Heavy metal resistance genes annotation conducted using Biocide and Metal Resistance Gene Database (BacMet) revealed the detection of genes responsible for the uptake, transport, detoxification, efflux, and regulation of copper, cadmium, zinc, nickel, chromium, cobalt, selenium, tungsten, mercury, and several others. ARG annotation using the Antibiotic Resistance Gene-annotation (ARG-ANNOT) revealed ARGs for 11 antibiotic classes with the preponderance of β-lactamases, mobilized colistin resistance determinant (mcr-1), macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside resistance genes, among others. The persistent use of pesticide and animal manure is strongly believed to play a major role in the proliferation of heavy metal and antibiotic resistance genes in the soil. This study revealed that agricultural soils inundated with pesticide and animal manure use are potential hotspots for ARG spread and may accentuate the spread of multidrug resistant clinical pathogens.
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Three new inhibitors of class A β-lactamases evaluated by molecular docking and dynamics simulations methods: relebactam, enmetazobactam, and QPX7728. J Mol Model 2022; 28:76. [PMID: 35243556 DOI: 10.1007/s00894-022-05073-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
Abstract
Antibiotic-resistant Acinetobacter baumannii, Pseudomonas aeruginosa, Mycobacterium tuberculosis, Staphylococcus aureus, and Enterobacterales infections are serious global health problems, and class A β-lactamases are one mechanism that leads to antibiotic resistance. QPX7728, relebactam, and enmetazobactam are new β-lactamase inhibitors to combat β-lactam resistance. in silico approach was used in the current study to find which of the three inhibitors would be more effective for all class A β-lactamases and to reveal molecular insights into the differences between their binding energies. The mutations in conserved residues of the active sites of β-lactamases were defined using BLDB and Clustal Omega. FastME and MMseq2 were used for cluster and phylogeny analysis. 3D protein structure models for β-lactamases were built using SWISS-MODEL. ERRAT and Galaxy Web Server were used to verify 42 β-lactamase protein structures. QPX7728, relebactam, and enmetazobactam were docked to β-lactamases by using AutoDock 4.2. The TEM76-relebactam, CTX-M-81-relebactam, TEM-76-enmetazobactam, and CTX-M-200-enmetazobactam complexes were simulated by molecular dynamics method for 500 ns. Based on molecular docking results, relebactam and QPX7728 were more favorable inhibitors for serine A β-lactamases. A 2D representation of the interactions between ligands and β-lactamases showed that S235, hydrogen bonded with TEM-76, might play a role in inhibitor design. A 500-ns MD analysis of complexes indicated that distance from S70, stability in the enzyme active cavity, and high atomic displacement would account for a significant difference in inhibitor binding affinity.
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