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Khademi Dehkordi M, Hoveida L, Fani N. Structure-based virtual screening, molecular docking, and molecular dynamics simulation approaches for identification of new potential inhibitors of class a β-lactamase enzymes. J Biomol Struct Dyn 2024; 42:5631-5641. [PMID: 37534493 DOI: 10.1080/07391102.2023.2227724] [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: 04/09/2023] [Accepted: 06/14/2023] [Indexed: 08/04/2023]
Abstract
Bacteria are smart organisms that create drug resistance by decreasing the effect of antibiotics in different ways, such as secretion of the β-lactamase enzymes. Finding the compounds that can act as the inhibitors of these enzymes is a great help in reducing drug resistance and treat all types of infections. In this study, using molecular docking and molecular dynamics simulation techniques, we introduced two Relebactam substructures as new inhibitors of class A β-lactamase enzymes. Results of molecular docking show that the conformation of these two compounds in the active site of class A β-lactamase enzymes has a good match with Relebactam and their binding affinity to enzymes is equal to or better than Relebactam. Results showed a good tendency for binding and the formation of van der Waals and hydrogen interactions between the desired compounds and the β-lactamase enzymes. The results of the analysis of the molecular dynamics simulation trajectories showed that in the presence of the desired compounds, the second structures of the enzymes did not undergo many changes and in none of the systems, the binding of the compounds to the enzyme did not cause much instability, and in most cases made the structure stable. The hydrogen bonds were stable during the simulation time and in most cases, the new compounds formed more hydrogen bonds and had better binding affinity than Relebactam confirms the docking results. The results of this study can be helpful in designing new beta-lactamase inhibitors and new treatment methods to deal with drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Laleh Hoveida
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Najmeh Fani
- Iliya Computational Research Center (ICRC), Isfahan University of Technology, Isfahan, Iran
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Sansone P, Giaccari LG, Di Flumeri G, Pace MC, Pota V, Coppolino F, Brunetti S, Aurilio C. Imipenem/Cilastatin/Relebactam for Complicated Infections: A Real-World Evidence. Life (Basel) 2024; 14:614. [PMID: 38792635 PMCID: PMC11122335 DOI: 10.3390/life14050614] [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: 03/09/2024] [Revised: 04/25/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
(1) Background: Infections caused by multidrug-resistant (MDR) bacteria represent one of the major global public health problems of the 21st century. Beta-lactam antibacterial agents are commonly used to treat infections due to Gram-negative pathogens. New β-lactam/β-lactamase inhibitor combinations are urgently needed. Combining relebactam (REL) with imipenem (IMI) and cilastatin (CS) can restore its activity against many imipenem-nonsusceptible Gram-negative pathogens. (2) Methods: we performed a systematic review of the studies reporting on the use of in vivo REAL/IPM/CS. (3) Results: A total of eight studies were included in this review. The primary diagnosis was as follows: complicated urinary tract infection (n = 234), complicated intra-abdominal infections (n = 220), hospital-acquired pneumonia (n = 276), and ventilator-associated pneumonia (n = 157). Patients with normal renal function received REL/IPM/CS (250 mg/500 mg/500 mg). The most frequently reported AEs occurring in patients treated with imipenem/cilastatin plus REL/IPM/CS were nausea (11.5%), diarrhea (9.8%), vomiting (9.8%), and infusion site disorders (4.0%). Treatment outcomes in these high-risk patients receiving REL/IPM/CS were generally favorable. A total of 70.6% of patients treated with REL/IPM/CS reported a favorable clinical response at follow-up. (4) Conclusions: this review indicates that REL/IPM/CS is active against important MDR Gram-negative organisms.
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Affiliation(s)
- Pasquale Sansone
- Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy; (P.S.); (L.G.G.); (M.C.P.); (V.P.); (F.C.); (S.B.)
| | - Luca Gregorio Giaccari
- Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy; (P.S.); (L.G.G.); (M.C.P.); (V.P.); (F.C.); (S.B.)
| | - Giusy Di Flumeri
- UOC Emerging Infectious Disease with High Contagiousness, AORN Ospedali dei Colli P.O. C Cotugno, 80131 Naples, Italy;
| | - Maria Caterina Pace
- Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy; (P.S.); (L.G.G.); (M.C.P.); (V.P.); (F.C.); (S.B.)
| | - Vincenzo Pota
- Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy; (P.S.); (L.G.G.); (M.C.P.); (V.P.); (F.C.); (S.B.)
| | - Francesco Coppolino
- Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy; (P.S.); (L.G.G.); (M.C.P.); (V.P.); (F.C.); (S.B.)
| | - Simona Brunetti
- Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy; (P.S.); (L.G.G.); (M.C.P.); (V.P.); (F.C.); (S.B.)
| | - Caterina Aurilio
- Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy; (P.S.); (L.G.G.); (M.C.P.); (V.P.); (F.C.); (S.B.)
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Al Asad M, Siddique Shanta A, Akter K, Binte Habib M, Nahar S, Haque M, Kumar S, Islam S. Using Quantitative Polymerase Chain Reaction (qPCR) to Identify a Myriad of Carbapenemase Genes in Fresh Cow Dung in Bangladesh. Cureus 2024; 16:e54644. [PMID: 38389567 PMCID: PMC10881286 DOI: 10.7759/cureus.54644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2024] [Indexed: 02/24/2024] Open
Abstract
Introduction The emergence of antimicrobial resistance (AMR) is driven by the selection pressure of frequent uses of antimicrobial agents in healthcare, the food chain, agriculture, fishery, and the food animal industry, which poses a serious health risk for transmission-linked humans and the surrounding environment. Livestock, particularly cattle, play an essential role in the food sector in Bangladesh. The food-animal chains can be the potential routes of exposure to AMR-microorganisms for every domain of one health. Antimicrobial resistance genes (ARGs) can impart a reservoir of AMR within the food supply chain, even without pathogenic microorganisms. This study investigated the history of infection for the last six-month period of antimicrobials utilized in cattle farms and the distribution of selected carbapenemase resistance genes, namely, bla-KPC, bla-IMP, bla-VIM, bla-NDM-1, bla-SIM, bla-GIM, bla-SPM, and bla-SME, in cattle feces in Bangladesh. Methods A cross-sectional study was designed to analyze ARGs in fresh cow dung samples collected from commercial farms and individual houses in four Bangladesh districts, namely, Dhaka, Gazipur, Manikganj, and Tangail. Types of cattle breeds, their existing diseases, recent antimicrobial uses, and vaccine uses were recorded. DNA was extracted from each cow dung sample using commercial kits (Qiagen GmbH, Germany). Real-time quantitative polymerase chain reaction (RT-qPCR) was employed to assess the eight carbapenem resistance genes in the extracted DNA. The eight carbapenem resistance genes in the extracted DNA were assessed by RT-qPCR using the qTOWER3 thermal cycler (Analytik Jena GmbH, Konrad-Zuse-Straße 1, 07745 Jena, Germany). Results Group A carbapenemase, bla-KPC, was detected in 66.7% of the samples. However, no bla-SME was identified in all of the test samples. Group B metallo carbapenemase, bla-IMP, bla-NDM-1, bla-VIM, bla-SIM, bla-GIM, and bla-SPM, were in 66.7% (80/120), 49.2% (59/120), 48.3% (58/120), 68.3% (82/120), 58.3% (70/120), and 12.5% (15/120), respectively. Only 8.3% of the tested samples contained no MBL gene; 10% carried a single-type carbapenemase gene; and the remaining 81.7% carried two or more carbapenemase genes concurrently. Co-carriage of four or more genes was found in over 59% of samples. As many as seven genes were found together in 6.7% of samples. ARG detection in commercial cattle samples and household feces is not statistically significant. Conclusions Substantial carbapenem-resistance ARGs were detected in commercially farmed cow dung and household cattle samples. Frequent use of antibiotics for cattle for treatment and prophylactic purposes may influence the high acquisition of ARGs. Bangladeshi cattle farms are reservoirs and routes of AMR, posing a significant threat to the country's public health.
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Affiliation(s)
| | | | - Kakoli Akter
- Microbiology, Jahangirnagar University, Dhaka, BGD
| | | | | | - Mainul Haque
- Dentistry, Karnavati University, Karnavati Scientific Research Center, Gandhinagar, IND
- Pharmacology and Therapeutics, National Defence University of Malaysia, Kuala Lumpur, MYS
| | - Santosh Kumar
- Periodontology and Implantology, Karnavati University, Karnavati School of Dentistry, Gandhinagar, IND
| | - Salequl Islam
- Microbiology, Jahangirnagar University, Dhaka, BGD
- Optometry and Vision Science, University of New South Wales, Faculty of Medicine and Health, Sydney, AUS
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Cooper AL, Low A, Wong A, Tamber S, Blais BW, Carrillo CD. Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools. BMC Microbiol 2024; 24:31. [PMID: 38245666 PMCID: PMC10799530 DOI: 10.1186/s12866-023-03148-6] [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: 08/21/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Although the spread of antimicrobial resistance (AMR) through food and its production poses a significant concern, there is limited research on the prevalence of AMR bacteria in various agri-food products. Sequencing technologies are increasingly being used to track the spread of AMR genes (ARGs) in bacteria, and metagenomics has the potential to bypass some of the limitations of single isolate characterization by allowing simultaneous analysis of the agri-food product microbiome and associated resistome. However, metagenomics may still be hindered by methodological biases, presence of eukaryotic DNA, and difficulties in detecting low abundance targets within an attainable sequence coverage. The goal of this study was to assess whether limits of detection of ARGs in agri-food metagenomes were influenced by sample type and bioinformatic approaches. RESULTS We simulated metagenomes containing different proportions of AMR pathogens and analysed them for taxonomic composition and ARGs using several common bioinformatic tools. Kraken2/Bracken estimates of species abundance were closest to expected values. However, analysis by both Kraken2/Bracken indicated presence of organisms not included in the synthetic metagenomes. Metaphlan3/Metaphlan4 analysis of community composition was more specific but with lower sensitivity than the Kraken2/Bracken analysis. Accurate detection of ARGs dropped drastically below 5X isolate genome coverage. However, it was sometimes possible to detect ARGs and closely related alleles at lower coverage levels if using a lower ARG-target coverage cutoff (< 80%). While KMA and CARD-RGI only predicted presence of expected ARG-targets or closely related gene-alleles, SRST2 (which allows read to map to multiple targets) falsely reported presence of distantly related ARGs at all isolate genome coverage levels. The presence of background microbiota in metagenomes influenced the accuracy of ARG detection by KMA, resulting in mcr-1 detection at 0.1X isolate coverage in the lettuce but not in the beef metagenome. CONCLUSIONS This study demonstrates accurate detection of ARGs in synthetic metagenomes using various bioinformatic methods, provided that reads from the ARG-encoding organism exceed approximately 5X isolate coverage (i.e. 0.4% of a 40 million read metagenome). While lowering thresholds for target gene detection improved sensitivity, this led to the identification of alternative ARG-alleles, potentially confounding the identification of critical ARGs in the resistome. Further advancements in sequencing technologies providing increased coverage depth or extended read lengths may improve ARG detection in agri-food metagenomic samples, enabling use of this approach for tracking clinically important ARGs in agri-food samples.
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Affiliation(s)
- Ashley L Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Andrew Low
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | - Burton W Blais
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Catherine D Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.
- Department of Biology, Carleton University, Ottawa, ON, Canada.
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Khadka C, Shyaula M, Syangtan G, Bista S, Tuladhar R, Singh A, Joshi DR, Pokhrel LR, Dawadi P. Extended-spectrum β-lactamases producing Enterobacteriaceae (ESBL-PE) prevalence in Nepal: A systematic review and meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166164. [PMID: 37572913 DOI: 10.1016/j.scitotenv.2023.166164] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/09/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
An alarming increase in the occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) has threatened the treatment and management of bacterial infections. This systematic review and meta-analysis aimed to provide a quantitative estimate of the prevalence of ESBL among the members of the Enterobacteriaceae family by analyzing the community-based and clinical studies published between 2011 and 2021 from Nepal and determine if ESBL-PE correlates with multidrug resistance (MDR). The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were followed for systematic review and meta-analysis and the articles' quality was assessed using the Newcastle-Ottawa scale. Of the 2529 articles screened, 65 articles were systematically reviewed, data extracted, and included in in-depth meta-analysis. The overall pooled prevalence of ESBL-producers in Enterobacteriaceae was 29 % (95 % CI: 26-32 %) with high heterogeneity (I2 = 96 %, p < 0.001). Escherichia coli was the predominant ESBL-producing member of the Enterobacteriaceae family, followed by Citrobacter spp. and Klebsiella spp. The prevalence of ESBL-PE increased from 18.7 % in 2011 to 29.5 % in 2021. A strong positive correlation (r = 0.98) was observed between ESBL production and MDR in Enterobacteriaceae. ESBL-PE isolates showed high resistance to ampicillin, cephalosporins, and amoxicillin-clavulanic acid, and blaCTX-M type was the most reported gene variant among ESBL-PE. In conclusion, this study demonstrated an increased prevalence of ESBL-PE in Nepal over the last decade, and such isolates showed a high level of MDR against the β-lactams and non-β-lactam antibiotics. Tackling the rising antibiotic resistance (AR) and MDR in ESBL-PE would require concerted efforts from all stakeholders to institute effective infection control programs in the community and clinical settings.
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Affiliation(s)
- Christina Khadka
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Manita Shyaula
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Gopiram Syangtan
- Shi-Gan International College of Science and Technology, Tribhuvan University, Kathmandu, Nepal
| | - Shrijana Bista
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Reshma Tuladhar
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Anjana Singh
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal; Faculty of Science, Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | - Dev Raj Joshi
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Lok R Pokhrel
- Department of Public Health, The Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA.
| | - Prabin Dawadi
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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Tariq FN, Shafiq M, Khawar N, Habib G, Gul H, Hayat A, Rehman MU, Moussa IM, Mahmoud EA, Elansary HO. The functional repertoire of AmpR in the AmpC β-lactamase high expression and decreasing β-lactam and aminoglycosides resistance in ESBL Citrobacter freundii. Heliyon 2023; 9:e19486. [PMID: 37662790 PMCID: PMC10472055 DOI: 10.1016/j.heliyon.2023.e19486] [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: 05/24/2023] [Revised: 08/12/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023] Open
Abstract
Citrobacter freundii is characterized by AmpC β-lactamases that develop resistance to β-lactam antibiotics. The production of extended-spectrum β-lactamase (ESBL) is substantially high in Escherichia coli, C. freundii, Enterobacter cloacae, and Serratia marcescens, but infrequently explored in C. freundii. The present investigation characterized the ESBL C. freundii and delineated the genes involved in decrease in antibiotics resistance. We used the VITEK-2 system and Analytical Profile Index (API) kit to characterize and identify the Citrobacter isolates. The mRNA level of AmpC and AmpR was determined by RT-qPCR, and gel-shift assay was performed to evaluate protein-DNA binding. Here, a total of 26 Citrobacter strains were isolated from COVID-19 patients that showed varying degrees of antibiotic resistance. We examined and characterized the multidrug resistant C. freundii that showed ESBL production. The RT-qPCR analysis revealed that the AmpC mRNA expression is significantly high followed by a high level of AmpR. We sequenced the AmpC and AmpR genes that revealed the AmpR has four novel mutations in comparison to the reference genome namely; Thr64Ile, Arg86Ser, Asp135Val, and Ile183Leu while AmpC remained intact. The ΔAmpR mutant analysis revealed that the AmpR positively regulates oxidative stress response and decreases β-lactam and aminoglycosides resistance. The AmpC and AmpR high expression was associated with resistance to tazobactam, ampicillin, gentamicin, nitrofurantoin, and cephalosporins whereas AmpR deletion reduced β-lactam and aminoglycosides resistance. We conclude that AmpR is a positive regulator of AmpC that stimulates β-lactamases which inactivate multiple antibiotics.
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Affiliation(s)
- Falak Naz Tariq
- Department of Microbiology, Abbottabad University of Science and Technology, Havelian, Abbottabad, 22500, Pakistan
| | - Mehreen Shafiq
- Department of Microbiology, Abbottabad University of Science and Technology, Havelian, Abbottabad, 22500, Pakistan
| | - Nadeem Khawar
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar, 25000, Pakistan
| | - Gul Habib
- Department of Microbiology, Abbottabad University of Science and Technology, Havelian, Abbottabad, 22500, Pakistan
| | - Haji Gul
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China
| | - Azam Hayat
- Department of Microbiology, Abbottabad University of Science and Technology, Havelian, Abbottabad, 22500, Pakistan
| | - Mujaddad Ur Rehman
- Department of Microbiology, Abbottabad University of Science and Technology, Havelian, Abbottabad, 22500, Pakistan
| | - Ihab Mohamed Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Eman A. Mahmoud
- Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta, Egypt
| | - Hosam O. Elansary
- Department of Plant Production, College of Food & Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
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Tripathi S, Nair NN. Temperature Accelerated Sliced Sampling to Probe Ligand Dissociation from Protein. J Chem Inf Model 2023; 63:5182-5191. [PMID: 37540828 DOI: 10.1021/acs.jcim.3c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
Modeling ligand unbinding in proteins to estimate the free energy of binding and probing the mechanism presents several challenges. They primarily pertain to the entropic bottlenecks resulting from protein and solvent conformations. While exploring the unbinding processes using enhanced sampling techniques, very long simulations are required to sample all of the conformational states as the system gets trapped in local free energy minima along transverse coordinates. Here, we demonstrate that temperature accelerated sliced sampling (TASS) is an ideal approach to overcome some of the difficulties faced by conventional sampling methods in studying ligand unbinding. Using TASS, we study the unbinding of avibactam inhibitor molecules from the Class C β-lactamase (CBL) active site. Extracting CBL-avibactam unbinding free energetics, unbinding pathways, and identifying critical interactions from the TASS simulations are demonstrated.
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Affiliation(s)
- Shubhandra Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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Krajnc A, Gobec S. Conjugates of monocyclic β-lactams and siderophore mimetics: a patent evaluation (WO2023023393). Expert Opin Ther Pat 2023; 33:471-476. [PMID: 37902072 DOI: 10.1080/13543776.2023.2262135] [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: 04/25/2023] [Accepted: 09/19/2023] [Indexed: 10/31/2023]
Abstract
INTRODUCTION β-Lactams, which include monobactams, remain the most important class of antibiotics worldwide. Aztreonam, the only monobactam in clinical use, has remarkable activity against many Gram-negative bacteria, but limited activity against some of the most problematic multidrug-resistant (MDR) pathogens, such as MDR Pseudomonas aeruginosa and Acinetobacter baumannii co-expressing extended-spectrum- and metallo-β-lactamases, which can inactivate aztreonam by hydrolysis. AREAS COVERED Structurally novel siderophore-conjugated aztreonam derivatives with improved antibacterial properties against several high-priority pathogens are claimed. This invention reports that sidechain extension of aztreonam is tolerated; the coupling of its aminothiazoloxime carboxylic acid part with a siderophore mimetic significantly improved the antibacterial activity against several problematic strains, including MDR A. baumannii isolates with carbapenemase/cephalosporinase activity. EXPERT OPINION Finding new strategies to tackle bacterial resistance to β-lactam antibiotics is critical. Considering that β lactams are validated and safe drugs, this research may stimulate the field to develop new ideas in the arena of antimicrobial drug discovery, particularly with respect to siderophore mimetics.
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Affiliation(s)
- Alen Krajnc
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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Infections in Glucose-6-Phosphate Dehydrogenase G6PD-Deficient Patients; Predictors for Infection-Related Mortalities and Treatment Outcomes. Antibiotics (Basel) 2023; 12:antibiotics12030494. [PMID: 36978361 PMCID: PMC10044656 DOI: 10.3390/antibiotics12030494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Disturbances in the count or maturity of blood cells weaken their microbial defensive capacity and render them more susceptible to infections. Glucose-6-phosphate deficient patients are affected by a genetic disease that affects cell integrity with increased liability to infections and death. We aimed to investigate the risk factors for infection mortality in this patient population. We retrospectively examined the records of G6PD adult patients with confirmed infections and collected data related to demographics, infections (pathogens, types, and treatment regimens) in addition to mortality and length of stay outcomes. Data were statistically analyzed using R Programming language to identify contributing factors to mortality and treatment regimens association with outcomes. Records of 202 unique patients over 5 years were included, corresponding to 379 microbiologically and clinically confirmed infections. Patients > 60 years [p = 0.001, OR: 5.6], number of comorbidities 4 (2–5) [p < 0.001, OR: 1.8], patients needed blood transfusion [p = 0.003, OR: 4.3]. Respiratory tract infections [p = 0.037, OR: 2.28], HAIs [p = 0.002, OR: 3.9], polymicrobial infections [p = 0.001, OR: 10.9], and concurrent infection Gram-negative [p < 0.001, OR: 7.1] were significant contributors to 28-day mortality. The history of exposure to many antimicrobial classes contributed significantly to deaths, including β-lactam/β-lactamase [p = 0.002, OR: 2.5], macrolides [p = 0.001, OR: 3.34], and β-lactams [p = 0.012, OR: 2.0]. G6PD patients are a unique population that is more vulnerable to infections. Prompt and appropriate antimicrobial therapy is warranted to combat infections. A strict application of stewardship principles (disinfection, shortening the length of stay, and controlling comorbid conditions) may be beneficial for this population. Finally, awareness of the special needs of this patient group may improve treatment outcomes.
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Obeng-Nkrumah N, Hansen DS, Awuah-Mensah G, Blankson NK, Frimodt-Møller N, Newman MJ, Opintan JA, Krogfelt KA. High level of colonization with 3rd-generation cephalosporin-resistant Enterobacterales in African community settings, Ghana. Diagn Microbiol Infect Dis 2023; 106:115918. [PMID: 37058979 DOI: 10.1016/j.diagmicrobio.2023.115918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/10/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
A cross-sectional survey was conducted in eight Ghanaian communities to investigate the extent of intestinal colonization with 3rd-generation cephalosporin-resistant Enterobacterales. The study collected faecal samples and corresponding lifestyle data from 736 healthy residents to assess the occurrence of cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae, with a focus on genotypes of plasmid-mediated ESBLs, AmpCs, and carbapenemases. The results showed that 371 participants (50.4%) carried 3rd-generation cephalosporin-resistant E. coli (n=362) and K. pneumoniae (n=9). Most of these were ESBL-producing E. coli (n=352, 94.9%), carrying CTX-M genes (96.0%, n=338/352), mostly for CTX-M-15 (98.9%, n=334/338). Nine participants (1.2%) carried AmpC-producing E. coli that harboured blaDHA-1 or blaCMY-2 genes, and two participants (0.3%) each carried a carbapenem-resistant E. coli that harboured both blaNDM-1 and blaCMY-2. Quinolone-resistant O25b: ST131 E. coli were recovered from six participants (0.8%) and were all CTX-M-15 ESBL-producers. Having a household toilet facility was significantly associated with a reduced risk of intestinal colonization (adjusted odds ratio, 0.71; 95% CI, 0.48-0.99; P-value=0.0095) in multivariate analysis. These findings raise serious public health concerns, and effective control of the spread of antibiotic-resistant bacteria is possible by providing better sanitary conditions for communities.
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Affiliation(s)
- Noah Obeng-Nkrumah
- Department of Medical Laboratory Sciences, University of Ghana School of Biomedical and Allied Health Sciences, University of Ghana, Legon, Accra, Ghana.
| | | | - Georgina Awuah-Mensah
- School of Life Sciences Medical School, Queen's Medical Centre, University of Nottingham, Nottingham England
| | - Nana Kweiba Blankson
- Department of Microbiological diagnostics, Statens Serum Institut, Copenhagen Denmark
| | - Niels Frimodt-Møller
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Mercy Jemima Newman
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Legon, Accra, Ghana
| | - Japheth Awuletey Opintan
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Legon, Accra, Ghana
| | - Karen Angeliki Krogfelt
- Department of Science and Environment, Pandemix Center Roskilde University, Roskilde, Denmark.
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11
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Castanheira M, Kimbrough JH, DeVries S, Mendes RE, Sader HS. Trends of β-Lactamase Occurrence Among Escherichia coli and Klebsiella pneumoniae in United States Hospitals During a 5-Year Period and Activity of Antimicrobial Agents Against Isolates Stratified by β-Lactamase Type. Open Forum Infect Dis 2023; 10:ofad038. [PMID: 36776778 PMCID: PMC9907474 DOI: 10.1093/ofid/ofad038] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/24/2023] [Indexed: 01/30/2023] Open
Abstract
Background The temporal and longitudinal trends of β-lactamases and their associated susceptibility patterns were analyzed for Escherichia coli and Klebsiella pneumoniae isolates consecutively collected in 56 United States hospitals during 2016-2020. Methods Isolates (n = 19 453) were susceptibility tested by reference broth microdilution methods. Isolates that displayed minimum inhibitory concentration (MIC) values ≥2 mg/L for at least 2 of the following compounds-ceftazidime, ceftriaxone, aztreonam, or cefepime-or resistance to the carbapenems were submitted to whole genome sequencing for identification of β-lactamases. Longitudinal and temporal trends were determined by slope coefficient. New CTX-M and OXA-1 variants were characterized. Results Extended-spectrum β-lactamases (ESBLs) were detected among 88.0% of the isolates that displayed elevated cephalosporin/aztreonam MICs without carbapenem resistance. bla CTX-M-15 was detected among 55.5% of the ESBL producers. ESBL rates were stable over time, but significant increases were noted among bloodstream infection and K pneumoniae isolates, mainly driven by an increase in bla CTX-M. Carbapenem resistance and carbapenemase genes were noted among 166 and 145 isolates, respectively, including 137 bla KPC, 6 bla SME, 3 bla OXA-48-like, and 3 bla NDM. Ceftazidime-avibactam and carbapenems were very active (>99% susceptibility) against ESBL producers without carbapenem resistance. Ceftazidime-avibactam inhibited 97.0% of the carbapenem-resistant isolates. This agent and meropenem-vaborbactam inhibited 96.4% and 85.0% of the 2020 isolates, respectively. Conclusions Overall, ESBL-producing isolates were stable, but an increase was noted for K pneumoniae isolates driven by CTX-M production. Carbapenem-resistant Enterobacterales rates decreased in the study period. The prevalence of metallo-β-lactamases and OXA-48-like remains low. Continuous surveillance of β-lactamase-producing isolates is prudent.
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Affiliation(s)
- Mariana Castanheira
- Correspondence: Mariana Castanheira, PhD, JMI Laboratories, 345 Beaver Kreek Center, Suite A, North Liberty, IA 52317 (); Helio S. Sader, MD, PhD, JMI Laboratories, 345 Beaver Kreek Center, Suite A, North Liberty, IA 52317 ()
| | | | | | | | - Helio S Sader
- Correspondence: Mariana Castanheira, PhD, JMI Laboratories, 345 Beaver Kreek Center, Suite A, North Liberty, IA 52317 (); Helio S. Sader, MD, PhD, JMI Laboratories, 345 Beaver Kreek Center, Suite A, North Liberty, IA 52317 ()
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12
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Li Y, Kumar S, Zhang L, Wu H, Wu H. Characteristics of antibiotic resistance mechanisms and genes of Klebsiella pneumoniae. Open Med (Wars) 2023; 18:20230707. [PMID: 37197355 PMCID: PMC10183727 DOI: 10.1515/med-2023-0707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 04/14/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen that can cause a range of infections in hospitalized patients. With the growing use of antibiotics, MDR K. pneumoniae is more prevalent, posing additional difficulties and obstacles in clinical therapy. To provide a valuable reference to deeply understand K. pneumoniae, and also to provide the theoretical basis for clinical prevention of such bacteria infections, the antibiotic resistance and mechanism of K. pneumoniae are discussed in this article. We conducted a literature review on antibiotic resistance of K. pneumoniae. We ran a thorough literature search of PubMed, Web of Science, and Scopus, among other databases. We also thoroughly searched the literature listed in the papers. We searched all antibiotic resistance mechanisms and genes of seven important antibiotics used to treat K. pneumoniae infections. Antibiotics such as β-lactams, aminoglycosides, and quinolones are used in the treatment of K. pneumoniae infection. With both chromosomal and plasmid-encoded ARGs, this pathogen has diverse resistance genes. Carbapenem resistance genes, enlarged-spectrum β-lactamase genes, and AmpC genes are the most often β-lactamase resistance genes. K. pneumoniae is a major contributor to antibiotic resistance worldwide. Understanding K. pneumoniae antibiotic resistance mechanisms and molecular characteristics will be important for the design of targeted prevention and novel control strategies against this pathogen.
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Affiliation(s)
- Yanping Li
- Pharmacy Department, Jiangsu Vocational College of Medicine, 224005Yancheng, Jiangsu Province, China
- Post Graduate Centre, Management and Science University, University Drive, Off Persiaran Olahraga, Section 13, 40100, Selangor, Malaysia
| | - Suresh Kumar
- Department of Diagnostic and Allied Health Science, Faculty of Health and Life Sciences, Management and Science University, Shah Alam, Malaysia
| | - Lihu Zhang
- Pharmacy Department, Jiangsu Vocational College of Medicine, 224005Yancheng, Jiangsu Province, China
| | - Hongjie Wu
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Hongyan Wu
- Pharmacy Department, Jiangsu Vocational College of Medicine, 224005Yancheng, Jiangsu Province, China
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13
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Yang X, Wang Z, Liu M, Yu X, Zhong Y, Wang F, Xu Y. Cefazolin and imipenem enhance AmpC expression and resistance in NagZ-dependent manner in Enterobacter cloacae complex. BMC Microbiol 2022; 22:284. [PMID: 36443681 PMCID: PMC9706910 DOI: 10.1186/s12866-022-02707-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 11/15/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Enterobacter cloacae complex (ECC) is a common opportunistic pathogen and is responsible for causing various infections in humans. Owing to its inducible chromosomal AmpC β-lactamase (AmpC), ECC is inherently resistant to the 1st- and 2nd- generation cephalosporins. However, whether β-lactams antibiotics enhance ECC resistance remains unclear. RESULTS In this study, we found that subinhibitory concentrations (SICs) of cefazolin (CFZ) and imipenem (IMP) can advance the expression of AmpC and enhance its resistance towards β-lactams through NagZ in Enterobacter cloacae (EC). Further, AmpC manifested a substantial upregulation in EC in response to SICs of CFZ and IMP. In nagZ knockout EC (ΔnagZ), the resistance to β-lactam antibiotics was rather weakened and the effect of CFZ and IMP on AmpC induction was completely abrogated. NagZ ectopic expression can rescue the induction effects of CFZ and IMP on AmpC and increase ΔnagZ resistance. More importantly, CFZ and IMP have the potential to induce the expression of AmpR's target genes in a NagZ-dependent manner. CONCLUSIONS Our findings suggest that NagZ is a critical determinant for CFZ and IMP to promote AmpC expression and resistance and that CFZ and IMP should be used with caution since they may aggravate ECC resistance. At the same time, this study further improves our understanding of resistance mechanisms in ECC.
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Affiliation(s)
- Xianggui Yang
- grid.414880.1Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan China
| | - Zhenguo Wang
- grid.414880.1Department of Stomatology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan China
| | - Mingquan Liu
- grid.414880.1Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan China
| | - Xuejing Yu
- grid.267313.20000 0000 9482 7121Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Yuanxiu Zhong
- grid.413856.d0000 0004 1799 3643Department of Biotechnology, Chengdu Medical College, Chengdu, Sichuan China
| | - Fuying Wang
- grid.413856.d0000 0004 1799 3643Department of Biotechnology, Chengdu Medical College, Chengdu, Sichuan China
| | - Ying Xu
- grid.414880.1Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan China
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14
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Irfan M, Almotiri A, AlZeyadi ZA. Antimicrobial Resistance and Its Drivers-A Review. Antibiotics (Basel) 2022; 11:1362. [PMID: 36290020 PMCID: PMC9598832 DOI: 10.3390/antibiotics11101362] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/25/2022] [Accepted: 10/01/2022] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) is a critical issue in health care in terms of mortality, quality of services, and financial damage. In the battle against AMR, it is crucial to recognize the impacts of all four domains, namely, mankind, livestock, agriculture, and the ecosystem. Many sociocultural and financial practices that are widespread in the world have made resistance management extremely complicated. Several pathways, including hospital effluent, agricultural waste, and wastewater treatment facilities, have been identified as potential routes for the spread of resistant bacteria and their resistance genes in soil and surrounding ecosystems. The overuse of uncontrolled antibiotics and improper treatment and recycled wastewater are among the contributors to AMR. Health-care organizations have begun to address AMR, although they are currently in the early stages. In this review, we provide a brief overview of AMR development processes, the worldwide burden and drivers of AMR, current knowledge gaps, monitoring methodologies, and global mitigation measures in the development and spread of AMR in the environment.
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15
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Affiliation(s)
- Vaishali Thakkur
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Chandan Kumar Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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16
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Zhang Y, Chen C, Cheng B, Gao L, Qin C, Zhang L, Zhang X, Wang J, Wan Y. Discovery of Quercetin and Its Analogs as Potent OXA-48 Beta-Lactamase Inhibitors. Front Pharmacol 2022; 13:926104. [PMID: 35814247 PMCID: PMC9258905 DOI: 10.3389/fphar.2022.926104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Carbapenem resistance in Enterobacteriaceae caused by OXA-48 β-lactamase is a growing global health threat and has rapidly spread in many regions of the world. Developing inhibitors is a promising way to overcome antibiotic resistance. However, there are few options for problematic OXA-48. Here we identified quercetin, fisetin, luteolin, 3′,4′,7-trihydroxyflavone, apigenin, kaempferol, and taxifolin as potent inhibitors of OXA-48 with IC50 values ranging from 0.47 to 4.54 μM. Notably, the structure-activity relationship revealed that the substitute hydroxyl groups in the A and B rings of quercetin and its structural analogs improved the inhibitory effect against OXA-48. Mechanism studies including enzymatic kinetic assay, isothermal titration calorimetry (ITC), and surface plasmon resonance (SPR) analysis demonstrated that quercetin reversibly inhibited OXA-48 through a noncompetitive mode. Molecular docking suggested that hydroxyl groups at the 3′, 4′ and 7 positions in flavonoids formed hydrogen-bonding interactions with the side chains of Thr209, Ala194, and Gln193 in OXA-48. Quercetin, fisetin, luteolin, and 3′,4′,7-trihydroxyflavone effectively restored the antibacterial efficacy of piperacillin or imipenem against E. coli producing OXA-48, resulting in 2–8-fold reduction in MIC. Moreover, quercetin combined with piperacillin showed antimicrobial efficacy in mice infection model. These studies provide potential lead compounds for the development of β-lactamase inhibitors and in combination with β-lactams to combat OXA-48 producing pathogen.
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Affiliation(s)
- Yuejuan Zhang
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Cheng Chen
- College of Forestry, Northwest A&F University, Yangling, China
| | - Bin Cheng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lei Gao
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Chuan Qin
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Lixia Zhang
- Clinical Laboratory, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Xu Zhang
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Jun Wang
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Yi Wan
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
- *Correspondence: Yi Wan,
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17
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Inhibiting the metallo-β-lactamases: challenges and strategies to overcome bacterial β-lactam resistance. Future Med Chem 2022; 14:1021-1025. [DOI: 10.4155/fmc-2022-0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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18
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Saebelfeld M, Das SG, Hagenbeek A, Krug J, de Visser JAGM. Stochastic establishment of β-lactam-resistant Escherichia coli mutants reveals conditions for collective resistance. Proc Biol Sci 2022; 289:20212486. [PMID: 35506221 PMCID: PMC9065960 DOI: 10.1098/rspb.2021.2486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
For antibiotic resistance to arise, new resistant mutants must establish in a bacterial population before they can spread via natural selection. Comprehending the stochastic factors that influence mutant establishment is crucial for a quantitative understanding of antibiotic resistance emergence. Here, we quantify the single-cell establishment probability of four Escherichia coli strains expressing β-lactamase alleles with different activity against the antibiotic cefotaxime, as a function of antibiotic concentration in both unstructured (liquid) and structured (agar) environments. We show that concentrations well below the minimum inhibitory concentration (MIC) can substantially hamper establishment, particularly for highly resistant mutants. While the pattern of establishment suppression is comparable in both tested environments, we find greater variability in establishment probability on agar. Using a simple branching model, we investigate possible sources of this stochasticity, including environment-dependent lineage variability, but cannot reject other possible causes. Lastly, we use the single-cell establishment probability to predict each strain's MIC in the absence of social interactions. We observe substantially higher measured than predicted MIC values, particularly for highly resistant strains, which indicates cooperative effects among resistant cells at large cell numbers, such as in standard MIC assays.
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Affiliation(s)
- Manja Saebelfeld
- Institute for Biological Physics, University of Cologne, Cologne, Germany,Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Suman G. Das
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Arno Hagenbeek
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Joachim Krug
- Institute for Biological Physics, University of Cologne, Cologne, Germany
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19
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Lucic A, Malla TR, Calvopiña K, Tooke CL, Brem J, McDonough MA, Spencer J, Schofield CJ. Studies on the Reactions of Biapenem with VIM Metallo β-Lactamases and the Serine β-Lactamase KPC-2. Antibiotics (Basel) 2022; 11:396. [PMID: 35326858 PMCID: PMC8944426 DOI: 10.3390/antibiotics11030396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
Carbapenems are important antibacterials and are both substrates and inhibitors of some β-lactamases. We report studies on the reaction of the unusual carbapenem biapenem, with the subclass B1 metallo-β-lactamases VIM-1 and VIM-2 and the class A serine-β-lactamase KPC-2. X-ray diffraction studies with VIM-2 crystals treated with biapenem reveal the opening of the β-lactam ring to form a mixture of the (2S)-imine and enamine complexed at the active site. NMR studies on the reactions of biapenem with VIM-1, VIM-2, and KPC-2 reveal the formation of hydrolysed enamine and (2R)- and (2S)-imine products. The combined results support the proposal that SBL/MBL-mediated carbapenem hydrolysis results in a mixture of tautomerizing enamine and (2R)- and (2S)-imine products, with the thermodynamically favoured (2S)-imine being the major observed species over a relatively long-time scale. The results suggest that prolonging the lifetimes of β-lactamase carbapenem complexes by optimising tautomerisation of the nascently formed enamine to the (2R)-imine and likely more stable (2S)-imine tautomer is of interest in developing improved carbapenems.
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Affiliation(s)
- Anka Lucic
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - Tika R. Malla
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - Karina Calvopiña
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - Catherine L. Tooke
- Biomedical Sciences Building, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK; (C.L.T.); (J.S.)
| | - Jürgen Brem
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - Michael A. McDonough
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - James Spencer
- Biomedical Sciences Building, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK; (C.L.T.); (J.S.)
| | - Christopher J. Schofield
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
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20
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Chiemchaisri W, Chiemchaisri C, Witthayaphirom C, Saengam C, Mahavee K. Reduction of antibiotic-resistant-E. coli, -K. pneumoniae, -A. baumannii in aged-sludge of membrane bioreactor treating hospital wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152470. [PMID: 34952056 DOI: 10.1016/j.scitotenv.2021.152470] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/23/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
A pilot-scale of membrane bioreactor (MBR) had functioned without sludge withdrawal for six months, proposed to minimize antibiotic-resistant bacteria (ARB) dissemination from hospital wastewater. With this proposal, an aging sludge in MBR has concerned as preserved-severe multidrug-resistant microorganisms. Thus, this study aims to investigate resistance alteration of ARB in the aging-sludge compared to that in the wastewater. Escherichia coli (EC), Klebsiella pneumoniae (KP), and Acinetobacter baumannii (AB) were antimicrobial-resistant indicators. In wastewater, AB showed the highest concentration followed by KP and EC, respectively, while an inverse order of those species showed in MBR-aging sludge. 60-isolates of each species per sample were tested on 8-antibiotics (AMAB) and 19-antibiotics (AMEC&AMKP) to evaluate antimicrobial resistance (AM) potency. The results show that high ARB variation of 0 to 100% population among those ARB had shown in the wastewater, while a significant reduction of those ARB population in MBR-aged-sludge had appeared surprisingly (P < 0.05). For example, the AMEC population of sludge to influent was <0.5 as of ESBL, Cefoperazone, Cefquinome, Imipenem, Gentamicin, Enrofloxacin, and Marbofloxacin. Among the three species studied, AB showed the highest antibiotic-resistant reduction of 8 antibiotics (100%), followed by KP (17 antibiotics, 99.44%) and EC (16 antibiotics, 88.89%), respectively. High dissolved oxygen levels and prolonged sludge age were possibly contributing to the reduction of those ARB in the MBR. This study gives a new point of view on potential ARB population reduction via the appropriate MBR operation.
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Affiliation(s)
- Wilai Chiemchaisri
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, 50 Phaholyothin Rd., Chatuchak, Bangkok 10900, Thailand.
| | - Chart Chiemchaisri
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, 50 Phaholyothin Rd., Chatuchak, Bangkok 10900, Thailand.
| | - Chayanid Witthayaphirom
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, 50 Phaholyothin Rd., Chatuchak, Bangkok 10900, Thailand
| | - Chitsuphang Saengam
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, 50 Phaholyothin Rd., Chatuchak, Bangkok 10900, Thailand
| | - Kanchanarin Mahavee
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, 50 Phaholyothin Rd., Chatuchak, Bangkok 10900, Thailand.
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21
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Martens-Lobenhoffer J, Angermair S, Bode-Böger SM. Quantification of ceftazidime/avibactam in human plasma and dried blood spots: Implications on stability and sample transport. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1193:123164. [PMID: 35196625 DOI: 10.1016/j.jchromb.2022.123164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/02/2022] [Accepted: 02/06/2022] [Indexed: 01/03/2023]
Abstract
Ceftazidime is an established third-generation cephalosporin antibiotic frequently administered to intensive care patients. To overcome drug resistance of pathogens, it is combined with the newly developed non-ß-lactam ß-lactamase inhibitor avibactam under the brand name Zavicefta®. To facilitate therapeutic drug monitoring (TDM), we developed a method for the simultaneous quantification of these substances by LC-MS/MS. A problem for TDM is the low stability of the analytes in plasma, requiring transport times of less than 6 h at 23 °C. Thus, we evaluated dried blood spots (DBS) as matrix for better stability. For both analytes, stable isotope labelled internal standards were applied. Plasma samples were prepared by protein precipitation, DBS by liquid extraction. The chromatographic separation took place on a polar-modified C18 column, and detection was achieved by tandem mass spectrometry with ESI ionization in positive mode for ceftazidime and negative mode for avibactam. Calibration was linear in the ranges of 5 - 100 µg/mL for ceftazidime and 1.25 - 25 µg/mL for avibactam in plasma and 2.5 - 50 µg/mL and 0.625 - 12.5 µg/mL in DBS, respectively. Precision was better than 7 % and accuracy better than 10% for plasma as well as for DBS. The stability of ceftazidime and avibactam was better in DBS than in plasma or full blood, extending maximal transport times at 23 °C from 6 h in plasma or full blood to 24 h for DBS samples. However, robust estimation of plasma concentrations from DBS measurements requires validation by future clinical studies.
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Affiliation(s)
| | - Stefan Angermair
- Department of Anesthesiology and Intensive Care Medicine, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Stefanie M Bode-Böger
- Institute of Clinical Pharmacology, Otto-von-Guericke University, Magdeburg, Germany
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22
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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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Bacterial Etiology of Bloodstream Infections and Antimicrobial Resistance Patterns from a Tertiary Care Hospital in Malé, Maldives. Int J Microbiol 2021; 2021:3088202. [PMID: 34707660 PMCID: PMC8545585 DOI: 10.1155/2021/3088202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/01/2021] [Indexed: 12/01/2022] Open
Abstract
Background Bloodstream infections pose a significant health problem worldwide and is a major cause of morbidity and mortality in many countries. It is important to have country-specific data for major pathogens causing bloodstream infections, in light of emerging resistance patterns of common bacterial isolates. Due to the scarcity of reports in this area, the aim of this study was to identify bacterial pathogens causing bloodstream infections among the study population. Methods A retrospective analysis of blood culture samples received at the Department of Laboratory Medicine, Indira Gandhi Memorial Hospital, Malé, Maldives, was performed for reports between January 2016 and December 2017. Results Out of the 471 culture-positive samples, 278 (59%) were males and 193 (41%) were females. Amongst the culture-positive samples, 338 (71.8%) Gram-positive organisms were isolated and 133 (28.2%) Gram-negative organisms were isolated. Coagulase-negative Staphylococcus (CoNS) was the most frequently isolated blood-borne bacterial pathogen in this study, accounting for 53.6% and 50.9% of the isolates in 2016 and 2017, respectively. Other frequently isolated pathogens included Staphylococcus aureus (15.9% and 10.3%), Klebsiella spp. (10.5% and 16.4%), and Escherichia coli (7.1% and 10.8%). Coagulase-negative Staphylococcus (CoNS) revealed high percentage of resistance among the tested antimicrobials, ampicillin, cephalexin, cefotaxime, and gentamicin. Over the two years, a significant difference between the percentage resistance among paediatric and adult patients was observed for coagulase-negative Staphylococcus (CoNS) isolate resistance to ampicillin (p ≤ 0.001), cephalexin (p ≤ 0.001), cefotaxime (p ≤ 0.001), gentamicin (p=0.008), and cotrimoxazole (SXT) (p ≤ 0.001). When comparing the significant antimicrobial resistance trends, it can be seen that Enterobacteriaceae isolates also demonstrated high resistance to ampicillin and gentamicin as well as second- and third-generation cephalosporins. Conclusions This study highlights the major bacterial pathogens involved in bloodstream infections in the healthcare setting of Malé, Maldives, and antibiotic resistance patterns. The results indicate that further characterization of bacteremia and its resistance patterns is needed to combat bloodstream infections.
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Zhang J, Li G, Zhang G, Kang W, Duan S, Wang T, Li J, Huangfu Z, Yang Q, Xu Y, Jia W, Sun H. Performance Evaluation of the Gradient Diffusion Strip Method and Disk Diffusion Method for Ceftazidime-Avibactam Against Enterobacterales and Pseudomonas aeruginosa: A Dual-Center Study. Front Microbiol 2021; 12:710526. [PMID: 34603236 PMCID: PMC8481768 DOI: 10.3389/fmicb.2021.710526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/13/2021] [Indexed: 12/02/2022] Open
Abstract
Objectives: Ceftazidime–avibactam is a novel synthetic beta-lactam + beta-lactamase inhibitor combination. We evaluated the performance of the gradient diffusion strip method and the disk diffusion method for the determination of ceftazidime–avibactam against Enterobacterales and Pseudomonas aeruginosa. Methods: Antimicrobial susceptibility testing of 302 clinical Enterobacterales and Pseudomonas aeruginosa isolates from two centers were conducted by broth microdilution (BMD), gradient diffusion strip method, and disk diffusion method for ceftazidime–avibactam. Using BMD as a gold standard, essential agreement (EA), categorical agreement (CA), major error (ME), and very major error (VME) were determined according to CLSI guidelines. CA and EA rate > 90%, ME rate < 3%, and VME rate < 1.5% were considered as acceptable criteria. Polymerase chain reaction and Sanger sequencing were performed to determine the carbapenem resistance genes of all 302 isolates. Results: A total of 302 strains were enrolled, among which 182 strains were from center 1 and 120 strains were from center 2. A percentage of 18.21% (55/302) of the enrolled isolates were resistant to ceftazidime–avibactam. The CA rates of the gradient diffusion strip method for Enterobacterales and P. aeruginosa were 100% and 98.65% (73/74), respectively, and the EA rates were 97.37% (222/228) and 98.65% (73/74), respectively. The CA rates of the disk diffusion method for Enterobacterales and P. aeruginosa were 100% and 95.95% (71/74), respectively. No VMEs were found by using the gradient diffusion strip method, while the ME rate was 0.40% (1/247). No MEs were found by using the disk diffusion method, but the VME rate was 5.45% (3/55). Therefore, all the parameters of the gradient diffusion strip method were in line with acceptable criteria. For 31 blaKPC, 33 blaNDM, 7 blaIMP, and 2 blaVIM positive isolates, both CA and EA rates were 100%; no MEs or VMEs were detected by either method. For 15 carbapenemase-non-producing resistant isolates, the CA and EA rates of the gradient diffusion strips method were 100%. Whereas the CA rate of the disk diffusion method was 80.00% (12/15), the VME rate was 20.00% (3/15). Conclusion: The gradient diffusion strip method can meet the needs of clinical microbiological laboratories for testing the susceptibility of ceftazidime–avibactam drugs. However, the VME rate > 1.5% (5.45%) by the disk diffusion method. By comparison, the performance of the gradient diffusion strip method was better than that of the disk diffusion method.
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Affiliation(s)
- Jingjia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Gang Li
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Ge Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Kang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Simeng Duan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Tong Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jin Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhiru Huangfu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Jia
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Hongli Sun
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Sakhrani VV, Ghosh RK, Hilario E, Weiss KL, Coates L, Mueller LJ. Toho-1 β-lactamase: backbone chemical shift assignments and changes in dynamics upon binding with avibactam. JOURNAL OF BIOMOLECULAR NMR 2021; 75:303-318. [PMID: 34218390 PMCID: PMC9122098 DOI: 10.1007/s10858-021-00375-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Backbone chemical shift assignments for the Toho-1 β-lactamase (263 amino acids, 28.9 kDa) are reported based on triple resonance solution-state NMR experiments performed on a uniformly 2H,13C,15N-labeled sample. These assignments allow for subsequent site-specific characterization at the chemical, structural, and dynamical levels. At the chemical level, titration with the non-β-lactam β-lactamase inhibitor avibactam is found to give chemical shift perturbations indicative of tight covalent binding that allow for mapping of the inhibitor binding site. At the structural level, protein secondary structure is predicted based on the backbone chemical shifts and protein residue sequence using TALOS-N and found to agree well with structural characterization from X-ray crystallography. At the dynamical level, model-free analysis of 15N relaxation data at a single field of 16.4 T reveals well-ordered structures for the ligand-free and avibactam-bound enzymes with generalized order parameters of ~ 0.85. Complementary relaxation dispersion experiments indicate that there is an escalation in motions on the millisecond timescale in the vicinity of the active site upon substrate binding. The combination of high rigidity on short timescales and active site flexibility on longer timescales is consistent with hypotheses for achieving both high catalytic efficiency and broad substrate specificity: the induced active site dynamics allows variously sized substrates to be accommodated and increases the probability that the optimal conformation for catalysis will be sampled.
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Affiliation(s)
- Varun V Sakhrani
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Rittik K Ghosh
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Eduardo Hilario
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA.
| | - Leonard J Mueller
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA.
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Abstract
Class D β-lactamases are composed of 14 families and the majority of the member enzymes are included in the OXA family. The genes for class D β-lactamases are frequently identified in the chromosome as an intrinsic resistance determinant in environmental bacteria and a few of these are found in mobile genetic elements carried by clinically significant pathogens. The most dominant OXA family among class D β-lactamases is superheterogeneous and the family needs to have an updated scheme for grouping OXA subfamilies through phylogenetic analysis. The OXA enzymes, even the members within a subfamily, have a diverse spectrum of resistance. Such varied activity could be derived from their active sites, which are distinct from those of the other serine β-lactamases. Their substrate profile is determined according to the size and position of the P-, Ω- and β5-β6 loops, assembling the active-site channel, which is very hydrophobic. Also, amino acid substitutions occurring in critical structures may alter the range of hydrolysed substrates and one subfamily could include members belonging to several functional groups. This review aims to describe the current class D β-lactamases including the functional groups, occurrence types (intrinsic or acquired) and substrate spectra and, focusing on the major OXA family, a new model for subfamily grouping will be presented.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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Discovery of Novel Chemical Series of OXA-48 β-Lactamase Inhibitors by High-Throughput Screening. Pharmaceuticals (Basel) 2021; 14:ph14070612. [PMID: 34202402 PMCID: PMC8308845 DOI: 10.3390/ph14070612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
The major cause of bacterial resistance to β-lactams is the production of hydrolytic β-lactamase enzymes. Nowadays, the combination of β-lactam antibiotics with β-lactamase inhibitors (BLIs) is the main strategy for overcoming such issues. Nevertheless, particularly challenging β-lactamases, such as OXA-48, pose the need for novel and effective treatments. Herein, we describe the screening of a proprietary compound collection against Klebsiella pneumoniae OXA-48, leading to the identification of several chemotypes, like the 4-ideneamino-4H-1,2,4-triazole (SC_2) and pyrazolo[3,4-b]pyridine (SC_7) cores as potential inhibitors. Importantly, the most potent representative of the latter series (ID2, AC50 = 0.99 μM) inhibited OXA-48 via a reversible and competitive mechanism of action, as demonstrated by biochemical and X-ray studies; furthermore, it slightly improved imipenem’s activity in Escherichia coli ATCC BAA-2523 β-lactam resistant strain. Also, ID2 showed good solubility and no sign of toxicity up to the highest tested concentration, resulting in a promising starting point for further optimization programs toward novel and effective non-β-lactam BLIs.
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The Carbapenemase BKC-1 from Klebsiella pneumoniae Is Adapted for Translocation by Both the Tat and Sec Translocons. mBio 2021; 12:e0130221. [PMID: 34154411 PMCID: PMC8262980 DOI: 10.1128/mbio.01302-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The cell envelope of Gram-negative bacteria consists of two membranes surrounding the periplasm and peptidoglycan layer. β-Lactam antibiotics target the periplasmic penicillin-binding proteins that synthesize peptidoglycan, resulting in cell death. The primary means by which bacterial species resist the effects of β-lactam drugs is to populate the periplasmic space with β-lactamases. Resistance to β-lactam drugs is spread by lateral transfer of genes encoding β-lactamases from one species of bacteria to another. However, the resistance phenotype depends in turn on these “alien” protein sequences being recognized and exported across the cytoplasmic membrane by either the Sec or Tat protein translocation machinery of the new bacterial host. Here, we examine BKC-1, a carbapenemase from an unknown bacterial source that has been identified in a single clinical isolate of Klebsiella pneumoniae. BKC-1 was shown to be located in the periplasm, and functional in both K. pneumoniae and Escherichia coli. Sequence analysis revealed the presence of an unusual signal peptide with a twin arginine motif and a duplicated hydrophobic region. Biochemical assays showed this signal peptide directs BKC-1 for translocation by both Sec and Tat translocons. This is one of the few descriptions of a periplasmic protein that is functionally translocated by both export pathways in the same organism, and we suggest it represents a snapshot of evolution for a β-lactamase adapting to functionality in a new host.
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29
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Hsu BM, Chen JS, Lin IC, Hsu GJ, Koner S, Hussain B, Huang SW, Tsai HC. Molecular and Anti-Microbial Resistance (AMR) Profiling of Methicillin-Resistant Staphylococcus aureus (MRSA) from Hospital and Long-Term Care Facilities (LTCF) Environment. Antibiotics (Basel) 2021; 10:antibiotics10060748. [PMID: 34205552 PMCID: PMC8235027 DOI: 10.3390/antibiotics10060748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
To provide evidence of the cross-contamination of emerging pathogenic microbes in a local network between long-term care facilities (LTCFs) and hospitals, this study emphasizes the molecular typing, the prevalence of virulence genes, and the antibiotic resistance pattern of methicillin-resistant Staphylococcus aureus. MRSA isolates were characterized from 246 samples collected from LTCFs, medical tubes of LTCF residents, and hospital environments of two cities, Chiayi and Changhua. Species identification, molecular characterization, and drug resistance analysis were performed. Hospital environments had a higher MRSA detection rate than that of LTCF environments, where moist samples are a hotspot of MRSA habitats, including tube samples from LTCF residents. All MRSA isolates in this study carried the exfoliative toxin eta gene (100%). The majority of MRSA isolates were resistant to erythromycin (76.7%), gentamicin (60%), and ciprofloxacin (55%). The percentage of multidrug-resistant MRSA isolates was approximately 50%. The enterobacterial repetitive intergenic consensus polymerase chain reaction results showed that 18 MRSA isolates belonged to a specific cluster. This implied that genetically similar isolates were spread between hospitals and LTCFs in Changhua city. This study highlights the threat to the health of LTCFs’ residents posed by hospital contact with MRSA.
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Affiliation(s)
- Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; (B.-M.H.); (S.K.); (B.H.)
- Center for Innovative on Aging Society, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung City 824, Taiwan;
| | - I-Ching Lin
- Department of Family Medicine, Asia University Hospital, Taichung City 413, Taiwan;
- Department of Kinesiology, Health and Leisure, Chienkuo Technology University, Chenghua County 500, Taiwan
| | - Gwo-Jong Hsu
- Division of Infectious Diseases, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chiayi City 600, Taiwan;
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; (B.-M.H.); (S.K.); (B.H.)
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; (B.-M.H.); (S.K.); (B.H.)
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Shih-Wei Huang
- Center for Environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung City 830, Taiwan;
- Super Micro Research and Technology Center, Cheng Shiu University, Kaohsiung City 830, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien County 970, Taiwan
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien County 970, Taiwan
- Correspondence: ; Tel.: +88-638-561-825
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30
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Bacterial Resistance to Antimicrobial Agents. Antibiotics (Basel) 2021; 10:antibiotics10050593. [PMID: 34067579 PMCID: PMC8157006 DOI: 10.3390/antibiotics10050593] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial pathogens as causative agents of infection constitute an alarming concern in the public health sector. In particular, bacteria with resistance to multiple antimicrobial agents can confound chemotherapeutic efficacy towards infectious diseases. Multidrug-resistant bacteria harbor various molecular and cellular mechanisms for antimicrobial resistance. These antimicrobial resistance mechanisms include active antimicrobial efflux, reduced drug entry into cells of pathogens, enzymatic metabolism of antimicrobial agents to inactive products, biofilm formation, altered drug targets, and protection of antimicrobial targets. These microbial systems represent suitable focuses for investigation to establish the means for their circumvention and to reestablish therapeutic effectiveness. This review briefly summarizes the various antimicrobial resistance mechanisms that are harbored within infectious bacteria.
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31
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Mathers AJ, Lewis JS. CON: Testing for ESBL production is unnecessary for ceftriaxone-resistant Enterobacterales. JAC Antimicrob Resist 2021; 3:dlab020. [PMID: 34223109 PMCID: PMC8210140 DOI: 10.1093/jacamr/dlab020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Phenotypic testing for Enterobacterales that harbour ESBLs is not additive to accurate in vitro β-lactam MICs for clinical decision-making. ESBL testing is an outdated practice established in an era of higher cephalosporin breakpoints to prevent resistant Enterobacterales carrying Ambler class A β-lactamases with affinity for later-generation β-lactams from being reported as susceptible to later-generation cephalosporins, leading to clinical failures. ESBL testing is problematic because of inaccuracies when multiple classes of β-lactamases are produced by the same organism, thus limiting the testing application to specific species and resistance types. Clinical laboratories should instead focus finite resources on accurate susceptibility testing using contemporary interpretative criteria to help guide therapeutic decisions. With continued emergence of antimicrobial resistance and in the setting of accurate susceptibility testing and current breakpoints the use of ESBL phenotypic testing is not helpful in clinical decision-making.
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Affiliation(s)
- Amy J Mathers
- Department of Medicine, Division of Infectious Diseases, University of Virginia Health System, Charlottesville, VA 22908, USA.,Department of Pathology, Clinical Microbiology Laboratory, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - James S Lewis
- Department of Pharmacy, Oregon Health & Science University, Portland, OR 97239, USA.,Department of Medicine, Division of Infectious Diseases, Oregon Health & Science University, Portland, OR, 97239, USA
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Mandal S, Thakkur V, Nair NN. Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based Ab Initio Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution. J Chem Theory Comput 2021; 17:2244-2255. [PMID: 33740375 DOI: 10.1021/acs.jctc.1c00009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio molecular dynamics (MD) with hybrid density functionals and a plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine adaptively compressed exchange (ACE) operator formulation and a multiple time step integration scheme to reduce the computational cost significantly [J. Chem. Phys. 2019, 151, 151102 ]. However, it was found that the construction of the ACE operator, which has to be done at least once in every MD time step, is computationally expensive. In the present work, systematic improvements are introduced to further speed up by employing localized orbitals for the construction of the ACE operator. By this, we could achieve a computational speedup of an order of magnitude for a periodic system containing 32 water molecules. Benchmark calculations were carried out to show the accuracy and efficiency of the method in predicting the structural and dynamical properties of bulk water. To demonstrate the applicability, computationally intensive free-energy computations at the level of hybrid density functional theory were performed to investigate (a) methyl formate hydrolysis reaction in neutral aqueous media and (b) proton-transfer reaction within the active-site residues of the class C β-lactamase enzyme.
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Affiliation(s)
- Sagarmoy Mandal
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India.,Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, Erlangen 91052, Germany
| | - Vaishali Thakkur
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
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Lopes SP, Jorge P, Sousa AM, Pereira MO. Discerning the role of polymicrobial biofilms in the ascent, prevalence, and extent of heteroresistance in clinical practice. Crit Rev Microbiol 2021; 47:162-191. [PMID: 33527850 DOI: 10.1080/1040841x.2020.1863329] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antimicrobial therapy is facing a worrisome and underappreciated challenge, the phenomenon of heteroresistance (HR). HR has been gradually documented in clinically relevant pathogens (e.g. Pseudomonas aeruginosa, Staphylococcus aureus, Burkholderia spp., Acinetobacter baumannii, Klebsiella pneumoniae, Candida spp.) towards several drugs and is believed to complicate the clinical picture of chronic infections. This type of infections are typically mediated by polymicrobial biofilms, wherein microorganisms inherently display a wide range of physiological states, distinct metabolic pathways, diverging refractory levels of stress responses, and a complex network of chemical signals exchange. This review aims to provide an overview on the relevance, prevalence, and implications of HR in clinical settings. Firstly, related terminologies (e.g. resistance, tolerance, persistence), sometimes misunderstood and overlapped, were clarified. Factors generating misleading HR definitions were also uncovered. Secondly, the recent HR incidences reported in clinically relevant pathogens towards different antimicrobials were annotated. The potential mechanisms underlying such occurrences were further elucidated. Finally, the link between HR and biofilms was discussed. The focus was to recognize the presence of heterogeneous levels of resistance within most biofilms, as well as the relevance of polymicrobial biofilms in chronic infectious diseases and their role in resistance spreading. These topics were subject of a critical appraisal, gaining insights into the ascending clinical implications of HR in antimicrobial resistance spreading, which could ultimately help designing effective therapeutic options.
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Affiliation(s)
- Susana Patrícia Lopes
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Paula Jorge
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Ana Margarida Sousa
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Maria Olívia Pereira
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
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34
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Cooper AL, Carter C, McLeod H, Wright M, Sritharan P, Tamber S, Wong A, Carrillo CD, Blais BW. Detection of carbapenem-resistance genes in bacteria isolated from wastewater in Ontario. Facets (Ott) 2021. [DOI: 10.1139/facets-2020-0101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacterial carbapenem resistance is a major public health concern since these antimicrobials are often the last resort to treat serious human infections. To evaluate methodologies for detection of carbapenem resistance, carbapenem-tolerant bacteria were isolated from wastewater treatment plants in Toronto, Ottawa, and Arnprior, Ontario. A total of 135 carbapenem-tolerant bacteria were recovered. Polymerase chain reaction (PCR) indicated the presence of carbapenem hydrolysing enzymes KPC ( n = 10), GES ( n = 5), VIM ( n = 7), and IMP ( n = 1), and β-lactamases TEM ( n = 7), PER ( n = 1), and OXA-variants ( n = 16). A subset of 46 isolates were sequenced and analysed using ResFinder and CARD-RGI. Both programs detected carbapenem resistance genes in 35 sequenced isolates and antimicrobial resistance genes (ARGs) conferring resistance to multiple class of other antibiotics. Where β-lactamase resistance genes were not initially identified, lowering the thresholds for ARG detection enabled identification of closely related β-lactamases. However, no known carbapenem resistance genes were found in seven sequenced Pseudomonas spp. isolates. Also of note was a multi-drug-resistant Klebsiella pneumoniae isolate from Ottawa, which harboured resistance to seven antimicrobial classes including β-lactams. These results highlight the diversity of genes encoding carbapenem resistance in Ontario and the utility of whole genome sequencing over PCR for ARG detection where resistance may result from an assortment of genes.
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Affiliation(s)
- Ashley L. Cooper
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Cassandra Carter
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Hana McLeod
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Marie Wright
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Prithika Sritharan
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Catherine D. Carrillo
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
| | - Burton W. Blais
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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35
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Gabrielyan NI, Sharapchenko SО, Kisil ОV, Kormilitsina VG, Drabkina IV, Safonova ТB, Petrukhina МI, Saitgareev RS, Zakharevich VМ. [The problem of global development of antibiotic resistant nosocomial pathogens]. TERAPEVT ARKH 2020; 92:110-116. [PMID: 33720615 DOI: 10.26442/00403660.2020.11.000783] [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: 12/26/2020] [Accepted: 12/26/2020] [Indexed: 11/22/2022]
Abstract
The problem of global expansion of multidrug-resistant nosocomial infections pathogens is under special attention at the moment. Antibiotic resistance increasing give us the limited treatment options. This problem is particularly acute for transplant clinics, because of patients need lifelong immunosuppressive therapy. From the one hand this ensures stable allograft functioning, but from the other increases the risk of severe infectious complications in the postoperative period. The purpose of this article is analysis carbapenem resistance dynamics of Klebsiella spp., Acinetobacter spp., Pseudomonas spp. and Staphylococcus spp. isolated from the blood of recipients of donor organs from 2009 to 2019 in the Shumakov National Medical Research Center of Transplantology and Artificial Organs. A significant annual decrease of carbapenem-sensitive strains of Klebsiella spp. and Acinetobacter spp. are shown. The study of a distinctive pathogen resistance profile specific to each institution can help one in selecting an adequate antimicrobial strategy and is an effective predictive tool for controlling the growth of multidrug-resistant microorganisms.
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Affiliation(s)
- N I Gabrielyan
- Shumakov National Medical Research Center of Transplantology and Artificial Organs
| | - S О Sharapchenko
- Shumakov National Medical Research Center of Transplantology and Artificial Organs
| | | | - V G Kormilitsina
- Shumakov National Medical Research Center of Transplantology and Artificial Organs
| | - I V Drabkina
- Shumakov National Medical Research Center of Transplantology and Artificial Organs
| | - Т B Safonova
- Russian Medical Academy of Continuous Professional Education
| | - М I Petrukhina
- Russian Medical Academy of Continuous Professional Education
| | - R S Saitgareev
- Shumakov National Medical Research Center of Transplantology and Artificial Organs
| | - V М Zakharevich
- Shumakov National Medical Research Center of Transplantology and Artificial Organs.,Sechenov First Moscow State Medical University (Sechenov University)
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Gupta S, Kumar M, Shergill SPS, Tandel K. Evaluation of ceftriaxone-sulbactam-disodium edetate adjuvant combination against multi-drug resistant Gram-negative organisms. Afr J Lab Med 2020; 9:991. [PMID: 33354525 PMCID: PMC7736688 DOI: 10.4102/ajlm.v9i1.991] [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: 02/04/2019] [Accepted: 08/27/2020] [Indexed: 11/23/2022] Open
Abstract
Background Multi-drug resistant (MDR) Gram-negative bacteria are an emerging threat, both in hospital and community settings. As very few antibiotics are effective against such infections, the need of the hour is a new antibiotic or drug combination which can overcome the effect of extended-spectrum β-lactamases (ESBL) and metallo β-lactamases (MBL). A new antibiotic combination of ceftriaxone, sulbactam and disodium edetate (CSE) has recently been proposed to tackle the MDR organisms. Objective Our study was carried out to assess the susceptibility of ESBL- and MBL-producing Gram-negative organisms to CSE. Methods The study was conducted in a tertiary-care hospital in Delhi, India, from February 2017 to June 2017. A total of 179 MDR (85 ESBL + 94 MBL) Gram-negative isolates from various clinical samples, identified by an automated system (Vitek 2) were tested against CSE using the Kirby-Bauer disc diffusion method. Susceptibility to CSE was recorded based on interpretative zone sizes of ceftriaxone as per 2017 Clinical and Laboratory Standards Institute guidelines. Results The most common isolate was Escherichia coli (76/179; 42.4%) followed by Klebsiella pneumoniae (53/179; 29.6%) and Acinetobacter baumanii (27/179; 15.1%). The in vitro susceptibility of ESBL- and MBL-producing Gram-negative isolates to CSE was found to be 58/85 (68.2%) for ESBL and 37/94 (39.4%) for MBL. Conclusion The in vitro susceptibility results obtained for CSE against ESBL-producing organisms is promising. It has the potential to emerge as a carbapenem-sparing antibiotic, active against ESBL-producing strains. Further clinical studies are required to establish the clinical efficacy of CSE against MDR pathogens.
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Affiliation(s)
- Shilpi Gupta
- Department of Microbiology, Military Hospital, Bhopal, India
| | - Mahadevan Kumar
- Department of Microbiology, Bharati Vidyapeeth University Medical College, Pune, India
| | | | - Kundan Tandel
- Department of Microbiology, Command Hospital (Central Command), Lucknow, India
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Wang G, Zhao G, Chao X, Xie L, Wang H. The Characteristic of Virulence, Biofilm and Antibiotic Resistance of Klebsiella pneumoniae. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17176278. [PMID: 32872324 PMCID: PMC7503635 DOI: 10.3390/ijerph17176278] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023]
Abstract
Klebsiella pneumoniae is an important gram-negative opportunistic pathogen that causes a variety of infectious diseases, including urinary tract infections, bacteremia, pneumonia, and liver abscesses. With the emergence of multidrug-resistant (MDR) and hypervirulent K. pneumoniae (hvKP) strains, the rapid spread of these clinical strains in geography is particularly worrying. However, the detailed mechanisms of virulence and antibiotic resistance in K. pneumoniae are still not very clear. Therefore, studying and elucidating the pathogenic mechanisms and drug resistance mechanism of K. pneumoniae infection are important parts of current medical research. In this paper, we systematically summarized the virulence, biofilm, and antibiotic tolerance mechanisms of K. pneumoniae, and explored the application of whole genome sequencing and global proteomics, which will provide new clues for clinical treatment of K. pneumoniae.
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Affiliation(s)
| | | | | | - Longxiang Xie
- Correspondence: (L.X.); (H.W.); Tel.: +86-0371-22892960 (L.X.)
| | - Hongju Wang
- Correspondence: (L.X.); (H.W.); Tel.: +86-0371-22892960 (L.X.)
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Virtual screening identifies broad-spectrum β-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases. Sci Rep 2020; 10:12763. [PMID: 32728062 PMCID: PMC7391774 DOI: 10.1038/s41598-020-69431-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteria are known to evade β-lactam antibiotic action by producing β-lactamases (BLs), including carbapenemases, which are able to hydrolyze nearly all available β-lactams. The production of BLs represents one of the best known and most targeted mechanisms of resistance in bacteria. We have performed the parallel screening of commercially available compounds against a panel of clinically relevant BLs: class A CTX-M-15 and KPC-2, subclass B1 NDM-1 and VIM-2 MBLs, and the class C P. aeruginosa AmpC. The results show that all BLs prefer scaffolds having electron pair donors: KPC-2 is preferentially inhibited by sulfonamide and tetrazole-based derivatives, NDM-1 by compounds bearing a thiol, a thiosemicarbazide or thiosemicarbazone moiety, while VIM-2 by triazole-containing molecules. Few broad-spectrum BLs inhibitors were identified; among these, compound 40 potentiates imipenem activity against an NDM-1-producing E. coli clinical strain. The binary complexes of the two most promising compounds binding NDM-1 and VIM-2 were obtained at high resolution, providing strong insights to improve molecular docking simulations, especially regarding the interaction of MBLs with inhibitors.
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Das CK, Nair NN. Elucidating the Molecular Basis of Avibactam‐Mediated Inhibition of Class A β‐Lactamases. Chemistry 2020; 26:9639-9651. [DOI: 10.1002/chem.202001261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/10/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Chandan Kumar Das
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
- Current Address: Lehrstuhl für Theoretische ChemieRuhr Universität Bochum 44780 Bochum Germany
| | - Nisanth N. Nair
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
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Structure and Molecular Recognition Mechanism of IMP-13 Metallo-β-Lactamase. Antimicrob Agents Chemother 2020; 64:AAC.00123-20. [PMID: 32205343 PMCID: PMC7269475 DOI: 10.1128/aac.00123-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/17/2020] [Indexed: 12/31/2022] Open
Abstract
Multidrug resistance among Gram-negative bacteria is a major global public health threat. Metallo-β-lactamases (MBLs) target the most widely used antibiotic class, the β-lactams, including the most recent generation of carbapenems. Interspecies spread renders these enzymes a serious clinical threat, and there are no clinically available inhibitors. We present the crystal structures of IMP-13, a structurally uncharacterized MBL from the Gram-negative bacterium Pseudomonas aeruginosa found in clinical outbreaks globally, and characterize the binding using solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The crystal structures of apo IMP-13 and IMP-13 bound to four clinically relevant carbapenem antibiotics (doripenem, ertapenem, imipenem, and meropenem) are presented. Active-site plasticity and the active-site loop, where a tryptophan residue stabilizes the antibiotic core scaffold, are essential to the substrate-binding mechanism. The conserved carbapenem scaffold plays the most significant role in IMP-13 binding, explaining the broad substrate specificity. The observed plasticity and substrate-locking mechanism provide opportunities for rational drug design of novel metallo-β-lactamase inhibitors, essential in the fight against antibiotic resistance.
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Taylor DM, Anglin J, Park S, Ucisik MN, Faver JC, Simmons N, Jin Z, Palaniappan M, Nyshadham P, Li F, Campbell J, Hu L, Sankaran B, Prasad BV, Huang H, Matzuk MM, Palzkill T. Identifying Oxacillinase-48 Carbapenemase Inhibitors Using DNA-Encoded Chemical Libraries. ACS Infect Dis 2020; 6:1214-1227. [PMID: 32182432 PMCID: PMC7673237 DOI: 10.1021/acsinfecdis.0c00015] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacterial resistance to β-lactam antibiotics is largely mediated by β-lactamases, which catalyze the hydrolysis of these drugs and continue to emerge in response to antibiotic use. β-Lactamases that hydrolyze the last resort carbapenem class of β-lactam antibiotics (carbapenemases) are a growing global health threat. Inhibitors have been developed to prevent β-lactamase-mediated hydrolysis and restore the efficacy of these antibiotics. However, there are few inhibitors available for problematic carbapenemases such as oxacillinase-48 (OXA-48). A DNA-encoded chemical library approach was used to rapidly screen for compounds that bind and potentially inhibit OXA-48. Using this approach, a hit compound, CDD-97, was identified with submicromolar potency (Ki = 0.53 ± 0.08 μM) against OXA-48. X-ray crystallography showed that CDD-97 binds noncovalently in the active site of OXA-48. Synthesis and testing of derivatives of CDD-97 revealed structure-activity relationships and informed the design of a compound with a 2-fold increase in potency. CDD-97, however, synergizes poorly with β-lactam antibiotics to inhibit the growth of bacteria expressing OXA-48 due to poor accumulation into E. coli. Despite the low in vivo activity, CDD-97 provides new insights into OXA-48 inhibition and demonstrates the potential of using DNA-encoded chemistry technology to rapidly identify β-lactamase binders and to study β-lactamase inhibition, leading to clinically useful inhibitors.
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Affiliation(s)
- Doris Mia Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin Anglin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suhyeorn Park
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Melek N. Ucisik
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John C. Faver
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas Simmons
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhuang Jin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pranavanand Nyshadham
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Feng Li
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James Campbell
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, CA, 94720, USA
| | - B.V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongbing Huang
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martin M. Matzuk
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
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Enany S, Zakeer S, Sayed AA, Magdeldin S. Shotgun proteomic analysis of ESBL-producing and non-ESBL-producing Klebsiella Pneumoniae clinical isolates. Microbiol Res 2020; 234:126423. [PMID: 32078895 DOI: 10.1016/j.micres.2020.126423] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/17/2019] [Accepted: 01/24/2020] [Indexed: 10/25/2022]
Abstract
Klebsiella pneumoniae is a pathogenic bacterium that is responsible for a wide range of infections in humans. An increased rate of infections caused by multi-drug-resistant K. pneumoniae has been noted in the last two decades. The association between antimicrobial resistance and virulence is an important topic of study. Genomic tools have been used widely for the detection of virulence. In our study, we used proteomic analysis with mass spectrometry and bioinformatics tools to explore the virulence factors of both ESBL-producing and non-ESBL-producing K. pneumoniae and to determine the association between virulence and antimicrobial resistance in these clinical isolates. We have revealed different proteomic profiles and different pathways between the ESBL- and non-ESBL-producing groups. Many proteins involved in stress responses have been reported in the shared proteome between ESBL-and non-ESBL producers, such as ElaB protein, Lon protease, and universal stress proteins G and A. The virulence and pathogenicity of ESBL-producing bacteria were stronger than those of the non-ESBL-producing bacteria. Several unique virulence determinants were identified in ESBL-producing K. pneumoniae, such as proteins with lyase, catalase, isochorismatase, and oxidoreductase activity.
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Affiliation(s)
- Shymaa Enany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt.
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Ahmed A Sayed
- Genomic Research Program, Basic Research Department, Children's Cancer Hospital Egypt 57357, 11441 Cairo, Egypt; Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Sameh Magdeldin
- Proteomics and Metabolomics Unit, Department of Basic Research, Children's Cancer Hospital Egypt 57357, 11441 Cairo, Egypt; Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, 41522 Ismailia, Egypt
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"It Takes a Village": Mechanisms Underlying Antimicrobial Recalcitrance of Polymicrobial Biofilms. J Bacteriol 2019; 202:JB.00530-19. [PMID: 31548277 DOI: 10.1128/jb.00530-19] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic infections are frequently caused by polymicrobial biofilms. Importantly, these infections are often difficult to treat effectively in part due to the recalcitrance of biofilms to antimicrobial therapy. Emerging evidence suggests that polymicrobial interactions can lead to dramatic and unexpected changes in the ability of antibiotics to eradicate biofilms and often result in decreased antimicrobial efficacy in vitro In this review, we discuss the influence of polymicrobial interactions on the antibiotic susceptibility of biofilms, and we highlight the studies that first documented the shifted antimicrobial susceptibilities of mixed-species cultures. Recent studies have identified several mechanisms underlying the recalcitrance of polymicrobial biofilm communities, including interspecies exchange of antibiotic resistance genes, β-lactamase-mediated inactivation of antibiotics, changes in gene expression induced by metabolites and quorum sensing signals, inhibition of the electron transport chain, and changes in properties of the cell membrane. In addition to elucidating multiple mechanisms that contribute to the altered drug susceptibility of polymicrobial biofilms, these studies have uncovered novel ways in which polymicrobial interactions can impact microbial physiology. The diversity of findings discussed highlights the importance of continuing to investigate the efficacy of antibiotics against biofilm communities composed of different combinations of microbial species. Together, the data presented here illustrate the importance of studying microbes as part of mixed-species communities rather than in isolation. In light of our greater understanding of how interspecies interactions alter the efficacy of antimicrobial agents, we propose that the methods for measuring the drug susceptibility of polymicrobial infections should be revisited.
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Obeng-Nkrumah N, Labi AK, Blankson H, Awuah-Mensah G, Oduro-Mensah D, Anum J, Teye J, Kwashie SD, Bako E, Ayeh-Kumi PF, Asmah R. Household cockroaches carry CTX-M-15-, OXA-48- and NDM-1-producing enterobacteria, and share beta-lactam resistance determinants with humans. BMC Microbiol 2019; 19:272. [PMID: 31801455 PMCID: PMC6894353 DOI: 10.1186/s12866-019-1629-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND This study was designed to investigate whether household cockroaches harbor cephalosporin-resistant enterobacteria that share resistance determinants with human inhabitants. From February through July 2016, whole cockroach homogenates and human fecal samples from 100 households were cultured for cephalosporin-resistant enterobacteria (CRe). The CRe were examined for plasmid-mediated AmpC, ESBL, and carbapenemase genes; antibiotic susceptibility patterns; and conjugative transfer of antibiotic resistance mechanisms. Clonal associations between CRe were determined by multi-locus sequence typing (MLST). RESULTS Twenty CRe were recovered from whole cockroach homogenates from 15 households. The prevalence of households with cockroaches that harbored CRe, AmpC- (based on phenotype, with no identifiable blaAmpC genes), ESBL-, and carbapenemase-producers were 15, 4, 5%(2 blaCTX-M-15/TEM-1; 1 blaCTX-M-15/TEM-4; 1 blaTEM-24; 1 blaSHV-4) and 3%(2 blaNDM-1 genes and 1 blaOXA-48 gene), respectively. Overall, 20 CRe were recovered from 61 fecal samples of inhabitants from all 15 households that had cockroach samples positive for CRe. Of these, 5CRe (1 per household) were positive for ESBLs (blaTEM-24, blaTEM-14, blaCTX-M-15/TEM-4, blaSHV-3, blaCTX-M-15/TEM-1) and none carried AmpCs or carbapenemases. From 4% of households, the pair of cockroach and human CRe shared the same sequence type (ST), clonal complex (CC), antibiogram, and conjugable bla gene sequence (house 34, E. coli ST9/CC20-blaTEM-4; house 37, E. coli ST44/CC10-blaCTX-15/TEM-4; house 41, E. coli ST443/CC205-blaCTX-15/TEM-1; house 49, K. pneumoniae ST231/CC131-blaSHV-13). CONCLUSION The findings provide evidence that household cockroaches may carry CTX-M-15-, OXA-48- and NDM-1-producers, and share clonal relationship and beta-lactam resistance determinants with humans.
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Affiliation(s)
- Noah Obeng-Nkrumah
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, P.O. Box KB 143, Accra, Ghana, West Africa
| | - Appiah-Korang Labi
- Department of Microbiology, Korle-Bu Teaching Hospital, P.O. Box 77, Accra, Ghana, West Africa
| | - Harriet Blankson
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, P.O. Box KB 143, Accra, Ghana, West Africa. .,Molecular and Experimental Mycobacteriology, Research Centre Bostel, Leibniz Lung Center, Parkallee 1-40, 23845, Borstel, Germany.
| | | | - Daniel Oduro-Mensah
- Department of Applied Chemistry and Biochemistry, University for Development Studies, Navrongo Campus, P.O. Box 24, Navrongo, Ghana, West Africa
| | - Judelove Anum
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, P.O. Box KB 143, Accra, Ghana, West Africa
| | - James Teye
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, P.O. Box KB 143, Accra, Ghana, West Africa
| | - Solomon Dzidzornu Kwashie
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, P.O. Box KB 143, Accra, Ghana, West Africa
| | - Evariste Bako
- Department of Biochemistry and Microbiology, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Patrick Ferdinand Ayeh-Kumi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, P.O. Box KB 143, Accra, Ghana, West Africa
| | - Richard Asmah
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, P.O. Box KB 143, Accra, Ghana, West Africa
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Khosravi MA, Najafi A, Esmaeili D. Design multiplex PCR for detection of rapid and correct the metallobetalactamase. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mechanistic Insights into β-Lactamase-Catalysed Carbapenem Degradation Through Product Characterisation. Sci Rep 2019; 9:13608. [PMID: 31541180 PMCID: PMC6754457 DOI: 10.1038/s41598-019-49264-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/15/2019] [Indexed: 01/20/2023] Open
Abstract
β-Lactamases are a major threat to the clinical use of carbapenems, which are often antibiotics of last resort. Despite this, the reaction outcomes and mechanisms by which β-lactamases degrade carbapenems are still not fully understood. The carbapenem bicyclic core consists of a β-lactam ring fused to a pyrroline ring. Following β-lactamase-mediated opening of the β-lactam, the pyrroline may interconvert between an enamine (2-pyrroline) form and two epimeric imine (1-pyrroline) forms; previous crystallographic and spectroscopic studies have reported all three of these forms in the contexts of hydrolysis by different β-lactamases. As we show by NMR spectroscopy, the serine β-lactamases (KPC-2, SFC-1, CMY-10, OXA-23, and OXA-48) and metallo-β-lactamases (NDM-1, VIM-1, BcII, CphA, and L1) tested all degrade carbapenems to preferentially give the Δ2 (enamine) and/or (R)-Δ1 (imine) products. Rapid non-enzymatic tautomerisation of the Δ2 product to the (R)-Δ1 product prevents assignment of the nascent enzymatic product by NMR. The observed stereoselectivity implies that carbapenemases control the form of their pyrroline ring intermediate(s)/product(s), thereby preventing pyrroline tautomerisation from inhibiting catalysis.
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Mallik D, Pal S, Ghosh AS. Involvement of AmpG in mediating a dynamic relationship between serine beta-lactamase induction and biofilm-forming ability of Escherichia coli. FEMS Microbiol Lett 2019; 365:4939471. [PMID: 29566229 DOI: 10.1093/femsle/fny065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/14/2018] [Indexed: 12/24/2022] Open
Abstract
AmpG permease is implicated both in beta-lactamase induction and peptidoglycan recycling in enterobacterial isolates. Here, physiological studies using molecular genetics show that deletion of AmpG permease dramatically increases beta-lactam susceptibility even in the presence of AmpC, TEM-1 and OXA beta-lactamases. Also, there is an appreciable decrease in the biofilm-forming ability of strains lacking this protein. Expression of this permease in excess probably compromises the integrity of the bacterial cells, leading to cell lysis. Based on these results, we propose that AmpG permease may be used as a potential antibiotic target and its suppression could efficiently inhibit both beta-lactamase induction and biofilm formation.
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Affiliation(s)
- Dhriti Mallik
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal-721302, India
| | - Shilpa Pal
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal-721302, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal-721302, India
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Abodakpi H, Wanger A, Tam VH. What the Clinical Microbiologist Should Know About Pharmacokinetics/Pharmacodynamics in the Era of Emerging Multidrug Resistance: Focusing on β-Lactam/β-Lactamase Inhibitor Combinations. Clin Lab Med 2019; 39:473-485. [PMID: 31383269 DOI: 10.1016/j.cll.2019.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
As a class, β-lactamase inhibitors have proved successful in extending the clinical utility of β-lactam antibiotics by circumventing β-lactamase-mediated resistance. However, the rapid evolution of these β-lactamases calls for a critical reevaluation of the relationships between susceptibility, drug exposures, and bacterial response. The existing paradigm for in vitro susceptibility testing and development of β-lactam/β-lactamase inhibitor combinations may not optimally facilitate clinical use. Thus, alternative approaches for pairing these combinations and evaluating in vitro susceptibility are needed to provide better guidance to clinicians.
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Affiliation(s)
- Henrietta Abodakpi
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, USA
| | - Audrey Wanger
- Department of Pathology and Laboratory Medicine, McGovern Medical School, 6431 Fannin, Houston, Texas 77030, USA
| | - Vincent H Tam
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, USA; Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, 4849 Calhoun Road, Houston, TX 77204, USA.
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High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1. Int J Mol Sci 2019; 20:ijms20040819. [PMID: 30769822 PMCID: PMC6412273 DOI: 10.3390/ijms20040819] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/10/2019] [Indexed: 01/04/2023] Open
Abstract
The bacteria expressing New Delhi Metallo-β-lactamase-1 (NDM-1) can hydrolyze all β-lactam antibiotics including carbapenems, causing multi-drug resistance. The worldwide emergence and dissemination of gene blaNDM-1 (produces NDM-1) in hospital and community settings, rising problems for public health. Indeed, there is an urgent need for NDM-1 inhibitors to manage antibiotic resistance. Here, we have identified novel non-β-lactam ring-containing inhibitors of NDM-1 by applying a high-throughput virtual screening of lead-like subset of ZINC database. The screened compounds were followed for the molecular docking, the molecular dynamics simulation, and then enzyme kinetics assessment. The adopted screening procedure funnels out five novel inhibitors of NDM-1 including ZINC10936382, ZINC30479078, ZINC41493045, ZINC7424911, and ZINC84525623. The molecular mechanics-generalized born surface area and molecular dynamics (MD) simulation showed that ZINC84525623 formed the most stable complex with NDM-1. Furthermore, analyses of the binding pose after MD simulation revealed that ZINC84525623 formed two hydrogen bonds (electrostatic and hydrophobic interaction) with key amino acid residues of the NDM-1 active site. The docking binding free energy and docking binding constant for the ZINC84525623 and NDM-1 interaction were estimated to be −11.234 kcal/mol, and 1.74 × 108 M−1 respectively. Steady-state enzyme kinetics in the presence of ZINC84525623 show the decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics. The findings of this study would be helpful in identifying novel inhibitors against other β-lactamases from a pool of large databases. Furthermore, the identified inhibitor (ZINC84525623) could be developed as efficient drug candidates.
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Exploring bacterial resistome and resistance dessemination: an approach of whole genome sequencing. Future Med Chem 2019; 11:247-260. [PMID: 30801197 DOI: 10.4155/fmc-2018-0201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
For several decades antibiotics are used to combat against pathogenic bacteria, but their misuse and overuse have caused the emergence of resistant bacteria. The scarcities of effective antibiotics along with unavailability of alternative solutions have exacerbated bacterial infections and mortality rate. This review provides the concept of bacterial resistome and mechanisms of resistance. It has also described the utility of whole genome sequencing in identifying resistance and its dissemination in association with available bioinformatics tools and databases. Moreover, the whole genome sequencing methodology described in this review will help to select effective antibiotics, maintain unparalleled surveillance of resistance and provide early diagnosis during resistance outbreaks. The provided information could be used to control infection caused by resistant microorganisms.
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