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Kastendiek N, Coletti R, Gross T, Lopes MB. Exploring glioma heterogeneity through omics networks: from gene network discovery to causal insights and patient stratification. BioData Min 2024; 17:56. [PMID: 39696678 DOI: 10.1186/s13040-024-00411-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 11/25/2024] [Indexed: 12/20/2024] Open
Abstract
Gliomas are primary malignant brain tumors with a typically poor prognosis, exhibiting significant heterogeneity across different cancer types. Each glioma type possesses distinct molecular characteristics determining patient prognosis and therapeutic options. This study aims to explore the molecular complexity of gliomas at the transcriptome level, employing a comprehensive approach grounded in network discovery. The graphical lasso method was used to estimate a gene co-expression network for each glioma type from a transcriptomics dataset. Causality was subsequently inferred from correlation networks by estimating the Jacobian matrix. The networks were then analyzed for gene importance using centrality measures and modularity detection, leading to the selection of genes that might play an important role in the disease. To explore the pathways and biological functions these genes are involved in, KEGG and Gene Ontology (GO) enrichment analyses on the disclosed gene sets were performed, highlighting the significance of the genes selected across several relevent pathways and GO terms. Spectral clustering based on patient similarity networks was applied to stratify patients into groups with similar molecular characteristics and to assess whether the resulting clusters align with the diagnosed glioma type. The results presented highlight the ability of the proposed methodology to uncover relevant genes associated with glioma intertumoral heterogeneity. Further investigation might encompass biological validation of the putative biomarkers disclosed.
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Affiliation(s)
- Nina Kastendiek
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Roberta Coletti
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology (NOVA FCT), Caparica, 2829-516, Portugal
| | - Thilo Gross
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, 26129, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Marta B Lopes
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology (NOVA FCT), Caparica, 2829-516, Portugal.
- UNIDEMI, Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology (NOVA FCT), Caparica, 2829-516, Portugal.
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Wang L, Wang Y, Wang Z, Zhang X, Chen H, Lin Q, Wang X, Wen Y, Pan X, Guo Z, Wan B. Anticancer potential of grifolin in lung cancer treatment through PI3K/AKT pathway inhibition. Heliyon 2024; 10:e29447. [PMID: 38644824 PMCID: PMC11033154 DOI: 10.1016/j.heliyon.2024.e29447] [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: 12/22/2023] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024] Open
Abstract
Objective Grifolin is a natural secondary metabolite isolated from edible fruiting bodies of the mushroom Albatrellus confluens. Grifolin has antitumor activities in several types of cancer. We aimed to determine the effects of grifolin on lung cancer. Methods We determined the proliferation, migration, invasion, and apoptosis of lung cancer cells using 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, Ethynyl deoxyuridine, colony formation, wound scratch, transwell, flow cytometry, and xenograft mouse assays. Molecular docking evaluated the binding relation between grifolin and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA). The levels of PIK3CA, AKT, and p-AKT were measured by western blot. Results Grifolin (10, 20, or 40 μM) inhibited the proliferation, migration, and invasion of lung cancer cells, and induced cell cycle arrest and apoptosis. Grifolin also decreased CDK4, CDK6, and CyclinD1 expression and significantly decreased PIK3CA and p-AKT expression in lung cancer cells. These anticancer effects were abolished by 740Y-P. Conclusions Grifolin regulates the PI3K/AKT pathway, thus inhibiting lung cancer progression.
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Affiliation(s)
- Li Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, China
| | - Yongjun Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, China
| | - Zexu Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, China
| | - Xiuwei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, China
| | - Huayong Chen
- Lanshan Central Hospital, Yongzhou, Hunan, 425899, China
| | - Qiuqi Lin
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, China
| | - Xin Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, China
| | - Yuting Wen
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, China
| | - Xia Pan
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, China
| | - Zhongliang Guo
- Department of Respiratory and Critical Care Medicine, The Affiliated Shanghai East Hospital of Nanjing Medical University, Shanghai, 200120, China
| | - Bing Wan
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, China
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Runa F, Ortiz-Soto G, de Barros NR, Kelber JA. Targeting SMAD-Dependent Signaling: Considerations in Epithelial and Mesenchymal Solid Tumors. Pharmaceuticals (Basel) 2024; 17:326. [PMID: 38543112 PMCID: PMC10975212 DOI: 10.3390/ph17030326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 04/01/2024] Open
Abstract
SMADs are the canonical intracellular effector proteins of the TGF-β (transforming growth factor-β). SMADs translocate from plasma membrane receptors to the nucleus regulated by many SMAD-interacting proteins through phosphorylation and other post-translational modifications that govern their nucleocytoplasmic shuttling and subsequent transcriptional activity. The signaling pathway of TGF-β/SMAD exhibits both tumor-suppressing and tumor-promoting phenotypes in epithelial-derived solid tumors. Collectively, the pleiotropic nature of TGF-β/SMAD signaling presents significant challenges for the development of effective cancer therapies. Here, we review preclinical studies that evaluate the efficacy of inhibitors targeting major SMAD-regulating and/or -interacting proteins, particularly enzymes that may play important roles in epithelial or mesenchymal compartments within solid tumors.
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Affiliation(s)
- Farhana Runa
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
| | | | | | - Jonathan A Kelber
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
- Department of Biology, Baylor University, Waco, TX 76706, USA
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Chagaleti BK, Saravanan V, Vellapandian C, Kathiravan MK. Exploring cyclin-dependent kinase inhibitors: a comprehensive study in search of CDK-6 inhibitors using a pharmacophore modelling and dynamics approach. RSC Adv 2023; 13:33770-33785. [PMID: 38019988 PMCID: PMC10655667 DOI: 10.1039/d3ra05672d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Cancer prevalence and resistance issues in cancer treatment are a significant public health concern globally. Among the existing strategies in cancer therapy, targeting cyclin-dependent kinases (CDKs), especially CDK-6 is found to be one of the most promising targets, as this enzyme plays a pivotal role in cell cycle stages and cell proliferation. Cell proliferation is the characteristic feature of cancer giving rise to solid tumours. Our research focuses on creating novel compounds, specifically, pyrazolopyrimidine fused azetidinones, using a groundbreaking molecular hybridization approach to target CDK-6. Through computational investigations, ligand-based pharmacophore modelling, pharmacokinetic studies (ADMET), molecular docking, and dynamics simulations, we identified 18 promising compounds. The pharmacophore model featured one aromatic hydrophobic centre (F1: Aro/Hyd) and two H-bond acceptors (F2 and F3: Acc). Molecular docking results showed favourable binding energies (-6.5 to -8.0 kcal mol-1) and effective hydrogen bonds and hydrophobic interactions. The designed compounds demonstrated good ADMET profiles. Specifically, B6 and B18 showed low energy conformation (-7.8 kcal and -7.6 kcal), providing insights into target inhibition compared to the standard drug Palbociclib. Extensive molecular dynamics simulations confirmed the stability of these derivatives. Throughout the 100 ns simulation, the ligand-protein complexes maintained structural stability, with acceptable RMSD values. These compounds hold promise as potential leads in cancer therapy.
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Affiliation(s)
- Bharath Kumar Chagaleti
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology Kattankulathur-603203 India
| | - Venkatesan Saravanan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology Kattankulathur-603203 India
| | - Chitra Vellapandian
- Department of Pharmacology, SRM College of Pharmacy SRMIST, Kattankulathur Chennai Tamil Nadu - 603 203 India
| | - Muthu K Kathiravan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology Kattankulathur-603203 India
- Dr A. P. J. Abdul Kalam Research Lab, Department of Pharmaceutical Chemistry, SRM College of Pharmacy SRMIST, Kattankulathur Chennai Tamil Nadu - 603 203 India
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Ni B, Yan J, Cai W, Xiao Y, Tu C. Tizoxanide as a novel theraputic candidate for osteoarthritis. Heliyon 2023; 9:e19472. [PMID: 37662752 PMCID: PMC10472306 DOI: 10.1016/j.heliyon.2023.e19472] [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: 11/27/2022] [Revised: 08/19/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023] Open
Abstract
Osteoarthritis (OA) is a frequently seen degenerative joint disease in the elderly. Its pathogenesis is highly related to the local inflammatory reaction and autophagy. Tizoxanide (Tiz), the main active metabolite of nitazoxanide, has proved its anti-inflammatory properties in several diseases. However, the exact role of Tiz in OA remains to explore. In this study, we investigated the anti-arthritic effects and the underlying molecular mechanisms of Tiz on rat OA. The results showed that Tiz could attenuate the IL-1β-induced inflammatory disorders, cartilage matrix damage and autophagy reduction in rat chondrocytes. Moreover, employment of autophagy inhibitor 3-methyladenine (3-MA) could antagonize the protective effects of Tiz in IL-1β-treated rat chondrocytes. Additionally, Tiz also inhibited the IL-1β-induced PI3K/AKT/mTOR and P38/JNK phosphorylation in chondrocytes. In vivo, intra-articular injection of Tiz could significantly alleviate the progression of cartilage damage in rat OA model. Briefly, our study demonstrated the therapeutic potential of Tiz in OA, suggesting that Tiz administration might serve as a promising strategy in OA therapy.
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Affiliation(s)
- Bowei Ni
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
- Department of Orthopedics, Tongren Hospital of Wuhan University, Wuhan Third Hopspital, Wuhan, Hubei, PR China
| | - Jiyuan Yan
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Wenxiang Cai
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Yifan Xiao
- Department of Pathology and Pathophysiology, Medical College, Jianghan University, Wuhan, Hubei, PR China
| | - Chang Tu
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
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Philo JE, Caudle JD, Moussa RN, Kampmeyer PM, Hasin TR, Seo DK, Sheaff RJ, Lamar AA. Synthesis and Biological Evaluation of a Library of Sulfonamide Analogs of Memantine to Target Glioblastoma. ChemMedChem 2023; 18:e202300134. [PMID: 37248422 DOI: 10.1002/cmdc.202300134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/29/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023]
Abstract
A library of 34 lipophilic sulfonamides based upon the memantine core has been synthesized to identify potential drug candidates to cross the blood-brain barrier and target glioblastoma. The library was screened for in vitro activity against 4 mammalian cell lines, including U-87 (glioblastoma). Additional synthetic variation of the active compounds has validated the importance of specific regions of the pharmacophore, with the sulfonamide functionality and S-aryl unit displaying the most significant impact. In silico investigations suggest the active compounds might target DDR1 or RET proteins. The investigation has resulted in several compounds that warrant further development for lead optimization.
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Affiliation(s)
- John E Philo
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Jenna D Caudle
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Reema N Moussa
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Patrick M Kampmeyer
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Tasfia R Hasin
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - David K Seo
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Robert J Sheaff
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Angus A Lamar
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
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Cavazzoni A, Palladini A. Editorial: Inhibitors of CDK family: New perspective and rationale for drug combination in preclinical models of solid tumors. Front Oncol 2023; 13:1180650. [PMID: 37056348 PMCID: PMC10086415 DOI: 10.3389/fonc.2023.1180650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Affiliation(s)
- Andrea Cavazzoni
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- *Correspondence: Andrea Cavazzoni,
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Huang Q, Liu M, Zhang D, Lin BB, Fu X, Zhang Z, Zhang B, Dong JT. Nitazoxanide inhibits acetylated KLF5-induced bone metastasis by modulating KLF5 function in prostate cancer. BMC Med 2023; 21:68. [PMID: 36810084 PMCID: PMC9945734 DOI: 10.1186/s12916-023-02763-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND Castration-resistant prostate cancer often metastasizes to the bone, and such bone metastases eventually become resistant to available therapies, leading to the death of patients. Enriched in the bone, TGF-β plays a pivotal role in bone metastasis development. However, directly targeting TGF-β or its receptors has been challenging for the treatment of bone metastasis. We previously found that TGF-β induces and then depends on the acetylation of transcription factor KLF5 at K369 to regulate multiple biological processes, including the induction of EMT, cellular invasiveness, and bone metastasis. Acetylated KLF5 (Ac-KLF5) and its downstream effectors are thus potential therapeutic targets for treating TGF-β-induced bone metastasis in prostate cancer. METHODS A spheroid invasion assay was applied to prostate cancer cells expressing KLF5K369Q, which mimics Ac-KLF5, to screen 1987 FDA-approved drugs for invasion suppression. Luciferase- and KLF5K369Q-expressing cells were injected into nude mice via the tail artery to model bone metastasis. Bioluminescence imaging, micro-CT), and histological analyses were applied to monitor and evaluate bone metastases. RNA-sequencing, bioinformatic, and biochemical analyses were used to understand nitazoxanide (NTZ)-regulated genes, signaling pathways, and the underlying mechanisms. The binding of NTZ to KLF5 proteins was evaluated using fluorescence titration, high-performance liquid chromatography (HPLC), and circular dichroism (CD) analysis. RESULTS NTZ, an anthelmintic agent, was identified as a potent invasion inhibitor in the screening and validation assays. In KLF5K369Q-induced bone metastasis, NTZ exerted a potent inhibitory effect in preventive and therapeutic modes. NTZ also inhibited osteoclast differentiation, a cellular process responsible for bone metastasis induced by KLF5K369Q. NTZ attenuated the function of KLF5K369Q in 127 genes' upregulation and 114 genes' downregulation. Some genes' expression changes were significantly associated with worse overall survival in patients with prostate cancer. One such change was the upregulation of MYBL2, which functionally promotes bone metastasis in prostate cancer. Additional analyses demonstrated that NTZ bound to the KLF5 protein, KLF5K369Q bound to the promoter of MYBL2 to activate its transcription, and NTZ attenuated the binding of KLF5K369Q to the MYBL2 promoter. CONCLUSIONS NTZ is a potential therapeutic agent for bone metastasis induced by the TGF-β/Ac-KLF5 signaling axis in prostate cancer and likely other cancers.
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Affiliation(s)
- Qingqing Huang
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen, 518055, China
| | - Mingcheng Liu
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen, 518055, China
| | - Duo Zhang
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen, 518055, China
| | - Bing-Biao Lin
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen, 518055, China.,Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518000, China
| | - Xing Fu
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen, 518055, China
| | - Zhiqian Zhang
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen, 518055, China
| | - Baotong Zhang
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen, 518055, China
| | - Jin-Tang Dong
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen, 518055, China.
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Carbapenem use correlates with percentage of patients with COVID-19 in intensive care units. Infection 2022; 51:331-336. [PMID: 35716341 PMCID: PMC9206090 DOI: 10.1007/s15010-022-01867-y] [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] [Received: 04/13/2022] [Accepted: 05/30/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND The first wave of COVID-19 pandemic may have significantly impacted antimicrobial consumption in hospitals. The objective of this study was to assess the evolution of carbapenem consumption and describe the implemented measures during the first year of the COVID-19 pandemic. METHODS We calculated carbapenem consumption for all the hospital and for intensive care units (ICU) for three periods: baseline (before COVID-19 cases, January 2019-February 2020), and the period of COVID-19 cases as a pre-intervention (March-August 2020) and a post-intervention phase (September 2020-December 2021). RESULTS During the study period, the percentage of admitted COVID-19 patients increased in the months of April-August of 2020 (pre-intervention period) from 5 to 26% of total admitted patients. The consumption of carbapenems (DDD/1000 patient days) increased from a mean of 67.1 at baseline to 142.9 pre-intervention. In ICUS, there was an increase in the mean from 125.7 to 240.8 DDD/1000 patient days. After interventions, the DDD/1000 patient days decreased by 49.5% overall the hospital and by 36% in ICUs. For the post-intervention period, there was a correlation between COVID-19 cases and carbapenem usage in the ICU but not the overall hospital. CONCLUSION An increase in the antimicrobial consumption during the first wave of COVID-19 pandemic was noticed, especially in the ICU. Antimicrobial stewardship programs are essential to reduce consumption rate.
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