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Kumar GS, Dubey A, Panda SP, Alawi MM, Sindi AA, Azhar EI, Dwivedi VD, Agrawal S. Repurposing of antibacterial compounds for suppression of Mycobacterium tuberculosis dormancy reactivation by targeting resuscitation-promoting factors B. J Biomol Struct Dyn 2023:1-13. [PMID: 37551014 DOI: 10.1080/07391102.2023.2245059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Tuberculosis infection has always been a global concern for public health, and the mortality rate has increased tremendously every year. The ability of the resuscitation Mycobacterium tuberculosis (Mtb) from the dormant state is one of the major reasons for the epidemic spread of tuberculosis infection, especially latent tuberculosis infection (LTBI). The element that encourages resuscitation, RpfB (resuscitation-promoting factors B), is mostly in charge of bringing Mtb out of slumber. This reason makes RpfB a promising target for developing tuberculosis drugs because of the effects of latent tuberculosis. Therefore, this work was executed using a computational three-level screening of the Selleckhem antibiotics database consisting of 462 antibiotics against the ligand binding region of the RpfB protein, followed by an estimation of binding free energy for ideal identification and confirmation of potential RpfB inhibitor. Subsequently, three antibiotic drug molecules, i.e., Amikacin hydrate (-66.87 kcal/mol), Isepamicin sulphate (-60.8 kcal/mol), and Bekanamycin (-46.89 kcal/mol), were selected on the basis of their binding free energy value for further computational studies in comparison to reference ligand, 4-benzoyl-2-nitrophenyl thiocyanate (NPT7). Based on the intermolecular interaction profiling, 200 ns molecular dynamic simulation (MD), post-simulation analysis and principal component analysis (PCA), the selected antibiotics showed substantial stability with the RpfB protein compared to the NPT7 inhibitor. Conclusively based on the computational results, the preferred drugs can be potent inhibitors of the RpfB protein, which can be further validated using in vivo research and in vitro enzyme inhibition to understand their therapeutic activity against tuberculosis infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India
| | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, India
| | - Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, India
| | - Maha M Alawi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anees A Sindi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pulmonary and Critical Care Department, International Medical Center Hospital, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Sharad Agrawal
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India
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Yasir M, Al-Sharif HA, Al-Subhi T, Sindi AA, Bokhary DH, El-Daly MM, Alosaimi B, Hamed ME, Karim AM, Hassan AM, AlShawdari MM, Alawi M, El-Kafrawy SA, Azhar EI. Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia. J Infect Public Health 2023; 16:680-688. [PMID: 36934642 PMCID: PMC9984237 DOI: 10.1016/j.jiph.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/11/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Infection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health. METHODS A total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 6S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens. RESULTS No significant (p > 0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p < 0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7 %) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1. CONCLUSIONS Overall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Hessa A Al-Sharif
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Tagreed Al-Subhi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Anees A Sindi
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Pulmonary & Critical Care Consultant, International Medical Center, Jeddah 21589, Saudi Arabia
| | - Diyaa H Bokhary
- Emergency Medicine Department, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mai M El-Daly
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Bandar Alosaimi
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Maaweya E Hamed
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Asad Mustafa Karim
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, the Republic of Korea
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mustafa M AlShawdari
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Maha Alawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Infection Control & Environmental Health Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sherif A El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Sindi AA, Tashkandi WA, Jastaniah MW, Bashanfar MA, Fakhri AF, Alsallum FS, Alguydi HB, Elhazmi A, Al-Khatib TA, Alawi MM, Abushoshah I. Impact of diabetes mellitus and co-morbidities on mortality in patients with COVID-19: A single-center retrospective study. Saudi Med J 2023; 44:67-73. [PMID: 36634951 PMCID: PMC9987682 DOI: 10.15537/smj.2023.44.1.20220462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/09/2022] [Indexed: 01/14/2023] Open
Abstract
OBJECTIVES To describe the effect of diabetes mellitus (DM) on clinical outcomes of patients admitted with COVID-19 infection. METHODS We carried out a single center, observational, retrospective study. We included adult patients with laboratory-confirmed diagnosis of COVID-19 admitted to a tertiary hospital in Jeddah, Saudi Arabia, from April 2020 to December 2020. Electronic medical records were reviewed for demographics, clinical status, hospital course, and outcome; and they were compared between the patients with or without DM. RESULTS Out of 198 patients included in the study, 86 (43.4%) were diabetic and 112 (56.5%) were non-diabetic. Majority of the patients were males 139 (70.2%) with a mean age of 54.14±14.89 years. In-hospital mortality rate was higher in diabetic patients than in non-diabetic patients (40 vs. 32; p=0.011). The most common comorbidity was hypertension (n=95, 48%) followed by ischemic heart disease (n=35, 17.7%), chronic kidney disease (n=17, 9.6%), and bronchial asthma (n=10, 5.1%). CONCLUSION The risk of SARS-CoV-2 infection is higher among diabetic patients; particularly, those with preexisting co-morbidities or geriatric patients. Diabetic patients are prone to a severe clinical course of COVID-19 and a significantly higher mortality rate.
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Affiliation(s)
- Anees A. Sindi
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
- Address correspondence and reprint request to: Dr. Anees A. Sindi, Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia. E-mail: ORCID ID: https://orcid.org/0000-0002-5854-6298
| | - Wail A. Tashkandi
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
| | - Mohammed W. Jastaniah
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
| | - Mohammed A. Bashanfar
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
| | - Ahmed F. Fakhri
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
| | - Fahad S. Alsallum
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
| | - Hamdan B. Alguydi
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
| | - Alyaa Elhazmi
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
| | - Talal A. Al-Khatib
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
| | - Maha M. Alawi
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
| | - Ibrahim Abushoshah
- From the Department of Anesthesia and Critical Care (Sindi, Abushoshah), from the Department of Surgery (Tashkandi), from the Department of Otolaryngology-Head Neck Surgery (Al-Khatib), from the Unit of Infection Control & Environmental Health (Alawi), Department of Medical Microbiology & Parasitology (Alawi), Faculty of Medicine (Jastaniah, Bashanfar, Fakhri, Alguydi, Alsallum), King Abdulaziz University and King Abdulaziz University Hospital, Jeddah, Saudi Arabia, from the College of Medicine (Elhazmi), Alfaisal University, and from the Research Center (Elhazmi), Dr. Sulaiman Al-Habib Medical Group, Riyadh, Kingdom of Saudi Arabia.
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Bajrai LH, Khateb AM, Alawi MM, Felemban HR, Sindi AA, Dwivedi VD, Azhar EI. Glycosylated Flavonoid Compounds as Potent CYP121 Inhibitors of Mycobacterium tuberculosis. Biomolecules 2022; 12:1356. [PMID: 36291570 PMCID: PMC9599785 DOI: 10.3390/biom12101356] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 07/30/2023] Open
Abstract
Due to the concerning rise in the number of multiple- and prolonged-drug-resistant (MDR and XDR) Mycobacterium tuberculosis (Mtb) strains, unprecedented demand has been created to design and develop novel therapeutic drugs with higher efficacy and safety. In this study, with a focused view on implementing an in silico drug design pipeline, a diverse set of glycosylated flavonoids were screened against the Mtb cytochrome-P450 enzyme 121 (CYP121), which is established as an approved drug target for the treatment of Mtb infection. A total of 148 glycosylated flavonoids were screened using structure-based virtual screening against the crystallized ligand, i.e., the L44 inhibitor, binding pocket in the Mtb CYP121 protein. Following this, only the top six compounds with the highest binding scores (kcal/mol) were considered for further intermolecular interaction and dynamic stability using 100 ns classical molecular dynamics simulation. These results suggested a considerable number of hydrogen and hydrophobic interactions and thermodynamic stability in comparison to the reference complex, i.e., the CYP121-L44 inhibitor. Furthermore, binding free energy via the MMGBSA method conducted on the last 10 ns interval of MD simulation trajectories revealed the substantial affinity of glycosylated compounds with Mtb CYP121 protein against reference complex. Notably, both the docked poses and residual energy decomposition via the MMGBSA method demonstrated the essential role of active residues in the interactions with glycosylated compounds by comparison with the reference complex. Collectively, this study demonstrates the viability of these screened glycosylated flavonoids as potential inhibitors of Mtb CYP121 for further experimental validation to develop a therapy for the treatment of drug-resistant Mtb strains.
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Affiliation(s)
- Leena Hussein Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Aiah M. Khateb
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Taibah University, Madinah 42353, Saudi Arabia
| | - Maha M. Alawi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Infection Control & Environmental Health Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hashim R. Felemban
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Anees A. Sindi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Bioinformatics Research Division, Quanta Calculus Pvt. Ltd., Greater Noida 201310, India
- Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
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Sindi AA, Alsayed SM, Abushoshah I, Bokhary DH, Tashkandy NR. Profile of the Gut Microbiome Containing Carbapenem-Resistant Enterobacteriaceae in ICU Patients. Microorganisms 2022; 10:microorganisms10071309. [PMID: 35889029 PMCID: PMC9320093 DOI: 10.3390/microorganisms10071309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) is a risk to public health worldwide and causes epidemic outbreaks in hospitals. The identification of alterations in the gut microbial profile can potentially serve as an early diagnostic tool to prevent harmful bacterial colonization. The purpose of this study was to characterize the gut microbiota profile of CRE-positive stool samples using 16S rRNA gene sequencing and to compare it with that of healthy control groups at King AbdulAziz University Hospital. Our results demonstrate that compared to the control group samples, the CRE-positive and CRE-negative group samples were less diverse and were dominated by a few operational taxonomic clusters of Enterococcus, Sphingomonas, and Staphylococcus. An analysis of samples from CRE-positive patients revealed Pseudomonas as the most abundant taxon. The existence of Pseudomonas in clinical samples undoubtedly indicates the development of resistance to a variety of antimicrobial drugs, with a less diverse microbiota. In our study, we found that the co-occurrence patterns of Klebsiella, Parabacteroides, Proteus and Pseudomonas differed between the CRE-negative and control stool groups.
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Affiliation(s)
- Anees A. Sindi
- Department of Anesthesia and Critical Care, Faculty of Medicine, King AbdulAziz University, Jeddah 21598, Saudi Arabia; (A.A.S.); (I.A.)
| | - Sarah M. Alsayed
- Department of Biological Sciences, Faculty of Science, King AbdulAziz University, Jeddah 21598, Saudi Arabia;
| | - Ibrahim Abushoshah
- Department of Anesthesia and Critical Care, Faculty of Medicine, King AbdulAziz University, Jeddah 21598, Saudi Arabia; (A.A.S.); (I.A.)
| | - Diyaa H. Bokhary
- Department of Emergency Medicine, King Abdulaziz University Hospital, Jeddah 22252, Saudi Arabia;
| | - Nisreen R. Tashkandy
- Department of Biological Sciences, Faculty of Science, King AbdulAziz University, Jeddah 21598, Saudi Arabia;
- Correspondence:
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Jose J, Al-Dorzi HM, Al-Omari A, Mandourah Y, Al-Hameed F, Sadat M, Al Qasim E, Alraddadi B, Al Harthy A, Al Mekhlafi GA, Almotairi A, Al Khatib K, Abdulmomen A, Qushmaq I, Sindi AA, Mady A, Solaiman O, Al-Raddadi R, Maghrabi K, Ragab A, Kharaba A, Shalhoub S, Al-Aithan AM, Vishwakarma GK, Bhattacharjee A, Arabi YM. Critically ill patients with diabetes and Middle East respiratory syndrome: a multi-center observational study. BMC Infect Dis 2021; 21:84. [PMID: 33468070 PMCID: PMC7814976 DOI: 10.1186/s12879-021-05771-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/06/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Diabetes is a risk factor for infection with coronaviruses. This study describes the demographic, clinical data, and outcomes of critically ill patients with diabetes and Middle East Respiratory Syndrome (MERS). METHODS This retrospective cohort study was conducted at 14 hospitals in Saudi Arabia (September 2012-January 2018). We compared the demographic characteristics, underlying medical conditions, presenting symptoms and signs, management and clinical course, and outcomes of critically ill patients with MERS who had diabetes compared to those with no diabetes. Multivariable logistic regression analysis was performed to determine if diabetes was an independent predictor of 90-day mortality. RESULTS Of the 350 critically ill patients with MERS, 171 (48.9%) had diabetes. Patients with diabetes were more likely to be older, and have comorbid conditions, compared to patients with no diabetes. They were more likely to present with respiratory failure requiring intubation, vasopressors, and corticosteroids. The median time to clearance of MERS-CoV RNA was similar (23 days (Q1, Q3: 17, 36) in patients with diabetes and 21.0 days (Q1, Q3: 10, 33) in patients with no diabetes). Mortality at 90 days was higher in patients with diabetes (78.9% versus 54.7%, p < 0.0001). Multivariable regression analysis showed that diabetes was an independent risk factor for 90-day mortality (odds ratio, 2.09; 95% confidence interval, 1.18-3.72). CONCLUSIONS Half of the critically ill patients with MERS have diabetes; which is associated with more severe disease. Diabetes is an independent predictor of mortality among critically patients with MERS.
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Affiliation(s)
- Jesna Jose
- Department of Biostatistics and Bioinformatics, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Department of Mathematics & Computing, Indian Institute of Technology (ISM), Dhanbad, Jharkhand 826004 India
| | - Hasan M. Al-Dorzi
- Intensive Care Department, Ministry of National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Awad Al-Omari
- Department of Intensive Care, College of Medicine, Alfaisal University, Dr Sulaiman Al-Habib Group Hospitals, Riyadh, Saudi Arabia
| | - Yasser Mandourah
- Military Medical Services, Ministry of Defense, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Fahad Al-Hameed
- Department of Intensive Care, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Musharaf Sadat
- Intensive Care Department, Ministry of National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Eman Al Qasim
- Intensive Care Department, Ministry of National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Basem Alraddadi
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
- Department of Medicine, University of Jeddah, Jeddah, Saudi Arabia
| | | | - Ghaleb A. Al Mekhlafi
- Department of Intensive Care Services, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Abdullah Almotairi
- Department of Critical Care Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Kasim Al Khatib
- Intensive Care Department, Al-Noor Specialist Hospital, Makkah, Saudi Arabia
| | - Ahmed Abdulmomen
- Department of Critical Care Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ismael Qushmaq
- Section of Critical Care Medicine, Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Anees A. Sindi
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Mady
- Intensive Care Department, King Saud Medical City, Riyadh, Saudi Arabia
- Tanta University Hospitals, Tanta, Egypt
| | - Othman Solaiman
- Intensive Care Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rajaa Al-Raddadi
- Department of Community Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalid Maghrabi
- Intensive Care Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ahmed Ragab
- Intensive Care Department, King Fahd Hospital, Jeddah, Saudi Arabia
| | - Ayman Kharaba
- Department of Critical Care, King Fahad Hospital, Ohoud Hospital, Al-Madinah, Saudi Arabia
| | - Sarah Shalhoub
- Department of Medicine, Division of Infectious Diseases, University of Western Ontario, London, Canada
- King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Abdulsalam M. Al-Aithan
- Department of Medicine, Critical Care Division, King Abdulaziz Hospital, Al Ahsa, Saudi Arabia
| | - Gajendra K. Vishwakarma
- Department of Mathematics & Computing, Indian Institute of Technology (ISM), Dhanbad, Jharkhand 826004 India
| | - Atanu Bhattacharjee
- Homi Bhaba National Institute, Section of Biostatistics, Centre for Cancer Epidemiology, Tata Memorial Centre, Navi Mumbai, India
| | - Yaseen M. Arabi
- Intensive Care Department, Ministry of National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - The Saudi Critical Care Trials Group
- Department of Biostatistics and Bioinformatics, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Department of Mathematics & Computing, Indian Institute of Technology (ISM), Dhanbad, Jharkhand 826004 India
- Intensive Care Department, Ministry of National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Department of Intensive Care, College of Medicine, Alfaisal University, Dr Sulaiman Al-Habib Group Hospitals, Riyadh, Saudi Arabia
- Military Medical Services, Ministry of Defense, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- Department of Intensive Care, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Jeddah, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
- Department of Medicine, University of Jeddah, Jeddah, Saudi Arabia
- Intensive Care Department, King Saud Medical City, Riyadh, Saudi Arabia
- Department of Intensive Care Services, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- Department of Critical Care Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
- Intensive Care Department, Al-Noor Specialist Hospital, Makkah, Saudi Arabia
- Department of Critical Care Medicine, King Saud University, Riyadh, Saudi Arabia
- Section of Critical Care Medicine, Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Tanta University Hospitals, Tanta, Egypt
- Intensive Care Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Community Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Intensive Care Department, King Fahd Hospital, Jeddah, Saudi Arabia
- Department of Critical Care, King Fahad Hospital, Ohoud Hospital, Al-Madinah, Saudi Arabia
- Department of Medicine, Division of Infectious Diseases, University of Western Ontario, London, Canada
- King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
- Department of Medicine, Critical Care Division, King Abdulaziz Hospital, Al Ahsa, Saudi Arabia
- Homi Bhaba National Institute, Section of Biostatistics, Centre for Cancer Epidemiology, Tata Memorial Centre, Navi Mumbai, India
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7
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Arabi YM, Shalhoub S, Mandourah Y, Al-Hameed F, Al-Omari A, Al Qasim E, Jose J, Alraddadi B, Almotairi A, Al Khatib K, Abdulmomen A, Qushmaq I, Sindi AA, Mady A, Solaiman O, Al-Raddadi R, Maghrabi K, Ragab A, Al Mekhlafi GA, Balkhy HH, Al Harthy A, Kharaba A, Gramish JA, Al-Aithan AM, Al-Dawood A, Merson L, Hayden FG, Fowler R. Ribavirin and Interferon Therapy for Critically Ill Patients With Middle East Respiratory Syndrome: A Multicenter Observational Study. Clin Infect Dis 2020; 70:1837-1844. [PMID: 31925415 PMCID: PMC7108209 DOI: 10.1093/cid/ciz544] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 06/21/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The objective of this study was to evaluate the effect of ribavirin and recombinant interferon (RBV/rIFN) therapy on the outcomes of critically ill patients with Middle East respiratory syndrome (MERS), accounting for time-varying confounders. METHODS This is a retrospective cohort study of critically ill patients with laboratory-confirmed MERS from 14 hospitals in Saudi Arabia diagnosed between September 2012 and January 2018. We evaluated the association of RBV/rIFN with 90-day mortality and MERS coronavirus (MERS-CoV) RNA clearance using marginal structural modeling to account for baseline and time-varying confounders. RESULTS Of 349 MERS patients, 144 (41.3%) patients received RBV/rIFN (RBV and/or rIFN-α2a, rIFN-α2b, or rIFN-β1a; none received rIFN-β1b). RBV/rIFN was initiated at a median of 2 days (Q1, Q3: 1, 3 days) from intensive care unit admission. Crude 90-day mortality was higher in patients with RBV/rIFN compared to no RBV/rIFN (106/144 [73.6%] vs 126/205 [61.5%]; P = .02]. After adjusting for baseline and time-varying confounders using a marginal structural model, RBV/rIFN was not associated with changes in 90-day mortality (adjusted odds ratio, 1.03 [95% confidence interval {CI}, .73-1.44]; P = .87) or with more rapid MERS-CoV RNA clearance (adjusted hazard ratio, 0.65 [95% CI, .30-1.44]; P = .29). CONCLUSIONS In this observational study, RBV/rIFN (RBV and/or rIFN-α2a, rIFN-α2b, or rIFN-β1a) therapy was commonly used in critically ill MERS patients but was not associated with reduction in 90-day mortality or in faster MERS-CoV RNA clearance.
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Affiliation(s)
- Yaseen M Arabi
- Intensive Care Department, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Sarah Shalhoub
- Department of Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada.,King Fahad Armed Forces Hospital, Jeddah
| | - Yasser Mandourah
- Military Medical Services, Ministry of Defense, Prince Sultan Military Medical City, Riyadh
| | - Fahad Al-Hameed
- Department of Intensive Care, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Jeddah
| | - Awad Al-Omari
- Department of Intensive Care, College of Medicine, Alfaisal University, Dr Sulaiman Al-Habib Group Hospitals, Riyadh
| | - Eman Al Qasim
- Intensive Care Department, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Jesna Jose
- Intensive Care Department, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Basem Alraddadi
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah.,Department of Medicine, University of Jeddah
| | | | - Kasim Al Khatib
- Intensive Care Department, Al-Noor Specialist Hospital, Makkah
| | - Ahmed Abdulmomen
- Department of Critical Care Medicine, King Saud University, Riyadh
| | - Ismael Qushmaq
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah
| | - Anees A Sindi
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah
| | - Ahmed Mady
- Intensive Care Department, King Saud Medical City, Riyadh, Saudi Arabia.,Tanta University Hospitals, Egypt
| | - Othman Solaiman
- Intensive Care Department, King Faisal Specialist Hospital and Research Center, Riyadh
| | - Rajaa Al-Raddadi
- Department of Community Medicine, Faculty of Medicine, King Abdulaziz University
| | - Khalid Maghrabi
- Intensive Care Department, King Faisal Specialist Hospital and Research Center, Riyadh
| | - Ahmed Ragab
- Intensive Care Department, King Fahd Hospital, Jeddah
| | | | - Hanan H Balkhy
- Department of Infection Prevention and Control, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh
| | | | - Ayman Kharaba
- Department of Critical Care, King Fahad Hospital, Ohoud Hospital, Al-Madinah
| | - Jawaher A Gramish
- Pharmaceutical Care Department, College of Pharmacy, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh
| | - Abdulsalam M Al-Aithan
- Department of Medicine, Critical Care Division, King Abdulaziz Hospital, Al Ahsa, Saudi Arabia
| | - Abdulaziz Al-Dawood
- Intensive Care Department, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Laura Merson
- International Severe Acute Respiratory and Emerging Infection Consortium, Infectious Diseases Data Observatory, Oxford University, United Kingdom
| | - Frederick G Hayden
- International Severe Acute Respiratory and Emerging Infection Consortium, Infectious Diseases Data Observatory, Oxford University, United Kingdom.,Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville
| | - Robert Fowler
- Institute of Health Policy Management and Evaluation, University of Toronto, Department of Critical Care Medicine and Department of Medicine, Sunnybrook Hospital, Ontario, Canada
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8
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Arabi YM, Mandourah Y, Al-Hameed F, Sindi AA, Almekhlafi GA, Hussein MA, Jose J, Pinto R, Al-Omari A, Kharaba A, Almotairi A, Al Khatib K, Alraddadi B, Shalhoub S, Abdulmomen A, Qushmaq I, Mady A, Solaiman O, Al-Aithan AM, Al-Raddadi R, Ragab A, Balkhy HH, Al Harthy A, Deeb AM, Al Mutairi H, Al-Dawood A, Merson L, Hayden FG, Fowler RA. Corticosteroid Therapy for Critically Ill Patients with Middle East Respiratory Syndrome. Am J Respir Crit Care Med 2019; 197:757-767. [PMID: 29161116 DOI: 10.1164/rccm.201706-1172oc] [Citation(s) in RCA: 762] [Impact Index Per Article: 152.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RATIONALE Corticosteroid therapy is commonly used among critically ill patients with Middle East Respiratory Syndrome (MERS), but its impact on outcomes is uncertain. Analyses of observational studies often do not account for patients' clinical condition at the time of corticosteroid therapy initiation. OBJECTIVES To investigate the association of corticosteroid therapy on mortality and on MERS coronavirus RNA clearance in critically ill patients with MERS. METHODS ICU patients with MERs were included from 14 Saudi Arabian centers between September 2012 and October 2015. We performed marginal structural modeling to account for baseline and time-varying confounders. MEASUREMENTS AND MAIN RESULTS Of 309 patients, 151 received corticosteroids. Corticosteroids were initiated at a median of 3.0 days (quartile 1 [Q1]-Q3, 1.0-7.0) from ICU admission. Patients who received corticosteroids were more likely to receive invasive ventilation (141 of 151 [93.4%] vs. 121 of 158 [76.6%]; P < 0.0001) and had higher 90-day crude mortality (112 of 151 [74.2%] vs. 91 of 158 [57.6%]; P = 0.002). Using marginal structural modeling, corticosteroid therapy was not significantly associated with 90-day mortality (adjusted odds ratio, 0.75; 95% confidence interval, 0.52-1.07; P = 0.12) but was associated with delay in MERS coronavirus RNA clearance (adjusted hazard ratio, 0.35; 95% CI, 0.17-0.72; P = 0.005). CONCLUSIONS Corticosteroid therapy in patients with MERS was not associated with a difference in mortality after adjustment for time-varying confounders but was associated with delayed MERS coronavirus RNA clearance. These findings highlight the challenges and importance of adjusting for baseline and time-varying confounders when estimating clinical effects of treatments using observational studies.
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Affiliation(s)
| | - Yasser Mandourah
- 3 Department of Intensive Care Services, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Fahad Al-Hameed
- 4 Department of Intensive Care, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Anees A Sindi
- 5 Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ghaleb A Almekhlafi
- 3 Department of Intensive Care Services, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | | | - Jesna Jose
- 6 Department of Biostatistics and Bioinformatics, and
| | - Ruxandra Pinto
- 7 Sunnybrook Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Awad Al-Omari
- 8 College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,9 Department of Intensive Care, Dr. Sulaiman Al-Habib Group Hospitals, Riyadh, Saudi Arabia
| | - Ayman Kharaba
- 10 Department of Critical Care, King Fahad Hospital, Al-Madinah Al-Monawarah, Saudi Arabia.,11 Department of Critical Care, Ohoud Hospital, Al-Madinah Al-Monawarah, Saudi Arabia
| | - Abdullah Almotairi
- 12 Department of Critical Care Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Kasim Al Khatib
- 13 Intensive Care Department, Al-Noor Specialist Hospital, Makkah, Saudi Arabia
| | - Basem Alraddadi
- 8 College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,14 Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Sarah Shalhoub
- 15 Division of Infectious Diseases, Department of Medicine, King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Ahmed Abdulmomen
- 16 Department of Critical Care Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ismael Qushmaq
- 14 Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Ahmed Mady
- 17 Department of Anesthesiology and Intensive Care, Tanta University Hospitals, Tanta, Egypt.,18 Intensive Care Department, King Saud Medical City, Riyadh, Saudi Arabia
| | - Othman Solaiman
- 19 King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Rajaa Al-Raddadi
- 21 Department of Research, Ministry of Health, Jeddah, Saudi Arabia
| | - Ahmed Ragab
- 22 Intensive Care Department, King Fahd Hospital, Jeddah, Saudi Arabia
| | - Hanan H Balkhy
- 1 College of Medicine.,23 Department of Infection Prevention and Control, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abdulrahman Al Harthy
- 17 Department of Anesthesiology and Intensive Care, Tanta University Hospitals, Tanta, Egypt
| | - Ahmad M Deeb
- 24 Research Office, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Hanan Al Mutairi
- 24 Research Office, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | | | - Laura Merson
- 25 International Severe Acute Respiratory and Emerging Infection Consortium, Infectious Diseases Data Observatory, Oxford University, Oxford, United Kingdom
| | - Frederick G Hayden
- 25 International Severe Acute Respiratory and Emerging Infection Consortium, Infectious Diseases Data Observatory, Oxford University, Oxford, United Kingdom.,26 Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Robert A Fowler
- 27 Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; and.,28 Department of Critical Care Medicine and.,29 Department of Medicine, Sunnybrook Hospital, Toronto, Ontario, Canada
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9
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Hashem AM, Azhar EI, Shalhoub S, Abujamel TS, Othman NA, Al Zahrani AB, Abdullah HM, Al-Alawi MM, Sindi AA. Genetic characterization and diversity of circulating influenza A/H1N1pdm09 viruses isolated in Jeddah, Saudi Arabia between 2014 and 2015. Arch Virol 2018; 163:1219-1230. [PMID: 29396684 DOI: 10.1007/s00705-018-3732-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 12/19/2017] [Indexed: 12/28/2022]
Abstract
The emerged influenza A/H1N1pdm09 viruses have replaced the previously circulating seasonal H1N1 viruses. The close antigenic properties of these viruses to the 1918 H1N1 pandemic viruses and their post-pandemic evolution pattern could further enhance their adaptation and pathogenicity in humans representing a major public health threat. Given that data on the dynamics and evolution of these viruses in Saudi Arabia is sparse we investigated the genetic diversity of circulating influenza A/H1N1pdm09 viruses from Jeddah, Saudi Arabia, by analyzing 39 full genomes from isolates obtained between 2014-2015, from patients with varying symptoms. Phylogenetic analysis of all gene segments and concatenated genomes showed similar topologies and co-circulation of clades 6b, 6b.1 and 6b.2, with clade 6b.1 being the most predominate since 2015. Most viruses were more closely related to the vaccine strain (Michigan/45/2015) recommended for the 2017/2018 season, than to the California/07/2009 strain. Low sequence variability was observed in the haemagglutinin protein compared to the neuraminidase protein. Resistance to neuraminidase inhibitors was limited as only one isolate had the H275Y substitution. Interestingly, two isolates had short PA-X proteins of 206 amino acids compared to the 232 amino acid protein found in most influenza A/H1N1pdm09 viruses. Together, the co-circulation of several clades and the predominance of clade 6b.1, despite its low circulation in Asia in 2015, suggests multiple introductions most probably during the mass gathering events of Hajj and Umrah. Jeddah represents the main port of entry to the holy cities of Makkah and Al-Madinah, emphasizing the need for vigilant surveillance in the kingdom.
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MESH Headings
- Amino Acid Substitution
- Female
- Genetic Variation
- Genome, Viral
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/transmission
- Influenza, Human/virology
- Male
- Nasopharynx/virology
- Neuraminidase/genetics
- Phylogeny
- RNA, Viral/genetics
- Saudi Arabia/epidemiology
- Seasons
- Sequence Analysis, DNA
- Viral Proteins/genetics
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Affiliation(s)
- Anwar M Hashem
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Esam I Azhar
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Sarah Shalhoub
- Division of Infectious Diseases, Department of Medicine, King Fahd Armed Forces Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Turki S Abujamel
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Norah A Othman
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abdulwahab B Al Zahrani
- Molecular Diagnostics Laboratory, King Fahd Armed Forces Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Hanan M Abdullah
- Students' Research and Innovation Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Maha M Al-Alawi
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Infection Control and Environmental Health Unit, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Anees A Sindi
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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