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Characterization of the Upper Respiratory Bacterial Microbiome in Critically Ill COVID-19 Patients. Biomedicines 2022; 10:biomedicines10050982. [PMID: 35625719 PMCID: PMC9138573 DOI: 10.3390/biomedicines10050982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/23/2022] Open
Abstract
The upper respiratory tract (URT) microbiome can contribute to the acquisition and severity of respiratory viral infections. The described associations between URT microbiota and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are limited at microbiota genus level and by the lack of functional interpretation. Our study, therefore, characterized the URT bacterial microbiome at species level and their encoded pathways in patients with COVID-19 and correlated these to clinical outcomes. Whole metagenome sequencing was performed on nasopharyngeal samples from hospitalized patients with critical COVID-19 (n = 37) and SARS-CoV-2-negative individuals (n = 20). Decreased bacterial diversity, a reduction in commensal bacteria, and high abundance of pathogenic bacteria were observed in patients compared to negative controls. Several bacterial species and metabolic pathways were associated with better respiratory status and lower inflammation. Strong correlations were found between species biomarkers and metabolic pathways associated with better clinical outcome, especially Moraxella lincolnii and pathways of vitamin K2 biosynthesis. Our study demonstrates correlations between the URT microbiome and COVID-19 patient outcomes; further studies are warranted to validate these findings and to explore the causal roles of the identified microbiome biomarkers in COVID-19 pathogenesis.
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2
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Kurra N, Woodard PI, Gandrakota N, Gandhi H, Polisetty SR, Ang SP, Patel KP, Chitimalla V, Ali Baig MM, Samudrala G. Opportunistic Infections in COVID-19: A Systematic Review and Meta-Analysis. Cureus 2022; 14:e23687. [PMID: 35505698 PMCID: PMC9055976 DOI: 10.7759/cureus.23687] [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] [Received: 03/16/2022] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
The prevalence, incidence, and characteristics of bacterial infections in patients infected with severe acute respiratory syndrome coronavirus 2 are not well understood and have been raised as an important knowledge gap. Therefore, our study focused on the most common opportunistic infections/secondary infections/superinfections in coronavirus disease 2019 (COVID-19) patients. This systematic review and meta-analysis was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Eligible studies were identified using PubMed/Medline since inception to June 25, 2021. Studies meeting the inclusion criteria were selected. Statistical analysis was conducted in Review Manager 5.4.1. A random-effect model was used when heterogeneity was seen to pool the studies, and the result was reported as inverse variance and the corresponding 95% confidence interval. We screened 701 articles comprising 22 cohort studies which were included for analysis. The pooled prevalence of opportunistic infections/secondary infections/superinfections was 16% in COVID-19 patients. The highest prevalence of secondary infections was observed among viruses at 33%, followed by bacteria at 16%, fungi at 6%, and 25% among the miscellaneous group/wrong outcome. Opportunistic infections are more prevalent in critically ill patients. The isolated pathogens included Epstein-Barr virus, Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, Hemophilus influenza, and invasive pulmonary aspergillosis. Large-scale studies are required to better identify opportunistic/secondary/superinfections in COVID-19 patients.
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Affiliation(s)
- Nithin Kurra
- Department of Neurology, University of Nebraska Medical Center, Omaha, USA
| | | | | | - Heli Gandhi
- Medicine and Surgery, Manipal Academy of Higher Education, Manipal, IND
| | | | - Song Peng Ang
- Medicine and Surgery, International Medical University, Kuala Lumpur, MYS
| | - Kinjalben P Patel
- Medicine and Surgery, Smt. B. K. Shah Medical Institute & Research Centre, Vadodara, IND
| | - Vishwaj Chitimalla
- Medicine and Surgery, Shri B M Patil Medical College Hospital and Research Centre, Bijapur Lingayat District Educational (BLDE) University, Vijayapura, IND
| | - Mirza M Ali Baig
- Department of Anaesthesiology, Dow University of Health Sciences, Karachi, PAK
| | - Gayathri Samudrala
- Obstetrics and Gynecology, National Board of Examinations, New Delhi, IND.,Medicine and Surgery, Dr. N. T. Ramarao University of Health Sciences, Vijayawada, IND
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3
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Markovskaya Y, Gavioli EM, Cusumano JA, Glatt AE. Coronavirus disease 2019 (COVID-19): Secondary bacterial infections and the impact on antimicrobial resistance during the COVID-19 pandemic. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2022; 2:e114. [PMID: 36483429 PMCID: PMC9726554 DOI: 10.1017/ash.2022.253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 05/16/2023]
Abstract
Secondary bacterial infections and bacterial coinfections are an important complication of coronavirus disease 2019 (COVID-19), leading to antibiotic overuse and increased rates of antimicrobial resistance (AMR) during the COVID-19 pandemic. In this literature review, we summarize the reported rates of secondary bacterial infections and bacterial coinfections in patients with COVID-19, the impact on patient outcomes, the antibiotic treatment approaches employed, and the resistance patterns observed. The reported data suggest that although the incidence of secondary bacterial infections or bacterial coinfections is relatively low, they are associated with worse outcomes such as prolonged hospitalization, intensive care unit admission, mechanical ventilator use, and increased mortality. Interestingly, antibiotic prescription rates are typically higher than secondary bacterial and bacterial coinfection rates, and reports of AMR are common. These findings highlight the need for an improved understanding of secondary bacterial and bacterial coinfection in patients with COVID-19, as well as improved treatment options, to mitigate inappropriate antibiotic prescribing and AMR.
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Affiliation(s)
- Yelena Markovskaya
- Department of Medicine, Mount Sinai South Nassau, Oceanside, NY, United States
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elizabeth M. Gavioli
- Department of Pharmacy Practice, Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, New York
| | - Jaclyn A. Cusumano
- Department of Pharmacy Practice, Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, New York
- Department of Pharmacy, Mount Sinai Queens, Queens, New York
| | - Aaron E. Glatt
- Department of Medicine, Mount Sinai South Nassau, Oceanside, NY, United States
- Icahn School of Medicine at Mount Sinai, New York, New York
- Author for correspondence: Aaron E. Glatt, MD, Mount Sinai South Nassau, Oceanside, NY 11791. E-mail:
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4
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Scott SJ, Pfotenhauer B, Weiner JJ, Hilleshiem J, Khubbar M, Bhattacharyya S. Respiratory Pathogen Coinfections in SARS-CoV-2-Positive Patients in Southeastern Wisconsin: A Retrospective Analysis. Microbiol Spectr 2021; 9:e0083121. [PMID: 34668725 PMCID: PMC8528126 DOI: 10.1128/spectrum.00831-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/21/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has infected all age groups and disproportionately impacted vulnerable populations globally. Polymicrobial infections may play an important role in the development of SARS-CoV-2 infection in susceptible hosts. These coinfections may increase the risk of disease severity and pose challenges to the diagnosis, treatment, and prognosis of COVID-19. There have been limited SARS-CoV-2 coinfection studies. In this retrospective study, residual nucleic acid extracts from 796 laboratory-confirmed COVID-19-positive specimens, collected between March 2020 and February 2021, were analyzed using a Luminex NxTAG respiratory pathogen panel (RPP). Of these, 745 returned valid results and were used for analysis; 53 (7.1%) were positive for one or more additional pathogens. Six different respiratory viruses were detected among the 53 SARS-CoV-2-positive patient specimens, and 7 of those specimens tested positive for more than one additional respiratory virus. The most common pathogens include rhinovirus/enterovirus (RV/EV) (n = 22, 41.51%), human metapneumovirus (hMPV) (n = 18, 33.9%), and adenovirus (n = 12, 22.6%). Interestingly, there were no SARS-CoV-2 coinfections involving influenza A or influenza B in the study specimens. The median age of the SARS-CoV-2-positive patients with coinfections was 38 years; 53% identified as female, and 47% identified as male. Based on our retrospective analysis, respiratory coinfections associated with SARS-CoV-2-positive patients were more common in young children (≤9 years old), with white being the most common race. Our findings will likely prompt additional investigation of polymicrobial infection associated with SARS-CoV-2 during seasonal respiratory pathogen surveillance by public health laboratories. IMPORTANCE This examination of respiratory pathogen coinfections in SARS-CoV-2 patients will likely shed light on our understanding of polymicrobial infection associated with COVID-19. Our results should prompt public health authorities to improve seasonal respiratory pathogen surveillance practices and address the risk of disease severity.
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Affiliation(s)
- Samantha J. Scott
- City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin, USA
| | - Beth Pfotenhauer
- City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin, USA
| | - Joshua J. Weiner
- City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin, USA
| | - Jordan Hilleshiem
- City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin, USA
| | - Manjeet Khubbar
- City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin, USA
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5
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Samoilov AE, Kaptelova VV, Bukharina AY, Shipulina OY, Korneenko EV, Saenko SS, Lukyanov AV, Grishaeva AA, Ploskireva AA, Speranskaya AS, Akimkin VG. Case report: change of dominant strain during dual SARS-CoV-2 infection. BMC Infect Dis 2021; 21:959. [PMID: 34530778 PMCID: PMC8443909 DOI: 10.1186/s12879-021-06664-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The dual infection with SARS-CoV-2 is poorly described and is currently under discussion. We present a study of two strains of SARS-CoV-2 detected in the same patient during the same disease presentation. CASE PRESENTATION A patient in their 90 s was hospitalised with fever. Oropharyngeal swab obtained on the next day (sample 1) tested positive for SARS-CoV-2. Five days later, the patient was transferred to the ICU (intensive care unit) of the hospital specialising in the treatment of COVID-19 patients, where the patient's condition progressively worsened and continuous oxygen insufflation was required. Repeated oropharyngeal swab (sample 2), which was taken eight days after the first one, also tested positive for SARS-CoV-2. After 5 days of ICU treatment, the patient died. The cause of death was a coronavirus infection, which progressed unfavourably due to premorbid status. We have performed sequencing of full SARS-CoV-2 genomes from oropharyngeal swabs obtained eight days apart. Genomic analysis revealed the presence of two genetically distant SARS-CoV-2 strains in both swabs. Detected strains belong to different phylogenetic clades (GH and GR) and differ in seven nucleotide positions. The relative abundance of strains was 70% (GH) and 30% (GR) in the first swab, and 3% (GH) and 97% (GR) in the second swab. CONCLUSIONS Our findings suggest that the patient was infected by two genetically distinct SARS-CoV-2 strains at the same time. One of the possible explanations is that the second infection was hospital-acquired. Change of the dominant strain ratio during disease manifestation could be explained by the advantage or higher virulence of the GR clade strain.
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Affiliation(s)
- Andrei E Samoilov
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia.
| | - Valeriia V Kaptelova
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia.
| | - Anna Y Bukharina
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia
| | - Olga Y Shipulina
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia
| | - Elena V Korneenko
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia
| | - Stepan S Saenko
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia
| | - Alexander V Lukyanov
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia
| | - Antonina A Grishaeva
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia
| | - Antonina A Ploskireva
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia
| | - Anna S Speranskaya
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia.
| | - Vasiliy G Akimkin
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia
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Malekifar P, Pakzad R, Shahbahrami R, Zandi M, Jafarpour A, Rezayat SA, Akbarpour S, Shabestari AN, Pakzad I, Hesari E, Farahani A, Soltani S. Viral Coinfection among COVID-19 Patient Groups: An Update Systematic Review and Meta-Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5313832. [PMID: 34485513 PMCID: PMC8416381 DOI: 10.1155/2021/5313832] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/10/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Coinfections have a potential role in increased morbidity and mortality rates during pandemics. Our investigation is aimed at evaluating the viral coinfection prevalence in COVID-19 patients. METHODS We systematically searched scientific databases, including Medline, Scopus, WOS, and Embase, from December 1, 2019, to December 30, 2020. Preprint servers such as medRxiv were also scanned to find other related preprint papers. All types of studies evaluating the viral coinfection prevalence in COVID-19 patients were considered. We applied the random effects model to pool all of the related studies. RESULTS Thirty-three studies including 10484 patients were identified. The viral coinfection estimated pooled prevalence was 12.58%; 95% CI: 7.31 to 18.96). Blood viruses (pooled prevalence: 12.48%; 95% CI: 8.57 to 16.93) had the most frequent viral coinfection, and respiratory viruses (pooled prevalence: 4.32%; 95% CI: 2.78 to 6.15) had less frequent viral coinfection. The herpesvirus pooled prevalence was 11.71% (95% CI: 3.02 to 24.80). Also, the maximum and minimum of viral coinfection pooled prevalence were in AMRO and EMRO with 15.63% (95% CI: 3.78 to 33.31) and 7.05% (95% CI: 3.84 to 11.07), respectively. CONCLUSION The lowest rate of coinfection belonged to respiratory viruses. Blood-borne viruses had the highest coinfection rate. Our results provide important data about the prevalence of blood-borne viruses among COVID-19 patients which can be critical when it comes to their treatment procedure.
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Affiliation(s)
- Pooneh Malekifar
- Department of Epidemiology, School of Public Health, Tehran University Medical Sciences, Tehran, Iran
| | - Reza Pakzad
- Department of Epidemiology, Faculty of Health, Ilam University Medical Sciences, Ilam, Iran
- Student Research Committee, Ilam University Medical Sciences, Ilam, Iran
| | - Ramin Shahbahrami
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Milad Zandi
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Jafarpour
- Gerash Amir-al-Momenin Medical and Educational Center, Gerash University of Medical Sciences, Gerash, Iran
| | - Sara Akhavan Rezayat
- Department of Management & Health Economics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Akbarpour
- Occupational Sleep Research Center, Baharloo Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Namazi Shabestari
- Department of Geriatric Medicine, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Iraj Pakzad
- Department of Microbiology, School of Medicine, Ilam University Medical Sciences, Ilam, Iran
| | - Elahe Hesari
- Department of Epidemiology, School of Public Health, Tehran University Medical Sciences, Tehran, Iran
| | - Abbas Farahani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Saber Soltani
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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7
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Soltani S, Faramarzi S, Zandi M, Shahbahrami R, Jafarpour A, Akhavan Rezayat S, Pakzad I, Abdi F, Malekifar P, Pakzad R. Bacterial coinfection among coronavirus disease 2019 patient groups: an updated systematic review and meta-analysis. New Microbes New Infect 2021; 43:100910. [PMID: 34226847 PMCID: PMC8245302 DOI: 10.1016/j.nmni.2021.100910] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/01/2021] [Accepted: 06/23/2021] [Indexed: 12/17/2022] Open
Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 raised the attention towards bacterial coinfection and its role in coronavirus disease 2019 (COVID-19) disease. This study aims to systematically review and identify the pooled prevalence of bacterial coinfection in the related articles. A comprehensive search was conducted in international databases, including MEDLINE, Scopus, Web of Science, and Embase, to identify the articles on the prevalence of bacterial coinfections in COIVD-19 patients from 1 December 2019 until 30 December 2020. All observational epidemiological studies that evaluated the prevalence of bacterial coinfections in patients with COVID-19 were included without any restriction. Forty-two studies including a total sample size of 54,695 were included in the analysis. The pooled estimate for the prevalence of bacterial coinfections was 20.97% (95% CI: 15.95-26.46), and the pooled prevalence of bacterial coinfections was 5.20% (95% CI: 2.39-8.91) for respiratory subtype and 4.79% (95% CI: 0.11-14.61) for the gastrointestinal subtype. The pooled prevalence for Eastern Mediterranean Regional Office and South-East Asia Regional Office was 100% (95% CI: 82.35-100.00) and 2.61% (95% CI: 1.74-3.62). This rate of coinfection poses a great danger towards patients, especially those in critical condition. Although there are multiple complications and adverse effects related to extensive use of antibiotics to treat patients with COVID-19, it seems there is no other option except applying them, and it needs to be done carefully.
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Affiliation(s)
- S. Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - S. Faramarzi
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - M. Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - R. Shahbahrami
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - A. Jafarpour
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
- Gerash Amir-al-Momenin Medical and Educational Center, Gerash University of Medical Sciences, Gerash, Iran
| | - S. Akhavan Rezayat
- Department of Management & Health Economics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - I. Pakzad
- Medical Microbiology, Department of Microbiology, School of Medicine, Ilam University Medical Sciences, Ilam, Iran
| | - F. Abdi
- School of Nursing and Midwifery, Alborz University of Medical Sciences, Karaj, Iran
| | - P. Malekifar
- Epidemiology, Department of Epidemiology, School of Public Health, Tehran University Medical Sciences, Tehran, Iran
| | - R. Pakzad
- Epidemiology, Department of Epidemiology, Faculty of Health, Ilam University Medical Sciences, Ilam, Iran
- Student Research Committee, Ilam University Medical Sciences, Ilam, Iran
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Yan H, Sun J, Wang K, Wang H, Wu S, Bao L, He W, Wang D, Zhu A, Zhang T, Gao R, Dong B, Li J, Yang L, Zhong M, Lv Q, Qin F, Zhuang Z, Huang X, Yang X, Li Y, Che Y, Jiang J. Repurposing carrimycin as an antiviral agent against human coronaviruses, including the currently pandemic SARS-CoV-2. Acta Pharm Sin B 2021; 11:2850-2858. [PMID: 33723501 PMCID: PMC7946546 DOI: 10.1016/j.apsb.2021.02.024] [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: 12/03/2020] [Revised: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 12/23/2022] Open
Abstract
COVID-19 pandemic caused by SARS-CoV-2 infection severely threatens global health and economic development. No effective antiviral drug is currently available to treat COVID-19 and any other human coronavirus infections. We report herein that a macrolide antibiotic, carrimycin, potently inhibited the cytopathic effects (CPE) and reduced the levels of viral protein and RNA in multiple cell types infected by human coronavirus 229E, OC43, and SARS-CoV-2. Time-of-addition and pseudotype virus infection studies indicated that carrimycin inhibited one or multiple post-entry replication events of human coronavirus infection. In support of this notion, metabolic labelling studies showed that carrimycin significantly inhibited the synthesis of viral RNA. Our studies thus strongly suggest that carrimycin is an antiviral agent against a broad-spectrum of human coronaviruses and its therapeutic efficacy to COVID-19 is currently under clinical investigation.
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Ventilator-Associated Pneumonia in Patients with COVID-19: A Systematic Review and Meta-Analysis. Antibiotics (Basel) 2021; 10:antibiotics10050545. [PMID: 34067186 PMCID: PMC8150614 DOI: 10.3390/antibiotics10050545] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/01/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
The aim of this systematic review and meta-analysis was to estimate the pooled occurrence of ventilator-associated pneumonia (VAP) among patients admitted to an intensive care unit with COVID-19 and mortality of those who developed VAP. We performed a systematic search on PubMed, EMBASE and Web of Science from inception to 2nd March 2021 for nonrandomized studies specifically addressing VAP in adult patients with COVID-19 and reporting data on at least one primary outcome of interest. Random effect single-arm meta-analysis was performed for the occurrence of VAP and mortality (at the longest follow up) and ICU length of stay. Twenty studies were included in the systematic review and meta-analysis, for a total of 2611 patients with at least one episode of VAP. The pooled estimated occurrence of VAP was of 45.4% (95% C.I. 37.8–53.2%; 2611/5593 patients; I2 = 96%). The pooled estimated occurrence of mortality was 42.7% (95% C.I. 34–51.7%; 371/946 patients; I2 = 82%). The estimated summary estimated metric mean ICU LOS was 28.58 days (95% C.I. 21.4–35.8; I2 = 98%). Sensitivity analysis showed that patients with COVID-19 may have a higher risk of developing VAP than patients without COVID-19 (OR 3.24; 95% C.I. 2.2–4.7; P = 0.015; I2 = 67.7%; five studies with a comparison group).
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8806 Russian patients demonstrate T cell count as better marker of COVID-19 clinical course severity than SARS-CoV-2 viral load. Sci Rep 2021; 11:9440. [PMID: 33941816 PMCID: PMC8093219 DOI: 10.1038/s41598-021-88714-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/13/2021] [Indexed: 12/11/2022] Open
Abstract
The article presents a comparative analysis of SARS-CoV-2 viral load (VL), T lymphocyte count and respiratory index PaO2:FiO2 ratio as prospective markers of COVID-19 course severity and prognosis. 8806 patients and asymptomatic carriers were investigated in time interval 15 March–19 December 2020. T cell count demonstrated better applicability as a marker of aggravating COVID-19 clinical course and unfavourable disease prognosis than SARS-CoV-2 VL or PaO2:FiO2 ratio taken alone. Using T cell count in clinical practice may provide an opportunity of early prediction of deteriorating a patient’s state.
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11
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Adeiza SS, Shuaibu AB, Shuaibu GM. Random effects meta-analysis of COVID-19/S. aureus partnership in co-infection. GMS HYGIENE AND INFECTION CONTROL 2020; 15:Doc29. [PMID: 33299742 PMCID: PMC7709160 DOI: 10.3205/dgkh000364] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aim: To assess the hypothesis that coinfection with SARS-CoV-2 and S. aureus exacerbates morbidity and mortality among patients, the study aims to report the pooled burden of S. aureus co-infections in patients hospitalized with COVID-19. Methods: We searched electronic databases and the bibliographies of pertinent papers for articles. We considered studies in which the core result was the number of patients with bacterial (S. aureus) co-infection. We performed random effects meta-analysis (REM) because the studies included were sampled from a universe of different populations and high heterogeneity was anticipated. Using the Cochran's Q statistic, the observed dispersion (heterogeneity) among effect sizes was assessed. The percentage of total variability in the estimates of the effect size was calculated with the I2 index. To check for publication bias, the Egger weighted regression, Begg rank correlation and meta-funnel plot were used. We conducted meta-regression analysis to evaluate the variability between our outcomes and the covariates using computational options such as "methods of moments" and then "maximum likelihood" ratio. Results: We included 18 studies and retrieved data for 63,370 patients hospitalized with influenza-like illness, of which about 14,369 (22.67%) tested positive for COVID-19 by rRT-PCR. Of this number, 8,249 (57.4%) patient samples were analyzed. Bacterial, fungal and viral agents were detected in 3,038 (36.8%); S. aureus in 1,192 (39.2%). Five studies reported MRSA co-infection. Study quality ranged from 6 to 9 (median 7.1) on a JBI scale. From the meta-analysis, 33.1% patients were found to be coinfected (95%, CI 18.0 to 52.6%, Q=3473: df=17, I2=99·48%, p=0.00). The rate of S. aureus /COVID-19 co-infection was 25.6% (95% CI: 15.6 to 39.0, Q=783.4, df=17, I2=97.702%, p=0.003).The proportion of COVID-19/S. aureus co-infected patients with MRSA was 53.9% (95% CI, 24.5 to 80.9, n=66, 5 studies, Q=29.32, df=4, I2=86.369%, p=0.000). With the multivariate meta-regression model, study type (p=0.029), quality (p=0.000) and country (p=0.000) were significantly associated with heterogeneity. Conclusions: The pooled rates of S. aureus among COVID-19 patients documented in this study support the concern of clinicians about the presence of S. aureus in co-infections. Improved antibiotic stewardship can be accomplished through rapid diagnosis by longitudinal sampling of patients.
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Affiliation(s)
- Suleiman Shuaibu Adeiza
- Department of Pharmaceutical Microbiology, Faculty of Pharmaceutical sciences, Ahmadu Bello University, Zaria, Kaduna, Nigeria
| | - Abdulmalik Bello Shuaibu
- Department of Veterinary Microbiology, Faculty of Veterinary medicine, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Gazali Mohammed Shuaibu
- Department of Microbiology, Faculty of sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
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Vlaeminck J, Raafat D, Surmann K, Timbermont L, Normann N, Sellman B, van Wamel WJB, Malhotra-Kumar S. Exploring Virulence Factors and Alternative Therapies against Staphylococcus aureus Pneumonia. Toxins (Basel) 2020; 12:toxins12110721. [PMID: 33218049 PMCID: PMC7698915 DOI: 10.3390/toxins12110721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/13/2022] Open
Abstract
Pneumonia is an acute pulmonary infection associated with high mortality and an immense financial burden on healthcare systems. Staphylococcus aureus is an opportunistic pathogen capable of inducing S. aureus pneumonia (SAP), with some lineages also showing multidrug resistance. Given the high level of antibiotic resistance, much research has been focused on targeting S. aureus virulence factors, including toxins and biofilm-associated proteins, in an attempt to develop effective SAP therapeutics. Despite several promising leads, many hurdles still remain for S. aureus vaccine research. Here, we review the state-of-the-art SAP therapeutics, highlight their pitfalls, and discuss alternative approaches of potential significance and future perspectives.
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Affiliation(s)
- Jelle Vlaeminck
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, 2610 Antwerp, Belgium; (J.V.); (L.T.)
| | - Dina Raafat
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, 17475 Greifswald, Germany; (D.R.); (N.N.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Kristin Surmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, 2610 Antwerp, Belgium; (J.V.); (L.T.)
| | - Nicole Normann
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, 17475 Greifswald, Germany; (D.R.); (N.N.)
| | - Bret Sellman
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA;
| | - Willem J. B. van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center Rotterdam, 3015 Rotterdam, The Netherlands;
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, 2610 Antwerp, Belgium; (J.V.); (L.T.)
- Correspondence: ; Tel.: +32-3-265-27-52
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Bresler SE, Vasil'eva NN, Kazbekov EN. [Mechanism of action of D-amino acid oxidase. II. Evidence for the free radical mechanism of the reaction catalysed by the monomer form of the enzyme]. Interact J Med Res 1976; 10:501-6. [PMID: 36548 PMCID: PMC9874988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
D-Amino acid oxidase was shown to dissociate into subunits in 2 M urea retaining the catalytic activity. This makes possible the direct observation of ESR spectra of the intermediate radical state of the enzyme when interacting with the substrate. We have shown that these radicals are really observable. Using the reversibility of the reaction and an equilibrium shift the amount of radicals can be increased up to 10% of all flavin groups present. The dependence of the radicals concentration on the amount of substrate and product can be predicted. The theory is confirmed by experimental data.
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