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Pokhrel V, Kuntal BK, Mande SS. Role and significance of virus-bacteria interactions in disease progression. J Appl Microbiol 2024; 135:lxae130. [PMID: 38830797 DOI: 10.1093/jambio/lxae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024]
Abstract
Understanding disease pathogenesis caused by bacteria/virus, from the perspective of individual pathogen has provided meaningful insights. However, as viral and bacterial counterparts might inhabit the same infection site, it becomes crucial to consider their interactions and contributions in disease onset and progression. The objective of the review is to highlight the importance of considering both viral and bacterial agents during the course of coinfection. The review provides a unique perspective on the general theme of virus-bacteria interactions, which either lead to colocalized infections that are restricted to one anatomical niche, or systemic infections that have a systemic effect on the human host. The sequence, nature, and underlying mechanisms of certain virus-bacteria interactions have been elaborated with relevant examples from literature. It also attempts to address the various applied aspects, including diagnostic and therapeutic strategies for individual infections as well as virus-bacteria coinfections. The review aims to aid researchers in comprehending the intricate interplay between virus and bacteria in disease progression, thereby enhancing understanding of current methodologies and empowering the development of novel health care strategies to tackle coinfections.
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Affiliation(s)
- Vatsala Pokhrel
- TCS Research, Tata Consultancy Services Ltd., TCS SP2 SEZ, Hinjewadi Phase 3, Pune 411057, India
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bhusan K Kuntal
- TCS Research, Tata Consultancy Services Ltd., TCS SP2 SEZ, Hinjewadi Phase 3, Pune 411057, India
| | - Sharmila S Mande
- TCS Research, Tata Consultancy Services Ltd., TCS SP2 SEZ, Hinjewadi Phase 3, Pune 411057, India
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Gavalda M, Fullana MI, Ferre A, Peña RR, Armendariz J, Torrallardona O, Magraner A, Lorenzo A, García C, Mut G, Planas L, Iglesias C, Fraile-Ribot P, Macia Romero MD, Riera M, García-Gasalla M. Clinical Characteristics and Microorganisms Isolated in Community-Acquired Pneumonia in the COVID-19 Period. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:5948747. [PMID: 38532828 PMCID: PMC10965275 DOI: 10.1155/2024/5948747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/15/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
Introduction Community-acquired pneumonia is a leading cause of mortality and hospital admissions. The aetiology remains unknown in 30-65% of the cases. Molecular tests are available for multiple pathogen detection and are under research to improve the causal diagnosis. Methods We carried out a prospective study to describe the clinical characteristics and aetiology of community-acquired pneumonia during the COVID-19 pandemic and to assess the diagnostic effectivity of the microbiological tests, including a molecular test of respiratory pathogens (FilmArray™ bioMérieux). Results From the 1st of February 2021 until the 31st of March 2022, 225 patients were included. Failure in microorganism identification occurred in approximately 70% of patients. Streptococcus pneumoniae was the most common isolate. There were 5 cases of viral pneumonia. The tested FilmArray exhibited a low positivity rate of 7% and mainly aided in the diagnosis of viral coinfections. Conclusions Despite our extensive diagnostic protocol, there is still a low rate of microorganism identification. We have observed a reduction in influenza and other viral pneumoniae during the COVID-19 pandemic. Having a high NEWS2 score on arrival at the emergency department, an active oncohematological disease or chronic neurological conditions and a positive microbiological test result were related to worse outcomes. Further research is needed to determine the role of molecular tests in the microbiological diagnosis of pneumonia.
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Affiliation(s)
- Meritxell Gavalda
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Maria Isabel Fullana
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Adrià Ferre
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Rebecca Rowena Peña
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Julen Armendariz
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Orla Torrallardona
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Aina Magraner
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Alejandro Lorenzo
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Carles García
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Gemma Mut
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Lluís Planas
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Carla Iglesias
- Microbiology Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Pablo Fraile-Ribot
- Microbiology Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
| | - Maria Dolores Macia Romero
- Microbiology Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
- Universitat de les Illes Balears, Illes Balears, Palma, Spain
| | - Melchor Riera
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
- Universitat de les Illes Balears, Illes Balears, Palma, Spain
| | - Mercedes García-Gasalla
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
- Universitat de les Illes Balears, Illes Balears, Palma, Spain
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O'Grady NP, Alexander E, Alhazzani W, Alshamsi F, Cuellar-Rodriguez J, Jefferson BK, Kalil AC, Pastores SM, Patel R, van Duin D, Weber DJ, Deresinski S. Society of Critical Care Medicine and the Infectious Diseases Society of America Guidelines for Evaluating New Fever in Adult Patients in the ICU. Crit Care Med 2023; 51:1570-1586. [PMID: 37902340 DOI: 10.1097/ccm.0000000000006022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
RATIONALE Fever is frequently an early indicator of infection and often requires rigorous diagnostic evaluation. OBJECTIVES This is an update of the 2008 Infectious Diseases Society of America and Society (IDSA) and Society of Critical Care Medicine (SCCM) guideline for the evaluation of new-onset fever in adult ICU patients without severe immunocompromise, now using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) methodology. PANEL DESIGN The SCCM and IDSA convened a taskforce to update the 2008 version of the guideline for the evaluation of new fever in critically ill adult patients, which included expert clinicians as well as methodologists from the Guidelines in Intensive Care, Development and Evaluation Group. The guidelines committee consisted of 12 experts in critical care, infectious diseases, clinical microbiology, organ transplantation, public health, clinical research, and health policy and administration. All task force members followed all conflict-of-interest procedures as documented in the American College of Critical Care Medicine/SCCM Standard Operating Procedures Manual and the IDSA. There was no industry input or funding to produce this guideline. METHODS We conducted a systematic review for each population, intervention, comparison, and outcomes question to identify the best available evidence, statistically summarized the evidence, and then assessed the quality of evidence using the GRADE approach. We used the evidence-to-decision framework to formulate recommendations as strong or weak or as best-practice statements. RESULTS The panel issued 12 recommendations and 9 best practice statements. The panel recommended using central temperature monitoring methods, including thermistors for pulmonary artery catheters, bladder catheters, or esophageal balloon thermistors when these devices are in place or accurate temperature measurements are critical for diagnosis and management. For patients without these devices in place, oral or rectal temperatures over other temperature measurement methods that are less reliable such as axillary or tympanic membrane temperatures, noninvasive temporal artery thermometers, or chemical dot thermometers were recommended. Imaging studies including ultrasonography were recommended in addition to microbiological evaluation using rapid diagnostic testing strategies. Biomarkers were recommended to assist in guiding the discontinuation of antimicrobial therapy. All recommendations issued were weak based on the quality of data. CONCLUSIONS The guidelines panel was able to formulate several recommendations for the evaluation of new fever in a critically ill adult patient, acknowledging that most recommendations were based on weak evidence. This highlights the need for the rapid advancement of research in all aspects of this issue-including better noninvasive methods to measure core body temperature, the use of diagnostic imaging, advances in microbiology including molecular testing, and the use of biomarkers.
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Affiliation(s)
- Naomi P O'Grady
- Internal Medicine Services, National Institutes of Health Clinical Center, Bethesda, MD
| | - Earnest Alexander
- Clinical Pharmacy Services, Department of Pharmacy, Tampa General Hospital, Tampa, FL
| | - Waleed Alhazzani
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Fayez Alshamsi
- Department of Internal Medicine, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Jennifer Cuellar-Rodriguez
- Laboratory of Clinical Immunology and Microbiology, National Institutes of Allergy and Infectious Diseases, Bethesda, MD
| | - Brian K Jefferson
- Division of Hepatobiliary and Pancreatic Surgery, Department of Internal Medicine-Critical Care Services, Atrium Health Cabarrus, Concord, NC
| | - Andre C Kalil
- Infectious Diseases Division, University of Nebraska Medical Center, Omaha, NE
| | - Stephen M Pastores
- Department of Anesthesiology and Critical Care Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Rochester, MN
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC
| | - David J Weber
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC
| | - Stanley Deresinski
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA
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Zhao J, He X, Min J, Yao RSY, Chen Y, Chen Z, Huang Y, Zhu Z, Gong Y, Xie Y, Li Y, Luo W, Shi D, Xu J, Shen A, Wang Q, Sun R, He B, Lin Y, Shen N, Cao B, Yang L, She D, Shi Y, Zhou J, Su X, Zhou H, Ma Z, Fan H, Lin Y, Ye F, Nie X, Zhang Q, Tian X, Lai G, Zhou M, Ma J, Zhang J, Qu J. A multicenter prospective study of comprehensive metagenomic and transcriptomic signatures for predicting outcomes of patients with severe community-acquired pneumonia. EBioMedicine 2023; 96:104790. [PMID: 37708700 PMCID: PMC10507133 DOI: 10.1016/j.ebiom.2023.104790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/29/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Severe community-acquired pneumonia (SCAP) results in high mortality as well as massive economic burden worldwide, yet limited knowledge of the bio-signatures related to prognosis has hindered the improvement of clinical outcomes. Pathogen, microbes and host are three vital elements in inflammations and infections. This study aims to discover the specific and sensitive biomarkers to predict outcomes of SCAP patients. METHODS In this study, we applied a combined metagenomic and transcriptomic screening approach to clinical specimens gathered from 275 SCAP patients of a multicentre, prospective study. FINDINGS We found that 30-day mortality might be independent of pathogen category or microbial diversity, while significant difference in host gene expression pattern presented between 30-day mortality group and the survival group. Twelve outcome-related clinical characteristics were identified in our study. The underlying host response was evaluated and enrichment of genes related to cell activation, immune modulation, inflammatory and metabolism were identified. Notably, omics data, clinical features and parameters were integrated to develop a model with six signatures for predicting 30-day mortality, showing an AUC of 0.953 (95% CI: 0.92-0.98). INTERPRETATION In summary, our study linked clinical characteristics and underlying multi-omics bio-signatures to the differential outcomes of patients with SCAP. The establishment of a comprehensive predictive model will be helpful for future improvement of treatment strategies and prognosis with SCAP. FUNDING National Natural Science Foundation of China (No. 82161138018), Shanghai Municipal Key Clinical Specialty (shslczdzk02202), Shanghai Top-Priority Clinical Key Disciplines Construction Project (2017ZZ02014), Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases (20dz2261100).
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Affiliation(s)
- Jingya Zhao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Xiangyan He
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Jiumeng Min
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Rosary Sin Yu Yao
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Yu Chen
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhonglin Chen
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Yi Huang
- Department of Pulmonary and Critical Care Medicine, Changhai Hospital, Shanghai, China
| | - Zhongyi Zhu
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Yanping Gong
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Yusang Xie
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Yuping Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital Wenzhou Medical College, Zhejiang, China
| | - Weiwei Luo
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Dongwei Shi
- Department of Emergency Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jinfu Xu
- Department of Pulmonary and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Ao Shen
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Qiuyue Wang
- Department of Pulmonary and Critical Care Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Ruixue Sun
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Bei He
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Yang Lin
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Ning Shen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Lingling Yang
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Danyang She
- Department of Pulmonary and Critical Care Medicine, The General Hospital of the People's Liberation Army, Beijing, China
| | - Yi Shi
- Department of Pulmonary and Critical Care Medicine, Jinling Hospital, Nanjing, China
| | - Jiali Zhou
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Xin Su
- Department of Pulmonary and Critical Care Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Hua Zhou
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital Zhejiang University, Hangzhou, China
| | - Zhenzi Ma
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Hong Fan
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Sichuan, China
| | - Yongquan Lin
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Feng Ye
- Department of Pulmonary and Critical Care Medicine, The First Affiliate Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xifang Nie
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | - Qiao Zhang
- Department of Pulmonary and Critical Care Medicine, Xinqiao Hospital of Army Medical University, Chongqing, China
| | - Xinlun Tian
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Guoxiang Lai
- Department of Pulmonary and Critical Care Medicine, Fuzhou General Hospital, Fuzhou, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China.
| | - Jinmin Ma
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China.
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China.
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Combe A, Kovacs D, de Mangou A, Miltgen G, Traversier N, Belmonte O, Simon O, Vidal C, Coolen-Allou N, Allyn J, Allou N. Impact of the COVID-19 pandemic on severe non-SARS-CoV-2 community-acquired pneumonia in Reunion Island: a multicenter retrospective observational study, 2016-2021. Sci Rep 2023; 13:14013. [PMID: 37640709 PMCID: PMC10462684 DOI: 10.1038/s41598-023-40791-5] [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: 10/03/2022] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
The Coronavirus 2019 (COVID-19) pandemic has had a considerable impact on the incidence of severe community-acquired pneumonia (CAP) worldwide. The aim of this study was to assess the early impact of the COVID-19 pandemic in the Reunion Island. This multicenter retrospective observational study was conducted from 2016 to 2021 in the hospitals of Reunion Island. The incidence of severe non-SARS-CoV-2 CAP, microorganisms, characteristics and outcomes of patients hospitalized in intensive care unit were compared between the pre-COVID-19 period (January 1, 2016 to February 29, 2020) and the early COVID-19 period (March 1, 2020 to October 31, 2021). Over the study period, 389 patients developed severe non-SARS-CoV-2 CAP. The incidence of severe non-SARS-CoV-2 CAP significantly decreased between the two periods (9.16 vs. 4.13 cases per 100,000 person-years). The influenza virus was isolated in 43.5% patients with severe non-SARS-CoV-2 CAP in the pre-COVID-19 period and in none of the 60 patients in the early COVID-19 period (P < 0.0001). The only virus that did not decrease was rhinovirus. Streptococcus pneumoniae was the most frequently isolated bacterial microorganism, with no significant difference between the two periods. In Reunion Island, the COVID-19 pandemic led to a significant decrease in the incidence of influenza, which likely explains the observed decrease in the incidence of severe non-SARS-CoV-2 CAP. The pandemic had no impact on the incidence of other viral and bacterial severe non-SARS-CoV-2 CAP. Monitoring influenza incidence is crucial now that COVID-19 control measures have been removed.
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Affiliation(s)
- Agathe Combe
- Intensive Care Unit, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
| | - David Kovacs
- Intensive Care Unit, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
| | - Axel de Mangou
- Intensive Care Unit, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
| | - Guillaume Miltgen
- Microbiology, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
- UMR Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
| | - Nicolas Traversier
- UMR Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
| | - Olivier Belmonte
- UMR Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
| | - Olivier Simon
- Intensive Care Unit, Centre Hospitalier Universitaire de La Réunion, Saint-Pierre, Reunion Island, France
| | - Charles Vidal
- Intensive Care Unit, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
| | - Nathalie Coolen-Allou
- Respiratory Medicine, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
| | - Jérôme Allyn
- Intensive Care Unit, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France
- Clinical Informatic Department, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, Reunion Island, France
| | - Nicolas Allou
- Intensive Care Unit, Centre Hospitalier Universitaire de La Réunion, Saint-Denis, Reunion Island, France.
- Clinical Informatic Department, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, Reunion Island, France.
- Hôpital Felix Guyon, Réanimation Polyvalente, Bellepierre, 97405, Saint-Denis, France.
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de Mangou A, Combe A, Coolen-Allou N, Miltgen G, Traversier N, Belmonte O, Vandroux D, Bohrer M, Cousty J, Caron M, Vidal C, Allyn J, Allou N. Severe community-acquired pneumonia in Reunion Island: Epidemiological, clinical, and microbiological characteristics, 2016-2018. PLoS One 2022; 17:e0267184. [PMID: 35427402 PMCID: PMC9012352 DOI: 10.1371/journal.pone.0267184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/04/2022] [Indexed: 12/17/2022] Open
Abstract
PURPOSE No data are available on severe community-acquired pneumonia (CAP) in the French overseas department of Reunion Island. This is unfortunate as the microorganisms responsible for the disease are likely to differ from those in temperate regions due to a tropical climate and proximity to other islands of the Indian Ocean region. The aim of this study was to assess the epidemiological, clinical, prognosis, and microbiological characteristics of patients with severe CAP in Reunion Island. MATERIALS AND METHODS This retrospective study evaluated all patients with CAP aged >18 years and hospitalized in one of the two intensive care units of Reunion Island between 2016 and 2018. Microorganisms were identified by culture from blood and respiratory samples, multiplex polymerase chain reaction from respiratory samples, urinary antigen tests, and serology. RESULTS Over the study period, 573 cases of severe CAP were recorded, with a mean incidence of 22 per 100,000 person-years. The most frequently isolated microorganism was influenza (21.9%) followed by Streptococcus pneumoniae (12%). The influenza virus was detected in affected patients all year round. Twenty-four patients with severe CAP came from another island of the Indian Ocean region (4.2%), mainly Madagascar (>50%). Two of these patients presented with melioidosis and 4 were infected with Acinetobacter spp. CONCLUSIONS Our findings have major implications for the management of severe CAP in tropical regions. The most frequently isolated microorganism in patients with severe CAP in Reunion Island is influenza followed by S. pneumoniae. Physicians should be aware that influenza is the main cause of severe CAP in patients living in or returning from Reunion Island, where this virus circulates all year round.
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Affiliation(s)
- Axel de Mangou
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Agathe Combe
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Nathalie Coolen-Allou
- Respiratory Disease, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Guillaume Miltgen
- Microbiology, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
- UMR Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de la Réunion, Saint-Denis, France
| | - Nicolas Traversier
- Microbiology, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Olivier Belmonte
- Microbiology, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - David Vandroux
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Michel Bohrer
- Department of Medical Information, Saint-Denis University Hospital, Saint-Denis, Reunion Island, France
| | - Julien Cousty
- Intensive Care Unit, Centre Hospitalier Universitaire Sud Réunion, Saint-Pierre, France
| | - Margot Caron
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Charles Vidal
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Jérôme Allyn
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
- Clinical Informatic Department, Saint-Denis University Hospital, Saint-Denis, Reunion Island, France
| | - Nicolas Allou
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
- Clinical Informatic Department, Saint-Denis University Hospital, Saint-Denis, Reunion Island, France
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Manufacturing Bacteriophages (Part 1 of 2): Cell Line Development, Upstream, and Downstream Considerations. Pharmaceuticals (Basel) 2021; 14:ph14090934. [PMID: 34577634 PMCID: PMC8471501 DOI: 10.3390/ph14090934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 01/21/2023] Open
Abstract
Within this first part of the two-part series on phage manufacturing, we will give an overview of the process leading to bacteriophages as a drug substance, before covering the formulation into a drug product in the second part. The principal goal is to provide the reader with a comprehensive framework of the challenges and opportunities that present themselves when developing manufacturing processes for bacteriophage-based products. We will examine cell line development for manufacture, upstream and downstream processes, while also covering the additional opportunities that engineered bacteriophages present.
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Daidoji T, Morales Vargas RE, Hagiwara K, Arai Y, Watanabe Y, Nishioka K, Murakoshi F, Garan K, Sadakane H, Nakaya T. Development of genus-specific universal primers for the detection of flaviviruses. Virol J 2021; 18:187. [PMID: 34526049 PMCID: PMC8442469 DOI: 10.1186/s12985-021-01646-5] [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: 04/14/2021] [Accepted: 08/23/2021] [Indexed: 12/03/2022] Open
Abstract
Background Flaviviruses are representative arboviruses carried by arthropods and/or vertebrates; these viruses can pose a public health concern in many countries. By contrast, it is known that a novel virus group called insect-specific flaviviruses (ISFs) also infects arthropods, although no such virus has yet been isolated from vertebrates. The characteristics of ISFs, which affect replication of human-pathogenic flaviviruses within co-infected mosquito cells or mosquitoes without affecting the mosquitoes themselves, mean that we should pay attention to both ISFs and human-pathogenic flaviviruses, despite the fact that ISFs appear not to be directly hazardous to human health. To assess the risk of diseases caused by flaviviruses, and to better understand their ecology, it is necessary to know the extent to which flaviviruses are harbored by arthropods. Methods We developed a novel universal primer for use in a PCR-based system to detect a broad range of flaviviruses. We then evaluated its performance. The utility of the novel primer pair was evaluated in a PCR assay using artificially synthesized oligonucleotides derived from a template viral genome sequence. The utility of the primer pair was also examined by reverse transcription PCR (RT-PCR) using cDNA templates prepared from virus-infected cells or crude supernatants prepared from virus-containing mosquito homogenates. Results The novel primer pair amplified the flavivirus NS5 sequence (artificially synthesized) in all samples tested (six species of flavivirus that can cause infectious diseases in humans, and flaviviruses harbored by insects). In addition, the novel primer pair detected viral genomes in cDNA templates prepared from mosquito cells infected with live flavivirus under different infectious conditions. Finally, the viral genome was detected with high sensitivity in crude supernatants prepared from pooled mosquito homogenates. Conclusion This PCR system based on a novel primer pair makes it possible to detect arthropod-borne flaviviruses worldwide (the primer pair even detected viruses belonging to different genetic subgroups). As such, an assay based on this primer pair may help to improve public health and safety, as well as increase our understanding of flavivirus ecology. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01646-5.
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Affiliation(s)
- Tomo Daidoji
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan.
| | | | - Katsuro Hagiwara
- Veterinary Virology, School of Veterinary Medicine , Rakuno Gakuen University, Hokkaido, 069-8501, Japan
| | - Yasuha Arai
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yohei Watanabe
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Keisuke Nishioka
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Fumi Murakoshi
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kotaro Garan
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Hiroki Sadakane
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
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Koo SH, Jiang B, Lim PQ, La MV, Tan TY. Development of a rapid multiplex PCR assay for the detection of common pathogens associated with community-acquired pneumonia. Trans R Soc Trop Med Hyg 2021; 115:1450-1455. [PMID: 34017992 DOI: 10.1093/trstmh/trab079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/04/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) is one of the most common infectious diseases and is a significant cause of mortality and morbidity globally. A microbial cause was not determined in a sizable percentage of patients with CAP; there are increasing data to suggest regional differences in bacterial aetiology. We devised a multiplex real-time PCR assay for detecting four microorganisms (Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae and Burkholderia pseudomallei) of relevance to CAP infections in Asia. METHODS Analytical validation was accomplished using bacterial isolates (n=10-33 of each target organism for analytical sensitivity and n=117 for analytical sensitivity) and clinical validation using 58 culture-positive respiratory tract specimens. RESULTS The qPCR assay exhibited 100% analytical sensitivity and analytical specificity, and 100% clinical sensitivity and 94-100% clinical specificity. The limit of detection and efficiency for the multiplex PCR assay were 3-33 CFU/mL and 93-110%, respectively. The results showed that the PCR-based method had higher sensitivity than traditional culture-based methods. The assay also demonstrated an ability to semiquantify bacterial loads. CONCLUSION We have devised a reliable laboratory-developed multiplex qPCR assay, with a turnaround time of within one working day, for detection of four clinically important CAP-associated microorganisms in Asia. The availability of a test with improved diagnostic capabilities potentially leads to an informed choice of antibiotic usage and appropriate management of the patient to achieve a better treatment outcome and financial savings.
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Affiliation(s)
- Seok Hwee Koo
- Clinical Trials and Research Unit, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Boran Jiang
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Pei Qi Lim
- Clinical Trials and Research Unit, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - My-Van La
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
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10
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Sangla F, Legouis D, Marti PE, Sgardello SD, Brebion A, Saint-Sardos P, Adda M, Lautrette A, Pereira B, Souweine B. One year after ICU admission for severe community-acquired pneumonia of bacterial, viral or unidentified etiology. What are the outcomes? PLoS One 2020; 15:e0243762. [PMID: 33315946 PMCID: PMC7735561 DOI: 10.1371/journal.pone.0243762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 11/29/2020] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Multiplex polymerase chain reaction (mPCR) for respiratory virus testing is increasingly used in community-acquired pneumonia (CAP), however data on one-year outcome in intensive care unit (ICU) patients with reference to the causative pathogen are scarce. MATERIALS AND METHODS We performed a single-center retrospective study in 123 ICU patients who had undergone respiratory virus testing for CAP by mPCR and with known one-year survival status. Functional status including dyspnea (mMRC score), autonomy (ADL Katz score) and need for new home-care ventilatory support was assessed at a one-year post-ICU follow-up. Mortality rates and functional status were compared in patients with CAP of a bacterial, viral or unidentified etiology one year after ICU admission. RESULTS The bacterial, viral and unidentified groups included 19 (15.4%), 37 (30.1%), and 67 (54.5%) patients, respectively. In multivariate analysis, one-year mortality in the bacterial group was higher compared to the viral group (HR 2.92, 95% CI 1.71-7.28, p = 0.02) and tended to be higher compared to the unidentified etiology group (p = 0.06); but no difference was found between the viral and the unidentified etiology group (p = 0.43). In 64/83 one-year survivors with a post-ICU follow-up consultation, there were no differences in mMRC score, ADL Katz score and new home-care ventilatory support between the groups (p = 0.52, p = 0.37, p = 0.24, respectively). Severe dyspnea (mMRC score = 4 or death), severe autonomy deficiencies (ADL Katz score ≤ 2 or death), and major adverse respiratory events (new home-care ventilatory support or death) were observed in 52/104 (50.0%), 47/104 (45.2%), and 65/104 (62.5%) patients, respectively; with no difference between the bacterial, viral and unidentified group: p = 0.58, p = 0.06, p = 0.61, respectively. CONCLUSIONS CAP of bacterial origin had a poorer outcome than CAP of viral or unidentified origin. At one-year, impairment of functional status was frequently observed, with no difference according to the etiology.
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Affiliation(s)
- Frédéric Sangla
- Service de Médecine intensive et réanimation, Centre Hospitalier Universitaire Gabriel Montpied, Clermont-Ferrand, France
- * E-mail:
| | - David Legouis
- Service de Soins intensifs adultes, Hôpitaux Universitaires de Genève, Geneva, Switzerland
| | - Pierre-Emmanuel Marti
- Service de Soins intensifs adultes, Hôpitaux Universitaires de Genève, Geneva, Switzerland
| | - Sebastian D. Sgardello
- Service de Soins intensifs adultes, Hôpitaux Universitaires de Genève, Geneva, Switzerland
| | - Amélie Brebion
- Laboratoire de Virologie, Centre Hospitalier Universitaire Gabriel Montpied, Clermont-Ferrand, France
| | - Pierre Saint-Sardos
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire Gabriel Montpied, Clermont-Ferrand, France
| | - Mireille Adda
- Service de Médecine intensive et réanimation, Centre Hospitalier Universitaire Gabriel Montpied, Clermont-Ferrand, France
| | - Alexandre Lautrette
- Service de Médecine intensive et réanimation, Centre Hospitalier Universitaire Gabriel Montpied, Clermont-Ferrand, France
| | - Bruno Pereira
- Département de Biostatistique, Centre Hospitalier Universitaire Gabriel Montpied, Clermont-Ferrand, France
| | - Bertrand Souweine
- Service de Médecine intensive et réanimation, Centre Hospitalier Universitaire Gabriel Montpied, Clermont-Ferrand, France
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11
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Ortac Ersoy E, Er B, Ciftci F, Gulleroglu A, Suner K, Arpinar B, Aygencel G, Bacakoglu F, Akpinar S, Comert B, Sungurtekin H, Altıntas D, Rollas K, Turan S, Topeli A. Outcome of Patients Admitted to Intensive Care Units due to Influenza-Related Severe Acute Respiratory Illness in 2017-2018 Flu Season: A Multicenter Study from Turkey. Respiration 2020; 99:954-960. [PMID: 33271560 DOI: 10.1159/000511092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 08/20/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Influenza can cause severe acute respiratory illness (SARI), which occurs as local outbreaks or seasonal epidemics with high intensive care unit (ICU) admission and mortality rates. Mortality is mainly due to SARI. OBJECTIVE The aim of this study was to evaluate the outcome of patients admitted to ICU due to influenza-related SARI in 2017-2018 flu season in Turkey. METHODS A retrospective multicenter study was conducted in 13 ICUs with a total of 216 beds from 6 cities in Turkey. All adult patients (over 18 years) admitted to the ICUs in 2017-2018 flu season (between September 1, 2017, and April 30, 2018) because of SARI and with a positive nasopharyngeal swab for influenza were included in the study. RESULTS A total of 123 cases were included in the study. The mean age of patients was 64.5 ± 17.5 years, and 66 (53.7%) patients were older than 65 years. The ICU mortality was 33.9%, and hospital mortality was 35.6%. Invasive mechanical ventilation (IMV), acute kidney injury (AKI), hematologic malignancy, and >65 years of age were the factors affecting mortality in influenza. CONCLUSION SARI due to influenza carries a high mortality rate, and IMV, AKI, presence of hematologic malignancy, and older age are independent risk factors for mortality.
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Affiliation(s)
- Ebru Ortac Ersoy
- Division of Intensive Care Medicine, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey,
| | - Berrin Er
- Division of Intensive Care Medicine, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Fatma Ciftci
- Department of Chest Diseases, Intensive Care Unit, Ankara University Faculty of Medicine, Ankara, Turkey
| | | | - Kezban Suner
- Intensive Care Unit, Sakarya University Education and Research Hospital, Sakarya, Turkey
| | - Burcu Arpinar
- Intensive Care Unit, Yedikule Chest Diseases and Chest Surgery Training and Research Hospital, Istanbul, Turkey
| | - Gulbin Aygencel
- Medical Intensive Care Unit, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Feza Bacakoglu
- Division of Chest Diseases, Intensive Care Unit, Ege University Faculty of Medicine, İzmir, Turkey
| | - Serdar Akpinar
- Medical Intensive Care Unit, Dışkapı Yıldırım Beyazıt Education and Research Hospital, Ankara, Turkey
| | - Bilgin Comert
- Medical Intensive Care Unit, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Hulya Sungurtekin
- Intensive Care Unit, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Defne Altıntas
- Medical Intensive Care Unit, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Kazim Rollas
- Intensive Care Unit, Tepecik Education Hospital, University of Health Sciences, Izmir, Turkey
| | - Sema Turan
- Intensive Care Unit, Ankara City Hospital, University of Health Sciences, Ankara, Turkey
| | - Arzu Topeli
- Division of Intensive Care Medicine, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
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12
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Cafferkey J, Coultas JA, Mallia P. Human rhinovirus infection and COPD: role in exacerbations and potential for therapeutic targets. Expert Rev Respir Med 2020; 14:777-789. [PMID: 32498634 DOI: 10.1080/17476348.2020.1764354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Respiratory virus infections (predominantly rhinoviruses) are the commonly identified in COPD exacerbations but debate about their role as a trigger of exacerbations continues. Experimental infection studies have provided significant new evidence establishing a causal relationship between virus infection and COPD exacerbations and contributed to a better understanding of the mechanisms of virus-induced exacerbations. However as yet no anti-viral treatments have undergone clinical trials in COPD patients. AREAS COVERED This review discusses the evidence for and against respiratory viruses being the main trigger of COPD exacerbations from both epidemiological studies and experimental infection studies. The host immune response to rhinovirus infection and how abnormalities in host immunity may underlie increased susceptibility to virus infection in COPD are discussed and the role of dual viral-bacterial infection in COPD exacerbations. Finally the current state of anti-viral therapy is discussed and how these may be used in the future treatment of COPD exacerbations. EXPERT OPINION Respiratory virus infections are the trigger of a substantial proportion of COPD exacerbations and rhinoviruses are the most common virus type. Clinical trials of anti-viral agents are needed in COPD patients to determine whether they are effective in virus-induced COPD exacerbations.
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Affiliation(s)
- John Cafferkey
- Department of Respiratory Medicine, Imperial College Healthcare NHS Trust , London, UK
| | | | - Patrick Mallia
- Department of Respiratory Medicine, Imperial College Healthcare NHS Trust , London, UK.,National Heart and Lung Institute, Imperial College London , London, UK
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13
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Lehel J, Yaucat-Guendi R, Darnay L, Palotás P, Laczay P. Possible food safety hazards of ready-to-eat raw fish containing product (sushi, sashimi). Crit Rev Food Sci Nutr 2020; 61:867-888. [PMID: 32270692 DOI: 10.1080/10408398.2020.1749024] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
It is undeniable that with the popularity of sushi and sashimi over the last decade the consumption of raw fish has extremely increased. Raw fish is very appreciated worldwide and has become a major component of human diet because of its fine taste and nutritional properties. Possible hazards concerning fish safety and quality are classified as biological and chemical hazards. They are contaminants that often accumulate in edible tissue of fish and transmit to humans via the food chain affecting the consumer's health. Although their concentration in fish and fishery products are found at non-alarming level of a daily basis period, they induce hazardous outcome on human health due to long and continuous consumption of raw fish. Regular sushi and sashimi eaters have to be aware of the contaminants found in the other components of their dish that often add up to acceptable residue limits found in fish. Hence, there is the urge for effective analytical methods to be developed as well as stricter regulations to be put in force between countries to monitor the safety and quality of fish for the interest of public health.
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Affiliation(s)
- József Lehel
- Department of Food Hygiene, University of Veterinary Medicine, Budapest, Hungary
| | | | - Lívia Darnay
- Department of Food Hygiene, University of Veterinary Medicine, Budapest, Hungary
| | | | - Péter Laczay
- Department of Food Hygiene, University of Veterinary Medicine, Budapest, Hungary
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14
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Converso TR, Assoni L, André GO, Darrieux M, Leite LCC. The long search for a serotype independent pneumococcal vaccine. Expert Rev Vaccines 2020; 19:57-70. [PMID: 31903805 DOI: 10.1080/14760584.2020.1711055] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Introduction: Serotype replacement - a consequence of polysaccharide vaccine use - will continue to drive the inclusion of new serotypes on conjugate vaccines, increasing production complexity and costs, and making an already expensive vaccine less accessible to developing countries, where prevalence is higher and resources available for health systems, scarcer. Serotype-independent formulations are a promising option, but so far they have not been successful in reducing colonization/transmission.Areas covered: Protein-based and whole-cell vaccine candidates studied in the past 30 years. Challenges for serotype-independent vaccine development and alternative approaches.Expert opinion: Clinical trials performed so far demonstrated the importance to establish more reliable animal models and better correlates of protection. Defining appropriate endpoints for clinical trials of serotype-independent vaccine candidates has been a challenge. Inhibition of colonization has been evaluated, but concern on the extent of bacterial elimination is still a matter of debate. Challenges on establishing representative sites for clinical trials, sample sizes and appropriate age groups are discussed. On a whole, although many challenges will have to be overcome, establishing protein-based antigens as serotype-independent vaccines is still the best alternative against the huge burden of pneumococcal diseases in the world.
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Affiliation(s)
- T R Converso
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - L Assoni
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - G O André
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - M Darrieux
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - L C C Leite
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, SP, Brazil
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15
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Torres A, Chalmers JD, Dela Cruz CS, Dominedò C, Kollef M, Martin-Loeches I, Niederman M, Wunderink RG. Challenges in severe community-acquired pneumonia: a point-of-view review. Intensive Care Med 2019; 45:159-171. [PMID: 30706119 PMCID: PMC7094947 DOI: 10.1007/s00134-019-05519-y] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/04/2019] [Indexed: 12/28/2022]
Abstract
Purpose Severe community-acquired pneumonia (SCAP) is still associated with substantial morbidity and mortality. In this point-of-view review paper, a group of experts discuss the main controversies in SCAP: the role of severity scores to guide patient settings of care and empiric antibiotic therapy; the emergence of pathogens outside the core microorganisms of CAP; viral SCAP; the best empirical treatment; septic shock as the most lethal complication; and the need for new antibiotics. Methods For all topics, the authors describe current controversies and evidence and provide recommendations and suggestions for future research. Evidence was based on meta-analyses, most recent RCTs and recent interventional or observational studies. Recommendations were reached by consensus of all the authors. Results and conclusions The IDSA/ATS criteria remain the most pragmatic tool to predict ICU admission. The authors recommend a combination of a beta-lactam/beta-lactamase inhibitor or a third G cephalosporin plus a macrolide in most SCAP patients, and to empirically cover PES (P. aeruginosa, extended spectrum beta-lactamase producing Enterobacteriaceae, methicillin-resistant S. aureus) pathogens when at least two specific risk factors are present. In patients with influenza CAP, the authors recommend the use of oseltamivir and avoidance of the use of steroids. Corticosteroids can be used in case of refractory shock and high systemic inflammatory response.
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Affiliation(s)
- Antoni Torres
- Department of Pulmonary Medicine, Hospital Clinic of Barcelona, C/Villarroel 170, 08036, Barcelona, Spain.
- August Pi i Sunyer Biomedical Research Institute, IDIBAPS, University of Barcelona, Barcelona, Spain.
- Biomedical Research Networking Centres in Respiratory Diseases (Ciberes), Barcelona, Spain.
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine and Microbial Pathogenesis, Center of Pulmonary Infection Research and Treatment, Yale University School of Medicine, New Haven, CT, USA
| | - Cristina Dominedò
- Department of Anesthesiology and Intensive Care Medicine, Fondazione Policlinico Universitario A. Gemelli, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marin Kollef
- Division of Pulmonary and Critical Care Medicine, Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Ignacio Martin-Loeches
- Biomedical Research Networking Centres in Respiratory Diseases (Ciberes), Barcelona, Spain
- St. James's Hospital, Multidisciplinary Intensive Care Research Organization (MICRO), Dublin, Ireland
| | - Michael Niederman
- Weill Cornell Medical College and New York Presbyterian/Weill Cornell Medical Center, New York City, USA
| | - Richard G Wunderink
- Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Li C, Zhu L, Gong X, Xu Z, Liu Y, Zhang M, Cao Q. Soluble triggering receptor expressed on myeloid cells-1 as a useful biomarker for diagnosing ventilator-associated pneumonia after congenital cardiac surgery in children. Exp Ther Med 2018; 17:147-152. [PMID: 30651775 PMCID: PMC6307413 DOI: 10.3892/etm.2018.6905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/04/2018] [Indexed: 01/26/2023] Open
Abstract
The present study aimed to assess the usefulness of soluble triggering receptor expressed on myeloid cells 1 (sTREM-1) in the diagnosis of ventilator-associated pneumonia (VAP) in paediatric patients with congenital heart disease (CHD) following cardiac surgery. The current prospective study enrolled 48 patients with congenital heart diseases who were suspected of having VAP; these patients were undergoing cardiac surgery between August 2016 and October 2017 in the Cardiac Intensive Care Unit of Shanghai Children's Medical Center (Shanghai, China). A total of 31 patients were diagnosed with VAP using a polymerase chain reaction (PCR) assay, while 17 patients without VAP were designated as the Non-VAP group. A bronchoscopy was performed and samples were collected for measurement on the day that VAP was diagnosed. The sTREM-1 levels were measured in bronchoalveolar lavage fluid (BALF) and exhaled ventilator condensate (EVC). BALF specimens were also sent to the microbiology laboratory for PCR assays and quantitative culturing. The positive detection rate of bacteria using the PCR assay and traditional culture was 64.6% (31/48) and 39.6% (19/48). sTREM-1 was significantly higher in the BALF (146.21 pg/ml vs. 118.06 pg/ml) and EVC (125.29 pg/ml vs. 120.48 pg/ml) of patients with VAP demonstrated compared with the patients without VAP. The findings suggest that the detection of sTREM-1 in BALF and EVC samples may be useful for the diagnosis of VAP following heart surgery in children.
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Affiliation(s)
- Chunxiang Li
- Department of Cardiac Intensive Care Unit, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Limin Zhu
- Department of Cardiac Intensive Care Unit, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Xiaolei Gong
- Department of Cardiac Intensive Care Unit, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Zhuoming Xu
- Department of Cardiac Intensive Care Unit, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Yujie Liu
- Department of Cardiac Intensive Care Unit, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Mingjie Zhang
- Department of Cardiac Intensive Care Unit, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Qing Cao
- Department of Infectious Disease, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
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Quah J, Jiang B, Tan PC, Siau C, Tan TY. Impact of microbial Aetiology on mortality in severe community-acquired pneumonia. BMC Infect Dis 2018; 18:451. [PMID: 30180811 PMCID: PMC6122562 DOI: 10.1186/s12879-018-3366-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 08/29/2018] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The impact of different classes of microbial pathogens on mortality in severe community-acquired pneumonia is not well elucidated. Previous studies have shown significant variation in the incidence of viral, bacterial and mixed infections, with conflicting risk associations for mortality. We aimed to determine the risk association of microbial aetiologies with hospital mortality in severe CAP, utilising a diagnostic strategy incorporating molecular testing. Our primary hypothesis was that respiratory viruses were important causative pathogens in severe CAP and was associated with increased mortality when present with bacterial pathogens in mixed viral-bacterial co-infections. METHODS A retrospective cohort study from January 2014 to July 2015 was conducted in a tertiary hospital medical intensive care unit in eastern Singapore, which has a tropical climate. All patients diagnosed with severe community-acquired pneumonia were included. RESULTS A total of 117 patients were in the study. Microbial pathogens were identified in 84 (71.8%) patients. Mixed viral-bacterial co-infections occurred in 18 (15.4%) of patients. Isolated viral infections were present in 32 patients (27.4%); isolated bacterial infections were detected in 34 patients (29.1%). Hospital mortality occurred in 16 (13.7%) patients. The most common bacteria isolated was Streptococcus pneumoniae and the most common virus isolated was Influenza A. Univariate and multivariate logistic regression showed that serum procalcitonin, APACHE II severity score and mixed viral-bacterial infection were associated with increased risk of hospital mortality. Mixed viral-bacterial co-infections were associated with an adjusted odds ratio of 13.99 (95% CI 1.30-151.05, p = 0.03) for hospital mortality. CONCLUSIONS Respiratory viruses are common organisms isolated in severe community-acquired pneumonia. Mixed viral-bacterial infections may be associated with an increased risk of mortality.
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Affiliation(s)
- Jessica Quah
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, SingHealth, 2 Simei Street 3, Postal Code, Singapore, 529889, Singapore.
| | - Boran Jiang
- Department of Laboratory Medicine, Changi General Hospital, SingHealth, Singapore, Singapore
| | - Poh Choo Tan
- Department of Advanced Nursing Practice, Changi General Hospital, SingHealth, Singapore, Singapore
| | - Chuin Siau
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, SingHealth, 2 Simei Street 3, Postal Code, Singapore, 529889, Singapore
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, SingHealth, Singapore, Singapore
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Trends in Pediatric Complicated Pneumonia in an Ontario Local Health Integration Network. CHILDREN-BASEL 2018; 5:children5030036. [PMID: 29510484 PMCID: PMC5867495 DOI: 10.3390/children5030036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 02/08/2018] [Accepted: 02/26/2018] [Indexed: 11/17/2022]
Abstract
Following the introduction of 7-valent pneumococcal vaccine (PCV7), while overall rates of invasive pneumococcal disease and pneumococcal pneumonia in children declined, rates of empyema increased. We examined changes in the incidence of hospitalization for pediatric complicated pneumonia (PCOMP) in Eastern Ontario, Canada, particularly since the introduction of the 13-valent vaccine (PCV13). A retrospective chart review was carried out evaluating previously healthy children admitted with PCOMP, which included empyema, parapneumonic effusion, necrotizing pneumonia, and lung abscess between 2002 and 2015. Three-hundred seventy-one children were included. Subjects had a median age of four years, and 188/370 (50.8%) required a chest tube. Admission rates changed markedly during this time period. The number of admissions per year rose most sharply between 2009 and 2012, corresponding to the period following introduction of PCV7 and then the occurrence of pandemic influenza A (H1N1). In children who likely received PCV13, the incidence of PCOMP returned to approximately pre-PCV7 levels. In contrast, rates of PCOMP in older children (who would not have received PCV13) remained elevated during the post-PCV13 time period. While rates of PCOMP, particularly in older children, remain elevated following the introduction of PCV13, this might be expected to resolve with more widespread vaccine coverage with PCV13 and herd immunity.
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Papan C, Meyer-Buehn M, Laniado G, Nicolai T, Griese M, Huebner J. Assessment of the multiplex PCR-based assay Unyvero pneumonia application for detection of bacterial pathogens and antibiotic resistance genes in children and neonates. Infection 2017; 46:189-196. [PMID: 29086343 DOI: 10.1007/s15010-017-1088-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/21/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND Pneumonia is a major healthcare problem. Rapid pathogen identification is critical, but often delayed due to the duration of culturing. Early, broad antibacterial therapy might lead to false-negative culture findings and eventually to the development of antibiotic resistances. We aimed to assess the accuracy of the new application Unyvero P50 based on multiplex PCR to detect bacterial pathogens in respiratory specimens from children and neonates. METHODS In this prospective study, bronchoalveolar lavage fluids, tracheal aspirates, or pleural fluids from neonates and children were analyzed by both traditional culture methods and Unyvero multiplex PCR. RESULTS We analyzed specimens from 79 patients with a median age of 1.8 (range 0.01-20.1). Overall, Unyvero yielded a sensitivity of 73.1% and a specificity of 97.9% compared to culture methods. Best results were observed for non-fermenting bacteria, for which sensitivity of Unyvero was 90% and specificity 97.3%, while rates were lower for Gram-positive bacteria (46.2 and 93.9%, respectively). For resistance genes, we observed a concordance with antibiogram of 75% for those specimens in which there was a cultural correlate. CONCLUSIONS Unyvero is a fast and easy-to-use tool that might provide additional information for clinical decision making, especially in neonates and in the setting of nosocomial pneumonia. Sensitivity of the PCR for Gram-positive bacteria and important resistance genes must be improved before this application can be widely recommended.
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Affiliation(s)
- Cihan Papan
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Lindwurmstr. 4, 80337, Munich, Germany. .,Pediatric Infectious Diseases, Medical Faculty Mannheim, University Children's Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
| | - Melanie Meyer-Buehn
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Lindwurmstr. 4, 80337, Munich, Germany
| | - Gudrun Laniado
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Lindwurmstr. 4, 80337, Munich, Germany
| | - Thomas Nicolai
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Lindwurmstr. 4, 80337, Munich, Germany
| | - Matthias Griese
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Lindwurmstr. 4, 80337, Munich, Germany
| | - Johannes Huebner
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Lindwurmstr. 4, 80337, Munich, Germany
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Lim TK, Siow WT. Pneumonia in the tropics. Respirology 2017; 23:28-35. [PMID: 28763150 PMCID: PMC7169137 DOI: 10.1111/resp.13137] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/27/2017] [Accepted: 06/12/2017] [Indexed: 12/19/2022]
Abstract
Pneumonia in the tropics poses a heavy disease burden. The complex interplay of climate change, human migration influences and socio-economic factors lead to changing patterns of respiratory infections in tropical climate but also increasingly in temperate countries. Tropical and poorer countries, especially South East Asia, also bear the brunt of the global tuberculosis (TB) pandemic, accounting for almost one-third of the burden. But, as human migration patterns evolve, we expect to see more TB cases in higher income as well as temperate countries, and rise in infections like scrub typhus from ecotourism activities. Fuelled by the ease of air travel, novel zoonotic infections originating from the tropics have led to global respiratory pandemics. As such, clinicians worldwide should be aware of these new conditions as well as classical tropical bacterial pneumonias such as melioidosis. Rarer entities such as co-infections of leptospirosis and chikungunya or dengue will need careful consideration as well. In this review, we highlight aetiologies of pneumonia seen more commonly in the tropics compared with temperate regions, their disease burden, variable clinical presentations as well as impact on healthcare delivery.
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Affiliation(s)
- Tow Keang Lim
- Division of Respiratory and Critical Care Medicine, National University Hospital, Singapore
| | - Wen Ting Siow
- Division of Respiratory and Critical Care Medicine, National University Hospital, Singapore
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Vatrella A. Answers Regarding the Etiology of Severe Community-Acquired Pneumonia: Usefulness of Polymerase Chain Reaction Techniques. Respiration 2016; 92:285. [PMID: 27701178 DOI: 10.1159/000450888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy
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