1
|
Porchera BR, da Silva CM, Miranda RP, Gomes ARQ, Fernandes PHDS, de Menezes CGO, Laurindo PDSDODC, Dolabela MF, Brígido HPC. Linezolid and vancomycin for nosocomial infections in pediatric patients: a systematic review. J Pediatr (Rio J) 2024; 100:242-249. [PMID: 38145631 PMCID: PMC11065658 DOI: 10.1016/j.jped.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/13/2023] [Accepted: 08/30/2023] [Indexed: 12/27/2023] Open
Abstract
OBJECTIVE To investigate the effectiveness of linezolid and vancomycin for the treatment of nosocomial infections in children under 12 years old. DATA SOURCES This is a systematic review in which five randomized clinical trials about the effectiveness of linezolid and vancomycin, involving a total of 429 children with nosocomial infections, were evaluated. They were searched in scientific databases: PubMed, Bvs, and SciELO. SUMMARY OF FINDINGS The main nosocomial infections that affected children were bacteremia, skin, and soft tissue infections followed by nosocomial pneumonia. Most infections were caused by Gram-positive bacteria, which all studies showed infections caused by Staphylococcus aureus, with methicillin-resistant S. aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci strains being isolated. Both linezolid and vancomycin showed high therapeutic efficacy against different types of nosocomial infections, ranging from 84.4% to 94% for linezolid and 76.9% to 90% for vancomycin. Patients receiving linezolid had lower rates of rash and red man syndrome compared to those receiving vancomycin. However, despite the adverse reactions, antimicrobials can be safely administered to children to treat nosocomial infections caused by resistant Gram-positive bacteria. CONCLUSION Both linezolid and vancomycin showed good efficacy in the treatment of bacterial infections caused by resistant Gram-positive bacteria in hospitalized children. However, linezolid stands out regarding its pharmacological safety. Importantly, to strengthen this conclusion, further clinical trials are needed to provide additional evidence.
Collapse
Affiliation(s)
- Bruno Russo Porchera
- Centro Universitário do Estado do Pará (CESUPA), Curso de Medicina, Belém, PA, Brazil
| | | | | | - Antônio Rafael Quadros Gomes
- Universidade Federal do Pará (UFPA), Programa de Pós-graduação em Inovação Farmacêutica (PPGIF), Belém, PA, Brazil
| | | | | | | | - Maria Fani Dolabela
- Universidade Federal do Pará (UFPA), Programa de Pós-graduação em Inovação Farmacêutica (PPGIF), Belém, PA, Brazil
| | - Heliton Patrick Cordovil Brígido
- Universidade Federal do Pará (UFPA), Programa de Pós-graduação em Inovação Farmacêutica (PPGIF), Belém, PA, Brazil; Centro Universitário Metropolitano da Amazônia (UNIFAMAZ), Curso de Medicina, Belém, PA, Brazil.
| |
Collapse
|
2
|
Rojo-Alba S, Martínez ZP, González-Alba JM, Boga JA, Varela CO, Álvarez MAA, Fonseca CP, Clemente MMG, Rodriguez JG, García EG, Pérez MR, García SM, Álvarez-Argüelles ME. Respiratory syncytial virus incidence and typing in the last six seasons in the north of Spain (Asturias). Genetic characterization during the SARS-CoV-2 pandemic. J Med Virol 2024; 96:e29499. [PMID: 38469919 DOI: 10.1002/jmv.29499] [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: 09/06/2023] [Revised: 01/04/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024]
Abstract
Respiratory syncytial virus is associated with lower respiratory tract infections. As several types and genotypes can circulate at the same time, genomic characterization is important for timely epidemiological control and treatment measures. In the last 6 seasons (2017-2023), 191 236 nasopharyngeal swabs were processed for respiratory viruses to determine the etiology of acute respiratory infections, describe the incidence and distribution of RSV types and enrich the data of epidemiological molecular studies on RSV in Spain. The incidence of RSV reached 7% in the pre-pandemic season. RSV was most frequent in children under 5 years of age (12.6%), but was also significant in those over 70 years of age (5.63%). The measures taken to control SARS-CoV-2 infection were useful for RSV control and the incidence decreased to 1.8%, but caused a change in the types. Pre-pandemic, the majority circulating types were RSV-B/RSV-B/RSV-A and in the pandemic it was RSV-B/RSV-B. In the last season, RSV-B and RSV-A were detected in the same proportion. Genetic characterization showed three new clades. This has been taken into account to understand the epidemiology as well as the development of therapeutic and preventive strategies.
Collapse
Affiliation(s)
- Susana Rojo-Alba
- Department of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Zulema Pérez Martínez
- Department of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - José María González-Alba
- Department of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - José Antonio Boga
- Department of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Cristina Ochoa Varela
- Department of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | | | - Carmen Pérez Fonseca
- Department of Emergency, Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | - José Gutierrez Rodriguez
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Department of Geriatrics, Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | - Mercedes Rodríguez Pérez
- Department of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Santiago Melón García
- Department of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Marta Elena Álvarez-Argüelles
- Department of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| |
Collapse
|
3
|
Chetty A, Blekhman R. Multi-omic approaches for host-microbiome data integration. Gut Microbes 2024; 16:2297860. [PMID: 38166610 PMCID: PMC10766395 DOI: 10.1080/19490976.2023.2297860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
The gut microbiome interacts with the host through complex networks that affect physiology and health outcomes. It is becoming clear that these interactions can be measured across many different omics layers, including the genome, transcriptome, epigenome, metabolome, and proteome, among others. Multi-omic studies of the microbiome can provide insight into the mechanisms underlying host-microbe interactions. As more omics layers are considered, increasingly sophisticated statistical methods are required to integrate them. In this review, we provide an overview of approaches currently used to characterize multi-omic interactions between host and microbiome data. While a large number of studies have generated a deeper understanding of host-microbiome interactions, there is still a need for standardization across approaches. Furthermore, microbiome studies would also benefit from the collection and curation of large, publicly available multi-omics datasets.
Collapse
Affiliation(s)
- Ashwin Chetty
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| |
Collapse
|
4
|
Oliveira FRCD, Trevisol LV, Salvador RA, Carvalho WBD. Is a viral panel testing worthy in our reality?? ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2023; 41:139-140. [PMID: 36759055 DOI: 10.1016/j.eimce.2022.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 02/10/2023]
Affiliation(s)
- Felipe Rezende Caino de Oliveira
- Santa Catarina Hospital, Department of Pediatrics, Brazil; Alvorada Hospital, Pediatric Intensive Care Unit, Brazil; GRAACC/IOP, Pediatric Intensive Care Unit, Brazil; Department of Pediatrics, Faculty of Medicine of the Nine of July University, Brazil.
| | | | | | - Werther Brunow de Carvalho
- Santa Catarina Hospital, Department of Pediatrics, Brazil; Department of Pediatrics, Neonatology Division, Faculty of Medicine of the University of São Paulo, Brazil
| |
Collapse
|
5
|
Oliveira FRCD, Trevisol LV, Salvador RA, Carvalho WBD. Is a viral panel testing worthy in our reality?? Enferm Infecc Microbiol Clin 2022. [DOI: 10.1016/j.eimc.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
6
|
Li Y, van Houten CB, Boers SA, Jansen R, Cohen A, Engelhard D, Kraaij R, Hiltemann SD, Ju J, Fernández D, Mankoc C, González E, de Waal WJ, de Winter-de Groot KM, Wolfs TFW, Meijers P, Luijk B, Oosterheert JJ, Sankatsing SUC, Bossink AWJ, Stein M, Klein A, Ashkar J, Bamberger E, Srugo I, Odeh M, Dotan Y, Boico O, Etshtein L, Paz M, Navon R, Friedman T, Simon E, Gottlieb TM, Pri-Or E, Kronenfeld G, Oved K, Eden E, Stubbs AP, Bont LJ, Hays JP. The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections. PLoS One 2022; 17:e0267140. [PMID: 35436301 PMCID: PMC9015155 DOI: 10.1371/journal.pone.0267140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 04/04/2022] [Indexed: 11/18/2022] Open
Abstract
Background The ability to accurately distinguish bacterial from viral infection would help clinicians better target antimicrobial therapy during suspected lower respiratory tract infections (LRTI). Although technological developments make it feasible to rapidly generate patient-specific microbiota profiles, evidence is required to show the clinical value of using microbiota data for infection diagnosis. In this study, we investigated whether adding nasal cavity microbiota profiles to readily available clinical information could improve machine learning classifiers to distinguish bacterial from viral infection in patients with LRTI. Results Various multi-parametric Random Forests classifiers were evaluated on the clinical and microbiota data of 293 LRTI patients for their prediction accuracies to differentiate bacterial from viral infection. The most predictive variable was C-reactive protein (CRP). We observed a marginal prediction improvement when 7 most prevalent nasal microbiota genera were added to the CRP model. In contrast, adding three clinical variables, absolute neutrophil count, consolidation on X-ray, and age group to the CRP model significantly improved the prediction. The best model correctly predicted 85% of the ‘bacterial’ patients and 82% of the ‘viral’ patients using 13 clinical and 3 nasal cavity microbiota genera (Staphylococcus, Moraxella, and Streptococcus). Conclusions We developed high-accuracy multi-parametric machine learning classifiers to differentiate bacterial from viral infections in LRTI patients of various ages. We demonstrated the predictive value of four easy-to-collect clinical variables which facilitate personalized and accurate clinical decision-making. We observed that nasal cavity microbiota correlate with the clinical variables and thus may not add significant value to diagnostic algorithms that aim to differentiate bacterial from viral infections.
Collapse
Affiliation(s)
- Yunlei Li
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Chantal B. van Houten
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | - Dan Engelhard
- Division of Paediatric Infectious Disease Unit, Hadassah-Hebrew University Medical Centre, Jerusalem, Israel
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Saskia D. Hiltemann
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jie Ju
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | | | - Wouter J. de Waal
- Department of Paediatrics, Diakonessenhuis, Utrecht, The Netherlands
| | - Karin M. de Winter-de Groot
- Department of Paediatric Respiratory Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tom F. W. Wolfs
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pieter Meijers
- Department of Paediatrics, Gelderse Vallei Hospital, Ede, The Netherlands
| | - Bart Luijk
- Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Jelrik Oosterheert
- Department of Internal Medicine and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Aik W. J. Bossink
- Department of Respiratory Medicine, Diakonessenhuis Utrecht, Utrecht, The Netherlands
| | - Michal Stein
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Adi Klein
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Jalal Ashkar
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Ellen Bamberger
- MeMed, Tirat Carmel, Israel
- Department of Paediatrics, Bnai Zion Medical Centre, Haifa, Israel
| | - Isaac Srugo
- Department of Paediatrics, Bnai Zion Medical Centre, Haifa, Israel
| | - Majed Odeh
- Department of Internal Medicine A, Bnai Zion Medical Centre, Haifa, Israel
| | - Yaniv Dotan
- Pulmonary Division, Rambam Health Care Campus, Haifa, Israel
| | | | | | | | | | | | | | | | | | | | | | | | - Andrew P. Stubbs
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Louis J. Bont
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - John P. Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- * E-mail:
| |
Collapse
|
7
|
Tan CD, Hagedoorn NN, Dewez JE, Borensztajn DM, von Both U, Carrol ED, Emonts M, van der Flier M, de Groot R, Herberg J, Kohlmaier B, Levin M, Lim E, Maconochie IK, Martinon-Torres F, Nijman RG, Pokorn M, Rivero-Calle I, Strle F, Tsolia M, Vermont CL, Yeung S, Zachariasse JM, Zenz W, Zavadska D, Moll HA. Rapid Viral Testing and Antibiotic Prescription in Febrile Children With Respiratory Symptoms Visiting Emergency Departments in Europe. Pediatr Infect Dis J 2022; 41:39-44. [PMID: 34862345 DOI: 10.1097/inf.0000000000003326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Inappropriate antibiotic prescribing often occurs in children with self-limiting respiratory tract infections, contributing to antimicrobial resistance. It has been suggested that rapid viral testing can reduce inappropriate antibiotic prescribing. We aimed to assess the association between rapid viral testing at the Emergency Department (ED) and antibiotic prescription in febrile children. METHODS This study is part of the MOFICHE study, which is an observational multicenter study including routine data of febrile children (0-18 years) attending 12 European EDs. In children with respiratory symptoms visiting 6 EDs equipped with rapid viral testing, we performed multivariable logistic regression analysis regarding rapid viral testing and antibiotic prescription adjusted for patient characteristics, disease severity, diagnostic tests, focus of infection, admission, and ED. RESULTS A rapid viral test was performed in 1061 children (8%) and not performed in 11,463 children. Rapid viral test usage was not associated with antibiotic prescription (aOR 0.9, 95% CI: 0.8-1.1). A positive rapid viral test was associated with less antibiotic prescription compared with children without test performed (aOR 0.6, 95% CI: 0.5-0.8), which remained significant after adjustment for CRP and chest radiograph result. Twenty percent of the positively tested children received antibiotics. A negative rapid viral test was not associated with antibiotic prescription (aOR 1.2, 95% CI: 1.0-1.4). CONCLUSIONS Rapid viral test usage did not reduce overall antibiotic prescription, whereas a positive rapid viral test did reduce antibiotic prescription at the ED. Implementation of rapid viral testing in routine emergency care and compliance to the rapid viral test outcome will reduce inappropriate antibiotic prescribing at the ED.
Collapse
Affiliation(s)
- Chantal D Tan
- From the Department of General Paediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Nienke N Hagedoorn
- From the Department of General Paediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Juan E Dewez
- Faculty of Tropical and Infectious Disease, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dorine M Borensztajn
- From the Department of General Paediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Ulrich von Both
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
- German Centre for Infection Research, DZIF, Partner Site Munich, Munich, Germany
| | - Enitan D Carrol
- Veterinary and Ecological Sciences Liverpool, Institute of Infection, University of Liverpool, Liverpool, United Kingdom
- Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Marieke Emonts
- Great North Children's Hospital, Paediatric Immunology, Infectious Diseases & Allergy, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- NIHR Newcastle Biomedical Research Centre based at Newcastle upon Tyne Hospitals NHS Trust and Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michiel van der Flier
- Section of Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, RadboudUMC, Nijmegen, the Netherlands
- Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Ronald de Groot
- Section of Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, RadboudUMC, Nijmegen, the Netherlands
| | - Jethro Herberg
- Section of Paediatric Infectious Diseases, Imperial College, London, United Kingdom
| | - Benno Kohlmaier
- Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Michael Levin
- Section of Paediatric Infectious Diseases, Imperial College, London, United Kingdom
| | - Emma Lim
- Great North Children's Hospital, Paediatric Immunology, Infectious Diseases & Allergy, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- NIHR Newcastle Biomedical Research Centre based at Newcastle upon Tyne Hospitals NHS Trust and Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ian K Maconochie
- Paediatric Emergency Medicine, Imperial College Healthcare Trust NHS, London, United Kingdom
| | - Federico Martinon-Torres
- Genetics, Vaccines, Infections and Paediatrics Research group (GENVIP), Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ruud G Nijman
- Section of Paediatric Infectious Diseases, Imperial College, London, United Kingdom
| | - Marko Pokorn
- Department of Infectious Diseases and Faculty of Medicine, University Medical Centre Ljubljana, University of Ljubljana, Ljubljana, Slovenia
| | - Irene Rivero-Calle
- Genetics, Vaccines, Infections and Paediatrics Research group (GENVIP), Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Franc Strle
- Department of Infectious Diseases and Faculty of Medicine, University Medical Centre Ljubljana, University of Ljubljana, Ljubljana, Slovenia
| | - Maria Tsolia
- Second Department of Paediatrics, P. and A. Kyriakou Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Clementien L Vermont
- Department of Paediatric Infectious diseases and Immunology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Shunmay Yeung
- Faculty of Tropical and Infectious Disease, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Joany M Zachariasse
- From the Department of General Paediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Werner Zenz
- Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Dace Zavadska
- Rīgas Stradiņa universitāte, Department of Paediatrics, Children Clinical University Hospital, Riga, Latvia
| | - Henriette A Moll
- From the Department of General Paediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| |
Collapse
|
8
|
Rethinking animal models of sepsis - working towards improved clinical translation whilst integrating the 3Rs. Clin Sci (Lond) 2021; 134:1715-1734. [PMID: 32648582 PMCID: PMC7352061 DOI: 10.1042/cs20200679] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022]
Abstract
Sepsis is a major worldwide healthcare issue with unmet clinical need. Despite extensive animal research in this area, successful clinical translation has been largely unsuccessful. We propose one reason for this is that, sometimes, the experimental question is misdirected or unrealistic expectations are being made of the animal model. As sepsis models can lead to a rapid and substantial suffering – it is essential that we continually review experimental approaches and undertake a full harm:benefit impact assessment for each study. In some instances, this may require refinement of existing sepsis models. In other cases, it may be replacement to a different experimental system altogether, answering a mechanistic question whilst aligning with the principles of reduction, refinement and replacement (3Rs). We discuss making better use of patient data to identify potentially useful therapeutic targets which can subsequently be validated in preclinical systems. This may be achieved through greater use of construct validity models, from which mechanistic conclusions are drawn. We argue that such models could provide equally useful scientific data as face validity models, but with an improved 3Rs impact. Indeed, construct validity models may not require sepsis to be modelled, per se. We propose that approaches that could support and refine clinical translation of research findings, whilst reducing the overall welfare burden on research animals.
Collapse
|
9
|
Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota. Genes (Basel) 2020; 11:genes11091105. [PMID: 32967250 PMCID: PMC7565314 DOI: 10.3390/genes11091105] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022] Open
Abstract
Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME (Oxford Nanopore Technologies—ONT, Oxford, UK) and an in-house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 (Oxford Nanopore Technologies—ONT, Oxford, UK) and R9.2 (Oxford Nanopore Technologies—ONT, Oxford, UK) were compared. In conclusion, the current study shows that the nanopore sequencing platform is comparable with the Illumina platform in detection bacterial genera of the nasal microbiota, but the nanopore platform does have problems in detecting bacteria within the genus Corynebacterium. Although advances are being made, thorough validation of the nanopore platform is still recommendable.
Collapse
|
10
|
Hagedoorn NN, Borensztajn DM, Nijman R, Balode A, von Both U, Carrol ED, Eleftheriou I, Emonts M, van der Flier M, de Groot R, Herberg J, Kohlmaier B, Lim E, Maconochie I, Martinon-Torres F, Nieboer D, Pokorn M, Strle F, Tsolia M, Yeung S, Zavadska D, Zenz W, Vermont C, Levin M, Moll HA. Variation in antibiotic prescription rates in febrile children presenting to emergency departments across Europe (MOFICHE): A multicentre observational study. PLoS Med 2020; 17:e1003208. [PMID: 32813708 PMCID: PMC7444592 DOI: 10.1371/journal.pmed.1003208] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 07/28/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The prescription rate of antibiotics is high for febrile children visiting the emergency department (ED), contributing to antimicrobial resistance. Large studies at European EDs covering diversity in antibiotic and broad-spectrum prescriptions in all febrile children are lacking. A better understanding of variability in antibiotic prescriptions in EDs and its relation with viral or bacterial disease is essential for the development and implementation of interventions to optimise antibiotic use. As part of the PERFORM (Personalised Risk assessment in Febrile illness to Optimise Real-life Management across the European Union) project, the MOFICHE (Management and Outcome of Fever in Children in Europe) study aims to investigate variation and appropriateness of antibiotic prescription in febrile children visiting EDs in Europe. METHODS AND FINDINGS Between January 2017 and April 2018, data were prospectively collected on febrile children aged 0-18 years presenting to 12 EDs in 8 European countries (Austria, Germany, Greece, Latvia, the Netherlands [n = 3], Spain, Slovenia, United Kingdom [n = 3]). These EDs were based in university hospitals (n = 9) or large teaching hospitals (n = 3). Main outcomes were (1) antibiotic prescription rate; (2) the proportion of antibiotics that were broad-spectrum antibiotics; (3) the proportion of antibiotics of appropriate indication (presumed bacterial), inappropriate indication (presumed viral), or inconclusive indication (unknown bacterial/viral or other); (4) the proportion of oral antibiotics of inappropriate duration; and (5) the proportion of antibiotics that were guideline-concordant in uncomplicated urinary and upper and lower respiratory tract infections (RTIs). We determined variation of antibiotic prescription and broad-spectrum prescription by calculating standardised prescription rates using multilevel logistic regression and adjusted for general characteristics (e.g., age, sex, comorbidity, referral), disease severity (e.g., triage level, fever duration, presence of alarming signs), use and result of diagnostics, and focus and cause of infection. In this analysis of 35,650 children (median age 2.8 years, 55% male), overall antibiotic prescription rate was 31.9% (range across EDs: 22.4%-41.6%), and among those prescriptions, the broad-spectrum antibiotic prescription rate was 52.1% (range across EDs: 33.0%-90.3%). After standardisation, differences in antibiotic prescriptions ranged from 0.8 to 1.4, and the ratio between broad-spectrum and narrow-spectrum prescriptions ranged from 0.7 to 1.8 across EDs. Standardised antibiotic prescription rates varied for presumed bacterial infections (0.9 to 1.1), presumed viral infections (0.1 to 3.3), and infections of unknown cause (0.1 to 1.8). In all febrile children, antibiotic prescriptions were appropriate in 65.0% of prescriptions, inappropriate in 12.5% (range across EDs: 0.6%-29.3%), and inconclusive in 22.5% (range across EDs: 0.4%-60.8%). Prescriptions were of inappropriate duration in 20% of oral prescriptions (range across EDs: 4.4%-59.0%). Oral prescriptions were not concordant with the local guideline in 22.3% (range across EDs: 11.8%-47.3%) of prescriptions in uncomplicated RTIs and in 45.1% (range across EDs: 11.1%-100%) of prescriptions in uncomplicated urinary tract infections. A limitation of our study is that the included EDs are not representative of all febrile children attending EDs in that country. CONCLUSIONS In this study, we observed wide variation between European EDs in prescriptions of antibiotics and broad-spectrum antibiotics in febrile children. Overall, one-third of prescriptions were inappropriate or inconclusive, with marked variation between EDs. Until better diagnostics are available to accurately differentiate between bacterial and viral aetiologies, implementation of antimicrobial stewardship guidelines across Europe is necessary to limit antimicrobial resistance.
Collapse
Affiliation(s)
- Nienke N. Hagedoorn
- Department of General Paediatrics, Erasmus MC–Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Dorine M. Borensztajn
- Department of General Paediatrics, Erasmus MC–Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Ruud Nijman
- Section of Paediatric Infectious Disease, Imperial College London, London, United Kingdom
| | - Anda Balode
- Department of Paediatrics, Children’s Clinical University Hospital, Rīgas Stradiņa Universitāte, Riga, Latvia
| | - Ulrich von Both
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig Maximilian University, Munich, Germany
- Partner Site Munich, German Center for Infection Research (DZIF), Munich, Germany
| | - Enitan D. Carrol
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Alder Hey Children’s NHS Foundation Trust, Liverpool, United Kingdom
| | - Irini Eleftheriou
- Second Department of Paediatrics, P. & A. Kyriakou Children’s Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Marieke Emonts
- Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
- NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust and Newcastle University, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michiel van der Flier
- Paediatric Infectious Diseases and Immunology, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
- Section of Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
- Paediatric Infectious Diseases and Immunology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ronald de Groot
- Paediatric Infectious Diseases and Immunology, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
- Section of Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Jethro Herberg
- Section of Paediatric Infectious Disease, Imperial College London, London, United Kingdom
| | - Benno Kohlmaier
- Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Emma Lim
- Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
- NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust and Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ian Maconochie
- Paediatric Emergency Medicine, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Federico Martinon-Torres
- Genetics, Vaccines, Infections and Paediatrics Research Group (GENVIP), Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daan Nieboer
- Department of Public Health, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marko Pokorn
- Department of Infectious Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Franc Strle
- Department of Infectious Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maria Tsolia
- Second Department of Paediatrics, P. & A. Kyriakou Children’s Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Shunmay Yeung
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Dace Zavadska
- Department of Paediatrics, Children’s Clinical University Hospital, Rīgas Stradiņa Universitāte, Riga, Latvia
| | - Werner Zenz
- Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Clementien Vermont
- Department of Paediatric Infectious Diseases and Immunology, Erasmus MC–Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Michael Levin
- Section of Paediatric Infectious Disease, Imperial College London, London, United Kingdom
| | - Henriëtte A. Moll
- Department of General Paediatrics, Erasmus MC–Sophia Children’s Hospital, Rotterdam, the Netherlands
- * E-mail:
| | | |
Collapse
|
11
|
Haag E, Molitor A, Gregoriano C, Müller B, Schuetz P. The value of biomarker-guided antibiotic therapy. Expert Rev Mol Diagn 2020; 20:829-840. [PMID: 32529871 DOI: 10.1080/14737159.2020.1782193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION There is an increasing interest to individualize patient management and decisions regarding antibiotic treatment. Biomarkers may provide relevant information for this purpose. AREAS COVERED Despite a growing number of clinical trials investigating several biomarkers, there remain open questions regarding the best type of biomarker, timing or frequency of testing, and optimal cutoffs among others. The most promising results in regard to diagnosis of bacterial infection and therapy monitoring are found for procalcitonin (PCT), although some recent trials were not able to validate the promising earlier findings. Furthermore, less specific markers like C-reactive protein (CRP) and new prognostic biomarkers such as proadrenomedullin (MR-proADM) may improve the prognostic assessment of patients and proteomics may help shorten time to microbiological results. The aim of this review is to summarize the current concept of biomarker-guided management and provide an outlook of promising ongoing investigations. EXPERT OPINION 'Antibiotic stewardship' is complex and needs more than just the measurement of one single biomarker. However, when integrated into the context of a thorough clinical examination, standard blood parameters and a well done risk stratification by clinical scores such as the SOFA-score, biomarkers have great potential to improve the diagnostic and prognostic assessment of patients.
Collapse
Affiliation(s)
- Ellen Haag
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Alexandra Molitor
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Claudia Gregoriano
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Beat Müller
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Philipp Schuetz
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| |
Collapse
|
12
|
van Houten CB, Cohen A, Engelhard D, Hays JP, Karlsson R, Moore E, Fernández D, Kreisberg R, Collins LV, de Waal W, de Winter-de Groot KM, Wolfs TFW, Meijers P, Luijk B, Oosterheert JJ, Heijligenberg R, Sankatsing SUC, Bossink AWJ, Stubbs A, Stein M, Reisfeld S, Klein A, Rachmilevitch R, Ashkar J, Braverman I, Kartun V, Chistyakov I, Bamberger E, Srugo I, Odeh M, Schiff E, Dotan Y, Boico O, Navon R, Friedman T, Etshtein L, Paz M, Gottlieb TM, Pri-Or E, Kronenfeld G, Simon E, Oved K, Eden E, Bont LJ. Antibiotic misuse in respiratory tract infections in children and adults-a prospective, multicentre study (TAILORED Treatment). Eur J Clin Microbiol Infect Dis 2019; 38:505-514. [PMID: 30707378 PMCID: PMC6394715 DOI: 10.1007/s10096-018-03454-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022]
Abstract
Respiratory tract infections (RTI) are more commonly caused by viral pathogens in children than in adults. Surprisingly, little is known about antibiotic use in children as compared to adults with RTI. This prospective study aimed to determine antibiotic misuse in children and adults with RTI, using an expert panel reference standard, in order to prioritise the target age population for antibiotic stewardship interventions. We recruited children and adults who presented at the emergency department or were hospitalised with clinical presentation of RTI in The Netherlands and Israel. A panel of three experienced physicians adjudicated a reference standard diagnosis (i.e. bacterial or viral infection) for all the patients using all available clinical and laboratory information, including a 28-day follow-up assessment. The cohort included 284 children and 232 adults with RTI (median age, 1.3 years and 64.5 years, respectively). The proportion of viral infections was larger in children than in adults (209(74%) versus 89(38%), p < 0.001). In case of viral RTI, antibiotics were prescribed (i.e. overuse) less frequently in children than in adults (77/209 (37%) versus 74/89 (83%), p < 0.001). One (1%) child and three (2%) adults with bacterial infection were not treated with antibiotics (i.e. underuse); all were mild cases. This international, prospective study confirms major antibiotic overuse in patients with RTI. Viral infection is more common in children, but antibiotic overuse is more frequent in adults with viral RTI. Together, these findings support the need for effective interventions to decrease antibiotic overuse in RTI patients of all ages.
Collapse
Affiliation(s)
- Chantal B van Houten
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, P.O. Box 85090, Office KC.03.063.0, 3508 AB, Utrecht, The Netherlands
| | | | - Dan Engelhard
- Division of Paediatric Infectious Disease Unit, Hadassah-Hebrew University Medical Centre, Jerusalem, Israel
| | - John P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Roger Karlsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Edward Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | | | | | - Wouter de Waal
- Department of Paediatrics, Diakonessenhuis, Utrecht, The Netherlands
| | - Karin M de Winter-de Groot
- Department of Paediatric Respiratory Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tom F W Wolfs
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, P.O. Box 85090, Office KC.03.063.0, 3508 AB, Utrecht, The Netherlands
| | - Pieter Meijers
- Department of Paediatrics, Gelderse Vallei Hospital, Ede, The Netherlands
| | - Bart Luijk
- Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Jelrik Oosterheert
- Department of Internal Medicine and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rik Heijligenberg
- Department of Internal Medicine, Gelderse Vallei Hospital, Ede, The Netherlands
| | | | - Aik W J Bossink
- Department of Respiratory Medicine, Diakonessenhuis Utrecht, Utrecht, The Netherlands
| | - Andrew Stubbs
- Department of Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Michal Stein
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Sharon Reisfeld
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Adi Klein
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | | | - Jalal Ashkar
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Itzhak Braverman
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Valery Kartun
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Irena Chistyakov
- Department of Paediatrics, Bnai Zion Medical Centre, Haifa, Israel
| | - Ellen Bamberger
- Department of Paediatrics, Bnai Zion Medical Centre, Haifa, Israel
| | - Isaac Srugo
- Department of Paediatrics, Bnai Zion Medical Centre, Haifa, Israel
| | - Majed Odeh
- Department of Paediatrics, Bnai Zion Medical Centre, Haifa, Israel
| | - Elad Schiff
- Department of Paediatrics, Bnai Zion Medical Centre, Haifa, Israel
| | - Yaniv Dotan
- Department of Internal Medicine, Bnai Zion Medical Centre, Haifa, Israel
| | | | | | | | | | | | | | | | | | | | | | | | - Louis J Bont
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, P.O. Box 85090, Office KC.03.063.0, 3508 AB, Utrecht, The Netherlands.
| |
Collapse
|