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González-López A, Cima-Cabal MD, Rioboó-Legaspi P, Costa-Rama E, García-Suárez MDM, Fernández-Abedul MT. Electrochemical Detection for Isothermal Loop-Mediated Amplification of Pneumolysin Gene of Streptococcus pneumoniae Based on the Oxidation of Phenol Red Indicator. Anal Chem 2022; 94:13061-13067. [PMID: 36106671 PMCID: PMC9523611 DOI: 10.1021/acs.analchem.2c02127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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A highly sensitive electrochemical methodology for end-point detection
of loop-mediated isothermal nucleic acid amplification reactions was
developed. It is based on the oxidation process of phenol red (PR),
commonly used as a visual indicator. The dependence of its redox process
on pH, which changes during amplification, allows performing quantitative
measurements. Thus, the change in the oxidation potential of PR during
the amplification is used, for the first time, as the analytical signal
that correlates with the number of initial DNA copies. As a proof-of-concept,
the amplification of the pneumolysin gene from Streptococcus
pneumoniae, one of the main pathogens causing community-acquired
pneumonia, is performed. Combination of isothermal amplification with
electrochemical detection, performed on small-size flexible electrodes,
allows easy decentralization. Adaptation to the detection of other
pathogens causing infectious diseases would be very useful in the
prevention of future epidemics.
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Affiliation(s)
- Andrea González-López
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | - María Dolores Cima-Cabal
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, Avda. de La Paz 137, Logroño 26006, Spain
| | - Pablo Rioboó-Legaspi
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | - Estefanía Costa-Rama
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | | | - M. Teresa Fernández-Abedul
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
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Dirkx KKT, Mulder B, Post AS, Rutten MH, Swanink CMA, Wertheim HFL, Cremers AJH. The drop in reported invasive pneumococcal disease among adults during the first COVID-19 wave in the Netherlands explained. Int J Infect Dis 2021; 111:196-203. [PMID: 34455081 PMCID: PMC8444629 DOI: 10.1016/j.ijid.2021.08.060] [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: 08/01/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 01/28/2023] Open
Abstract
Objectives: Streptococcus pneumoniae is the leading bacterial pathogen causing respiratory infections. Since the COVID-19 pandemic emerged, less invasive pneumococcal disease (IPD) was identified by surveillance systems worldwide. Measures to prevent transmission of SARS-CoV-2 also reduce transmission of pneumococci, but this would gradually lead to lower disease rates. Design: Here, we explore additional factors contributing to the instant drop in pneumococcal disease cases captured in surveillance. Results: Our observations on referral practices and other impediments to diagnostic testing indicate that residual IPD has likely occurred but remained undetected by conventional hospital-based surveillance. Conclusions: Depending on the setting, we discuss alternative monitoring strategies that could improve understanding of pneumococcal disease dynamics.
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Affiliation(s)
- Kirsten K T Dirkx
- Department of Clinical Microbiology and Infectious Diseases, Canisius-Wilhelmina Ziekenhuis, Nijmegen, the Netherlands; Department of Clinical Microbiology, Radboud Centre for Infectious Diseases, Radboudumc, Nijmegen, the Netherlands
| | - Bert Mulder
- Department of Clinical Microbiology and Infectious Diseases, Canisius-Wilhelmina Ziekenhuis, Nijmegen, the Netherlands
| | - Annelies S Post
- Department of Clinical Microbiology and Infectious Diseases, Canisius-Wilhelmina Ziekenhuis, Nijmegen, the Netherlands
| | - Martijn H Rutten
- Department of Primary and Community Care, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Caroline M A Swanink
- Department of Clinical Microbiology and Immunology, Rijnstate, Arnhem, the Netherlands
| | - Heiman F L Wertheim
- Department of Clinical Microbiology, Radboud Centre for Infectious Diseases, Radboudumc, Nijmegen, the Netherlands
| | - Amelieke J H Cremers
- Department of Clinical Microbiology, Radboud Centre for Infectious Diseases, Radboudumc, Nijmegen, the Netherlands
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3
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Application of a Pneumococcal Serotype-specific Urinary Antigen Detection Test for Identification of Pediatric Pneumonia in Burkina Faso. Pediatr Infect Dis J 2021; 40:418-425. [PMID: 33464020 DOI: 10.1097/inf.0000000000003065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Serotype-specific diagnosis of pneumococcal community-acquired pneumonia in children under age 5 years would mark a major advancement for understanding pneumococcal epidemiology and supporting vaccine decision-making. METHODS A Luminex technology-based multiplex urinary antigen detection (UAD) diagnostic assay was developed and subsequently validated in adults, but its applicability to children is unknown. This study aimed to set appropriate cutoffs for use of the UAD in a healthy pediatric population and apply these cutoffs in children with pneumonia in sub-Saharan Africa. The cutoffs were determined by assessing 379 urines obtained from healthy children under age 5 years from the Bobo-Dioulasso area for serotypes included in 13-valent pneumococcal conjugate vaccine (UAD-1) and the 11 other serotypes unique to 23-valent pneumococcal polysaccharide vaccine (UAD-2). RESULTS Based on the assigned cutoff values, among 108 children who met the World Health Organization consolidation endpoint criteria, UAD-1 and UAD-2 were positive in 23.3% and 8.3%, respectively; among 364 children with clinically suspected pneumonia who did not meet the World Health Organization criteria, UAD-1 and UAD-2 were positive for 6.6% and 3.6%, respectively. Pneumococcal carriage prevalence was similar among pneumonia cases (30%) versus controls (35%) as was semiquantitative carriage density. CONCLUSIONS UAD-1 and UAD-2 were able to distinguish community controls from children with pneumonia, particularly pneumonia with consolidation. Future studies are needed to confirm these results and more fully assess the contribution of pneumococcal carriage and concurrent viral infection.
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Groeneveld GH, van der Reyden TJ, Joosten SA, Bootsma HJ, Cobbaert CM, de Vries JJC, Kuijper EJ, van Dissel JT. Non-lytic antibiotic treatment in community-acquired pneumococcal pneumonia does not attenuate inflammation: the PRISTINE trial. J Antimicrob Chemother 2020; 74:2385-2393. [PMID: 31106377 PMCID: PMC6640306 DOI: 10.1093/jac/dkz207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 12/18/2022] Open
Abstract
Background The inflammatory response in pneumococcal infection is primarily driven by immunoreactive bacterial cell wall components [lipoteichoic acid (LTA)]. An acute release of these components occurs when pneumococcal infection is treated with β-lactam antibiotics. Objectives We hypothesized that non-lytic rifampicin compared with lytic β-lactam antibiotic treatment would attenuate the inflammatory response in patients with pneumococcal pneumonia. Methods In the PRISTINE (Pneumonia treated with RIfampicin aTtenuates INflammation) trial, a randomized, therapeutic controlled, exploratory study in patients with community-acquired pneumococcal pneumonia, we looked at LTA release and inflammatory and clinical response during treatment with both rifampicin and β-lactam compared with treatment with β-lactam antibiotics only. The trial is registered in the Dutch trial registry, number NTR3751 (European Clinical Trials Database number 2012-003067-22). Results Forty-one patients with community-acquired pneumonia were included; 17 of them had pneumococcal pneumonia. LTA release, LTA-mediated inflammatory responses, clinical outcomes, inflammatory biomarkers and transcription profiles were not different between treatment groups. Conclusions The PRISTINE study demonstrated the feasibility of adding rifampicin to β-lactam antibiotics in the treatment of community-acquired pneumococcal pneumonia, but, despite solid in vitro and experimental animal research evidence, failed to demonstrate a difference in plasma LTA concentrations and subsequent inflammatory and clinical responses. Most likely, an inhibitory effect of human plasma contributes to the low immune response in these patients. In addition, LTA plasma concentration could be too low to mount a response via Toll-like receptor 2 in vitro, but may nonetheless have an effect in vivo.
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Affiliation(s)
- Geert H Groeneveld
- Department of Internal Medicine and Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Tanny J van der Reyden
- Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Hester J Bootsma
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (Rijksinstituut voor Volksgezondheid en Milieu, RIVM), Bilthoven, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Jaap T van Dissel
- Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (Rijksinstituut voor Volksgezondheid en Milieu, RIVM), Bilthoven, The Netherlands
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5
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Cremers AJH, Mobegi FM, van der Gaast-de Jongh C, van Weert M, van Opzeeland FJ, Vehkala M, Knol MJ, Bootsma HJ, Välimäki N, Croucher NJ, Meis JF, Bentley S, van Hijum SAFT, Corander J, Zomer AL, Ferwerda G, de Jonge MI. The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease. Clin Infect Dis 2020; 68:61-69. [PMID: 29788414 DOI: 10.1093/cid/ciy417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 05/10/2018] [Indexed: 01/02/2023] Open
Abstract
Background Different clinical manifestations of invasive pneumococcal disease (IPD) have thus far mainly been explained by patient characteristics. Here we studied the contribution of pneumococcal genetic variation to IPD phenotype. Methods The index cohort consisted of 349 patients admitted to 2 Dutch hospitals between 2000-2011 with pneumococcal bacteremia. We performed genome-wide association studies to identify pneumococcal lineages, genes, and allelic variants associated with 23 clinical IPD phenotypes. The identified associations were validated in a nationwide (n = 482) and a post-pneumococcal vaccination cohort (n = 121). The contribution of confirmed pneumococcal genotypes to the clinical IPD phenotype, relative to known clinical predictors, was tested by regression analysis. Results Among IPD patients, the presence of pneumococcal gene slaA was a nationwide confirmed independent predictor of meningitis (odds ratio [OR], 10.5; P = .001), as was sequence cluster 9 (serotype 7F: OR, 3.68; P = .057). A set of 4 pneumococcal genes co-located on a prophage was a confirmed independent predictor of 30-day mortality (OR, 3.4; P = .003). We could detect the pneumococcal variants of concern in these patients' blood samples. Conclusions In this study, knowledge of pneumococcal genotypic variants improved the clinical risk assessment for detrimental manifestations of IPD. This provides us with novel opportunities to target, anticipate, or avert the pathogenic effects related to particular pneumococcal variants, and indicates that information on pneumococcal genotype is important for the diagnostic and treatment strategy in IPD. Ongoing surveillance is warranted to monitor the clinical value of information on pneumococcal variants in dynamic microbial and susceptible host populations.
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Affiliation(s)
- Amelieke J H Cremers
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands.,Department of Medical Microbiology, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
| | - Fredrick M Mobegi
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands.,Bacterial Genomics Group, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
| | - Christa van der Gaast-de Jongh
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
| | - Michelle van Weert
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
| | - Fred J van Opzeeland
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
| | - Minna Vehkala
- Department of Mathematics and Statistics, University of Helsinki, Finland
| | - Mirjam J Knol
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Hester J Bootsma
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Niko Välimäki
- Department of Mathematics and Statistics, University of Helsinki, Finland
| | - Nicholas J Croucher
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Stephen Bentley
- Wellcome Trust Sanger Institute, Pathogen Genomics Group, Hinxton, Cambridge, United Kingdom
| | - Sacha A F T van Hijum
- Radboud Center for Infectious Diseases, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands.,Bacterial Genomics Group, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands.,NIZO, Ede, The Netherlands
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Finland.,Wellcome Trust Sanger Institute, Pathogen Genomics Group, Hinxton, Cambridge, United Kingdom.,Department of Biostatistics, University of Oslo, Norway
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Gerben Ferwerda
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
| | - Marien I de Jonge
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
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Viasus D, Calatayud L, McBrown MV, Ardanuy C, Carratalà J. Urinary antigen testing in community-acquired pneumonia in adults: an update. Expert Rev Anti Infect Ther 2019; 17:107-115. [PMID: 30618315 DOI: 10.1080/14787210.2019.1565994] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Community-acquired pneumonia (CAP) continues to be a leading cause of hospitalization and mortality worldwide. Streptococcus pneumoniae and Legionella pneumophila remain the major etiological agents and are responsible for a significant proportion of CAP mortality. Among diagnostic tests for CAP, urine antigen detection of S. pneumoniae and L. pneumophila is widely accepted due to the simplicity of collection and the rapidity of the test results. Areas covered: This comprehensive review outlines the urinary antigen tests available, discusses their sensitivity and specificity, and assesses the usefulness of their results as the basis for targeted therapy. Expert commentary: There have been advances in urine antigen detection tests for patients with CAP. New methodologies show greater sensitivity, detect S. pneumoniae and L. pneumophila in a single test, and also detect pneumococcal serotypes. In addition, urine antigen detection tests have shown a high specificity, which means that a positive result practically indicates the causative pathogen of CAP. Therefore, a positive result can lead to a targeted therapy that is likely to improve patient outcomes and reduce the risk of resistance and adverse events. However, well-designed studies are needed to evaluate the usefulness of urine antigen detection tests with regard to clinical outcomes.
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Affiliation(s)
- Diego Viasus
- a Department of Medicine, Health Sciences Division , Universidad del Norte and Hospital Universidad del Norte , Barranquilla , Colombia
| | - Laura Calatayud
- b Department of Microbiology , Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), University of Barcelona , Barcelona , Spain.,c Research Network for Respiratory Diseases (CIBERES) , Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - María V McBrown
- a Department of Medicine, Health Sciences Division , Universidad del Norte and Hospital Universidad del Norte , Barranquilla , Colombia
| | - Carmen Ardanuy
- b Department of Microbiology , Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), University of Barcelona , Barcelona , Spain.,c Research Network for Respiratory Diseases (CIBERES) , Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Jordi Carratalà
- d Department of Infectious Diseases , Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), University of Barcelona , Barcelona , Spain.,e Spanish Network for Research in Infectious Diseases (REIPI) , Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
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Chen J, Xu Y, Yan H, Zhu Y, Wang L, Zhang Y, Lu Y, Xing W. Sensitive and rapid detection of pathogenic bacteria from urine samples using multiplex recombinase polymerase amplification. LAB ON A CHIP 2018; 18:2441-2452. [PMID: 30014076 DOI: 10.1039/c8lc00399h] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Bacterial infections may cause severe diseases such as tuberculosis, sepsis, nephritis and cystitis. The rapid and sensitive detection of bacteria is a prerequisite for the treatment of these diseases. The current gold standard for bacterial identification is bacteriological culture. However, culture-based identification takes 3-7 days, which is time-consuming and laborious. In this study, bacteria in urine samples were enriched using a portable filter-based pipette. Then, a centrifugal chip was constructed to detect multiple pathogenic bacteria from urine samples by integrating the DNA extraction, multiplex recombinase polymerase amplification (RPA) and fluorescent detection together. This eliminated the time-consuming cultivation step, and thus accelerated the diagnosis of the urinary tract infections (UTIs). The five major pathogenic bacteria in UTIs were detected in this study, which are Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, Staphylococcus aureus and Salmonella typhimurium. Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa and Staphylococcus aureus were successfully detected with limits of detection of 100 CFU mL-1 from urine samples within 40 min. Salmonella typhimurium was successfully detected with a limit of detection of 1000 CFU mL-1 from urine samples. The chip-based bacteria detection proposed in this study is a promising tool for sensitive, accurate, and multiplex identification of bacteria in clinical urine samples of UTIs and bacteriuria.
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Affiliation(s)
- Junge Chen
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China.
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8
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Development of an Extended-Specificity Multiplex Immunoassay for Detection of Streptococcus pneumoniae Serotype-Specific Antigen in Urine by Use of Human Monoclonal Antibodies. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:CVI.00262-17. [PMID: 28978509 DOI: 10.1128/cvi.00262-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/30/2017] [Indexed: 11/20/2022]
Abstract
Current pneumococcal vaccines cover the 10 to 23 most common serotypes of the 92 presently described. However, with the increased usage of pneumococcal-serotype-based vaccines, the risk of serotype replacement and an increase in disease caused by nonvaccine serotypes remains. Serotype surveillance of pneumococcal infections relies heavily on culture techniques, which are known to be insensitive, particularly in cases of noninvasive disease. Pneumococcal-serotype-specific urine assays offer an alternative method of serotyping for both invasive and noninvasive disease. However, the assays described previously cover mainly conjugate vaccine serotypes, give little information about circulating nonvaccine serotypes, and are currently available only in one or two specialist laboratories. Our laboratory has developed a Luminex-based extended-range antigen capture assay to detect pneumococcal-serotype-specific antigens in urine samples. The assay targets 24 distinct serotypes/serogroups plus the cell wall polysaccharide (CWP) and some cross-reactive serotypes. We report that the assay is capable of detecting all the targeted serotypes and the CWP at 0.1 ng/ml, while some serotypes are detected at concentrations as low as 0.3 pg/ml. The analytical serotype specificity was determined to be 98.4% using a panel of polysaccharide-negative urine specimens spiked with nonpneumococcal bacterial antigens. We also report clinical sensitivities of 96.2% and specificities of 89.9% established using a panel of urine specimens from patients diagnosed with community-acquired pneumonia or pneumococcal disease. This assay can be extended for testing other clinical samples and has the potential to greatly improve serotype-specific surveillance in the many cases of pneumococcal disease in which a culture is never obtained.
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Pneumococcal conjugate vaccination response in patients after community-acquired pneumonia, differences in patients with S. pneumoniae versus other pathogens. Vaccine 2017; 35:4886-4895. [DOI: 10.1016/j.vaccine.2017.07.088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/15/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022]
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10
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Torres A, Lee N, Cilloniz C, Vila J, Van der Eerden M. Laboratory diagnosis of pneumonia in the molecular age. Eur Respir J 2016; 48:1764-1778. [PMID: 27811073 DOI: 10.1183/13993003.01144-2016] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/17/2016] [Indexed: 01/20/2023]
Abstract
Pneumonia remains a worldwide health problem with a high rate of morbidity and mortality. Identification of microbial pathogens which cause pneumonia is an important area for optimum clinical management of pneumonia patients and is a big challenge for conventional microbiological methods. The development and implementation of molecular diagnostic tests for pneumonia has been a major advance in the microbiological diagnosis of respiratory pathogens in recent years. However, with new knowledge regarding the microbiome, together with the recognition that the lungs are a dynamic microbiological ecosystem, our current concept of pneumonia is not totally realistic as this new concept of pneumonia involves a dysbiosis or alteration of the lung microbiome. A new challenge for microbiologists and clinicians has therefore arisen. There is much to learn regarding the information provided by this new diagnostic technology, which will lead to improvements in the time to antibiotic therapy, targeted antibiotic selection and more effective de-escalation and improved stewardship for pneumonia patients. This article provides an overview of current methods of laboratory diagnosis of pneumonia in the molecular age.
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Affiliation(s)
- Antoni Torres
- Dept of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Ciber de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Nelson Lee
- Division of Infectious Diseases, Dept of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Catia Cilloniz
- Dept of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Ciber de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Jordi Vila
- Servei de Microbiologia, Hospital Clinic, ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Menno Van der Eerden
- Dept of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
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Application of capsular sequence typing (CST) to serotype non-viable Streptococcus pneumoniae isolates from an old collection. Eur J Clin Microbiol Infect Dis 2016; 35:2025-2031. [PMID: 27580910 DOI: 10.1007/s10096-016-2755-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 10/21/2022]
Abstract
Serotyping of Streptococcus pneumoniae is essential for monitoring changes in the pneumococcal population and the impact of vaccines. Recently, various DNA-based methods have become available and are increasingly used because they are cheaper and easier to perform than the Quellung reaction. Our aim was to apply a DNA-based method, capsular sequence typing (CST), to a collection of non-viable lyophilized pneumococcal isolates dating from the 1980s to elucidate the serotypes circulating in Italy 30 years ago. As a preliminary evaluation of the method, CST was applied to 68 recent pneumococcal isolates representative of the most common serotypes circulating in Italy in invasive pneumococcal disease (IPD) previously serotyped by the Quellung reaction. CST was then applied to 132 lyophilized non-viable isolates. A serotype-specific polymerase chain reaction (PCR), using primers suggested by the Centers for Disease Control and Prevention (CDC), was performed when CST did not yield a univocal serotype. Considering the control isolates, CST concordance with the Quellung reaction was 95.6 %. For the non-viable lyophilized isolates, CST identified a univocal serotype for 59.4 % of the isolates. This percentage increased to 78.1 % if CST was combined with serotype-specific PCR. The most frequent serotypes in the collection of non-viable strains were: 3 (15.6 %), 14 (11.7 %), 35B (5.5 %), 19A (5.5 %), and 8 (4.7 %). CST proved to be a valid method for serotyping pneumococcal strains and provided information about pneumococcal serotypes present in Italy 30 years ago. The combination of CST with serotype-specific PCR was an effective strategy to identify pneumococcal serotypes that can be suggested also for routine laboratories.
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Earle K, Williams S. Burden of pneumococcal disease in adults aged 65 years and older: an Australian perspective. Pneumonia (Nathan) 2016; 8:9. [PMID: 28702288 PMCID: PMC5471924 DOI: 10.1186/s41479-016-0008-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/31/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The burden of pneumococcal disease in adults aged 65 years and older in Australia is not well defined. This retrospective cross-sectional study calculated rates for pneumococcal pneumonia using data from the Australian Institute of Health and Welfare and from the Bettering Evaluation and Care of Health program. METHODS Invasive pneumococcal disease (IPD) incidence was calculated using National Notifiable Diseases Surveillance System data. Population estimates and pneumonia mortality data were from the Australian Bureau of Statistics. Medical costs were derived from Australian Refined Diagnosis Related Groups and the literature. Clinical and economic burden of pneumococcal pneumonia hospitalisations and general practitioner (GP) visits were described and compared with IPD. RESULTS For adults aged ≥65 years, pneumococcal pneumonia hospitalisation incidence was 274 per 100,000 population in 2011-2012. From 2004 to 2012, a mean of 2235 pneumonia hospitalisation deaths were recorded, corresponding to a case fatality rate of 6.1 %. GP visits accounted for the largest portion of healthcare encounters, with an annual average of 455 pneumococcal pneumonia GP visits per 100,000 population from 2008 to 2013. In 2012, IPD incidence was 19 per 100,000 population. The estimated annual costs of treating pneumococcal pneumonia hospitalisations and GP visits were A$55,722,136 and A$1,604,189, respectively. Estimated costs for IPD were A$1,172,986. CONCLUSIONS The healthcare and economic burden of pneumococcal disease in adults aged ≥65 years in Australia is substantial, with the incidence of pneumococcal pneumonia hospitalisation nearly 15-fold higher than for IPD. Despite this, it remains less recognised than other infectious diseases such as influenza.
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Affiliation(s)
- Kylie Earle
- Pfizer Australia, Access and Public Affairs, Australia 38-42 Wharf Road, West Ryde, Sydney, 2114 NSW Australia
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Molecular surveillance of nasopharyngeal carriage of Streptococcus pneumoniae in children vaccinated with conjugated polysaccharide pneumococcal vaccines. Sci Rep 2016; 6:23809. [PMID: 27046258 PMCID: PMC4820691 DOI: 10.1038/srep23809] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/15/2016] [Indexed: 11/16/2022] Open
Abstract
Following the introduction of pneumococcal conjugate vaccines (PCVs) for infants, surveillance studies on Streptococcus pneumoniae carriage have proven valuable for monitoring vaccine effects. Here, we compared molecular versus conventional diagnostic methods in prospective cross-sectional surveillances in vaccinated infants in the Netherlands. Nasopharyngeal samples (n = 1169) from 11- and 24-month-old children, collected during autumn/winter 2010/2011 and 2012/2013, were tested by conventional culture for S. pneumoniae. DNA extracted from all culture-plate growth was tested by qPCR for pneumococcal-specific genes (lytA/piaB) and selected serotypes (including PCV13-serotypes). qPCR significantly increased the number of carriers detected compared to culture (69% vs. 57%, p < 0.0001). qPCR assays targeting vaccine-serotypes 4 and 5 proved non-specific (results excluded). For serotypes reliably targeted by qPCR, the number of serotype-carriage events detected by qPCR (n = 709) was 1.68× higher compared to culture (n = 422). There was a strong correlation (rho = 0.980; p < 0.0001) between the number of serotypes detected using qPCR and by culture. This study demonstrates the high potential of molecular methods in pneumococcal surveillances, particularly for enhanced serotype detection. We found no evidence of a hidden circulation of vaccine-targeted serotypes, despite vaccine-serotypes still significantly contributing to invasive pneumococcal disease in unvaccinated individuals, supporting the presence of a substantial S. pneumoniae reservoir outside vaccinated children.
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Falguera M, Ramírez M. Neumonía adquirida en la comunidad. Rev Clin Esp 2015; 215:458-67. [DOI: 10.1016/j.rce.2015.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 05/30/2015] [Accepted: 06/02/2015] [Indexed: 11/30/2022]
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15
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Falguera M, Ramírez M. Community-acquired pneumonia. Rev Clin Esp 2015. [DOI: 10.1016/j.rceng.2015.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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TRUCCHI C, PAGANINO C, ANSALDI F. Methodological criticisms in the evaluation of Pneumococcal Conjugate Vaccine effectiveness. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2015; 56:E144-9. [PMID: 26788736 PMCID: PMC4755124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 08/22/2015] [Indexed: 11/13/2022]
Abstract
Globally, lower respiratory tract infections (LRTIs), including community-acquired pneumonia (CAP), cause considerable of morbidity and mortality in adults, especially in the elderly. In addition to age, underlying medical conditions are associated with an increased risk of CAP. From an aetiological point of view, Streptococcus pneumoniae is the leading cause of adult CAP throughout the world. Two types of vaccine are available for the prevention of pneumococcal diseases: the pneumococcal polysaccharide vaccine (PPV23) and the pneumococcal conjugate vaccine (PCV7, PCV10 and PCV13). An accurate understanding of the LRTIs burden and the types of subjects at risk of CAP, allow to find an appropriately targeted immunization strategy and provide baseline data to evaluate pneumococcal vaccine effectiveness. Given the high variability in available estimates of LRTIs burden and associated risk factors, the objective of the study was to discuss the methodological criticism in its evaluation, in the light of the gradual introduction of PCV13 immunization strategy targeted to elderly and risk groups in middle-high income countries.
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Affiliation(s)
- C. TRUCCHI
- Department of Health Sciences (DiSSal), University of Genoa, Italy;,Cecilia Trucchi, Department of Health Sciences (DiSSal), University of Genoa, via A. Pastore, 1, 16132 Genoa, Italy - Tel. +39 010 5552333 - E-mail:
| | - C. PAGANINO
- Department of Health Sciences (DiSSal), University of Genoa, Italy
| | - F. ANSALDI
- Department of Health Sciences (DiSSal), University of Genoa, Italy;, OU Clinical Governance and Hospital Organization, IRCCS AOU San Martino – IST, Genoa, Italy
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