1
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Yasuo S, Murata M, Nakagawa N, Kawasaki T, Yoshida T, Ando K, Okamori S, Okada Y. Diagnostic accuracy of urinary antigen tests for pneumococcal pneumonia among patients with acute respiratory failure suspected pneumonia: a systematic review and meta-analysis. BMJ Open 2022; 12:e057216. [PMID: 35953247 PMCID: PMC9379505 DOI: 10.1136/bmjopen-2021-057216] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND/OBJECTIVES Urinary antigen tests have been used for the rapid identification of Streptococcus pneumoniae infection in patients with pneumonia, thereby leading to earlier targeted therapy than when using conventional diagnostic culture methods. This study aimed to update the knowledge on the diagnostic accuracy of urinary antigen tests for S. pneumoniae among patients with acute respiratory failure suspected of pneumonia based on a systematic review and meta-analysis. METHODS A systematic search was performed using MEDLINE and the Cochrane Central Register of Controlled Trials for studies published up to 3 June 2020. Prospective and retrospective cohort studies (in English) that reported on the diagnostic performance of urinary antigen tests versus culture or smear diagnostic methods in adult patients with clinically diagnosed pneumonia were selected and analysed. The QUADAS-2 tool was used to assess the risk of bias, and a bivariate random effects model was applied to perform a meta-analysis of the selected studies. RESULTS A total of 2179 studies were screened, of which 30 met the eligibility criteria for quality assessment and meta-analysis. Overall, data from 12 366 patients, including 1548 patients (12.5%) with the target condition and suspected pneumococcal pneumonia, were included in the analysis. The overall quality of the included studies was determined to be serious. The calculated pooled sensitivity and specificity were of 0.66 (95% CI 0.62 to 0.69) and 0.90 (95% CI 0.85 to 0.93), respectively. CONCLUSIONS The urinary antigen test is useful for achieving a definitive diagnosis of S. pneumoniae infection in patients with pneumonia.
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Affiliation(s)
- Shunsuke Yasuo
- Department of Emergency and Critical Care Medicine, Kyoto Katsura Hospital, Kyoto, Kyoto, Japan
| | - Maki Murata
- Department of Emergency medicine and Critical care, National Hospital Organization Kyoto Medical Center, Kyoto, Kyoto, Japan
| | - Natsuki Nakagawa
- Department of Respiratory Medicine, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Takeshi Kawasaki
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Takuo Yoshida
- Department of Intensive Care Medicine, Tokyo Women's Medical University, Shinjuku-ku, Tokyo, Japan
| | - Koichi Ando
- Division of Respiratory Medicine and Allergology, Department of Medicine, Showa University, School of Medicine, Shinagawa-ku, Tokyo, Japan
| | - Satoshi Okamori
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yohei Okada
- Department of Primary Care and Emergency Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
- Preventive Services, School of Public Health in the Graduate School of Medicine, Kyoto University, Kyoto, Japan
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2
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Tasaka S, Ohshimo S, Takeuchi M, Yasuda H, Ichikado K, Tsushima K, Egi M, Hashimoto S, Shime N, Saito O, Matsumoto S, Nango E, Okada Y, Hayashi K, Sakuraya M, Nakajima M, Okamori S, Miura S, Fukuda T, Ishihara T, Kamo T, Yatabe T, Norisue Y, Aoki Y, Iizuka Y, Kondo Y, Narita C, Kawakami D, Okano H, Takeshita J, Anan K, Okazaki SR, Taito S, Hayashi T, Mayumi T, Terayama T, Kubota Y, Abe Y, Iwasaki Y, Kishihara Y, Kataoka J, Nishimura T, Yonekura H, Ando K, Yoshida T, Masuyama T, Sanui M. ARDS Clinical Practice Guideline 2021. J Intensive Care 2022; 10:32. [PMID: 35799288 PMCID: PMC9263056 DOI: 10.1186/s40560-022-00615-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/10/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The joint committee of the Japanese Society of Intensive Care Medicine/Japanese Respiratory Society/Japanese Society of Respiratory Care Medicine on ARDS Clinical Practice Guideline has created and released the ARDS Clinical Practice Guideline 2021. METHODS The 2016 edition of the Clinical Practice Guideline covered clinical questions (CQs) that targeted only adults, but the present guideline includes 15 CQs for children in addition to 46 CQs for adults. As with the previous edition, we used a systematic review method with the Grading of Recommendations Assessment Development and Evaluation (GRADE) system as well as a degree of recommendation determination method. We also conducted systematic reviews that used meta-analyses of diagnostic accuracy and network meta-analyses as a new method. RESULTS Recommendations for adult patients with ARDS are described: we suggest against using serum C-reactive protein and procalcitonin levels to identify bacterial pneumonia as the underlying disease (GRADE 2D); we recommend limiting tidal volume to 4-8 mL/kg for mechanical ventilation (GRADE 1D); we recommend against managements targeting an excessively low SpO2 (PaO2) (GRADE 2D); we suggest against using transpulmonary pressure as a routine basis in positive end-expiratory pressure settings (GRADE 2B); we suggest implementing extracorporeal membrane oxygenation for those with severe ARDS (GRADE 2B); we suggest against using high-dose steroids (GRADE 2C); and we recommend using low-dose steroids (GRADE 1B). The recommendations for pediatric patients with ARDS are as follows: we suggest against using non-invasive respiratory support (non-invasive positive pressure ventilation/high-flow nasal cannula oxygen therapy) (GRADE 2D), we suggest placing pediatric patients with moderate ARDS in the prone position (GRADE 2D), we suggest against routinely implementing NO inhalation therapy (GRADE 2C), and we suggest against implementing daily sedation interruption for pediatric patients with respiratory failure (GRADE 2D). CONCLUSIONS This article is a translated summary of the full version of the ARDS Clinical Practice Guideline 2021 published in Japanese (URL: https://www.jsicm.org/publication/guideline.html ). The original text, which was written for Japanese healthcare professionals, may include different perspectives from healthcare professionals of other countries.
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Affiliation(s)
- Sadatomo Tasaka
- Department of Respiratory Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori, 036-8562, Japan.
| | - Shinichiro Ohshimo
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Muneyuki Takeuchi
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Hideto Yasuda
- Department of Emergency and Critical Care Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Kazuya Ichikado
- Division of Respiratory Medicine, Saiseikai Kumamoto Hospital, Kumamoto, Japan
| | - Kenji Tsushima
- International University of Health and Welfare, Tokyo, Japan
| | - Moritoki Egi
- Department of Anesthesiology, Kobe University Hospital, Hyogo, Japan
| | - Satoru Hashimoto
- Department of Anesthesiology and Intensive Care Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Nobuaki Shime
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Osamu Saito
- Department of Pediatric Emergency and Critical Care Medicine, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Shotaro Matsumoto
- Division of Critical Care Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Eishu Nango
- Department of Family Medicine, Seibo International Catholic Hospital, Tokyo, Japan
| | - Yohei Okada
- Department of Primary Care and Emergency Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichiro Hayashi
- Department of Pediatrics, The University of Tokyo Hospital, Tokyo, Japan
| | - Masaaki Sakuraya
- Department of Emergency and Intensive Care Medicine, JA Hiroshima General Hospital, Hiroshima, Japan
| | - Mikio Nakajima
- Emergency and Critical Care Center, Tokyo Metropolitan Hiroo Hospital, Tokyo, Japan
| | - Satoshi Okamori
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shinya Miura
- Paediatric Intensive Care Unit, The Royal Children's Hospital, Melbourne, Australia
| | - Tatsuma Fukuda
- Department of Emergency and Critical Care Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Tadashi Ishihara
- Department of Emergency and Critical Care Medicine, Urayasu Hospital, Juntendo University, Chiba, Japan
| | - Tetsuro Kamo
- Department of Critical Care Medicine, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Tomoaki Yatabe
- Department of Anesthesiology, Nishichita General Hospital, Tokai, Japan
| | | | - Yoshitaka Aoki
- Department of Anesthesiology and Intensive Care Medicine, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Yusuke Iizuka
- Department of Anesthesiology and Critical Care Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Yutaka Kondo
- Department of Emergency and Critical Care Medicine, Juntendo University Urayasu Hospital, Chiba, Japan
| | - Chihiro Narita
- Department of Emergency Medicine, Shizuoka General Hospital, Shizuoka, Japan
| | - Daisuke Kawakami
- Department of Anesthesia and Critical Care, Kobe City Medical Center General Hospital, Hyogo, Japan
| | - Hiromu Okano
- Department of Critical Care and Emergency Medicine, National Hospital Organization Yokohama Medical Center, Kanagawa, Japan
| | - Jun Takeshita
- Department of Anesthesiology, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Keisuke Anan
- Division of Respiratory Medicine, Saiseikai Kumamoto Hospital, Kyoto, Japan
| | | | - Shunsuke Taito
- Division of Rehabilitation, Department of Clinical Practice and Support, Hiroshima University Hospital, Hiroshima, Japan
| | - Takuya Hayashi
- Pediatric Emergency and Critical Care Center, Saitama Children's Medical Center, Saitama, Japan
| | - Takuya Mayumi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Takero Terayama
- Department of Psychiatry, School of Medicine, National Defense Medical College, Saitama, Japan
| | - Yoshifumi Kubota
- Kameda Medical Center Department of Infectious Diseases, Chiba, Japan
| | - Yoshinobu Abe
- Division of Emergency and Disaster Medicine Tohoku Medical and Pharmaceutical University, Miyagi, Japan
| | - Yudai Iwasaki
- Department of Anesthesiology and Perioperative Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yuki Kishihara
- Department of Emergency Medicine, Japanese Red Cross Musashino Hospital, Tokyo, Japan
| | - Jun Kataoka
- Department of Critical Care Medicine, Nerima Hikarigaoka Hospital, Tokyo, Japan
| | - Tetsuro Nishimura
- Department of Traumatology and Critical Care Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Hiroshi Yonekura
- Department of Anesthesiology and Pain Medicine, Fujita Health University Bantane Hospital, Aichi, Japan
| | - Koichi Ando
- Division of Respiratory Medicine and Allergology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Takuo Yoshida
- Intensive Care Unit, Department of Anesthesiology, Jikei University School of Medicine, Tokyo, Japan
| | - Tomoyuki Masuyama
- Department of Emergency and Critical Care Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Masamitsu Sanui
- Department of Anesthesiology and Critical Care Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
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3
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Tasaka S, Ohshimo S, Takeuchi M, Yasuda H, Ichikado K, Tsushima K, Egi M, Hashimoto S, Shime N, Saito O, Matsumoto S, Nango E, Okada Y, Hayashi K, Sakuraya M, Nakajima M, Okamori S, Miura S, Fukuda T, Ishihara T, Kamo T, Yatabe T, Norisue Y, Aoki Y, Iizuka Y, Kondo Y, Narita C, Kawakami D, Okano H, Takeshita J, Anan K, Okazaki SR, Taito S, Hayashi T, Mayumi T, Terayama T, Kubota Y, Abe Y, Iwasaki Y, Kishihara Y, Kataoka J, Nishimura T, Yonekura H, Ando K, Yoshida T, Masuyama T, Sanui M. ARDS clinical practice guideline 2021. Respir Investig 2022; 60:446-495. [PMID: 35753956 DOI: 10.1016/j.resinv.2022.05.003] [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: 04/19/2022] [Revised: 05/07/2022] [Accepted: 05/13/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND The joint committee of the Japanese Society of Intensive Care Medicine/Japanese Respiratory Society/Japanese Society of Respiratory Care Medicine on ARDS Clinical Practice Guideline has created and released the ARDS Clinical Practice Guideline 2021. METHODS The 2016 edition of the Clinical Practice Guideline covered clinical questions (CQs) that targeted only adults, but the present guideline includes 15 CQs for children in addition to 46 CQs for adults. As with the previous edition, we used a systematic review method with the Grading of Recommendations Assessment Development and Evaluation (GRADE) system as well as a degree of recommendation determination method. We also conducted systematic reviews that used meta-analyses of diagnostic accuracy and network meta-analyses as a new method. RESULTS Recommendations for adult patients with ARDS are described: we suggest against using serum C-reactive protein and procalcitonin levels to identify bacterial pneumonia as the underlying disease (GRADE 2D); we recommend limiting tidal volume to 4-8 mL/kg for mechanical ventilation (GRADE 1D); we recommend against managements targeting an excessively low SpO2 (PaO2) (GRADE 2D); we suggest against using transpulmonary pressure as a routine basis in positive end-expiratory pressure settings (GRADE 2B); we suggest implementing extracorporeal membrane oxygenation for those with severe ARDS (GRADE 2B); we suggest against using high-dose steroids (GRADE 2C); and we recommend using low-dose steroids (GRADE 1B). The recommendations for pediatric patients with ARDS are as follows: we suggest against using non-invasive respiratory support (non-invasive positive pressure ventilation/high-flow nasal cannula oxygen therapy) (GRADE 2D); we suggest placing pediatric patients with moderate ARDS in the prone position (GRADE 2D); we suggest against routinely implementing NO inhalation therapy (GRADE 2C); and we suggest against implementing daily sedation interruption for pediatric patients with respiratory failure (GRADE 2D). CONCLUSIONS This article is a translated summary of the full version of the ARDS Clinical Practice Guideline 2021 published in Japanese (URL: https://www.jrs.or.jp/publication/jrs_guidelines/). The original text, which was written for Japanese healthcare professionals, may include different perspectives from healthcare professionals of other countries.
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Affiliation(s)
- Sadatomo Tasaka
- Department of Respiratory Medicine, Hirosaki University Graduate School of Medicine, Aomori, Japan.
| | - Shinichiro Ohshimo
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Muneyuki Takeuchi
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Hideto Yasuda
- Department of Emergency and Critical Care Medicine, Jichi Medical University, Saitama Medical Center, Saitama, Japan
| | - Kazuya Ichikado
- Division of Respiratory Medicine, Saiseikai Kumamoto Hospital, Kumamoto, Japan
| | - Kenji Tsushima
- International University of Health and Welfare, Tokyo, Japan
| | - Moritoki Egi
- Department of Anesthesiology, Kobe University Hospital, Hyogo, Japan
| | - Satoru Hashimoto
- Department of Anesthesiology and Intensive Care Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Nobuaki Shime
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Osamu Saito
- Department of Pediatric Emergency and Critical Care Medicine, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Shotaro Matsumoto
- Division of Critical Care Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Eishu Nango
- Department of Family Medicine, Seibo International Catholic Hospital, Tokyo, Japan
| | - Yohei Okada
- Department of Primary Care and Emergency Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichiro Hayashi
- Department of Pediatrics, The University of Tokyo Hospital, Tokyo, Japan
| | - Masaaki Sakuraya
- Department of Emergency and Intensive Care Medicine, JA Hiroshima General Hospital, Hiroshima, Japan
| | - Mikio Nakajima
- Emergency and Critical Care Center, Tokyo Metropolitan Hiroo Hospital, Tokyo, Japan
| | - Satoshi Okamori
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shinya Miura
- Paediatric Intensive Care Unit, The Royal Children's Hospital Melbourne, Melbourne, Australia
| | - Tatsuma Fukuda
- Department of Emergency and Critical Care Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Tadashi Ishihara
- Department of Emergency and Critical Care Medicine, Juntendo University, Urayasu Hospital, Chiba, Japan
| | - Tetsuro Kamo
- Department of Critical Care Medicine, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Tomoaki Yatabe
- Department of Anesthesiology, Nishichita General Hospital, Aichi, Japan
| | | | - Yoshitaka Aoki
- Department of Anesthesiology and Intensive Care Medicine, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Yusuke Iizuka
- Department of Anesthesiology and Critical Care Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Yutaka Kondo
- Department of Emergency and Critical Care Medicine, Juntendo University, Urayasu Hospital, Chiba, Japan
| | - Chihiro Narita
- Department of Emergency Medicine, Shizuoka General Hospital, Shizuoka, Japan
| | - Daisuke Kawakami
- Department of Anesthesia and Critical Care, Kobe City Medical Center General Hospital, Hyogo, Japan
| | - Hiromu Okano
- Department of Critical Care and Emergency Medicine, National Hospital Organization Yokohama Medical Center, Kanagawa, Japan
| | - Jun Takeshita
- Department of Anesthesiology, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Keisuke Anan
- Division of Respiratory Medicine, Saiseikai Kumamoto Hospital, Kumamoto, Japan
| | | | - Shunsuke Taito
- Division of Rehabilitation, Department of Clinical Practice and Support, Hiroshima University Hospital, Hiroshima, Japan
| | - Takuya Hayashi
- Pediatric Emergency and Critical Care Center, Saitama Children's Medical Center, Saitama, Japan
| | - Takuya Mayumi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Takero Terayama
- Department of Psychiatry, School of Medicine, National Defense Medical College, Saitama, Japan
| | - Yoshifumi Kubota
- Department of Infectious Diseases, Kameda Medical Center, Chiba, Japan
| | - Yoshinobu Abe
- Division of Emergency and Disaster Medicine, Tohoku Medical and Pharmaceutical University, Miyagi, Japan
| | - Yudai Iwasaki
- Department of Anesthesiology and Perioperative Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yuki Kishihara
- Department of Emergency Medicine, Japanese Red Cross Musashino Hospital, Tokyo, Japan
| | - Jun Kataoka
- Department of Critical Care Medicine, Nerima Hikarigaoka Hospital, Tokyo, Japan
| | - Tetsuro Nishimura
- Department of Traumatology and Critical Care Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Hiroshi Yonekura
- Department of Anesthesiology and Pain Medicine, Fujita Health University Bantane Hospital, Aichi, Japan
| | - Koichi Ando
- Division of Respiratory Medicine and Allergology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Takuo Yoshida
- Intensive Care Unit, Department of Anesthesiology, Jikei University School of Medicine, Tokyo, Japan
| | - Tomoyuki Masuyama
- Department of Emergency and Critical Care Medicine, Jichi Medical University, Saitama Medical Center, Saitama, Japan
| | - Masamitsu Sanui
- Department of Anesthesiology and Critical Care Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
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Salvador M, Marqués-Fernández JL, Bunge A, Martínez-García JC, Turcu R, Peddis D, García-Suárez MDM, Cima-Cabal MD, Rivas M. Magnetic Nanoclusters Increase the Sensitivity of Lateral Flow Immunoassays for Protein Detection: Application to Pneumolysin as a Biomarker for Streptococcus pneumoniae. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:2044. [PMID: 35745381 PMCID: PMC9228753 DOI: 10.3390/nano12122044] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
Lateral flow immunoassays for detecting biomarkers in body fluids are simple, quick, inexpensive point-of-care tests widely used in disease surveillance, such as during the coronavirus disease 2019 (COVID-19) pandemic. Improvements in sensitivity would increase their utility in healthcare, food safety, and environmental control. Recently, biofunctional magnetic nanoclusters have been used to selectively label target proteins, which allows their detection and quantification with a magneto-inductive sensor. This type of detector is easily integrated with the lateral flow immunoassay format. Pneumolysin is a cholesterol-dependent cytolysin and one of the most important protein virulence factors of pneumonia produced by Streptococcus pneumoniae. It is recognized as an important biomarker for diagnosis in urine samples. Pneumonia is the infectious disease that causes the most deaths globally, especially among children under five years and adults over 65 years, most of them in low- and middle-income countries. There especially, a rapid diagnostic urine test for pneumococcal pneumonia with high sensitivity and specificity would be helpful in primary care. In this work, a lateral flow immunoassay with magnetic nanoclusters conjugated to anti-pneumolysin antibodies was combined with two strategies to increase the technique's performance. First, magnetic concentration of the protein before the immunoassay was followed by quantification by means of a mobile telephone camera, and the inductive sensor resulted in detection limits as low as 0.57 ng (telephone camera) and 0.24 ng (inductive sensor) of pneumolysin per milliliter. Second, magnetic relocation of the particles within the test strip after the immunoassay was completed increased the detected signal by 20%. Such results obtained with portable devices are promising when compared to non-portable conventional pneumolysin detection techniques such as enzyme-linked immunosorbent assays. The combination and optimization of these approaches would have excellent application in point-of-care biodetection to reduce antibiotic misuse, hospitalizations, and deaths from community-acquired pneumonia.
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Affiliation(s)
- María Salvador
- Department of Physics & IUTA, University of Oviedo, Campus de Viesques, 33203 Gijón, Spain; (M.S.); (J.L.M.-F.); (J.C.M.-G.)
- Institute of Structure of Matter—National Research Council (CNR), 00016 Monterotondo Scalo (RM), Rome, Italy;
| | - José Luis Marqués-Fernández
- Department of Physics & IUTA, University of Oviedo, Campus de Viesques, 33203 Gijón, Spain; (M.S.); (J.L.M.-F.); (J.C.M.-G.)
| | - Alexander Bunge
- National Institute for Research and Development of Isotopic and Molecular Technologies, 400293 Cluj-Napoca, Romania; (A.B.); (R.T.)
| | - José Carlos Martínez-García
- Department of Physics & IUTA, University of Oviedo, Campus de Viesques, 33203 Gijón, Spain; (M.S.); (J.L.M.-F.); (J.C.M.-G.)
| | - Rodica Turcu
- National Institute for Research and Development of Isotopic and Molecular Technologies, 400293 Cluj-Napoca, Romania; (A.B.); (R.T.)
| | - Davide Peddis
- Institute of Structure of Matter—National Research Council (CNR), 00016 Monterotondo Scalo (RM), Rome, Italy;
- Department of Chemistry and Industrial Chemistry, Università degli Studi di Genova, 16146 Genova, Italy
| | - María del Mar García-Suárez
- Escuela Superior de Ingeniería y Tecnología (ESIT), Universidad Internacional de la Rioja (UNIR), Avenida de la Paz, 137, 26006 Logroño, Spain; (M.d.M.G.-S.); (M.D.C.-C.)
| | - María Dolores Cima-Cabal
- Escuela Superior de Ingeniería y Tecnología (ESIT), Universidad Internacional de la Rioja (UNIR), Avenida de la Paz, 137, 26006 Logroño, Spain; (M.d.M.G.-S.); (M.D.C.-C.)
| | - Montserrat Rivas
- Department of Physics & IUTA, University of Oviedo, Campus de Viesques, 33203 Gijón, Spain; (M.S.); (J.L.M.-F.); (J.C.M.-G.)
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Gomez JL, Himes BE, Kaminski N. Molecular Diagnostics in Pulmonary Infections. PRECISION IN PULMONARY, CRITICAL CARE, AND SLEEP MEDICINE 2020. [PMCID: PMC7121992 DOI: 10.1007/978-3-030-31507-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Infection of the lung parenchyma, or pneumonia, accounts for over four million deaths per year worldwide (Ferkol and Schraufnagel, Ann Am Thorac Soc 11:404–406, 2014). The condition is common, but also over-diagnosed, in part due to relatively poor laboratory and radiographic diagnostics. Indeed, we continue to rely on antiquated tools such as sputum culture and chest X-ray – the former of which lacks speed and sensitivity, and the latter specificity (Albaum et al. Chest 110:343–50, 1996). The resulting presumptive diagnoses of pneumonia lead to excessive use of empiric broad spectrum antibiotics; indeed, by some estimates, 30–70% of antibiotic prescriptions for lower respiratory tract infection are inappropriate (Kraus, PLoS One 12(3): e0174584, 2017). This approach begets microbial resistance, exposes patients to medication side effects, and puts patients at risk of potentially life-threatening complications including Clostridium difficile colitis. To improve diagnostic certainty in patients with suspected pneumonia, we must begin to consider and implement emerging technologies for efficient and accurate characterization of host responses to infection and identification of pathogens. In this chapter, we will discuss precision diagnostics already in common practice and those poised to be, and how these tools may ultimately enable personalization in the diagnosis of pneumonia.
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Affiliation(s)
- Jose L. Gomez
- Assistant Professor Pulmonary, Critical Care and Sleep Medicine Section, Department of Medicine, Yale University School of Medicine, New Haven, CT USA
| | - Blanca E. Himes
- Assistant Professor of Informatics, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Naftali Kaminski
- Boehringer-Ingelheim Endowed, Professor of Internal Medicine, Chief of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT USA
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Edouard S, Al-Tawfiq JA, Memish ZA, Yezli S, Gautret P. Impact of the Hajj on pneumococcal carriage and the effect of various pneumococcal vaccines. Vaccine 2018; 36:7415-7422. [PMID: 30236632 DOI: 10.1016/j.vaccine.2018.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Islamic Hajj pilgrimage is the largest annual mass gathering in the world. The overcrowding of people promotes the acquisition, spread and transmission of respiratory pathogens, including Streptococcus pneumoniae. METHODS We conducted a methodological review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. The objective was to summarize the available data regarding the prevalence of pneumococcal carriage among Hajj pilgrims and about carriage acquisition and circulation of S. pneumoniae among pilgrims before and after participating in the Hajj according to their vaccination status. RESULTS Eight articles met eligibility criteria for pneumococcal carriage and impact of pneumococcal vaccination on carriage. Seven of them showed a significant increase in nasopharyngeal carriage of pneumococci following the pilgrimage, with acquisition rates ranging from 18 to 36%. Serotypes 3, 19F and 34 are the most common. A significant increase in antibiotic resistant strains was observed following participation in the Hajj. A lower prevalence was found in pilgrims treated with antibiotics, those who used a hand sanitizer, or those who washed their hands more frequently than usual. An increased carriage of pneumococcal serotypes included in pneumococcal vaccines (10-valent pneumococcal conjugate vaccine (PCV10), 13-valent pneumococcal conjugate vaccine (PCV13), 23-valent pneumococcal polysaccharide vaccine (PPV23)) was observed following participation in the Hajj. To date, no study has shown a significant reduction in pneumococcal carriage among pilgrims after vaccination with PPV23 or PCV. In fact, no significant difference was currently observed in the prevalence ratio of pneumococcal carriage between vaccinated and unvaccinated pilgrims. CONCLUSION The studies analyzed in this review showed an increased carriage of pneumococcus in post-Hajj pilgrims compared to pre-Hajj pilgrims, including vaccine serotypes. Further studies are needed to investigate the possible relationships between carriage, disease and vaccine in pilgrims.
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Affiliation(s)
- Sophie Edouard
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine Unit, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ziad A Memish
- Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Saber Yezli
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.
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Edouard S, Al-Tawfiq JA, Memish ZA, Yezli S, Gautret P. WITHDRAWN: Impact of the Hajj on pneumococcal carriage and the effect of various pneumococcal vaccines. Vaccine 2017:S0264-410X(17)31028-9. [PMID: 28780980 DOI: 10.1016/j.vaccine.2017.03.109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/25/2017] [Accepted: 03/01/2017] [Indexed: 12/27/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Sophie Edouard
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée-Infection, Marseille, France
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine Unit, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ziad A Memish
- Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Saber Yezli
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Philippe Gautret
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée-Infection, Marseille, France.
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Bjarnason A, Lindh M, Westin J, Andersson LM, Baldursson O, Kristinsson KG, Gottfredsson M. Utility of oropharyngeal real-time PCR for S. pneumoniae and H. influenzae for diagnosis of pneumonia in adults. Eur J Clin Microbiol Infect Dis 2017; 36:529-536. [PMID: 27822652 PMCID: PMC5309271 DOI: 10.1007/s10096-016-2829-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/20/2016] [Indexed: 12/11/2022]
Abstract
A lack of sensitive tests and difficulties obtaining representative samples contribute to the challenge in identifying etiology in pneumonia. Upper respiratory tract swabs can be easily collected and analyzed with real-time PCR (rtPCR). Common pathogens such as S. pneumoniae and H. influenzae can both colonize and infect the respiratory tract, complicating the interpretation of positive results. Oropharyngeal swabs were collected (n = 239) prospectively from adults admitted to hospital with pneumonia. Analysis with rtPCR targeting S. pneumoniae and H. influenzae was performed and results compared with sputum cultures, blood cultures, and urine antigen testing for S. pneumoniae. Different Ct cutoff values were applied to positive tests to discern colonization from infection. Comparing rtPCR with conventional testing for S. pneumoniae in patients with all tests available (n = 57) resulted in: sensitivity 87 %, specificity 79 %, PPV 59 % and NPV 94 %, and for H. influenzae (n = 67): sensitivity 75 %, specificity 80 %, PPV 45 % and NPV 94 %. When patients with prior antimicrobial exposure were excluded sensitivity improved: 92 % for S. pneumoniae and 80 % for H. influenzae. Receiver operating characteristic curve analysis demonstrated for S. pneumoniae: AUC = 0.65 (95 % CI 0.51-0.80) and for H. influenzae: AUC = 0.86 (95 % CI 0.72-1.00). Analysis of oropharyngeal swabs using rtPCR proved both reasonably sensitive and specific for diagnosing pneumonia caused by S. pneumoniae and H. influenzae. This method may be a useful diagnostic adjunct to other methods and of special value in patients unable to provide representative lower airway samples.
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Affiliation(s)
- A Bjarnason
- Faculty of Medicine, University of Iceland, Reykjavik, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
- Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - M Lindh
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Medicinaregatan 3a-5b, 40530, Gothenburg, Sweden
| | - J Westin
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Medicinaregatan 3a-5b, 40530, Gothenburg, Sweden
| | - L-M Andersson
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Medicinaregatan 3a-5b, 40530, Gothenburg, Sweden
| | - O Baldursson
- Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - K G Kristinsson
- Faculty of Medicine, University of Iceland, Reykjavik, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
- Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - M Gottfredsson
- Faculty of Medicine, University of Iceland, Reykjavik, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland.
- Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland.
- Division of Infectious Diseases, Landspitali University Hospital, Fossvogur, 108, Reykjavik, Iceland.
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Using Nucleic Acid Amplification Techniques in a Syndrome-Oriented Approach: Detection of Respiratory Agents. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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10
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11
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Schulte B, Eickmeyer H, Heininger A, Juretzek S, Karrasch M, Denis O, Roisin S, Pletz MW, Klein M, Barth S, Lüdke GH, Thews A, Torres A, Cillóniz C, Straube E, Autenrieth IB, Keller PM. Detection of pneumonia associated pathogens using a prototype multiplexed pneumonia test in hospitalized patients with severe pneumonia. PLoS One 2014; 9:e110566. [PMID: 25397673 PMCID: PMC4232251 DOI: 10.1371/journal.pone.0110566] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 09/23/2014] [Indexed: 11/18/2022] Open
Abstract
Severe pneumonia remains an important cause of morbidity and mortality. Polymerase chain reaction (PCR) has been shown to be more sensitive than current standard microbiological methods – particularly in patients with prior antibiotic treatment – and therefore, may improve the accuracy of microbiological diagnosis for hospitalized patients with pneumonia. Conventional detection techniques and multiplex PCR for 14 typical bacterial pneumonia-associated pathogens were performed on respiratory samples collected from adult hospitalized patients enrolled in a prospective multi-center study. Patients were enrolled from March until September 2012. A total of 739 fresh, native samples were eligible for analysis, of which 75 were sputa, 421 aspirates, and 234 bronchial lavages. 276 pathogens were detected by microbiology for which a valid PCR result was generated (positive or negative detection result by Curetis prototype system). Among these, 120 were identified by the prototype assay, 50 pathogens were not detected. Overall performance of the prototype for pathogen identification was 70.6% sensitivity (95% confidence interval (CI) lower bound: 63.3%, upper bound: 76.9%) and 95.2% specificity (95% CI lower bound: 94.6%, upper bound: 95.7%). Based on the study results, device cut-off settings were adjusted for future series production. The overall performance with the settings of the CE series production devices was 78.7% sensitivity (95% CI lower bound: 72.1%) and 96.6% specificity (95% CI lower bound: 96.1%). Time to result was 5.2 hours (median) for the prototype test and 43.5 h for standard-of-care. The Pneumonia Application provides a rapid and moderately sensitive assay for the detection of pneumonia-causing pathogens with minimal hands-on time. Trial Registration Deutsches Register Klinischer Studien (DRKS) DRKS00005684
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Affiliation(s)
- Berit Schulte
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Holm Eickmeyer
- Heart and Diabetes Center North Rhine-Westphalia, Institute for Laboratory- and Transfusion Medicine, University Hospital of the Ruhr-University Bochum, Bad Oeynhausen, Germany
- Heart and Diabetes Center North Rhine-Westphalia, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Alexandra Heininger
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Anesthesiology and Intensive Care Medicine, Tübingen University Hospital, Tübingen, Germany
| | - Stephanie Juretzek
- University Hospital Jena, Institute of Medical Microbiology, Jena, Germany
| | - Matthias Karrasch
- University Hospital Jena, Institute of Medical Microbiology, Jena, Germany
| | - Olivier Denis
- Université Libre de Bruxelles, Laboratory of Microbiology, Bruxelles, Belgium
| | - Sandrine Roisin
- Université Libre de Bruxelles, Laboratory of Microbiology, Bruxelles, Belgium
| | - Mathias W. Pletz
- University Hospital Jena, Center for Infectious Diseases and Infection Control, and Center for Sepsis Care and Control, Jena, Germany
| | | | | | | | | | - Antoni Torres
- Department of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB) - Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
| | - Catia Cillóniz
- Department of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB) - Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
| | - Eberhard Straube
- University Hospital Jena, Institute of Medical Microbiology, Jena, Germany
- University Hospital Jena, Center for Infectious Diseases and Infection Control, and Center for Sepsis Care and Control, Jena, Germany
| | - Ingo B. Autenrieth
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Peter M. Keller
- University Hospital Jena, Institute of Medical Microbiology, Jena, Germany
- University Hospital Jena, Center for Infectious Diseases and Infection Control, and Center for Sepsis Care and Control, Jena, Germany
- * E-mail:
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Genomic load from sputum samples and nasopharyngeal swabs for diagnosis of pneumococcal pneumonia in HIV-infected adults. J Clin Microbiol 2014; 52:4224-9. [PMID: 25253798 DOI: 10.1128/jcm.01553-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quantitative lytA real-time PCR (rtPCR) results from nasopharyngeal (NP) swabs distinguish community-acquired pneumococcal pneumonia (CAP) from asymptomatic colonization. The use of an optimized cutoff value improved pneumococcal etiology determination compared to that of traditional diagnostic methods. Here, we compare the utility of lytA rtPCR from induced sputum and from NP swabs. Pneumococcus was considered the cause of CAP in HIV-infected South African adults if blood culture, induced-sputum culture or Gram stain, urine antigen test, or whole-blood lytA rtPCR revealed pneumococcus or if lytA rtPCR from NP swabs gave a result of >8,000 copies/ml. lytA rtPCR was also performed on induced sputum. Pneumococcus was detected by lytA rtPCR from sputum in 149 (67.1%) of 222 patients with available induced sputum, whereas the results of either Gram stain or culture of sputum were positive in 105 of 229 patients (45.9%; P < 0.001). The mean copy numbers from sputum were higher when the sputum cultures were positive than when the sputum cultures were negative (7.9 versus 5.6 log10 copies/ml; P < 0.001). Against the composite diagnostic standard, a cutoff value of 10,000 copies/ml for good-quality sputum lytA rtPCR had a sensitivity of 78.1% and a specificity of 80.0%. This cutoff value performed similarly to the previously identified cutoff value of 8,000 copies/ml for NP swab lytA rtPCR (area under the curve receiver operating characteristic [AUC-ROC], 80.4% for sputum of any quality versus 79.6% for NP swabs). The AUC-ROC for good-quality sputum was 83.2%. Overall, lytA rtPCR performs similarly well on induced sputum as on NP swabs for most patients but performs slightly better if good-quality sputum can be obtained. Due to the ease of specimen collection, NP swabs may be preferable for the diagnosis of pneumococcal pneumonia.
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Huijskens EGW, Rossen JWA, Kluytmans JAJW, van der Zanden AGM, Koopmans M. Evaluation of yield of currently available diagnostics by sample type to optimize detection of respiratory pathogens in patients with a community-acquired pneumonia. Influenza Other Respir Viruses 2014; 8:243-9. [PMID: 23957707 PMCID: PMC4186473 DOI: 10.1111/irv.12153] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND For the detection of respiratory pathogens, the sampling strategy may influence the diagnostic yield. Ideally, samples from the lower respiratory tract are collected, but they are difficult to obtain. OBJECTIVES In this study, we compared the diagnostic yield in sputum and oropharyngeal samples (OPS) for the detection of respiratory pathogens in patients with community-acquired pneumonia (CAP), with the objective to optimize our diagnostic testing algorithm. METHODS Matched sputum samples, OPS, blood cultures, serum, and urine samples were taken from patients (>18 years) with CAP and tested for the presence of possible respiratory pathogens using bacterial cultures, PCR for 17 viruses and five bacteria and urinary antigen testing. RESULTS When using only conventional methods, that is, blood cultures, sputum culture, urinary antigen tests, a pathogen was detected in 49·6% of patients (n = 57). Adding molecular detection assays increased the yield to 80%. A pathogen was detected in 77 of the 115 patients in OPS or sputum samples by PCR. The sensitivity of the OPS was lower than that of the sputum samples (57% versus 74%). In particular, bacterial pathogens were more often detected in sputum samples. The sensitivity of OPS for the detection of most viruses was higher than in sputum samples (72% versus 66%), except for human rhinovirus and respiratory syncytial virus. CONCLUSION Addition of PCR on both OPS and sputum samples significantly increased the diagnostic yield. For molecular detection of bacterial pathogens, a sputum sample is imperative, but for detection of most viral pathogens, an OPS is sufficient.
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Affiliation(s)
- Elisabeth G W Huijskens
- Laboratory of Medical Microbiology and Immunology, St. Elisabeth Hospital, Tilburg, The Netherlands; Department of Medical Microbiology, Albert Schweitzer Hospital, Dordrecht, The Netherlands
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14
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Comparison of sputum and nasopharyngeal aspirate samples and of the PCR gene targets lytA and Spn9802 for quantitative PCR for rapid detection of pneumococcal pneumonia. J Clin Microbiol 2013; 52:83-9. [PMID: 24153121 DOI: 10.1128/jcm.01742-13] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We aimed to compare sputum and nasopharyngeal aspirate (NpA) samples and the PCR gene targets lytA and Spn9802 in quantitative PCR (qPCR) assays for rapid detection of pneumococcal etiology in community-acquired pneumonia (CAP). Seventy-eight adult patients hospitalized for radiologically confirmed CAP had both good-quality sputum and NpA specimens collected at admission. These samples were subjected to lytA qPCR and Spn9802 qPCR assays with analytical times of <3 h. Thirty-two patients had CAP with a pneumococcal etiology, according to conventional diagnostic criteria. The following qPCR positivity rates were noted in CAP cases with and without pneumococcal etiology: 96% and 15% (sputum lytA assay), 96% and 17% (sputum Spn9802 assay), 81% and 11% (NpA lytA assay), and 81% and 20% (NpA Spn9802 assay), respectively. The mean lytA and Spn9802 DNA levels were significantly higher in qPCR-positive sputum samples from cases with pneumococcal etiology than in qPCR-positive sputum samples from CAP cases without pneumococcal etiology or qPCR-positive NpA samples from cases with pneumococcal etiology (P < 0.02 for all comparisons). For detection of pneumococcal etiology, receiver operating characteristic curve analysis showed that sputum specimens were superior to NpA specimens as the sample type (P < 0.02 for both gene targets) and lytA tended to be superior to Spn9802 as the gene target. The best-performing test, the sputum lytA qPCR assay, showed high sensitivity (94%) and specificity (96%) with a cutoff value of 10(5) DNA copies/ml. In CAP patients with good sputum production, this test has great potential to be used for the rapid detection of pneumococcal etiology and to target penicillin therapy.
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Huijskens EGW, van Erkel AJM, Palmen FMH, Buiting AGM, Kluytmans JAJW, Rossen JWA. Viral and bacterial aetiology of community-acquired pneumonia in adults. Influenza Other Respir Viruses 2013; 7:567-73. [PMID: 22908940 PMCID: PMC5781003 DOI: 10.1111/j.1750-2659.2012.00425.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Modern molecular techniques reveal new information on the role of respiratory viruses in community-acquired pneumonia. In this study, we tried to determine the prevalence of respiratory viruses and bacteria in patients with community-acquired pneumonia who were admitted to the hospital. METHODS Between April 2008 and April 2009, 408 adult patients (aged between 20 and 94 years) with community-acquired pneumonia were tested for the presence of respiratory pathogens using bacterial cultures, real-time PCR for viruses and bacteria, urinary antigen testing for Legionella and Pneumococci and serology for the presence of viral and bacterial pathogens. RESULTS Pathogens were identified in 263 (64·5%) of the 408 patients. The most common single organisms in these 263 patients were Streptococcus pneumoniae (22·8%), Coxiella burnetii (6·8%) and influenza A virus (3·8%). Of the 263 patients detected with pathogens, 117 (44·5%) patients were positive for one or more viral pathogens. Of these 117 patients, 52 (44·4%) had no bacterial pathogen. Multiple virus infections (≥2) were found in 16 patients. CONCLUSION In conclusion, respiratory viruses are frequently found in patients with CAP and may therefore play an important role in the aetiology of this disease.
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Affiliation(s)
- Elisabeth G W Huijskens
- Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands.
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Dugard A, Chainier D, Barraud O, Garnier F, Ploy MC, Vignon P, François B. Early bacterial genome detection in body fluids from patients with severe sepsis: A pilot study. J Crit Care 2012; 27:416.e1-6. [DOI: 10.1016/j.jcrc.2011.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/03/2011] [Accepted: 11/07/2011] [Indexed: 10/14/2022]
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Werno AM, Anderson TP, Murdoch DR. Association between pneumococcal load and disease severity in adults with pneumonia. J Med Microbiol 2012; 61:1129-1135. [DOI: 10.1099/jmm.0.044107-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Anja M. Werno
- Department of Pathology, University of Otago, Christchurch, New Zealand
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Trevor P. Anderson
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, New Zealand
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
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Novel molecular method for identification of Streptococcus pneumoniae applicable to clinical microbiology and 16S rRNA sequence-based microbiome studies. J Clin Microbiol 2012; 50:1968-73. [PMID: 22442329 DOI: 10.1128/jcm.00365-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The close phylogenetic relationship of the important pathogen Streptococcus pneumoniae and several species of commensal streptococci, particularly Streptococcus mitis and Streptococcus pseudopneumoniae, and the recently demonstrated sharing of genes and phenotypic traits previously considered specific for S. pneumoniae hamper the exact identification of S. pneumoniae. Based on sequence analysis of 16S rRNA genes of a collection of 634 streptococcal strains, identified by multilocus sequence analysis, we detected a cytosine at position 203 present in all 440 strains of S. pneumoniae but replaced by an adenosine residue in all strains representing other species of mitis group streptococci. The S. pneumoniae-specific sequence signature could be demonstrated by sequence analysis or indirectly by restriction endonuclease digestion of a PCR amplicon covering the site. The S. pneumoniae-specific signature offers an inexpensive means for validation of the identity of clinical isolates and should be used as an integrated marker in the annotation procedure employed in 16S rRNA-based molecular studies of complex human microbiotas. This may avoid frequent misidentifications such as those we demonstrate to have occurred in previous reports and in reference sequence databases.
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Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples. J Clin Microbiol 2012; 50:1171-7. [PMID: 22278834 DOI: 10.1128/jcm.06609-11] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The identification and detection of mitis group streptococci, which contain Streptococcus pneumoniae, have been hampered by the lack of sensitive and specific assays. In this study, we evaluated several biochemical and molecular assays for the identification of S. pneumoniae and Streptococcus pseudopneumoniae and their distinction from other mitis group streptococci using a collection of 54 isolates obtained by the routine culturing of 53 respiratory specimens from patients with community-acquired pneumonia. The combined results of the biochemical and molecular assays indicated the presence of 23 S. pneumoniae, 2 S. pseudopneumoniae, and 29 other mitis group streptococcal isolates. The tube bile solubility test that is considered gold standard for the identification of S. pneumoniae showed concordant results with optochin susceptibility testing (CO(2) atmosphere) and a real-time multiplex PCR assay targeting the Spn9802 fragment and the autolysin gene. Optochin susceptibility testing upon incubation in an O(2) atmosphere, bile solubility testing by oxgall disk, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and sequence analysis of the tuf and rpoB genes resulted in several false-positive, false-negative, or inconclusive results. The S. pseudopneumoniae isolates could be identified only by molecular assays, and the multiplex real-time PCR assay was concluded to be most convenient for the identification of S. pneumoniae and S. pseudopneumoniae isolates. Using this method, S. pneumoniae and S. pseudopneumoniae DNA could be detected in the respiratory samples from which they were isolated and in an additional 11 samples from which only other streptococci were isolated.
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Azzari C, Cortimiglia M, Moriondo M, Canessa C, Lippi F, Ghiori F, Becciolini L, de Martino M, Resti M. Pneumococcal DNA is not detectable in the blood of healthy carrier children by real-time PCR targeting the lytA gene. J Med Microbiol 2011; 60:710-714. [PMID: 21349984 PMCID: PMC3167920 DOI: 10.1099/jmm.0.028357-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The diagnosis of invasive pneumococcal disease (IPD) is currently based on culture methods, which lack sensitivity, especially after antibiotic therapy. Molecular methods have improved sensitivity and do not require viable bacteria; however, their use is complicated by reports of low specificity with some assays. The present study investigated the specificity of a real-time PCR targeting lytA for the detection of IPD. A group of 147 healthy children, aged 6 months to 16 years (mean 6.4 years, median 4.9 years, interquartile range 6.4 years), who were in hospital for routine examinations, were tested for pneumococcal carrier status and for the presence of detectable pneumococcal DNA in their blood by real-time PCR targeting the pneumococcal lytA gene. In addition, 35 culture-positive biological samples were analysed. Urine was examined for the presence of pneumococcal DNA and C-polysaccharide antigen. Carriage was detected in 77 of the 147 subjects (52.4 %); however, regardless of carrier status, none of the subjects had a positive result from blood. Analysis of the culture-positive biological samples yielded positive results in 100 % (15/15) of cerebrospinal fluid samples and 95 % (19/20) of blood samples. All urine samples from healthy carriers were negative for DNA, whilst antigenuria was detected in 44/77 carriers (57.1 %). In conclusion, real-time PCR is both sensitive and specific and can be a useful tool in the routine diagnosis of IPD. Its sensitivity, which surpasses that of other methods for this purpose, does not come at the cost of reduced specificity.
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Affiliation(s)
- Chiara Azzari
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Martina Cortimiglia
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Maria Moriondo
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Clementina Canessa
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Francesca Lippi
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Federica Ghiori
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Laura Becciolini
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Maurizio de Martino
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Massimo Resti
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
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recA-based PCR assay for accurate differentiation of Streptococcus pneumoniae from other viridans streptococci. J Clin Microbiol 2010; 49:523-7. [PMID: 21147955 DOI: 10.1128/jcm.01450-10] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proper identification of Streptococcus pneumoniae by conventional methods remains problematic. The discriminatory power of the 16S rRNA gene, which can be considered the "gold standard" for molecular identification, is too low to differentiate S. pneumoniae from closely related species such as Streptococcus pseudopneumoniae, Streptococcus mitis, and Streptococcus oralis in the routine clinical laboratory. A 313-bp part of recA was selected on the basis of variability within the S. mitis group, showing <95.8% interspecies homology. In addition, 6 signature nucleotides specific for S. pneumoniae were identified within the 313-bp recA fragment. We show that recA analysis is a useful tool for proper identification to species level within the S. mitis group, in particular, for pneumococci.
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Kurola P, Erkkilä L, Kaijalainen T, Palmu AA, Hausdorff WP, Poolman J, Jokinen J, Kilpi TM, Leinonen M, Saukkoriipi A. Presence of capsular locus genes in immunochemically identified encapsulated and unencapsulated Streptococcus pneumoniae sputum isolates obtained from elderly patients with acute lower respiratory tract infection. J Med Microbiol 2010; 59:1140-1145. [PMID: 20616188 DOI: 10.1099/jmm.0.016956-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The principal virulence factor of Streptococcus pneumoniae is capsular polysaccharide, and encapsulated pneumococci are more common causes of disease than unencapsulated strains. This study analysed the presence of capsular genes in 59 pneumococcal isolates using two PCR methods targeted at the cpsA and cpsB genes of the capsular biosynthesis locus. The PCR method targeted at the cpsB gene, reported to be essential for encapsulation, was developed in this study. Of 59 pneumococcal isolates, 49 (83 %) were obtained from the sputum samples of elderly patients (≥65 years) with community-acquired pneumonia (CAP) and 10 (17 %) were from those with other acute lower respiratory tract infections (ARIs). Forty (82 %) of the CAP isolates and two (20 %) of the ARI isolates were encapsulated, as assessed by conventional immunochemical methods. Forty-one (98 %) of the 42 encapsulated strains had the cpsB gene present, and in 38 strains the cpsA gene was also detected. One of the unencapsulated isolates gave a positive result for the cpsB gene, and neither of the capsular locus genes were present in all the other unencapsulated strains. The distribution of encapsulated and unencapsulated isolates differed significantly between the two patient groups regardless of whether the presence of capsule was determined immunochemically (P<0.001) or by cpsB PCR (P=0.002). The cpsB PCR developed here was found to be a rapid and reliable method to detect the pneumococcal capsule locus and may have potential in sputum diagnostics when investigating the pneumococcal aetiology of CAP.
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Affiliation(s)
- Paula Kurola
- National Institute for Health and Welfare, Oulu, Finland
| | - Leena Erkkilä
- National Institute for Health and Welfare, Oulu, Finland
| | | | - Arto A Palmu
- National Institute for Health and Welfare, Helsinki, Finland
| | | | - Jan Poolman
- GlaxoSmithKline Biologicals, Rixensart, Belgium
| | - Jukka Jokinen
- National Institute for Health and Welfare, Helsinki, Finland
| | - Terhi M Kilpi
- National Institute for Health and Welfare, Helsinki, Finland
| | - Maija Leinonen
- National Institute for Health and Welfare, Oulu, Finland
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Johansson N, Kalin M, Tiveljung-Lindell A, Giske CG, Hedlund J. Etiology of community-acquired pneumonia: increased microbiological yield with new diagnostic methods. Clin Infect Dis 2010; 50:202-9. [PMID: 20014950 PMCID: PMC7107844 DOI: 10.1086/648678] [Citation(s) in RCA: 325] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The microbial etiology of community-acquired pneumonia (CAP) is still not well characterized. During the past few years, polymerase chain reaction (PCR)-based methods have been developed for many pathogens causing respiratory tract infections. The aim of this study was to determine the etiology of CAP among adults-especially the occurrence of mixed infections among patients with CAP-by implementing a new diagnostic PCR platform combined with conventional methods. METHODS Adults admitted to Karolinska University Hospital were studied prospectively during a 12-month period. Microbiological testing methods included culture from blood, sputum, and nasopharyngeal secretion samples; sputum samples analyzed by real-time quantitative PCR for Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis; nasopharyngeal specimens analyzed by use of PCR; serological testing for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and viruses common in the respiratory tract; and urine antigen assays for detection of pneumococcal and Legionella pneumophila antigens. RESULTS A microbial etiology could be identified for 67% of the patients (n = 124). For patients with complete sampling, a microbiological agent was identified for 89% of the cases. The most frequently detected pathogens were S. pneumoniae (70 patients [38%]) and respiratory virus (53 patients [29%]). Two or more pathogens were present in 43 (35%) of 124 cases with a determined etiology. CONCLUSIONS By supplementing traditional diagnostic methods with new PCR-based methods, a high microbial yield was achieved. This was especially evident for patients with complete sampling. Mixed infections were frequent (most commonly S. pneumoniae together with a respiratory virus).
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Affiliation(s)
- Niclas Johansson
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
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Abdeldaim G, Herrmann B, Mölling P, Holmberg H, Blomberg J, Olcén P, Strålin K. Usefulness of real-time PCR for lytA, ply, and Spn9802 on plasma samples for the diagnosis of pneumococcal pneumonia. Clin Microbiol Infect 2009; 16:1135-41. [PMID: 19832718 DOI: 10.1111/j.1469-0691.2009.03069.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the present study, we evaluated rapid real-time PCR assays for ply, Spn9802, and lytA applied to plasma samples for the detection of Streptococcus pneumoniae in patients with community-acquired pneumonia (CAP). In a prospective study of CAP aetiology, an EDTA plasma sample was collected together with blood culture in 92 adult CAP patients and 91 adult controls. Among the 92 CAP patients, lytA PCR was positive in eight (9%), Spn9802 PCR was positive in 11 (12%) and ply PCR was positive in 19 (21%) cases. Of 91 controls, the ply PCR was positive in eight cases (9%), but no positive cases were noted by Spn9802 or lytA PCRs. Ten CAP patients had pneumococcal bacteraemia. Compared to blood culture, PCR for lytA, Spn9802 and ply had sensitivities of 70% (7/10), 60% (6/10) and 70% (7/10), and specificities of 96% (79/82), 94% (77/82) and 85% (70/82) respectively. With blood culture and/or culture of representative sputum, and/or urinary antigen detection, S. pneumoniae was identified in 31 CAP patients. Compared to these tests in combination, PCR for lytA, Spn9802 and ply showed sensitivities of 26% (8/31), 32% (10/31) and 42% (13/31), and specificities of 100% (61/61), 98% (60/61) and 90% (55/61) respectively. We conclude that Spn9802 and lytA PCRs may be useful for the rapid detection of bacteraemic pneumococcal pneumonia, whereas ply PCR is not specific enough for routine use and blood PCR with small plasma volumes is not useful for the detection of nonbacteraemic pneumococcal pneumonia.
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Affiliation(s)
- G Abdeldaim
- Department of Clinical Microbiology, Uppsala University Hospital, Uppsala, Sweden.
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