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Wang X, Shi Y, Guo S, Qu X, Xie F, Duan Z, Hu Y, Fu H, Shi X, Quan T, Wang K, Xie L. A Clinical Bacterial Dataset for Deep Learning in Microbiological Rapid On-Site Evaluation. Sci Data 2024; 11:608. [PMID: 38851809 PMCID: PMC11162412 DOI: 10.1038/s41597-024-03370-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/13/2024] [Indexed: 06/10/2024] Open
Abstract
Microbiological Rapid On-Site Evaluation (M-ROSE) is based on smear staining and microscopic observation, providing critical references for the diagnosis and treatment of pulmonary infectious disease. Automatic identification of pathogens is the key to improving the quality and speed of M-ROSE. Recent advancements in deep learning have yielded numerous identification algorithms and datasets. However, most studies focus on artificially cultured bacteria and lack clinical data and algorithms. Therefore, we collected Gram-stained bacteria images from lower respiratory tract specimens of patients with lung infections in Chinese PLA General Hospital obtained by M-ROSE from 2018 to 2022 and desensitized images to produce 1705 images (4,912 × 3,684 pixels). A total of 4,833 cocci and 6,991 bacilli were manually labelled and differentiated into negative and positive. In addition, we applied the detection and segmentation networks for benchmark testing. Data and benchmark algorithms we provided that may benefit the study of automated bacterial identification in clinical specimens.
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Affiliation(s)
- Xiuli Wang
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Yinghan Shi
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Shasha Guo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xuzhong Qu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Fei Xie
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Zhimei Duan
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Ye Hu
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Han Fu
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Xin Shi
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Tingwei Quan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Kaifei Wang
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China.
| | - Lixin Xie
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China.
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Ito H, Tomura Y, Oshida J, Fukui S, Kodama T, Kobayashi D. The role of gram stain in reducing broad-spectrum antibiotic use: A systematic literature review and meta-analysis. Infect Dis Now 2023; 53:104764. [PMID: 37482245 DOI: 10.1016/j.idnow.2023.104764] [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: 04/04/2023] [Revised: 05/20/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
The number of studies that verify whether Gram stain can help to reduce the use of broad-spectrum antibiotics is relatively limited compared to those evaluating its concordance with culture test results. Thereby, we aimed to evaluate the effectiveness of Gram staining in the reduction of broad-spectrum antibiotics and its impact on clinical outcomes. We systematically reviewed studies having used Gram stain to guide antibiotic selection and evaluated performance measures between 1996 and 2022. We extracted available data on broad-spectrum antibiotic use as a primary outcome of the studies in view of an exploratory meta-analysis designed to estimate the clinical effect of Gram stain. We also evaluated the clinical response and coverage rates of the initial antibiotic therapy. One randomized study and four non-randomized studies were eligible, all of which were conducted in tertiary care hospitals in Japan. Gram stain was associated with reduced broad-spectrum antibiotic use, including antipseudomonal antibiotics (odds ratio [OR], 0.05; 95% confidence interval [CI], 0.01-0.34), anti-methicillin-resistant Staphylococcus aureus antibiotics (OR, 0.21; 95% CI, 0.07-0.63), and carbapenems (OR, 0.07; 95% CI, 0.02-0.19), without impairing clinical outcomes, including clinical response rate (OR, 1.48; 95% CI, 0.95-2.31) and coverage rate of initial antibiotic therapy (OR, 0.70; 95% CI, 0.40-1.22) using random-effects models in our meta-analysis. In conclusion, Gram stain may be useful in guiding initial antibiotic selection without apparent adverse clinical outcomes. However, currently available studies evaluating the clinical usefulness of Gram stain are limited to specific clinical settings.
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Affiliation(s)
- Hiroshi Ito
- Division of General Internal Medicine, Department of Internal Medicine, Tokyo Medical University Ibaraki Medical Center, Inashiki, Ibaraki, Japan.
| | - Yuna Tomura
- Tokyo Medical University Library, Shinjuku, Tokyo, Japan
| | - Jura Oshida
- Division of General Internal Medicine, Department of Internal Medicine, Tokyo Medical University Ibaraki Medical Center, Inashiki, Ibaraki, Japan
| | - Sayato Fukui
- Division of General Internal Medicine, Department of Internal Medicine, Tokyo Medical University Ibaraki Medical Center, Inashiki, Ibaraki, Japan
| | - Taisuke Kodama
- Division of General Internal Medicine, Department of Internal Medicine, Tokyo Medical University Ibaraki Medical Center, Inashiki, Ibaraki, Japan
| | - Daiki Kobayashi
- Division of General Internal Medicine, Department of Internal Medicine, Tokyo Medical University Ibaraki Medical Center, Inashiki, Ibaraki, Japan
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Bronchoalveolar Lavage Gram Stains for Early Bacterial Identification in Pneumonia: Should They Stay or Should They Go? Crit Care Explor 2021; 3:e0501. [PMID: 34368769 PMCID: PMC8330965 DOI: 10.1097/cce.0000000000000501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES: The primary endpoint was to determine the sensitivity and specificity of the bronchoalveolar lavage Gram stain in predicting culture results. Secondary endpoints included determining the proportion of Gram stains from bronchoalveolar lavages that accurately identify culture isolates and the duration of antibiotic treatment before bronchoalveolar lavage collection. DESIGN: Retrospective, observational study. SETTING: Four ICUs at a single academic medical center. SUBJECTS: Patients at least 18 years old admitted to an ICU with a diagnosis of pneumonia, collection of a bronchoalveolar lavage sample, and receipt of antibiotics. MEASUREMENTS AND MAIN RESULTS: Two-hundred five isolates were included. Gram stains for Gram-positive and Gram-negative isolates showed high specificity, 97.3% and 100%, respectively, but lower sensitivity at 61.9% and 54.2%, respectively. The positive predictive value and negative predictive value were 77.2% and 95.7% for Gram-positive isolates and 100% and 84.4% for Gram-negative isolates, respectively. Gram stains correctly identified isolates on the bronchoalveolar lavage culture in 61.9% of Gram-positive organisms and in 54.2% of Gram-negative organisms. CONCLUSIONS: Gram stains accurately identified causative organisms in a limited number of patients making the utility of the Gram stain an uncertain modality for predicting causative respiratory pathogens from bronchoalveolar lavage samples.
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Ranzani OT, Motos A, Chiurazzi C, Ceccato A, Rinaudo M, Li Bassi G, Ferrer M, Torres A. Diagnostic accuracy of Gram staining when predicting staphylococcal hospital-acquired pneumonia and ventilator-associated pneumonia: a systematic review and meta-analysis. Clin Microbiol Infect 2020; 26:1456-1463. [PMID: 32822880 DOI: 10.1016/j.cmi.2020.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/06/2020] [Accepted: 08/11/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND There is no clear guidance on empirical antibiotic coverage against Staphylococcus aureus for hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP). OBJECTIVE To evaluate whether the presence of clusters of Gram-positive cocci in Gram staining of respiratory samples predicts S. aureus as HAP/VAP pathogen. METHODS Data sources were MEDLINE, PubMed, Embase, Scielo, CINAHL and Scopus, from inception to 15/07/2017 (update on 31/10/2019), and original data from a single-centre database (PROSPERO: CRD42017072138). We included studies reporting the diagnostic accuracy of a Gram-staining evaluation suggestive of Staphylococcus compared with a positive culture for S. aureus in any type of lower respiratory tract sample. Participants were adult patients with HAP/VAP. The index test was morphological evaluation of Gram staining of respiratory samples. We followed PRISMA guidelines and assessed risk of bias and applicability with the QUADAS-2 tool. We conducted a meta-analysis using a bivariate random effects model. RESULTS We selected five studies that included only VAP and data from a single-centre database including VAP and HAP. We pooled six studies for VAP and analysed 1665 respiratory samples. Pooled sensitivity was 68% (95%CI 49-83 and specificity 95% (95%CI 86-98). The pooled positive likelihood ratio was 12.7 (95%CI 5.1-31.6), negative likelihood ratio 0.34 (95%CI 0.20-0.57), diagnostic odds ratio 38 (95%CI 13-106) and area under the summary receiver operating curve (SROC) 0.91 (95%CI 0.88-0.93). There was great heterogeneity between sensitivity and specificity. In scenarios in which the prevalence of S. aureus was between 5% and 20%, the positive and negative predictive values were 62% (95%CI 47-77) and 95% (95%CI 82-100), respectively. CONCLUSIONS Detection of Gram-positive cocci in clusters in respiratory samples of patients with VAP has the potential to guide risk assessments of S. aureus for more personalized antibiotic coverage. Randomized clinical trials with patient-centred outcomes are needed for strong clinical recommendations.
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Affiliation(s)
- Otavio T Ranzani
- Department of Pneumology, Institut Clinic de Respiratori Hospital Clinic, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Pulmonary Division, Heart Institute (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil; Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain
| | - Ana Motos
- Department of Pneumology, Institut Clinic de Respiratori Hospital Clinic, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomedica En Red-Enfermedades Respiratorias (CIBERES), Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Chiara Chiurazzi
- Department of Pneumology, Institut Clinic de Respiratori Hospital Clinic, Barcelona, Spain; Department of Anaesthesiology and Intensive Care Medicine, Humanitas Clinical and Research Centre, Milano, Italy
| | - Adrian Ceccato
- Department of Pneumology, Institut Clinic de Respiratori Hospital Clinic, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mariano Rinaudo
- Department of Pneumology, Institut Clinic de Respiratori Hospital Clinic, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Gianluigi Li Bassi
- Department of Pneumology, Institut Clinic de Respiratori Hospital Clinic, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomedica En Red-Enfermedades Respiratorias (CIBERES), Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Miquel Ferrer
- Department of Pneumology, Institut Clinic de Respiratori Hospital Clinic, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomedica En Red-Enfermedades Respiratorias (CIBERES), Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Antoni Torres
- Department of Pneumology, Institut Clinic de Respiratori Hospital Clinic, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomedica En Red-Enfermedades Respiratorias (CIBERES), Barcelona, Spain; University of Barcelona, Barcelona, Spain.
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Li H, Li L, Chi Y, Tian Q, Zhou T, Han C, Zhu Y, Zhou Y. Development of a standardized Gram stain procedure for bacteria and inflammatory cells using an automated staining instrument. Microbiologyopen 2020; 9:e1099. [PMID: 32592452 PMCID: PMC7520987 DOI: 10.1002/mbo3.1099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/27/2020] [Accepted: 05/30/2020] [Indexed: 11/14/2022] Open
Abstract
Gram stain is a subjective and poorly controlled test, and the resultant errors often perplex laboratory scientists. To reduce errors and make Gram stain a precisely controllable and meritorious test, a standardized Gram stain procedure for bacteria and inflammatory cells was developed using an automated staining instrument in this study. Freshly expectorated sputum specimens, used as the optimized targets, were smeared on slides by laboratory technicians, defining each slide loaded with uniform matrix and monolayer cell. And then, the staining and decolorizing time, as well as the stain and decolorant volume, were optimized as 15, 105, 1, and 25 s and 1.1, 1.4, 0.3, and 0.7 ml, respectively. Culture‐positive blood specimens and original purulent fluids were used for confirming the developed standardized Gram stain procedure. Distinct tinctures of bacteria and inflammatory cells adhered to slide uniformly in a monolayer were observed, and the obtained staining results of these samples were highly consistent with their cultured results. Furthermore, according to the staining results under different staining conditions, an updated molecular mechanism of Gram stain for bacteria and the probable staining mechanism for inflammatory cells were also proposed in this study.
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Affiliation(s)
- Hui Li
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lele Li
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yuanyuan Chi
- Qingdao Women and Children's Hospital, Qingdao, China
| | - Qingwu Tian
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tingting Zhou
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chunhua Han
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yuanqi Zhu
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yusun Zhou
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
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Gunasekaran J, Saksena R, Jain M, Gaind R. Can sputum gram stain be used to predict lower respiratory tract infection and guide empiric antimicrobial treatment: Experience from a tertiary care hospital. J Microbiol Methods 2019; 166:105731. [PMID: 31629914 DOI: 10.1016/j.mimet.2019.105731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/23/2019] [Accepted: 09/27/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND The mortality associated with lower respiratory tract infection is high. Indiscriminate use of antimicrobials leads to alteration of respiratory tract flora and development of multi-drug resistance. Rapid diagnostic tests to confirm infection can guide the clinicians about antimicrobial treatment. So the present study was planned to evaluate the role of direct gram stain examination as a rapid and simple test to help clinicians for appropriate patient management. METHODS The present study was conducted on 1000 respiratory specimens which were processed using conventional microbiological techniques. Gram stain smear and culture results were compared statistically to assess the sensitivity, specificity, positive and negative predictive value. The agreement between gram stain smear examination and culture was calculated using kappa statistics. RESULTS Potential pathogens were obtained from 28 of 209 deeply coughed out sputum samples (13.3%) and from 19 of 315 saliva mixed sputum samples (6%). Out of 473 tracheal aspirates, 115 (24.3%) had potential pathogens. The sensitivity for predicting infection was higher for good quality sputum samples (54%) as compared to poor quality sputum samples (37%). The gram stain and culture of tracheal samples had a good agreement for predicting infection whereas there was only moderate agreement for sputum sample. CONCLUSION Gram stain smear examination from respiratory samples can be used to guide empiric antibiotic therapy pending final culture sensitivity results if the attending physicians ensure appropriate sample collection and transport. In absence of these supportive measures smear examination should not be relied upon for empiric treatment.
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Affiliation(s)
- Jayanthi Gunasekaran
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, Delhi 110029, India
| | - Rushika Saksena
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, Delhi 110029, India
| | - Manisha Jain
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, Delhi 110029, India.
| | - Rajni Gaind
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, Delhi 110029, India
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7
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Ekren PK, Ranzani OT, Ceccato A, Li Bassi G, Muñoz Conejero E, Ferrer M, Niederman MS, Torres A. Evaluation of the 2016 Infectious Diseases Society of America/American Thoracic Society Guideline Criteria for Risk of Multidrug-Resistant Pathogens in Patients with Hospital-acquired and Ventilator-associated Pneumonia in the ICU. Am J Respir Crit Care Med 2019; 197:826-830. [PMID: 28902529 DOI: 10.1164/rccm.201708-1717le] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Pervin Korkmaz Ekren
- 1 University of Barcelona Barcelona, Spain.,2 Medicine School of Ege University Izmir, Turkey
| | - Otavio T Ranzani
- 1 University of Barcelona Barcelona, Spain.,3 Universidade de Sao Paulo Sao Paulo, Brazil
| | - Adrian Ceccato
- 1 University of Barcelona Barcelona, Spain.,4 Hospital Nacional Prof. Alejandro Posadas Palomar, Argentina
| | | | - Eva Muñoz Conejero
- 1 University of Barcelona Barcelona, Spain.,5 Universidad de Valladolid Valladolid, Spain and
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Shi Y, Huang Y, Zhang TT, Cao B, Wang H, Zhuo C, Ye F, Su X, Fan H, Xu JF, Zhang J, Lai GX, She DY, Zhang XY, He B, He LX, Liu YN, Qu JM. Chinese guidelines for the diagnosis and treatment of hospital-acquired pneumonia and ventilator-associated pneumonia in adults (2018 Edition). J Thorac Dis 2019; 11:2581-2616. [PMID: 31372297 PMCID: PMC6626807 DOI: 10.21037/jtd.2019.06.09] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/19/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Yi Shi
- Department of Pulmonary and Critical Care Medicine, Nanjing Jinling Hospital, Nanjing University, School of Medicine, Nanjing 210002, China
| | - Yi Huang
- Department of Pulmonary and Critical Care Medicine, Shanghai Changhai hospital, Navy Medical University, Shanghai 200433, China
| | - Tian-Tuo Zhang
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing 100029, China
| | - Hui Wang
- Department of Clinical Laboratory Medicine, Peking University People’s Hospital, Beijing 100044, China
| | - Chao Zhuo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Feng Ye
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Xin Su
- Department of Pulmonary and Critical Care Medicine, Nanjing Jinling Hospital, Nanjing University, School of Medicine, Nanjing 210002, China
| | - Hong Fan
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jin-Fu Xu
- Department of Pulmonary and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Jing Zhang
- Department of Pulmonary Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Guo-Xiang Lai
- Department of Pulmonary and Critical Care Medicine, Dongfang Hospital, Xiamen University, Fuzhou 350025, China
| | - Dan-Yang She
- Department of Pulmonary and Critical Care Medicine, the First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Xiang-Yan Zhang
- Department of Pulmonary and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guizhou 550002, China
| | - Bei He
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Li-Xian He
- Department of Pulmonary Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - You-Ning Liu
- Department of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Jie-Ming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Giuliano C, Patel CR, Kale-Pradhan PB. A Guide to Bacterial Culture Identification And Results Interpretation. P & T : A PEER-REVIEWED JOURNAL FOR FORMULARY MANAGEMENT 2019; 44:192-200. [PMID: 30930604 PMCID: PMC6428495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
PURPOSE To provide a guide to interpreting bacterial culture results. METHODS Studies were identified via a PubMed literature search (from 1966 to January 2018). Search terms included microbial sensitivity tests, microbial drug resistance, and anti-infective agents/pharmacology. Articles were included if they were published in English. References within identified articles were also reviewed. RESULTS This paper reviewed core concepts of interpreting bacterial culture results, including timing of cultures, common culture sites, potential for contamination, interpreting the Gram stain, role of rapid diagnostic tests, conventional antibiotic susceptibility testing, and automated testing. CONCLUSION This guide can assist pharmacists in their role as integral members of the antimicrobial stewardship team in an effort to improve patient care.
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Yoshimura J, Yamakawa K, Kinoshita T, Ohta Y, Morimoto T. GRam stain-guided Antibiotics ChoicE for Ventilator-Associated Pneumonia (GRACE-VAP) trial: rationale and study protocol for a randomised controlled trial. Trials 2018; 19:614. [PMID: 30409160 PMCID: PMC6225572 DOI: 10.1186/s13063-018-2971-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/08/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Optimising the use of antibiotic agents is a pressing challenge to overcoming the rapid emergence and spread of multidrug-resistant pathogens in intensive care units (ICUs). Although Gram staining may possibly provide immediate information for predicting pathogenic bacteria, Gram stain-guided initial antibiotic treatment is not well established in the ICU setting. We planned the GRam stain-guided Antibiotics ChoicE for Ventilator-Associated Pneumonia (GRACE-VAP) trial to investigate whether Gram staining can safely restrict the use of broad-spectrum antibiotics in patients with ventilator-associated pneumonia (VAP), which is one of the most common hospital-acquired infections in ICUs. METHODS/DESIGN The GRACE-VAP trial is a multicentre, randomised, open-label parallel-group trial to assess the non-inferiority of Gram stain-guided initial antibiotic treatment to guidelines-based initial antibiotic treatment for the primary endpoint of clinical response rate in patients with VAP. Secondary endpoints include the coverage rates of initial antibiotic therapies, the selected rates of anti-pseudomonal agents and anti-methicillin-resistant Staphylococcus aureus (anti-MRSA) agents as initial antibiotic therapies, 28-day all-cause mortality, ICU-free days, ventilator-free days and adverse events. Patients are randomly assigned to receive Gram stain-guided treatment or guidelines-based treatment at a ratio of 1:1. In the Gram stain group, results of Gram staining of endotracheal aspirate are used to guide the selection of antibiotics. In the guidelines group, the combination of an anti-pseudomonal agent and an anti-MRSA agent is administered. A total sample size of 200 was estimated to provide a power of 80% with a one-sided alpha level of 2.5% and a non-inferiority margin of 20%, considering 10% non-evaluable patients. DISCUSSION The GRACE-VAP trial is expected to reveal whether Gram staining can reduce the use of broad-spectrum antibiotics without impairing patient outcomes and thereby provide evidence for an antibiotic selection strategy in patients with VAP. TRIAL REGISTRATION Clinicaltrials.gov, NCT03506113 . Registered on 29 March 2018. University Hospital Medical Information Network, UMIN000031933. Registered on 26 March 2018.
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Affiliation(s)
- Jumpei Yoshimura
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, 3-1-56 Bandai-Higashi, Sumiyoshi, Osaka, 558-8558, Japan
| | - Kazuma Yamakawa
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, 3-1-56 Bandai-Higashi, Sumiyoshi, Osaka, 558-8558, Japan.
| | - Takahiro Kinoshita
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, 3-1-56 Bandai-Higashi, Sumiyoshi, Osaka, 558-8558, Japan
| | - Yoshinori Ohta
- Division of General Medicine, Department of Internal Medicine, Hyogo College of Medicine, 1-1 Mukogawa, Nishinomiya, Hyogo, 663-8501, Japan
| | - Takeshi Morimoto
- Department of Clinical Epidemiology, Hyogo College of Medicine, 1-1 Mukogawa, Nishinomiya, Hyogo, 663-8501, Japan
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Vandana Kalwaje E, Rello J. Management of ventilator-associated pneumonia: Need for a personalized approach. Expert Rev Anti Infect Ther 2018; 16:641-653. [DOI: 10.1080/14787210.2018.1500899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Eshwara Vandana Kalwaje
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Jordi Rello
- Critical Care Department, Vall d’Hebron Barcelona Hospital Campus & Centro de Investigacion Biomedica en Red (CIBERES), Barcelona, Spain
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12
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Boyanova L. Direct Gram staining and its various benefits in the diagnosis of bacterial infections. Postgrad Med 2017; 130:105-110. [PMID: 29091518 DOI: 10.1080/00325481.2018.1398049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the era of rapid development of molecular and other diagnostic methods, direct Gram staining (DGS) tends to remain in the background, although it can provide both microbiologists and clinicians numerous benefits. The aim of this review was to emphasize the importance of DGS for the diagnosis of many clinically important infections. A PubMed search was carried out using relevant keywords for articles published primarily since 2010. The DGS can provide early information for a timely diagnosis of infections, can reveal the causative agents of the infections even under suboptimal conditions of specimen collection, transport or identification methods, can detect the presence of rare/unusual pathogens, moreover, the method shows the specimen quality, by distinguishing between contamination and true infection, it can direct or change initial antibiotic treatment before the availability of culture results, can indicate the need of other methods for pathogen identification and, in some cases, can show the need for emergency attention such as urgent antibiotic therapy and surgical measures. Briefly, the DGS remains an easy, rapid, inexpensive and important method, which use should be encouraged in conditions of a standardized and controlled performance to avoid technical or interpretation errors.
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Affiliation(s)
- Lyudmila Boyanova
- a Department of Medical Microbiology , Medical University of Sofia , Sofia , Bulgaria
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Eliakim-Raz N, Hellerman M, Yahav D, Cohen J, Margalit I, Fisher S, Zusman O, Shaked H, Bishara J. Trimethoprim/sulfamethoxazole versus vancomycin in the treatment of healthcare/ventilator-associated MRSA pneumonia: a case-control study. J Antimicrob Chemother 2017; 72:882-887. [PMID: 27999052 DOI: 10.1093/jac/dkw510] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/26/2016] [Indexed: 02/06/2023] Open
Abstract
Objectives Therapeutic options available to treat MRSA pneumonia are limited. Trimethoprim/sulfamethoxazole is an attractive treatment because of its bactericidal anti-MRSA activity, oral and parenteral formulations and good penetration to the lung tissue. We aimed to compare the efficacy and safety of trimethoprim/sulfamethoxazole with vancomycin in the treatment of healthcare/ventilator-associated MRSA pneumonia. Methods We carried out a retrospective case-control study of all consecutive hospitalized adult patients diagnosed with MRSA pneumonia at Beilinson Hospital during 2010-15 and treated with either vancomycin or trimethoprim/sulfamethoxazole. The primary outcomes were all-cause mortality at 30 days and clinical failure at the end of treatment. In order to reduce bias affecting the decision to use a specific antibiotic and as a sensitivity analysis, a propensity-score model for choosing between vancomycin and trimethoprim/sulfamethoxazole was used. Results We identified 42 patients with MRSA pneumonia treated with trimethoprim/sulfamethoxazole and 39 treated with vancomycin. There were no significant differences in the baseline characteristics between the groups. Vancomycin-treated patients showed significantly higher 30 day mortality on both multivariate analysis (HR = 5.28; 95% CI = 1.50-18.60; P < 0.05) and sensitivity analysis with propensity score [vancomycin 13/24 (54.1%) versus trimethoprim/sulfamethoxazole 4/24 (16.7%); P < 0.05], and higher clinical failure rates [vancomycin 23/39 (59%) versus trimethoprim/sulfamethoxazole 15/42 (35.7%); P < 0.05], also in the sensitivity analysis with propensity score [vancomycin 14/24 (58.3%) versus trimethoprim/sulfamethoxazole 6/24 (25%); P < 0.05]. The rates of side effects in both arms were comparable. Conclusions Trimethoprim/sulfamethoxazole appears to be superior to vancomycin in the treatment of MRSA pneumonia. A large-scale randomized controlled trial is needed to evaluate these findings.
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Affiliation(s)
- Noa Eliakim-Raz
- Infectious Diseases Unit, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel.,Department of Internal Medicine E, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Moran Hellerman
- Department of Internal Medicine F, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel
| | - Dafna Yahav
- Infectious Diseases Unit, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Jonathan Cohen
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel.,Intensive Care Unit, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel
| | - Ili Margalit
- Department of Internal Medicine F, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel
| | - Sharon Fisher
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Oren Zusman
- Department of Internal Medicine E, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Hila Shaked
- Infectious Diseases Unit, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Jihad Bishara
- Infectious Diseases Unit, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
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14
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Impact of Gram stain results on initial treatment selection in patients with ventilator-associated pneumonia: a retrospective analysis of two treatment algorithms. Crit Care 2017. [PMID: 28625166 PMCID: PMC5474871 DOI: 10.1186/s13054-017-1747-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ventilator-associated pneumonia (VAP) is a common and serious problem in intensive care units (ICUs). Several studies have suggested that the Gram stain of endotracheal aspirates is a useful method for accurately diagnosing VAP. However, the usefulness of the Gram stain in predicting which microorganisms cause VAP has not been established. The purpose of this study was to evaluate whether a Gram stain of endotracheal aspirates could be used to determine appropriate initial antimicrobial therapy for VAP. METHODS Data on consecutive episodes of microbiologically confirmed VAP were collected from February 2013 to February 2016 in the ICU of a tertiary care hospital in Japan. We constructed two hypothetical empirical antimicrobial treatment algorithms for VAP: a guidelines-based algorithm (GLBA) based on the recommendations of the American Thoracic Society-Infectious Diseases Society of America (ATS-IDSA) guidelines and a Gram stain-based algorithm (GSBA) which limited the choice of initial antimicrobials according to the results of bedside Gram stains. The GLBA and the GSBA were retrospectively reviewed for each VAP episode. The initial coverage rates and the selection of broad-spectrum antimicrobial agents were compared between the two algorithms. RESULTS During the study period, 219 suspected VAP episodes were observed and 131 episodes were assessed for analysis. Appropriate antimicrobial coverage rates were not significantly different between the two algorithms (GLBA 95.4% versus GSBA 92.4%; p = 0.134). The number of episodes for which antimethicillin-resistant Staphylococcus aureus agents were selected as an initial treatment was larger in the GLBA than in the GSBA (71.0% versus 31.3%; p < 0.001), as were the number of episodes for which antipseudomonal agents were recommended as an initial treatment (70.2% versus 51.9%; p < 0.001). CONCLUSIONS Antimicrobial treatment based on Gram stain results may restrict the administration of broad-spectrum antimicrobial agents without increasing the risk of treatment failure. TRIAL REGISTRATION UMIN-CTR, UMIN000026457 . Registered 8 March 2017 (retrospectively registered).
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15
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Lin W, Guan X, Cao J, Niu B, Chen Q. Bactericidal mechanism of glutaraldehyde-didecyldimethylammonium bromide as a disinfectant againstEscherichia coli. J Appl Microbiol 2017; 122:676-685. [DOI: 10.1111/jam.13384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/05/2016] [Accepted: 12/09/2016] [Indexed: 11/29/2022]
Affiliation(s)
- W. Lin
- Shanghai Key Laboratory of Bio-Energy Crops; School of Life Sciences, Shanghai University; Shanghai China
| | - X. Guan
- Shanghai Key Laboratory of Bio-Energy Crops; School of Life Sciences, Shanghai University; Shanghai China
| | - J. Cao
- Shanghai Key Laboratory of Bio-Energy Crops; School of Life Sciences, Shanghai University; Shanghai China
| | - B. Niu
- Shanghai Key Laboratory of Bio-Energy Crops; School of Life Sciences, Shanghai University; Shanghai China
| | - Q. Chen
- Shanghai Key Laboratory of Bio-Energy Crops; School of Life Sciences, Shanghai University; Shanghai China
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16
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Kalil AC, Metersky ML, Klompas M, Muscedere J, Sweeney DA, Palmer LB, Napolitano LM, O'Grady NP, Bartlett JG, Carratalà J, El Solh AA, Ewig S, Fey PD, File TM, Restrepo MI, Roberts JA, Waterer GW, Cruse P, Knight SL, Brozek JL. Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society. Clin Infect Dis 2016; 63:e61-e111. [PMID: 27418577 PMCID: PMC4981759 DOI: 10.1093/cid/ciw353] [Citation(s) in RCA: 1981] [Impact Index Per Article: 247.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 02/06/2023] Open
Abstract
It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.These guidelines are intended for use by healthcare professionals who care for patients at risk for hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), including specialists in infectious diseases, pulmonary diseases, critical care, and surgeons, anesthesiologists, hospitalists, and any clinicians and healthcare providers caring for hospitalized patients with nosocomial pneumonia. The panel's recommendations for the diagnosis and treatment of HAP and VAP are based upon evidence derived from topic-specific systematic literature reviews.
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Affiliation(s)
- Andre C. Kalil
- Departmentof Internal Medicine, Division of Infectious Diseases,
University of Nebraska Medical Center,
Omaha
| | - Mark L. Metersky
- Division of Pulmonary and Critical Care Medicine,
University of Connecticut School of Medicine,
Farmington
| | - Michael Klompas
- Brigham and Women's Hospital and Harvard Medical School
- Harvard Pilgrim Health Care Institute, Boston,
Massachusetts
| | - John Muscedere
- Department of Medicine, Critical Care Program,Queens University, Kingston, Ontario,
Canada
| | - Daniel A. Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine,
University of California, San
Diego
| | - Lucy B. Palmer
- Department of Medicine, Division of Pulmonary Critical Care and Sleep
Medicine, State University of New York at Stony
Brook
| | - Lena M. Napolitano
- Department of Surgery, Division of Trauma, Critical Care and Emergency
Surgery, University of Michigan, Ann
Arbor
| | - Naomi P. O'Grady
- Department of Critical Care Medicine, National
Institutes of Health, Bethesda
| | - John G. Bartlett
- Johns Hopkins University School of Medicine,
Baltimore, Maryland
| | - Jordi Carratalà
- Department of Infectious Diseases, Hospital Universitari
de Bellvitge, Bellvitge Biomedical Research Institute, Spanish Network for Research in
Infectious Diseases, University of Barcelona,
Spain
| | - Ali A. El Solh
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep
Medicine, University at Buffalo, Veterans Affairs Western New
York Healthcare System, New York
| | - Santiago Ewig
- Thoraxzentrum Ruhrgebiet, Department of Respiratory and Infectious
Diseases, EVK Herne and Augusta-Kranken-Anstalt
Bochum, Germany
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of
Nebraska Medical Center, Omaha
| | | | - Marcos I. Restrepo
- Department of Medicine, Division of Pulmonary and Critical Care
Medicine, South Texas Veterans Health Care System and University
of Texas Health Science Center at San Antonio
| | - Jason A. Roberts
- Burns, Trauma and Critical Care Research Centre, The
University of Queensland
- Royal Brisbane and Women's Hospital,
Queensland
| | - Grant W. Waterer
- School of Medicine and Pharmacology, University of
Western Australia, Perth,
Australia
| | - Peggy Cruse
- Library and Knowledge Services, National Jewish
Health, Denver, Colorado
| | - Shandra L. Knight
- Library and Knowledge Services, National Jewish
Health, Denver, Colorado
| | - Jan L. Brozek
- Department of Clinical Epidemiology and Biostatistics and Department of
Medicine, McMaster University, Hamilton,
Ontario, Canada
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