1
|
Ji Y, Li J, Chen C, Piao C, Zhou X, Yoon J. Wash-Free Bacterial Gram-Typing and Photodynamic Inactivation with Long-Chain-Tailed BODIPY Derivatives. Biomater Res 2024; 28:0069. [PMID: 39228999 PMCID: PMC11370751 DOI: 10.34133/bmr.0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024] Open
Abstract
The rapid identification of bacterial Gram types and their viability, as well as efficient bacterial elimination are crucial for managing bacterial infections yet present important challenges. In this research, we utilized long-chain-tailed BODIPY derivatives to address these hurdles. Our data indicated that these derivatives can distinguish bacteria types and their viability in aqueous solutions through a concise turn-on fluorescent response. Among them, B-8 stained both live and dead bacteria, and B-14 offered a wash-free staining. B-18 demonstrated the highest affinity to selectively fluorescent label viable gram-positive bacteria with a 53.2-fold fluorescent enhancement. Confocal imaging confirmed that B-18 can serve as an effective membrane-specific probe for facilitating the typing between gram-negative and gram-positive bacteria in a wash-free manner. Additionally, B-18 displayed selective photodynamic inactivation at 1 μM toward gram-positive bacteria. In vivo studies variformed the ideal photodynamic therapeutic efficacy of B-18 against methicillin-resistant Staphylococcus aureus in mice wound infections.
Collapse
Affiliation(s)
- Yuefeng Ji
- College of Agriculture,
Yanbian University, Yanji, 133002, China
| | - Jigai Li
- College of Chemistry and Chemical Engineering,
Qingdao University, Qingdao, 266071, China
| | - Chunping Chen
- College of Agriculture,
Yanbian University, Yanji, 133002, China
| | - Chunxiang Piao
- College of Agriculture,
Yanbian University, Yanji, 133002, China
| | - Xin Zhou
- College of Chemistry and Chemical Engineering,
Qingdao University, Qingdao, 266071, China
| | - Juyoung Yoon
- Department of Chemistry and Nano Science,
Ewha Womans University, Seoul, 120-750, Korea
| |
Collapse
|
2
|
Guo X, Che W. Improvement of gram staining effect by ethanol pretreatment and quantization of staining image by unsupervised machine learning. Arch Microbiol 2024; 206:318. [PMID: 38904719 DOI: 10.1007/s00203-024-04045-w] [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: 05/01/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
In this study, we propose an Ethanol Pretreatment Gram staining method that significantly enhances the color contrast of the stain, thereby improving the accuracy of judgement, and demonstrated the effectiveness of the modification by eliminating unaided-eye observational errors with unsupervised machine learning image analysis. By comparing the traditional Gram staining method with the improved method on various bacterial samples, results showed that the improved method offers distinct color contrast. Using multimodal assessment strategies, including unaided-eye observation, manual image segmentation, and advanced unsupervised machine learning automatic image segmentation, the practicality of ethanol pretreatment on Gram staining was comprehensively validated. In our quantitative analysis, the application of the CIEDE2000, and CMC color difference standards confirmed the significant effect of the method in enhancing the discrimination of Gram staining.This study not only improved the efficacy of Gram staining, but also provided a more accurate and standardized strategy for analyzing Gram staining results, which might provide an useful analytical tool in microbiological diagnostics.
Collapse
Affiliation(s)
- Xuan Guo
- Guangzhou Higher Education Mega Centre, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, Guangdong, China.
| | - Wenming Che
- Guangzhou Higher Education Mega Centre, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, Guangdong, China
| |
Collapse
|
3
|
Walter C, Weissert C, Gizewski E, Burckhardt I, Mannsperger H, Hänselmann S, Busch W, Zimmermann S, Nolte O. Performance evaluation of machine-assisted interpretation of Gram stains from positive blood cultures. J Clin Microbiol 2024; 62:e0087623. [PMID: 38506525 PMCID: PMC11005413 DOI: 10.1128/jcm.00876-23] [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: 08/08/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024] Open
Abstract
Manual microscopy of Gram stains from positive blood cultures (PBCs) is crucial for diagnosing bloodstream infections but remains labor intensive, time consuming, and subjective. This study aimed to evaluate a scan and analysis system that combines fully automated digital microscopy with deep convolutional neural networks (CNNs) to assist the interpretation of Gram stains from PBCs for routine laboratory use. The CNN was trained to classify images of Gram stains based on staining and morphology into seven different classes: background/false-positive, Gram-positive cocci in clusters (GPCCL), Gram-positive cocci in pairs (GPCP), Gram-positive cocci in chains (GPCC), rod-shaped bacilli (RSB), yeasts, and polymicrobial specimens. A total of 1,555 Gram-stained slides of PBCs were scanned, pre-classified, and reviewed by medical professionals. The results of assisted Gram stain interpretation were compared to those of manual microscopy and cultural species identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The comparison of assisted Gram stain interpretation and manual microscopy yielded positive/negative percent agreement values of 95.8%/98.0% (GPCCL), 87.6%/99.3% (GPCP/GPCC), 97.4%/97.8% (RSB), 83.3%/99.3% (yeasts), and 87.0%/98.5% (negative/false positive). The assisted Gram stain interpretation, when compared to MALDI-TOF MS species identification, also yielded similar results. During the analytical performance study, assisted interpretation showed excellent reproducibility and repeatability. Any microorganism in PBCs should be detectable at the determined limit of detection of 105 CFU/mL. Although the CNN-based interpretation of Gram stains from PBCs is not yet ready for clinical implementation, it has potential for future integration and advancement.
Collapse
Affiliation(s)
- Christian Walter
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- University Hospital Heidelberg, Heidelberg, Germany
| | - Christoph Weissert
- Division of Human Microbiology, Centre for Laboratory Medicine, St. Gall, Switzerland
| | - Eve Gizewski
- MetaSystems Hard & Software GmbH, Altlussheim, Germany
| | - Irene Burckhardt
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | - Stefan Zimmermann
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- University Hospital Heidelberg, Heidelberg, Germany
| | - Oliver Nolte
- Division of Human Microbiology, Centre for Laboratory Medicine, St. Gall, Switzerland
| |
Collapse
|
4
|
Tsehay AK, Sineshaw HM, Eshetu K, Gize A, Abebe SA, Mihret A, Tullu KD. Competency Assessment on Gram Stain Examination and Interpretation Among Medical Laboratory Professionals Working in Selected Hospitals of Addis Ababa, Ethiopia. J Multidiscip Healthc 2024; 17:1007-1021. [PMID: 38476254 PMCID: PMC10929549 DOI: 10.2147/jmdh.s442127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Background Laboratory test results are the cornerstone for patient diagnosis and treatment. Gram staining is a classic laboratory test method used to differentiate between bacteria. Competence assessment can help identify gaps and provide suggestions to academics, researchers, and policymakers to address competency gaps. In Ethiopia, there is no evidence of competency assessment by medical laboratory professionals using the Gram-staining technique. Objective To assess the competency of medical laboratory professionals on Gram stain examination and interpretation in selected hospitals of Addis Ababa, Ethiopia. Methods A cross-sectional study was conducted to assess the competency of medical laboratory professionals on Gram stain examination and interpretation from September 2015 to December 2017. Results Of 190 participants, 55 (28.9%) participants scored low knowledge, 131 (68.9%) scored medium knowledge, and only 4 (2.1%) respondents scored high knowledge. From the study variables, education level, supervision by regional or federal government bodies, and training about Gram staining were significantly associated with the knowledge level of study participants. Forty eight (25.3%), 78 (41%), and 64 (33.7%) participants scored low, medium, and high skill level, respectively, from a total of 190 participants. From skill level analysis, hospital type, microscope type, and availability of health information resources were significantly associated with skill levels. There were 44 observations (4%) with major errors and 321 observations (28%) with very major errors from all 1140 observations. Of all observations, 321 (28.2%) reported without grading, 39 observations (3.4%) reported gram-positive bacteria as gram-negative bacteria, and 15 observations (1.4%) reported gram-negative bacteria as gram-positive bacteria. Conclusion The current study found that most medical laboratory professionals work without supervision or refresher training in Gram stain examination and interpretation. Hence, medical laboratory professionals' knowledge and skill levels are unsatisfactory. Regular competence assessments, training, and follow-up are necessary to improve the professional competence in medical laboratories.
Collapse
Affiliation(s)
- Adugna Kassie Tsehay
- Laboratory Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Kirubel Eshetu
- Diagnostics Team, Management Sciences for Health, Addis Ababa, Ethiopia
| | - Addisu Gize
- Department of Microbiology, St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Samuel Ayele Abebe
- Data Management and Biostatistics, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Adane Mihret
- Bacterial and Viral Diseases, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Kassu Desta Tullu
- Department of Medical Laboratory Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| |
Collapse
|
5
|
Zhang H, Yang Y, Jiang Y, Zhang M, Xu Z, Wang X, Jiang J. Mass Spectrometry Analysis for Clinical Applications: A Review. Crit Rev Anal Chem 2023:1-20. [PMID: 37910438 DOI: 10.1080/10408347.2023.2274039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Mass spectrometry (MS) has become an attractive analytical method in clinical analysis due to its comprehensive advantages of high sensitivity, high specificity and high throughput. Separation techniques coupled MS detection (e.g., LC-MS/MS) have shown unique advantages over immunoassay and have developed as golden criterion for many clinical applications. This review summarizes the characteristics and applications of MS, and emphasizes the high efficiency of MS in clinical research. In addition, this review also put forward further prospects for the future of mass spectrometry technology, including the introduction of miniature MS instruments, point-of-care detection and high-throughput analysis, to achieve better development of MS technology in various fields of clinical application. Moreover, as ambient ionization mass spectrometry (AIMS) requires little or no sample pretreatment and improves the flux of MS, this review also summarizes its potential applications in clinic.
Collapse
Affiliation(s)
- Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Yali Yang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Yanxiao Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Meng Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Zhilong Xu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Xiaofei Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| |
Collapse
|
6
|
Srinivasan S, Austin MN, Fiedler TL, Strenk SM, Agnew KJ, Gowda GAN, Raftery D, Beamer MA, Achilles SL, Wiesenfeld HC, Fredricks DN, Hillier SL. Amygdalobacter indicium gen. nov., sp. nov., and Amygdalobacter nucleatus sp. nov., gen. nov.: novel bacteria from the family Oscillospiraceae isolated from the female genital tract. Int J Syst Evol Microbiol 2023; 73:006017. [PMID: 37787404 PMCID: PMC11318147 DOI: 10.1099/ijsem.0.006017] [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: 03/15/2023] [Accepted: 07/17/2023] [Indexed: 10/04/2023] Open
Abstract
Four obligately anaerobic Gram-positive bacteria representing one novel genus and two novel species were isolated from the female genital tract. Both novel species, designated UPII 610-JT and KA00274T, and an additional isolate of each species were characterized utilizing biochemical, genotypic and phylogenetic analyses. All strains were non-motile and non-spore forming, asaccharolytic, non-cellulolytic and indole-negative coccobacilli. Fatty acid methyl ester analysis for UPII 610-JT and KA00274T and additional isolates revealed C16 : 0, C18 : 0, C18:1ω9c and C18:2ω6,9c to be the major fatty acids for both species. UPII 610-JT had a 16S rRNA gene sequence similarity of 99.4 % to an uncultured clone sequence (AY724740) designated as Bacterial Vaginosis Associated Bacterium 2 (BVAB2). KA00274T had a 16S rRNA gene sequence similarity of 96.5 % to UPII 610-JT. Whole genomic DNA mol% G+C content was 42.2 and 39.3 % for UPII 610-JT and KA00274T, respectively. Phylogenetic analyses indicate these isolates represent a novel genus and two novel species within the Oscillospiraceae family. We propose the names Amygdalobacter indicium gen. nov., sp. nov., for UPII 610-JT representing the type strain of this species (=DSM 112989T, =ATCC TSD-274T) and Amygdalobacter nucleatus gen. nov., sp. nov., for KA00274T representing the type strain of this species (=DSM 112988T, =ATCC TSD-275T).
Collapse
Affiliation(s)
- Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Tina L. Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Susan M. Strenk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kathy J. Agnew
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Washington Medical Center, Seattle, WA, USA
| | - G. A. Nagana Gowda
- Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - May A. Beamer
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Sharon L. Achilles
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
| | - Harold C. Wiesenfeld
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
| | - David N. Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sharon L. Hillier
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
| |
Collapse
|
7
|
Brault D, Olivier T, Faure N, Dixneuf S, Kolytcheff C, Charmette E, Soulez F, Fournier C. Multispectral in-line hologram reconstruction with aberration compensation applied to Gram-stained bacteria microscopy. Sci Rep 2023; 13:14437. [PMID: 37660181 PMCID: PMC10475072 DOI: 10.1038/s41598-023-41079-4] [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: 06/13/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023] Open
Abstract
In multispectral digital in-line holographic microscopy (DIHM), aberrations of the optical system affect the repeatability of the reconstruction of transmittance, phase and morphology of the objects of interest. Here we address this issue first by model fitting calibration using transparent beads inserted in the sample. This step estimates the aberrations of the optical system as a function of the lateral position in the field of view and at each wavelength. Second, we use a regularized inverse problem approach (IPA) to reconstruct the transmittance and phase of objects of interest. Our method accounts for shift-variant chromatic and geometrical aberrations in the forward model. The multi-wavelength holograms are jointly reconstructed by favouring the colocalization of the object edges. The method is applied to the case of bacteria imaging in Gram-stained blood smears. It shows our methodology evaluates aberrations with good repeatability. This improves the repeatability of the reconstructions and delivers more contrasted spectral signatures in transmittance and phase, which could benefit applications of microscopy, such as the analysis and classification of stained bacteria.
Collapse
Affiliation(s)
- Dylan Brault
- Université Jean Monnet Saint-Etienne, CNRS, Institut d Optique Graduate School, Laboratoire Hubert Curien UMR 5516, 42023, Saint-Etienne, France
| | - Thomas Olivier
- Université Jean Monnet Saint-Etienne, CNRS, Institut d Optique Graduate School, Laboratoire Hubert Curien UMR 5516, 42023, Saint-Etienne, France
| | - Nicolas Faure
- bioMérieux, Centre Christophe Mérieux, 38024, Grenoble, France
| | - Sophie Dixneuf
- BIOASTER, Bioassays, Microsystems and Optical Engineering Unit, Lyon, France
| | | | | | - Ferréol Soulez
- Univ. de Lyon, Université Lyon1, ENS de Lyon, CNRS, Centre de Recherche Astrophysique de Lyon, UMR 5574, 69230, Saint-Genis-Laval, France
| | - Corinne Fournier
- Université Jean Monnet Saint-Etienne, CNRS, Institut d Optique Graduate School, Laboratoire Hubert Curien UMR 5516, 42023, Saint-Etienne, France.
| |
Collapse
|
8
|
Yu M, Shi H, Shen H, Chen X, Zhang L, Zhu J, Qian G, Feng B, Yu S. Simple and Rapid Discrimination of Methicillin-Resistant Staphylococcus aureus Based on Gram Staining and Machine Vision. Microbiol Spectr 2023; 11:e0528222. [PMID: 37395643 PMCID: PMC10433844 DOI: 10.1128/spectrum.05282-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a clinical threat with high morbidity and mortality. Here, we describe a new simple, rapid identification method for MRSA using oxacillin sodium salt, a cell wall synthesis inhibitor, combined with Gram staining and machine vision (MV) analysis. Gram staining classifies bacteria as positive (purple) or negative (pink) according to the cell wall structure and chemical composition. In the presence of oxacillin, the integrity of the cell wall for methicillin-susceptible S. aureus (MSSA) was destroyed immediately and appeared Gram negative. In contrast, MRSA was relatively stable and appeared Gram positive. This color change can be detected by MV. The feasibility of this method was demonstrated in 150 images of the staining results for 50 clinical S. aureus strains. Based on effective feature extraction and machine learning, the accuracies of the linear linear discriminant analysis (LDA) model and nonlinear artificial neural network (ANN) model for MRSA identification were 96.7% and 97.3%, respectively. Combined with MV analysis, this simple strategy improved the detection efficiency and significantly shortened the time needed to detect antibiotic resistance. The whole process can be completed within 1 h. Unlike the traditional antibiotic susceptibility test, overnight incubation is avoided. This new strategy could be used for other bacteria and represents a new rapid method for detection of clinical antibiotic resistance. IMPORTANCE Oxacillin sodium salt destroys the integrity of the cell wall of MSSA immediately, appearing Gram negative, whereas MRSA is relatively stable and still appears Gram positive. This color change can be detected by microscopic examination and MV analysis. This new strategy has significantly reduced the time to detect resistance. The results show that using oxacillin sodium salt combined with Gram staining and MV analysis is a new, simple and rapid method for identification of MRSA.
Collapse
Affiliation(s)
- Menghuan Yu
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Haimei Shi
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Hao Shen
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Xueqin Chen
- Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Li Zhang
- Department of Clinical Lab, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy Medical Science, Beijing, China
| | - Jianhua Zhu
- Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Guoqing Qian
- Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Bin Feng
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| |
Collapse
|
9
|
Samuel L. Direct-from-Blood Detection of Pathogens: a Review of Technology and Challenges. J Clin Microbiol 2023; 61:e0023121. [PMID: 37222587 PMCID: PMC10358183 DOI: 10.1128/jcm.00231-21] [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] [Indexed: 05/25/2023] Open
Abstract
Blood cultures have been the staple of clinical microbiology laboratories for well over half a century, but gaps remain in our ability to identify the causative agent in patients presenting with signs and symptoms of sepsis. Molecular technologies have revolutionized the clinical microbiology laboratory in many areas but have yet to present a viable alternative to blood cultures. There has been a recent surge of interest in utilizing novel approaches to address this challenge. In this minireview, I discuss whether molecular tools will finally give us the answers we need and the practical challenges of incorporating them into the diagnostic algorithm.
Collapse
Affiliation(s)
- Linoj Samuel
- Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, Michigan, USA
| |
Collapse
|
10
|
Vijayakumar T, Divya B, Vasanthi V, Narayan M, Kumar AR, Krishnan R. Diagnostic Utility of Gram Stain for Oral Smears - A Review. J Microsc Ultrastruct 2023; 11:130-134. [PMID: 38025180 PMCID: PMC10679832 DOI: 10.4103/jmau.jmau_108_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/05/2023] [Accepted: 02/12/2023] [Indexed: 12/01/2023] Open
Abstract
For rapid and successful treatment of infectious diseases, detection of the presence of microorganisms is essential. Traditional culture-based approaches are limiting and time consuming for microbial identification. The most popular staining technique for identifying Gram-positive and Gram-negative microorganisms in various tissues is called Gram staining. This method is utilized in both clinical practice and research. Gram staining of the oral smears is the preliminary step in the identification of any pathological shift in normal oral microbiota. This review discusses the principle of gram stain emphasizing its significance in diagnostic utility for oral smears.
Collapse
Affiliation(s)
- Tharani Vijayakumar
- Department of Oral Pathology and Microbiology, SRM Dental College, Ramapuram, Chennai, Tamil Nadu, India
| | - Bose Divya
- Department of Oral Pathology and Microbiology, SRM Dental College, Ramapuram, Chennai, Tamil Nadu, India
| | - V. Vasanthi
- Department of Oral Pathology and Microbiology, SRM Dental College, Ramapuram, Chennai, Tamil Nadu, India
| | - Madhu Narayan
- Department of Oral Pathology and Microbiology, SRM Dental College, Ramapuram, Chennai, Tamil Nadu, India
| | - Annasamy Ramesh Kumar
- Department of Oral Pathology and Microbiology, SRM Dental College, Ramapuram, Chennai, Tamil Nadu, India
| | - Rajkumar Krishnan
- Department of Oral Pathology and Microbiology, SRM Dental College, Ramapuram, Chennai, Tamil Nadu, India
| |
Collapse
|
11
|
Diedrich CM, Verhorstert KWJ, Riool M, Schuster H, de Boer L, Kikhney J, Moter A, Zaat SAJ, Roovers JPWR. Transvaginal Mesh-related Complications and the Potential Role of Bacterial Colonization: An Exploratory Observational Study. J Minim Invasive Gynecol 2023; 30:205-215. [PMID: 36442754 DOI: 10.1016/j.jmig.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/12/2022] [Accepted: 11/19/2022] [Indexed: 11/27/2022]
Abstract
STUDY OBJECTIVE This study aimed to investigate the potential role of transvaginal mesh bacterial colonization in the development of mesh-related complications (MRCs). DESIGN An observational and exploratory study. SETTING Tertiary referral center (Amsterdam UMC, location AMC, Amsterdam, The Netherlands). PATIëNTS: 49 patients indicated for mesh removal and 20 women of whom vaginal tissue was retrieved during prolapse surgery as a reference cohort. INTERVENTIONS collection of mesh-tissue complex (patient cohort) or vaginal tissue (reference cohort) MEASUREMENTS AND MAIN RESULTS: Homogenized samples were used for quantitative microbiological culture. Inflammation and fibrosis were semiquantitatively histologically scored; Gram staining and fluorescence in situ hybridization were used to detect bacteria and bacterial biofilms. Of the 49 patients, 44 samples (90%) were culture positive, with a higher diversity of species and more Gram-negative bacteria and polymicrobial cultures in the MRC cohort than the reference cohort, with mostly staphylococci, streptococci, Actinomyces spp., Cutibacterium acnes, and Escherichia coli. Patients with clinical signs of infection or exposure had the highest bacterial counts. Histology demonstrated moderate to severe inflammation in most samples. Gram staining showed bacteria in 57% of culture-positive samples, and in selected samples, fluorescence in situ hybridization illustrated a polymicrobial biofilm. CONCLUSION In this study, we observed distinct differences in bacterial numbers and species between patients with MRCs and a reference cohort. Bacteria were observed at the mesh-tissue interface in a biofilm. These results strongly support the potential role of bacterial mesh colonization in the development of MRCs.
Collapse
Affiliation(s)
- Chantal M Diedrich
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Schuster, and Roovers), Amsterdam, The Netherlands; Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands.
| | - Kim W J Verhorstert
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Schuster, and Roovers), Amsterdam, The Netherlands; Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Martijn Riool
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Heleen Schuster
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Schuster, and Roovers), Amsterdam, The Netherlands; Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Leonie de Boer
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Judith Kikhney
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Microbiology, Infectious Diseases, and Immunology, Biofilmcenter, Hindenburgdamm 30 (Drs. Kikhney and Moter), 12203 Berlin, Germany; MoKi Analytics GmbH, Hindenburgdamm 30 (Drs. Kikhney and Moter) 12203 Berlin, Germany
| | - Annette Moter
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Microbiology, Infectious Diseases, and Immunology, Biofilmcenter, Hindenburgdamm 30 (Drs. Kikhney and Moter), 12203 Berlin, Germany; MoKi Analytics GmbH, Hindenburgdamm 30 (Drs. Kikhney and Moter) 12203 Berlin, Germany; Practice Moter Diagnostics (practice), Marienplatz 9 (Dr. Moter), 12207 Berlin, Germany
| | - Sebastian A J Zaat
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Jan-Paul W R Roovers
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Schuster, and Roovers), Amsterdam, The Netherlands
| |
Collapse
|
12
|
Test Performance and Potential Clinical Utility of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel. Microbiol Spectr 2023; 11:e0409222. [PMID: 36688641 PMCID: PMC9927486 DOI: 10.1128/spectrum.04092-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The test performance and potential clinical utility of the ePlex blood culture identification Gram-negative (BCID-GN) panel was evaluated relative to matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry on bacterial isolates and conventional antimicrobial susceptibility testing. The majority (106/108, 98.1%) of GN bacteria identified by MALDI were on the BCID-GN panel, and valid tests (107/108, 99.1%) yielded results on average 26.7 h earlier. For all valid tests with on-panel organisms, the positive percent agreement was 102/105 (97.2%) with 3 false negatives and the negative percent agreement was 105/105. Chart review (n = 98) showed that in conjunction with Gram stain results, negative pan-Gram-positive (GP) markers provided the opportunity to discontinue GP antibiotic coverage in 63/98 (64.3%) cases on average 26.2 h earlier. Only 8/12 (66.7%) Enterobacterales isolates with resistance to third-generation cephalosporins harbored the CTX-M gene. In contrast, 8/8 CTX-M+ samples yielded a resistant isolate. Detection of 1 Stenotrophomonas maltophilia (18 h), 1 OXA23/48+ Acinetobacter baumannii (52.4 h), and 3 CTX-M+ Enterobacterales isolates on ineffective treatment (47.1 h) and 1 on suboptimal therapy (72.6 h) would have additionally enabled early antimicrobial optimization in 6/98 (6.1%) patients. IMPORTANCE The GenMark Dx ePlex rapid blood culture diagnostic system enables earlier time to identification of antimicrobial-resistant Gram-negative bacteria causing bloodstream infections. Its ability to rule out Gram-positive bacteria enabled early discontinuation of unnecessary antibiotics in 63/98 (64.3%) cases on average 26.2 h earlier. Detection of bacteria harboring the CTX-M gene as well as early identification of highly resistant bacteria such as Stenotrophomonas maltophilia and Acinetobacter baumannii enabled optimization of ineffective therapy in 6/98 (6.1%) patients. Its implementation in clinical microbiology laboratories optimizes therapy and improves patient care.
Collapse
|
13
|
Nik Zuraina NMN, Mohamad S, Hasan H, Goni MD, Suraiya S. Diagnostic performance of an in-house multiplex PCR assay and the retrospective surveillance of bacterial respiratory pathogens at a teaching hospital, Kelantan, Malaysia. Pathog Glob Health 2023; 117:63-75. [PMID: 35331083 PMCID: PMC9848298 DOI: 10.1080/20477724.2022.2028378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Respiratory tract infections (RTIs), including pneumonia and pulmonary tuberculosis, are among the leading causes of death worldwide. The use of accurate diagnostic tests is crucial to initiate proper treatment and therapy to reduce the mortality rates for RTIs. A PCR assay for simultaneous detection of six respiratory bacteria: Haemophilus influenzae, Klebsiella pneumoniae, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae, was developed in our lab. The current study aimed to evaluate the performance of this assay along with the retrospective surveillance of respiratory pathogens at a teaching hospital in Kelantan, Malaysia. Leftover sputa (n = 200) from clinical laboratories were collected and undergone DNA template preparation for PCR analysis. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the PCR assay were determined in comparison with the gold standard sputum culture. Overall, the accuracy performance of this assay was 94.67% (95% CI: 90.87% to 97.21%) with sensitivity, specificity, PPV and NPV of 100%, 91.67%, 87.1% and 100%, respectively. Based on the organisms detected from sputa, K. pneumoniae ranked as the top isolate (n = 48), followed by P. aeruginosa (n = 13) and H. influenzae (n = 10). Surveillance among the patients showed that the associations of bacterial positive with gender and means of acquisition were found significant (p values = 0.049 and 0.001, respectively). Besides the promising performance of this ready-to-use molecular-based assay for the rapid detection of selected bacteria pathogens, this study also highlighted significant spread of K. pneumoniae RTIs in the community.
Collapse
Affiliation(s)
- Nik Mohd Noor Nik Zuraina
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Malaysia
| | - Suharni Mohamad
- School of Dental Sciences, Universiti Sains Malaysia, Kota Bharu, Malaysia
| | - Habsah Hasan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Malaysia
| | - Mohammed Dauda Goni
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | - Siti Suraiya
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Malaysia
- Infectious Disease Control and Epidemiology Unit, Hospital Universiti Sains Malaysia, Kota Bharu, Malaysia
- CONTACT Siti Suraiya Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150Kota Bharu, Kelantan, Malaysia; Infectious Disease Control and Epidemiology Unit, Hospital Universiti Sains Malaysia, 16150 Kota Bharu, Kelantan, Malaysia
| |
Collapse
|
14
|
Sukweenadhi J, Theda JA, Artadana IBM, Kang SC. Isolation and in vitro Screening of Plant Growth Promoting Rhizospheric Bacteria from Corn (Zea mays var. indentata). APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s000368382206014x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
|
15
|
Analytical Performance and Potential Clinical Utility of the GenMark Dx ePlex® Blood Culture Identification Gram-Positive Panel. Diagn Microbiol Infect Dis 2022; 104:115762. [DOI: 10.1016/j.diagmicrobio.2022.115762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/26/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
|
16
|
The Hidden Crisis in the Times of COVID-19: Critical Shortages of Medical Laboratory Professionals in Clinical Microbiology. J Clin Microbiol 2022; 60:e0024122. [PMID: 35658527 PMCID: PMC9383190 DOI: 10.1128/jcm.00241-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The COVID pandemic has put a spotlight on laboratory medicine, showcasing how vital diagnostic testing is for society and the health care system. It has also brought to light and accelerated the critical shortage of trained and experienced laboratory personnel that has been felt for decades. The need for laboratory professionals is expected to grow by 11% between 2020 and 2030, a higher rate of growth than the overall average for all other health care occupations. Here, the background to this workforce shortage is reviewed. Some proposed actions to help address the issue are put forth, including increasing awareness of the medical laboratory science profession along with bolstering training opportunities and awareness of alternate routes to obtaining certification as a medical laboratory scientist. In addition, recent survey data specifically related to the employee shortages in microbiology are presented which demonstrate that 80% of microbiology laboratories have vacant positions and that filling these positions is challenging for a number of reasons, including a lack of qualified applicants.
Collapse
|
17
|
Tuft S, Somerville TF, Li JPO, Neal T, De S, Horsburgh MJ, Fothergill JL, Foulkes D, Kaye S. Bacterial keratitis: identifying the areas of clinical uncertainty. Prog Retin Eye Res 2021; 89:101031. [PMID: 34915112 DOI: 10.1016/j.preteyeres.2021.101031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
Bacterial keratitis is a common corneal infection that is treated with topical antimicrobials. By the time of presentation there may already be severe visual loss from corneal ulceration and opacity, which may persist despite treatment. There are significant differences in the associated risk factors and the bacterial isolates between high income and low- or middle-income countries, so that general management guidelines may not be appropriate. Although the diagnosis of bacterial keratitis may seem intuitive there are multiple uncertainties about the criteria that are used, which impacts the interpretation of investigations and recruitment to clinical studies. Importantly, the concept that bacterial keratitis can only be confirmed by culture ignores the approximately 50% of cases clinically consistent with bacterial keratitis in which investigations are negative. The aetiology of these culture-negative cases is unknown. Currently, the estimation of bacterial susceptibility to antimicrobials is based on data from systemic administration and achievable serum or tissue concentrations, rather than relevant corneal concentrations and biological activity in the cornea. The provision to the clinician of minimum inhibitory concentrations of the antimicrobials for the isolated bacteria would be an important step forward. An increase in the prevalence of antimicrobial resistance is a concern, but the effect this has on disease outcomes is yet unclear. Virulence factors are not routinely assessed although they may affect the pathogenicity of bacteria within species and affect outcomes. New technologies have been developed to detect and kill bacteria, and their application to bacterial keratitis is discussed. In this review we present the multiple areas of clinical uncertainty that hamper research and the clinical management of bacterial keratitis, and we address some of the assumptions and dogma that have become established in the literature.
Collapse
Affiliation(s)
- Stephen Tuft
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, UK.
| | - Tobi F Somerville
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Ji-Peng Olivia Li
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, UK.
| | - Timothy Neal
- Department of Clinical Microbiology, Liverpool Clinical Laboratories, Liverpool University Hospital NHS Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK.
| | - Surjo De
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London, NW1 2PG, UK.
| | - Malcolm J Horsburgh
- Department of Infection and Microbiomes, University of Liverpool, Crown Street, Liverpool, L69 7BX, UK.
| | - Joanne L Fothergill
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Daniel Foulkes
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Stephen Kaye
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| |
Collapse
|
18
|
Abstract
Antibiotic resistance is a public health concern. A critical care clinician is faced with a clinical dilemma of using the appropriate treatment without compromising the antibiotic armamentarium. Postoperative and trauma patients in the intensive care unit (ICU) pose a unique challenge of mounting a systemic inflammatory response, which makes it even more difficult to differentiate inflammation from infection. The decision for type of empirical therapy should be individualized to the patient and local ecology data and resistance profiles. After initiation of empirical therapy, deescalation should be done once microbiology data are available. Antibiotic stewardship programs are essential in the ICU.
Collapse
|
19
|
Diagnostic armamentarium of infectious keratitis: A comprehensive review. Ocul Surf 2021; 23:27-39. [PMID: 34781020 PMCID: PMC8810150 DOI: 10.1016/j.jtos.2021.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 01/23/2023]
Abstract
Infectious keratitis (IK) represents the leading cause of corneal blindness worldwide, particularly in developing countries. A good outcome of IK is contingent upon timely and accurate diagnosis followed by appropriate interventions. Currently, IK is primarily diagnosed on clinical grounds supplemented by microbiological investigations such as microscopic examination with stains, and culture and sensitivity testing. Although this is the most widely accepted practice adopted in most regions, such an approach is challenged by several factors, including indistinguishable clinical features shared among different causative organisms, polymicrobial infection, long diagnostic turnaround time, and variably low culture positivity rate. In this review, we aim to provide a comprehensive overview of the current diagnostic armamentarium of IK, encompassing conventional microbiological investigations, molecular diagnostics (including polymerase chain reaction and mass spectrometry), and imaging modalities (including anterior segment optical coherence tomography and in vivo confocal microscopy). We also highlight the potential roles of emerging technologies such as next-generation sequencing, artificial intelligence-assisted platforms. and tele-medicine in shaping the future diagnostic landscape of IK.
Collapse
|
20
|
Sirohi M, Lall M, Yenishetti S, Panat L, Kumar A. Development of a Machine learning image segmentation-based algorithm for the determination of the adequacy of Gram-stained sputum smear images. Med J Armed Forces India 2021; 78:339-344. [DOI: 10.1016/j.mjafi.2021.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022] Open
|
21
|
Melter O, Abdulla L, Harwill M, Vaniš V, Pavlíková M, Tkadlec J. SensiGram as a modified Gram staining procedure with higher sensitivity for detection of Gram-negative bacteria in blood culture. J Microbiol Methods 2021; 191:106344. [PMID: 34653524 DOI: 10.1016/j.mimet.2021.106344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Affiliation(s)
- O Melter
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic.
| | - L Abdulla
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - M Harwill
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - V Vaniš
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - M Pavlíková
- Department of Probability and Mathematical Statistics, Charles University-Faculty of Mathematics and Physics, Prague, Czech Republic
| | - J Tkadlec
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic
| |
Collapse
|
22
|
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.
Collapse
|
23
|
Samuel LP, Hansen GT, Kraft CS, Pritt BS. The Need for Dedicated Microbiology Leadership in the Clinical Microbiology Laboratory. J Clin Microbiol 2021; 59:e0154919. [PMID: 33597258 PMCID: PMC8288296 DOI: 10.1128/jcm.01549-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Clinical microbiology laboratories play a crucial role in patient care using traditional and innovative diagnostics. Challenges faced by laboratories include emerging pathogens, rapidly evolving technologies, health care-acquired infections, antibiotic-resistant organisms, and diverse patient populations. Despite these challenges, many clinical microbiology laboratories in the United States are not directed by doctoral level microbiology-trained individuals with sufficient time dedicated to laboratory leadership. The manuscript highlights the need for medical microbiology laboratory directors with appropriate training and qualifications.
Collapse
Affiliation(s)
- Linoj P. Samuel
- Department of Pathology and Laboratory Medicine, Henry Ford Health System, Detroit, Michigan, USA
| | - Glen T. Hansen
- Department of Pathology and Laboratory Medicine, Hennepin County Medical Center, Minneapolis, Minnesota, USA
- Department of Pathology and Laboratory Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Medicine, Division of Infectious Diseases, University of Minnesota, Minneapolis, Minnesota, USA
| | - Colleen S. Kraft
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
- Department Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Bobbi S. Pritt
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Internal Medicine, Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
24
|
Fischer A, Azam N, Rasga L, Barras V, Tangomo M, Renzi G, Vuilleumier N, Schrenzel J, Cherkaoui A. Performances of automated digital imaging of Gram-stained slides with on-screen reading against manual microscopy. Eur J Clin Microbiol Infect Dis 2021; 40:2171-2176. [PMID: 33963927 PMCID: PMC8449764 DOI: 10.1007/s10096-021-04233-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/21/2021] [Indexed: 11/25/2022]
Abstract
The objective of this study was to evaluate the performances of the automated digital imaging of Gram-stained slides against manual microscopy. Four hundred forty-three identified Gram-stained slides were included in this study. When both methods agreed, we considered the results as correct, and no further examination was carried out. Whenever the methods gave discrepant results, we reviewed the digital images and the glass slides by manual microscopy to avoid incorrectly read smears. The final result was a consensus of multiple independent reader interpretations. Among the 443 slides analyzed in this study, 101 (22.8%) showed discrepant results between the compared methods. The rates of discrepant results according to the specimen types were 5.7% (9/157) for positive blood cultures, 42% (60/142) for respiratory tract specimens, and 22% (32/144) for sterile site specimens. After a subsequent review of the discrepant slides, the final rate of discrepancies dropped to 7.0% (31/443). The overall agreement between the compared methods and the culture results reached 78% (345/443) and 79% (349/443) for manual microscopy and automated digital imaging, respectively. According to culture results, the specificity for automated digital imaging and manual microscopy were 90.8% and 87.7% respectively. In contrast, sensitivity was 84.1% for the two compared methods. The discrepant results were mostly encountered with microorganism morphologies of rare occurrence. The results reported in this study emphasize that on-screen reading is challenging, since the recognition of morphologies on-screen can appear different as compared to routine manual microscopy. Monitoring of Gram stain errors, which is facilitated by automated digital imaging, remains crucial for the quality control of reported Gram stain results.
Collapse
Affiliation(s)
- Adrien Fischer
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Nouria Azam
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Lara Rasga
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Valérie Barras
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Manuela Tangomo
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Gesuele Renzi
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Abdessalam Cherkaoui
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland.
| |
Collapse
|
25
|
Yi X, Song Y, Xu X, Peng D, Wang J, Qie X, Lin K, Yu M, Ge M, Wang Y, Zhang D, Yang Q, Wang M, Huang WE. Development of a Fast Raman-Assisted Antibiotic Susceptibility Test (FRAST) for the Antibiotic Resistance Analysis of Clinical Urine and Blood Samples. Anal Chem 2021; 93:5098-5106. [PMID: 33728890 DOI: 10.1021/acs.analchem.0c04709] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Human health is at great risk due to the spreading of antimicrobial resistance (AMR). The lengthy procedure of conventional antimicrobial susceptibility testing (AST) usually requires a few days. We developed a fast Raman-assisted antibiotic susceptibility test (FRAST), which detects single bacterial metabolic activity in the presence of antibiotics, using Raman single-cell spectroscopy. It was found that single-cell Raman spectra (SCRS) would show a clear and distinguishable Raman band at the "silent zone" (2000-2300 cm-1), due to the active incorporation of deuterium from heavy water (D2O) by antibiotic-resistant bacteria. This pilot study has compared the FRAST and the conventional AST for six clinical standard quality controls (four Gram-negative and two Gram-positive bacteria strains) in response to 38 antibiotics. In total, 3200 treatments have been carried out and approximately 64 000 SCRS have been acquired for FRAST analysis. The result showed an overall agreement of 88.0% between the FRAST and the conventional AST assay. The gram-staining classification based on the linear discriminant analysis (LDA) model of SCRS was developed, seamlessly coupling with the FRAST to further reduce the turnaround time. We applied the FRAST to real clinical analysis for nine urinary infectious samples and three sepsis samples. The results were consistent with MALDI-TOF identification and the conventional AST. Under the optimal conditions, the "sample to report" of the FRAST could be reduced to 3 h for urine samples and 21 h for sepsis samples. The FRAST provides fast and reliable susceptibility tests, which could speed up microbiological analysis for clinical practice and facilitate antibiotic stewardship.
Collapse
Affiliation(s)
- Xiaofei Yi
- Shanghai D-band Medical Instrument Co., Shanghai 201802, China
| | - Yizhi Song
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Di Peng
- Shanghai D-band Medical Instrument Co., Shanghai 201802, China
| | - Jingkai Wang
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
| | - Xingwang Qie
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Kaicheng Lin
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Miao Yu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
| | - Mingfeng Ge
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Yun Wang
- Shanghai D-band Medical Instrument Co., Shanghai 201802, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, P. R. China
| | - Qiwen Yang
- Department of clinical laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Beijing 100730, China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, U.K
| |
Collapse
|
26
|
Blondeau JM, Rankin SC. Diagnostic clinical microbiology. J Vet Pharmacol Ther 2021; 44:250-269. [PMID: 33686661 DOI: 10.1111/jvp.12962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/27/2021] [Accepted: 02/09/2021] [Indexed: 01/07/2023]
Abstract
Technological advancements have changed the way clinical microbiology laboratories are detecting and identifying bacterial, viral, parasitic, and yeast/fungal pathogens. Such advancements have improved sensitivity and specificity and reduce turnaround time to reporting of clinically important results. This article discusses and reviews some traditional methodologies along with some of the technological innovations introduced into diagnostic microbiology laboratories. Some insight to what might be available in the coming years is also discussed.
Collapse
Affiliation(s)
- Joseph M Blondeau
- Division of Clinical Microbiology, Royal University Hospital and Saskatchewan Health Authority, Saskatoon, SK, Canada.,Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Ophthalmology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Shelley C Rankin
- Department of Pathobiology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA
| |
Collapse
|
27
|
Ombelet S, Natale A, Ronat JB, Vandenberg O, Hardy L, Jacobs J. Evaluation of MicroScan Bacterial Identification Panels for Low-Resource Settings. Diagnostics (Basel) 2021; 11:349. [PMID: 33669829 PMCID: PMC7922174 DOI: 10.3390/diagnostics11020349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial identification is challenging in low-resource settings (LRS). We evaluated the MicroScan identification panels (Beckman Coulter, Brea, CA, USA) as part of Médecins Sans Frontières' Mini-lab Project. The MicroScan Dried Overnight Positive ID Type 3 (PID3) panels for Gram-positive organisms and Dried Overnight Negative ID Type 2 (NID2) panels for Gram-negative organisms were assessed with 367 clinical isolates from LRS. Robustness was studied by inoculating Gram-negative species on the Gram-positive panel and vice versa. The ease of use of the panels and readability of the instructions for use (IFU) were evaluated. Of species represented in the MicroScan database, 94.6% (185/195) of Gram-negative and 85.9% (110/128) of Gram-positive isolates were correctly identified up to species level. Of species not represented in the database (e.g., Streptococcus suis and Bacillus spp.), 53.1% out of 49 isolates were incorrectly identified as non-related bacterial species. Testing of Gram-positive isolates on Gram-negative panels and vice versa (n = 144) resulted in incorrect identifications for 38.2% of tested isolates. The readability level of the IFU was considered too high for LRS. Inoculation of the panels was favorably evaluated, whereas the visual reading of the panels was considered error-prone. In conclusion, the accuracy of the MicroScan identification panels was excellent for Gram-negative species and good for Gram-positive species. Improvements in stability, robustness, and ease of use have been identified to assure adaptation to LRS constraints.
Collapse
Affiliation(s)
- Sien Ombelet
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (L.H.); (J.J.)
- Immunology & Microbiology Department, KU Leuven, 3000 Leuven, Belgium
| | - Alessandra Natale
- Médecins Sans Frontières, Operational Center Paris, 75019 Paris, France; (A.N.); (J.-B.R.)
| | - Jean-Baptiste Ronat
- Médecins Sans Frontières, Operational Center Paris, 75019 Paris, France; (A.N.); (J.-B.R.)
- Team ReSIST, INSERM U1184, School of Medicine, University Paris-Saclay, 94807 Villejuif, France
- Bacteriology-Hygiene Unit, Assistance Publique—Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
| | - Olivier Vandenberg
- Center for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium;
- Innovation and Business Development Unit, Laboratoire Hospitalier Universitaire de Bruxelles—Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London WC1E 6BT, UK
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (L.H.); (J.J.)
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (L.H.); (J.J.)
- Immunology & Microbiology Department, KU Leuven, 3000 Leuven, Belgium
| |
Collapse
|
28
|
Wu KY, Yang TX. A Novel Improved Gram Staining Method Based on the Capillary Tube. Pol J Microbiol 2021; 69:503-508. [PMID: 33574878 PMCID: PMC7812360 DOI: 10.33073/pjm-2020-043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/11/2020] [Accepted: 09/02/2020] [Indexed: 11/06/2022] Open
Abstract
In this work, an exploratory study was conducted to examine Gram staining based on the capillary tube. Each Gram staining step for all bacterial strains tested was completed in capillary tubes. The results showed that different Gram staining morphologies were clearly visible in the capillary tubes. The results presented here demonstrated that the improved method could effectively distinguish between Gram-positive and Gram-negative bacteria, and only small volumes of reagents were required in this method. Collectively, this efficient method could rapidly and accurately identify the types of bacteria. Therefore, our findings could be used as a useful reference study for other staining methods.
Collapse
Affiliation(s)
- Kong-Yang Wu
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Tong-Xiang Yang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| |
Collapse
|
29
|
Bann SJ, Ballantine RD, Cochrane SA. The tridecaptins: non-ribosomal peptides that selectively target Gram-negative bacteria. RSC Med Chem 2021; 12:538-551. [PMID: 34041489 PMCID: PMC8127968 DOI: 10.1039/d0md00413h] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tridecaptins are a re-emerging class of non-ribosomal antibacterial peptides (NRAPs) with potent activity against highly problematic strains of Gram-negative bacteria. An intricate mode of action has been reported to explain the bactericidal activity of these NRAPs, wherein they bind selectivity to the Gram-negative version of the peptidoglycan precursor lipid II on the outer leaflet of the inner membrane and disrupt the proton-motive force. Tridecaptins are highly amenable to synthetic modification owing to their linear structure, therefore, various synthetic analogues have been reported, several of which have enhanced antimicrobial activity, reduced cost of synthesis and/or improved stability towards d-peptidase mediated hydrolysis. It has also been demonstrated that unacylated tridecaptins can act synergistically with clinically relevant antibiotics by sensitizing the outer membrane. This review will summarize past literature on the development/discovery of novel tridecaptin analogues (up until the end of 2020), some of which may be useful therapeutic agents to treat insidious Gram-negative bacterial infections.
Collapse
Affiliation(s)
- Samantha J Bann
- School of Chemistry and Chemical Engineering, Queens University Belfast David Keir Building, Stranmillis Road Belfast BT9 5AG UK
| | - Ross D Ballantine
- School of Chemistry and Chemical Engineering, Queens University Belfast David Keir Building, Stranmillis Road Belfast BT9 5AG UK
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queens University Belfast David Keir Building, Stranmillis Road Belfast BT9 5AG UK
| |
Collapse
|
30
|
Gram Staining: a Comparison of Two Automated Systems and Manual Staining. J Clin Microbiol 2020; 58:JCM.01914-20. [PMID: 32938735 DOI: 10.1128/jcm.01914-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/09/2020] [Indexed: 11/20/2022] Open
Abstract
Various Gram staining automated systems are available to accelerate and standardize the staining process, but a systematic comparison of different systems is largely lacking. The objective of this study was to evaluate two devices in comparison to manual Gram staining. Clinical samples (n = 500; University Hospital Münster, Germany; May to June 2020) were simultaneously Gram stained manually and with two automated Gram stainers (Previ Color Gram, bioMérieux, and ColorAX2, Axonlab). The quality was assessed based on four criteria: (i) homogeneous staining of bacteria/fungi, (ii) uniform staining of the background, (iii) absence of staining artifacts, and (iv) congruency between culture and microscopy. Each criterion was rated with 0 (absence) or 1 (presence) point to calculate a quality score (0 to 4 points). The costs for each staining procedure were calculated based on consumables and hands-on time (applying the average wage of a laboratory technician in the public service for Germany and the United States). The mean (± standard deviation [SD]) quality scores were comparable for manual staining (3.06 ± 0.91) and Previ Color Gram (3.04 ± 0.90; P = 0.6), while significantly lower scores were achieved by ColorAX2 (2.57 ± 1.09; P < 0.0001). The total cost per Gram stain was €1.13/$1.34 for Previ Color Gram, €0.80/$0.83 for manual, and €0.60/$0.71 for ColorAX2, respectively. The quality and costs per slide vary significantly between instruments of different manufacturers.
Collapse
|
31
|
Butina K, Tomac A, Choong FX, Shirani H, Nilsson KPR, Löffler S, Richter-Dahlfors A. Optotracing for selective fluorescence-based detection, visualization and quantification of live S. aureus in real-time. NPJ Biofilms Microbiomes 2020; 6:35. [PMID: 33037198 PMCID: PMC7547713 DOI: 10.1038/s41522-020-00150-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/10/2020] [Indexed: 11/09/2022] Open
Abstract
Methods for bacterial detection are needed to advance the infection research and diagnostics. Based on conformation-sensitive fluorescent tracer molecules, optotracing was recently established for dynamic detection and visualization of structural amyloids and polysaccharides in the biofilm matrix of gram-negative bacteria. Here, we extend the use of optotracing for detection of gram-positive bacteria, focussing on the clinically relevant opportunistic human pathogen Staphylococcus aureus. We identify a donor-acceptor-donor-type optotracer, whose binding-induced fluorescence enables real-time detection, quantification, and visualization of S. aureus in monoculture and when mixed with gram-negative Salmonella Enteritidis. An algorithm-based automated high-throughput screen of 1920 S. aureus transposon mutants recognized the cell envelope as the binding target, which was corroborated by super-resolution microscopy of bacterial cells and spectroscopic analysis of purified cell wall components. The binding event was essentially governed by hydrophobic interactions, which permitted custom-designed tuning of the binding selectivity towards S. aureus versus Enterococcus faecalis by appropriate selection of buffer conditions. Collectively this work demonstrates optotracing as an enabling technology relevant for any field of basic and applied research, where visualization and detection of S. aureus is needed.
Collapse
Affiliation(s)
- Karen Butina
- AIMES-Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Ana Tomac
- AIMES-Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Ferdinand X Choong
- AIMES-Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Hamid Shirani
- Department of Chemistry, IFM, Linköping University, SE-581 83, Linköping, Sweden
| | - K Peter R Nilsson
- AIMES-Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Chemistry, IFM, Linköping University, SE-581 83, Linköping, Sweden
| | - Susanne Löffler
- AIMES-Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Agneta Richter-Dahlfors
- AIMES-Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden. .,Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
| |
Collapse
|
32
|
Pisitpayat P, Sirikul T, Hongmanee P, Santanirand P, Lekhanont K. Mycobacterium haemophilum scleritis: two case reports and review of literature. BMC Ophthalmol 2020; 20:378. [PMID: 32967654 PMCID: PMC7513486 DOI: 10.1186/s12886-020-01649-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/17/2020] [Indexed: 11/25/2022] Open
Abstract
Background Mycobacterium haemophilum is a rare and emerging nontuberculous mycobacteria (NTM). It normally causes localized or disseminated systemic diseases, particularly skin infections and arthritis in severely immunocompromised patients. There have been 5 cases of M. haemophilum ocular infections reported in the literature. Only 1 case presented with scleritis with keratitis. Here, we reported 2 cases of M. haemophilum scleritis. One of them was immunocompetent host and had keratitis with radial keratoneuritis as a presenting sign. Case presentation Case 1: A 52-year-old Thai female with rheumatoid arthritis presented with scleritis. Conjunctival scraping was carried out and the culture result was positive for M. haemophilum. Despite receiving systemic and topical antibiotics, her clinical symptoms and signs worsened. Surgical debridement was performed. After surgery, the lesion was significantly improved and finally turned to conjunctival scarring. Case 2: A 32-year old healthy Thai male without underlying disease presented with nodular scleritis and keratouveitis with multiple radial keratoneuritis. Surgical debridement of the scleral nodule was performed. Initial microbiological investigations were negative. Herpes ocular infections was suspected. Topical antibiotics, oral acyclovir, low-dose topical steroids and systemic steroids were started. The scleral inflammation subsided but later the keratitis relapsed, requiring corneal biopsy. Histopathology of the specimen revealed acid-fast bacteria and M. haemophilum was identified by polymerase chain reaction (PCR) and sequencing. The diagnosis of Mycobacterial keratitis was made. Although using the combination of systemic and topical antibiotics, his clinical status progressively deteriorated. Multiple therapeutic penetrating keratoplasties were required to eradicate the infection. No recurrence was found during the 1-year follow-up in both cases. Conclusions M. haemophilum can cause scleritis and keratitis, even in immunocompenent host. Radial keraoneuritis is first described in M. haemophilum keratitis. NTM keratitis should be considered in the differential diagnosis of patients with radial keratoneuritis. Increased awareness and early diagnosis using appropriate culture conditions and molecular techniques are important for the proper treatment of this infection. Prompt surgical intervention appears to be vital for successful management of M. haemophilum scleritis and keratitis.
Collapse
Affiliation(s)
- Punyanuch Pisitpayat
- Department of Ophthalmology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Rama VI Rd., Rajathevi, Bangkok, 10400, Thailand
| | - Tasanee Sirikul
- Department of Ophthalmology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Rama VI Rd., Rajathevi, Bangkok, 10400, Thailand
| | - Poonpilas Hongmanee
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kaevalin Lekhanont
- Department of Ophthalmology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Rama VI Rd., Rajathevi, Bangkok, 10400, Thailand.
| |
Collapse
|
33
|
Eickelberg G, Sanchez-Pinto LN, Luo Y. Predictive modeling of bacterial infections and antibiotic therapy needs in critically ill adults. J Biomed Inform 2020; 109:103540. [PMID: 32814200 PMCID: PMC7530142 DOI: 10.1016/j.jbi.2020.103540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/17/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022]
Abstract
Unnecessary antibiotic regimens in the intensive care unit (ICU) are associated with adverse patient outcomes and antimicrobial resistance. Bacterial infections (BI) are both common and deadly in ICUs, and as a result, patients with a suspected BI are routinely started on broad-spectrum antibiotics prior to having confirmatory microbiologic culture results or when an occult BI is suspected, a practice known as empiric antibiotic therapy (EAT). However, EAT guidelines lack consensus and existing methods to quantify patient-level BI risk rely largely on clinical judgement and inaccurate biomarkers or expensive diagnostic tests. As a consequence, patients with low risk of BI often are continued on EAT, exposing them to unnecessary side effects. Augmenting current intuition-based practices with data-driven predictions of BI risk could help inform clinical decisions to shorten the duration of unnecessary EAT and improve patient outcomes. We propose a novel framework to identify ICU patients with low risk of BI as candidates for earlier EAT discontinuation. For this study, patients suspected of having a community-acquired BI were identified in the Medical Information Mart for Intensive Care III (MIMIC-III) dataset and categorized based on microbiologic culture results and EAT duration. Using structured longitudinal data collected up to 24-, 48-, and 72-hours after starting EAT, our best models identified patients at low risk of BI with AUROCs up to 0.8 and negative predictive values >93%. Overall, these results demonstrate the feasibility of forecasting BI risk in a critical care setting using patient features found in the electronic health record and call for more extensive research in this promising, yet relatively understudied, area.
Collapse
Affiliation(s)
- Garrett Eickelberg
- Department of Preventitive Medicine (Health & Biomedical Informatics), Feinberg School of Medicine, 750 N Lake Shore, Chicago, IL 60611, USA
| | - L Nelson Sanchez-Pinto
- Department of Preventitive Medicine (Health & Biomedical Informatics), Feinberg School of Medicine, 750 N Lake Shore, Chicago, IL 60611, USA; Department of Pediatrics (Critical Care), 225 E. Chicago Avenue, Chicago, IL 60611, USA.
| | - Yuan Luo
- Department of Preventitive Medicine (Health & Biomedical Informatics), Feinberg School of Medicine, 750 N Lake Shore, Chicago, IL 60611, USA.
| |
Collapse
|
34
|
Huang WY, Lee MS, Lin LM, Liu YC. Diagnostic performance of the Sputum Gram Stain in predicting sputum culture results for critically ill pediatric patients with pneumonia. Pediatr Neonatol 2020; 61:420-425. [PMID: 32349917 DOI: 10.1016/j.pedneo.2020.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 01/21/2020] [Accepted: 03/31/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The sputum Gram stain is an inexpensive, rapid, and convenient laboratory method that predicts the bacterial pathogens in patients with pneumonia. This study aimed to evaluate the diagnostic performance of this method in predicting sputum culture results for critically ill pediatric patients. METHODS From June 2008 to June 2018, patients with pneumonia with an endotracheal or a tracheostomy tube in place in the Pediatric Intensive Care Unit at Changhua Christian Hospital were enrolled retrospectively. Sputum was collected from each patient via the artificial airway for Gram stain and culture evaluations of bacterial pathogens. Mixed culture results were excluded. A successful prediction was defined as a match of the sputum Gram stain and culture results. RESULTS A total of 622 records were reviewed, of which 542 were analyzed. Haemophilus influenzae, Pseudomonas aeruginosa, and Streptococcus pneumoniae were the three most common pathogens found. The overall prediction success rate of the sputum Gram stain was 59.23%. The sensitivity of the method in predicting gram-negative bacilli (GNB), gram-negative cocci (GNC), and gram-positive cocci (GPC) was 0.45, 0.67, and 0.61, respectively. Its specificity in predicting GNB, GNC, and GPC was 0.87, 0.98, and 0.87, respectively. Its positive likelihood ratio in predicting GNB, GNC, and GPC was 3.46, 33.50, and 4.69, respectively. The highest prediction success rate among all pathogens was for GNC. CONCLUSION The sputum Gram stain had high specificity and relatively low sensitivity in predicting the bacterial pathogens in critically ill pediatric patients. Its high specificity in predicting sputum culture results means that clinicians can confidently use sputum Gram stain results to guide their antibiotic choice for treatment.
Collapse
Affiliation(s)
- Wun-Yan Huang
- Department of Pediatric Emergency Medicine, China Medical University Children's Hospital, China Medical University, Taichung, Taiwan
| | - Ming-Sheng Lee
- Department of Pediatric Pulmonology and Critical Care, Changhua Christian Children Hospital, Changhua, Taiwan; Graduate Program in Nutrition, Chung Shan Medical University, Taichung, Taiwan
| | - Liang-Mei Lin
- Respiratory Therapy Section for Children, Changhua Christian Children Hospital, Changhua, Taiwan
| | - Yi-Chen Liu
- Respiratory Therapy Section for Children, Changhua Christian Children Hospital, Changhua, Taiwan.
| |
Collapse
|
35
|
Fecal Gram stain morphotype and their distribution patterns in a Cameroonian cohort with and without HIV infection. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Clinical Performance of the Novel GenMark Dx ePlex Blood Culture ID Gram-Positive Panel. J Clin Microbiol 2020; 58:JCM.01730-19. [PMID: 31996444 PMCID: PMC7098771 DOI: 10.1128/jcm.01730-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 01/18/2020] [Indexed: 12/14/2022] Open
Abstract
Rapid identification from positive blood cultures is standard of care (SOC) in many clinical microbiology laboratories. The GenMark Dx ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a multiplex nucleic acid amplification assay based on competitive DNA hybridization and electrochemical detection using eSensor technology. This multicenter study compared the investigational-use-only (IUO) BCID-GP Panel to other methods of identification of 20 Gram-positive bacteria, four antimicrobial resistance genes, and both Pan Candida and Pan Gram-Negative targets that are unique to the BCID-GP Panel. Rapid identification from positive blood cultures is standard of care (SOC) in many clinical microbiology laboratories. The GenMark Dx ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a multiplex nucleic acid amplification assay based on competitive DNA hybridization and electrochemical detection using eSensor technology. This multicenter study compared the investigational-use-only (IUO) BCID-GP Panel to other methods of identification of 20 Gram-positive bacteria, four antimicrobial resistance genes, and both Pan Candida and Pan Gram-Negative targets that are unique to the BCID-GP Panel. Ten microbiology laboratories throughout the United States collected residual, deidentified positive blood culture samples for analysis. Five laboratories tested both clinical and contrived samples with the BCID-GP Panel. Comparator identification methods included each laboratory’s SOC, which included matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and automated identification systems as well as targeted PCR/analytically validated real-time PCR (qPCR) with bidirectional sequencing. A total of 2,342 evaluable samples (1,777 clinical and 565 contrived) were tested with the BCID-GP Panel. The overall sample accuracy for on-panel organisms was 89% before resolution of discordant results. For pathogenic Gram-positive targets (Bacillus cereus group, Enterococcus spp., Enterococcus faecalis, Enterococcus faecium, Staphylococcus spp., Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lugdunensis, Listeria spp., Listeria monocytogenes, Streptococcus spp., Streptococcus agalactiae, Streptococcus anginosus group, Streptococcus pneumoniae, and Streptococcus pyogenes), positive percent agreement (PPA) and negative percent agreement (NPA) ranged from 93.1% to 100% and 98.8% to 100%, respectively. For contamination rule-out targets (Bacillus subtilis group, Corynebacterium, Cutibacterium acnes, Lactobacillus, and Micrococcus), PPA and NPA ranged from 84.5% to 100% and 99.9% to 100%, respectively. Positive percent agreement and NPA for the Pan Candida and Pan Gram-Negative targets were 92.4% and 95.7% for the former and 99.9% and 99.6% for the latter. The PPAs for resistance markers were as follows: mecA, 97.2%; mecC, 100%; vanA, 96.8%; and vanB, 100%. Negative percent agreement ranged from 96.6% to 100%. In conclusion, the ePlex BCID-GP Panel compares favorably to SOC and targeted molecular methods for the identification of 20 Gram-positive pathogens and four antimicrobial resistance genes in positive blood culture bottles. This panel detects a broad range of pathogens and mixed infections with yeast and Gram-negative organisms from the same positive blood culture bottle.
Collapse
|
38
|
Smith KP, Kirby JE. Image analysis and artificial intelligence in infectious disease diagnostics. Clin Microbiol Infect 2020; 26:1318-1323. [PMID: 32213317 DOI: 10.1016/j.cmi.2020.03.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/06/2020] [Accepted: 03/13/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Microbiologists are valued for their time-honed skills in image analysis, including identification of pathogens and inflammatory context in Gram stains, ova and parasite preparations, blood smears and histopathologic slides. They also must classify colony growth on a variety of agar plates for triage and assessment. Recent advances in image analysis, in particular application of artificial intelligence (AI), have the potential to automate these processes and support more timely and accurate diagnoses. OBJECTIVES To review current AI-based image analysis as applied to clinical microbiology; and to discuss future trends in the field. SOURCES Material sourced for this review included peer-reviewed literature annotated in the PubMed or Google Scholar databases and preprint articles from bioRxiv. Articles describing use of AI for analysis of images used in infectious disease diagnostics were reviewed. CONTENT We describe application of machine learning towards analysis of different types of microbiologic image data. Specifically, we outline progress in smear and plate interpretation as well as the potential for AI diagnostic applications in the clinical microbiology laboratory. IMPLICATIONS Combined with automation, we predict that AI algorithms will be used in the future to prescreen and preclassify image data, thereby increasing productivity and enabling more accurate diagnoses through collaboration between the AI and the microbiologist. Once developed, image-based AI analysis is inexpensive and amenable to local and remote diagnostic use.
Collapse
Affiliation(s)
- K P Smith
- Department of Pathology, Beth Israel Deaconess Medical Center, USA; Harvard Medical School, Boston, MA, USA
| | - J E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, USA; Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
39
|
Kurra C, Caldwell M, Taylor K, Nwachukwu C, Salar M, Kaye MB, Gopinath A, Altunkaynak C, Wasserman P. Candida Parapsilosis associated rice bodies in the extensor compartment of the wrist--an emerging finding. Radiol Case Rep 2019; 14:1539-1544. [PMID: 31709023 PMCID: PMC6831843 DOI: 10.1016/j.radcr.2019.09.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 11/25/2022] Open
Abstract
Candida parapsilosis has been considered an emerging pathogen with increasing incidence reported in the literature. As a normal commensal of human skin, it is likely that Candida species could gain access to soft tissues of the hand and wrist by direct inoculation, resulting in an infectious tenosynovitis. With the increased prevalence of intravenous drug use (IVDU), users are at increasing risk for musculoskeletal infections including soft tissue abscesses, cellulitis, tenosynovitis, and septic arthritis. Chronic tenosynovitis, with rice body formation in particular, is a comparatively rare musculoskeletal infection. Knowledge of this entity, the related pathogens, imaging findings, and the treatment plan is important not only to the treating clinician, but also to radiologists as the physiological and anatomic consequences can be detrimental to patient recovery.
Collapse
Affiliation(s)
- Chandana Kurra
- Department of Radiology, University of Florida, 655 West 8th Street, Jacksonville, FL 32209 USA
| | | | - Kristin Taylor
- Department of Radiology, University of Florida, 655 West 8th Street, Jacksonville, FL 32209 USA
| | - Chidi Nwachukwu
- Department of Radiology, University of Florida, 655 West 8th Street, Jacksonville, FL 32209 USA
| | - Mohammad Salar
- Department of Orthopedic Surgery, University of Florida, 655 West 8th Street, Jacksonville, FL 32209 USA
| | - Marc B Kaye
- Department of Orthopedic Surgery, University of Florida, 655 West 8th Street, Jacksonville, FL 32209 USA
| | - Arun Gopinath
- Department of Pathology, University of Florida, 655 West 8th Street, Jacksonville, FL 32209 USA
| | - Civan Altunkaynak
- Department of Pathology, University of Florida, 655 West 8th Street, Jacksonville, FL 32209 USA
| | - Paul Wasserman
- Department of Radiology, University of Florida, 655 West 8th Street, Jacksonville, FL 32209 USA
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Wolfe B, Kerr AR, Mejia A, Simmons HA, Czuprynski CJ, Golos TG. Sequelae of Fetal Infection in a Non-human Primate Model of Listeriosis. Front Microbiol 2019; 10:2021. [PMID: 31572310 PMCID: PMC6749046 DOI: 10.3389/fmicb.2019.02021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
Listeria monocytogenes (Lm) is a common environmental bacterium that thrives on vegetation and soil matter, but can infect humans if contaminated food products are ingested, resulting in severe disease in immunosuppressed populations, including pregnant women and newborns. To better understand how the unique immunological milieu of pregnancy increases susceptibility to infection, we study listeriosis in cynomolgus macaques, a non-human primate that closely resembles humans in placentation and in the physiology, and immunology of pregnancy. Non-human primates are naturally susceptible to Lm infection, and spontaneous abortions due to listeriosis are known to occur in outdoor macaque colonies, making them ideal models to understand the disease pathogenesis and host-pathogen relationship of listeriosis. We have previously shown that Lm infection in the first trimester has a high rate of miscarriage. This study expands on our previous findings by assessing how the quantity of Lm as well as stage of pregnancy at the time of exposure may influence disease susceptibility. In the current study we inoculated a cohort of macaques with a lower dose of Lm than our previous study and although this did not result in fetal demise, there was evidence of in utero inflammation and fetal distress. Animals that were reinfected with an equivalent or higher dose of the same strain of Lm resulted in approximately half of cases continuing to term and half ending in fetal demise. These cases had inconsistent bacterial colonization of the fetal compartment, suggesting that Lm does not need to directly infect the placenta to cause adverse pregnancy outcomes. Timed surgical collection of tissues following inoculation demonstrated that transmission from mother to fetus can occur as soon as 5 days post-inoculation. Lastly, third trimester inoculation resulted in pregnancy loss in 3 out of 4 macaques, accompanied by characteristic pathology and Lm colonization. Collectively, our studies demonstrate that common laboratory culture tests may not always recover Lm despite known maternal ingestion. Notably, we also find it is possible for maternal infection to resolve in some cases with no discernible adverse outcome; however, such cases had evidence of a sterile intrauterine inflammatory response, with unknown consequences for fetal development.
Collapse
Affiliation(s)
- Bryce Wolfe
- Department of Pathology and Laboratory Medicine, University of Wisconsin - Madison, Madison, WI, United States.,Wisconsin National Primate Research Center, University of Wisconsin - Madison, Madison, WI, United States
| | - Andrea R Kerr
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, United States
| | - Andres Mejia
- Wisconsin National Primate Research Center, University of Wisconsin - Madison, Madison, WI, United States
| | - Heather A Simmons
- Wisconsin National Primate Research Center, University of Wisconsin - Madison, Madison, WI, United States
| | - Charles J Czuprynski
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin -Madison, Madison, WI, United States
| | - Thaddeus G Golos
- Wisconsin National Primate Research Center, University of Wisconsin - Madison, Madison, WI, United States.,Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, United States.,Department of Obstetrics and Gynecology, University of Wisconsin - Madison, Madison, WI, United States
| |
Collapse
|
42
|
Kim D, Cho CH, Lee SB. Clinical Analysis of Bacterial Keratitis According to Culture Positivity. JOURNAL OF THE KOREAN OPHTHALMOLOGICAL SOCIETY 2019. [DOI: 10.3341/jkos.2019.60.11.1027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Doyeon Kim
- Department of Ophthalmology, Yeungnam University College of Medicine, Daegu, Korea
| | - Chan Ho Cho
- Department of Ophthalmology, Yeungnam University College of Medicine, Daegu, Korea
| | - Sang-Bumm Lee
- Department of Ophthalmology, Yeungnam University College of Medicine, Daegu, Korea
| |
Collapse
|
43
|
Yagupsky P. Microbiological Diagnosis of Skeletal System Infections in Children. Curr Pediatr Rev 2019; 15:154-163. [PMID: 30961502 DOI: 10.2174/1573396315666190408114653] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/23/2019] [Accepted: 03/26/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND If not timely diagnosed and adequately treated, skeletal system infections in children may result in severe and permanent disability. Prompt identification of the etiology of the disease and determination of its antibiotic susceptibility are crucial for the successful management of septic arthritis, osteomyelitis, and spondylodiscitis. However, the bacteriological diagnosis of these infections has been traditionally limited by the low yield of conventional cultures and, on average, one-third of cases of pediatric joint and bone infections remained unconfirmed. OBJECTIVE To review the medical literature to summarize the current approach diagnosing the pediatric skeletal system infections. METHODS The relevant publications for the last three decades were reviewed. RESULTS In recent years, the detection of skeletal system pathogens has been revolutionized by the use of improved laboratory methods, including seeding of synovial fluid and bone exudates into blood culture vials, and the development and implementation of sensitive nucleic acid amplification assays. These advances have resulted in the recognition of Kingella kingae as the predominant etiology of hematogenous infections of bones, joints, intervertebral discs and tendon sheaths in children aged 6-48 months, and reduced the fraction of culture-negative osteoarthritis. CONCLUSION As the exudate and tissue samples obtained from young children with skeletal system infections are frequently insufficient for a comprehensive laboratory workup, physicians should take in consideration the patient's age, predisposing medical conditions and possible exposure to zoonotic organisms, and use a judicious combination of Gram's stain, culture on blood culture vials, and molecular tests to maximize the microbiological diagnosis of these diseases.
Collapse
Affiliation(s)
- Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer-Sheva 84101, Israel
| |
Collapse
|
44
|
Abstract
BACKGROUND The diagnosis of pediatric septic arthritis (SA) can be challenging due to wide variability in the presentation of musculoskeletal infection. Synovial fluid Gram stain is routinely obtained and often used as an initial indicator of the presence or absence of pediatric SA. The purpose of this study was to examine the clinical utility of the Gram stain results from a joint aspiration in the diagnosis and management of pediatric SA. METHODS All patients with suspected SA who underwent arthrocentesis and subsequent surgical irrigation and debridement at an urban tertiary care children's hospital between January 2007 and October 2016 were identified. Results of the synovial fluid Gram stain, as well as synovial cell count/differential and serum markers, were evaluated. RESULTS A total of 302 patients that underwent incision and drainage for suspected SA were identified. In total, 102 patients (34%) had positive synovial fluid cultures and 47 patients (16%) had a microorganism detected on Gram stain. Gram stain sensitivity and specificity for the detection of SA were 0.40 and 0.97, respectively. This yielded a number needed to misdiagnose of 4.5 (ie, every fifth patient was misdiagnosed by Gram stain). For gram-negative organisms, the sensitivity dropped further to 0.13, with only 2/16 gram-negative organisms identified on Gram stain. Stepwise regression showed that age, serum white blood cell, and absolute neutrophil count were significant independent predictors for having a true positive Gram stain result. Elevated synovial white blood cell count was a significant predictor of having an accurate (culture matching the Gram stain) result. CONCLUSIONS The Gram stain result is a poor screening tool for the detection of SA and is particularly ineffective for the detection of gram-negative organisms. The clinical relevance of the Gram stain and cost-effectiveness of this test performed on every joint aspiration sent for culture requires additional evaluation. Patients with gram-negative SA may be at high risk for inadequate coverage with empiric antibiotics due to poor detection of gram-negative organisms on initial Gram stain. LEVEL OF EVIDENCE Level III-case-control study.
Collapse
|
45
|
Samuel LP. Harmonization of microbiology processes and standards: work in progress. ACTA ACUST UNITED AC 2018; 56:1624-1628. [DOI: 10.1515/cclm-2017-1074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 05/03/2018] [Indexed: 11/15/2022]
Abstract
Abstract
Clinical microbiology is a highly challenging technical discipline, which makes it difficult to harmonize processes and protocols. In addition, the lack of scientific consensus on some diagnostic algorithms and the need to address the diverse needs of different patient populations contribute to the lack of interlaboratory consistency. Laboratories utilize a number of measures and metrics, but the lack of standardized approaches and data collection means that they cannot effectively evaluate their performance against their peers. Coordinated efforts are required to develop tools that can be used across laboratories regardless of size or complexity.
Collapse
Affiliation(s)
- Linoj P. Samuel
- Division Head, Clinical Microbiology, Henry Ford Health System , Detroit, MI 48202 , USA
| |
Collapse
|
46
|
Abstract
Appropriate antimicrobial therapy is essential to ensuring positive patient outcomes. Inappropriate or suboptimal utilization of antibiotics can lead to increased length of stay, multidrug-resistant infections, and mortality. Critically ill intensive care patients, particularly those with severe sepsis and septic shock, are at risk of antibiotic failure and secondary infections associated with incorrect antibiotic use. Through the initiation of active empiric antibiotic therapy based upon local susceptibilities, daily evaluation of signs and symptoms of infection and narrowing of antibiotic therapy when feasible, providers can streamline the treatment of common intensive care unit (ICU) infections. Optimizing antibiotic dosing through prolonged infusions can be beneficial in intensive care populations with altered pharmacokinetics. Antimicrobial stewardship teams can assist ICU providers in managing and implementing these tactics. This review will discuss the current literature on antibiotic use in the ICU applying antimicrobial stewardship strategies. Based upon the most recent evidence, ICUs would benefit from employing empiric guidelines for antibiotic use, collecting appropriate specimens and implementing molecular diagnostics, optimizing the dosing of antibiotics, and reducing the duration of total therapy. These strategies for antibiotic use have the potential to enhance patient care while preventing adverse outcomes.
Collapse
Affiliation(s)
- Maureen Campion
- 1 Division of Infectious Disease, Department of Medicine, UMass Memorial Medical Center, Worcester, MA, USA
| | - Gail Scully
- 1 Division of Infectious Disease, Department of Medicine, UMass Memorial Medical Center, Worcester, MA, USA
| |
Collapse
|
47
|
Smith KP, Kang AD, Kirby JE. Automated Interpretation of Blood Culture Gram Stains by Use of a Deep Convolutional Neural Network. J Clin Microbiol 2018; 56:e01521-17. [PMID: 29187563 PMCID: PMC5824030 DOI: 10.1128/jcm.01521-17] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/09/2017] [Indexed: 02/04/2023] Open
Abstract
Microscopic interpretation of stained smears is one of the most operator-dependent and time-intensive activities in the clinical microbiology laboratory. Here, we investigated application of an automated image acquisition and convolutional neural network (CNN)-based approach for automated Gram stain classification. Using an automated microscopy platform, uncoverslipped slides were scanned with a 40× dry objective, generating images of sufficient resolution for interpretation. We collected 25,488 images from positive blood culture Gram stains prepared during routine clinical workup. These images were used to generate 100,213 crops containing Gram-positive cocci in clusters, Gram-positive cocci in chains/pairs, Gram-negative rods, or background (no cells). These categories were targeted for proof-of-concept development as they are associated with the majority of bloodstream infections. Our CNN model achieved a classification accuracy of 94.9% on a test set of image crops. Receiver operating characteristic (ROC) curve analysis indicated a robust ability to differentiate between categories with an area under the curve of >0.98 for each. After training and validation, we applied the classification algorithm to new images collected from 189 whole slides without human intervention. Sensitivity and specificity were 98.4% and 75.0% for Gram-positive cocci in chains and pairs, 93.2% and 97.2% for Gram-positive cocci in clusters, and 96.3% and 98.1% for Gram-negative rods. Taken together, our data support a proof of concept for a fully automated classification methodology for blood-culture Gram stains. Importantly, the algorithm was highly adept at identifying image crops with organisms and could be used to present prescreened, classified crops to technologists to accelerate smear review. This concept could potentially be extended to all Gram stain interpretive activities in the clinical laboratory.
Collapse
Affiliation(s)
- Kenneth P Smith
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Anthony D Kang
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- United States Army Medical Department Center and School, Fort Sam Houston, Texas, USA
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
48
|
Abstract
Our mostly manual, agar-based clinical microbiology laboratory is slowly but steadily being redefined by automation and innovation. Ironically, the oldest test, the Gram stain test, is still manually read and interpreted by trained personnel. In a proof-of-concept study, Smith et al. (J. Clin. Microbiol. 56:e01521-17, 2018, https://doi.org/10.1128/JCM.01521-17) used computer imaging with a deep convolutional neural network to examine and interpret Gram-stained slides from positive blood culture bottles. In light of the shortage of medical technologists/microbiologists and the need for results from positive blood culture bottles 24/7, this paper paves the way for the next innovations for the clinical microbiology laboratory of the future.
Collapse
|
49
|
How Reliable Is Microscopy and Culture for the Diagnosis of Gonorrhea? An 11-Year Experience from INDIA. Sex Transm Dis 2017; 44:111-113. [PMID: 28079747 DOI: 10.1097/olq.0000000000000550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Positivity of microscopy and culture was greater (P < 0.0001) in men with urethral discharge syndrome (65.8%) than in women with vaginal/cervical discharge (0.5%), indicating that basic diagnostic tests may not be cost-effective for diagnosis of vaginal/cervical discharge syndrome. Microscopy when compared with culture showed sensitivity, specificity, positive predictive value and negative predictive value of 95.4%, 77.6%, 84.6%, and 95.3%, in men, whereas in women, it was 77.8%, 99.9%, 92.1%, and 99.9%, respectively.
Collapse
|
50
|
Scherz V, Durussel C, Greub G. Internal quality assurance in diagnostic microbiology: A simple approach for insightful data. PLoS One 2017; 12:e0187263. [PMID: 29135992 PMCID: PMC5685576 DOI: 10.1371/journal.pone.0187263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/17/2017] [Indexed: 11/18/2022] Open
Abstract
Given the importance of microbiology results on patient care, high quality standards are expected. Internal quality assurance (IQA) could mitigate the limitations of internal quality control, competency assessment and external quality assurance, adding a longitudinal insight, including pre- and post-analytical steps. Here, we implemented an IQA program in our clinical microbiology facilities with blind resubmission of routine samples during 22 months. One-hundred-and-twenty-one out of 123 (98.4%) serological analyses and 112 out of 122 (91.8%) molecular analyses were concordant. Among the discordances in molecular biology analyses, 6 results were low positive samples that turned out negative, likely due to stochastic repartition of nucleic acids. Moreover, one identified retranscription error led us to implement automated results transmission from the Applied Biosystems instruments to the laboratory information system (LIS). Regarding Gram stain microscopy, 560 out of 745 (75.2%) of compared parameters were concordant. As many as 67 out of 84 (79.8%) pairs of culture results were similar, including 16 sterile pairs, 27 having identical identification or description and semi-quantification and 24 only showing variations in semi-quantification with identical description or identification of colonies. Seventeen pairs had diverging identification or description of colonies. Culture was twice only done for one member of the pairs. Regarding antibiotic susceptibility testing, a major discrepancy was observed in 5 out of 48 results (10.4%). In conclusion, serological tests were highly reproducible. Molecular diagnosis also revealed to be robust except when the amounts of nucleic acids present in the sample were close to the limits of detection. Conventional microbiology was less robust with major discrepancies reaching 39.5% of the samples for microscopy. Similarly, culture and antibiotic susceptibility testing were prone to discrepancies. This work was ground for reconsidering multiples aspects of our practices and demonstrates the importance of IQA to complete the other quality management procedures.
Collapse
Affiliation(s)
- Valentin Scherz
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Christian Durussel
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
- * E-mail:
| |
Collapse
|