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Tang Z, Wang H, Liu Y, Wang C, Li X, Yang Q. Current status and new experimental diagnostic methods of invasive fungal infections after hematopoietic stem cell transplantation. Arch Microbiol 2024; 206:237. [PMID: 38678508 DOI: 10.1007/s00203-024-03905-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/19/2024] [Indexed: 05/01/2024]
Abstract
Invasive fungal infections (IFIs) are common and life-threatening complications in post-hematopoietic stem cell transplantation (post-HSCT) recipients, Severe IFIs can lead to systemic infection and organ damage, which results in high mortality in HSCT recipients. With the development of the field of fungal infection diagnosis, more and more advanced non-culture diagnostic tools have been developed, such as glip biosensors, metagenomic next-generation sequencing, Magnetic Nanoparticles and Identified Using SERS via AgNPs+ , and artificial intelligence-assisted diagnosis. The advanced diagnostic approaches contribute to the success of HSCT and improve the overall survival of post-HSCT leukemia patients by supporting therapeutical decisions. This review provides an overview of the characteristics of two high-incidence IFIs in post-HSCT recipients and discusses some of the recently developed IFI detection technologies. Additionally, it explores the potential application of cationic conjugated polymer fluorescence resonance energy transfer (CCP-FRET) technology for IFI detection. The aim is to offer insights into selecting appropriate IFI detection methods and gaining an understanding of novel fungal diagnostic approaches in laboratory settings.
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Affiliation(s)
- Zhenhua Tang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - HaiTao Wang
- Department of Hematology, The Fifth Medical Center of Chinese, PLA General Hospital, Beijing, 100071, China
| | - Yuankai Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Chen Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xinye Li
- Lanzhou Petrochemical General Hospital (The Fourth Affiliated Hospital of Gansu University of Chinese Medicine), Gansu, 730060, China.
| | - Qiong Yang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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Azim A, Ahmed A. Diagnosis and management of invasive fungal diseases in non-neutropenic ICU patients, with focus on candidiasis and aspergillosis: a comprehensive review. Front Cell Infect Microbiol 2024; 14:1256158. [PMID: 38505289 PMCID: PMC10948617 DOI: 10.3389/fcimb.2024.1256158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
Invasive fungal diseases pose a significant threat to non-neutropenic ICU patients, with Candida and Aspergillus infections being the most common. However, diagnosing these infections in the ICU population remains challenging due to overlapping clinical features, poor sensitivity of blood cultures, and invasive sampling requirements. The classical host criteria for defining invasive fungal disease do not fully apply to ICU patients, leading to missed or delayed diagnoses. Recent advancements have improved our understanding of invasive fungal diseases, leading to revised definitions and diagnostic criteria. However, the diagnostic difficulties in ICU patients remain unresolved, highlighting the need for further research and evidence generation. Invasive candidiasis is the most prevalent form of invasive fungal disease in non-neutropenic ICU patients, presenting as candidemia and deep-seated candidiasis. Diagnosis relies on positive blood cultures or histopathology, while non-culture-based techniques such as beta-D-glucan assay and PCR-based tests show promise. Invasive aspergillosis predominantly manifests as invasive pulmonary aspergillosis in ICU patients, often associated with comorbidities and respiratory deterioration in viral pneumonia. Diagnosis remains challenging due to poor sensitivity of blood cultures and difficulties in performing lung biopsies. Various diagnostic criteria have been proposed, including mycological evidence, clinical/radiological factors and expanded list of host factors. Non-culture-based techniques such as galactomannan assay and PCR-based tests can aid in diagnosis. Antifungal management involves tailored therapy based on guidelines and individual patient factors. The complexity of diagnosing and managing invasive fungal diseases in ICU patients underscore the importance of ongoing research and the need for updated diagnostic criteria and treatment approaches. Invasive fungal disease, Invasive fungal infection, Invasive candidiasis, Invasive aspergillosis, Antifungal drugs.
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Affiliation(s)
- Afzal Azim
- Department of Critical Care Medicine, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGI), Lucknow, India
| | - Armin Ahmed
- Department of Critical Care Medicine, King George’s Medical University, Lucknow, India
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Soriano-Martín A, Muñoz P, García-Rodríguez J, Cantón R, Vena A, Bassetti M, Bouza E. Unresolved issues in the diagnosis of catheter related candidemia: A position paper. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2024; 37:1-16. [PMID: 37953593 PMCID: PMC10874659 DOI: 10.37201/req/112.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 11/14/2023]
Abstract
The incidence and recent trends of candidemia and the contribution of the COVID-19 pandemic to its evolution are not well documented. The catheter is a major focus of Candida spp. infections, but the methods used to confirm the origin of candidemia are still based on the data generated for bacterial infection. The presence of Candida spp. on the tip of a removed catheter is the gold standard for confirmation but it is not always possible to remove it. Conservative methods, without catheter removal, have not been specifically studied for microorganisms whose times of growth are different from those of bacteria and therefore these results are not applicable to candidemia. The different Candida species do not have a particular tropism for catheter colonization and fungal biomarkers have not yet been able to contribute to the determination of the origin of candidemia. Techniques such Candida T2 Magnetic Resonance (T2MR) has not yet been applied for this purpose. Finally, there is not yet a consensus of how to proceed when Candida spp. is isolated from an extracted catheter and blood cultures obtained from simultaneous peripheral veins are negative. In this lack of firm data, a group of experts has formulated a series of questions trying to answer them based on the literature, indicating the current deficiencies and offering their own opinion. All authors agree with the conclusions of the manuscript and offer it as a position and discussion paper.
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Affiliation(s)
- A Soriano-Martín
- Ana Soriano Martín, Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón. Calle Doctor Esquerdo 46, 28007 Madrid, Spain.
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Jiang Y, Wang J, Zhang H, Tian X, Liang Z, Xu X, Bao J, Chen B. Biological Activity and Sterilization Mechanism of Marine Fungi-derived Aromatic Butenolide Asperbutenolide A Against Staphylococcus aureus. Chem Biodivers 2024; 21:e202301826. [PMID: 38155523 DOI: 10.1002/cbdv.202301826] [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: 11/15/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 12/30/2023]
Abstract
Marine fungi represent a huge untapped resource of natural products. The bio-activity of a new asperbutenolide A from marine fungus Aspergillus terreus was not well known. In the present study, the minimum inhibitory concentration (MIC) and RNA-Sequencing were used to analyze the bio-activity and sterilization mechanism of asperbutenolide A against clinical pathogenic microbes. The results showed that the MICs of asperbutenolide A against methicillin-resistant Staphylococcus aureus (MRSA) were 4.0-8.0 μg/mL. The asperbutenolide A present poor bio-activity against with candida. The sterilization mechanism of asperbutenolide A against MRSA showed that there were 1426 differentially-expressed genes (DEGs) between the groups of MRSA treated with asperbutenolide A and negative control. Gene Ontology (GO) classification analysis indicated that the DEGs were mainly involved in cellular process, metabolic process, cellular anatomical entity, binding, catalytic activity, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) classification analysis showed that these DEGs were mainly enriched in amino acid metabolism, carbohydrate metabolism, membrane transport, etc. Moreover, qRT-PCR showed similar trends in the expressions of argF, ureA, glmS and opuCA with the RNA-Sequencing. These results indicated that asperbutenolide A was with ideal bio-activity against with MRSA and could be as a new antibacterial agent.
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Affiliation(s)
- Yufeng Jiang
- Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Jinan, China
- Medical Laboratory, Jining No.1 People's Hospital, Jining, Shandong, China
- Key Laboratory of Jining high-throughput gene sequencing, Jining No.1 People's Hospital, Jining, Shandong, China
- Key Laboratory of Jining Prenatal Monitoring and Genetic Disease Research, Jining No.1 People's Hospital, Jining, Shandong, China
| | - Jiule Wang
- Central Laboratory, Jining No.1 People's Hospital, Jining, Shandong, China
- Jining Key Laboratory for the Intelligent Diagnosis of Emerging Infectious Diseases, Jining No.1 People's Hospital, Jining, Shandong, China
| | - Hua Zhang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xuelu Tian
- Department of Laboratory, Jining Dermatosis Prevention and Treatment Hospital, Jining, Shandong, China
| | - Zhiqiang Liang
- Medical Laboratory, Jining No.1 People's Hospital, Jining, Shandong, China
- Key Laboratory of Jining high-throughput gene sequencing, Jining No.1 People's Hospital, Jining, Shandong, China
- Key Laboratory of Jining Prenatal Monitoring and Genetic Disease Research, Jining No.1 People's Hospital, Jining, Shandong, China
| | - Xinli Xu
- Medical Laboratory, Jining No.1 People's Hospital, Jining, Shandong, China
- Key Laboratory of Jining high-throughput gene sequencing, Jining No.1 People's Hospital, Jining, Shandong, China
- Key Laboratory of Jining Prenatal Monitoring and Genetic Disease Research, Jining No.1 People's Hospital, Jining, Shandong, China
| | - Jie Bao
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Biao Chen
- Central Laboratory, Jining No.1 People's Hospital, Jining, Shandong, China
- Jining Key Laboratory for the Intelligent Diagnosis of Emerging Infectious Diseases, Jining No.1 People's Hospital, Jining, Shandong, China
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Bian W, Xie Y, Shang Y, Zhao L, Yang Z, Ma X, He Y, Yu W, Xi W, Yang D, Wang F, Chen Y, Gong P, Gao Z. Relationship between clinical features and droplet digital PCR copy number in non-HIV patients with pneumocystis pneumonia. BMC Infect Dis 2023; 23:833. [PMID: 38012564 PMCID: PMC10683233 DOI: 10.1186/s12879-023-08580-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 09/04/2023] [Indexed: 11/29/2023] Open
Abstract
OBJECTIVE Droplet digital PCR (ddPCR) is a novel assay to detect pneumocystis jjrovecii (Pj) which has been defined to be more sensitive than qPCR in recent studies. We aimed to explore whether clinical features of pneumocystis pneumonia (PCP) were associated with ddPCR copy numbers of Pj. METHODS A total of 48 PCP patients were retrospectively included. Pj detection was implemented by ddPCR assay within 4 h. Bronchoalveolar fluid (BALF) samples were collected from 48 patients with molecular diagnosis as PCP via metagenomic next generation sequencing (mNGS) or quantitative PCR detection. Univariate and multivariate logistic regression were performed to screen out possible indicators for the severity of PCP. The patients were divided into two groups according to ddPCR copy numbers, and their clinical features were further analyzed. RESULTS Pj loading was a pro rata increase with serum (1,3)-beta-D glucan, D-dimmer, neutrophil percentage, procalcitonin and BALF polymorphonuclear leucocyte percentage, while negative correlation with albumin, PaO2/FiO2, BALF cell count, and BALF lymphocyte percentage. D-dimmer and ddPCR copy number of Pj were independent indicators for moderate/severe PCP patients with PaO2/FiO2 lower than 300. We made a ROC analysis of ddPCR copy number of Pj for PaO2/FiO2 index and grouped the patients according to the cut-off value (2.75). The high copy numbers group was characterized by higher level of inflammatory markers. Compared to low copy number group, there was lower level of the total cell count while higher level of polymorphonuclear leucocyte percentage in BALF in the high copy numbers group. Different from patients with high copy numbers, those with high copy numbers had a tendency to develop more severe complications and required advanced respiratory support. CONCLUSION The scenarios of patients infected with high ddPCR copy numbers of Pj showed more adverse clinical conditions. Pj loading could reflect the severity of PCP to some extent.
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Affiliation(s)
- Wenjie Bian
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Yu Xie
- Department of Respiratory Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Shang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Zhengwu Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Wen Xi
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Donghong Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Fang Wang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Yanwen Chen
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China
| | - Pihua Gong
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China.
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, No.11, Xizhimen South Street, Beijing, China.
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Jenks JD, White PL, Kidd SE, Goshia T, Fraley SI, Hoenigl M, Thompson GR. An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections. Expert Rev Mol Diagn 2023; 23:1135-1152. [PMID: 37801397 PMCID: PMC10842420 DOI: 10.1080/14737159.2023.2267977] [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: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens. AREAS COVERED We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS). EXPERT OPINION PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.
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Affiliation(s)
- Jeffrey D Jenks
- Durham County Department of Public Health, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - P Lewis White
- Public Health Wales Microbiology Cardiff, UHW, United Kingdom and Centre for trials research/Division of Infection/Immunity, Cardiff University, Cardiff, UK
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, Australia
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - George R Thompson
- University of California Davis Center for Valley Fever, Sacramento, CA, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, CA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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Yang J, Xu H, Ke Z, Kan N, Zheng E, Qiu Y, Huang M. Absolute quantification of viable Vibrio cholerae in seawater samples using multiplex droplet digital PCR combined with propidium monoazide. Front Microbiol 2023; 14:1149981. [PMID: 37362935 PMCID: PMC10288211 DOI: 10.3389/fmicb.2023.1149981] [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] [Received: 01/24/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Toxigenic Vibrio cholerae serogroup O1 and O139 are the pathogens responsible for the global cholera epidemic. V. cholerae can settle in the water and spread via the fecal-oral route. Rapid and accurate monitoring of live V. cholerae in environmental water has become an important strategy to prevent and control cholera transmission. Conventional plate counting is widely used to detect viable bacteria but requires time and effort. Methods This study aims to develop a new assay that combines triplex droplet digital PCR (ddPCR) with propidium monoazide (PMA) treatment for quantitatively detecting live V. cholerae O1/O139 and cholera enterotoxin. Specific primers and probes were designed according to the conserved regions of gene rfb O1, rfb O139, and ctxA. The amplification procedures and PMA treatment conditions were optimized. The specificity, sensitivity, and ability of PMA-ddPCR to detect viable bacteria-derived DNA were evaluated in simulated seawater samples. Results and Discussion The results revealed that the optimal primer concentrations of rfb O1, rfb O139, and ctxA were 1 μM, while the concentrations of the three probes were 0.25, 0.25, and 0.4 μM, respectively. The best annealing temperature was 58°C to obtain the most accurate results. The optimal strategy for distinguishing dead and live bacteria from PMA treatment was incubation at the concentration of 20 μM for 15 min, followed by exposure to a 650-W halogen lamp for 20 min. In pure culture solutions, the limit of detection (LODs) of V. cholerae O1 and O139, and ctxA were 127.91, 120.23 CFU/mL, and 1.5 copies/reaction in PMA-triplex ddPCR, respectively, while the LODs of the three targets were 150.66, 147.57 CFU/mL, and 2 copies/reaction in seawater samples. The PMA-ddPCR sensitivity was about 10 times higher than that of PMA-qPCR. When detecting spiked seawater samples with live bacterial concentrations of 1.53 × 102 and 1.53 × 105 CFU/mL, the assay presented a higher sensitivity (100%, 16/16) than qPCR (50.00%, 8/16) and a perfect specificity (100%, 9/9). These results indicate that the developed PMA-triplex ddPCR is superior to the qPCR regarding sensitivity and specificity and can be used to rapidly detect viable toxigenic V. cholerae O1 and O139 in suspicious seawater samples.
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Affiliation(s)
- Jinsong Yang
- Fujian Center for Disease Control and Prevention, Fuzhou, China
- Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Haibin Xu
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Zili Ke
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Naipeng Kan
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Enhui Zheng
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Yufeng Qiu
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Mengying Huang
- Fujian Center for Disease Control and Prevention, Fuzhou, China
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Xu D, Zhang W, Li H, Li N, Lin JM. Advances in droplet digital polymerase chain reaction on microfluidic chips. LAB ON A CHIP 2023; 23:1258-1278. [PMID: 36752545 DOI: 10.1039/d2lc00814a] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The PCR technique has been known to the general public since the pandemic outbreak of COVID-19. This technique has progressed through three stages: from simple PCR to real-time fluorescence PCR to digital PCR. Among them, the microfluidic-based droplet digital PCR technique has attracted much attention and has been widely applied due to its advantages of high throughput, high sensitivity, low reagent consumption, low cross-contamination, and absolute quantification ability. In this review, we introduce various designs of microfluidic-based ddPCR developed within the last decade. The microfluidic-based droplet generation methods, thermal cycle strategies, and signal counting approaches are described, and the applications in the fields of single-cell analysis, disease diagnosis, and pathogen detection are introduced. Further, the challenges and prospects of microfluidic-based ddPCR are discussed. We hope that this review can contribute to the further development of the microfluidic-based ddPCR technique.
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Affiliation(s)
- Danfeng Xu
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.
| | - Weifei Zhang
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.
| | - Hongmei Li
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.
| | - Nan Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), China.
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), China.
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Koc Ö, Kessler HH, Hoenigl M, Wagener J, Suerbaum S, Schubert S, Dichtl K. Performance of Multiplex PCR and β-1,3-D-Glucan Testing for the Diagnosis of Candidemia. J Fungi (Basel) 2022; 8:jof8090972. [PMID: 36135696 PMCID: PMC9504845 DOI: 10.3390/jof8090972] [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: 08/26/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
Bloodstream infections caused by Candida yeasts (candidemia) are associated with high morbidity and mortality. Diagnosis remains challenging, with the current gold standard—isolation from blood culture (BC)—being limited by low sensitivity and long turnaround time. This study evaluated the performance of two nonculture methods: PCR and β-1,3-D-glucan (BDG) testing. The sera of 103 patients with BC-proven candidemia and of 46 controls were analyzed with the Fungiplex Candida Real-Time PCR and the Wako β-Glucan Test. The BDG assay demonstrated higher sensitivity than the multiplex PCR (58% vs. 33%). This was particularly evident in ICU patients (60% vs. 28%) and in C. albicans candidemia (57% vs. 37%). The earlier prior to BC sampling the sera were obtained, the more the PCR sensitivity decreased (46% to 18% in the periods of 0−2 and 3−5 days before BC, respectively), while BDG testing was independent of the sampling date. No positive PCR results were obtained in sera sampled more than five days before BC. Specificities were 89% for BDG and 93% for PCR testing. In conclusion, BDG testing demonstrated several advantages over PCR testing for the diagnosis of candidemia, including higher sensitivity and earlier diagnosis. However, BC remains essential, as BDG does not allow for species differentiation.
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Affiliation(s)
- Özlem Koc
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
| | - Harald H. Kessler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Johannes Wagener
- Microbiology Department, St. James’s Hospital, D08 RX0X Dublin, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, The University of Dublin, St. James’s Hospital Campus, D08 RX0X Dublin, Ireland
| | - Sebastian Suerbaum
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
| | - Sören Schubert
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
- Correspondence: (S.S.); (K.D.)
| | - Karl Dichtl
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
- Correspondence: (S.S.); (K.D.)
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Merino I, de la Fuente A, Domínguez-Gil M, Eiros JM, Tedim AP, Bermejo-Martín JF. Digital PCR applications for the diagnosis and management of infection in critical care medicine. Crit Care 2022; 26:63. [PMID: 35313934 PMCID: PMC8935253 DOI: 10.1186/s13054-022-03948-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10–25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.
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Affiliation(s)
- Irene Merino
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José María Eiros
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain. .,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.
| | - Jesús F Bermejo-Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
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