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Assiri AM, Alshahrani AM, Sakkijha H, AlGeer A, Zeitouni M, AlGohary M, Dhaini L, Verma R, Singh H. Transforming respiratory tract infection diagnosis in the kingdom of saudi arabia through point-of-care testing: A white paper for policy makers. Diagn Microbiol Infect Dis 2024; 110:116530. [PMID: 39321629 DOI: 10.1016/j.diagmicrobio.2024.116530] [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: 11/30/2023] [Revised: 09/03/2024] [Accepted: 09/05/2024] [Indexed: 09/27/2024]
Abstract
With the evident increased prevalence of respiratory tract infections (RTIs) such as Respiratory Syncytial Virus (RSV), influenza, Group A Streptococcus (GAS), and COVID-19, the conventional diagnostic methods are considered sub-optimal in providing timely management to patients in the Kingdom of Saudi Arabia (KSA). Gaps in current diagnostics are magnified by the Kingdom's unique demographic composition, comprising 11.9 million foreign workers, and the annual influx of over 10 million pilgrims. Current gaps in timely diagnosis leads to delays in treatment, misuse of antibiotics, and protracted hospital stays, subsequently compromising patient care, and escalating healthcare costs. KSA healthcare stakeholders suggest that the integration of rapid molecular Point-of-Care Testing (POCT) into the Kingdom's healthcare infrastructure is an absolute necessity. This publication serves as an urgent call for action aimed at healthcare policymakers in Saudi Arabia, to review the existing diagnostic challenges and include rapid POCTs in the Saudi healthcare strategy for respiratory infections.
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Affiliation(s)
- Abdullah M Assiri
- Deputyship for Preventive Health, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | | | | | - Abdulrahman AlGeer
- Center for Infection Prevention and Control, Ministry of Defense Health Services, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Zeitouni
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | | | - Liliane Dhaini
- Consulting and Analytics, IQVIA, Dubai, United Arab Emirates
| | - Rashi Verma
- Consulting and Analytics, IQVIA, Bengaluru, India
| | - Harmandeep Singh
- Engagement Manager, Consulting and Analytics, IQVIA, Dubai, United Arab Emirates.
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Luo X, Wong YC, Chen X, Tan H, Wen W. In-vitro blood purification using tiny pinch holographic optical tweezers based on deep learning. Biosens Bioelectron 2024; 267:116781. [PMID: 39293268 DOI: 10.1016/j.bios.2024.116781] [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: 06/14/2024] [Revised: 09/05/2024] [Accepted: 09/11/2024] [Indexed: 09/20/2024]
Abstract
In-vitro blood purification is essential to a wide range of medical treatments, requiring fine-grained analysis and precise separation of blood components. Despite existing methods that can extract specific components from blood by size or by magnetism, there is not yet a general approach to efficiently filter blood components on demand. In this work, we introduce the first programmable non-contact blood purification system for accurate blood component detection and extraction. To accurately identify different cells and artificial particles in the blood, we collected and annotated a new blood component object detection dataset and trained a collection of deep-learning-based object detectors upon it. To precisely capture and extract desired blood components, we fabricated a microfluidic chip and set up a customized holographic optical tweezer to trap and move cells/particles in the blood. Empirically, we demonstrate that our proposed system can perform real-time blood fractionation with high precision reaching up to 96.89%, as well as high efficiency. Its scalability and flexibility open new research directions in blood treatment.
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Affiliation(s)
- Xiao Luo
- Department of Physics, The Hong Kong University of Science and Technology, China
| | - Yu Ching Wong
- Department of Physics, The Hong Kong University of Science and Technology, China
| | - Xiangyu Chen
- Department of Computer Science, Cornell University, Ithaca, 14850, New York, United States
| | - Handong Tan
- Department of Individualized Interdisciplinary Program (Advanced Materials), The Hong Kong University of Science and Technology, China
| | - Weijia Wen
- Department of Physics, The Hong Kong University of Science and Technology, China; Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, 511400, China.
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Wang W, Chauhan V, Luo Y, Sharma S, Li C, Chen H. Comparing NGS-Based identification of bloodstream infections to traditional culture methods for enhanced ICU care: a comprehensive study. Front Cell Infect Microbiol 2024; 14:1454549. [PMID: 39328359 PMCID: PMC11424606 DOI: 10.3389/fcimb.2024.1454549] [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: 06/25/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
Background Accurate identification of infectious diseases using molecular techniques, such as PCR and NGS, is well-established. This study aims to assess the utility of Bactfast and Fungifast in diagnosing bloodstream infections in ICU settings, comparing them against traditional culture methods. The objectives include evaluating sensitivity and specificity and identifying a wide range of pathogens, including non-culturable species. Methods We collected 500 non-duplicate blood samples from ICU patients between January 2023 and December 2023. Specimens underwent traditional culture, MALDI-TOF, VITEK®2 compact system, and NGS-based Bactfast and Fungifast analyses. Results Out of the 500 samples, 26.8% (n=134) showed bacterial growth via traditional culture methods, while 4.8% (n=24) were positive for fungal growth. MALDI-TOF and VITEK®2 compact system yielded comparable results, identifying 26.4% (n=132) of specimens with bacterial growth. NGS-based Bactfast detected bacterial presence in 38.2% (n=191) of samples, including non-culturable bacteria missed by traditional methods. However, NGS-based Fungifast showed concordant fungal detection rates with culture methods. Among identified pathogens by culture method included Klebsiella pneumoniae 20.89% (n=28), Enterococcus faecalis 18.65% (n=25), Escherichia coli 15.67% (n=21), Pseudomonas aeruginosa 12.68% (n=17), Acinetobacter baumannii 10.44% (n=14), various Streptococcus species 7.46% (n=10), Mycobacterium tuberculosis 6.71% (n=9), Mycobacterium abscessus 4.47% (n=6), and Salmonella spp 2.98% (n=4). Non-culture-based NGS identified additional (n=33) pathogens, including Klebsiella pneumoniae 27.27% (n=9), Bacteroides fragilis 21.21% (n=7), Aerococcus viridans 15.15% (n=5), Elizabethkingia anopheles 12.12% (n=4), Aeromonas salmonicida 9% (n=3), Clostridium 9% (n=3), and Bacteroides vulgatus 6% (n=2). Candida albicans was reported in 5% (n=24) of samples by both methods. Conclusion NGS-based Bactfast and Fungifast demonstrate high sensitivity in identifying a wide array of bacterial and fungal pathogens in ICU patients, outperforming traditional culture methods in detecting non-culturable organisms. These molecular assays offer rapid and comprehensive diagnostic capabilities, potentially improving clinical outcomes through timely and accurate pathogen identification.
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Affiliation(s)
- Wei Wang
- Department of Endocrinology, Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Varun Chauhan
- Department of Microbiology, Post-Graduate Institute of Medical Education, Chandigarh, India
| | - Yutian Luo
- Department of Critical Care Medicine, Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Sonu Sharma
- Department of Pharmacy, DIT University, Mussoorie, Uttarakhand, India
| | - Chenxi Li
- Department of Critical Care Medicine, Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Huaisheng Chen
- Department of Critical Care Medicine, Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
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Çelik H, Caf BB, Çebi G. Innovative Biosensor Technologies in the Diagnosis of Urinary Tract Infections: A Comprehensive Literature Review. Indian J Microbiol 2024; 64:894-909. [PMID: 39282176 PMCID: PMC11399381 DOI: 10.1007/s12088-024-01359-7] [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: 03/28/2024] [Accepted: 07/21/2024] [Indexed: 09/18/2024] Open
Abstract
Urinary tract infections (UTIs) are prevalent bacterial infections globally, posing significant challenges due to their frequency, recurrence, and antibiotic resistance. This review delves into the advancements in UTI diagnostics over the past decade, particularly focusing on the development of biosensor technologies. The emergence of biosensors, including microfluidic, optical, electrochemical, immunosensors, and nanotechnology-based sensors, offers enhanced diagnostic accuracy, reduced healthcare costs. Despite these advancements, challenges such as technical limitations, the need for cross-population validation, and economic barriers for widespread implementation persist. The integration of artificial intelligence and smart devices in UTI diagnostics, highlighting the innovative approaches and their implications for patient care. The article envisions a future where multidisciplinary research and innovation overcome current obstacles, fully leveraging the potential of biosensor technologies to transform biosensor-based UTIs diagnosis. The ultimate goal is to achieve rapid, accurate, and non-invasive diagnostics, making healthcare more accessible and effective.
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Affiliation(s)
- Haluk Çelik
- Vivosens, Inc., 44 Tehama Street, Suite 409, San Francisco, CA 94105 USA
- Program of Stem Cell and Tissue Engineering, Institute of Graduate Education, Istinye University, 34010 Istanbul, Turkey
| | - Balım Bengisu Caf
- Vivosens, Inc., 44 Tehama Street, Suite 409, San Francisco, CA 94105 USA
- Program of Bioengineering, Graduate School of Science and Engineering, Yıldız Technical University, 34220 Esenler, Istanbul, Turkey
| | - Gizem Çebi
- Vivosens, Inc., 44 Tehama Street, Suite 409, San Francisco, CA 94105 USA
- Program of Chemical Engineering, Institute of Graduate School, Istanbul Technical University, ITU Ayazaga Kampusu, 34469 Maslak, Istanbul, Turkey
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Zhou YZ, Zhao YH, Fang WZ, Zhou YL, Chen CM, Gao ZH, Gu B, Guo XG, Duan CH. Establishment of droplet digital PCR for the detection of Neisseria gonorrhoeae. Diagn Microbiol Infect Dis 2024; 110:116351. [PMID: 38896891 DOI: 10.1016/j.diagmicrobio.2024.116351] [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: 12/15/2023] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Infection with Neisseria gonorrhoeae in adults usually leads to vaginitis and acute urethritis, and infection through the birth canal in newborns can lead to acute neonatal conjunctivitis. In view of certain factors such as a high missed detection rate of N.gonorrhoeae from staining microscopy method, the time-consuming nature and limited sensitivity of bacterial culture method, complicated and inability of absolute quantification from the ordinary PCR method. METHODS This study aims to establish a ddPCR system to detect N.gonorrhoeae in a absolute quantification, high specificity, high stability and accurate way. We selected the pgi1 gene as the target gene for the detection of N.gonorrhoeae. RESULTS The amplification efficiency was good in the ddPCR reaction, and the whole detection process could be completed in 94 min. It has a high sensitivity of up to 5.8 pg/μL. With a high specificity, no positive microdroplets were detected in 9 negative control pathogens in this experiment. In addition, ddPCR detection of N.gonorrhoeae has good repeatability, and the calculated CV is 4.2 %. CONCLUSIONS DdPCR detection technology has the characteristics of absolute quantification, high stability, high specificity and high accuracy of N.gonorrhoeae. It can promote the accuracy of the detecting of N.gonorrhoeae, providing a more scientific basis for clinical diagnosis and treatment.
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Affiliation(s)
- Yong-Zhuo Zhou
- Laboratory of Clinical, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Yanjiangxi Road, Guangzhou, Guangdong 510120, China; The Third Affiliated Hospital of Guangzhou Medical University, 510150, China
| | - Yun-Hu Zhao
- Department of Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Wei-Zhen Fang
- Laboratory of Clinical, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Yanjiangxi Road, Guangzhou, Guangdong 510120, China
| | - Yu-Lin Zhou
- The Third Affiliated Hospital of Guangzhou Medical University, 510150, China
| | - Chu-Mao Chen
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ze-Hang Gao
- Department of Clinical Laboratory Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China; School of Microelectronics, Shanghai University, Shanghai 200444, China
| | - Bing Gu
- Department of Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou 511436, China; Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, King Med School of Laboratory Medicine, Guangzhou Medical University, Guangzhou 510000, China
| | - Chao-Hui Duan
- Laboratory of Clinical, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Yanjiangxi Road, Guangzhou, Guangdong 510120, China.
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Wang K, Zhang T, Jiao T, Pang F, Dai F, Zhang Z, Li X, Chen Y, Zhang H, Chen Z, Song J. Mini-Program Enabled IoT Intelligent Molecular Diagnostic Device for Co-Detection and Spatiotemporal Mapping of Infectious Disease Pathogens. Anal Chem 2024; 96:13494-13503. [PMID: 39082644 DOI: 10.1021/acs.analchem.4c01762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Effective detection of infectious pathogens is crucial for disease prevention and control. We present an innovative Internet of Things (IoT) molecular diagnostic device featuring a WeChat mini-program for simultaneous detection and spatiotemporal mapping of respiratory pathogens. Leveraging social software's widespread usage, our device integrates seamlessly with WeChat, eliminating the need for app downloads and installations. Through a comprehensive detection system, including a user-friendly mini-program, a portable Point-of-Care fluorescence detector, and a diagnostic information management platform (EzDx Cloud), we demonstrate high sensitivity and specificity in detecting common respiratory viruses. Our SARS-CoV-2/H1N1 combo test kit, developed using a novel one-tube/one-step loop-mediated isothermal amplification-CRISPR method, shows remarkable performance. We address challenges in at-home nucleic acid testing by providing a cost-effective solution capable of detecting multiple pathogens simultaneously. Our system's versatility accommodates various assays operating at different temperatures and fluorescence intensities, offering significant advantages over traditional methods. Moreover, integration with EzDx Cloud facilitates disease monitoring and early warning systems, enhancing public health management. This study highlights the potential of our IoT molecular diagnostic device in revolutionizing infectious disease detection and control, with wide-ranging applications in both human and animal population.
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Affiliation(s)
- Kaizheng Wang
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Tao Zhang
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Tianjiao Jiao
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Feibiao Pang
- Hangzhou EzDx Technology Co., Ltd., Hangzhou, Zhejiang 311231, China
| | - Fengyi Dai
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhanfang Zhang
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Xiang Li
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Yao Chen
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Hongyu Zhang
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhiguang Chen
- Hangzhou EzDx Technology Co., Ltd., Hangzhou, Zhejiang 311231, China
| | - Jinzhao Song
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Lagopati N, Trachanas GP, Doukas H. Multi-Criteria Decision-Making Approach for Pre-Synthesis Selection of the Optimal Physicochemical Properties of TiO 2 Photocatalytic Nanoparticles for Biomedical and Environmental Applications. Molecules 2024; 29:3726. [PMID: 39202805 PMCID: PMC11357246 DOI: 10.3390/molecules29163726] [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: 06/30/2024] [Revised: 07/26/2024] [Accepted: 08/05/2024] [Indexed: 09/03/2024] Open
Abstract
Nanomaterials are widely used in several biomedical and environmental applications, due to their ideal properties. However, the synthetic and characterization procedure requires significant costs and has a negative environmental impact. Various methods are available in order to control the pre-synthesis design of the produced materials, predicting their behavior and minimizing the series of experiments. Multi-Criteria Decision-Making is proposed in this study in order to determine the best combination of the physicochemical parameters and to define the best alternative among fifteen different samples of nanostructured titanium dioxide. In particular, the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) method was applied to achieve a final ranking of the available alternatives by avoiding several of the trials that would follow testing the biological effect and the photocatalytic degradation of organic pollutants. Thus, this approach helps us to stay environmentally and ethically correct, saving time, money, and energy and also providing an optimization of the nanomaterials that are developed.
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Affiliation(s)
- Nefeli Lagopati
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Georgios P. Trachanas
- Decision Support Systems Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, 9, Iroon Polytechniou Str., 15773 Athens, Greece
| | - Haris Doukas
- Decision Support Systems Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, 9, Iroon Polytechniou Str., 15773 Athens, Greece
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Fung M, Patel N, DeVoe C, Ryan CN, McAdams S, Pamula M, Dwivedi A, Teraoka J, Smollin M, Sam S, Perkins B, Chin-Hong P. Utility of Serial Microbial Cell-free DNA Sequencing for Inpatient and Outpatient Pathogen Surveillance Among Allogeneic Hematopoietic Stem Cell Transplant Recipients. Open Forum Infect Dis 2024; 11:ofae330. [PMID: 39086465 PMCID: PMC11288372 DOI: 10.1093/ofid/ofae330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Indexed: 08/02/2024] Open
Abstract
Background This study characterizes the clinical utility and validity of the Karius test (KT), a plasma microbial cell-free DNA sequencing platform, as an infection surveillance tool among hematopoietic stem cell transplant (HCT) recipients, including monitoring for cytomegalovirus (CMV) and detecting infections relative to standard microbiologic testing (SMT). Methods A prospective, observational cohort study was performed among adult HCT recipients as inpatients and outpatients. Serial KTs were performed starting with 1 sample within 14 days before HCT, then weekly from 7-63 days posttransplant then monthly from 3-12 months post-HCT. Diagnostic performance of KT versus CMV polymerase chain reaction was evaluated with positive percent agreement and negative percent agreement. Infectious events (<12 months post-HCT) were extracted from medical records. For infectious events without positive SMT, 2 clinicians adjudicated KT results to determine if any detections were a probable cause. Difference in time from KT pathogen detection and infection onset was calculated. Results Of the 70 participants, mean age was 49.9 years. For CMV surveillance, positive percent agreement was 100% and negative percent agreement was 90%. There was strong correlation between CMV DNA and KT molecules per microliter (r 2: 0.84, P < .001). Of the 32 SMT+/KT+ infectious events, KT identified 26 earlier than SMT (median: -12 days) and an additional 5 diagnostically difficult pathogens identified by KT but not SMT. Conclusions KT detected CMV with high accuracy and correlation with quantitative polymerase chain reaction. Among infectious events, KT demonstrated additive clinical utility by detecting pathogens earlier than SMT and those not detected by SMT.
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Affiliation(s)
- Monica Fung
- Division of Infectious Diseases, University of California San Francisco, San Francisco, California, USA
| | - Nimish Patel
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Catherine DeVoe
- Division of Infectious Diseases, University of California San Francisco, San Francisco, California, USA
| | | | | | - Meenakshi Pamula
- Division of Infectious Diseases, University of California San Francisco, San Francisco, California, USA
| | - Aditya Dwivedi
- Division of Infectious Diseases, University of California San Francisco, San Francisco, California, USA
| | - Justin Teraoka
- Division of Infectious Diseases, University of California San Francisco, San Francisco, California, USA
| | | | - Srey Sam
- Karius, Inc., Redwood City, California, USA
| | | | - Peter Chin-Hong
- Division of Infectious Diseases, University of California San Francisco, San Francisco, California, USA
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Ullah MK, Dayam F, Ahmed A, Ahmad S, Munawar M, Jahangir S, Daftani MH, Ali Z, Kakar B, Farooq A, Ullah N. A Multidisciplinary Approach in the Management of Infectious Diarrhea in the Emergency Department. Cureus 2024; 16:e67788. [PMID: 39323695 PMCID: PMC11423180 DOI: 10.7759/cureus.67788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2024] [Indexed: 09/27/2024] Open
Abstract
Background Globally, infectious diarrhea poses a serious threat to public health, especially in emergency department (ED) settings where timely and efficient treatment is essential. The primary objective of this study was to explore and evaluate the efficacy of a multidisciplinary approach (MDA) in the management of infectious diarrhea within the ED setting. Methodology This prospective cohort study was conducted from January to December 2023 at the Lady Reading Hospital ED in Peshawar, Pakistan. Individuals 18 years of age or older with a confirmed diagnosis of infectious diarrhea were included in the study. Those who refused to participate or had non-infectious reasons were excluded from the study. Through successive sampling, 650 patients comprised the study sample. Using a standardized form, demographic information, clinical presentations, test results, treatment methods, and patient outcomes were collected. Descriptive statistics and logistic regression were used in statistical studies to assess treatment outcomes and complications. Results Of the 650 patients, the majority (203 patients, 31.23%) were between the ages of 30 and 39 years. The gender distribution was about equal (332 men, 51.08%; 318 females, 48.92%). Abdominal pain (383 patients, 58.92%) was the most common presenting complaint. In 310 instances, bacterial pathogens were found, 160 had viral infections, and 110 had parasitic infections. There were notable complications, such as sepsis (37 patients, 5.69%), although the response to treatment effectiveness was notably high (593 patients, 91.08%). Upon follow-up, 590 (90.77%) patients had symptom and sign resolution, while 80 (12.31%) patients had a low recurrence rate. Longer symptom duration (odds ratio (OR) = 1.45, 95% confidence interval (CI) 1.12-1.88, p = 0.005) and specific antibiotics (OR = 1.68, 95% CI = 1.25-2.25, p = 0.001) were found to improve treatment success using logistic regression, whereas the risks of complications increased with age (OR = 1.05, 95% CI = 1.01-1.09, p = 0.012) and severe dehydration (OR = 1.75, 95% CI = 1.32-2.31, p < 0.001). Conclusions The MDA to manage infectious diarrhea in the ED significantly improved patient outcomes and reduced complications.
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Affiliation(s)
| | - Fahad Dayam
- Internal Medicine, Mercy Teaching Hospital, Peshawar, PAK
| | - Aamir Ahmed
- Community Health Sciences, Peshawar Medical College, Peshawar, PAK
| | - Sohail Ahmad
- Internal Medicine, Lady Reading Hospital, Peshawar, PAK
| | | | - Sidra Jahangir
- General Practice, Burjeel Medical Hospital, Abu Dhabi, ARE
| | | | - Zeeshan Ali
- Medicine and Surgery, Liaquat College of Medicine and Dentistry, Karachi, PAK
| | | | - Ammara Farooq
- General Practice, Rahat Family Clinic, Peshawar, PAK
| | - Naqeeb Ullah
- Internal Medicine, Lady Reading Hospital, Peshawar, PAK
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Raichur A, Sinha N. Narrow spectrum nano-antibiotic for selective removal of ARB from contaminated water: New insights into stimuli response based on cellular attachment, lysis, and excretion. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134475. [PMID: 38733781 DOI: 10.1016/j.jhazmat.2024.134475] [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: 01/07/2024] [Revised: 04/14/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024]
Abstract
Narrow spectrum nano-antibiotics are supposedly the future trouble-shooters to improve the efficacy of conventional antimicrobials for treatment of severe bacterial infections, remove contamination from water and diminish the development of antibiotic resistance. In this study, antimicrobial peptide functionalized boron-carbon-nitride nanosheets ((Ant)pep@BCN NSs) are developed that are a promising wastewater disinfector and antibiotic resistant bactericide agent. These nanosheets are developed for selective removal and effective inactivation of antibiotic resistant bacteria (ARB) from water in presence of two virulent bacteria. The (Ant)pep@BCN NSs provide reactive surface receptors specific to the ARB. They mimic muralytic enzymes to damage the cell membrane of ARB. These NSs demonstrate 3-fold higher antimicrobial efficiency against the targeted ARB compared to pristine BCN even at lower concentrations. To the best of our knowledge, this is the first time that functionalized BCN has been developed to remove ARB selectively from wastewater. Furthermore, the (Ant)pep@BCN selectively reduced the microbiological load and led to morphological changes in Gram negative ARB in a mixed bacterial inoculum. These ARBs excreted outer-inner membrane vesicles (OIMVs) of triangular shape as a stimuli response to (Ant)pep@BCN NSs. These novel antimicrobial peptide-NSs have potential to improve treatment efficacy against ARB infections and water contamination.
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Affiliation(s)
- Archana Raichur
- Department of Mechanical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.
| | - Niraj Sinha
- Department of Mechanical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.
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Iftimie S, Gabaldó-Barrios X, Penadés-Nadal J, Canela-Capdevila M, Piñana R, Jiménez-Franco A, López-Azcona AF, Castañé H, Cárcel M, Camps J, Castro A, Joven J. Serum Levels of Arachidonic Acid, Interleukin-6, and C-Reactive Protein as Potential Indicators of Pulmonary Viral Infections: Comparative Analysis of Influenza A, Respiratory Syncytial Virus Infection, and COVID-19. Viruses 2024; 16:1065. [PMID: 39066228 PMCID: PMC11281451 DOI: 10.3390/v16071065] [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: 05/20/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Acute respiratory tract infections, including influenza A (FluA), respiratory syncytial virus (RSV) infection, and COVID-19, can aggravate to levels requiring hospitalization, increasing morbidity and mortality. Identifying biomarkers for an accurate diagnosis and prognosis of these infections is a clinical need. We performed a cross-sectional study aimed to investigate the changes in circulating levels of arachidonic acid, interleukin 6 (IL-6), and C-reactive protein (CRP) in patients with FluA, RSV, or COVID-19, and to analyze the potential of these parameters as diagnosis or prognosis biomarkers. We analyzed serum samples from 172 FluA, 80 RSV, and 217 COVID-19 patients, and 104 healthy volunteers. Individuals with lung viral diseases showed reduced arachidonic acid concentrations compared to healthy people, with these differences being most pronounced in the order COVID-19 > RSV > FluA. Conversely, IL-6 and CRP levels were elevated across diseases, with IL-6 emerging as the most promising diagnostic biomarker, with areas under the curve (AUC) of the receiver operating characteristics plot higher than 0.85 and surpassing arachidonic acid and CRP. Moreover, IL-6 displayed notable efficacy in distinguishing between FluA patients who survived and those who did not (AUC = 0.80). These findings may provide useful tools for diagnosing and monitoring the severity of acute viral respiratory tract infections, ultimately improving patient outcomes.
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Affiliation(s)
- Simona Iftimie
- Department of Internal Medicine, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (S.I.); (J.P.-N.); (A.F.L.-A.); (A.C.)
| | - Xavier Gabaldó-Barrios
- Department of Clinical Laboratory, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (R.P.); (M.C.)
| | - Joan Penadés-Nadal
- Department of Internal Medicine, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (S.I.); (J.P.-N.); (A.F.L.-A.); (A.C.)
| | - Marta Canela-Capdevila
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (M.C.-C.); (A.J.-F.); (H.C.); (J.J.)
| | - Rubén Piñana
- Department of Clinical Laboratory, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (R.P.); (M.C.)
| | - Andrea Jiménez-Franco
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (M.C.-C.); (A.J.-F.); (H.C.); (J.J.)
| | - Ana F. López-Azcona
- Department of Internal Medicine, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (S.I.); (J.P.-N.); (A.F.L.-A.); (A.C.)
| | - Helena Castañé
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (M.C.-C.); (A.J.-F.); (H.C.); (J.J.)
| | - María Cárcel
- Department of Clinical Laboratory, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (R.P.); (M.C.)
| | - Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (M.C.-C.); (A.J.-F.); (H.C.); (J.J.)
| | - Antoni Castro
- Department of Internal Medicine, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (S.I.); (J.P.-N.); (A.F.L.-A.); (A.C.)
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43204 Reus, Spain; (M.C.-C.); (A.J.-F.); (H.C.); (J.J.)
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12
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Henkel R. Leukocytospermia and/or Bacteriospermia: Impact on Male Infertility. J Clin Med 2024; 13:2841. [PMID: 38792382 PMCID: PMC11122306 DOI: 10.3390/jcm13102841] [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: 04/05/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Infertility is a globally underestimated public health concern affecting almost 190 million people, i.e., about 17.5% of people during their lifetime, while the prevalence of male factor infertility is about 7%. Among numerous other causes, the prevalence of male genital tract infections reportedly ranges between 10% and 35%. Leukocytospermia is found in 30% of infertile men and up to 20% in fertile men. Bacterial infections cause an inflammatory response attracting leukocytes, which produce reactive oxygen species (ROS) and release cytokines, both of which can cause damage to sperm, rendering them dysfunctional. Although leukocytospermia and bacteriospermia are both clinical conditions that can negatively affect male fertility, there is still debate about their impact on assisted reproduction outcomes and management. According to World Health Organization (WHO) guidelines, leukocytes should be determined by means of the Endtz test or with monoclonal antibodies against CD15, CD68 or CD22. The cut-off value proposed by the WHO is 1 × 106 peroxidase-positive cells/mL. For bacteria, Gram staining and semen culture are regarded as the "gold standard", while modern techniques such as PCR and next-generation sequencing (NGS) are allowing clinicians to detect a wider range of pathogens. Whereas the WHO manual does not specify a specific value as a cut-off for bacterial contamination, several studies consider semen samples with more than 103 colony-forming units (cfu)/mL as bacteriospermic. The pathogenic mechanisms leading to sperm dysfunction include direct interaction of bacteria with the male germ cells, bacterial release of spermatotoxic substances, induction of pro-inflammatory cytokines and ROS, all of which lead to oxidative stress. Clinically, bacterial infections, including "silent" infections, are treatable, with antibiotics being the treatment of choice. Yet, non-steroidal antiphlogistics or antioxidants should also be considered to alleviate inflammatory lesions and improve semen quality. In an assisted reproduction set up, sperm separation techniques significantly reduce the bacterial load in the semen. Nonetheless, contamination of the semen sample with skin commensals should be prevented by applying relevant hygiene techniques. In patients where leukocytospermia is detected, the causes (e.g. infection, inflammation, varicocele, smoking, etc.) of the leukocyte infiltration have to be identified and addressed with antibiotics, anti-inflammatories or antioxidants in cases where high oxidative stress levels are detected. However, no specific strategy is available for the management of leukocytospermia. Therefore, the relationship between bacteriospermia and leukocytospermia as well as their specific impact on functional sperm parameters and reproductive outcome variables such as fertilization or clinical pregnancy must be further investigated. The aim of this narrative review is to provide an update on the current knowledge on leukocytospermia and bacteriospermia and their impact on male fertility.
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Affiliation(s)
- Ralf Henkel
- LogixX Pharma Ltd., Merlin House, Brunel Road, Theale, Reading RG7 4AB, UK;
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0HS, UK
- Department of Medical Bioscience, University of the Western Cape, Bellville 7535, South Africa
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Clodi-Seitz T, Baumgartner S, Turner M, Mader T, Hind J, Wenisch C, Zoufaly A, Presterl E. Point-of-Care Method T2Bacteria ®Panel Enables a More Sensitive and Rapid Diagnosis of Bacterial Blood Stream Infections and a Shorter Time until Targeted Therapy than Blood Culture. Microorganisms 2024; 12:967. [PMID: 38792796 PMCID: PMC11124434 DOI: 10.3390/microorganisms12050967] [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: 04/13/2024] [Revised: 04/25/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Rapid diagnosis and identification of pathogens are pivotal for appropriate therapy of blood stream infections. The T2Bacteria®Panel, a culture-independent assay for the detection of Escherichia coli, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa in blood, was evaluated under real-world conditions as a point-of-care method including patients admitted to the internal medicine ward due to suspected blood stream infection. METHODS Patients were assigned to two groups (standard of care-SOC vs. T2). In the SOC group 2 × 2 blood culture samples were collected, in the T2 group the T2Bacteria®Panel was performed additionally for pathogen identification. RESULTS A total of 94 patients were included. Pathogens were detected in 19 of 50 patients (38%) in the T2 group compared to 16 of 44 patients (36.4%) in the SOC group. The median time until pathogen detection was significantly shorter in the T2 group (4.5 h vs. 60 h, p < 0.001), as well as the time until targeted therapy (antibiotic with the narrowest spectrum and maximal effectiveness) (6.4 h vs. 42.2 h, p = 0.043). CONCLUSIONS The implementation of the T2Bacteria®Panel for patients with sepsis leads to an earlier targeted antimicrobial therapy resulting in earlier sufficient treatment and decreased excessive usage of broad-spectrum antimicrobials.
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Affiliation(s)
- Tamara Clodi-Seitz
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Sebastian Baumgartner
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Michael Turner
- Department of Rheumatology and Osteology, Klinik Favoriten, 1100 Vienna, Austria
| | - Theresa Mader
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Julian Hind
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Christoph Wenisch
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Alexander Zoufaly
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
- Faculty of Medicine, Sigmund Freud University Vienna, 1020 Vienna, Austria
| | - Elisabeth Presterl
- Department of Hospital Epidemiology and Infection Control, Medical University of Vienna, 1090 Vienna, Austria
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14
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Sun C, Zhou C, Wang L, Wei S, Shi M, Li J, Lin L, Liu X. Clinical application of metagenomic next-generation sequencing for the diagnosis of suspected infection in adults: A cross-sectional study. Medicine (Baltimore) 2024; 103:e37845. [PMID: 38640284 PMCID: PMC11029930 DOI: 10.1097/md.0000000000037845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/21/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has become an available method for pathogen detection. The clinical application of mNGS requires further evaluation. We conducted a cross-sectional study of 104 patients with suspected infection between May 2019 and May 2021. The risk factors associated with infection were analyzed using univariate logistic analysis. The diagnostic performance of pathogens was compared between mNGS and conventional microbiological tests. About 104 patients were assigned into 3 groups: infected group (n = 69), noninfected group (n = 20), and unknown group (n = 15). With the composite reference standard (combined results of all microbiological tests, radiological testing results, and a summary of the hospital stay of the patient) as the gold standard, the sensitivity, specificity, positive predictive value, negative predictive value of mNGS was 84.9%, 50.0%, 88.6%, and 42.1%, respectively. Compared with conventional microbiological tests, mNGS could detect more pathogens and had obvious advantages in Mycobacterium tuberculosis, Aspergillus, and virus detection. Moreover, mNGS had distinct benefits in detecting mixed infections. Bacteria-fungi-virus mixed infections were the most common in patients with severe pneumonia. mNGS had a higher sensitivity than conventional microbiological tests, especially for M. tuberculosis, Aspergillus, viruses, and mixed infections. We suggest that mNGS should be used more frequently in the early diagnosis of pathogens in critically ill patients in the future.
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Affiliation(s)
- Chunping Sun
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
- Department of Critical Care Medicine, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Chaoe Zhou
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Lina Wang
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Shanchen Wei
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Mingwei Shi
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Jun Li
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Lianjun Lin
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Xinmin Liu
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
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15
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Gray CF. CORR Insights®: Neutrophil Extracellular Trap-related Biomarkers Are Increased in the Synovial Fluid of Patients With Periprosthetic Joint Infections. Clin Orthop Relat Res 2024; 482:734-736. [PMID: 38231019 PMCID: PMC10936967 DOI: 10.1097/corr.0000000000002971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024]
Affiliation(s)
- Chancellor F Gray
- Orthopaedic Surgeon, Florida Orthopaedic Institute, Gainesville, FL, USA
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16
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Wood JB, Russell K, Davis TE, Park SY, Smollin MJ, Schneider JG. Plasma Microbial Cell-Free DNA Sequencing for Pathogen Detection and Quantification in Children With Musculoskeletal Infections. J Pediatric Infect Dis Soc 2024; 13:211-219. [PMID: 38330338 DOI: 10.1093/jpids/piae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Nearly half of all pediatric musculoskeletal infections (MSKIs) are culture negative. Plasma microbial cell-free DNA (mcfDNA) sequencing is noninvasive and not prone to the barriers of culture. We evaluated the performance of plasma mcfDNA sequencing in identifying a pathogen, and examined the duration of pathogen detection in children with MSKIs. METHODS We conducted a prospective study of children, aged 6 months to 18 years, hospitalized from July 2019 to May 2022 with MSKIs, in whom we obtained serial plasma mcfDNA sequencing samples and compared the results with cultures. RESULTS A pathogen was recovered by culture in 23 of 34 (68%) participants, and by initial mcfDNA sequencing in 25 of 31 (81%) participants. Multiple pathogens were detected in the majority (56%) of positive initial samples. Complete concordance with culture (all organisms accounted for by both methods) was 32%, partial concordance (at least one of the same organism(s) identified by both methods) was 36%, and discordance was 32%. mcfDNA sequencing was more likely to show concordance (complete or partial) if obtained prior to a surgical procedure (82%), compared with after (20%), (RR 4.12 [95% CI 1.25, 22.93], p = .02). There was no difference in concordance based on timing of antibiotics (presample antibiotics 60% vs no antibiotics 75%, RR 0.8 [95% CI 0.40, 1.46], p = .65]). mcfDNA sequencing was positive in 67% of culture-negative infections and detected a pathogen for a longer interval than blood culture (median 2 days [IQR 1, 6 days] vs 1 day [1, 1 day], p < .01). CONCLUSIONS Plasma mcfDNA sequencing may be useful in culture-negative pediatric MSKIs if the sample is obtained prior to surgery. However, results must be interpreted in the appropriate clinical context as multiple pathogens are frequently detected supporting the need for diagnostic stewardship.
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Affiliation(s)
- James B Wood
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Pediatric and Adolescent Comparative Effectiveness Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kelsey Russell
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Tom E Davis
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | | | - Jack G Schneider
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA
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17
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Knoth C, Humphries R, Johnson JK, Patel A, Lima A, Silbert S, Vinjé J. Multicenter evaluation of BioCode GPP for syndromic molecular detection of gastrointestinal pathogens from stool specimens. J Clin Microbiol 2024; 62:e0154523. [PMID: 38329337 PMCID: PMC10935640 DOI: 10.1128/jcm.01545-23] [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: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Acute gastroenteritis (AGE) is a leading cause of morbidity and mortality worldwide across all age groups that disproportionally affects young children in low- and middle-income countries and immunocompromised patients in high-income countries. Regional outbreaks of AGE are typically detected by traditional microbiological detection methods that target limited organisms and are associated with low sensitivity and lengthy time-to-results. Combined, these may result in repeat testing, imprecise or delayed treatment, and delayed recognition of outbreaks. We conducted a multi-site prospective study comparing the BioCode Gastrointestinal Pathogen Panel (BioCode GPP) for the detection of 17 common bacterial, viral, and protozoan causes of gastroenteritis with reference methods, including stool culture, enzyme immunoassays, pathogen-specific PCR assays, and sequencing. One thousand five hundred fifty-eight residual, de-identified stool samples (unpreserved stool and stool in Cary-Blair transport medium) were enrolled and tested for 11 bacterial, 3 viral, and 3 protozoan pathogens. BioCode GPP and reference methods were positive for 392 (25.2%) and 283 (18.2%) samples, respectively (P < 0.0001). In this study, the BioCode GPP and reference methods detected 69 and 65 specimens positive for Clostridioides difficile, 51 and 48 for enteroaggregative Escherichia coli, 33 and 27 for enterotoxigenic E. coli, 50 and 47 for norovirus GI/GII, and 30 and 22 for rotavirus A, respectively. The BioCode GPP showed good positive and negative agreements for each pathogen ranging from 89.5% to 100%, with overall sensitivity and specificity of 96.1% and 99.7%, post adjudication. The BioCode GPP detected >1 pathogens in 49 samples, representing 12.5% of the total 392 positive specimens. IMPORTANCE This study highlights performance of a novel technology for timely and accurate detection and differentiation of 17 common bacterial, viral, and protozoan causes of gastroenteritis. Utilizing molecular tests such as the BioCode Gastrointestinal Pathogen Panel may improve the detection of gastrointestinal pathogens and provide actionable results, particularly for patient populations at most risk.
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Affiliation(s)
| | - Romney Humphries
- University of California Los Angeles Medical Center, Los Angeles, California, USA
| | - J. Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Anami Patel
- Le Bonheur Children’s Hospital, Memphis, Tennessee, USA
| | | | | | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Lehnert T, Gijs MAM. Microfluidic systems for infectious disease diagnostics. LAB ON A CHIP 2024; 24:1441-1493. [PMID: 38372324 DOI: 10.1039/d4lc00117f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.
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Affiliation(s)
- Thomas Lehnert
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
| | - Martin A M Gijs
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
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19
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Ioannou P, Baliou S, Samonis G. Nanotechnology in the Diagnosis and Treatment of Antibiotic-Resistant Infections. Antibiotics (Basel) 2024; 13:121. [PMID: 38391507 PMCID: PMC10886108 DOI: 10.3390/antibiotics13020121] [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: 01/04/2024] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
The development of antimicrobial resistance (AMR), along with the relative reduction in the production of new antimicrobials, significantly limits the therapeutic options in infectious diseases. Thus, novel treatments, especially in the current era, where AMR is increasing, are urgently needed. There are several ongoing studies on non-classical therapies for infectious diseases, such as bacteriophages, antimicrobial peptides, and nanotechnology, among others. Nanomaterials involve materials on the nanoscale that could be used in the diagnosis, treatment, and prevention of infectious diseases. This review provides an overview of the applications of nanotechnology in the diagnosis and treatment of infectious diseases from a clinician's perspective, with a focus on pathogens with AMR. Applications of nanomaterials in diagnosis, by taking advantage of their electrochemical, optic, magnetic, and fluorescent properties, are described. Moreover, the potential of metallic or organic nanoparticles (NPs) in the treatment of infections is also addressed. Finally, the potential use of NPs in the development of safe and efficient vaccines is also reviewed. Further studies are needed to prove the safety and efficacy of NPs that would facilitate their approval by regulatory authorities for clinical use.
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Affiliation(s)
- Petros Ioannou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Stella Baliou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George Samonis
- School of Medicine, University of Crete, 71003 Heraklion, Greece
- First Department of Medical Oncology, Metropolitan Hospital of Neon Faliron, 18547 Athens, Greece
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Wang JZ, Yuan D, Yang XH, Sun CH, Hou LL, Zhang Y, Gao YX. Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study. Front Cell Infect Microbiol 2024; 13:1291980. [PMID: 38264726 PMCID: PMC10803656 DOI: 10.3389/fcimb.2023.1291980] [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: 09/10/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Pneumonia are the leading cause of death worldwide, and antibiotic treatment remains fundamental. However, conventional sputum smears or cultures are still inefficient for obtaining pathogenic microorganisms.Metagenomic next-generation sequencing (mNGS) has shown great value in nucleic acid detection, however, the NGS results for lower respiratory tract microorganisms are still poorly studied. Methods This study dealt with investigating the efficacy of mNGS in detecting pathogens in the lower respiratory tract of patients with pulmonary infections. A total of 112 patients admitted at the First Affiliated Hospital of Zhengzhou University between April 30, 2018, and June 30, 2020, were enrolled in this retrospective study. The bronchoalveolar lavage fluid (BALF) was obtained from lower respiratory tract from each patient. Routine methods (bacterial smear and culture) and mNGS were employed for the identification of pathogenic microorganisms in BALF. Results The average patient age was 53.0 years, with 94.6% (106/112) obtaining pathogenic microorganism results. The total mNGS detection rate of pathogenic microorganisms significantly surpassed conventional methods (93.7% vs. 32.1%, P < 0.05). Notably, 75% of patients (84/112) were found to have bacteria by mNGS, but only 28.6% (32/112) were found to have bacteria by conventional approaches. The most commonly detected bacteria included Acinetobacter baumannii (19.6%), Klebsiella pneumoniae (17.9%), Pseudomonas aeruginosa (14.3%), Staphylococcus faecium (12.5%), Enterococcus faecium (12.5%), and Haemophilus parainfluenzae (11.6%). In 29.5% (33/112) of patients, fungi were identified using mNGS, including 23 cases of Candida albicans (20.5%), 18 of Pneumocystis carinii (16.1%), and 10 of Aspergillus (8.9%). However, only 7.1 % (8/112) of individuals were found to have fungi when conventional procedures were used. The mNGS detection rate of viruses was significantly higher than the conventional method rate (43.8% vs. 0.9%, P < 0.05). The most commonly detected viruses included Epstein-Barr virus (15.2%), cytomegalovirus (13.4%), circovirus (8.9%), human coronavirus (4.5%), and rhinovirus (4.5%). Only 29.4% (33/112) of patients were positive, whereas 5.4% (6/112) of patients were negative for both detection methods as shown by Kappa analysis, indicating poor consistency between the two methods (P = 0.340; Kappa analysis). Conclusion Significant benefits of mNGS have been shown in the detection of pathogenic microorganisms in patients with pulmonary infection. For those with suboptimal therapeutic responses, mNGS can provide an etiological basis, aiding in precise anti-infective treatment.
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Affiliation(s)
- Jin-zhu Wang
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ding Yuan
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiang-hong Yang
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chang-hua Sun
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lin-lin Hou
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Zhang
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan-xia Gao
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Wilde AM, Song M, Allen WP, Junkins AD, Frazier JM, Moore SE, Schulz PS. Implementation of a pharmacy-driven rapid bacteremia response program. Am J Health Syst Pharm 2024; 81:74-82. [PMID: 37658845 DOI: 10.1093/ajhp/zxad211] [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: 08/31/2023] [Indexed: 09/05/2023] Open
Abstract
PURPOSE This report describes a comprehensive pharmacy-driven rapid bacteremia response program. SUMMARY This novel program positioned the pharmacy department at a large, community health system to receive and respond to critical microbiologic diagnostic testing results, 24/7/365. The program empowered pharmacists to provide centralized, comprehensive care including assessing blood culture Gram stain results, adjusting antibiotic therapy per protocol, ordering repeat blood cultures, analyzing and interpreting rapid molecular diagnostic test results, placing orders for contact isolation, and communicating antibiotic recommendations to the treatment team. In the first year after program implementation, 2,282 blood culture Gram stains and 2,046 rapid diagnostic test results were called in to the pharmacy department. The program reduced the median time to effective therapy in patients who did not already have active antimicrobial orders from over 10 hours to less than 1 hour. Based on the Gram stain results, antibiotics were started per protocol in 34.2% of patients. Based on the rapid molecular diagnostic test results, adjustments were made to antibiotic regimens in 55.7% of cases after discussion with a provider. Of these adjustments, 39.9% were for escalation of antibiotics and 37.7% were for de-escalation of antibiotics. CONCLUSION By expanding the scope of pharmacy practice, barriers to optimizing clinical care were overcome.
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Affiliation(s)
- Ashley M Wilde
- Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY, USA
| | - Matthew Song
- Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY, USA
| | - W Paul Allen
- Pharmacy Services, Norton Healthcare, Louisville, KY, USA
| | - Alan D Junkins
- Department of Microbiology, Norton Healthcare, Louisville, KY, USA
| | | | - Sarah E Moore
- Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY, USA
| | - Paul S Schulz
- Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY, USA
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22
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Chavda VP, Vuppu S, Mishra T, Kamaraj S, Sharma N, Punetha S, Sairam A, Vaghela D, Dargahi N, Apostolopoulos V. Combatting infectious diarrhea: innovations in treatment and vaccination strategies. Expert Rev Vaccines 2024; 23:246-265. [PMID: 38372023 DOI: 10.1080/14760584.2023.2295015] [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: 12/11/2023] [Indexed: 02/20/2024]
Abstract
INTRODUCTION The escalating prevalence of infectious diseases is an important cause of concern in society. Particularly in several developing countries, infectious diarrhea poses a major problem, with a high fatality rate, especially among young children. The condition is divided into four classes, namely, acute diarrhea, invasive diarrhea, acute bloody diarrhea, and chronic diarrhea. Various pathogenic agents, such as bacteria, viruses, protozoans, and helminths, contribute to the onset of this condition. AREAS COVERED The review discusses the scenario of infectious diarrhea, the prevalent types, as well as approaches to management including preventive, therapeutic, and vaccination strategies. The vaccination techniques are extensively discussed including the available vaccines, their advantages as well as limitations. EXPERT OPINION There are several approaches available to develop new-improved vaccines. In addition, route of immunization is important and aerosols/nasal sprays, oral route, skin patches, powders, and liquid jets to minimize needles can be used. Plant-based vaccines, such as rice, might save packing and refrigeration costs by being long-lasting, non-refrigerable, and immunogenic. Future research should utilize predetermined PCR testing intervals and symptom monitoring to identify persistent pathogens after therapy and symptom remission.
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Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, LM College of Pharmacy, Ahmedabad, Gujarat, India
| | - Suneetha Vuppu
- Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Toshika Mishra
- Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Sathvika Kamaraj
- Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Nikita Sharma
- Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Swati Punetha
- Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Sairam
- Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Dixa Vaghela
- Pharmacy Section, L.M. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Narges Dargahi
- Institute for Health and Sport, Victoria University, Melbourne, Australia
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Immunology Program, Sunshine Hospital Campus, Saint Albans, Victoria, Australia
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23
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Vloemans D, Van Hileghem L, Ordutowski H, Dal Dosso F, Spasic D, Lammertyn J. Self-Powered Microfluidics for Point-of-Care Solutions: From Sampling to Detection of Proteins and Nucleic Acids. Methods Mol Biol 2024; 2804:3-50. [PMID: 38753138 DOI: 10.1007/978-1-0716-3850-7_1] [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: 05/21/2024]
Abstract
Self-powered microfluidics presents a revolutionary approach to address the challenges of healthcare in decentralized and point-of-care settings where limited access to resources and infrastructure prevails or rapid clinical decision-making is critical. These microfluidic systems exploit physical and chemical phenomena, such as capillary forces and surface tension, to manipulate tiny volumes of fluids without the need for external power sources, making them cost-effective and highly portable. Recent technological advancements have demonstrated the ability to preprogram complex multistep liquid operations within the microfluidic circuit of these standalone systems, which enabled the integration of sensitive detection and readout principles. This chapter first addresses how the accessibility to in vitro diagnostics can be improved by shifting toward decentralized approaches like remote microsampling and point-of-care testing. Next, the crucial role of self-powered microfluidic technologies to enable this patient-centric healthcare transition is emphasized using various state-of-the-art examples, with a primary focus on applications related to biofluid collection and the detection of either proteins or nucleic acids. This chapter concludes with a summary of the main findings and our vision of the future perspectives in the field of self-powered microfluidic technologies and their use for in vitro diagnostics applications.
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Affiliation(s)
- Dries Vloemans
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium
| | | | - Henry Ordutowski
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium
| | | | - Dragana Spasic
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium.
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24
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Astatke M, Tiburzi O, Connolly A, Robinson ML. RNA Analysis Using Immunoassay Detection Format. Methods Mol Biol 2024; 2822:175-186. [PMID: 38907919 DOI: 10.1007/978-1-0716-3918-4_13] [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: 06/24/2024]
Abstract
Oligonucleotide probe tagging and reverse transcriptase polymerase-chain reaction (RT-PCR) are the most widely used techniques currently used for detecting and analyzing RNA. RNA detection using labeled oligonucleotide probe-based approaches is suitable for point-of-care (POC) applications but lacks assay sensitivity, whereas RT-PCR requires complex instrumentation. As an alternative, immunoassay detection formats coupled with isothermal RNA amplification techniques have been proposed for handheld assay development. In this chapter, we describe a robust technique comprising of: (a) target RNA tagging with a complementary oligonucleotide probe labeled with a hapten moiety to form a DNA/RNA duplex hybrid; (b) complexing the DNA/RNA duplex with a pre-coated antibody (Ab) directed at the hapten moiety; (c) sandwich complex formation with an Ab that selectively recognizes the DNA/RNA structural motif; and (d) detection of the sandwich complex using a secondary Ab enzyme conjugate targeting the anti-DNA/RNA Ab followed by standard enzyme-linked immunosorbent assay (ELISA) visualization.
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Affiliation(s)
- Mekbib Astatke
- Asymmetric Operations Sector, Applied Biological Sciences, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA.
| | - Olivia Tiburzi
- Asymmetric Operations Sector, Applied Biological Sciences, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | | | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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25
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Deng Z, Li C, Wang Y, Wu F, Liang C, Deng W, Wang Y. Targeted next-generation sequencing for pulmonary infection diagnosis in patients unsuitable for bronchoalveolar lavage. Front Med (Lausanne) 2023; 10:1321515. [PMID: 38179267 PMCID: PMC10764475 DOI: 10.3389/fmed.2023.1321515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Background Targeted next-generation sequencing (tNGS) has emerged as a rapid diagnostic technology for identifying a wide spectrum of pathogens responsible for pulmonary infections. Methods Sputum samples were collected from patients unable or unwilling to undergo bronchoalveolar lavage. These samples underwent tNGS analysis to diagnose pulmonary infections. Retrospective analysis was performed on clinical data, and the clinical efficacy of tNGS was compared to conventional microbiological tests (CMTs). Results This study included 209 pediatric and adult patients with confirmed pulmonary infections. tNGS detected 45 potential pathogens, whereas CMTs identified 23 pathogens. The overall microbial detection rate significantly differed between tNGS and CMTs (96.7% vs. 36.8%, p < 0.001). Among the 76 patients with concordant positive results from tNGS and CMTs, 86.8% (66/76) exhibited full or partial agreement. For highly pathogenic and rare/noncolonized microorganisms, tNGS, combined with comprehensive clinical review, directly guided pathogenic diagnosis and antibiotic treatment in 21 patients. This included infections caused by Mycobacterium tuberculosis complex, certain atypical pathogens, Aspergillus, and nontuberculous Mycobacteria. Among the enrolled population, 38.8% (81/209) of patients adjusted their treatment based on tNGS results. Furthermore, tNGS findings unveiled age-specific heterogeneity in pathogen distribution between children and adults. Conclusion CMTs often fall short in meeting the diagnostic needs of pulmonary infections. This study highlights how tNGS of sputum samples from patients who cannot or will not undergo bronchoalveolar lavage yield valuable insights into potential pathogens, thereby enhancing the diagnosis of pulmonary infections in specific cases.
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Affiliation(s)
- Zhenfeng Deng
- Clinical Genome Center, Guangxi KingMed Diagnostics, Nanning, China
| | - Chunhong Li
- Clinical Genome Center, Guangxi KingMed Diagnostics, Nanning, China
| | - Yingjin Wang
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Fengwen Wu
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Chunfang Liang
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Wei Deng
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Yuanli Wang
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
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26
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Ali SB, Cecchin A, Lucchesi C, Putty T, Edwards S, Petrou T, Coates P, Ferrante A, Pucar PA, King J, Banovic T. Can C-reactive protein be used as a surrogate marker of IL-6 in a broad array of clinical entities? Biomark Med 2023; 17:1001-1010. [PMID: 38235562 DOI: 10.2217/bmm-2023-0708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Abstract
Background: C-reactive protein (CRP) is commonly performed, whereas cytokine testing is limited to research. Aims: To determine CRP correlation to cytokines IL-6, IL-1β and TNF-α. Results: Consecutive samples (n = 307) were collected over 24 h. Ninety-six patients (31%) had acute infections, and 23 patients (7.5%) had autoimmune or inflammatory disease presentations. A strong correlation between CRP and two IL-6 assays (r = 0.74 and r = 0.71; p < 0.001) was present. CRP did not correlate with IL-1β and TNF-α across the data set. Bacterial infection had a significantly higher CRP and IL-6 (p < 0.001), while only CRP was elevated in inflammatory and autoimmune diseases (p < 0.001). Discussion: CRP may be used as a surrogate marker of IL-6 levels in the routine diagnostic laboratories.
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Affiliation(s)
- Syed B Ali
- Department of Clinical Immunology & Allergy, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
- Department of Immunopathology, Adelaide, 5000, Australia
- School of Medicine & Public Health, University of Adelaide, 5000, Australia
| | - Amelia Cecchin
- Department of Immunopathology, Adelaide, 5000, Australia
| | | | - Trishni Putty
- Department of Immunopathology, SA Pathology Womens' & Childrens' Hospital, Adelaide, 5000, Australia
| | - Suzanne Edwards
- Adelaide Health Technology Assessment, School of Public Health, University of Adelaide, Adelaide, 5000, Australia
| | - Tina Petrou
- Department of Biochemistry, Royal Adelaide Hospital, Adelaide, 5000, Australia
| | - Penelope Coates
- Department of Biochemistry, Royal Adelaide Hospital, Adelaide, 5000, Australia
- Department of Biochemistry, SA Pathology, Adelaide, 5000, Australia
| | - Antonio Ferrante
- Department of Immunopathology, SA Pathology Womens' & Childrens' Hospital, Adelaide, 5000, Australia
| | - Phillippa A Pucar
- Department of Clinical Immunology & Allergy, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
- Department of Immunopathology, Adelaide, 5000, Australia
| | - Jovanka King
- Department of Immunopathology, Adelaide, 5000, Australia
- School of Medicine & Public Health, University of Adelaide, 5000, Australia
- Department of Immunopathology, SA Pathology Womens' & Childrens' Hospital, Adelaide, 5000, Australia
| | - Tatjana Banovic
- Department of Clinical Immunology & Allergy, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
- Department of Immunopathology, Adelaide, 5000, Australia
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27
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Yigci D, Atçeken N, Yetisen AK, Tasoglu S. Loop-Mediated Isothermal Amplification-Integrated CRISPR Methods for Infectious Disease Diagnosis at Point of Care. ACS OMEGA 2023; 8:43357-43373. [PMID: 38027359 PMCID: PMC10666231 DOI: 10.1021/acsomega.3c04422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023]
Abstract
Infectious diseases continue to pose an imminent threat to global public health, leading to high numbers of deaths every year and disproportionately impacting developing countries where access to healthcare is limited. Biological, environmental, and social phenomena, including climate change, globalization, increased population density, and social inequity, contribute to the emergence of novel communicable diseases. Rapid and accurate diagnoses of infectious diseases are essential to preventing the transmission of infectious diseases. Although some commonly used diagnostic technologies provide highly sensitive and specific measurements, limitations including the requirement for complex equipment/infrastructure and refrigeration, the need for trained personnel, long sample processing times, and high cost remain unresolved. To ensure global access to affordable diagnostic methods, loop-mediated isothermal amplification (LAMP) integrated clustered regularly interspaced short palindromic repeat (CRISPR) based pathogen detection has emerged as a promising technology. Here, LAMP-integrated CRISPR-based nucleic acid detection methods are discussed in point-of-care (PoC) pathogen detection platforms, and current limitations and future directions are also identified.
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Affiliation(s)
- Defne Yigci
- School
of Medicine, Koç University, Istanbul 34450, Turkey
| | - Nazente Atçeken
- Koç
University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Ali K. Yetisen
- Department
of Chemical Engineering, Imperial College
London, London SW7 2AZ, U.K.
| | - Savas Tasoglu
- Koç
University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Boğaziçi
Institute of Biomedical Engineering, Boğaziçi
University, Istanbul 34684, Turkey
- Koç
University Arçelik Research Center for Creative Industries
(KUAR), Koç University, Istanbul 34450, Turkey
- Physical
Intelligence Department, Max Planck Institute
for Intelligent Systems, Stuttgart 70569, Germany
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28
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Tanniche I, Behkam B. Engineered live bacteria as disease detection and diagnosis tools. J Biol Eng 2023; 17:65. [PMID: 37875910 PMCID: PMC10598922 DOI: 10.1186/s13036-023-00379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/18/2023] [Indexed: 10/26/2023] Open
Abstract
Sensitive and minimally invasive medical diagnostics are essential to the early detection of diseases, monitoring their progression and response to treatment. Engineered bacteria as live sensors are being developed as a new class of biosensors for sensitive, robust, noninvasive, and in situ detection of disease onset at low cost. Akin to microrobotic systems, a combination of simple genetic rules, basic logic gates, and complex synthetic bioengineering principles are used to program bacterial vectors as living machines for detecting biomarkers of diseases, some of which cannot be detected with other sensing technologies. Bacterial whole-cell biosensors (BWCBs) can have wide-ranging functions from detection only, to detection and recording, to closed-loop detection-regulated treatment. In this review article, we first summarize the unique benefits of bacteria as living sensors. We then describe the different bacteria-based diagnosis approaches and provide examples of diagnosing various diseases and disorders. We also discuss the use of bacteria as imaging vectors for disease detection and image-guided surgery. We conclude by highlighting current challenges and opportunities for further exploration toward clinical translation of these bacteria-based systems.
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Affiliation(s)
- Imen Tanniche
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bahareh Behkam
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
- School of Biomedical Engineered and Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
- Center for Engineered Health, Institute for Critical Technology and Applied Science, Virginia Tech, Blacksburg, VA, 24061, USA.
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29
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Hetta HF, Rashed ZI, Ramadan YN, Al-Kadmy IMS, Kassem SM, Ata HS, Nageeb WM. Phage Therapy, a Salvage Treatment for Multidrug-Resistant Bacteria Causing Infective Endocarditis. Biomedicines 2023; 11:2860. [PMID: 37893232 PMCID: PMC10604041 DOI: 10.3390/biomedicines11102860] [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: 09/18/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Infective endocarditis (IE) is defined as an infection of the endocardium, or inner surface of the heart, most frequently affecting the heart valves or implanted cardiac devices. Despite its rarity, it has a high rate of morbidity and mortality. IE generally occurs when bacteria, fungi, or other germs from another part of the body, such as the mouth, spread through the bloodstream and attach to damaged areas in the heart. The epidemiology of IE has changed as a consequence of aging and the usage of implantable cardiac devices and heart valves. The right therapeutic routes must be assessed to lower complication and fatality rates, so this requires early clinical suspicion and a fast diagnosis. It is urgently necessary to create new and efficient medicines to combat multidrug-resistant bacterial (MDR) infections because of the increasing threat of antibiotic resistance on a worldwide scale. MDR bacteria that cause IE can be treated using phages rather than antibiotics to combat MDR bacterial strains. This review will illustrate how phage therapy began and how it is considered a powerful potential candidate for the treatment of MDR bacteria that cause IE. Furthermore, it gives a brief about all reported clinical trials that demonstrated the promising effect of phage therapy in combating resistant bacterial strains that cause IE and how it will become a hope in future medicine.
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Affiliation(s)
- Helal F. Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Zainab I. Rashed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt; (Z.I.R.); (Y.N.R.)
| | - Yasmin N. Ramadan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt; (Z.I.R.); (Y.N.R.)
| | - Israa M. S. Al-Kadmy
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, Baghdad P.O. Box 10244, Iraq
| | - Soheir M. Kassem
- Department of Internal Medicine and Critical Care, Faculty of Medicine, Assuit University, Assiut 71515, Egypt;
| | - Hesham S. Ata
- Department of Pathology, College of Medicine, Qassim University, Buraydah 51452, Qassim, Saudi Arabia;
| | - Wedad M. Nageeb
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
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30
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Martin-Loeches I, Reyes LF, Nseir S, Ranzani O, Povoa P, Diaz E, Schultz MJ, Rodríguez AH, Serrano-Mayorga CC, De Pascale G, Navalesi P, Panigada M, Coelho LM, Skoczynski S, Esperatti M, Cortegiani A, Aliberti S, Caricato A, Salzer HJF, Ceccato A, Civljak R, Soave PM, Luyt CE, Ekren PK, Rios F, Masclans JR, Marin J, Iglesias-Moles S, Nava S, Chiumello D, Bos LD, Artigas A, Froes F, Grimaldi D, Taccone FS, Antonelli M, Torres A. European Network for ICU-Related Respiratory Infections (ENIRRIs): a multinational, prospective, cohort study of nosocomial LRTI. Intensive Care Med 2023; 49:1212-1222. [PMID: 37812242 PMCID: PMC10562498 DOI: 10.1007/s00134-023-07210-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023]
Abstract
PURPOSE Lower respiratory tract infections (LRTI) are the most frequent infectious complication in patients admitted to the intensive care unit (ICU). We aim to report the clinical characteristics of ICU-admitted patients due to nosocomial LRTI and to describe their microbiology and clinical outcomes. METHODS A prospective observational study was conducted in 13 countries over two continents from 9th May 2016 until 16th August 2019. Characteristics and outcomes of ventilator-associated pneumonia (VAP), ventilator-associated tracheobronchitis (VAT), ICU hospital-acquired pneumonia (ICU-HAP), HAP that required invasive ventilation (VHAP), and HAP in patients transferred to the ICU without invasive mechanical ventilation were collected. The clinical diagnosis and treatments were per clinical practice and not per protocol. Descriptive statistics were used to compare the study groups. RESULTS 1060 patients with LRTI (72.5% male sex, median age 64 [50-74] years) were included in the study; 160 (15.1%) developed VAT, 556 (52.5%) VAP, 98 (9.2%) ICU-HAP, 152 (14.3%) HAP, and 94 (8.9%) VHAP. Patients with VHAP had higher serum procalcitonin (PCT) and Sequential Organ Failure Assessment (SOFA) scores. Patients with VAP or VHAP developed acute kidney injury, acute respiratory distress syndrome, multiple organ failure, or septic shock more often. One thousand eight patients had microbiological samples, and 711 (70.5%) had etiological microbiology identified. The most common microorganisms were Pseudomonas aeruginosa (18.4%) and Klebsiella spp (14.4%). In 382 patients (36%), the causative pathogen shows some antimicrobial resistance pattern. ICU, hospital and 28-day mortality were 30.8%, 37.5% and 27.5%, respectively. Patients with VHAP had the highest ICU, in-hospital and 28-day mortality rates. CONCLUSION VHAP patients presented the highest mortality among those admitted to the ICU. Multidrug-resistant pathogens frequently cause nosocomial LRTI in this multinational cohort study.
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Affiliation(s)
- Ignacio Martin-Loeches
- St James's University Hospital, Trinity College, Dublin 8, D08 NHY, Ireland.
- Universidad de Barcelona, CIBERes, Barcelona, Spain.
| | - Luis Felipe Reyes
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Clinica Universidad de La Sabana, Chia, Colombia
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Saad Nseir
- University Hospital of Lille, Lille, France
| | | | - Pedro Povoa
- Hospital de Sao Francisco Xavier, Lisbon, Portugal
| | - Emili Diaz
- Corporacio Sanitaria Parc Tauli, Sabadell, Spain
| | - Marcus J Schultz
- Academic Medical Center, Amsterdam, The Netherlands
- Department of Intensive Care Laboratory for Experimental Intensive Care and Anesthesiology (LEICA), Amsterdam, The Netherlands
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, UK
| | | | - Cristian C Serrano-Mayorga
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Clinica Universidad de La Sabana, Chia, Colombia
| | | | - Paolo Navalesi
- Magna Graecia University, Catanzaro, Italy
- Sant'Andrea (ASL VC), Vercelli, Italy
| | - Mauro Panigada
- Anesthesia and Critical Care, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | | | | | - Stefano Aliberti
- Medical University of Silesia, Katowice, Poland
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Respiratory Unit, Milan, Italy
| | | | - Helmut J F Salzer
- Department of Internal Medicine 4-Pneumology, Kepler University Hospital, Linz, Austria
- Medical Faculty, Johannes Kepler University Linz, Linz, Austria
- Division of Infectious Diseases and Tropical Medicine, Kepler University Hospital, Linz, Austria
| | | | - Rok Civljak
- "Dr. Fran Mihaljevic" University Hospital for Infectious Diseases, Zagreb, Croatia
| | | | | | | | - Fernando Rios
- Hospital Nacional Alejandro Posadas, Buenos Aires, Argentina
| | - Joan Ramon Masclans
- Hospital del Mar, Barcelona, Spain
- Intensive Care Medicine, Hospital del Mar & IMIM, Barcelona, Spain
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Judith Marin
- Intensive Care Medicine, Hospital del Mar & IMIM, Barcelona, Spain
| | | | - Stefano Nava
- S. Orsola-Malpighi Hospital, Bologna, Italy
- Respiratory and Critical Care Unit, IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy
- Alma Mater Studiorum, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | | | - Lieuwe D Bos
- Academic Medical Center, Amsterdam, The Netherlands
| | | | | | - David Grimaldi
- Hospital Erasme Universit Libre de Bruxelles, Brussels, Belgium
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31
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Dubey AK, Mostafavi E. Biomaterials-mediated CRISPR/Cas9 delivery: recent challenges and opportunities in gene therapy. Front Chem 2023; 11:1259435. [PMID: 37841202 PMCID: PMC10568484 DOI: 10.3389/fchem.2023.1259435] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023] Open
Abstract
The use of biomaterials in delivering CRISPR/Cas9 for gene therapy in infectious diseases holds tremendous potential. This innovative approach combines the advantages of CRISPR/Cas9 with the protective properties of biomaterials, enabling accurate and efficient gene editing while enhancing safety. Biomaterials play a vital role in shielding CRISPR/Cas9 components, such as lipid nanoparticles or viral vectors, from immunological processes and degradation, extending their effectiveness. By utilizing the flexibility of biomaterials, tailored systems can be designed to address specific genetic diseases, paving the way for personalized therapeutics. Furthermore, this delivery method offers promising avenues in combating viral illnesses by precisely modifying pathogen genomes, and reducing their pathogenicity. Biomaterials facilitate site-specific gene modifications, ensuring effective delivery to infected cells while minimizing off-target effects. However, challenges remain, including optimizing delivery efficiency, reducing off-target effects, ensuring long-term safety, and establishing scalable production techniques. Thorough research, pre-clinical investigations, and rigorous safety evaluations are imperative for successful translation from the laboratory to clinical applications. In this review, we discussed how CRISPR/Cas9 delivery using biomaterials revolutionizes gene therapy and infectious disease treatment, offering precise and safe editing capabilities with the potential to significantly improve human health and quality of life.
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Affiliation(s)
- Ankit Kumar Dubey
- Global Research and Publishing Foundation, New Delhi, India
- Institute of Scholars, Bengaluru, Karnataka, India
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
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Borah Slater K, Ahmad M, Poirier A, Stott A, Siedler BS, Brownsword M, Mehat J, Urbaniec J, Locker N, Zhao Y, La Ragione R, Silva SRP, McFadden J. Development of a loop-mediated isothermal amplification (LAMP)-based electrochemical test for rapid detection of SARS-CoV-2. iScience 2023; 26:107570. [PMID: 37664622 PMCID: PMC10470312 DOI: 10.1016/j.isci.2023.107570] [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: 02/06/2023] [Revised: 03/10/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Rapid, reliable, sensitive, portable, and accurate diagnostics are required to control disease outbreaks such as COVID-19 that pose an immense burden on human health and the global economy. Here we developed a loop-mediated isothermal amplification (LAMP)-based electrochemical test for the detection of SARS-CoV-2 that causes COVID-19. The test is based on the oxidation-reduction reaction between pyrophosphates (generated from positive LAMP reaction) and molybdate that is detected by cyclic voltammetry using inexpensive and disposable carbon screen printed electrodes. Our test showed higher sensitivity (detecting as low as 5.29 RNA copies/μL) compared to the conventional fluorescent reverse transcriptase (RT)-LAMP. We validated our tests using human serum and saliva spiked with SARS-CoV-2 RNA and clinical (saliva and nasal-pharyngeal) swab samples demonstrating 100% specificity and 93.33% sensitivity. Our assay provides a rapid, specific, and sensitive test with an electrochemical readout in less than 45 min that could be adapted for point-of-care settings.
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Affiliation(s)
- Khushboo Borah Slater
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Muhammad Ahmad
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Aurore Poirier
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Ash Stott
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Bianca Sica Siedler
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Matthew Brownsword
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Jai Mehat
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Joanna Urbaniec
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Nicolas Locker
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Yunlong Zhao
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Roberto La Ragione
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - S. Ravi P. Silva
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Johnjoe McFadden
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
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Leanse LG, Marasini S, dos Anjos C, Dai T. Antimicrobial Resistance: Is There a 'Light' at the End of the Tunnel? Antibiotics (Basel) 2023; 12:1437. [PMID: 37760734 PMCID: PMC10525303 DOI: 10.3390/antibiotics12091437] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/30/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
In recent years, with the increases in microorganisms that express a multitude of antimicrobial resistance (AMR) mechanisms, the threat of antimicrobial resistance in the global population has reached critical levels. The introduction of the COVID-19 pandemic has further contributed to the influx of infections caused by multidrug-resistant organisms (MDROs), which has placed significant pressure on healthcare systems. For over a century, the potential for light-based approaches targeted at combatting both cancer and infectious diseases has been proposed. They offer effective killing of microbial pathogens, regardless of AMR status, and have not typically been associated with high propensities of resistance development. To that end, the goal of this review is to describe the different mechanisms that drive AMR, including intrinsic, phenotypic, and acquired resistance mechanisms. Additionally, the different light-based approaches, including antimicrobial photodynamic therapy (aPDT), antimicrobial blue light (aBL), and ultraviolet (UV) light, will be discussed as potential alternatives or adjunct therapies with conventional antimicrobials. Lastly, we will evaluate the feasibility and requirements associated with integration of light-based approaches into the clinical pipeline.
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Affiliation(s)
- Leon G. Leanse
- Health and Sports Sciences Hub, University of Gibraltar, Europa Point Campus, Gibraltar GX11 1AA, Gibraltar
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (C.d.A.); (T.D.)
| | - Sanjay Marasini
- New Zealand National Eye Centre, Department of Ophthalmology, The University of Auckland, Auckland 1142, New Zealand;
| | - Carolina dos Anjos
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (C.d.A.); (T.D.)
| | - Tianhong Dai
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (C.d.A.); (T.D.)
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Habgood-Coote D, Wilson C, Shimizu C, Barendregt AM, Philipsen R, Galassini R, Calle IR, Workman L, Agyeman PKA, Ferwerda G, Anderson ST, van den Berg JM, Emonts M, Carrol ED, Fink CG, de Groot R, Hibberd ML, Kanegaye J, Nicol MP, Paulus S, Pollard AJ, Salas A, Secka F, Schlapbach LJ, Tremoulet AH, Walther M, Zenz W, Van der Flier M, Zar HJ, Kuijpers T, Burns JC, Martinón-Torres F, Wright VJ, Coin LJM, Cunnington AJ, Herberg JA, Levin M, Kaforou M. Diagnosis of childhood febrile illness using a multi-class blood RNA molecular signature. MED 2023; 4:635-654.e5. [PMID: 37597512 DOI: 10.1016/j.medj.2023.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND Appropriate treatment and management of children presenting with fever depend on accurate and timely diagnosis, but current diagnostic tests lack sensitivity and specificity and are frequently too slow to inform initial treatment. As an alternative to pathogen detection, host gene expression signatures in blood have shown promise in discriminating several infectious and inflammatory diseases in a dichotomous manner. However, differential diagnosis requires simultaneous consideration of multiple diseases. Here, we show that diverse infectious and inflammatory diseases can be discriminated by the expression levels of a single panel of genes in blood. METHODS A multi-class supervised machine-learning approach, incorporating clinical consequence of misdiagnosis as a "cost" weighting, was applied to a whole-blood transcriptomic microarray dataset, incorporating 12 publicly available datasets, including 1,212 children with 18 infectious or inflammatory diseases. The transcriptional panel identified was further validated in a new RNA sequencing dataset comprising 411 febrile children. FINDINGS We identified 161 transcripts that classified patients into 18 disease categories, reflecting individual causative pathogen and specific disease, as well as reliable prediction of broad classes comprising bacterial infection, viral infection, malaria, tuberculosis, or inflammatory disease. The transcriptional panel was validated in an independent cohort and benchmarked against existing dichotomous RNA signatures. CONCLUSIONS Our data suggest that classification of febrile illness can be achieved with a single blood sample and opens the way for a new approach for clinical diagnosis. FUNDING European Union's Seventh Framework no. 279185; Horizon2020 no. 668303 PERFORM; Wellcome Trust (206508/Z/17/Z); Medical Research Foundation (MRF-160-0008-ELP-KAFO-C0801); NIHR Imperial BRC.
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Affiliation(s)
- Dominic Habgood-Coote
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Clare Wilson
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Chisato Shimizu
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Anouk M Barendregt
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Ria Philipsen
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Rachel Galassini
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Irene Rivero Calle
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Lesley Workman
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Philipp K A Agyeman
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gerben Ferwerda
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Suzanne T Anderson
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - J Merlijn van den Berg
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Marieke Emonts
- Great North Children's Hospital, Department of Paediatric Immunology, Infectious Diseases & Allergy and NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Enitan D Carrol
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Colin G Fink
- Micropathology Ltd Research and Diagnosis, Coventry, UK; University of Warwick, Coventry, UK
| | - Ronald de Groot
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - John Kanegaye
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Mark P Nicol
- Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Stéphane Paulus
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Antonio Salas
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Fatou Secka
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Luregn J Schlapbach
- Pediatric and Neonatal Intensive Care Unit, and Children`s Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Child Health Research Centre, The University of Queensland, and Paediatric Intensive Care Unit, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Adriana H Tremoulet
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Walther
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Werner Zenz
- University Clinic of Paediatrics and Adolescent Medicine, Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Michiel Van der Flier
- Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Paediatric Infectious Diseases and Immunology Amalia Children's Hospital, Radboudumc, Nijmegen, the Netherlands
| | - Heather J Zar
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands; Department of Blood Cell Research, Sanquin Blood Supply, Division Research and Landsteiner Laboratory of Amsterdam UMC (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Jane C Burns
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Federico Martinón-Torres
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Victoria J Wright
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Jethro A Herberg
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK.
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Eid R, Zahar JR, Ait Ali C, Mizrahi A, Ibrahim R, Banh E, Halouani H, Jauréguy F, Pilmis B, Saliba R. Bloodstream Infections: Comparison of Diagnostic Methods and Therapeutic Consequences between a Hospital in a Resource-Limited Setting and Two French Hospitals. Microorganisms 2023; 11:2136. [PMID: 37763979 PMCID: PMC10535486 DOI: 10.3390/microorganisms11092136] [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: 06/15/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
In recent years, the diagnosis of bloodstream infections has been complemented by rapid microbiological methods, unattainable to most clinical laboratories in resource-limited settings. We evaluated the impact of their shortage on antibiotic therapy adequacy. We conducted a prospective multicenter cohort study including 150 adult Gram-negative bacilli bacteremia episodes, evenly distributed across three university hospitals: one in Lebanon, a resource-limited setting, and two in France, a resource-rich setting. Previous colonization by multidrug-resistant organisms (MDRO) was significantly more prevalent among the Lebanese than the French group of patients (16/50 vs. 5/100; p < 0.01). Bloodstream infections by carbapenemase-producing Enterobacterales and other MDRO were higher among the Lebanese than the French group of patients (25/50 vs. 12/100; p < 0.01). For the French group, rapid identification of species and mechanisms of resistance significantly shortened turnaround time for definitive laboratory diagnosis and increased antibiotic therapy adequacy. No statistically significant differences were noted in targeted antibiotic therapy between the two groups. This study suggests that, in settings where bacterial resistance is prevalent, rapid microbiological methods have not provided any additional value. The clinical and economic impact of rapid microbiological methods will likely depend on local CPE, VRE, and other MDRO epidemiology and are areas for future research.
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Affiliation(s)
- Racha Eid
- Clinical Microbiology Department, Hotel Dieu de France Teaching Hospital, Saint-Joseph University of Beirut, Beirut 1100, Lebanon; (R.E.); (R.I.); (R.S.)
| | - Jean-Ralph Zahar
- Clinical Microbiology Department, Avicenne Hospital, 93000 Bobigny, France; (C.A.A.); (H.H.); (F.J.)
- UMR1137-IAME, Inserm, Paris Cite University, 75006 Paris, France
| | - Chahrazed Ait Ali
- Clinical Microbiology Department, Avicenne Hospital, 93000 Bobigny, France; (C.A.A.); (H.H.); (F.J.)
- UMR1137-IAME, Inserm, Paris Cite University, 75006 Paris, France
| | - Assaf Mizrahi
- Clinical Microbiology Department, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France; (A.M.); (E.B.); (B.P.)
| | - Racha Ibrahim
- Clinical Microbiology Department, Hotel Dieu de France Teaching Hospital, Saint-Joseph University of Beirut, Beirut 1100, Lebanon; (R.E.); (R.I.); (R.S.)
| | - Emeline Banh
- Clinical Microbiology Department, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France; (A.M.); (E.B.); (B.P.)
| | - Habib Halouani
- Clinical Microbiology Department, Avicenne Hospital, 93000 Bobigny, France; (C.A.A.); (H.H.); (F.J.)
- UMR1137-IAME, Inserm, Paris Cite University, 75006 Paris, France
| | - Françoise Jauréguy
- Clinical Microbiology Department, Avicenne Hospital, 93000 Bobigny, France; (C.A.A.); (H.H.); (F.J.)
- UMR1137-IAME, Inserm, Paris Cite University, 75006 Paris, France
| | - Benoit Pilmis
- Clinical Microbiology Department, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France; (A.M.); (E.B.); (B.P.)
| | - Rindala Saliba
- Clinical Microbiology Department, Hotel Dieu de France Teaching Hospital, Saint-Joseph University of Beirut, Beirut 1100, Lebanon; (R.E.); (R.I.); (R.S.)
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Kalpana S, Lin WY, Wang YC, Fu Y, Wang HY. Alternate Antimicrobial Therapies and Their Companion Tests. Diagnostics (Basel) 2023; 13:2490. [PMID: 37568853 PMCID: PMC10417861 DOI: 10.3390/diagnostics13152490] [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: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023] Open
Abstract
New antimicrobial approaches are essential to counter antimicrobial resistance. The drug development pipeline is exhausted with the emergence of resistance, resulting in unsuccessful trials. The lack of an effective drug developed from the conventional drug portfolio has mandated the introspection into the list of potentially effective unconventional alternate antimicrobial molecules. Alternate therapies with clinically explicable forms include monoclonal antibodies, antimicrobial peptides, aptamers, and phages. Clinical diagnostics optimize the drug delivery. In the era of diagnostic-based applications, it is logical to draw diagnostic-based treatment for infectious diseases. Selection criteria of alternate therapeutics in infectious diseases include detection, monitoring of response, and resistance mechanism identification. Integrating these diagnostic applications is disruptive to the traditional therapeutic development. The challenges and mitigation methods need to be noted. Applying the goals of clinical pharmacokinetics that include enhancing efficacy and decreasing toxicity of drug therapy, this review analyses the strong correlation of alternate antimicrobial therapeutics in infectious diseases. The relationship between drug concentration and the resulting effect defined by the pharmacodynamic parameters are also analyzed. This review analyzes the perspectives of aligning diagnostic initiatives with the use of alternate therapeutics, with a particular focus on companion diagnostic applications in infectious diseases.
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
| | - Wan-Ying Lin
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA;
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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Chatelard PA, Rousseau N, Parmeland L, Metral P, Pariset C, Vivier E. Shortening identification times: comparative observational study of three early blood culture testing protocols. Front Cell Infect Microbiol 2023; 13:1192002. [PMID: 37533929 PMCID: PMC10390722 DOI: 10.3389/fcimb.2023.1192002] [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: 03/22/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Background While early appropriate antibiotic therapy is a proven means of limiting the progression of infections, especially bacteremia, empirical antibiotic therapy in sepsis is ineffective up to 30%. The aim of this study was to compare early blood culture testing protocols in terms of their ability to shorten the delay between blood sampling and appropriate antibiotic therapy. Methods In this french observational study, we compared three blood culture testing protocols. Positive blood cultures were tested using either GenMark ePlex panels (multiplex PCR period), a combination of MRSA/SA PCR, β-Lacta and oxidase tests (multitest period), or conventional identification and susceptibility tests only (reference period). Conventional identification and susceptibility tests were performed in parallel for all samples, as the gold standard. Results Among the 270 patients with positive blood cultures included, early and conventional results were in good agreement, especially for the multitest period. The delay between a blood culture positivity and initial results was 3.8 (2.9-6.9) h in the multiplex PCR period, 2.6 (1.3-4.5) h in the multitest period and 3.7 (1.8-8.2) h in the reference period (p<0.01). Antibiotic therapy was initiated or adjusted in 68 patients based on early analysis results. The proportion of patients receiving appropriate antibiotic therapy within 48 h of blood sampling was higher in the multiplex PCR and multitest periods, (respectively 90% and 88%) than in the reference period (71%). Conclusion These results suggest rapid bacterial identification and antibiotic resistance tests are feasible, efficient and can expedite appropriate antibiotic therapy.
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Affiliation(s)
| | - Nathalie Rousseau
- Centre Hospitalier Saint Joseph Saint Luc, Laboratoire de biologie médicale, Lyon, France
| | - Laurence Parmeland
- Centre Hospitalier Saint Joseph Saint Luc, Laboratoire de biologie médicale, Lyon, France
| | - Pierre Metral
- Centre Hospitalier Saint Joseph Saint Luc, Département d’Information Médicale, Lyon, France
| | - Caroline Pariset
- Centre Hospitalier Saint Joseph Saint Luc, Maladies Infectieuses, Lyon, France
| | - Emmanuel Vivier
- Centre Hospitalier Saint Joseph Saint Luc, Médecine Intensive Réanimation, Lyon, France
- Centre Hospitalier Saint Joseph Saint Luc, Unité de Recherche Clinique, Lyon, France
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Huang Z, Lyon CJ, Wang J, Lu S, Hu TY. CRISPR Assays for Disease Diagnosis: Progress to and Barriers Remaining for Clinical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301697. [PMID: 37162202 PMCID: PMC10369298 DOI: 10.1002/advs.202301697] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Numerous groups have employed the special properties of CRISPR/Cas systems to develop platforms that have broad potential applications for sensitive and specific detection of nucleic acid (NA) targets. However, few of these approaches have progressed to commercial or clinical applications. This review summarizes the properties of known CRISPR/Cas systems and their applications, challenges associated with the development of such assays, and opportunities to improve their performance or address unmet assay needs using nano-/micro-technology platforms. These include rapid and efficient sample preparation, integrated single-tube, amplification-free, quantifiable, multiplex, and non-NA assays. Finally, this review discusses the current outlook for such assays, including remaining barriers for clinical or point-of-care applications and their commercial development.
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Affiliation(s)
- Zhen Huang
- National Clinical Research Center for Infectious DiseasesShenzhen Third People's HospitalSouthern University of Science and Technology29 Bulan RoadShenzhenGuangdong518112China
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
| | - Christopher J. Lyon
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
| | - Jin Wang
- Tolo Biotechnology Company Limited333 Guiping RoadShanghai200233China
| | - Shuihua Lu
- National Clinical Research Center for Infectious DiseasesShenzhen Third People's HospitalSouthern University of Science and Technology29 Bulan RoadShenzhenGuangdong518112China
| | - Tony Y. Hu
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
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Oruganti S, Lakshmi Gundimeda S, Buddolla V, Anantha Lakshmi B, Kim YJ. Paper-based diagnostic chips for viral detection. Clin Chim Acta 2023:117413. [PMID: 37263536 DOI: 10.1016/j.cca.2023.117413] [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: 01/20/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
Viruses cause various diseases in humans, and pose serious health risks to individuals and populations worldwide. As a result, various diagnostic procedures and methods have been developed to prevent, manage, and reduce the burden of viral diseases, each with its own benefits and drawbacks. Among these, paper-based diagnostic chips are becoming increasingly common because of their speed, accuracy, convenience, and economical and environmental friendliness. These paper-based diagnostic tests have ideal point-of-care (POC) diagnostic applications, particularly in personalized healthcare. Paper-based diagnostics have emerged as innovative and low-cost solutions for diagnosing viral diseases in remote and underdeveloped regions where traditional diagnostic methods are not readily available. These tests are easy to use, require minimal equipment, and can be performed by nonspecialized personnel, making them accessible even in resource-constrained settings. In this review, we discuss recent developments in paper-based diagnostic chips, the importance of improved methods for identifying viral pathogens, drawbacks of traditional detection techniques, and challenges and prospects of paper-based diagnostic chips for the detection of viruses.
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Affiliation(s)
- Srividya Oruganti
- Dr. Buddolla's Institute of Life Sciences, Tirupati-517506, Andhra Pradesh, India
| | | | - Viswanath Buddolla
- Dr. Buddolla's Institute of Life Sciences, Tirupati-517506, Andhra Pradesh, India
| | - Buddolla Anantha Lakshmi
- Department of Electronic Engineering, Gachon University, 1342 Seongnam-Daero, Seongnam, Gyeonggi-Do 13120, Republic of Korea.
| | - Young-Joon Kim
- Department of Electronic Engineering, Gachon University, 1342 Seongnam-Daero, Seongnam, Gyeonggi-Do 13120, Republic of Korea.
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Mwakibete L, Takahashi S, Ahyong V, Black A, Rek J, Ssewanyana I, Kamya M, Dorsey G, Jagannathan P, Rodríguez-Barraquer I, Tato CM, Greenhouse B. Metagenomic next-generation sequencing to characterize potential etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001675. [PMID: 37134083 PMCID: PMC10156012 DOI: 10.1371/journal.pgph.0001675] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/12/2023] [Indexed: 05/04/2023]
Abstract
Causes of non-malarial fevers in sub-Saharan Africa remain understudied. We hypothesized that metagenomic next-generation sequencing (mNGS), which allows for broad genomic-level detection of infectious agents in a biological sample, can systematically identify potential causes of non-malarial fevers. The 212 participants in this study were of all ages and were enrolled in a longitudinal malaria cohort in eastern Uganda. Between December 2020 and August 2021, respiratory swabs and plasma samples were collected at 313 study visits where participants presented with fever and were negative for malaria by microscopy. Samples were analyzed using CZ ID, a web-based platform for microbial detection in mNGS data. Overall, viral pathogens were detected at 123 of 313 visits (39%). SARS-CoV-2 was detected at 11 visits, from which full viral genomes were recovered from nine. Other prevalent viruses included Influenza A (14 visits), RSV (12 visits), and three of the four strains of seasonal coronaviruses (6 visits). Notably, 11 influenza cases occurred between May and July 2021, coinciding with when the Delta variant of SARS-CoV-2 was circulating in this population. The primary limitation of this study is that we were unable to estimate the contribution of bacterial microbes to non-malarial fevers, due to the difficulty of distinguishing bacterial microbes that were pathogenic from those that were commensal or contaminants. These results revealed the co-circulation of multiple viral pathogens likely associated with fever in the cohort during this time period. This study illustrates the utility of mNGS in elucidating the multiple potential causes of non-malarial febrile illness. A better understanding of the pathogen landscape in different settings and age groups could aid in informing diagnostics, case management, and public health surveillance systems.
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Affiliation(s)
- Lusajo Mwakibete
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Saki Takahashi
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Allison Black
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - John Rek
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University, Kampala, Uganda
| | - Grant Dorsey
- Department of Medicine, Division of HIV, ID, and Global Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | - Prasanna Jagannathan
- Department of Medicine, Stanford University, Palo Alto, CA, United States of America
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA, United States of America
| | - Isabel Rodríguez-Barraquer
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Bryan Greenhouse
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
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Rankin DA, Peetluk LS, Deppen S, Slaughter JC, Katz S, Halasa NB, Khankari NK. Diagnostic models predicting paediatric viral acute respiratory infections: a systematic review. BMJ Open 2023; 13:e067878. [PMID: 37085296 PMCID: PMC10124282 DOI: 10.1136/bmjopen-2022-067878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/03/2023] [Indexed: 04/23/2023] Open
Abstract
OBJECTIVES To systematically review and evaluate diagnostic models used to predict viral acute respiratory infections (ARIs) in children. DESIGN Systematic review. DATA SOURCES PubMed and Embase were searched from 1 January 1975 to 3 February 2022. ELIGIBILITY CRITERIA We included diagnostic models predicting viral ARIs in children (<18 years) who sought medical attention from a healthcare setting and were written in English. Prediction model studies specific to SARS-CoV-2, COVID-19 or multisystem inflammatory syndrome in children were excluded. DATA EXTRACTION AND SYNTHESIS Study screening, data extraction and quality assessment were performed by two independent reviewers. Study characteristics, including population, methods and results, were extracted and evaluated for bias and applicability using the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies and PROBAST (Prediction model Risk Of Bias Assessment Tool). RESULTS Of 7049 unique studies screened, 196 underwent full text review and 18 were included. The most common outcome was viral-specific influenza (n=7; 58%). Internal validation was performed in 8 studies (44%), 10 studies (56%) reported discrimination measures, 4 studies (22%) reported calibration measures and none performed external validation. According to PROBAST, a high risk of bias was identified in the analytic aspects in all studies. However, the existing studies had minimal bias concerns related to the study populations, inclusion and modelling of predictors, and outcome ascertainment. CONCLUSIONS Diagnostic prediction can aid clinicians in aetiological diagnoses of viral ARIs. External validation should be performed on rigorously internally validated models with populations intended for model application. PROSPERO REGISTRATION NUMBER CRD42022308917.
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Affiliation(s)
- Danielle A Rankin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Epidemiology PhD Program, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lauren S Peetluk
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephen Deppen
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Sophie Katz
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Natasha B Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nikhil K Khankari
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Strouts FR, McAllister LB, Tsalik EL. Viewing both sides of the coin for infectious disease diagnosis. J Clin Invest 2023; 133:169242. [PMID: 37066874 PMCID: PMC10104889 DOI: 10.1172/jci169242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Optimal management of lower respiratory tract infection relies on distinguishing infectious from noninfectious etiologies and identifying the microbiologic cause if applicable. This process is complicated by overlapping clinical symptoms and the colonizing lung microbiota. In a recent issue of the JCI, Mick, Tsitsiklis, and colleagues apply RNA-Seq to tracheal aspirates from critically ill children and demonstrate how integration of the host response with microbial identification results in a harmonious and accurate diagnostic classifier. Though promising, there are numerous barriers to realizing a combined host and pathogen diagnostic.
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Affiliation(s)
| | | | - Ephraim L Tsalik
- Danaher Diagnostics, Washington, DC, USA
- Durham VA Health Care System, Durham, North Carolina, USA
- Duke University School of Medicine, Durham, North Carolina, USA
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Lin Z, Lawrence WR, Gong W, Lin L, Hu J, Zhu S, Meng R, He G, Xu X, Liu T, Zhong J, Yu M, Reinhold K, Ma W. The impact of mortality underreporting on the association of ambient temperature and PM10 with mortality risk in time series study. Heliyon 2023; 9:e14648. [PMID: 37025823 PMCID: PMC10070596 DOI: 10.1016/j.heliyon.2023.e14648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Properly analyzing and reporting data remains a challenging task in epidemiologic research, as underreporting of data is often overlooked. The evaluation on the effect of underreporting remains understudied. In this study, we examined the effect of different scenarios of mortality underreporting on the relationship between PM10, temperature, and mortality. Mortality data, PM10, and temperature data in seven cities were obtained from Provincial Center for Disease Control and Prevention (CDC), China Meteorological Data Sharing Service System, and China National Environmental Monitoring Center, respectively. A time-series design with a distributed lag nonlinear model (DLNM) was used to examine the effects of five mortality underreporting scenarios: 1) Random underreporting of mortality; 2) Underreporting is monotonically increasing (MI) or monotonically decreasing (MD); 3) Underreporting due to holiday and weekends; 4) Underreporting occurs before the 20th day of each month, and these underreporting will be added after the 20th day of the month; and 5) Underreporting due to holiday, weekends, MI, and MD. We observed that underreporting at random (UAR) scenario had little effect on the association between PM10, temperature, and daily mortality. However, other four underreporting not at random (UNAR) scenarios mentioned above had varying degrees of influence on the association between PM10, temperature, and daily mortality. Additionally, in addition to imputation under UAR, the variation of minimum mortality temperature (MMT) and attributable fraction (AF) of mortality attributed to temperature in the same imputation scenarios is inconsistent in different cities. Finally, we observed that the pooled excess risk (ER) below MMT was negatively associated with mortality and the pooled ER above MMT was positively associated with mortality. This study showed that UNAR impacted the association between PM10, temperature, and mortality, and potential underreporting should be dealt with before analyzing data to avoid drawing invalid conclusions.
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Affiliation(s)
- Ziqiang Lin
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, 511443, China
| | - Wayne R. Lawrence
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, State University of New York, 1 University Place, Rensselaer, NY, 12144, United States
| | - Weiwei Gong
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310009, China
| | - Lifeng Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Jianxiong Hu
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Sui Zhu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, 511443, China
| | - Ruilin Meng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Guanhao He
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, 511443, China
| | - Xiaojun Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Tao Liu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, 511443, China
| | - Jieming Zhong
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310009, China
| | - Min Yu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310009, China
| | - Karin Reinhold
- Department of Mathematics and Statistics, College of Arts and Sciences, University at Albany, State University of New York, 1400 Washington Ave, Albany, NY, 12222, United States
| | - Wenjun Ma
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, 511443, China
- Corresponding author.
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44
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Bramer S, Cheung HY, Do W, Leeflang MMG. Overinterpretation of findings in diagnostic accuracy studies of infectious diseases. Clin Microbiol Infect 2023:S1198-743X(23)00120-9. [PMID: 36925106 DOI: 10.1016/j.cmi.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/03/2023] [Accepted: 03/05/2023] [Indexed: 03/17/2023]
Abstract
OBJECTIVES To assess the prevalence of overly positive interpretation - also called 'spin'- of results in diagnostic accuracy studies of infectious diseases and to identify suggestions for improvement. METHODS A PubMed search was performed to identify diagnostic accuracy studies of infectious diseases published between January and March 2019. Each article was assessed by two authors independently to identify study characteristics and forms of actual and potential overinterpretation. 'Actual overinterpretation' was defined as conclusions that were not based on the study aims or conclusions that were more favourable than was justified by the study findings. There are other practices that may result in the overinterpretation of study findings and these have been described as 'potential overinterpretation'. RESULTS The final analysis included 120 studies. Favourable or promising recommendations were made in the main text of 101 (84%) of the included studies. Evidence of actual overinterpretation (spin) was found in 30 (25%) articles, with 22 studies reporting a conclusion that did not match the study aims and 56 studies with a more positive conclusion in the abstract than in the main text. All analysed studies exhibited at least one form of potential overinterpretation, with was most commonly a lack of sample size calculation (n = 109, 91%) and not reporting a null hypothesis (n = 115, 96%). CONCLUSIONS Evidence of overinterpretation of results was found in a third of the included studies. We propose possible interventions to prevent overly positive interpretation of results in diagnostic accuracy studies.
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Affiliation(s)
- Solange Bramer
- Oxford University Hospitals, Oxford University, Oxford, United Kingdom
| | - Ho Yee Cheung
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Wesley Do
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Mariska M G Leeflang
- Department of Epidemiology and Data Science, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
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45
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Bošković F, Zhu J, Tivony R, Ohmann A, Chen K, Alawami MF, Đorđević M, Ermann N, Pereira-Dias J, Fairhead M, Howarth M, Baker S, Keyser UF. Simultaneous identification of viruses and viral variants with programmable DNA nanobait. NATURE NANOTECHNOLOGY 2023; 18:290-298. [PMID: 36646828 PMCID: PMC10020084 DOI: 10.1038/s41565-022-01287-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
Abstract
Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.
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Affiliation(s)
- Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Milan Đorđević
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Niklas Ermann
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Joana Pereira-Dias
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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46
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Gumus E, Bingol H, Zor E. Lateral flow assays for detection of disease biomarkers. J Pharm Biomed Anal 2023; 225:115206. [PMID: 36586382 DOI: 10.1016/j.jpba.2022.115206] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Early diagnosis saves lives in many diseases. In this sense, monitoring of biomarkers is crucial for the diagnosis of diseases. Lateral flow assays (LFAs) have attracted great attention among paper-based point-of-care testing (POCT) due to their low cost, user-friendliness, and time-saving advantages. Developments in the field of health have led to an increase of interest in these rapid tests. LFAs are used in the diagnosis and monitoring of many diseases, thanks to biomarkers that can be observed in body fluids. This review covers the recent advances dealing with the design and strategies for the development of LFA for the detection of biomarkers used in clinical applications in the last 5 years. We focus on various strategies such as choosing the nanoparticle type, single or multiple test approaches, and equipment for signal transducing for the detection of the most common biomarkers in different diseases such as cancer, cardiovascular, infectious, and others including Parkinson's and Alzheimer's diseases. We expect that this study will contribute to the different approaches in LFA and pave the way for other clinical applications.
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Affiliation(s)
- Eda Gumus
- Biomaterials and Biotechnology Laboratory, Science and Technology Research and Application Center (BITAM), Necmettin Erbakan University, 42140 Konya, Turkey
| | - Haluk Bingol
- Biomaterials and Biotechnology Laboratory, Science and Technology Research and Application Center (BITAM), Necmettin Erbakan University, 42140 Konya, Turkey; Department of Chemistry Education, A.K. Education Faculty, Necmettin Erbakan University, 42090 Konya, Turkey
| | - Erhan Zor
- Biomaterials and Biotechnology Laboratory, Science and Technology Research and Application Center (BITAM), Necmettin Erbakan University, 42140 Konya, Turkey; Department of Science Education, A.K. Education Faculty, Necmettin Erbakan University, 42090 Konya, Turkey.
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47
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Shim H. Three Innovations of Next-Generation Antibiotics: Evolvability, Specificity, and Non-Immunogenicity. Antibiotics (Basel) 2023; 12:antibiotics12020204. [PMID: 36830114 PMCID: PMC9952447 DOI: 10.3390/antibiotics12020204] [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: 11/29/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance is a silent pandemic exacerbated by the uncontrolled use of antibiotics. Since the discovery of penicillin, we have been largely dependent on microbe-derived small molecules to treat bacterial infections. However, the golden era of antibiotics is coming to an end, as the emergence and spread of antimicrobial resistance against these antibacterial compounds are outpacing the discovery and development of new antibiotics. The current antibiotic market suffers from various shortcomings, including the absence of profitability and investment. The most important underlying issue of traditional antibiotics arises from the inherent properties of these small molecules being mostly broad-spectrum and non-programmable. As the scientific knowledge of microbes progresses, the scientific community is starting to explore entirely novel approaches to tackling antimicrobial resistance. One of the most prominent approaches is to develop next-generation antibiotics. In this review, we discuss three innovations of next-generation antibiotics compared to traditional antibiotics as specificity, evolvability, and non-immunogenicity. We present a number of potential antimicrobial agents, including bacteriophage-based therapy, CRISPR-Cas-based antimicrobials, and microbiome-derived antimicrobial agents. These alternative antimicrobial agents possess innovative properties that may overcome the inherent shortcomings of traditional antibiotics, and some of these next-generation antibiotics are not merely far-fetched ideas but are currently in clinical development. We further discuss some related issues and challenges such as infection diagnostics and regulatory frameworks that still need to be addressed to bring these next-generation antibiotics to the antibiotic market as viable products to combat antimicrobial resistance using a diversified set of strategies.
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Affiliation(s)
- Hyunjin Shim
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon 21985, Republic of Korea
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48
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A Comparative Study on Visual Detection of Mycobacterium tuberculosis by Closed Tube Loop-Mediated Isothermal Amplification: Shedding Light on the Use of Eriochrome Black T. Diagnostics (Basel) 2023; 13:diagnostics13010155. [PMID: 36611447 PMCID: PMC9818645 DOI: 10.3390/diagnostics13010155] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/29/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Loop-mediated isothermal amplification is a promising candidate for the rapid detection of Mycobacterium tuberculosis. However, the high potential for carry-over contamination is the main obstacle to its routine use. Here, a closed tube LAMP was intended for the visual detection of Mtb to compare turbidimetric and two more favorable colorimetric methods using calcein and hydroxy naphthol blue (HNB). Additionally, a less studied dye (i.e., eriochrome black T (EBT)) was optimized in detail in the reaction for the first time. Mtb purified DNA and 30 clinical specimens were used to respectively determine the analytical and diagnostic sensitivities of each method. The turbidimetric method resulted in the best analytical sensitivity (100 fg DNA/reaction), diagnostic sensitivity and specificity (100%), and time-to-positivity of the test (15 min). However, this method is highly prone to subjective error in reading the results. Moreover, HNB-, calcein-, and EBT-LAMP could respectively detect 100 fg, 1 pg, and 1 pg DNA/reaction (the analytical sensitivities) in 30, 15, and 30 min, while the diagnostic sensitivity and specificity were respectively 93.3% and 100% for them all. Interestingly, EBT-LAMP showed the lowest potential for subjective error in reading the results. This report helps judiciously choose the most appropriate visual method, taking a step forward toward the field applicability of LAMP for the detection of Mtb, particularly in resource-limited settings.
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Somanader DS, Brunskill I, Perrin M, Barkema HW, Hillier S, Hindmarch S, Weese JS, Wright GD, Morris AM. Canada has an opportunity to address antimicrobial resistance through COVID-19 recovery spending. LANCET REGIONAL HEALTH. AMERICAS 2022; 16:100393. [PMID: 36415218 PMCID: PMC9672386 DOI: 10.1016/j.lana.2022.100393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/06/2022] [Accepted: 10/21/2022] [Indexed: 11/19/2022]
Abstract
Antimicrobial Resistance (AMR) causes more than a million deaths globally per year due to infections incurable with currently available antibiotics. Failing to effectively address AMR will have significant negative consequences for Canadians and the Canadian economy. Canada is behind on allocation of required funding and nationally coordinated AMR mitigation strategies relative to other high-income countries. A Pan-Canadian AMR action plan and development of a new governance model is pending. Recent AMR-specific funding commitments are significant but fall short while distribution of funds indicate a siloed approach. Canada could initiate progress towards AMR mitigation through incorporation within the scope of budget allocations intended for COVID-19 recovery and mitigation efforts. We discuss the following components for inclusion: development of infectious disease diagnostics and therapeutics; antimicrobial stewardship interventions in long-term care and Indigenous communities; environmental monitoring of AMR; comprehensive antimicrobial use, and AMR surveillance; and support for capacity-building in low and middle-income countries.
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Affiliation(s)
- Deborah S. Somanader
- Antimicrobial Stewardship Program, Sinai Health-University Health Network, Toronto, ON, Canada
| | | | | | | | - Sean Hillier
- Faculty of Health, York University, Toronto, ON, Canada
| | - Suzanne Hindmarch
- Department of Political Science, University of New Brunswick, Fredericton, NB, Canada
| | - J. Scott Weese
- Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Gerard D. Wright
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Andrew M. Morris
- Antimicrobial Stewardship Program, Sinai Health-University Health Network, Toronto, ON, Canada
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50
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Dai Y, Sheng K, Hu L. Diagnostic efficacy of targeted high-throughput sequencing for lower respiratory infection in preterm infants. Am J Transl Res 2022; 14:8204-8214. [PMID: 36505277 PMCID: PMC9730095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/26/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To examine the pathogen diagnostic performance of targeted high-throughput next-gen sequencing (tNGS) in respiratory infectious diseases in preterm infants using dynamic follow-up. METHODS Clinical samples of respiratory secretions were consecutively collected from 20 preterm infants weekly for 5 weeks, during which 10 developed bronchopulmonary dysplasia. Pathogen identification from these collected specimens was performed by both conventional cultivation and tNGS. RESULTS We found that targeted next-generation sequencing shared a 90.9% full or partial consistency for lower respiratory pathogen detection with the traditional culture-based approach, and increased the detection rate by 105.9%. Moreover, most of the pathogens identified by tNGS were diminished in patients after treatment. CONCLUSION This study reveals the high sensitivity and performance of targeted high-throughput sequencing for respiratory infectious disease diagnosis and pathogen identification. The trial registry number is NCT03850457, and the trial URL is https://clinicaltrials.gov/ct2/show/NCT03850457.
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Affiliation(s)
- Yi Dai
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical CenterShanghai, China
| | - Kai Sheng
- Geriatrics Department, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Lan Hu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical CenterShanghai, China
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