Diagnosis Of Infectious Diseases Research Articles

High‐Precision Viral Detection Using Electrochemical Kinetic Profiling of Aptamer‐Antigen Recognition in Clinical Samples and Machine Learning

AbstractHigh‐precision viral detection at point of need with clinical samples plays a pivotal role in the diagnosis of infectious diseases and the control of a global pandemic. However, the complexity of clinical samples that often contain very low viral concentrations makes it a huge challenge to develop simple diagnostic devices that do not require any sample processing and yet are capable of meeting performance metrics such as very high sensitivity and specificity. Herein we describe a new single‐pot and single‐step electrochemical method that uses real‐time kinetic profiling of the interaction between a high‐affinity aptamer and an antigen on a viral surface. This method generates many data points per sample, which when combined with machine learning, can deliver highly accurate test results in a short testing time. We demonstrate this concept using both SARS‐CoV‐2 and Influenza A viruses as model viruses with specifically engineered high‐affinity aptamers. Utilizing this technique to diagnose COVID‐19 with 37 real human saliva samples results in a sensitivity and specificity of both 100 % (27 true negatives and 10 true positives, with 0 false negative and 0 false positive), which showcases the superb diagnostic precision of this method.

Utilizing natural language processing and large language models in the diagnosis and prediction of infectious diseases: A systematic review

Natural Language Processing (NLP) and Large Language Models (LLMs) hold largely untapped potential in infectious disease management. This review explores their current use and uncovers areas needing more attention. This analysis followed systematic review procedures, registered with the Prospective Register of Systematic Reviews. We conducted a search across major databases including PubMed, Embase, Web of Science, and Scopus, up to December 2023, using keywords related to NLP, LLM, and infectious diseases. We also employed the Quality Assessment of Diagnostic Accuracy Studies-2 tool for evaluating the quality and robustness of the included studies. Our review identified 15 studies with diverse applications of NLP in infectious disease management. Notable examples include GPT-4's application in detecting urinary tract infections and BERTweet's use in Lyme Disease surveillance through social media analysis. These models demonstrated effective disease monitoring and public health tracking capabilities. However, the effectiveness varied across studies. For instance, while some NLP tools showed high accuracy in pneumonia detection and high sensitivity in identifying invasive mold diseases from medical reports, others fell short in areas like bloodstream infection management. This review highlights the yet-to-be-fully-realized promise of NLP and LLMs in infectious disease management. It calls for more exploration to fully harness AI's capabilities, particularly in the areas of diagnosis, surveillance, predicting disease courses, and tracking epidemiological trends.

Illumina and Nanopore sequencing in culture-negative samples from suspected lower respiratory tract infection patients.

To evaluate the diagnostic value of metagenomic sequencing technology based on Illumina and Nanopore sequencing platforms for patients with suspected lower respiratory tract infection whose pathogen could not be identified by conventional microbiological tests. Patients admitted to the Respiratory and Critical Care Medicine in Shanghai Ruijin Hospital were retrospectively studied from August 2021 to March 2022. Alveolar lavage or sputum was retained in patients with clinically suspected lower respiratory tract infection who were negative in conventional tests. Bronchoalveolar lavage fluid (BALF) samples were obtained using bronchoscopy. Sputum samples were collected, while BALF samples were not available due to bronchoscopy contraindications. Samples collected from enrolled patients were simultaneously sent for metagenomic sequencing on both platforms. Thirty-eight patients with suspected LRTI were enrolled in this study, consisting of 36 parts of alveolar lavage and 2 parts of sputum. According to the infection diagnosis, 31 patients were confirmed to be infected with pathogens, while 7 patients were diagnosed with non-infectious disease. With regard to the diagnosis of infectious diseases, the sensitivity and specificity of Illumina and Nanopore to diagnose infection in patients were 80.6% vs. 93.5% and 42.9 vs. 28.6%, respectively. In patients diagnosed with bacterial, Mycobacterium, and fungal infections, the positive rates of Illumina and Nanopore sequencer were 71.4% vs. 78.6%, 36.4% vs. 90.9%, and 50% vs. 62.5%, respectively. In terms of pathogen diagnosis, the sensitivity and specificity of pathogens detected by Illumina and Nanopore were 55.6% vs. 77.8% and 42.9% vs. 28.6%, respectively. Among the patients treated with antibiotics in the last 2 weeks, 61.1% (11/18) and 77.8% (14/18) cases of pathogens were accurately detected by Illumina and Nanopore, respectively, among which 8 cases were detected jointly. The consistency between Illumina and diagnosis was 63.9% (23/36), while the consistency between Nanopore and diagnosis was 83.3% (30/36). Between Illumina and Nanopore sequencing methods, the consistency ratio was 55% (22/42) based on pathogen diagnosis. Both platforms play a certain value in infection diagnosis and pathogen diagnosis of CMT-negative suspected LRTI patients, providing a theoretical basis for clinical accurate diagnosis and symptomatic treatment. The Nanopore platform demonstrated potential advantages in the identification of Mycobacterium and could further provide another powerful approach for patients with suspected Mycobacterium infection.

Molecular Imaging Techniques in the Diagnosis and Monitoring of Infectious Diseases

Molecular Imaging Techniques in the Diagnosis and Monitoring of Infectious Diseases

Indirect hemagglutination assay for diagnosing brucellosis: Past, present, and future

Brucellosis is a zoonotic disease that causes enormous losses in livestock production worldwide and has a significant public health impact. None of the brucellosis-free countries is currently able to guarantee their ability to prevent the introduction of the pathogen due to the increase in tourism and the expansion of migration. The timely identification of infected animals is an effective means of preventing brucellosis and minimizing the epidemiological risk. The tube agglutination test, Rose Bengal plate test, complement fixation test, and enzyme-linked immunosorbent assay, which are routinely used to identify seropositive productive animals, have limitations and results that do not always correlate. The indirect hemagglutination assay (IHA) stands out among non-traditional methods because it is affordable, has a simple protocol, and is more reliable than classical serological tests, especially in cases of questionable and/or false-negative results. The diagnostic value of the IHA has long been studied by laboratories in several countries, but mostly by post-soviet research teams; therefore, the results continue to be published in Russian-language journals, ensuring that the local scientific community can access the results. In addition, the efficacy of this test for the diagnosis of brucellosis and other infectious diseases has not yet been reviewed. The purpose of this review was to summarize the results of studies on the development and use of IHA for the diagnosis of brucellosis and to determine the prospects for further improvement Keywords: brucellosis, diagnostic value, indirect hemagglutination assay, prospects for improving the test, serological tests.

Metronidazole Refractory Giardiasis Complicating the Management of Rhabdomyosarcoma in a Child

Giardiasis caused by Giardia duodenalis is one of the leading causes of gastroenteritis, especially in developing countries. The scenario may be further complicated by emerging metronidazole refractory cases worldwide. We present a case of a 2-year-old girl on chemotherapy for metastatic para meningeal rhabdomyosarcoma. She had a 15 day history of persistent diarrhea of foul-smelling loose stools, without fever. Light microscopy of stool wet mounts revealed cysts and trophozoites of Giardia duodenalis. The patient was managed with nitazoxanide after metronidazole proved ineffective clinically. This case highlights the importance of timely diagnosis and management of infectious diseases and rising antimicrobial resistance among parasites.

Differential Diagnosis of Infectious and Inflammatory Diseases of the Maxillofacial Area, Taking into Account Immunological Parameters of Oral Fluid

Differential Diagnosis of Infectious and Inflammatory Diseases of the Maxillofacial Area, Taking into Account Immunological Parameters of Oral Fluid

Diagnostic yield and complications of flexible bronchoscopy performed at Charlotte Maxeke Johannesburg academic hospital: A 5 year restrospective study

Objectives: There is a high incidence of lung diseases but very little data in South Africa relating to bronchoscopy practice. The objectives of the study are to determine the diagnostic yield, indications, and complications as well as determine the effectiveness of biopsy and bronchoalveolar lavage (BAL) in making diagnoses of infectious and non-infectious diseases. Materials and Methods: Six hundred and ninety-two patients were identified and 647 cases were analyzed due to 45 cases with inadequate data for analyses. A single-center retrospective cross-sectional review of patients who underwent bronchoscopy between January 2015 and December 2019 was conducted at the Charlotte Maxeke Johannesburg Academic Hospital. Results: The epidemiology of the subjects showed a significant male predominance (64.14%), with a mean age of 55.9 years of age. The most common indication was suspected malignancy, followed by non-resolving pneumonia, 63.99%, and 14.53%, respectively. A total of 120 (18.55%) patients were diagnosed with a malignancy on biopsy and 83 (12.83%) on BAL. Of all bronchoscopies performed, 85.94% had no complications during or after bronchoscopy, whereas 10.97% were complicated with bleeding. Conclusion: This audit revealed that flexible bronchoscopy is safe and effective and associated with minimal risk. This study revealed the use of bronchoscopy in diagnosing lung malignancies/carcinomas and highlights the necessity of the availability of bronchoscopy.

Exploring hospital resilience protective or risk factors: lessons for future disaster response efforts.

Hospital resilience is essential in responding to disasters, but current research focuses mainly on frameworks and models rather than the protection of resilience and analysis of risk factors during public health emergencies. This study aims to examine the development of resilience in Chinese frontline hospitals during the initial COVID-19 outbreak in 2020, providing insights for future disaster response efforts. We conducted interviews with 26 hospital staff members who were involved in the initial response to the COVID-19 outbreak in China. We used a semi-structured interview approach and employed purposive sampling and snowball sampling techniques. The interview outline was guided by the 'Action Framework' proposed by the World Health Organization (WHO) for responding to infectious disease emergencies. This framework includes dimensions such as command, surveillance, risk communication, medical response, and public health response. We analyzed the collected data using Colaizzi's seven-step data analysis method and the template analysis method. WHO's 'action framework' effectively highlights the factors that contribute to hospital resilience. While medical response, including the availability of materials and facilities, the use of information technology, and the capacity for infectious disease diagnosis and treatment, remains crucial, other important aspects include awareness and beliefs about infections, treatment experience, interdisciplinary collaboration, and more. Additionally, it is essential to establish an intelligent command system, foster trusting partnerships between teams, improve monitoring capabilities for infectious disease agents, enhance risk communication through information synchronization and transparency, strengthen infection control planning, and improve environmental disinfection capabilities for effective public health emergency response. These contradictions significantly impact the enhancement of hospital resilience in dealing with major infectious disease outbreaks. In responding to sudden major infectious diseases, hospitals play a vital role within the healthcare system. Enhancing hospital resilience involves more than just improving treatment capabilities. It also requires effective command coordination at the hospital level, infection control planning, and the deployment of intelligent equipment. Additionally, planning for effective communication and coordination between hospitals, communities, and the national healthcare system can further enhance hospital resilience.

Performance of metagenomic next-generation sequencing in cerebrospinal fluid for diagnosis of tuberculous meningitis.

Purpose. Metagenomic next-generation sequencing (mNGS) has been widely used in the diagnosis of infectious diseases, while its performance in diagnosis of tuberculous meningitis (TBM) is incompletely characterized. The aim of this study was to assess the performance of mNGS in the diagnosis of TBM, and illustrate the sensitivity and specificity of different methods.Methods. We retrospectively recruited TBM patients between January 2021 and March 2023 to evaluate the performance of mNGS on cerebrospinal fluid (CSF) samples, in comparison with conventional microbiological testing, including culturing of Mycobacterium tuberculosis (MTB), acid-fast bacillus (AFB) stain, reverse transcription PCR and Xpert MTB/RIF.Results. Of the 40 enrolled, 34 participants were diagnosed with TBM, including 15(44.12 %) definite and 19(55.88 %) clinical diagnosis based upon clinical manifestations, CSF parameters, brain imaging, pathogen evidence and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MTBC) in 11 CSF samples. In patients with definite TBM, the sensitivity, specificity, positive predictive value, negative predictive value and accuracy of mNGS were 78.57, 100, 100, 66.67 and 85 %, respectively. Compared to conventional diagnostic methods, the sensitivity of mNGS (78.57 %) was higher than AFB (0 %), culturing (0 %), RT-PCR (60 %) and Xpert MTB/RIF (14.29 %).Conclusions. Our study indicates that mNGS of CSF exhibited an overall improved sensitivity over conventional diagnostic methods for TBM and can be considered a front-line CSF test.

ACM’s transition to an English journal: A leap towards international recognition

The Annals of Clinical Microbiology (Ann Clin Microbiol, ACM) serves as the official journal of the Korean Society of Clinical Microbiology. It is dedicated to publishing research articles encompassing all facets of clinical microbiology, intending to disseminate research findings pertinent to scholarly endeavors within the realm of clinical microbiology for the diagnosis, treatment, and prevention of infections in humans. Clinical microbiology stands as a pivotal discipline for the prevention, diagnosis, and treatment of infectious diseases in modern society. The publication of articles within the domain of clinical microbiology assumes a significant role in the dissemination and progression of advanced medical technology and knowledge. It provides a platform for various issues such as the discovery and treatment of new infectious diseases and the problem of antibiotic resistance. In Korea, this journal stands as the sole academic publication primarily dedicated to clinical microbiology, garnering substantial recognition for its academic contributions in this arena.

The Big Three diagnostic errors through reflections of Japanese internists.

To analyze the Big Three diagnostic errors (malignant neoplasms, cardiovascular diseases, and infectious diseases) through internists' self-reflection on their most memorable diagnostic errors. This secondary analysis study, based on a web-based cross-sectional survey, recruited participants from January 21 to 31, 2019. The participants were asked to recall the most memorable diagnostic error cases in which they were primarily involved. We gathered data on internists' demographics, time to error recognition, and error location. Factors causing diagnostic errors included environmental conditions, information processing, and cognitive bias. Participants scored the significance of each contributing factor on a Likert scale (0, unimportant; 10, extremely important). The Big Three comprised 54.1 % (n=372) of the 687 cases reviewed. The median physician age was 51.5 years (interquartile range, 42-58 years); 65.6 % of physicians worked in hospital settings. Delayed diagnoses were the most common among malignancies (n=64, 46 %). Diagnostic errors related to malignancy were frequent in general outpatient settings on weekdays and in the mornings and were not identified for several months following the event. Environmental factors often contributed to cardiovascular disease-related errors, which were typically identified within days in emergency departments, during night shifts, and on holidays. Information gathering and interpretation significantly impacted infectious disease diagnoses. The Big Three accounted for the majority of cases recalled by Japanese internists. The most relevant contributing factors were different for each of the three categories. Addressing these errors may require a unique approach based on the disease associations.

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.

Metagenomic sequencing has emerged as a transformative tool in infectious disease diagnosis, offering a comprehensive and unbiased approach to pathogen detection. Leveraging international standards and guidelines is essential for ensuring the quality and reliability of metagenomic sequencing in clinical practice. This review explores the implications of international standards and guidelines for the application of metagenomic sequencing in infectious disease diagnosis. By adhering to established standards, such as those outlined by regulatory bodies and expert consensus, healthcare providers can enhance the accuracy and clinical utility of metagenomic sequencing. The integration of international standards and guidelines into metagenomic sequencing workflows can streamline diagnostic processes, improve pathogen identification, and optimize patient care. Strategies in implementing these standards for infectious disease diagnosis using metagenomic sequencing are discussed, highlighting the importance of standardized approaches in advancing precision infectious disease diagnosis initiatives.

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications.

The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.

CRISPR-Cas12/Cas13: Bibliometric analysis and systematic review of its application in infectious disease detection

BackgroundInfectious diseases impose a significant burden on the global public health and economy, resulting in an estimated 15 million deaths out of 57 million annually worldwide. This study examines the current state of CRISPR-Cas12/Cas13 research, focusing on its applications in infectious disease detection and its evolutionary trajectory. MethodsA bibliometric analysis and systematic review were conducted by retrieving CRISPR-Cas12/Cas13-related articles published between January 1, 2015 to December 31, 2022, from the Web of Science database. The research protocol was registered with International Platform of Registered Systematic Review and Meta-analysis Protocols (INPLASY202380062). ResultsOur search identified 1987 articles, of which, 1856 were included in the bibliometric analysis and 445 were used in qualitative analysis. The study reveals a substantial increase in scientific production on CRISPR-Cas12/Cas13, with an annual growth rate of 104.5%. The United States leads in the number of published articles. The systematic review identified 580 different diagnostic assays targeting 170 pathogens, with SARS-CoV-2 dominating with 158 assays. Recombinase polymerase amplification (RPA)/reverse transcription-RPA (RT-RPA) emerged as the predominant amplification method, while lateral flow assay was the most common readout method. Approximately 72% of the diagnostic assays developed are suitable for point-of-care testing. ConclusionThe rapid increase in research on CRISPR-Cas12/Cas13 between 2015 and 2022 suggests promising potential for advancements in infectious disease diagnosis. Given the numerous advantages of CRISPR-Cas technology for disease detection over other methods, and the dedicated efforts of scientists from around the world, it is reasonable to anticipate that CRISPR-Cas technology may emerge as a formidable alternative, offering the possibility of expedited point-of-care testing in the not-too-distant future.

Effectiveness of metagenomic next-generation sequencing in the diagnosis of infectious diseases: A systematic review and meta-analysis

ObjectivesEarly diagnosis of infectious diseases remains a challenge. This study assessed the diagnostic value of mNGS in infections and explored the effect of various factors on the accuracy of mNGS. MethodsAn electronic article search of PubMed, Cochrane Library, and Embase was performed. A total of 85 papers were eligible for inclusion and analysis. Stata 12.0 was used for statistical calculation to evaluate the efficacy of mNGS for the diagnosis of infectious diseases. ResultsThe AUC of 85 studies was 0.88 (95%CI, 0.85-0.90). The AUC of the clinical comprehensive diagnosis and conventional test groups was 0.92 (95%CI, 0.89-0.94) and 0.82 (95%CI, 0.78-0.85), respectively. The results of subgroup analysis indicated that the PLR and NLR were 12.67 (95%CI, 6.01-26.70) and 0.05 (95%CI, 0.03-0.10), respectively, in arthrosis infections. The PLR was 24.41 (95%CI, 5.70-104.58) in central system infections and the NLR of immunocompromised patients was 0.08 (95%CI, 0.01-0.62). ConclusionmNGS demonstrated satisfactory diagnostic performance for infections, especially for bone and joint infections and central system infections. Moreover, mNGS also has a high value in the exclusion of infection in immunocompromised patients.

Recent Developments in the Diagnosis and Management of Infectious Diseases

Recent Developments in the Diagnosis and Management of Infectious Diseases

Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2024 Update by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM).

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by experts in both adult and pediatric laboratory and clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including arboviral Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also addressed. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.

Application of metagenomic next-generation sequencing in the clinical diagnosis of infectious diseases after allo-HSCT: a single-center analysis

BackgroundWe investigated the value of metagenomic next-generation sequencing (mNGS) in diagnosing infectious diseases in patients receiving allogeneic hematopoietic stem cell transplantation (allo-HSCT).MethodsFifty-four patients who had fever following allo-HSCT from October 2019 to February 2022 were enrolled. Conventional microbiological tests (CMTs) and mNGS, along with imaging and clinical manifestations, were used to diagnose infection following allo-HSCT. The clinical diagnostic value of mNGS was evaluated.ResultsA total of 61 mNGS tests were performed, resulting in the diagnosis of 46 cases of infectious diseases. Among these cases, there were 22 cases of viral infection, 13 cases of fungal infection, and 11 cases of bacterial infection. Moreover, 27 cases (58.7%) were classified as bloodstream infections, 15 (32.6%) as respiratory infections, 2 (4.3%) as digestive system infections, and 2 (4.3%) as central nervous system infections. Additionally, there were 8 cases with non-infectious diseases (8/54, 14.81%), including 2 cases of interstitial pneumonia, 2 cases of bronchiolitis obliterans, 2 cases of engraftment syndrome, and 2 cases of acute graft-versus-host disease. The positive detection rates of mNGS and CMT were 88.9% and 33.3%, respectively, with significant differences (P < 0.001). The sensitivity of mNGS was 97.82%, the specificity was 25%, the positive predictive value was 93.75%, and the negative predictive value was 50%. Following treatment, 51 patients showed improvement, and 3 cases succumbed to multidrug-resistant bacterial infections.ConclusionsmNGS plays an important role in the early clinical diagnosis of infectious diseases after allo-HSCT, which is not affected by immunosuppression status, empiric antibiotic therapy, and multi-microbial mixed infection.

Exonuclease III-propelled DNAzyme walker: an electrochemical strategy for microRNA diagnostics.

MicroRNA detection is crucial for early infectious disease diagnosis and rapid cancer screening. However, conventional techniques like reverse transcription-quantitative polymerase chain reaction, requiring specialized training and intricate procedures, are less suitable for point-of-care analyses. To address this, we've developed a straightforward amplifier based on an exonuclease III (exo III)-propelled DNAzyme walker for sensitive and selective microRNA detection. This amplifier employs a specially designed hairpin probe with two exposed segments for strand recognition. Once the target microRNA is identified by the hairpin's extended single-strand DNA, exo III initiates its digestion, allowing microRNA regeneration and subsequent hairpin probe digestion cycles. This cyclical process produces a significant amount of DNAzyme, leading to a marked reduction in electrochemical signals. The biosensor exhibits a detection range from 10 fM to 100pM and achieves a detection limit of 5 fM (3σcriterion). Importantly, by integrating an "And logic gate," our system gains the capacity for simultaneous diagnosis of multiple microRNAs, enhancing its applicability in RNA-based disease diagnostics.