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Suwara MI, Bennett M, Voto IAP, Brownlie CA, Gillies EA. Development and Validation of the MAST ISOPLEX ®VTEC Kit for Simultaneous Detection of Shiga Toxin/Verotoxin 1 and 2 ( stx1/vt1 and stx2/vt2) with Inhibition Control (IC) in a Rapid Loop-Mediated Isothermal Amplification (LAMP) Multiplex Assay. Int J Mol Sci 2024; 25:10067. [PMID: 39337553 PMCID: PMC11432264 DOI: 10.3390/ijms251810067] [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: 08/15/2024] [Revised: 09/10/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a cost-effective, rapid, and highly specific method of replicating nucleic acids. Adding multiple targets into a single LAMP assay to create a multiplex format is highly desirable for clinical applications but has been challenging due to a need to develop specific detection techniques and strict primer design criteria. This study describes the evaluation of a rapid triplex LAMP assay, MAST ISOPLEX®VTEC, for the simultaneous detection of Shiga toxin/verotoxin 1 and 2 (stx1/vt1 and stx2/vt2) genes in verotoxigenic Escherichia coli (E. coli) (VTEC) isolates with inhibition control (IC) synthetic DNA using a single fluorophore-oligonucleotide probe, MAST ISOPLEX®Probes, integrated into the primer set of each target. MAST ISOPLEX®Probes used in the MAST ISOPLEX®VTEC kit produce fluorescent signals as they integrate with reaction products specific to each target, allowing tracking of multiple amplifications in real time using a real-time analyzer. Initial validation on DNA extracts from fecal cultures and synthetic DNA sequences (gBlocks) showed that the MAST ISOPLEX®VTEC kit provides a method for sensitive simultaneous triplex detection in a single assay with a limit of detection (LOD) of less than 100 target copies/assay and 96% and 100% sensitivity and specificity, respectively.
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Affiliation(s)
- Monika Iwona Suwara
- Mast Group Ltd., Mast House, Derby Rd, Bootle L20 1EA, UK; (M.B.); (I.A.P.V.); (C.A.B.); (E.A.G.)
| | - Matthew Bennett
- Mast Group Ltd., Mast House, Derby Rd, Bootle L20 1EA, UK; (M.B.); (I.A.P.V.); (C.A.B.); (E.A.G.)
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Ilaria Anna Pia Voto
- Mast Group Ltd., Mast House, Derby Rd, Bootle L20 1EA, UK; (M.B.); (I.A.P.V.); (C.A.B.); (E.A.G.)
| | | | - Elizabeth Ann Gillies
- Mast Group Ltd., Mast House, Derby Rd, Bootle L20 1EA, UK; (M.B.); (I.A.P.V.); (C.A.B.); (E.A.G.)
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Yang M, Wang Z, Su M, Zhu S, Xie Y, Ying B. Smart Nanozymes for Diagnosis of Bacterial Infection: The Next Frontier from Laboratory to Bedside Testing. ACS APPLIED MATERIALS & INTERFACES 2024; 16:44361-44375. [PMID: 39162136 DOI: 10.1021/acsami.4c07043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
The global spread of infectious diseases caused by pathogenic bacteria significantly poses public health concerns, and methods for sensitive, selective, and facile diagnosis of bacteria can efficiently prevent deterioration and further spreading of the infections. The advent of nanozymes has broadened the spectrum of alternatives for diagnosing bacterial infections. Compared to natural enzymes, nanozymes exhibit the same enzymatic characteristics but offer greater economic efficiency, enhanced durability, and adjustable dimensions. The importance of early diagnosis of bacterial infection and conventional diagnostic approaches is introduced. Subsequently, the review elucidates the definition, properties, and catalytic mechanism of nanozymes. Eventually, the detailed application of nanozymes in detecting bacteria is explored, highlighting their utilization as biosensors that allow for accelerated and highly sensitive identification of bacterial infections and reflecting on the potential of nanozyme-based bacterial detection as a point-of-care testing (POCT) tool. A brief summary of obstacles and future perspectives in this field is presented at the conclusion of this review.
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Affiliation(s)
- Mei Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhonghao Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Mi Su
- Functional Science Laboratory, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shuairu Zhu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yi Xie
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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Djiman TA, Biguezoton AS, Saegerman C. Tick-Borne Diseases in Sub-Saharan Africa: A Systematic Review of Pathogens, Research Focus, and Implications for Public Health. Pathogens 2024; 13:697. [PMID: 39204297 PMCID: PMC11356977 DOI: 10.3390/pathogens13080697] [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: 07/29/2024] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 09/03/2024] Open
Abstract
Sub-Saharan Africa, with its hot and humid climate, is a conducive zone for tick proliferation. These vectors pose a major challenge to both animal and human health in the region. However, despite the relevance of emerging diseases and evidence of tick-borne disease emergence, very few studies have been dedicated to investigating zoonotic pathogens transmitted by ticks in this area. To raise awareness of the risks of tick-borne zoonotic diseases in sub-Saharan Africa, and to define a direction for future research, this systematic review considers the trends of research on tick-borne bacteria, parasites, and viruses from 2012 to 2023, aiming to highlight the circulation of these pathogens in ticks, cattle, sheep, goats, and humans. For this purpose, three international databases were screened to select 159 papers fitting designed inclusion criteria and used for qualitative analyses. Analysis of these studies revealed a high diversity of tick-borne pathogens in sub-Saharan Africa, with a total of 37 bacterial species, 27 parasite species, and 14 viruses identified. Among these, 27% were zoonotic pathogens, yet only 11 studies investigated their presence in humans. Furthermore, there is growing interest in the investigation of bacteria and parasites in both ticks and ruminants. However, research into viruses is limited and has only received notable interest from 2021 onwards. While studies on the detection of bacteria, including those of medical interest, have focused on ticks, little consideration has been given to these vectors in studies of parasites circulation. Regarding the limited focus on zoonotic pathogens transmitted by ticks, particularly in humans, despite documented cases of emerging zoonoses and the notable 27% proportion reported, further efforts should be made to fill these gaps. Future studies should prioritize the investigation of zoonotic pathogens, especially viruses, which represent the primary emerging threats, by adopting a One Health approach. This will enhance the understanding of their circulation and impact on both human and animal health. In addition, more attention should be given to the risk factors/drivers associated to their emergence as well as the perception of the population at risk of infection from these zoonotic pathogens.
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Affiliation(s)
- Tidjani A. Djiman
- Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULiège), Fundamental and Applied Research for Animals and Health (FARAH) Center, Faculty of Veterinary Medicine, University of Liege, 4000 Liège, Belgium;
- Vector-Borne Diseases and Biodiversity Unit (UMaVeB), International Research and Development Centre on Livestock in Sub-humid Areas (CIRDES), Bobo-Dioulasso 454, Burkina Faso;
| | - Abel S. Biguezoton
- Vector-Borne Diseases and Biodiversity Unit (UMaVeB), International Research and Development Centre on Livestock in Sub-humid Areas (CIRDES), Bobo-Dioulasso 454, Burkina Faso;
| | - Claude Saegerman
- Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULiège), Fundamental and Applied Research for Animals and Health (FARAH) Center, Faculty of Veterinary Medicine, University of Liege, 4000 Liège, Belgium;
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Gutiérrez-Santana JC, Rosas-Espinosa V, Martinez E, Casiano-García E, Coria-Jiménez VR. Metal Nanoparticle-Based Biosensors for the Early Diagnosis of Infectious Diseases Caused by ESKAPE Pathogens in the Fight against the Antimicrobial-Resistance Crisis. BIOSENSORS 2024; 14:339. [PMID: 39056615 PMCID: PMC11274948 DOI: 10.3390/bios14070339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 07/28/2024]
Abstract
The species included in the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and the genus Enterobacter) have a high capacity to develop antimicrobial resistance (AMR), a health problem that is already among the leading causes of death and could kill 10 million people a year by 2050. The generation of new potentially therapeutic molecules has been insufficient to combat the AMR "crisis", and the World Health Organization (WHO) has stated that it will seek to promote the development of rapid diagnostic strategies. The physicochemical properties of metallic nanoparticles (MNPs) have made it possible to design biosensors capable of identifying low concentrations of ESKAPE bacteria in the short term; other systems identify antimicrobial susceptibility, and some have been designed with dual activity in situ (bacterial detection and antimicrobial activity), which suggests that, in the near future, multifunctional biosensors could exist based on MNPs capable of quickly identifying bacterial pathogens in clinical niches might become commercially available. This review focuses on the use of MNP-based systems for the rapid and accurate identification of clinically important bacterial pathogens, exhibiting the necessity for exhaustive research to achieve these objectives. This review focuses on the use of metal nanoparticle-based systems for the rapid and accurate identification of clinically important bacterial pathogens.
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Affiliation(s)
- Juan Carlos Gutiérrez-Santana
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco, Coyoacán C.P. 04530, Mexico (V.R.C.-J.)
| | - Viridiana Rosas-Espinosa
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco, Coyoacán C.P. 04530, Mexico (V.R.C.-J.)
| | - Evelin Martinez
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Coyoacán C.P. 04960, Mexico;
| | - Esther Casiano-García
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Coyoacán C.P. 04960, Mexico;
| | - Victor Rafael Coria-Jiménez
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco, Coyoacán C.P. 04530, Mexico (V.R.C.-J.)
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Puspitasari H, Suwanti LT, Mufasirin M, Kusnoto K, Yudaniayanti IS, Setiawan B, Suprihati E, Aksono EB, Widodo DP, Wardhana AH, Matsubayashi M, Indasari EN. Molecular detection of toxoplasmosis in wild rats using loop-mediated isothermal amplification assay. Vet World 2024; 17:1575-1580. [PMID: 39185038 PMCID: PMC11344104 DOI: 10.14202/vetworld.2024.1575-1580] [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: 03/21/2024] [Accepted: 06/18/2024] [Indexed: 08/27/2024] Open
Abstract
Background and Aim Toxoplasmosis is caused by the parasite Toxoplasma gondii. Cats are the only known hosts that excrete resistant oocysts. Wild rats serve as crucial reservoirs and intermediate hosts for T. gondii's survival and dissemination. Consuming soil and water containing oocysts can lead to illness. This study aimed to estimate the prevalence of toxoplasmosis in wild rats through molecular detection as an indicator of environmental contamination in Surabaya. Materials and Methods One hundred rats were collected from the three areas (housing, dense settlements, and traditional markets) and distributed into the five zones: West, East, Central, North, and South of Surabaya. Brain tissue samples were extracted using a Geneaid™ (New Taipei City, Taiwan) DNA isolation kit and analyzed through the loop-mediated isothermal amplification (LAMP) method. Results The study analyzed brain tissue from 100 wild rats, consisting of 77 Rattus tanezumi and 33 Rattus norvegicus, displaying 30% LAMP positivity. The study revealed that 30% (30/100) of wild rats tested were infected with T. gondii. The molecular prevalence rate in male rats was 32.35% (22/68), compared to females with 25% (8/32). 41.9% of the housing population, 33.3% of traditional markets, and 22.6% of dense settlements had the highest molecular prevalence. The high positive molecular rate at the trapping site can be attributed to cats and dense populations. Conclusion Thirty percentage wild rats were tested positive for toxoplasmosis in Surabaya, East Java, Indonesia using LAMP method. Implementing strict control and monitoring is crucial in preventing the transmission of diseases from wild rats to humans. It is necessary to carry out further research related to genetic analysis of T. gondii to determine the type of T. gondii that infects animals and humans in Surabaya through bioassay and molecular test.
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Affiliation(s)
- Heni Puspitasari
- Doctoral Program of Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
- Toxoplasma Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Lucia Tri Suwanti
- Toxoplasma Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
- Division of Parasitology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Mufasirin Mufasirin
- Toxoplasma Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
- Division of Parasitology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Kusnoto Kusnoto
- Division of Parasitology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Ira Sari Yudaniayanti
- Division of Clinic Veterinary, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Boedi Setiawan
- Division of Clinic Veterinary, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Endang Suprihati
- Division of Parasitology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Eduardus Bimo Aksono
- Division of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Dwi Priyo Widodo
- Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - April Hari Wardhana
- Research Center for Veterinary Sciences, Organization for Health, National Research Center for Veterinary Sciences, Cibinong, 16911, Indonesia
| | - Makoto Matsubayashi
- Department of Veterinary Immunology, Graduate School of Veterinary Sciences, Osaka Metropolitan Univesity, Osaka, Japan, 598-8531
| | - Elly Nur Indasari
- Toxoplasma Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Brawijaya, Malang, 65144, Indonesia
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Ziaei Chamgordani S, Yadegar A, Ghourchian H. C. difficile biomarkers, pathogenicity and detection. Clin Chim Acta 2024; 558:119674. [PMID: 38621586 DOI: 10.1016/j.cca.2024.119674] [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: 02/04/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is the main etiologic agent of antibiotic-associated diarrhea. CDI contributes to gut inflammation and can lead to disruption of the intestinal epithelial barrier. Recently, the rate of CDI cases has been increased. Thus, early diagnosis of C. difficile is critical for controlling the infection and guiding efficacious therapy. APPROACH A search strategy was set up using the terms C. difficile biomarkers and diagnosis. The found references were classified into two general categories; conventional and advanced methods. RESULTS The pathogenicity and biomarkers of C. difficile, and the collection manners for CDI-suspected specimens were briefly explained. Then, the conventional CDI diagnostic methods were subtly compared in terms of duration, level of difficulty, sensitivity, advantages, and disadvantages. Thereafter, an extensive review of the various newly proposed techniques available for CDI detection was conducted including nucleic acid isothermal amplification-based methods, biosensors, and gene/single-molecule microarrays. Also, the detection mechanisms, pros and cons of these methods were highlighted and compared with each other. In addition, approximately complete information on FDA-approved platforms for CDI diagnosis was collected. CONCLUSION To overcome the deficiencies of conventional methods, the potential of advanced methods for C. difficile diagnosis, their direction, perspective, and challenges ahead were discussed.
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Affiliation(s)
- Sepideh Ziaei Chamgordani
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hedayatollah Ghourchian
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.
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Qin Y, Huo M, Liu X, Li SC. Biomarkers and computational models for predicting efficacy to tumor ICI immunotherapy. Front Immunol 2024; 15:1368749. [PMID: 38524135 PMCID: PMC10957591 DOI: 10.3389/fimmu.2024.1368749] [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: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
Numerous studies have shown that immune checkpoint inhibitor (ICI) immunotherapy has great potential as a cancer treatment, leading to significant clinical improvements in numerous cases. However, it benefits a minority of patients, underscoring the importance of discovering reliable biomarkers that can be used to screen for potential beneficiaries and ultimately reduce the risk of overtreatment. Our comprehensive review focuses on the latest advancements in predictive biomarkers for ICI therapy, particularly emphasizing those that enhance the efficacy of programmed cell death protein 1 (PD-1)/programmed cell death-ligand 1 (PD-L1) inhibitors and cytotoxic T-lymphocyte antigen-4 (CTLA-4) inhibitors immunotherapies. We explore biomarkers derived from various sources, including tumor cells, the tumor immune microenvironment (TIME), body fluids, gut microbes, and metabolites. Among them, tumor cells-derived biomarkers include tumor mutational burden (TMB) biomarker, tumor neoantigen burden (TNB) biomarker, microsatellite instability (MSI) biomarker, PD-L1 expression biomarker, mutated gene biomarkers in pathways, and epigenetic biomarkers. TIME-derived biomarkers include immune landscape of TIME biomarkers, inhibitory checkpoints biomarkers, and immune repertoire biomarkers. We also discuss various techniques used to detect and assess these biomarkers, detailing their respective datasets, strengths, weaknesses, and evaluative metrics. Furthermore, we present a comprehensive review of computer models for predicting the response to ICI therapy. The computer models include knowledge-based mechanistic models and data-based machine learning (ML) models. Among the knowledge-based mechanistic models are pharmacokinetic/pharmacodynamic (PK/PD) models, partial differential equation (PDE) models, signal networks-based models, quantitative systems pharmacology (QSP) models, and agent-based models (ABMs). ML models include linear regression models, logistic regression models, support vector machine (SVM)/random forest/extra trees/k-nearest neighbors (KNN) models, artificial neural network (ANN) and deep learning models. Additionally, there are hybrid models of systems biology and ML. We summarized the details of these models, outlining the datasets they utilize, their evaluation methods/metrics, and their respective strengths and limitations. By summarizing the major advances in the research on predictive biomarkers and computer models for the therapeutic effect and clinical utility of tumor ICI, we aim to assist researchers in choosing appropriate biomarkers or computer models for research exploration and help clinicians conduct precision medicine by selecting the best biomarkers.
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Affiliation(s)
- Yurong Qin
- Department of Computer Science, City University of Hong Kong, Kowloon, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong, China
| | - Miaozhe Huo
- Department of Computer Science, City University of Hong Kong, Kowloon, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong, China
| | - Xingwu Liu
- School of Mathematical Sciences, Dalian University of Technology, Dalian, Liaoning, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong, China
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Gradisteanu Pircalabioru G, Raileanu M, Dionisie MV, Lixandru-Petre IO, Iliescu C. Fast detection of bacterial gut pathogens on miniaturized devices: an overview. Expert Rev Mol Diagn 2024; 24:201-218. [PMID: 38347807 DOI: 10.1080/14737159.2024.2316756] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024]
Abstract
INTRODUCTION Gut microbes pose challenges like colon inflammation, deadly diarrhea, antimicrobial resistance dissemination, and chronic disease onset. Development of early, rapid and specific diagnosis tools is essential for improving infection control. Point-of-care testing (POCT) systems offer rapid, sensitive, low-cost and sample-to-answer methods for microbe detection from various clinical and environmental samples, bringing the advantages of portability, automation, and simple operation. AREAS COVERED Rapid detection of gut microbes can be done using a wide array of techniques including biosensors, immunological assays, electrochemical impedance spectroscopy, mass spectrometry and molecular biology. Inclusion of Internet of Things, machine learning, and smartphone-based point-of-care applications is an important aspect of POCT. In this review, the authors discuss various fast diagnostic platforms for gut pathogens and their main challenges. EXPERT OPINION Developing effective assays for microbe detection can be complex. Assay design must consider factors like target selection, real-time and multiplex detection, sample type, reagent stability and storage, primer/probe design, and optimizing reaction conditions for accuracy and sensitivity. Mitigating these challenges requires interdisciplinary collaboration among scientists, clinicians, engineers, and industry partners. Future efforts are essential to enhance sensitivity, specificity, and versatility of POCT systems for gut microbe detection and quantification, advancing infectious disease diagnostics and management.
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Affiliation(s)
- Gratiela Gradisteanu Pircalabioru
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Division of Earth, Environmental and Life Sciences, The Research Institute of University of Bucharest (ICUB), Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
| | - Mina Raileanu
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Department of Life and Environmental Physics, Horia Hulubei National Institute of Physics and Nuclear Engineering, Magurele, Romania
| | - Mihai Viorel Dionisie
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
| | - Irina-Oana Lixandru-Petre
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
| | - Ciprian Iliescu
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- Microsystems in Biomedical and Environmental Applications, National Research and Development Institute for Microtechnology, Bucharest, Romania
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Huang A, Krueger R, Moeller KD. Microelectrode Arrays, Electrocatalysis, and the Need for Proper Characterization. ChemElectroChem 2023; 10:e202300457. [PMID: 38450252 PMCID: PMC10914339 DOI: 10.1002/celc.202300457] [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: 09/08/2023] [Indexed: 03/08/2024]
Abstract
Indirect electrochemical methods are a powerful tool for synthetic chemistry because they allow for the optimization of chemical selectivity in a reaction while maintaining the advantages of electrochemistry in terms of sustainability. Recently, we have found that such methods provide a handle for not only the synthesis of complex molecules, but also the construction of complex, addressable molecular surfaces. In this effort, the indirect electrochemical methods enable the placement or synthesis of molecules by any electrode or set of electrodes in a microelectrode array. The success of these surface-based reactions are typically evaluated with the use of fluorescence labelling studies. However, these fluorescence-based evaluations can be misleading. While they are excellent for determining that a reaction has occurred in a site-selective fashion on an array, they do not provide information on whether that reaction is the one desired or how well it worked. We describe here how the use of a "safety-catch" linker strategy allows for a more accurate assessment of reaction quality on an array, and then use that capability to illustrate how the use of transition metal mediated cross-coupling reactions on an array prevent unwanted background reactions that can occur on a polymer-coated electrode surface. The method enables a unique level of quality control for array-based transformations.
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Affiliation(s)
- Albert Huang
- Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Ruby Krueger
- Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Kevin D. Moeller
- Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
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Silva APSP, Almeida M, Michael A, Rahe MC, Siepker C, Magstadt DR, Piñeyro P, Arruda BL, Macedo NR, Sahin O, Gauger PC, Krueger KM, Mugabi R, Streauslin JS, Trevisan G, Linhares DCL, Silva GS, Fano E, Main RG, Schwartz KJ, Burrough ER, Derscheid RJ, Sitthicharoenchai P, Clavijo MJ. Detection and disease diagnosis trends (2017-2022) for Streptococcus suis, Glaesserella parasuis, Mycoplasma hyorhinis, Actinobacillus suis and Mycoplasma hyosynoviae at Iowa State University Veterinary Diagnostic Laboratory. BMC Vet Res 2023; 19:268. [PMID: 38087358 PMCID: PMC10714645 DOI: 10.1186/s12917-023-03807-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Accurate measurement of disease associated with endemic bacterial agents in pig populations is challenging due to their commensal ecology, the lack of disease-specific antemortem diagnostic tests, and the polymicrobial nature of swine diagnostic cases. The main objective of this retrospective study was to estimate temporal patterns of agent detection and disease diagnosis for five endemic bacteria that can cause systemic disease in porcine tissue specimens submitted to the Iowa State University Veterinary Diagnostic Laboratory (ISU VDL) from 2017 to 2022. The study also explored the diagnostic value of specific tissue specimens for disease diagnosis, estimated the frequency of polymicrobial diagnosis, and evaluated the association between phase of pig production and disease diagnosis. RESULTS S. suis and G. parasuis bronchopneumonia increased on average 6 and 4.3%, while S. suis endocarditis increased by 23% per year, respectively. M. hyorhinis and A. suis associated serositis increased yearly by 4.2 and 12.8%, respectively. A significant upward trend in M. hyorhinis arthritis cases was also observed. In contrast, M. hyosynoviae arthritis cases decreased by 33% average/year. Investigation into the diagnostic value of tissues showed that lungs were the most frequently submitted sample, However, the use of lung for systemic disease diagnosis requires caution due to the commensal nature of these agents in the respiratory system, compared to systemic sites that diagnosticians typically target. This study also explored associations between phase of production and specific diseases caused by each agent, showcasing the role of S. suis arthritis in suckling pigs, meningitis in early nursery and endocarditis in growing pigs, and the role of G. parasuis, A. suis, M. hyorhinis and M. hyosynoviae disease mainly in post-weaning phases. Finally, this study highlighted the high frequency of co-detection and -disease diagnosis with other infectious etiologies, such as PRRSV and IAV, demonstrating that to minimize the health impact of these endemic bacterial agents it is imperative to establish effective viral control programs. CONCLUSIONS Results from this retrospective study demonstrated significant increases in disease diagnosis for S. suis, G. parasuis, M. hyorhinis, and A. suis, and a significant decrease in detection and disease diagnosis of M. hyosynoviae. High frequencies of interactions between these endemic agents and with viral pathogens was also demonstrated. Consequently, improved control programs are needed to mitigate the adverse effect of these endemic bacterial agents on swine health and wellbeing. This includes improving diagnostic procedures, developing more effective vaccine products, fine-tuning antimicrobial approaches, and managing viral co-infections.
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Affiliation(s)
- Ana Paula Serafini Poeta Silva
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Marcelo Almeida
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Alyona Michael
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Michael C Rahe
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Christopher Siepker
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Drew R Magstadt
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Pablo Piñeyro
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Bailey L Arruda
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
- United States Department of Agriculture (USDA), Ames, IA, USA
| | - Nubia R Macedo
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Orhan Sahin
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Philip C Gauger
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Karen M Krueger
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Robert Mugabi
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jessica S Streauslin
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Giovani Trevisan
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Daniel C L Linhares
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Gustavo S Silva
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Eduardo Fano
- Boehringer Ingelheim Animal Health USA Inc, Atlanta, GA, USA
| | - Rodger G Main
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Kent J Schwartz
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Eric R Burrough
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Rachel J Derscheid
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Panchan Sitthicharoenchai
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Maria J Clavijo
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
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11
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Giacobbe DR, Di Pilato V, Karaiskos I, Giani T, Marchese A, Rossolini GM, Bassetti M. Treatment and diagnosis of severe KPC-producing Klebsiella pneumoniae infections: a perspective on what has changed over last decades. Ann Med 2023; 55:101-113. [PMID: 36856521 PMCID: PMC9980017 DOI: 10.1080/07853890.2022.2152484] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Antimicrobial resistance is a global health threat. Among Gram-negative bacteria, resistance to carbapenems, a class of β-lactam antibiotics, is usually a proxy for difficult-to-treat resistance, since carbapenem-resistant organisms are often resistant to many classes of antibiotics. Carbapenem resistance in the Gram-negative pathogen Klebsiella pneumoniae is mostly due to the production of carbapenemases, enzymes able to hydrolyze carbapenems, and K. pneumoniae carbapenemase (KPC)-type enzymes are overall the most prevalent carbapenemases in K. pneumoniae. In the last decade, the management of severe infections due to KPC-producing K. pneumoniae (KPC-Kp) in humans has presented many peculiar challenges to clinicians worldwide. In this perspective, we discuss how the treatment of severe KPC-Kp infections has evolved over the last decades, guided by the accumulating evidence from clinical studies, and how recent advances in diagnostics have allowed to anticipate identification of KPC-Kp in infected patients.KEY MESSAGESIn the last decade, the management of severe infections due to KPC-Kp has presented many peculiar challenges to clinicians worldwideFollowing the introduction in clinical practice of novel β-lactam/β-lactamase inhibitor combinations and novel β-lactams active against KPC-producing bacteria, the management of severe KPC-Kp infections has witnessed a remarkable evolutionTreatment of severe KPC-Kp infections is a highly dynamic process, in which the wise use of novel antimicrobials should be accompanied by a continuous refinement based on evolving clinical evidence and laboratory diagnostics.
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Affiliation(s)
- Daniele Roberto Giacobbe
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy.,UO Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Ilias Karaiskos
- First Department of Internal Medicine - Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Tommaso Giani
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Anna Marchese
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy.,UO Microbiologia, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Matteo Bassetti
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy.,UO Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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12
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Shelke YP, Badge AK, Bankar NJ. Applications of Artificial Intelligence in Microbial Diagnosis. Cureus 2023; 15:e49366. [PMID: 38146579 PMCID: PMC10749263 DOI: 10.7759/cureus.49366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/24/2023] [Indexed: 12/27/2023] Open
Abstract
The diagnosis is an important factor in healthcare care, and it is essential to identify microorganisms that cause infections and diseases. The application of artificial intelligence (AI) systems can improve disease management, drug development, antibiotic resistance prediction, and epidemiological monitoring in the field of microbial diagnosis. AI systems can quickly and accurately detect infections, including new and drug-resistant strains, and enable early detection of antibiotic resistance and improved diagnostic techniques. The application of AI in bacterial diagnosis focuses on the speed, precision, and identification of pathogens and the ability to predict antibiotic resistance.
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Affiliation(s)
- Yogendra P Shelke
- Microbiology, Bhaktshreshtha Kamalakarpant Laxmanrao Walawalkar Rural Medical College, Ratnagiri, IND
| | - Ankit K Badge
- Microbiology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research (Deemed to Be University), Wardha, IND
| | - Nandkishor J Bankar
- Microbiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research (Deemed to Be University), Wardha, IND
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13
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Signoroni A, Ferrari A, Lombardi S, Savardi M, Fontana S, Culbreath K. Hierarchical AI enables global interpretation of culture plates in the era of digital microbiology. Nat Commun 2023; 14:6874. [PMID: 37898607 PMCID: PMC10613199 DOI: 10.1038/s41467-023-42563-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 10/13/2023] [Indexed: 10/30/2023] Open
Abstract
Full Laboratory Automation is revolutionizing work habits in an increasing number of clinical microbiology facilities worldwide, generating huge streams of digital images for interpretation. Contextually, deep learning architectures are leading to paradigm shifts in the way computers can assist with difficult visual interpretation tasks in several domains. At the crossroads of these epochal trends, we present a system able to tackle a core task in clinical microbiology, namely the global interpretation of diagnostic bacterial culture plates, including presumptive pathogen identification. This is achieved by decomposing the problem into a hierarchy of complex subtasks and addressing them with a multi-network architecture we call DeepColony. Working on a large stream of clinical data and a complete set of 32 pathogens, the proposed system is capable of effectively assist plate interpretation with a surprising degree of accuracy in the widespread and demanding framework of Urinary Tract Infections. Moreover, thanks to the rich species-related generated information, DeepColony can be used for developing trustworthy clinical decision support services in laboratory automation ecosystems from local to global scale.
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Affiliation(s)
- Alberto Signoroni
- Department of Information Engineering, University of Brescia, Brescia, Italy.
- Department of Medical and Surgical specialties Radiological Sciences and Public Health, University of Brescia, Brescia, Italy.
| | | | - Stefano Lombardi
- Department of Information Engineering, University of Brescia, Brescia, Italy
- Copan WASP, Brescia, Italy
| | - Mattia Savardi
- Department of Information Engineering, University of Brescia, Brescia, Italy
- Department of Medical and Surgical specialties Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | | | - Karissa Culbreath
- Department of Infectious Disease, Tricore Laboratories, Albuquerque, New Mexico, USA
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14
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Šakarnytė L, Šiugždinienė R, Žymantienė J, Ruzauskas M. Comparison of Oral Microbial Composition and Determinants Encoding Antimicrobial Resistance in Dogs and Their Owners. Antibiotics (Basel) 2023; 12:1554. [PMID: 37887255 PMCID: PMC10604839 DOI: 10.3390/antibiotics12101554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
Consolidated studies on animal, human, and environmental health have become very important for understanding emerging zoonotic diseases and the spread of antimicrobial resistance (AMR). The aim of this study was to analyse the oral microbiomes of healthy dogs and their owners, including determinants of AMR. Shotgun metagenomic sequencing detected 299 bacterial species in pets and their owners, from which 70 species were carried by dogs and 229 species by humans. Results demonstrated a unique microbial composition of dogs and their owners. At an order level, Bacteroidales were the most prevalent oral microbiota of dogs with significantly lower prevalence in their owners where Actinomycetales and Lactobacillales predominated. Porphyromonas and Corynebacterium were the most prevalent genera in dogs, whereas Streptococcus and Actinomyces were in animal owners. The resistances to macrolides, tetracyclines, lincosamides and Cfx family A class broad-spectrum β-lactamase were detected in both animal and human microbiomes. Resistance determinants to amphenicols, aminoglycosides, sulphonamides, and quaternary ammonium compounds were detected exceptionally in dogs. In conclusion, the study demonstrated different bacterial composition in oral microbiomes of healthy dogs without clinical signs of periodontal disease and their owners. Due to the low numbers of the samples tested, further investigations with an increased number of samples should be performed.
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Affiliation(s)
- Laura Šakarnytė
- Microbiology and Virology Institute, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.Š.); (R.Š.)
| | - Rita Šiugždinienė
- Microbiology and Virology Institute, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.Š.); (R.Š.)
| | - Judita Žymantienė
- Department of Anatomy and Physiology, Veterinary Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania;
| | - Modestas Ruzauskas
- Microbiology and Virology Institute, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.Š.); (R.Š.)
- Department of Anatomy and Physiology, Veterinary Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania;
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15
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Hu L, Zhang S, Song W, Dong F, Xie Z, Chen X, Liu M, Cui B, Zhang Y, Zhang R, Wang Q. A sensitive mass spectrometry-based method to identify common respiratory pathogens in children. Microbiol Spectr 2023; 11:e0185823. [PMID: 37754782 PMCID: PMC10580997 DOI: 10.1128/spectrum.01858-23] [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: 05/05/2023] [Accepted: 07/11/2023] [Indexed: 09/28/2023] Open
Abstract
Public health threats posed by emerging respiratory infections are a significant concern, particularly in children and infants. Traditional culture-based detection methods are time-consuming and typically require 1-3 days. Herein, we developed and evaluated a 23-plex common respiratory pathogen mass spectrometry assay that enables the simultaneous detection of 18 common respiratory pathogens in children. This assay combines matrix-assisted laser desorption/ionization time of flight mass spectrometry with multiplex reverse transcription-PCR and targets 11 bacterial and 7 viral pathogens (including 10 subtypes), and two internal controls. The detection limit of the common respiratory pathogen mass spectrometry assay was as low as 1 copy/µL, with no cross-reactivity with other organisms. We assessed the clinical performance of the common respiratory pathogen mass spectrometry assay using respiratory samples from 450 children. The total 450 clinical specimens underwent analysis via matrix-assisted laser desorption/ionization time of flight mass spectrometry, and the outcomes were juxtaposed with those derived from real-time reverse-transcriptase PCR conducted concurrently. The concordance between these methods was 96.0%, and the multiple infection identification rate was 7.1%. This innovative approach enables the simultaneous analysis of numerous outcomes from a solitary examination across 192 specimens within a timeframe of approximately 7 hours, with a dramatically reduced sample use and cost. In summary, the common respiratory pathogen mass spectrometry assay is a sensitive, accurate, and cost-effective method for detecting common respiratory pathogens in children and has the potential to revolutionize the diagnosis of respiratory tract infections. IMPORTANCE This study aimed to present and evaluate a novel co-detection method that enables the simultaneous identification of 11 bacterial and 7 viral pathogens in about 7 hours using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Our approach utilizes a combination of multiplex reverse transcription-PCR and matrix-assisted laser desorption/ionization time of flight mass spectrometry, which overcomes the limitations of conventional assays, which include a long assessment time, technical difficulty, and high costs. As a screening method for common respiratory pathogens in children, common respiratory pathogen mass spectrometry assay has the potential to revolutionize the diagnosis of respiratory tract infections by providing an accurate etiological diagnosis. The common respiratory pathogen mass spectrometry assay is expected to be a critical tool for the diagnosis of respiratory infections in children, offering a more efficient, cost-effective, and accurate approach for the detection of common respiratory pathogens.
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Affiliation(s)
- Lixin Hu
- Capital Medical University, Beijing, China
- Department of Clinical Laboratory, Beijing Chao-Yang Hospita, Capital Medical University, Beijing, China
- Department of Clinical Laboratory, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Shenyan Zhang
- Beijing BGI-GBI Biotech Co., Ltd., Beijing, China
- BGI Genomics, Shenzhen, China
| | - Wenqi Song
- Department of Clinical Laboratory, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Fang Dong
- Department of Clinical Laboratory, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Zhengde Xie
- Department of Clinical Laboratory, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Xiangpeng Chen
- Department of Clinical Laboratory, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Meng Liu
- Beijing BGI-GBI Biotech Co., Ltd., Beijing, China
| | - Baoxue Cui
- Beijing BGI-GBI Biotech Co., Ltd., Beijing, China
| | | | - Rui Zhang
- Department of Clinical Laboratory, Beijing Chao-Yang Hospita, Capital Medical University, Beijing, China
| | - Qingtao Wang
- Department of Clinical Laboratory, Beijing Chao-Yang Hospita, Capital Medical University, Beijing, China
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16
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Mwapagha LM. Why pathogen genomics is crucial in Africa's public health. Afr J Lab Med 2023; 12:2166. [PMID: 37822518 PMCID: PMC10563014 DOI: 10.4102/ajlm.v12i1.2166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/04/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Lamech M Mwapagha
- Department of Biology, Chemistry and Physics, Faculty of Health, Natural Resources and Applied Sciences, Namibia University of Science and Technology, Windhoek, Namibia
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17
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Alotaibi BS, Tantry BA, Bandy A, Ahmad R, Khursheed SQ, Ahmad A, Hakami MA, Shah NN. Simultaneous Detection of Influenza A/B, Respiratory Syncytial Virus, and SARS-CoV-2 in Nasopharyngeal Swabs by One-Tube Multiplex Reverse Transcription Polymerase Chain Reaction. Trop Med Infect Dis 2023; 8:326. [PMID: 37368744 DOI: 10.3390/tropicalmed8060326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
The treatment and outcome of respiratory virus infections differ. SARS-CoV-2, as well as other respiratory viruses such as influenza virus (A and B) and respiratory syncytial virus (RSV), require simultaneous, cost-effective, and rapid differential detection. We used a gold standard five-target single-step RT-PCR to detect influenza viruses, RSV, and SARS-CoV-2, and this method can be extended to detect influenza virus subtypes. As a result, this five-target single-step RT-PCR method is ideal for differentiating respiratory viruses. The 5' nuclease activity of Taq DNA polymerase is used in the real-time reverse transcription PCR assay. The Taq man fast viral 1-step enzyme is a 4× Master mix and five-target primer probe mix that detects influenza A, influenza B, SARS-CoV-2 ORF1ab, respiratory syncytial viruses A/B and actin. When compared with TaqMan TM and Invitrogen superscript TM III Platinum and the Meril Kit for SARS-CoV-2, the assay demonstrated 100% sensitivity, specificity, and amplification efficiency of 90.1% for target genes. In conclusion, our one-tube multiplex RT-PCR assay offers a rapid and reliable method for the simultaneous detection of influenza A/B, RSV, and SARS-CoV-2 from nasopharyngeal swabs. This assay has the potential to enhance diagnostic capabilities and improve public health responses during respiratory outbreaks, enabling timely interventions and informed decision making.
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Affiliation(s)
- Bader S Alotaibi
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 19257, Saudi Arabia
| | - Bilal Ahmad Tantry
- Department of Microbiology, Government Medical College, Srinagar 190010, India
| | - Altaf Bandy
- Department of Community Medicine, College of Medicine, Shaqra University, Shaqra 15273, Saudi Arabia
| | - Reyaz Ahmad
- Department of Microbiology, Government Medical College, Srinagar 190010, India
| | | | - Arshid Ahmad
- Department of Pulmonary Medicine, Government Medical College, Srinagar 190001, India
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 19257, Saudi Arabia
| | - Naveed Nazir Shah
- Department of Pulmonary Medicine, Government Medical College, Srinagar 190001, India
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18
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Bispo PJM, Belanger N, Li A, Liu R, Susarla G, Chan W, Chodosh J, Gilmore MS, Sobrin L. An All-in-One Highly Multiplexed Diagnostic Assay for Rapid, Sensitive, and Comprehensive Detection of Intraocular Pathogens. Am J Ophthalmol 2023; 250:82-94. [PMID: 36709019 PMCID: PMC10760444 DOI: 10.1016/j.ajo.2023.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
Abstract
PURPOSE Intraocular infections are sight-threatening conditions that can lead to vision loss. Rapid identification of the etiologies plays a key role in early initiation of effective therapy to save vision. However, current diagnostic modalities are time consuming and lack sensitivity and inclusiveness. We present here a newly developed comprehensive ocular panel designed to improve diagnostic yields and provide a tool for rapid and sensitive pathogen detection. DESIGN Experimental laboratory investigation. METHODS A panel containing 46 pathogens and 2 resistance/virulence markers that are commonly detected in intraocular infections was developed. Genomic targets were scrutinized for stretches predicted to be specific for a particular species while being conserved across different strains. A set of primers for sample enrichment, and two 50mer NanoString compatible probes were then designed for each target. Probe-target hybrids were detected and quantified using the NanoString nCounter SPRINT Profiler. Diagnostic feasibility was assessed in a pilot clinical study testing samples from infectious retinitis (n = 15) and endophthalmitis (n = 12) patients, for which the etiologies were confirmed by polymerase chain reaction (PCR) or culture. RESULTS Analytical studies demonstrated highly sensitive detection of a broad spectrum of pathogens, including bacteria, viruses, and parasites, with limits of detection being as low as 2.5 femtograms per reaction. We also found excellent target specificity, with minimal cross-reactivity detected. The custom-designed NanoString ocular panel correctly identified the causative agent from all clinical specimens positive for a variety of pathogens. CONCLUSION This highly multiplexed panel for pathogen detection offers a sensitive, comprehensive, and uniform assay run directly on ocular fluids that could significantly improve diagnostics of sight-threatening intraocular infections.
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Affiliation(s)
- Paulo J M Bispo
- From the Department of Ophthalmology (P.J.M.B., N.B., A.L., R.L., G.S., W.C., J.C., M.S.G., L.S.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA; Infectious Disease Institute (P.J.M.B., N.B., J.C., M.S.G., L.S.), Harvard Medical School, Boston, Massachusetts, USA.
| | - Nicole Belanger
- From the Department of Ophthalmology (P.J.M.B., N.B., A.L., R.L., G.S., W.C., J.C., M.S.G., L.S.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA; Infectious Disease Institute (P.J.M.B., N.B., J.C., M.S.G., L.S.), Harvard Medical School, Boston, Massachusetts, USA
| | - Ashley Li
- From the Department of Ophthalmology (P.J.M.B., N.B., A.L., R.L., G.S., W.C., J.C., M.S.G., L.S.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Renee Liu
- From the Department of Ophthalmology (P.J.M.B., N.B., A.L., R.L., G.S., W.C., J.C., M.S.G., L.S.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Gayatri Susarla
- From the Department of Ophthalmology (P.J.M.B., N.B., A.L., R.L., G.S., W.C., J.C., M.S.G., L.S.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Weilin Chan
- From the Department of Ophthalmology (P.J.M.B., N.B., A.L., R.L., G.S., W.C., J.C., M.S.G., L.S.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - James Chodosh
- From the Department of Ophthalmology (P.J.M.B., N.B., A.L., R.L., G.S., W.C., J.C., M.S.G., L.S.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA; Infectious Disease Institute (P.J.M.B., N.B., J.C., M.S.G., L.S.), Harvard Medical School, Boston, Massachusetts, USA
| | - Michael S Gilmore
- From the Department of Ophthalmology (P.J.M.B., N.B., A.L., R.L., G.S., W.C., J.C., M.S.G., L.S.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA; Infectious Disease Institute (P.J.M.B., N.B., J.C., M.S.G., L.S.), Harvard Medical School, Boston, Massachusetts, USA; Department of Microbiology and Immunobiology (M.S.G.), Harvard Medical School, Boston, Massachusetts, USA
| | - Lucia Sobrin
- From the Department of Ophthalmology (P.J.M.B., N.B., A.L., R.L., G.S., W.C., J.C., M.S.G., L.S.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA; Infectious Disease Institute (P.J.M.B., N.B., J.C., M.S.G., L.S.), Harvard Medical School, Boston, Massachusetts, USA
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Jena S, Gaur D, Dubey NC, Tripathi BP. Advances in paper based isothermal nucleic acid amplification tests for water-related infectious diseases. Int J Biol Macromol 2023:125089. [PMID: 37245760 DOI: 10.1016/j.ijbiomac.2023.125089] [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: 02/11/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Water-associated or water-related infectious disease outbreaks are caused by pathogens such as bacteria, viruses, and protozoa, which can be transmitted through contaminated water sources, poor sanitation practices, or insect vectors. Low- and middle-income countries bear the major burden of these infections due to inadequate hygiene and subpar laboratory facilities, making it challenging to monitor and detect infections in a timely manner. However, even developed countries are not immune to these diseases, as inadequate wastewater management and contaminated drinking water supplies can also contribute to disease outbreaks. Nucleic acid amplification tests have proven to be effective for early disease intervention and surveillance of both new and existing diseases. In recent years, paper-based diagnostic devices have made significant progress and become an essential tool in detecting and managing water-associated diseases. In this review, we highlight the importance of paper and its variants as a diagnostic tool and discuss the properties, design modifications, and various paper-based device formats developed and used for detecting water-associated pathogens.
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Affiliation(s)
- Saikrushna Jena
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Divya Gaur
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Nidhi C Dubey
- Department of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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20
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Thulasinathan B, D S, Murugan S, Panda SK, Veerapandian M, Manickam P. DNA-functionalized carbon quantum dots for electrochemical detection of pyocyanin: A quorum sensing molecule in Pseudomonas aeruginosa. Biosens Bioelectron 2023; 227:115156. [PMID: 36842368 DOI: 10.1016/j.bios.2023.115156] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 02/21/2023]
Abstract
The electrochemical biosensing strategy for pyocyanin (PYO), a virulent quorum-sensing molecule responsible for Pseudomonas aeruginosa infections, was developed by mimicking its extracellular DNA interaction. Calf thymus DNA (ct-DNA) functionalized amine-containing carbon quantum dots (CQDs) were used as a biomimetic receptor for electrochemical sensing of PYO as low as 37 nM in real urine sample. The ct-DNA-based biosensor enabled the selective measurement of PYO in the presence of other interfering species. Calibration and validation of the PYO sensor platform were demonstrated in buffer solution (0-100 μM), microbial culture media (0-100 μM), artificial urine (0-400 μM), and real urine sample (0-250 μM). The sensor capability was successfully implemented for point-of-care (POC) detection of PYO release from Pseudomonas aeruginosa strains during lag and stationary phases. Cross-reactivity of the sensing platform was also tested in other bacterial species such as Bacillus subtilis, Escherichia coli, Klebsiella pneumoniae, Shigella dysenteriae, Staphylococcus aureus, and Streptococcus pneumoniae. Potential clinical implementation of the ct-DNA-based sensor was manifested in detecting the PYO in P. aeruginosa cultured baby diaper and sanitary napkin. Our results highlight that the newly developed ct-DNA-based sensing platform can be used as a potential candidate for real-time POC diagnosis of Pseudomonas aeruginosa infection in clinical samples.
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Affiliation(s)
- Boobalan Thulasinathan
- Electrodics & Electrocatalysis Division, CSIR - Central Electrochemical Research Institute (CECRI), Karaikudi, 630003, India
| | - Sujatha D
- Electroplating and Metal Finishing Division, CSIR - Central Electrochemical Research Institute (CECRI), Karaikudi, 630003, India
| | - Sethupathi Murugan
- Electroplating and Metal Finishing Division, CSIR - Central Electrochemical Research Institute (CECRI), Karaikudi, 630003, India
| | - Subhendu K Panda
- Electroplating and Metal Finishing Division, CSIR - Central Electrochemical Research Institute (CECRI), Karaikudi, 630003, India
| | - Murugan Veerapandian
- Electrodics & Electrocatalysis Division, CSIR - Central Electrochemical Research Institute (CECRI), Karaikudi, 630003, India
| | - Pandiaraj Manickam
- Electrodics & Electrocatalysis Division, CSIR - Central Electrochemical Research Institute (CECRI), Karaikudi, 630003, India.
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21
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Deshamukhya C, Bhowmik D, (Chanda) DD, Bhattacharjee A. Optimization of loop-mediated isothermal amplification-based method for detection of macrolide-lincosamide-streptogramin B resistance in Staphylococcus aureus. Indian J Med Res 2023; 157:477-481. [PMID: 37955222 PMCID: PMC10443712 DOI: 10.4103/ijmr.ijmr_3304_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Indexed: 11/14/2023] Open
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22
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Tosun AI, Kolukirik M, Yılmaz M, Ötgün SN, Aygun G, Kolukirik CZK, Zeybek U, Ozgumus GG, Turan M, Kuskucu M, Ince O, Ince B, Kilic S. Development of a new multiplex real-time PCR assay for rapid screening of hospital-acquired infection agents. J Microbiol Methods 2023; 206:106690. [PMID: 36801238 DOI: 10.1016/j.mimet.2023.106690] [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: 07/13/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
AIMS A new multiplex real-time PCR (qPCR) assay was developed to detect antibiotic-resistant hospital-acquired infectious agents in nasal and rectal swab samples in 1.5 h without the need for nucleic acid extraction. METHODS Spiked negative clinical specimens were used for the analytical performance evaluation. Double-blind samples were collected from 1788 patients to assess the relative clinical performance of the qPCR assay to the conventional culture-based methods. Bio-Speedy® Fast Lysis Buffer (FLB) and 2× qPCR-Mix for hydrolysis probes (Bioeksen R&D Technologies, Istanbul, Turkey) and LightCycler® 96 Instrument (Roche Inc., Branchburg, NJ, USA) were used for all molecular analyses. The samples were transferred into 400 L FLB, homogenized and immediately used in qPCRs. The target DNA regions are vanA and vanB genes for vancomycin-resistant Enterococcus (VRE); blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-23, blaOXA-48, blaOXA-58 genes for carbapenem-resistant Enterobacteriaceae (CRE); and mecA, mecC and spa for methicillin-resistant Staphylococcus aureus (MRSA). RESULTS No qPCR tests produced positive results for the samples spiked with the potential cross-reacting organisms. The limit of detection (LOD) of the assay for all targets was 100 colony-forming unit (cfu)/swab-sample. Results of the repeatability studies in two different centers were in 96%-100% (69/72-72/72) agreement. The relative specificity and sensitivity of the qPCR assay were respectively 96.8% and 98.8% for VRE; 94.9% and 95.1% for CRE; 99.9% and 97.1% for MRSA. CONCLUSIONS The developed qPCR assay can screen antibiotic-resistant hospital-acquired infectious agents in infected/colonized patients with an equal clinical performance to the culture-based methods.
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Affiliation(s)
- Ayse Istanbullu Tosun
- Medical Microbiology, School of Medicine, Istanbul Medipol University, İIstanbu, Turkey.
| | - Mustafa Kolukirik
- Bioeksen R&D Technologies Ltd., Istanbul Technical University Ari-3 Technopark, Istanbul, Turkey
| | - Mesut Yılmaz
- Infectious Diseases and Clinical Microbiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Selin Nar Ötgün
- Public Health General Directorate, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| | - Gokhan Aygun
- Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | | | - Umit Zeybek
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Gozde Girgin Ozgumus
- Bioeksen R&D Technologies Ltd., Istanbul Technical University Ari-3 Technopark, Istanbul, Turkey
| | - Meral Turan
- Public Health General Directorate, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| | - Mert Kuskucu
- Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Orhan Ince
- ENGY Environmental and Energy Technologies Biotechnology R&D Ltd., Bogazici University Technopark, Istanbul, Turkey
| | - Bahar Ince
- ENGY Environmental and Energy Technologies Biotechnology R&D Ltd., Bogazici University Technopark, Istanbul, Turkey
| | - Selcuk Kilic
- Public Health General Directorate, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
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23
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Dysin AP, Egorov AR, Godzishevskaya AA, Kirichuk AA, Tskhovrebov AG, Kritchenkov AS. Biologically Active Supplements Affecting Producer Microorganisms in Food Biotechnology: A Review. Molecules 2023; 28:molecules28031413. [PMID: 36771079 PMCID: PMC9921933 DOI: 10.3390/molecules28031413] [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: 12/18/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Microorganisms, fermentation processes, and the resultant metabolic products are a key driving force in biotechnology and, in particular, in food biotechnology. The quantity and/or quality of final manufactured food products are directly related to the efficiency of the metabolic processes of producer microorganisms. Food BioTech companies are naturally interested in increasing the productivity of their biotechnological production lines. This could be achieved via either indirect or direct influence on the fundamental mechanisms governing biological processes occurring in microbial cells. This review considers an approach to improve the efficiency of producer microorganisms through the use of several types of substances or complexes affecting the metabolic processes of microbial producers that are of interest for food biotechnology, particularly fermented milk products. A classification of these supplements will be given, depending on their chemical nature (poly- and oligosaccharides; poly- and oligopeptides, individual amino acids; miscellaneous substances, including vitamins and other organic compounds, minerals, and multicomponent supplements), and the approved results of their application will be comprehensively surveyed.
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Affiliation(s)
- Artem P. Dysin
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
| | - Anton R. Egorov
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
| | - Anastasia A. Godzishevskaya
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
| | - Anatoly A. Kirichuk
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
| | - Alexander G. Tskhovrebov
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
- Correspondence: (A.G.T.); (A.S.K.)
| | - Andreii S. Kritchenkov
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
- Metal Physics Laboratory, Institute of Technical Acoustics NAS of Belarus, Ludnikova Prosp. 13, 210009 Vitebsk, Belarus
- Correspondence: (A.G.T.); (A.S.K.)
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24
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Hijano DR, Ferrolino JA, Hidinger J, Brazelton JN, Gu Z, Suganda S, Glasgow HL, Allison KJ, Peterson M, Dallas RH, Maron G, Hayden RT. Clinical Correlation of Adenoviral Load in the Respiratory Tract Measured by Digital PCR in Immunocompromised Children. Open Forum Infect Dis 2023; 10:ofad030. [PMID: 36776777 PMCID: PMC9907548 DOI: 10.1093/ofid/ofad030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Immunocompromised patients can have life-threatening adenoviral infection. Viral load in blood and stool is commonly used to guide antiviral therapy. We developed and evaluated a digital polymerase chain reaction assay to quantify human adenovirus in the respiratory tract and showed that higher peak load correlates with disseminated infection, mechanical ventilation, and death.
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Affiliation(s)
- Diego R Hijano
- Correspondence: Randall T. Hayden, MD, Department of Pathology, Mail Stop 250, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 (); or Diego R. Hijano, MD, MSc, Department of Infectious Diseases, Mail Stop 230, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 ()
| | | | - Jennifer Hidinger
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Jessica N Brazelton
- Department of Pathology, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Zhengming Gu
- Department of Pathology, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Sri Suganda
- Department of Pathology, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Heather L Glasgow
- Department of Pathology, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Kim J Allison
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Megan Peterson
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Ronald H Dallas
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Maron
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Randall T Hayden
- Correspondence: Randall T. Hayden, MD, Department of Pathology, Mail Stop 250, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 (); or Diego R. Hijano, MD, MSc, Department of Infectious Diseases, Mail Stop 230, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 ()
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25
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De R, Kanungo S, Mukhopadhyay AK, Dutta S. The gut microbiome of the healthy population in Kolkata, India, is a reservoir of antimicrobial resistance genes emphasizing the need of enforcing antimicrobial stewardship. FEMS Microbiol Lett 2023; 370:fnad090. [PMID: 37697657 DOI: 10.1093/femsle/fnad090] [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: 07/14/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Antimicrobial resistance (AMR) alleviation warrants antimicrobial stewardship (AS) entailing the indispensability of epidemiological surveillance. We undertook a small-scale surveillance in Kolkata to detect the presence of antimicrobial resistance genes (ARGs) in the healthy gut microbiome. We found that it was a reservoir of ARGs against common antibiotics. A targeted Polymerase Chain Reaction (PCR) and sequencing-based ARGs detection against tetracyclines, macrolides, trimethoprim, sulfamethoxazole, aminoglycosides, amphenicol, and mobile genetic element (MGE) markers were deployed in 25 fecal samples. Relative abundance and frequency of ARGs were calculated. We detected markers against all these classes of antibiotics. 100% samples carried aminoglycoside resistance marker and int1U. A comparison with our previously published diarrheal resistome from the same spatial and temporal frame revealed that a higher diversity of ARGs were detected in the community and a higher rate of isolation of tetC, msrA, tmp, and sul-2 was found. The presence of common markers in the two cohorts proves that the gut microbiome has been contaminated with ARGs and which are being disseminated among different ecosystems. This is an issue of discerning concern for public health. The study raises an alarming picture of the AMR crisis in low-middle and emergent economies. It emphasizes the strict enforcement of AS in the community.
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Affiliation(s)
- Rituparna De
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Suman Kanungo
- Division of Epidemiology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Asish Kumar Mukhopadhyay
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
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26
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Rawson TM, Antcliffe DB, Wilson RC, Abdolrasouli A, Moore LSP. Management of Bacterial and Fungal Infections in the ICU: Diagnosis, Treatment, and Prevention Recommendations. Infect Drug Resist 2023; 16:2709-2726. [PMID: 37168515 PMCID: PMC10166098 DOI: 10.2147/idr.s390946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/22/2023] [Indexed: 05/13/2023] Open
Abstract
Bacterial and fungal infections are common issues for patients in the intensive care unit (ICU). Large, multinational point prevalence surveys have identified that up to 50% of ICU patients have a diagnosis of bacterial or fungal infection at any one time. Infection in the ICU is associated with its own challenges. Causative organisms often harbour intrinsic and acquired mechanisms of drug-resistance, making empiric and targeted antimicrobial selection challenging. Infection in the ICU is associated with worse clinical outcomes for patients. We review the epidemiology of bacterial and fungal infection in the ICU. We discuss risk factors for acquisition, approaches to diagnosis and management, and common strategies for the prevention of infection.
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Affiliation(s)
- Timothy M Rawson
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Hammersmith Hospital, London, UK
- Centre for Antimicrobial Optimisation, Imperial College London, Imperial College London, London, UK
- David Price Evan’s Group in Infectious Diseases and Global Health, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
- Correspondence: Timothy M Rawson, Health Protection Research Unit in Healthcare Associated Infections & Antimicrobial Resistance, Hammersmith Hospital, Du Cane Road, London, W12 0NN, United Kingdom, Email
| | - David B Antcliffe
- Centre for Antimicrobial Optimisation, Imperial College London, Imperial College London, London, UK
- Division Anaesthesia, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Richard C Wilson
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Hammersmith Hospital, London, UK
- Centre for Antimicrobial Optimisation, Imperial College London, Imperial College London, London, UK
- David Price Evan’s Group in Infectious Diseases and Global Health, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | | | - Luke S P Moore
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Hammersmith Hospital, London, UK
- Chelsea & Westminster NHS Foundation Trust, London, UK
- North West London Pathology, Imperial College Healthcare NHS Trust, London, UK
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27
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Engineering CRISPR/Cas-based nanosystems for therapeutics, diagnosis and bioimaging. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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28
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Detection of Salmonella enterica subsp. enterica via Quenching of Unincorporated Amplification Signal Reporters in Loop-Mediated Isothermal Amplification. ScientificWorldJournal 2022; 2022:4567817. [PMID: 36619257 PMCID: PMC9822744 DOI: 10.1155/2022/4567817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/31/2022] Open
Abstract
Salmonella enterica is a major cause of diarrheal diseases in developing countries where timely surveillance and proper clinical management are inadequate. In this study, a rapid and cheap method of detecting S. enterica DNA was developed by employing the Quenching of Unincorporated Amplification Signal Reporters in Loop-Mediated Isothermal Amplification (QUASR LAMP) platform. QUASR LAMP provides a closed-tube, target-specific endpoint detection of pathogens, wherein results can be analyzed visually through an LED transilluminator and verified through agarose gel electrophoresis. Based on the chromosomal SopD gene, primers and probes were first designed, then screened. The assay was subsequently optimized so that the presence of S. enterica is determined by incubating the extracted DNA at 65°C for only 60 minutes. The assay was repeatable and can be performed by simply using a thermal cycler or even a dry bath incubator. S. enterica positives appear bright yellow green when viewed through a yellow filter excited with blue LED. The developed assay had an in silico and in vitro specificity towards Salmonella enterica subsp. enterica serovars with a limit of detection of 104 copies per microliter. The Salmonella QUASR LAMP assay has the potential for food and environmental applications. Chiefly, as an alternative to traditional microbiology and PCR, this QUASR LAMP assay can be used for point-of-care salmonellosis testing of clinical specimens in low-resource settings.
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Nyaruaba R, Mwaliko C, Dobnik D, Neužil P, Amoth P, Mwau M, Yu J, Yang H, Wei H. Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks. Clin Microbiol Rev 2022; 35:e0016821. [PMID: 35258315 PMCID: PMC9491181 DOI: 10.1128/cmr.00168-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
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Affiliation(s)
- Raphael Nyaruaba
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- International College, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Caroline Mwaliko
- International College, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Pavel Neužil
- Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Matilu Mwau
- Center for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute, Busia, Kenya
| | - Junping Yu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hang Yang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
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30
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Deng Q, Cao Y, Wan X, Wang B, Sun A, Wang H, Wang Y, Wang H, Gu H. Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections. Front Cell Infect Microbiol 2022; 12:943859. [PMID: 36204638 PMCID: PMC9530710 DOI: 10.3389/fcimb.2022.943859] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer patients are at high risk of infections and infection-related mortality; thereby, prompt diagnosis and precise anti-infectives treatment are critical. This study aimed to evaluate the performance of nanopore amplicon sequencing in identifying microbial agents among immunocompromised cancer patients with suspected infections. This prospective study enlisted 56 immunocompromised cancer patients with suspected infections. Their body fluid samples such as sputum and blood were collected, and potential microbial agents were detected in parallel by nanopore amplicon sequencing and the conventional culture method. Among the 56 body fluid samples, 47 (83.9%) samples were identified to have at least one pathogen by nanopore amplicon sequencing, but only 25 (44.6%) samples exhibited a positive finding by culture. Among 31 culture-negative samples, nanopore amplicon sequencing successfully detected pathogens in 22 samples (71.0%). Nanopore amplicon sequencing showed a higher sensitivity in pathogen detection than that of the conventional culture method (83.9% vs. 44.6%, P<0.001), and this advantage both existed in blood samples (38.5% vs. 0%, P=0.039) and non-blood samples (97.7% vs. 58.1%, P<0.001). Compared with the culture method, nanopore amplicon sequencing illustrated more samples with bacterial infections (P<0.001), infections from fastidious pathogens (P=0.006), and co-infections (P<0.001). The mean turnaround time for nanopore amplicon sequencing was about 17.5 hours, which was shorter than that of the conventional culture assay. This study suggested nanopore amplicon sequencing as a rapid and precise method for detecting pathogens among immunocompromised cancer patients with suspected infections. The novel and high-sensitive method will improve the outcomes of immunocompromised cancer patients by facilitating the prompt diagnosis of infections and precise anti-infectives treatment.
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Affiliation(s)
- Qingmei Deng
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Yongqing Cao
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Xiaofeng Wan
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Bin Wang
- Zhejiang ShengTing Biotechnology Company, Hangzhou, China
| | - Aimin Sun
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Huanzhong Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotechnology Company, Hangzhou, China
| | - Hongzhi Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
- *Correspondence: Hongzhi Wang, ; Hongcang Gu,
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
- *Correspondence: Hongzhi Wang, ; Hongcang Gu,
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31
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Tvrdá E, Ďuračka M, Benko F, Lukáč N. Bacteriospermia - A formidable player in male subfertility. Open Life Sci 2022; 17:1001-1029. [PMID: 36060647 PMCID: PMC9386612 DOI: 10.1515/biol-2022-0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/29/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022] Open
Abstract
Bacterial colonization of male reproductive tissues, cells, and fluids, and the subsequent impact of bacteria on the sperm architecture, activity, and fertilizing potential, has recently gained increased attention from the medical and scientific community. Current evidence strongly emphasizes the fact that the presence of bacteria in semen may have dire consequences on the resulting male fertility. Nevertheless, the molecular basis underlying bacteriospermia-associated suboptimal semen quality is sophisticated, multifactorial, and still needs further understanding. Bacterial adhesion and subsequent sperm agglutination and immobilization represent the most direct pathway of sperm-bacterial interactions. Furthermore, the release of bacterial toxins and leukocytic infiltration, associated with a massive outburst of reactive oxygen species, have been repeatedly associated with sperm dysfunction in bacteria-infested semen. This review serves as a summary of the present knowledge on bacteriospermia-associated male subfertility. Furthermore, we strived to outline the currently available methods for assessing bacterial profiles in semen and to outline the most promising strategies for the prevention and/or management of bacteriospermia in practice.
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Affiliation(s)
- Eva Tvrdá
- Department of Animal Physiology, Institute of Applied Biology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, Nitra-Chrenová, 949 76, Slovakia
| | - Michal Ďuračka
- Department of Animal Physiology, Institute of Applied Biology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, Nitra-Chrenová, 949 76, Slovakia
| | - Filip Benko
- Department of Animal Physiology, Institute of Applied Biology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, Nitra-Chrenová, 949 76, Slovakia
| | - Norbert Lukáč
- Department of Animal Physiology, Institute of Applied Biology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, Nitra-Chrenová, 949 76, Slovakia
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Wan J, Duan L, Chen Q, Wang L, Bai J, Hu J, Lu X, Zhang T, Song W, Yang D, Shan Y, Yan Z. Potential clinical impact of metagenomic next-generation sequencing of plasma for cervical spine injury with sepsis in intensive care unit: A retrospective study. Front Cell Infect Microbiol 2022; 12:948602. [PMID: 36017370 PMCID: PMC9397569 DOI: 10.3389/fcimb.2022.948602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Cervical spine injury (CSI) accounts for significant mortality in the intensive care unit (ICU), whereas sepsis remains one of the major causes of death in patients with CSI. However, there is no effective method to diagnose sepsis timely. The aim of this study is to investigate the effect of metagenomic next-generation sequencing (mNGS) on the pathogen features and the prognostic prediction of CSI patients with sepsis. A total of 27 blood samples from 17 included patients were tested by mNGS. Data of mNGS were compared with the conventional culture method. The Kaplan–Meier plots were used to visualize survival curves. A Cox proportional hazards model was used to identify independent prognostic factors for survival. Results showed that mNGS detected a wide spectrum of pathogens in CSI patients with sepsis, including 129 bacterial species, 8 viral species, and 51 fungal species. mNGS indicated 85.2% positive results, while the conventional culture method only showed 11.1% positive results in the blood samples. Further analyses revealed that mNGS had no prognostic effect on the septic CSI patients in ICU, whereas positive results of blood culture were closely correlated with an increased hazard ratio (HR) (HR 77.7067, 95%CI 2.860–2641.4595, p = 0.0155). Our results suggested that the mNGS application may provide evidence for clinicians to use antibiotics when a CSI case is diagnosed with sepsis.
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Affiliation(s)
- Jian Wan
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Liwei Duan
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
| | - Qitong Chen
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
| | - Lv Wang
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
| | - Jinxia Bai
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Jingyun Hu
- Central Lab, Shanghai Key Laboratory of Pathogenic Fungi Medical Testing, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Xinyuan Lu
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Tao Zhang
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Wei Song
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Degang Yang
- Department of Infectious Diseases, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Degang Yang, ; Yi Shan, ; Zhu Yan,
| | - Yi Shan
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
- *Correspondence: Degang Yang, ; Yi Shan, ; Zhu Yan,
| | - Zhu Yan
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
- *Correspondence: Degang Yang, ; Yi Shan, ; Zhu Yan,
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Smith LD, Nalla S, Kuo CW, Kohli M, Smith AM. Rapid quantification of microRNA-375 through one-pot primer-generating rolling circle amplification. Analyst 2022; 147:2936-2941. [PMID: 35695478 PMCID: PMC11247439 DOI: 10.1039/d2an00263a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
A recent surge of interest in microRNA has been driven by its discovery as a circulating biomarker of disease, with many diagnostic test platforms currently under development. Alternatives to widely used microRNA quantification methods such as quantitative reverse transcriptase PCR (qRT-PCR) are needed for use in portable and point-of-care devices which are incompatible with complex sample processing workflows and thermal cycling. Rolling circle amplification (RCA) is a one-pot assay technique which directly amplifies nucleic acids using sequence-specific microRNA priming to initiate a single-step isothermal reaction that is compatible with simple devices. Sensitivity remains a limitation of RCA methods, however, and detection limits do not typically reach the femtomolar level in which microRNA targets are present in blood. RCA assays have previously been improved by digestion of the amplification products using a nicking endonuclease to exponentially generate new reaction primers. Here we describe how a ligation-free version of this technique performed in a single tube can be used to improve the limit of detection for microRNA-375, an important blood biomarker for prostate cancer. Endonuclease addition changes a linear process into an exponential amplification reaction which results in a 61-fold improvement of the limit of detection (5.9 fM), a dynamic range wider than 5-log(10), and a shorter reaction time. By eliminating the need for microRNA reverse transcription and thermal cycling, this single-step one-pot method provides a more rapid and simplified alternative to qRT-PCR for ultrasensitive microRNA quantification in blood extracts.
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Affiliation(s)
- Lucas D Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Siva Nalla
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Manish Kohli
- Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Materials Science & Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, Urbana, Illinois 61801, USA
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Close RM, Sutcliffe CG, Galdun P, Reid A, Askew MR, Davidson AM, Kellywood K, Parker D, Patel J, Romancito E, Brown LB, McAuley JB, Hammitt LL. Point-of-care molecular diagnostics for the detection of group A Streptococcus in non-invasive skin and soft tissue infections: a validation study. Diagn Microbiol Infect Dis 2022; 103:115729. [DOI: 10.1016/j.diagmicrobio.2022.115729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/15/2022] [Accepted: 05/20/2022] [Indexed: 01/21/2023]
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35
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Baumkircher A, Seme K, Munih M, Mihelj M. Collaborative Robot Precision Task in Medical Microbiology Laboratory. SENSORS 2022; 22:s22082862. [PMID: 35458847 PMCID: PMC9025832 DOI: 10.3390/s22082862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022]
Abstract
This study focuses on the feasibility of collaborative robot implementation in a medical microbiology laboratory by demonstrating fine tasks using kinesthetic teaching. Fine tasks require sub-millimetre positioning accuracy. Bacterial colony picking and identification was used as a case study. Colonies were picked from Petri dishes and identified using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry. We picked and identified 56 colonies (36 colonies of Gram-negative Acinetobacter baumannii and 20 colonies of Gram-positive Staphylococcus epidermidis). The overall identification error rate was around 11%, although it was significantly lower for Gram-positive bacteria (5%) than Gram-negative bacteria (13.9%). Based on the identification scores, it was concluded that the system works similarly well as a manual operator. It was determined that tasks were successfully demonstrated using kinesthetic teaching and generalized using dynamic movement primitives (DMP). Further improvement of the identification error rate is possible by choosing a different deposited sample treatment method (e.g., semi-extraction, wet deposition).
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Affiliation(s)
- Aljaz Baumkircher
- Laboratory of Robotics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška Cesta 25, 1000 Ljubljana, Slovenia
| | - Katja Seme
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Marko Munih
- Laboratory of Robotics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška Cesta 25, 1000 Ljubljana, Slovenia
| | - Matjaž Mihelj
- Laboratory of Robotics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška Cesta 25, 1000 Ljubljana, Slovenia
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36
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MALDI-TOF Mass Spectrometry Analysis and Human Post-Mortem Microbial Community: A Pilot Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074354. [PMID: 35410034 PMCID: PMC8998342 DOI: 10.3390/ijerph19074354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023]
Abstract
Introduction: The human post-mortem microbiome (HPM) plays a major role in the decomposition process. Successional changes in post-mortem bacterial communities have been recently demonstrated using high throughput metagenomic sequencing techniques, showing great potential as a post-mortem interval (PMI) predictor. The aim of this study is to verify the application of the mass spectrometry technique, better known as MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), as a cheap and quick method for microbe taxonomic identification and for studying the PM microbiome. Methods: The study was carried out on 18 human bodies, ranging from 4 months to 82 years old and with a PMI range from 24 h up to 15 days. The storage time interval in the coolers was included in the final PMI estimates. Using the PMI, the sample study was divided into three main groups: seven cases with a PMI < 72 h; six cases with a PMI of 72−168 h and five cases with a PMI > 168 h. For each body, microbiological swabs were sampled from five external anatomical sites (eyes, ears, nose, mouth, and rectum) and four internal organs (brain, spleen, liver, and heart). Results: The HPM became increasingly different from the starting communities over time in the internal organs as well as at skin sites; the HPM microbiome was mostly dominated by Firmicutes and Proteobacteria phyla; and a PM microbial turnover existed during decomposition, evolving with the PMI. Conclusions: MALDI-TOF is a promising method for PMI estimation, given its sample handling, good reproducibility, and high speed and throughput. Although several intrinsic and extrinsic factors can affect the structure of the HPM, MALDI-TOF can detect the overall microbial community turnover of most prevalent phyla during decomposition. Limitations are mainly related to its sensitivity due to the culture-dependent method and bias in the identification of new isolates.
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37
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Zhang X, Meng H, Liu H, Ye Q. Advances in laboratory detection methods and technology application of SARS-CoV-2. J Med Virol 2022; 94:1357-1365. [PMID: 34854101 PMCID: PMC9015480 DOI: 10.1002/jmv.27494] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023]
Abstract
At present, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is raging worldwide, and the coronavirus disease 2019 outbreak caused by SARS-CoV-2 seriously threatens the life and health of all humankind. There is no specific medicine for novel coronavirus yet. So, laboratory diagnoses of novel coronavirus as soon as possible and isolation of the source of infection play a vital role in preventing and controlling the epidemic. Therefore, selecting appropriate detection techniques and methods is particularly important to improve the efficiency of disease diagnosis and treatment and to curb the outbreak of infectious diseases. In this paper, virus nucleic acid, protein, and serum immunology were reviewed to provide a reference for further developing virus detection technology to provide better prevention and treatment strategies and research ideas for clinicians and researchers.
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Affiliation(s)
- Xiucai Zhang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Hanyan Meng
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Huihui Liu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Qing Ye
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
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38
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Merino I, de la Fuente A, Domínguez-Gil M, Eiros JM, Tedim AP, Bermejo-Martín JF. Digital PCR applications for the diagnosis and management of infection in critical care medicine. Crit Care 2022; 26:63. [PMID: 35313934 PMCID: PMC8935253 DOI: 10.1186/s13054-022-03948-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10–25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.
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Affiliation(s)
- Irene Merino
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José María Eiros
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain. .,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.
| | - Jesús F Bermejo-Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
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Garcia Gonzalez J, Hernandez FJ. Nuclease activity: an exploitable biomarker in bacterial infections. Expert Rev Mol Diagn 2022; 22:265-294. [PMID: 35240900 DOI: 10.1080/14737159.2022.2049249] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION In the increasingly challenging field of clinical microbiology, diagnosis is a cornerstone whose accuracy and timing are crucial for the successful management, therapy, and outcome of infectious diseases. Currently employed biomarkers of infectious diseases define the scope and limitations of diagnostic techniques. As such, expanding the biomarker catalog is crucial to address unmet needs and bring about novel diagnostic functionalities and applications. AREAS COVERED This review describes the extracellular nucleases of 15 relevant bacterial pathogens and discusses the potential use of nuclease activity as a diagnostic biomarker. Articles were searched for in PubMed using terms: "nuclease", "bacteria", "nuclease activity" or "biomarker". For overview sections, original and review articles between 2000 and 2019 were searched for using terms: "infections", "diagnosis", "bacterial", "burden", "challenges". Informative articles were selected. EXPERT OPINION Using the catalytic activity of nucleases offers new possibilities compared to established biomarkers. Nucleic acid activatable reporters in combination with different transduction platforms and delivery methods can be used to detect disease-associated nuclease activity patterns in vitro and in vivo for prognostic and diagnostic applications. Even when these patterns are not obvious or of unknown etiology, screening platforms could be used to identify new disease reporters.
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Affiliation(s)
- Javier Garcia Gonzalez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
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Development of a loop-mediated isothermal amplification (LAMP) assay for molecular identification of Trueperella abortisuis isolated from pigs. Mol Cell Probes 2022; 62:101795. [DOI: 10.1016/j.mcp.2022.101795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 01/19/2022] [Accepted: 02/02/2022] [Indexed: 11/21/2022]
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Oussou-Azo FA, Futagami T, Vestergaard MCM. Immuno-Dipstick for Colletotrichum gloeosporioides Detection: Towards On-Farm Application. BIOSENSORS 2022; 12:49. [PMID: 35200310 PMCID: PMC8869205 DOI: 10.3390/bios12020049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 11/16/2022]
Abstract
Early and quick detection of pathogens are crucial for managing the spread of infections in the biomedical, biosafety, food, and agricultural fields. While molecular diagnostics can offer the specificity and reliability in acute infectious diseases, detection of pathogens is often slowed down by the current benchtop molecular diagnoses, which are time consuming, labor intensive, and lack the mobility for application at the point-of-need. In this work, we developed a complete on-farm use detection protocol for the plant-devastating anthracnose agent: Colletotrichum gloeosporioides. Our methods combined a simplified DNA extraction on paper that is compatible with loop-mediated isothermal amplification (LAMP), coupled with paper-based immunoassay lateral flow sensing. Our results offer simple, quick, easy, and a minimally instrumented toolkit for Colletotrichum gloeosporioides detection. This scalable and adaptable platform is a valuable alternative to traditional sensing systems towards on-the-go pathogen detection in food and agriculture, biomedical, and other fields.
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Affiliation(s)
- Fifame Auriane Oussou-Azo
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; (F.A.O.-A.); (T.F.)
| | - Taiki Futagami
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; (F.A.O.-A.); (T.F.)
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Mun’delanji Catherine M. Vestergaard
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; (F.A.O.-A.); (T.F.)
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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42
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Rawson TM, Peiffer-Smadja N, Holmes A. Artificial Intelligence in Infectious Diseases. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Ordóñez-Mena JM, Fanshawe TR, Foster D, Andersson M, Oakley S, Stoesser N, Walker AS, Hayward G. Frequencies and patterns of microbiology test requests from primary care in Oxfordshire, UK, 2008-2018: a retrospective cohort study of electronic health records to inform point-of-care testing. BMJ Open 2021; 11:e048527. [PMID: 34815274 PMCID: PMC8611454 DOI: 10.1136/bmjopen-2020-048527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES To inform point-of-care test (POCT) development, we quantified the primary care demand for laboratory microbiology tests by describing their frequencies overall, frequencies of positives, most common organisms identified, temporal trends in testing and patterns of cotesting on the same and subsequent dates. DESIGN Retrospective cohort study. SETTING Primary care practices in Oxfordshire. PARTICIPANTS 393 905 patients (65% female; 49% aged 18-49). PRIMARY AND SECONDARY OUTCOME MEASURES The frequencies of all microbiology tests requested between 2008 and 2018 were quantified. Patterns of cotesting were investigated with heat maps. All analyses were done overall, by sex and age categories. RESULTS 1 596 752 microbiology tests were requested. Urine culture±microscopy was the most common of all tests (n=673 612, 42%), was mainly requested without other tests and was the most common test requested in follow-up within 7 and 14 days. Of all urine cultures, 180 047 (27%) were positive and 172 651 (26%) showed mixed growth, and Escherichia coli was the most prevalent organism (132 277, 73% of positive urine cultures). Antenatal urine cultures and blood tests in pregnancy (hepatitis B, HIV and syphilis) formed a common test combination, consistent with their use in antenatal screening. CONCLUSIONS The greatest burden of microbiology testing in primary care is attributable to urine culture ± microscopy; genital and routine antenatal urine and blood testing are also significant contributors. Further research should focus on the feasibility and impact of POCTs for these specimen types.
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Affiliation(s)
- J M Ordóñez-Mena
- Department of Primary Care Health Sciences, University of Oxford Nuffield, Oxford, Oxfordshire, UK
- NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Thomas R Fanshawe
- Department of Primary Care Health Sciences, University of Oxford Nuffield, Oxford, Oxfordshire, UK
| | - Dona Foster
- Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Monique Andersson
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Sarah Oakley
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Nicole Stoesser
- NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - A Sarah Walker
- NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Gail Hayward
- Department of Primary Care Health Sciences, University of Oxford Nuffield, Oxford, Oxfordshire, UK
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Sciuto EL, Leonardi AA, Calabrese G, Luca GD, Coniglio MA, Irrera A, Conoci S. Nucleic Acids Analytical Methods for Viral Infection Diagnosis: State-of-the-Art and Future Perspectives. Biomolecules 2021; 11:1585. [PMID: 34827583 PMCID: PMC8615992 DOI: 10.3390/biom11111585] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
The analysis of viral nucleic acids (NA), DNA or RNA, is a crucial issue in the diagnosis of infections and the treatment and prevention of related human diseases. Conventional nucleic acid tests (NATs) require multistep approaches starting from the purification of the pathogen genetic material in biological samples to the end of its detection, basically performed by the consolidated polymerase chain reaction (PCR), by the use of specialized instruments and dedicated laboratories. However, since the current NATs are too constraining and time and cost consuming, the research is evolving towards more integrated, decentralized, user-friendly, and low-cost methods. These will allow the implementation of massive diagnoses addressing the growing demand of fast and accurate viral analysis facing such global alerts as the pandemic of coronavirus disease of the recent period. Silicon-based technology and microfluidics, in this sense, brought an important step up, leading to the introduction of the genetic point-of-care (PoC) systems. This review goes through the evolution of the analytical methods for the viral NA diagnosis of infection diseases, highlighting both advantages and drawbacks of the innovative emerging technologies versus the conventional approaches.
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Affiliation(s)
- Emanuele Luigi Sciuto
- Azienda Ospedaliero, Universitaria Policlinico “G. Rodolico-San Marco”, Via Santa Sofia 78, 95123 Catania, Italy
| | - Antonio Alessio Leonardi
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy; (A.A.L.); (A.I.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
| | - Giovanna Calabrese
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
| | - Giovanna De Luca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
| | - Maria Anna Coniglio
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, University of Catania, Via Sofia 87, 95123 Catania, Italy;
| | - Alessia Irrera
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy; (A.A.L.); (A.I.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
| | - Sabrina Conoci
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy; (A.A.L.); (A.I.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy; (G.C.); (G.D.L.)
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM), Ottava Strada n.5, 95121 Catania, Italy
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Teoh T, McNamara R, Powell J, O’Connell NH, Dunne CP. A retrospective observational study of the impact of 16s and 18s ribosomal RNA PCR on antimicrobial treatment over seven years: A tertiary hospital experience. PLoS One 2021; 16:e0258552. [PMID: 34637486 PMCID: PMC8509882 DOI: 10.1371/journal.pone.0258552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/29/2021] [Indexed: 01/15/2023] Open
Abstract
Background Although culture-based methods remain a staple element of microbiology analysis, advanced molecular methods increasingly supplement the testing repertoire. Since the advent of 16s and 18s ribosomal RNA PCR in the 2000s, there has been interest in its utility for pathogen detection. Nonetheless, studies assessing the impact on antimicrobial prescribing are limited. We report a single-centre experience of the influence of 16s and 18s PCR testing on antimicrobial treatment, including a cost-analysis. Methods Data were collected retrospectively for all samples sent for 16s and 18s PCR testing between January 2014 and December 2020. Results were compared to any culture-based result. Assessment focused on any change of antimicrobial treatment based on PCR result, or use of the result as supportive evidence for microbiological diagnosis. Results 310 samples relevant to 268 patients were referred for 16s/18s rRNA PCR testing during the period. Culture was performed for 234 samples. Enrichment culture was performed for 83 samples. 82 of 300 samples sent for 16s PCR had positive results (20.8%). When culture was performed, enrichment reduced the outcome of 16s PCR only positive results (4/36 [11.1%] versus 14/35 [40.0%], p = 0.030 where a pathogen found). 18s PCR yielded 9 positive results from 67 samples. The 16s PCR result influenced antimicrobial change for 6 patients (2.2%). We estimated the cost for 16s PCR testing to result in one significant change in antimicrobial therapy to be €3,340. 18s PCR did not alter antimicrobial treatment. Conclusion There was limited impact of 16s PCR results on antimicrobial treatments. Relevance to practice was affected by relatively long turn-around-time for results. Utility may be increased in specialised surgical centres, or by reducing turn-around-time. Enrichment culture should be considered on samples where 16s PCR is requested. There remains limited evidence for use of 18s PCR in clinical management, and further studies in this area are likely warranted.
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Affiliation(s)
- TeeKeat Teoh
- Department of Clinical Microbiology, University Limerick Hospital Group, Limerick, Ireland
- Centre for Interventions in Infection, Inflammation & Immunity (4i) and School of Medicine, University of Limerick, Limerick, Ireland
| | - Rachel McNamara
- Department of Medicine and Infectious Diseases, University Hospital Limerick, Limerick, Ireland
| | - James Powell
- Department of Clinical Microbiology, University Limerick Hospital Group, Limerick, Ireland
| | - Nuala H. O’Connell
- Department of Clinical Microbiology, University Limerick Hospital Group, Limerick, Ireland
- Centre for Interventions in Infection, Inflammation & Immunity (4i) and School of Medicine, University of Limerick, Limerick, Ireland
| | - Colum P. Dunne
- Centre for Interventions in Infection, Inflammation & Immunity (4i) and School of Medicine, University of Limerick, Limerick, Ireland
- * E-mail:
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Dumkow LE, Worden LJ, Rao SN. Syndromic diagnostic testing: a new way to approach patient care in the treatment of infectious diseases. J Antimicrob Chemother 2021; 76:iii4-iii11. [PMID: 34555157 PMCID: PMC8460095 DOI: 10.1093/jac/dkab245] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Advanced microbiology technologies such as multiplex molecular assays (i.e. syndromic diagnostic tests) are a novel approach to the rapid diagnosis of common infectious diseases. As the global burden of antimicrobial resistance continues to rise, the judicious use of antimicrobials is of utmost importance. Syndromic panels are now being recognized in some clinical practice guidelines as a 'game-changer' in the diagnosis of infectious diseases. These syndromic panels, if implemented thoughtfully and interpreted carefully, have the potential to improve patient outcomes through improved clinical decision making, optimized laboratory workflow, and enhanced antimicrobial stewardship. This paper reviews the potential benefits of and considerations regarding various infectious diseases syndromic panels, and highlights how to maximize impact through collaboration between clinical microbiology laboratory and antimicrobial stewardship programmes.
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Affiliation(s)
- Lisa E Dumkow
- Mercy Health Saint Mary's Hospital, Grand Rapids, MI, USA
| | - Lacy J Worden
- Mercy Health Saint Mary's Hospital, Grand Rapids, MI, USA
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Nichols ZE, Geddes CD. Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review. Molecules 2021; 26:5666. [PMID: 34577137 PMCID: PMC8470389 DOI: 10.3390/molecules26185666] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Sample preparation is an essential step for nearly every type of biochemical analysis in use today. Among the most important of these analyses is the diagnosis of diseases, since their treatment may rely greatly on time and, in the case of infectious diseases, containing their spread within a population to prevent outbreaks. To address this, many different methods have been developed for use in the wide variety of settings for which they are needed. In this work, we have reviewed the literature and report on a broad range of methods that have been developed in recent years and their applications to point-of-care (POC), high-throughput screening, and low-resource and traditional clinical settings for diagnosis, including some of those that were developed in response to the coronavirus disease 2019 (COVID-19) pandemic. In addition to covering alternative approaches and improvements to traditional sample preparation techniques such as extractions and separations, techniques that have been developed with focuses on integration with smart devices, laboratory automation, and biosensors are also discussed.
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Affiliation(s)
- Zach E. Nichols
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
| | - Chris D. Geddes
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
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Zhao H, Yang Y, Lyu J, Ren X, Cheng W. Development and application of a method to detect 27 respiratory pathogens using multiplex RT-PCR combined with MassARRAY technology. BMC Infect Dis 2021; 21:870. [PMID: 34433411 PMCID: PMC8385475 DOI: 10.1186/s12879-021-06404-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/18/2021] [Indexed: 12/28/2022] Open
Abstract
Background Respiratory tract infections are the most common infections that lead to morbidity and mortality worldwide. Early recognition and precise diagnosis of microbial etiology is important to treat LRTIs promptly, specifically and effectively. Objectives To establish a method based on multiplex reverse transcription (MRT)-PCR and MassARRAY technology for the simultaneous detection of 27 respiratory pathogens and explore its clinical application value. Methods Analytical sensitivity and specificity of the MRT-PCR-MassARRAY system were validated using inactivated bacterial and viral strains. Also we analyzed samples from 207 patients by MassARRAY methods and compared the results with consensus PCR/reverse transcription (RT)-PCR. Results The minimum detection limit of our MRT-PCR-MassARRAY method for pathogens was 10–100 copies/μl, with high specificity. Comparison test with consensus PCR/RT-PCR on 207 clinical samples, the positive, negative, and total correlation rates were 100, 98.68, and 99.03%, respectively. There was a high degree of agreement between the test results of the two methods (P < 0.01 by McNemar’s test). Conclusion Our detection system of 27 respiratory pathogens based on MassARRAY technology has high sensitivity and specificity, high throughput, and is simple to operate. It provides diagnostic value for the clinical diagnosis of respiratory pathogens and is of great significance in the screening of respiratory pathogens.
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Affiliation(s)
- Huan Zhao
- Department of Respiratory Medicine, The Sixth People's Hospital of Nantong, Nantong, Jiangsu, China
| | - Yichao Yang
- Research and Development Centre, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang, China
| | - Jiangfeng Lyu
- Research and Development Centre, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang, China
| | - Xuyi Ren
- Research and Development Centre, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang, China.
| | - Wei Cheng
- Department of Respiratory Diseases, Nantong Tongzhou People's Hospital, Nantong, Jiangsu, China.
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Nasopharyngeal metabolomics and machine learning approach for the diagnosis of influenza. EBioMedicine 2021; 71:103546. [PMID: 34419924 PMCID: PMC8385175 DOI: 10.1016/j.ebiom.2021.103546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/03/2022] Open
Abstract
Background Respiratory virus infections are significant causes of morbidity and mortality, and may induce host metabolite alterations by infecting respiratory epithelial cells. We investigated the use of liquid chromatography quadrupole time-of-flight mass spectrometry (LC/Q-TOF) combined with machine learning for the diagnosis of influenza infection. Methods We analyzed nasopharyngeal swab samples by LC/Q-TOF to identify distinct metabolic signatures for diagnosis of acute illness. Machine learning models were performed for classification, followed by Shapley additive explanation (SHAP) analysis to analyze feature importance and for biomarker discovery. Findings A total of 236 samples were tested in the discovery phase by LC/Q-TOF, including 118 positive samples (40 influenza A 2009 H1N1, 39 influenza H3 and 39 influenza B) as well as 118 age and sex-matched negative controls with acute respiratory illness. Analysis showed an area under the receiver operating characteristic curve (AUC) of 1.00 (95% confidence interval [95% CI] 0.99, 1.00), sensitivity of 1.00 (95% CI 0.86, 1.00) and specificity of 0.96 (95% CI 0.81, 0.99). The metabolite most strongly associated with differential classification was pyroglutamic acid. Independent validation of a biomarker signature based on the top 20 differentiating ion features was performed in a prospective cohort of 96 symptomatic individuals including 48 positive samples (24 influenza A 2009 H1N1, 5 influenza H3 and 19 influenza B) and 48 negative samples. Testing performed using a clinically-applicable targeted approach, liquid chromatography triple quadrupole mass spectrometry, showed an AUC of 1.00 (95% CI 0.998, 1.00), sensitivity of 0.94 (95% CI 0.83, 0.98), and specificity of 1.00 (95% CI 0.93, 1.00). Limitations include lack of sample suitability assessment, and need to validate these findings in additional patient populations. Interpretation This metabolomic approach has potential for diagnostic applications in infectious diseases testing, including other respiratory viruses, and may eventually be adapted for point-of-care testing.
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Safiabadi Tali SH, LeBlanc JJ, Sadiq Z, Oyewunmi OD, Camargo C, Nikpour B, Armanfard N, Sagan SM, Jahanshahi-Anbuhi S. Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection. Clin Microbiol Rev 2021; 34:e00228-20. [PMID: 33980687 PMCID: PMC8142517 DOI: 10.1128/cmr.00228-20] [Citation(s) in RCA: 179] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.
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Affiliation(s)
- Seyed Hamid Safiabadi Tali
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
- Department of Mechanical, Industrial, and Aerospace Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Jason J LeBlanc
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine (Infectious Diseases), Dalhousie University, Halifax, Nova Scotia, Canada
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Zubi Sadiq
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Oyejide Damilola Oyewunmi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Carolina Camargo
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Bahareh Nikpour
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
| | - Narges Armanfard
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
- Mila-Quebec AI Institute, Montréal, Québec, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Sana Jahanshahi-Anbuhi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
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