ABSTRACT
Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.
Subject(s)
Chromatography, Liquid/methods , Communicable Diseases/diagnosis , Mass Spectrometry/methods , Microbiological Techniques/methods , Proteomics/methods , Body Fluids , COVID-19 Testing/methods , Humans , Tandem Mass SpectrometryABSTRACT
The eighth Applied Bioinformatics and Public Health Microbiology (ABPHM) conference showcased the recent acceleration of bioinformatic approaches used in public health settings. This included approaches for the surveillance of infectious diseases, understanding microbial evolution and diversity and pathogen interactions. Overall, the meeting highlighted the importance of data-driven approaches used by scientists during the COVID-19 pandemic.
Subject(s)
Bacterial Infections/epidemiology , COVID-19/epidemiology , Computational Biology/methods , Microbiological Techniques/methods , Public Health/methods , Bacterial Infections/microbiology , Bacterial Infections/prevention & control , COVID-19/prevention & control , COVID-19/virology , HumansABSTRACT
With advanced technology and its development, bioinformatics is one of the avant-garde fields that has managed to make amazing progress in the pharmaceutical-medical field by modeling the infrastructural dimensions of healthcare and integrating computing tools in drug innovation, facilitating prevention, detection/more accurate diagnosis, and treatment of disorders, while saving time and money. By association, bioinformatics and pharmacovigilance promoted both sample analyzes and interpretation of drug side effects, also focusing on drug discovery and development (DDD), in which systems biology, a personalized approach, and drug repositioning were considered together with translational medicine. The role of bioinformatics has been highlighted in DDD, proteomics, genetics, modeling, miRNA discovery and assessment, and clinical genome sequencing. The authors have collated significant data from the most known online databases and publishers, also narrowing the diversified applications, in order to target four major areas (tetrad): DDD, anti-microbial research, genomic sequencing, and miRNA research and its significance in the management of current pandemic context. Our analysis aims to provide optimal data in the field by stratification of the information related to the published data in key sectors and to capture the attention of researchers interested in bioinformatics, a field that has succeeded in advancing the healthcare paradigm by introducing developing techniques and multiple database platforms, addressed in the manuscript.
Subject(s)
Computational Biology , Drug Development , Drug Discovery , MicroRNAs , Microbiological Techniques/methods , Whole Genome Sequencing , Animals , COVID-19 , Drug Industry , Genome-Wide Association Study , Humans , Pharmacovigilance , Public Health , Translational Research, BiomedicalSubject(s)
Bacterial Infections/diagnosis , COVID-19/epidemiology , Clinical Laboratory Techniques/methods , Cross Infection/diagnosis , Specimen Handling/methods , COVID-19/transmission , Cross Infection/microbiology , Humans , Microbiological Techniques/methods , Pneumonia, Ventilator-Associated/diagnosis , Pneumonia, Ventilator-Associated/microbiology , SARS-CoV-2ABSTRACT
We describe rapid spread of multidrug-resistant gram-negative bacteria among patients in dedicated coronavirus disease care units in a hospital in Maryland, USA, during May-June 2020. Critical illness, high antibiotic use, double occupancy of single rooms, and modified infection prevention practices were key contributing factors. Surveillance culturing aided in outbreak recognition and control.
Subject(s)
Anti-Bacterial Agents , COVID-19 , Critical Illness , Gram-Negative Bacteria , Infection Control , Practice Patterns, Nurses' , Superinfection , Anti-Bacterial Agents/classification , Anti-Bacterial Agents/therapeutic use , COVID-19/epidemiology , COVID-19/physiopathology , COVID-19/therapy , Critical Illness/epidemiology , Critical Illness/therapy , Drug Resistance, Multiple, Bacterial , Gram-Negative Bacteria/classification , Gram-Negative Bacteria/drug effects , Gram-Negative Bacteria/isolation & purification , Humans , Infection Control/methods , Infection Control/organization & administration , Intensive Care Units/organization & administration , Maryland/epidemiology , Microbiological Techniques/methods , Microbiological Techniques/statistics & numerical data , Practice Patterns, Nurses'/organization & administration , Practice Patterns, Nurses'/standards , Precipitating Factors , Risk Factors , SARS-CoV-2 , Superinfection/diagnosis , Superinfection/microbiologyABSTRACT
We observed bacterial or fungal coinfections in COVID-19 patients admitted between March 1 and April 18, 2020 (152 of 4,267, 3.6%). Among these patients, mortality was 57%; 74% were intubated; 51% with bacteremia had central venous catheters. Time to culture positivity was 6-7 days, and 79% had received prior antibiotics. Metallo-ß-lactamase-producing E. cloacae coinfections occurred in 5 patients.
Subject(s)
Anti-Bacterial Agents/therapeutic use , Bacteremia , COVID-19 , Coinfection , Mycoses , SARS-CoV-2/isolation & purification , Bacteremia/diagnosis , Bacteremia/epidemiology , Bacteremia/therapy , COVID-19/epidemiology , COVID-19/microbiology , COVID-19/therapy , Central Venous Catheters/microbiology , Central Venous Catheters/statistics & numerical data , Coinfection/epidemiology , Coinfection/microbiology , Coinfection/virology , Drug Resistance, Bacterial , Female , Humans , Male , Microbiological Techniques/methods , Microbiological Techniques/statistics & numerical data , Middle Aged , Mycoses/diagnosis , Mycoses/epidemiology , Mycoses/therapy , New York/epidemiology , Outcome and Process Assessment, Health Care , Respiration, Artificial/statistics & numerical data , Severity of Illness IndexABSTRACT
Endemic species of coronavirus (HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1) are frequent causes of upper respiratory tract infections. Three highly pathogenic coronaviruses have been associated with outbreaks and epidemics and have challenged clinical microbiology laboratories to quickly develop assays for diagnosis. Their initial characterization was achieved by molecular methods. With the great advance in metagenomic whole-genome sequencing directly from clinical specimens, diagnosis of novel coronaviruses could be quickly implemented into the workflow of managing cases of pneumonia of unknown cause, which will markedly affect the time of the initial characterization and accelerate the initiation of outbreak control measures.
Subject(s)
Communicable Disease Control/methods , Coronavirus , Disease Outbreaks/prevention & control , Microbiological Techniques/methods , Respiratory Tract Infections , Clinical Laboratory Services , Coronavirus/classification , Coronavirus/genetics , Coronavirus/isolation & purification , Coronavirus/pathogenicity , Humans , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Whole Genome SequencingABSTRACT
Since 2014, porcine epidemic diarrhea virus (PEDV) has reemerged in Europe. RT-PCR methods have been described for the detection of PEDV, but none have been validated according to a norm. In this study we described the development and validation of a SYBR™ Green one-step RT-qPCR according to the French norm NF U47-600, for the detection and quantification of PEDV viral RNA. The method was validated from sample preparation (feces or jejunum) through to nucleic acid extraction and RT-qPCR detection. Specificity and sensitivity, limit of detection (LoD), limit of quantification (LQ), linearity, intra and inter assay variability were evaluated using transcribed RNA and fecal and jejunum matrices spiked with virus. The analytical and diagnostic specificities and sensitivities of this RT-qPCR were 100% in this study. A LoD of 50 genome copies/5 µl of extract from fecal matrices spiked with virus or RNA transcript and 100 genome copies/5 µl of extract from jejunum matrices spiked with virus were obtained. The Lower LQ (LLQ) was 100 genome copies/5 µl and the Upper LQ (ULQ) 108 copies/5 µl. This method is the first, validated according a norm for PEDV and may serve as a global reference method to harmonize detection and quantification of PEDV viral RNA in both field and experimental settings.