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The Journal of Foot and Ankle Surgery :... 2022Identification of bacteria by polymerase chain reaction (PCR) is known to be more sensitive than culture, which brings to question the clinical applicability of the...
Identification of bacteria by polymerase chain reaction (PCR) is known to be more sensitive than culture, which brings to question the clinical applicability of the results. In this study, we evaluate the ability of PCR to detect clinically relevant bacterial species in lower extremity wound infections requiring operative debridement, as well as the quantitative change in biodiversity and bacterial load reflected by PCR during the course of treatment. Thirty-four infected lower extremity were examined by analysis of 16S ribosomal RNA subunit and by culture. McNemar's test was used to measure the concordance of clinically relevant bacterial species identified by PCR compared to culture during each debridement. Change in wound biodiversity from initial presentation to final closure was evaluated by Wilcoxon signed-rank test. Kaplan-Meier survival curve was used to characterize change in measured bacterial load over the course of operative debridement. A total of 15 and 12 clinically relevant bacterial species were identified by PCR and culture, respectively. The most common bacterial species identified were Coagulase-negative Staphylococcus, Staphylococcus aureus, and Enterococcus spp. PCR was less likely to detect Enterococcus spp. on initial debridement and Coagulase-negative Staphylococcus on closure in this study population. A significant decrease in mean number of clinically relevant species detected from initial debridement to closure was reflected by culture (p = .0188) but not by PCR (p = .1848). Both PCR (p = .0128) and culture (p = .0001) depicted significant reduction in mean bacterial load from initial debridement to closure. PCR is able to identify common clinically relevant bacterial species in lower extremity surgical wound infections. PCR displays increased sensitivity compared to culture with relation to detection of biodiversity, rather than bacterial load. Molecular diagnostics and conventional culture may serve a joint purpose to assist with rendering clinical judgment in complex wound infections.
Topics: Bacteria; Coagulase; Humans; Lower Extremity; Polymerase Chain Reaction; Surgical Wound Infection
PubMed: 34895822
DOI: 10.1053/j.jfas.2020.07.009 -
The Veterinary Clinics of North... Mar 2023Laboratory testing is one part of clinical diagnosis, and quick and reliable testing results provide important data to support treatment decision and develop control... (Review)
Review
Laboratory testing is one part of clinical diagnosis, and quick and reliable testing results provide important data to support treatment decision and develop control strategies. Clinical viral testing has been shifting from traditional virus isolation and electron microscopy to molecular polymerase chain reaction and point-of-care antigen tests. This shift in diagnostic methodology also means change from looking for infectious virions or viral particles to hunting viral antigens and genomes. With technological development, it is predicted that metagenomic sequencing will be commonly used in veterinary clinical diagnosis for unveiling the whole picture of microbes involved in diseases in the future.
Topics: Animals; Laboratories; Polymerase Chain Reaction
PubMed: 36731993
DOI: 10.1016/j.cvfa.2022.09.002 -
Journal of Bioscience and Bioengineering Jul 2022A variety of methods have been reported using polymerase chain reaction (PCR)-based nucleic acid testing (NAT) because of its potential to be used in highly sensitive...
A variety of methods have been reported using polymerase chain reaction (PCR)-based nucleic acid testing (NAT) because of its potential to be used in highly sensitive inspection systems. Among these NATs, fusion-PCR (also called as overlap-extension-PCR) has been focused on this study and adopted to generate the fused amplicon composed of plural marker gene fragments for detection. Generally, conventional agarose gel electrophoresis followed by gel staining is employed to check the PCR results. However, these are time-consuming processes that use specific equipment. To overcome these disadvantages, the immunochromatographic test (ICT) for the detection of PCR amplicons with hapten-labels that were generated by PCR using hapten-labeled primers was also adopted in this study. Based on these concepts, we constructed the systems of hapten-labeled fusion-PCR (HL-FuPCR) followed by ICT (HL-FuPCR-ICT) for the two and three marker genes derived from pathogenic microbe. As a result, we successfully developed a two marker genes system for the pathogenic influenza A virus and a three marker genes system for the penicillin-resistant Streptococcus pneumoniae. These detection systems of HL-FuPCR-ICT are characterized by simple handling and rapid detection within few minutes, and also showed the results as clear lines. Thus, the HL-FuPCR-ICT system introduced in this study has potential for use as a user-friendly inspection tool with the advantages especially in the detection of specific strains or groups expressing the characteristic phenotype(s) such as antibiotic resistance and/or high pathogenicity even in the same species.
Topics: DNA Primers; Haptens; Immunologic Tests; Polymerase Chain Reaction; Sensitivity and Specificity
PubMed: 35450786
DOI: 10.1016/j.jbiosc.2022.03.006 -
BioMed Research International 2021This study presents a discussion on the fundamentals of polymerase chain reaction (PCR) and its use as a diagnostic tool in periodontology. (Review)
Review
OBJECTIVES
This study presents a discussion on the fundamentals of polymerase chain reaction (PCR) and its use as a diagnostic tool in periodontology.
MATERIALS AND METHODS
A computer-aided as well as hand-made search in PubMed and Scopus indexed journals (relevant to the topic) was done by keywords of molecular technique in periodontology, PCR, applications of PCR, and PCR in periodontics. Only the papers in the English language and outlining PCR and its association with periodontology were collected and utilized to provide a succinct review. There was no limitation for publication time.
RESULTS
The results of our search showed that PCR has turned into a standard in diagnosis in the field of periodontology. A variety of researches has demonstrated that its sensitive, and specific characteristics make it a quick and effective technique of recognition, identification, and quantification of microorganisms. Identification of various immunoinflammatory markers at the mRNA expression level as well as ascertaining gene-related polymorphisms can also be performed.
CONCLUSIONS
The mechanisms of periodontal disease can further become clarified using PCR. . PCR as a diagnostic method can play a main part in the validation of the clinical diagnosis of periodontal disease indicating the reason, pathogenesis, clinical steps, progress, and prognosis of the disease.
Topics: Biomarkers; Humans; Molecular Diagnostic Techniques; Periodontal Diseases; Periodontics; Polymerase Chain Reaction; Polymorphism, Genetic
PubMed: 34337068
DOI: 10.1155/2021/9979948 -
Klinicka Onkologie : Casopis Ceske a... 2021Nowadays, modern treatment methods for cancer patients are based on targeting specific molecules involved in cellular signaling system associated with tumor initiation... (Review)
Review
BACKGROUND
Nowadays, modern treatment methods for cancer patients are based on targeting specific molecules involved in cellular signaling system associated with tumor initiation and progression. The success of such approach depends on a correctly chosen dia-gnostic test with high sensitivity that identifies the occurrence and level of bio-markers in patients to select those who will respond and benefit from the treatment. The development of new technologies and the upgrades of the known ones contribute to the innovations in molecular characterization of cancer, which allows the detection of patients mutational status with high sensitivity and specificity.
PURPOSE
Here, we discuss the utilization of the third-generation type of polymerase chain reaction (PCR), droplet digital PCR (ddPCR), in the molecular dia-gnostics of oncology diseases. According to the studies reported in our review, ddPCR represents a promising tool in genetic profiling of cancer patients. Therefore, the optimization and precise validation may enable gradual implementation of ddPCR into clinical practice in the field of oncology.
Topics: Humans; Neoplasm, Residual; Neoplasms; Polymerase Chain Reaction
PubMed: 33657817
DOI: 10.48095/ccko202133 -
Infection Control and Hospital... Jun 2022In June 2018, the Ministry of Health received notification from 2 hospitals about 2 patients who presented with overwhelming sepsis that developed within 24 hours after...
BACKGROUND
In June 2018, the Ministry of Health received notification from 2 hospitals about 2 patients who presented with overwhelming sepsis that developed within 24 hours after a dental procedure. We describe the investigation of this outbreak.
METHODS
The epidemiologic investigation included site visits in 2 dental clinics and interviews with all involved healthcare workers. Chart reviews were conducted for case and control subjects. Samples were taken from medications and antiseptics, environmental surfaces, dental water systems, and from the involved healthcare professionals. Isolate similarity was assessed using repetitive element sequence-based polymerase chain reaction (REP-PCR).
RESULTS
The 2 procedures were conducted in different dental clinics by different surgeons and dental technicians. A single anesthesiologist administered the systemic anesthetic in both cases. Cultures from medications, fluids and healthcare workers' hands were negative, but was detected from the anesthesiologist's portable medication cart. The 2 human isolates and the environmental isolate shared the same REP-PCR fingerprinting profile. None of the 21 patients treated by the anesthesiologist in a general hospital during the same period, using the hospital's medications, developed infection following surgery.
CONCLUSIONS
An outbreak of post-dental-procedure sepsis was linked to a contaminated medication cart, emphasizing the importance of medication storage standards and strict aseptic technique when preparing intravenous drugs during anesthesia. Immediate reporting of sepsis following these outpatient procedures enabled early identification and termination of the outbreak.
Topics: Dental Clinics; Disease Outbreaks; Humans; Polymerase Chain Reaction; Sepsis
PubMed: 34011423
DOI: 10.1017/ice.2021.176 -
Analytical Biochemistry Mar 2021A system devised to conduct Polymerase Chain Reaction (PCR) in-flight on drones that uses the spatial displacement of capillary tubes on thermal blocks kept at 94 °C,...
A system devised to conduct Polymerase Chain Reaction (PCR) in-flight on drones that uses the spatial displacement of capillary tubes on thermal blocks kept at 94 °C, 58 °C and 72 °C corresponding to cycling temperatures for denaturation, annealing and extension is demonstrated here. The use of acetal as the thermal block material reduced heat loss and the input power (within 18.5 W) needed to maintain the required temperatures. Tests showed that concentrations of samples down to 1.16 × 10 DNA copies/μL could be significantly and consistently detected above the background emission of the fluorescence signal intensity.
Topics: Air Travel; Aircraft; DNA; Humans; Polymerase Chain Reaction; Specimen Handling; Temperature; Time Factors
PubMed: 33388295
DOI: 10.1016/j.ab.2020.114098 -
Biosensors & Bioelectronics Sep 2019Over the last decade, nucleic acid amplification tests (NAATs) including polymerase chain reaction (PCR) were an indispensable methodology for diagnosing cancers, viral... (Review)
Review
Over the last decade, nucleic acid amplification tests (NAATs) including polymerase chain reaction (PCR) were an indispensable methodology for diagnosing cancers, viral and bacterial infections owing to their high sensitivity and specificity. Because the NAATs can recognize and discriminate even a few copies of nucleic acid (NA) and species-specific NA sequences, NAATs have become the gold standard in a wide range of applications. However, limitations of NAAT approaches have recently become more apparent by reason of their lengthy run time, large reaction volume, and complex protocol. To meet the current demands of clinicians and biomedical researchers, new NAATs have developed to achieve ultrafast sample-to-answer protocols for the point-of-care testing (POCT). In this review, ultrafast NA-POCT platforms are discussed, outlining their NA amplification principles as well as delineating recent advances in ultrafast NAAT applications. The main focus is to provide an overview of NA-POCT platforms in regard to sample preparation of NA, NA amplification, NA detection process, interpretation of the analysis, and evaluation of the platform design. Increasing importance will be given to innovative, ultrafast amplification methods and tools which incorporate artificial intelligence (AI)-associated data analysis processes and mobile-healthcare networks. The future prospects of NA POCT platforms are promising as they allow absolute quantitation of NA in individuals which is essential to precision medicine.
Topics: Animals; Artificial Intelligence; Biosensing Techniques; Equipment Design; Humans; Nucleic Acid Amplification Techniques; Nucleic Acids; Point-of-Care Systems; Polymerase Chain Reaction; Time Factors
PubMed: 31252258
DOI: 10.1016/j.bios.2019.111448 -
The Journal of Applied Laboratory... Jan 2024Digital polymerase chain reaction (dPCR) is an accurate and sensitive molecular method that can be used in clinical diagnostic, prognostic, and predictive tests. The key...
BACKGROUND
Digital polymerase chain reaction (dPCR) is an accurate and sensitive molecular method that can be used in clinical diagnostic, prognostic, and predictive tests. The key component of the dPCR method is the partitioning of a single reaction into many thousands of droplets, nanochannels or other nano- or picoliter-sized reactions. This results in high enough sensitivity to detect rare nucleic acid targets and provides an absolute quantification of target sequences or alleles compared to other PCR-based methods.
CONTENT
An increasing number of dPCR platforms have been introduced commercially in recent years and more are being developed. These platforms differ in the method of partitioning, degree of automation, and multiplexing capabilities but all can be used in similar ways for sensitive and highly accurate quantification of a variety of nucleic acid targets. Currently, clinical applications of dPCR include oncology, microbiology and infectious disease, genetics, and prenatal/newborn screening. Commercially available tests for clinical applications are being developed for variants with diagnostic, prognostic, and therapeutic significance in specific disease types.
SUMMARY
The power of dPCR technology relies on the partitioning of the reactions and results in increased sensitivity and accuracy compared to qPCR. More recently, the sensitivity of dPCR has been applied to the detection of known variants in cell-free DNA and circulating tumor DNA. Future clinical applications of dPCR include liquid biopsy, treatment resistance detection, screening for minimal residual disease, and monitoring allograft engraftment in transplanted patients.
Topics: Pregnancy; Female; Infant, Newborn; Humans; Polymerase Chain Reaction; Prenatal Diagnosis; Nucleic Acids
PubMed: 38167753
DOI: 10.1093/jalm/jfad103 -
Trends in Biochemical Sciences Feb 2020
Review
Topics: Photons; Polymerase Chain Reaction; Temperature
PubMed: 31866304
DOI: 10.1016/j.tibs.2019.11.007