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Journal of Applied Microbiology Nov 2012The polymerase chain reaction (PCR) is increasingly used as the standard method for detection and characterization of microorganisms and genetic markers in a variety of... (Review)
Review
The polymerase chain reaction (PCR) is increasingly used as the standard method for detection and characterization of microorganisms and genetic markers in a variety of sample types. However, the method is prone to inhibiting substances, which may be present in the analysed sample and which may affect the sensitivity of the assay or even lead to false-negative results. The PCR inhibitors represent a diverse group of substances with different properties and mechanisms of action. Some of them are predominantly found in specific types of samples thus necessitating matrix-specific protocols for preparation of nucleic acids before PCR. A variety of protocols have been developed to remove the PCR inhibitors. This review focuses on the general properties of PCR inhibitors and their occurrence in specific matrices. Strategies for their removal from the sample and for quality control by assessing their influence on the individual PCR test are presented and discussed.
Topics: False Negative Reactions; Nucleic Acid Synthesis Inhibitors; Polymerase Chain Reaction; Quality Control; Specimen Handling
PubMed: 22747964
DOI: 10.1111/j.1365-2672.2012.05384.x -
Clinical Microbiology and Infection :... Apr 2020Blood culture contamination carries risks for patients, such as unnecessary antimicrobial therapy and other additional hazards and costs. One method shown to be... (Randomized Controlled Trial)
Randomized Controlled Trial
OBJECTIVES
Blood culture contamination carries risks for patients, such as unnecessary antimicrobial therapy and other additional hazards and costs. One method shown to be effective in reducing contamination is initial blood specimen diversion during collection. We hypothesized that initial blood specimen diversion without a designated device or procedure would suffice for reduction in blood culture contamination rate.
METHODS
From 1 September 2017 through to 6 September 2018, we conducted a randomized controlled trial to assess the effect of an initial-specimen diversion technique (ISDT) on the rate of blood-culture contamination by changing the order of sampling using regular vacuum specimen tubes instead of commercially available sterile diversion devices. We included adults from whom the treating physician planned to take blood cultures and additional blood chemistry tests. Additionally, we evaluated the potential economic benefits of an ISDT. This was a researcher-initiated trial, Clinicaltrials.gov NCT03088865.
RESULTS
In all, 756 patients were enrolled. This method, compared with the standard procedure in use at our medical centre, reduced contamination by 66% (95% CI 17%-86%), from 20/400 (5%) with the standard method to 6/356 (1.6%) with the ISDT, without compromising detection of true bloodstream infection and at no additional cost. Hospital-wide implementation of ISDT was associated with a 1.1% saving in hospitalization days.
CONCLUSIONS
We offer this novel approach as a simple, cost-effective measure to reduce risks to patient safety from contaminated blood cultures, without the need for using costly devices.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Blood Culture; Blood Specimen Collection; Costs and Cost Analysis; Female; Hospitals; Humans; Male; Middle Aged; Prospective Studies; Specimen Handling; Young Adult
PubMed: 31539635
DOI: 10.1016/j.cmi.2019.09.005 -
Tidsskrift For Den Norske Laegeforening... Aug 2023In Norway, approximately 360 000 cervical screening samples were taken in 2020, of which 11 000 were registered as inadequate. We therefore wished to investigate...
BACKGROUND
In Norway, approximately 360 000 cervical screening samples were taken in 2020, of which 11 000 were registered as inadequate. We therefore wished to investigate doctors' knowledge of cervical sample-taking in the primary health service.
MATERIAL AND METHOD
An anonymous survey on cervical sample-taking was sent by email to around 4 700 members of the Norwegian College of General Practice in September 2021.
RESULTS
Of the 1 039 doctors who responded to the survey, 820 (79 %) reported that they always indicate the reason for taking the sample in the requisition form, and 898 (86 %) reported that they avoid taking a sample during menstruation. Only one in three doctors (343) correctly indicated the location of the squamocolumnar junction in postmenopausal women. In response to a question aimed at users of the ThinPrep method, which is particularly sensitive to sampling errors, 426 out of 697 (61 %) answered that they either avoid using a lubricant or use a water-based lubricant, while only 35 % of the doctors responded that they stop taking the sample if bleeding occurs.
INTERPRETATION
The results show that although many doctors have satisfactory knowledge, a continuous focus on cervical sample-taking is essential. Correct sampling and knowledge of anatomical factors in postmenopausal women may be significant for reducing the number of inadequate samples.
Topics: Female; Humans; Early Detection of Cancer; General Practice; Lubricants; Primary Health Care; Uterine Cervical Neoplasms; Specimen Handling; Health Knowledge, Attitudes, Practice; Norway; Physicians, Primary Care
PubMed: 37589352
DOI: 10.4045/tidsskr.23.0066 -
The National Medical Journal of India 1992
Topics: Amniocentesis; Clinical Protocols; Female; Humans; Pregnancy; Pregnancy Trimester, Second; Pregnancy Trimester, Third; Specimen Handling
PubMed: 1304245
DOI: No ID Found -
The Veterinary Clinics of North... Jan 2017Synovial fluid analysis is a key component of the minimum database needed to diagnose and manage primary and secondary articular joint disorders. Unfortunately,... (Review)
Review
Synovial fluid analysis is a key component of the minimum database needed to diagnose and manage primary and secondary articular joint disorders. Unfortunately, preanalytical variables can drastically alter samples submitted for evaluation to veterinary laboratories and it is considered the stage at which most laboratory error occurs. This article addresses common sources of preanalytical variability and error that are seen in veterinary medicine. With consistent quality control and reporting of specimens, downstream clinical decision making and management of patients can be accelerated and improved.
Topics: Animals; Cytological Techniques; Specimen Handling; Synovial Fluid
PubMed: 27720280
DOI: 10.1016/j.cvsm.2016.07.007 -
Nature Communications Jan 2017Nuclear spin hyperpolarization of C-labelled metabolites by dissolution dynamic nuclear polarization can enhance the NMR signals of metabolites by several orders of...
Nuclear spin hyperpolarization of C-labelled metabolites by dissolution dynamic nuclear polarization can enhance the NMR signals of metabolites by several orders of magnitude, which has enabled in vivo metabolic imaging by MRI. However, because of the short lifetime of the hyperpolarized magnetization (typically <1 min), the polarization process must be carried out close to the point of use. Here we introduce a concept that markedly extends hyperpolarization lifetimes and enables the transportation of hyperpolarized metabolites. The hyperpolarized sample can thus be removed from the polarizer and stored or transported for use at remote MRI or NMR sites. We show that hyperpolarization in alanine and glycine survives 16 h storage and transport, maintaining overall polarization enhancements of up to three orders of magnitude.
Topics: Alanine; Carbon Isotopes; Cyclic N-Oxides; Glycine; Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Metabolomics; Specimen Handling; Spin Labels
PubMed: 28072398
DOI: 10.1038/ncomms13975 -
Neonatology 2014Ventilator-associated pneumonia (VAP) is a serious complication related to mechanical ventilation in the neonatal period. However, lack of a specific definition and... (Review)
Review
Ventilator-associated pneumonia (VAP) is a serious complication related to mechanical ventilation in the neonatal period. However, lack of a specific definition and difficulties obtaining noncontaminated samples of the lower respiratory airway render microbiological diagnosis and etiological treatment extremely difficult. Thus far, only few studies have approached VAP using accepted Centers for Disease Control and Prevention criteria and reliable sampling techniques. In recent years, however, the blind-protected bronchoalveolar lavage technique with protected specimen brush and the development of validated biomarkers have attempted to overcome the diagnostic difficulties and assess the response to therapy. This updated review on neonatal VAP aims to stimulate neonatologists' interest in this subtle but serious complication of mechanical ventilation.
Topics: Biomarkers; Humans; Incidence; Infant, Extremely Premature; Infant, Newborn; Infant, Premature, Diseases; Pneumonia, Ventilator-Associated; Risk Factors; Specimen Handling
PubMed: 24296586
DOI: 10.1159/000355539 -
American Journal of Clinical Pathology Jan 2021Millions of biospecimens will be collected during the coronavirus disease 2019 (COVID-19) pandemic. As learned from severe acute respiratory syndrome (SARS), proper... (Review)
Review
OBJECTIVES
Millions of biospecimens will be collected during the coronavirus disease 2019 (COVID-19) pandemic. As learned from severe acute respiratory syndrome (SARS), proper biospecimen handling is necessary to prevent laboratory-related infections.
METHODS
Centers for Disease Control and Prevention and World Health Organization severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interim biosafety guidelines continue to be updated. Presented here are additional considerations intended to complement the interim guidance. These considerations draw on prior SARS recommendations and recent COVID-19 reports.
RESULTS
SARS-CoV-2 viral RNA has been detected in various biospecimen types; however, studies are needed to determine whether viral load indicates viable virus. Throughout the pandemic, biospecimens will be collected for various purposes from COVID-19 known and suspected cases, as well as presymptomatic and asymptomatic individuals. Current data suggest the pandemic start may be as early as October 2019; thus, all biospecimens collected since could be considered potentially infectious.
CONCLUSIONS
All entities handling these biospecimens should do risk assessments in accordance with institutional policies and adhere to any guidance provided. The scientific community has a responsibility to safely handle and maintain all biospecimens collected during the COVID-19 pandemic. Soon, it will be imperative to convene expert working groups to address the current and long-term storage and use of these biospecimens. Ideally, worldwide guidelines will be established to protect the personnel handling these biospecimens and communities at large.
Topics: Biological Specimen Banks; COVID-19; Clinical Laboratory Services; Global Health; Humans; Infection Control; Occupational Diseases; Pandemics; Practice Guidelines as Topic; Specimen Handling; Viral Load
PubMed: 32974640
DOI: 10.1093/ajcp/aqaa171 -
The Journal of Molecular Diagnostics :... Sep 2019An enduring goal of personalized medicine in cancer is the ability to identify patients who are likely to respond to specific therapies. Our growing understanding of the... (Review)
Review
An enduring goal of personalized medicine in cancer is the ability to identify patients who are likely to respond to specific therapies. Our growing understanding of the biology and molecular signatures of individual tumor types has facilitated the identification of predictive biomarkers and has led to an increasing number of diagnostic tests to be performed, often as serial and distinct assays on limited tumor specimens. The biomarker diagnostics field has been revolutionized by next-generation sequencing (NGS), which provides a comprehensive overview of the genomic profile of a tumor. Many preanalytic variables can influence the accuracy and reliability of NGS results. Standardization of preanalytic variables is, however, complicated by the plethora of specimen acquisition and processing methods. Variables across the tissue journey, including specimen acquisition, specimen fixation, and sectioning, as well as postfixation processing, such as nucleic acid extraction, library preparation, and choice of sequencing methods, are critical for the reliability of NGS analysis; thus, standardization would be beneficial. In this article, each step in the tissue journey is outlined, with specific focus on preanalytic variables that can influence NGS results. Practical considerations for standardization of these variables are provided to facilitate accurate, reliable, and reproducible NGS-based molecular characterization of tumors, ultimately informing diagnosis and guiding treatment.
Topics: Gene Library; High-Throughput Nucleotide Sequencing; Humans; Neoplasms; Precision Medicine; Sequence Analysis, DNA; Specimen Handling
PubMed: 31251989
DOI: 10.1016/j.jmoldx.2019.05.004 -
Clinical Infectious Diseases : An... Apr 2012Diagnosing the etiologic agent of pneumonia has an essential role in ensuring the most appropriate and effective therapy for individual patients and is critical to... (Review)
Review
Diagnosing the etiologic agent of pneumonia has an essential role in ensuring the most appropriate and effective therapy for individual patients and is critical to guiding the development of treatment and prevention strategies. However, establishing the etiology of pneumonia remains challenging because of the relative inaccessibility of the infected tissue and the difficulty in obtaining samples without contamination by upper respiratory tract secretions. Here, we review the published and unpublished literature on various specimens available for the diagnosis of pediatric pneumonia. We discuss the advantages and limitations of each specimen, and discuss the rationale for the specimens to be collected for the Pneumonia Etiology Research for Child Health study.
Topics: Blood; Bodily Secretions; Child; Humans; Lung Diseases; Patient Selection; Pediatrics; Pneumonia; Respiratory Tract Infections; Serologic Tests; Specimen Handling; Sputum; Urine
PubMed: 22403227
DOI: 10.1093/cid/cir1068