Frequency and types of pre-analytical errors in a clinical laboratory of a specialized healthcare hospital

Background & Objective

The pre-analytical phase, encompassing all preparatory steps leading to the analytical process, represents a critical stage prone to laboratory errors. An assessment of the occurrence and categories of laboratory errors, specifically within the pre-analytical phase of laboratory procedures, can guide in taking timely actions for rectifying errors responsible for damage and loss of samples. This study aimed to assess the frequency and types of pre-analytical errors within a clinical laboratory at the Multan Institute of Kidney Diseases over two years.

Methods

This research took place at the Multan Institute of Kidney Diseases. Data was extracted from the hospital laboratory records of the period from 1st January 2021 to 31st December 2022. After data compilation, a retrospective cross-sectional methodology was adopted to assess frequency and types of pre-analytical errors within a clinical laboratory. The records underwent a thorough examination to identify pre-analytical errors, which were classified according to their type and occurrence rate.

Results

Among the 254810 specimens received during the data collection period, a total of 1,722 specimens (0.67% of all collected samples) were found unsuitable for further processing. Amongst the rejected specimens, 718 (41.6%) displayed indications of hemolysis, 388 (22.5%) exhibited clotting, 217 (12.6%) had an insufficient volume and the remaining specimens fell into other miscellaneous categories such as insufficient quantity, unlabeled samples etc.

Conclusion

The overall percentage of sample rejections in the laboratory was 0.67%. This study provided valuable insights into various reasons, and causes that require improvements to enhance the efficiency and quality of laboratory processes.

The AIDS and Cancer Specimen Resource (ACSR): HIV malignancy specimens and data available at no cost

The goal of the AIDS and Cancer Specimen Resource (ACSR) is to play a major role in the advancement of HIV/AIDS cancer-related research/treatment by providing richly annotated biospecimens and data to researchers at no cost. The ACSR acquires, stores, and equitably distributes these samples and associated clinical data to investigators conducting HIV/AIDS-related research, at no costs. Currently, it is the only biorepository of human biospecimens from people with HIV and cancer available to eligible researchers globally who are studying HIV associated malignancies.This review describes the history and organizational structure of the ACSR, its types of specimens in its inventory, and the process of requesting specimens. In addition, the review provides an overview of research that was performed over the last 5 years with its support and gives a summary of important new findings acquired by this research into the development of cancers in people with HIV, including both Aids-related and non-Aids-related malignancies.

Patterns of floristic inventory and plant collections in Myanmar

Myanmar is one of the most biodiverse countries in the Asia-Pacific region due to a wide range of climatic and environmental heterogeneity. Floristic diversity in Myanmar is largely unknown, resulting in a lack of comprehensive conservation plans. We developed a database of higher plants in Myanmar derived from herbarium specimens and literature sources, and analyzed patterns of diversity inventories and collection inconsistencies, aiming to provide a baseline floristic data of Myanmar and act as a guide for future research efforts. We collected 1,329,354 records of 16,218 taxa. Results show that the collection densities at the township level was variable, with 5% of townships having no floristic collections. No ecoregion had an average collection density of greater than 1 specimen/km2 and the lowest collection density was found in the Kayah-Karen Montane Rainforests, which covered 8% of Myanmar's total area. The highest sampling densities were found in Mandalay Region, Chin State, and Yangon Region. Despite floristic collections over the past three centuries, knowledge of the distribution of the vast majority of plant taxa remained limited, particularly for gymnosperms, pteridophytes, and bryophytes. More botanical surveys and further analyses are needed to better describe Myanmar's floristic diversity. An important strategy to promote knowledge of the biodiversity patterns in Myanmar is to improve the collection and digitalization of specimens and to strengthen cooperation among countries.

Alternative sampling specimens for the molecular detection of mpox (formerly monkeypox) virus

BACKGROUND

Mpox (formerly monkeypox) is a viral disease caused by the mpox virus (MPXV), endemic in Central and West Africa and currently causing a global outbreak of international concern. Much remains unknown about sample types most suited for mpox laboratory diagnosis. While it is established that high viral loads can be found in active skin lesions (currently the recommended mpox laboratory confirmation specimen type), WHO mpox testing guidelines encourage the use of oropharyngeal swabs as an additional sample type for mpox diagnosis and suggest investigating the value of other specimens like blood samples.

OBJECTIVE

In this study, we verified the value of select alternative specimen types for mpox laboratory confirmation.

METHODS

We included 25 patients with MPXV-confirmed skin lesions to compare diagnostic sensitivity of MPXV PCR testing on EDTA plasma and two upper respiratory specimens: oropharyngeal swabs and saliva.

RESULTS

In our patient cohort with MPXV-confirmed skin lesions, diagnostic sensitivity of MPXV PCR was 80% in EDTA plasma, 64% in oropharyngeal swabs, and 88% in saliva. MPXV viral loads were significantly higher in saliva compared to oropharyngeal swabs and EDTA plasma.

DISCUSSION

The WHO recommendation to collect oropharyngeal swabs as an additional specimen for mpox diagnosis might need to be revised to include saliva wherever feasible. We suggest investigating saliva as a diagnostic specimen in the absence of active skin lesions or during the phase preceding skin manifestations. Moreover, the relatively high MPXV DNA content of saliva warrants elucidating its potential role in disease transmission.

[Chinese experts consensus on standardized surgical management of specimens from radical gastrectomy (2022 edition)]

In the standardized diagnosis and treatment process of advanced gastric cancer, there is a unappreciated key link between standard radical surgery and accurate pathological reports. That is, the process of dissection, fixation, sampling and recording of the specimen by the surgeons, starting from specimen isolation to the management of the pathologist. Standardizing this process can not only accurately reflect the detailed distribution and exact number of lymph nodes, but also clarify the pathological stage of gastric cancer, so as to make adjuvant treatment plans. Moreover, it can also reflect the scope of intraoperative lymph node dissection to ensure the standardized implementation of surgery, including the overall dissection principle (en bloc resection), and therefore can provide a solid foundation for later related researches. So far, there is still a lack of complete and unified standard for the surgical management of specimens after radical gastrectomy in China. On the basis of the relevant researches and clinical practice about specimen management at home and abroad, the Chinese Journal of Gastrointestinal Surgery, in the name of the Gastric Cancer Professional Committee, Chinese Anticancer Association, as well as the Oncogastroenterology Professional Committee, Chinese Anticancer Association, organized dozens of experts to formulate a consensus on the standardized surgical management of specimens after repeated discussions and revisions for two years. This consensus is aimed to standardize the preparations, basic requirements and sample processing procedures before the surgical treatment of postoperative specimens after a radical surgery for gastric cancer patients, including the processing time of specimens, the processing and data archiving of gastric specimens, and lymph node grouping, sorting and fine sorting records, etc and with the purpose of standardizing the surgical treatment of postoperative specimens on the basis of standardized diagnosis and treatment of gastric cancer, in order to further promote the high-quality development of gastric cancer surgery in China.

Scale in the history of medicine

This is a history of medicine that takes its point of departure in the specimens of human bodily material used to produce medical knowledge. An ordering principle of scale prompts a material and epistemic history of 18th-21st century medicine that highlights shifts in interest towards smaller and smaller units of study: from organs in pathological collections, over microscope slides, to samples in biobanks. The account reveals a set of connected scales of the site of disease, time of diagnosis, size of cohorts, number of disease categories, and technologies of investigation. Moreover, the principle of following the scale of specimens demonstrates the continued importance of physical specimens in medicine, it synthesizes studies of important epistemic objects of medicine such as the organ specimen, the microscope slide and the blood sample, and it draws new historical connections from pathological collections to biobanks.

A diagnostic testing for people with appendicitis using machine learning techniques

Appendicitis is a common disease that occurs particularly often in childhood and adolescence. The accurate diagnosis of acute appendicitis is the most significant precaution to avoid severe unnecessary surgery. In this paper, the author presents a machine learning (ML) technique to predict appendix illness whether it is acute or subacute, especially between 10 and 30 years and whether it requires an operation or just taking medication for treatment. The dataset has been collected from public hospital-based citizens between 2016 and 2019. The predictive results of the models achieved by different ML techniques (Logistic Regression, Naïve Bayes, Generalized Linear, Decision Tree, Support Vector Machine, Gradient Boosted Tree, Random Forest) are compared. The covered dataset are 625 specimens and the total of the medical records that are applied in this paper include 371 males (60.22%) and 254 females (40.12%). According to the dataset, the records consist of 318 (50.88%) operated and 307 (49.12%) unoperated patients. It is observed that the random forest algorithm obtains the optimal result with an accurately predicted result of 83.75%, precision of 84.11%, sensitivity of 81.08%, and the specificity of 81.01%. Moreover, an estimation method based on ML techniques is improved and enhanced to detect individuals with acute appendicitis.

Spot specimen testing with GeneXpert MTB/RIF results compared to morning specimen in a programmatic setting in Cotonou, Benin

BACKGROUND

The diagnosis of tuberculosis (TB) using smear microscopy has been based on testing two specimens: one spot and one early morning sputa. Recently, the World Health Organization (WHO) has recommended to replace, whenever possible, microscopy with GeneXpert® MTB/RIF performed on a single specimen. However, as the bacterial load is higher in early morning specimens than in spot specimens, one could expect lower sensitivity of GeneXpert® MTB/RIF performed only on spot specimens. In this study, we compared results of GeneXpert® MTB/RIF on spot specimens versus early morning specimens, under programmatic conditions in Cotonou, Benin.

METHODS

From June to September 2018, all sputa received from presumptive TB patients at the Supranational Reference Laboratory for Tuberculosis of Cotonou were included in the study. From each patient, two specimens were collected (one spot and one early morning) and GeneXpert® MTB/RIF was performed on both specimens.

RESULTS

In total, 886 participants were included in the study, of whom 737 provided both sputa and 149 (16.8%) gave only the spot specimen. For the 737 participants who provided both sputa, GeneXpert® MTB/RIF was positive for both specimens in 152 participants; for three participants GeneXpert® MTB/RIF was positive on spot specimen but negative on morning specimen while for another three, the test was positive on morning specimen but negative on spot specimen. The overall percentage of agreement was excellent (99.2%) with a positive and negative percent agreement greater than 98%.

CONCLUSION

For TB diagnosis under programmatic conditions in Cotonou, GeneXpert® MTB/RIF in spot specimens gave similar results with the test in morning specimens. Performing GeneXpert® MTB/RIF in both specimens did not significantly increase the number of cases detected. To avoid losing patients from the diagnostic cascade, it is preferable to test sputa produced at the time of the first visit at the health center.

A review of coral bleaching specimen collection, preservation, and laboratory processing methods

Under current climate warming predictions, the future of coral reefs is dire. With projected coral reef decline, it is likely that coral specimens for bleaching research will increasingly become a more limited resource in the future. By adopting a holistic approach through increased collaborations, coral bleaching scientists can maximize a specimen’s investigative yield, thus reducing the need to remove more coral material from the reef. Yet to expand a specimen’s utility for additional analytic methods, information on how corals are collected is essential as many methods are variably sensitive to upstream handling and processing. In an effort to identify common practices for coral collection, sacrifice, preservation, and processing in coral bleaching research, we surveyed the literature from the last 6.5 years and created and analyzed the resulting dataset of 171 publications. Since January 2014, at least 21,890 coral specimens were collected for bleaching surveys or bleaching experiments. These specimens spanned 122 species of scleractinian corals where the most frequently sampled were Acropora millepora, Pocillopora damicornis, and Stylophora pistillata. Almost 90% of studies removed fragments from the reef, 6% collected skeletal cores, and 3% collected mucus specimens. The most common methods for sacrificing specimens were snap freezing with liquid nitrogen, chemical preservation (e.g., with ethanol or nucleic acid stabilizing buffer), or airbrushing live fragments. We also characterized 37 distinct methodological pathways from collection to processing of specimens in preparation for a variety of physiological, -omic, microscopy, and imaging analyses. Interestingly, almost half of all studies used only one of six different pathways. These similarities in collection, preservation, and processing methods illustrate that archived coral specimens could be readily shared among researchers for additional analyses. In addition, our review provides a reference for future researchers who are considering which methodological pathway to select to maximize the utility of coral bleaching specimens that they collect.

Mixed-reality view of cardiac specimens: a new approach to understanding complex intracardiac congenital lesions

Digital reality is an emerging platform for three-dimensional representation of medical imaging data. In this technical innovation paper, the authors evaluated the accuracy and utility of mixed-reality technology in the morphological evaluation of complex congenital heart disease. The authors converted CT datasets of 12 heart specimens with different subtypes of double-outlet right ventricle to stereoscopic images and interrogated them using a mixed-reality system. The morphological features identified on the stereoscopic models were compared with findings at macroscopic examination of the actual heart specimens. The results showed that the mixed-reality system provided highly accurate stereoscopic display of spatially complex congenital cardiac lesions, with interactive features that might enhance 3-D understanding of morphology. Additionally, the authors found that high-resolution digital reproduction of cardiac specimens using clinical CT scanners is feasible for preservation and educational purposes.

Usefulness of Nested Polymerase Chain Reaction with Clinical Specimens for Diagnosis of Leptospirosis: a Case Series and a Review of Literature

A culture of the Leptospira species and the microscopic agglutination test (MAT) are considered as the reference standard for the diagnosis of leptospirosis, but both tests are imperfect for early diagnosis. We describe 4 patients diagnosed with leptospirosis using nested polymerase chain reaction (N-PCR) that targeted the 16S rRNA gene and the passive hemagglutination assay (PHA). In our 4 cases, Leptospira DNA in the urine, plasma, or cerebrospinal fluid (CSF), was detected by N-PCR in the early phase of leptospirosis, except in the sample from the buffy coat. Especially, case 3 showed that N-PCR with the urine and CSF was positive 8 days after symptom onset, but not for the plasma or buffy coat. We report 4 cases of leptospirosis that were diagnosed by N-PCR that targeted the 16S rRNA gene with urine, plasma, or CSF, but not the buffy coat. Three were cured by doxycycline but the case 4 was fatal. Detection of Leptospira DNA by PCR from the urine and CSF, in addition to plasma, may be helpful to confirm the diagnosis.

Reducing delays to multidrug-resistant tuberculosis case detection through a revised routine surveillance system

BACKGROUND

Implementation of an effective Tuberculosis Routine Surveillance System in low-income countries like Tanzania is problematic, despite being an essential tool for the detection and effective monitoring of drug resistant tuberculosis. Long delays in specimen transportation from the facilities to reference laboratory and results dissemination back to the health facilities, result in poor patient management, particularly where multidrug-resistant tuberculosis disease is present.

METHODS

Following a detailed qualitative study, a pilot intervention of a revised Tuberculosis Routine Surveillance System was implemented in Mwanza region, Tanzania. This included the use of rapid molecular methods for the detection of both tuberculosis and drug resistance using Xpert MTB/RIF in some Mwanza sites, the use of Xpert MTB/RIF and Line Probe Assay at the Central Tuberculosis Reference Laboratory, a revised communication strategy and interventions to address the issue of poor form completion. A before and after comparison of the intervention on the number of drug resistant tuberculosis cases identified and the time taken for results feedback to the requesting site was reported.

RESULTS

The revised system for previously treated cases tested at the Central Reference Laboratory was able to obtain the following findings; the number of cases tested increased from 75 in 2016 to 185 in 2017. The times for specimen transportation from health facilities to the reference laboratory were reduced by 22% (from 9 to 7 days). The median time for the district to receive results was reduced by 36% (from 11 to 7 days). Overall the number of drug resistant tuberculosis cases starting treatment increased by 67% (from 12 to 20).

CONCLUSION

Detection of drug resistance could significantly be enhanced, and delays reduced by introduction of new technologies and improved routine surveillance system, including better communication using mobile applications such as 'WhatsApp' and close follow-ups. A larger scale study is now merited to ascertain if these benefits are robust across different contexts.

Contributions to the flora of Myanmar from 2000 to 2019

Myanmar is botanically rich and floristically diverse: one of the world's biodiversity hotspots. However, Myanmar is still very unevenly explored, and until a plant checklist was published in 2003, relatively little work was done on its flora. This checklist included 11,800 species of spermatophytes in 273 families. Since this checklist was published, the botanical exploration of Myanmar has accelerated and there have been many additional publications. We therefore surveyed the literature of taxonomic contributions to Myanmar's vascular flora over the last 20 years (2000-2019) and compiled a list of new and newly described taxa. Our list includes 13 genera, 193 species, 7 subspecies, 19 varieties, and 2 forms new to science; and 3 families, 34 genera, 347 species, 4 subspecies, 7 varieties, and 1 form newly recorded in Myanmar. Altogether, they represent 91 families and 320 genera. Most of the new discoveries belong to 15 families, with more than 25% (146 taxa) belonging to Orchidaceae. These new discoveries are unevenly distributed in the country, with about 41% of the newly discovered species described from Kachin State in northeast Myanmar. This reflects the incompleteness of our current knowledge of the flora of Myanmar and the urgent need for a greatly expanded effort. The completion of the flora of Myanmar requires more fieldwork from north to south, taxonomic studies on new and existing collections, and some mechanism that both coordinates the efforts of various international institutions and initiatives and encourages continued international cooperation. In addition, producing modern taxonomic treatments of the flora of Myanmar requires the participation of experts on all vascular plant families and genera. There is also an urgent need to attract young scientists to plant taxonomy, to work on inventories, identification, nomenclature, herbarium work, and comparative studies.

Application of 16S rRNA gene sequencing in Helicobacter pylori detection

Helicobacter pylori is one of the major stomach microbiome components, promoting development of inflammation and gastric cancer in humans. H. pylori has a unique ability to transform into a coccoidal form which is difficult to detect by many diagnostic methods, such as urease activity detection, and even histopathological examination. Here we present a comparison of three methods for H. pylori identification: histological assessment (with eosin, hematoxylin, and Giemsa staining), polymerase chain reaction (PCR) detection of urease (ureA specific primers), and detection by 16S rRNA gene sequencing. The study employed biopsies from the antral part of the stomach (N = 40). All samples were assessed histologically which revealed H. pylori in eight patients. Bacterial DNA isolated from the bioptates was used as a template for PCR reaction and 16S rRNA gene sequencing that revealed H. pylori in 13 and in 20 patients, respectively. Thus, 16S rRNA gene sequencing was the most sensitive method for detection of H. pylori in stomach biopsy samples.

The Global Museum: natural history collections and the future of evolutionary science and public education

Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.

Fluid Preservation of Zoological Specimens

Preservation of organic materials in fluids for later dissection and education in biobanking stems from the need to prevent their degradation by the action of decomposers. Decomposers can be endogenous (e.g., enzymes) or exogenous (fungi, bacteria, protists, etc.) to the organism. In this chapter, we discuss the different causes of decomposition and methods to prevent decay of zoological specimens, for the purpose of biobanking, using taxidermy and fluid preservation.

Moving past serology: Diagnostic options without serum

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Traditional serology has moved beyond blood as a test medium.

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A number of different samples and tissues are now frequently used in veterinary diagnosis.

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Testing can be robust and accurate and opens up the field to a variety of new opportunities.

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Molecular testing allows direct testing for the agent on a variety of tissues and samples, and pools.

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Pooling of samples can allow for more efficient and cost-effective testing.

Detecting antibodies formed in serum in response to infection is the traditional function of serology. Diagnostic modalities have included complement fixation tests, agar gel immune-diffusion, radioimmunoassay, ELISA and immunofluorescence. More recent technology now allows for the direct detection of pathogens by PCR. This review details the options for diagnostic testing using specimen types other than serum, identifying the advantages and disadvantages of these options and providing evidence for more widespread use of these techniques and specimen types.

The Myriapoda and Onychophora collection (MY) of the Muséum national d'Histoire naturelle (MNHN, Paris)

The Myriapoda and Onychophora collection dataset inventories the occurrence records of the collection of myriapods and onychophorans in the Muséum national d’Histoire naturelle, Paris. The dataset currently consists of 202 lots of onychophorans, representing all of those present, and almost ten thousand (9 795) lots of myriapods, representing 33 to 40% of the MNHN Myriapoda collection. This collection, which is of key historic importance, represents the results of two centuries of myriapod and onychophoran studies. The sources of the collection are worldwide, with a high representation for metropolitan France for the myriapods. None of the occurrences are yet georeferenced. Access to the dataset via the data portals of the MNHN and the GBIF has been made possible through the e-ReColNat project (ANR-11-INBS-0004).

The Myriapoda and Onychophora collection of MNHN is actively expanding, hence both the collection and dataset are in continuous growth. The dataset can be accessed through the portals of GBIF at http://www.gbif.org/dataset/3287044c-8c48-4ad6-81d4-4908071bc8db and the MNHN at http://science.mnhn.fr/institution/mnhn/collection/my/item/search/form.

Birds of Antioquia: Georeferenced database of specimens from the Colección de Ciencias Naturales del Museo Universitario de la Universidad de Antioquia (MUA)

The department of Antioquia, Colombia, lies in the northwestern corner of South America and provides a biogeographical link among divergent faunas, including Caribbean, Andean, Pacific and Amazonian. Information about the distribution of biodiversity in this area is of relevance for academic, practical and social purposes. This data paper describes the dataset containing all bird specimens deposited in the Colección de Ciencias Naturales del Museo Universitario de la Universidad de Antioquia (MUA). We curated all the information associated with the bird specimens, including the georeferences and taxonomy, and published the database through the Global Biodiversity Information Facility network. During this process we checked the species identification and existing georeferences and completed the information when possible. The collection holds 663 bird specimens collected between 1940 and 2011. Even though most specimens are from Antioquia (70%), the collection includes material from several other departments and one specimen from the United States. The collection holds specimens from three endemic and endangered species (Coeligena orina, Diglossa gloriossisima, and Hypopirrhus pyrohipogaster), and includes localities poorly represented in other collections. The information contained in the collection has been used for biodiversity modeling, conservation planning and management, and we expect to further facilitate these activities by making it publicly available.

The clinical relevance of microbiology specimens in head and neck space infections of odontogenic origin

It is common surgical practice to take a specimen for microbial culture and sensitivity when incising and draining infections of odontogenic origin in the head and neck. We aimed to find out if routine testing has any therapeutic value. We retrospectively studied 90 patients (57 male and 33 female) admitted to Northampton General Hospital for treatment of odontogenic infections, and reviewed admission details, antimicrobial treatment, microbiological findings and their sensitivity or resistance, and complications. Specimens were sent from 72 (80%) patients of which 61 (85%) were infected. The most commonly isolated organism was Streptococcus viridans. Interim reports were published after a mean of 3 days (range 1-4), and 94% of patients were discharged within a mean of 2 days (range 0-9) postoperatively. Almost 95% of patients were discharged before results were available, and there were no reported complications. We therefore suggest that microbial culture has little therapeutic value in the management of these patients. With culture and sensitivity tests costing £25 - £30, omission of this practice in the case of uncomplicated (single tissue space) odontogenic infections could save resources in the National Health Service without affecting the care of patients.