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BMC Infectious Diseases Jun 2024When COVID-19 hit the world in 2019, an enhanced focus on diagnostic testing for SARS-CoV-2 was essential for a successful pandemic response. Testing laboratories...
INTRODUCTION
When COVID-19 hit the world in 2019, an enhanced focus on diagnostic testing for SARS-CoV-2 was essential for a successful pandemic response. Testing laboratories stretched their capabilities for the new coronavirus by adopting different test methods. The necessity of having external quality assurance (EQA) mechanisms was even more critical due to this rapid expansion. However, there was a lack of experience in providing the necessary SARS-CoV-2 EQA materials, especially in locations with constrained resources.
OBJECTIVE
We aimed to create a PT (Proficiency testing) programme based on the Dried Tube Specimens (DTS) method that would be a practical option for molecular based SARS-CoV-2 EQA in Low- and Middle-Income Countries.
METHODS
Based on previous ISO/IEC 17043:2010 accreditation experiences and with assistance from the US Centers for Disease Control and Prevention, The Supranational Reference Laboratory of Uganda (adapted the DTS sample preparation method and completed a pilot EQA program between 2020 and 2021. Stability and panel validation testing was conducted on the designed materials before shipping to pilot participants in six African countries. Participants received a panel containing five SARS-CoV-2 DTS samples, transported at ambient conditions. Results submitted by participants were compared to validation results. Participants were graded as satisfactory (≥ 80%) or unsatisfactory (< 80%) and performance reports disseminated.
RESULTS
Our SARS-CoV-2 stability experiments showed that SARS-CoV-2 RNA was stable (-15 to -25 °C, 4 to 8 °C, (18 to 28 °C) room temperature and 35 to 38 °C) as well as DTS panels (4 to 8 °C, 18 to 28 °C, 35 to 38 °C and 45 °C) for a period of 4 weeks. The SARS-CoV-2 DTS panels were successfully piloted in 35 test sites from Zambia, Malawi, Mozambique, Nigeria, and Seychelles. The pilot results of the participants showed good accuracy, with an average of 86% (30/35) concordance with the original SARS CoV-2 expectations.
CONCLUSION
The SARS-CoV-2 DTS PT panel is reliable, stable at ambient temperature, simple to prepare and requires minimal resources.
Topics: Humans; COVID-19; SARS-CoV-2; Specimen Handling; Laboratory Proficiency Testing; Developing Countries; COVID-19 Testing; Uganda; Pilot Projects
PubMed: 38937708
DOI: 10.1186/s12879-024-09555-y -
Materials (Basel, Switzerland) Jun 2024The paper presents and discusses the results of a study of the thermal properties of cement composites with different contents of magnetite aggregate (0%, 20%, 40% and...
The paper presents and discusses the results of a study of the thermal properties of cement composites with different contents of magnetite aggregate (0%, 20%, 40% and 60% by volume). The effect of grain size on the evaluated thermal properties was also investigated. For this purpose, concrete containing 50% by volume of magnetite aggregate with four different fractions (1-2 mm, 2-4 mm, 4-8 mm and 8-16 mm) was used. Thermal parameters were evaluated on specimens fully saturated with water and dried to a constant mass at 65 °C. The series with varying grain sizes of magnetite achieved thermal conductivity values in the range of 2.76-3.03 W/(m·K) and 2.00-2.21 W/(m·K) at full water saturation and after drying to a constant mass, respectively. In the case of the series with 20% magnetite by volume, the thermal conductivity was 2.65 W/(m·K) and 1.99 W/(m·K) for the material fully saturated with water and dried to a constant mass, respectively. The series with a 60% volume share of magnetite obtained values of this parameter of 3.47 W/(m·K) and 2.66 W/(m·K), respectively, under the same assumptions.
PubMed: 38930306
DOI: 10.3390/ma17122936 -
Diagnostics (Basel, Switzerland) Jun 2024The present study focuses on establishing the quality assurance of laboratories for recent infections (RTRI) in Thailand. We developed a cold-chain independent method,...
The present study focuses on establishing the quality assurance of laboratories for recent infections (RTRI) in Thailand. We developed a cold-chain independent method, using fully characterized plasma obtained from the Thai Red Cross Society, and prepared as dried tube specimens (DTS). Twenty microliters of HIV-seronegative, recent, and long-term infected samples were aliquoted into individual tubes and dried at room temperature, 20-30 degrees Celsius, in a biosafety cabinet overnight to ensure optimal preservation. The DTS external quality control and external quality assessment were tested for homogeneity and stability following the ISO/Guide 35 guidelines. The DTS panels were distributed to 48 sites (FY 2022) and 27 sites (FY 2023) across 14 and 9 provinces, respectively, in Thailand. The results from participating laboratories were collected and evaluated for performance. The results were scored, and acceptable performance criteria were defined as the proportion of panels correctly tested, which was set at 100%. The satisfactory performance ranged from 96% to 100% and was not significantly different among the 13 health regions. The developed and implemented DTS panels can be used to monitor the quality of RTRI testing in Thailand.
PubMed: 38928636
DOI: 10.3390/diagnostics14121220 -
Insects Jun 2024The skin beetle is regularly found beyond North America where it originated. The larvae cause considerable concern in museums, as they damage hides or furs in addition...
The skin beetle is regularly found beyond North America where it originated. The larvae cause considerable concern in museums, as they damage hides or furs in addition to being a special source of damage to collections of dried plants in herbaria or collections of insects and other zoological specimens. arrived in Europe in the mid-20th century and was associated mostly with stored food products, but over time, it has become recognised as a museum pest. Although it is still uncommon and may only be observed in a small fraction of museums, when the insect is found in large numbers, it can cause problems. Catches from blunder traps in Austrian museums and from an online database in the UK were used to track changing concern over the insect. As a single female beetle can continue to reproduce because the species is parthenogenetic, its presence can persist over long periods of time. Although small populations in museums are typically found in the adult form, the larval forms are more common where a site is infested by high numbers, perhaps because the larvae and adults must range more widely for food. Although can be controlled using pesticides, it is also possible to kill the larvae within infested materials through freezing or anoxia.
PubMed: 38921120
DOI: 10.3390/insects15060405 -
Polymers Jun 2024The freeze-drying of biopolymers presents a fresh option with greater potential for application in soil subgrade stabilization. A freeze-dried combination of β-glucan...
The freeze-drying of biopolymers presents a fresh option with greater potential for application in soil subgrade stabilization. A freeze-dried combination of β-glucan (BG) and γ-poly-glutamic acid (GPA) biopolymers was used to treat low compressible clay (CL) and low compressible silt (ML) soils in dosages of 0.5%, 1%, 1.5%, and 2%. The California bearing ratio (CBR) test for the treated specimens was performed under three curing conditions: (i) thermal curing at 60 °C, (ii) air-curing for seven days followed by submergence for 4 days, and (iii) no curing, i.e., tested immediately after mixing. To investigate the influence of shear strength on the freeze-dried biopolymer-stabilized soil specimens and their variations with aging, unconfined compressive strength (UCS) tests were conducted after thermal curing at 60 °C for 3 days, 7 days, and 7 days of thermal curing followed by 21 days of air curing. The maximum CBR of 125.3% was observed for thermally cured CL and a minimum CBR of 6.1% was observed under soaked curing conditions for ML soils. Scanning electron microscopy (SEM), infrared spectroscopy, average particle size, permeability, and adsorption tests revealed the pore filling, biopolymer adsorption and coating on the soil surface, and agglomeration of the soil along with the presence of hydrogen bonds, covalent amide bonds, and Van der Waals forces that contributed to the stiffening of the stabilized soil. Using three-dimensional (3D) finite element analysis (FEA) and layered elastic analysis (LEA), a mechanistic-empirical pavement design was carried out for the stabilized soil and a design thickness catalog was prepared for the maximum CBR. The cost reductions for a 1 km section of the pavement were expected to be 12.5%.
PubMed: 38891532
DOI: 10.3390/polym16111586 -
Italian Journal of Food Safety May 2024The aim of this work is the description and characterization of a severe microsporidian infection in a batch of salted and dried cod. Particularly, the case involves a...
The aim of this work is the description and characterization of a severe microsporidian infection in a batch of salted and dried cod. Particularly, the case involves a batch of approximately 800 kg obtained from (Food and Agriculture Organization Zone 61 - Northwest Pacific Ocean), which, after rehydration and sectioning operations, underwent routine company checks before packaging. In about 20% of the samples, the presence of whitish nodules with a diameter ranging from 1 to 2 mm was observed on the surface of the fillets and in cross-section. The lesions ranged from a few units to 10 per cm. Some samples were subjected to fresh microscopic observation with the stereomicroscope, confirming the nodular nature of the lesions, which were often confluent, alternating with empty spaces, giving the tissue a honeycombing aspect. The histological examination at low magnification allowed us to observe the heavy vacuolization of nodular lesions irregularly surrounded by a spongy-like wall. The observation at higher magnification of other sections allowed us to identify intra-myofibrillar cists containing presumptive microsporidian elements. The tissue damage derived from the technological processes and gravity of lesions did not allow a morphological characterization of presumptive protozoans. The molecular examination of the nodular lesions and the analysis of the sequence of an 897 bp fragment of the small subunit 16S rRNA revealed 100% identity with (GenBank accession number MT928885-89) first isolated from the skeletal muscles of specimens from the Sea of Okhotsk. This finding confirms the importance of selecting suppliers and raw materials in the seafood industry, as well as the usefulness of an effective traceability system.
PubMed: 38887589
DOI: 10.4081/ijfs.2024.12333 -
MethodsX Jun 2024Next-generation sequencing requires intact and high-quality DNA. However, typical liquid-nitrogen DNA extraction methods are expensive and not practical for field sample...
Next-generation sequencing requires intact and high-quality DNA. However, typical liquid-nitrogen DNA extraction methods are expensive and not practical for field sample collections. Hence, we present a cost-effective method for DNA extraction from silica-dried leaf samples, eliminating the need for liquid nitrogen. Two protocols were evaluated to determine the effectiveness of grinding dried plant samples without liquid nitrogen in comparison to the standard protocol for tissue homogenization and cell lysis. Protocol 1 involved grinding fresh leaf samples with liquid nitrogen, while Protocol 2 entailed incubating dried plant samples at-20 °C for 1 h before grinding in the absence of liquid nitrogen. Both protocols produced comparable DNA yields with an average A260/A280 ratio of 1.78±0.02, suitable for short- and long-read sequencing. Using Protocol 2, we successfully assembled ten plastomes. It also demonstrated versatility as comparable DNA quality was obtained from dried mollusks and actinomycetes, resulting in the successful assembly of two complete mitochondrial genomes. The protocol is advantageous for research workflows involving the collection of samples in the field as a long-term source of genetic material.•Drying: Fresh samples were silica-dried at silica-to-sample ratio of 2:1.•Pre-lysis: Dried samples were frozen at -20 °C for 1 hour before grinding.•Frozen samples were subjected to tissue homogenization followed by the standard CTAB DNA extraction.
PubMed: 38883586
DOI: 10.1016/j.mex.2024.102758 -
Journal of Pharmacy & Bioallied Sciences Apr 2024Complex anatomy of the root canal system results in incomplete debridement with mechanical instrumentation, leaving some areas or root canal walls untouched. There comes...
INTRODUCTION
Complex anatomy of the root canal system results in incomplete debridement with mechanical instrumentation, leaving some areas or root canal walls untouched. There comes the significance of endodontic irrigants with residual antibacterial substantivity which prolongs the post-antibiotic effect, thereby improving the success and predictability of endodontic treatment.
AIM
To comparatively evaluate the residual antibacterial substantivity of 2% chlorhexidine, Biopure MTAD and 2% chitosan against at intervals of 1, 14 and 28 days.
MATERIALS AND METHODS
Seventy-five therapeutically extracted permanent single rooted mandibular premolars teeth were selected. Dentin blocks of 4 mm thickness were prepared and enlarged to 1.6 mm. The autoclaved blocks were inoculated with 24-hour colonies of pure cultures of for 14 days. After the contamination period, canals of each dentin block were irrigated with 5 ml of sterile saline and dried with sterile paper points. A total of 75 dentin blocks were randomly divided into five groups as follows: Group A (21 specimens): 2% chlorhexidine, Group B (21 specimens): Biopure MTAD, Group C (21 specimens): 2% chitosan, Group D (6 specimens): positive control (infected dentin tubes) and Group E (six specimens): negative control (sterile dentin tubes). Then, the lumens of dentin blocks were irrigated with the respective irrigants for 10 mins and were dried using sterile paper points. The specimens were then incubated at 37°C for 28 days to maintain humidity. At experimental intervals of 1, 14 and 28 days, dentin shavings were removed from the canals of respective groups by circumferential filing with sterile no. 35 Hedstrom files. The powdered dentin samples obtained with each dentin block were observed for colony forming units (CFUs) using a Digital Colony counter and were expressed as CFUs/mL.
RESULT
All the irrigants in the study showed a significant decrease in CFUs from day 1 to day 28 indicating that they have residual antibacterial substantivity against . Group B (Biopure MTAD) showed significantly least mean CFUs compared to Group A (2% CHX) and Group C (2% chitosan) against at B1(day 1), B2(day 14) and B3(day 28). Group A (2% CHX) showed significantly higher mean CFUs than Group C (2% chitosan) at A1(day 1). Group C (2% chitosan) showed significantly higher mean CFUs compared to Group A (2% CHX) at C2(day 14) and C3 (day 28).
CONCLUSION
MTAD showed statistically higher residual antibacterial substantivity against at experimental periods of 1, 14 and 28 days. The residual antibacterial effect of 2% chitosan was better compared to 2% CHX at day 1. The residual antimicrobial substantivity of 2% CHX was higher compared to 2% chitosan at intervals of 14 and 28 days.
PubMed: 38882860
DOI: 10.4103/jpbs.jpbs_693_23 -
PLOS Global Public Health 2024Testing for human immunodeficiency virus (HIV) and hepatitis C virus (HCV) using dried blood spot (DBS) specimens has been an integral part of bio-behavioural...
Testing for human immunodeficiency virus (HIV) and hepatitis C virus (HCV) using dried blood spot (DBS) specimens has been an integral part of bio-behavioural surveillance in Canada for almost two decades, though less is known regarding the use of DBS in surveillance of other sexually transmitted and blood-borne infections (STBBI). A systematic review was conducted using a peer-reviewed search strategy to assess the current evidence regarding the validity of STBBI testing using DBS specimens. Eligibility criteria included studies reporting use of DBS specimens for STBBI testing with either commercially available or "in-house" tests in populations 15 years of age or older. Studies reporting a measure of validity such as sensitivity, specificity, positive and negative predictive values were eligible for inclusion. Quality of studies and risk of bias were assessed using the QUADAS-2 tool. A total of 7,132 records were identified. Of these, 174 met the criteria for inclusion. Among the studies that reported validity measures, a substantial proportion demonstrated high sensitivity (≥90%) in 62.5% of cases (N = 334/534 sensitivity measurements), and high specificity (≥90%) was observed in 84.9% of instances (N = 383/451 specificity measurements). However, the quality of the studies varied greatly. Our findings support the validity of the use of DBS specimens in STBBI testing where sufficient evidence was available, but validity is highly dependent on thorough method development and validation.
PubMed: 38875246
DOI: 10.1371/journal.pgph.0003320 -
IMA Fungus Jun 2024Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in...
Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in axenic culture, and lack of reliable and cost-efficient DNA extraction protocols. In particular, the genus Laboulbenia is notorious for low success with DNA extraction and polymerase chain reaction (PCR) amplification. This is attributed to the presence of melanin, a molecule known to inhibit PCR, in the cells. We evaluated the efficacy of a standard single cell-based DNA extraction protocol by halving the recommended amount of reagents to reduce the cost per extraction and adding bovine serum albumin (BSA) during the multiple displacement amplification step to reverse the effect of melanin. A total of 196 extractions were made, 111 of which were successful. We found that halving the reagents used in the single cell-based extraction kit did not significantly affect the probability of successful DNA extraction. Using the halved protocol reduces cost and resource consumption. Moreover, there was no significant difference in the probability of successfully extracting DNA based on whether BSA was added or not, suggesting that the amount of melanin present in cells of the thallus has no major inhibitory effect on PCR. We generated 277 sequences from five loci, but amplification of the internal transcribed spacer region, the mitochondrial small subunit rDNA, and protein-coding genes remains challenging. The probability of successfully extracting DNA from Laboulbeniales was also impacted by specimen storage methods, with material preserved in > 95% ethanol yielding higher success rates compared to material stored in 70% ethanol and dried material. We emphasize the importance of proper preservation of material and propose the design of Laboulbeniales-specific primers to overcome the problems of primer mismatches and contaminants. Our new insights apply not only to the genus Laboulbenia; Laboulbeniales generally are understudied, and the vast majority of species remain unsequenced. New and approachable molecular developments will benefit the study of Laboulbeniales, helping to elucidate the true diversity and evolutionary relationships of these peculiar microfungi.
PubMed: 38863065
DOI: 10.1186/s43008-024-00146-9