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Different specimen types are used for influenza diagnosis but comparative data for viral loads from different swab types are limited. We compared influenza viral loads (determined by quantitative reverse transcription polymerase chain reaction [RT‐PCR]) in 93 paired midturbinate and nasopharyngeal swab aliquots from influenza infected patients enrolled in a phase 3 randomized‐controlled study with the objective of maximizing the number of swabs available for sequence analysis. Midturbinate swabs yielded a 53% lower viral load versus nasopharyngeal swabs, and this difference was similar for influenza A and B. These data suggest that nasopharyngeal swabs might be preferred in diagnostic settings when obtaining higher viral load is important. [ABSTRACT FROM AUTHOR]

Hainan Wen,1 Shoujun Xie,1 Yanchao Liu,1 Yueyi Liang,1 Pan Zhang,1 Xiaohui Wang,1 Jianhui Li2 1Department of Clinical Laboratory, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, People’s Republic of China; 2Department of Preventive Medicine, Chengde Medical University, Chengde, Hebei, People’s Republic of ChinaCorrespondence: Jianhui Li, Email wow99wow@126.comObjective: Enterobacteriaceae have displayed widespread trends of antimicrobial resistance in recent years. Therefore, we aimed to analyse the antimicrobial susceptibility of common bacteria and explore the significance in treatment and research of infections induced by Enterobacteriaceae.Methods: We retrospectively analysed 10,775 antimicrobial susceptibility test results acquired over a 6-year period in the affiliated hospital of Chengde Medical University. We divided the data based on specimen type (blood, sputum, pus, or urine), and population characteristics (age bracket and sex) for analysis. We mainly analysed the antimicrobial susceptibility of Escherichia coli (Eco), Klebsiella pneumoniae (Kpn), and Enterobacter cloacae (Ecl).Results: In our study, it was found that the resistance rates of Eco, Kpn, and Ecl to most antimicrobial agents were significantly different (P < 0.05) on specimen type and age bracket. The Eco from sputum had the highest resistance rates except ciprofloxacin (CIP), levofloxacin (LVX), and gentamicin (GEN); the Kpn from urine had the highest resistance rates to all antimicrobial agents; the Ecl from urine had the highest resistance rates to most antimicrobial agents. The Eco from geriatric patients had the highest resistance rates except GEN and SXT; the Kpn from adult patients had the lowest resistance rates to most antimicrobial agents except LVX. The Eco isolated from males had higher resistance rates to most antimicrobial agents except CIP, LVX, and NIT than those isolated from females; the Kpn showed significant differences in antimicrobial susceptibility to only 5 out of 22 antimicrobial agents (P < 0.05); the Ecl showed significant differences in susceptibility only to two antimicrobial agents, LVX and TOB (P < 0.01).Conclusion: The antimicrobial susceptibility of Enterobacteriaceae was significantly different among specimen type, age bracket and sex of patients, which is of great significance for the treatment and research of infection.Keywords: Enterobacteriaceae, antimicrobial sensitivity, drug resistance, specimen type, infection

Not many reports have covered large-scale point of care testing (POCT) blood glucose comparisons, and many interfering factors affect detection. This study aims to verify the performance of POCT blood glucose meters and discusses the factors that interfere with detection.

Material samples form an important portion of the data infrastructure for many disciplines. Here, a material sample is a physical object, representative of some physical thing, on which observations can be made. Material samples may be collected for one project initially, but can also be valuable resources for other studies in other disciplines. Collecting and curating material samples can be a costly process. Integrating institutionally managed sample collections, along with those sitting in individual offices or labs, is necessary to faciliate large-scale evidence-based scientific research. Many have recognized the problems and are working to make data related to material samples FAIR: findable, accessible, interoperable, and reusable. The Internet of Samples (i.e., iSamples) is one of these projects. iSamples was funded by the United States National Science Foundation in 2020 with the following aims: 1. enable previously impossible connections between diverse and disparate samplebased observations; 2. support existing research programs and facilities that collect and manage diverse sample types; 3. facilitate new interdisciplinary collaborations; and 4. provide an efficient solution for FAIR samples, avoiding duplicate efforts in different domains (Davies et al. 2021) The initial sample collections that will make up the internet of samples include those from the System for Earth Sample Registration (SESAR), Open Context, the Genomic Observatories Meta-Database (GEOME), and Smithsonian Institution Museum of Natural History (NMNH), representing the disciplines of geoscience, archaeology/anthropology, and biology. To achieve these aims, the proposed iSamples infrastructure (Fig. 1) has two key components: iSamples in a Box (iSB) and iSamples Central (iSC). The iSC component will be a permanent Internet service that preserves, indexes, and provides access to sample metadata aggregated from iSBs. It will also ensure that persistent identifiers and sample descriptions assigned and used by individual iSBs are synchronized with the records in iSC and with identifier authorities like International Geo Sample Number (IGSN) or Archival Resource Key (ARK). The iSBs create and maintain identifiers and metadata for their respective collection of samples. While providing access to the samples held locally, an iSB also allows iSC to harvest its metadata records. The metadata modeling strategy adopted by the iSamples project is a metadata profilebased approach, where core metadata fields that are applicable to all samples, form the core metadata schema for iSamples. Each individual participating collectionis free to include additional metadata in their records, which will also be harvested by iSC and are discoverable through the iSC user interface or APIs (Application Programming Interfaces), just like the core. In-depth analysis of metadata profiles used by participating collections, including Darwin Core, has resulted in an iSamples core schema currently being tested and refined through use. See the current version of the iSamples core schema. A number of properties require a controlled vocabulary. Controlled vocabularies used by existing records are kept, while new vocabularies are also being developed to support high-level grouping with consistent semantics across collection types. Examples include vocabularies for Context Category, Material Category, and Specimen Type (Table 1). These vocabularies were also developed in a bottom-up manner, based on the terms used in the existing collections. For each vocabulary, a decision tree graph was created to illustrate relations among the terms, and a card sorting exercise was conducted within the project team to collect feedback. Domain experts are invited to take part in this exercise here, here, and here. These terms will be used as upper-level terms to the existing category terms used in the participating collections and hence create connections among individual participating collections. iSample project members are also active in the TDWG Material Sample Task Group and the global consultation on Digital Extended Specimens. Many members of the iSamples project also lead or participate in a sister research coordination network (RCN), Sampling Nature. The goal of this RCN is to develop and refine metadata standards and controlled vocabularies for the iSamples and other projects focusing on material samples. We cordially invite you to participate in the Sampling Nature RCN and help shape the future standards for material samples. Contact Sarah Ramdeen (sramdeen@ideo.columbia.edu) to engage with the RCN. [ABSTRACT FROM AUTHOR]

As infectious disease diagnostics increasingly incorporates molecular techniques, there are unique preanalytical concerns that must be considered. First, noninvasive specimen types that may be inadequate for culture-based diagnostics may be acceptable when using molecular tests. Second, specimen containers must be evaluated for the presence of substances that may interfere with amplification or sequencing reactions. Finally, the capacity of transport, storage, and processing conditions to maintain nucleic acid integrity and avoid contamination must be assessed. This review explores these issues and the effects they may have on result quality., Competing Interests: Disclosure A. Misra has no disclosures. E.A. Powell has received research funding from GenMark Diagnostics., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Highlights • Independent f t and K IC can be determined by using various concrete specimens. • Average Δ a fic ≈ 1.0 d max can be assumed for 3-p-b and WS concrete specimens. • Structural failure of concrete can be constructed by using independent f t and K IC. • Safe design diagrams with limits (±15%) can cover all experimental results. • Theoretical specimen size meeting linear elastic fracture mechanics are obtained. • Predicted peak loads using the Δ a fic ≈ 1.0 d max fit experimental peak loads. Abstract Concrete tensile strength and fracture toughness are two important material constants that should be independent of specimen size, geometry or type. In this study, on the basis of the improved boundary effect model, independent tensile strength and fracture toughness of concrete, which are unaffected by the specimen type, were determined by using various specimens, e.g., three-point-bending and wedge-splitting specimens. The concrete structural failure was fully predicted using independent material constants, and the constructed safe design diagrams with upper and lower limits (±15%) can cover all experimental results. The theoretical minimum size of the concrete meeting the linear elastic fracture mechanics were quantified, and the peak loads of concrete specimens were predicted using various average fictitious crack growth length. [ABSTRACT FROM AUTHOR]

We evaluated the field diagnostic accuracy of a syphilis rapid test (RDT), using serum and whole blood by non-laboratorians in two Canadian Arctic communities. We implemented a multisite prospective field evaluation wherein patients were screened by an RDT containing treponemal and non-treponemal components (Chembio DPP® Syphilis Screen & Confirm) between January 2020 and December 2021. Venous whole blood and serum were collected for rapid testing and compared with laboratory-based serology reference testing using a reverse sequence algorithm of treponemal and rapid plasma reagin (RPR) testing. Overall, 135 whole blood and 139 serum specimens were collected from 161 participants during clinical encounters. Treponemal-RDT sensitivity against a treponemal-reference standard (38/161 confirmed cases) was similar for serum (78% [95% CI: 61–90%]) and whole blood (81% [95% CI: 63–93%]). In those with RPR titres ≥1:8 (i.e. suggestive of recent/active infection), sensitivity increased to 93% (95% CI: 77–99%) for serum and 92% (95% CI: 73–99%) for whole blood. Treponemal-RDT specificity was excellent (99% [95% CI: 95–100%]) for both specimen types. Non-treponemal-RDT sensitivity against RPR was 94% (95% CI: 80–99%) for serum and 79% (95% CI: 60–92%) for whole blood. Sensitivity increased to 100% (95% CI: 88–100%) for serum and 92% (95% CI: 73–99%) for whole blood when RPR titres ≥1:8. RDT performance with whole blood was similar to that with serum. Non-laboratorians using the RDT accurately identified individuals with infectious syphilis under real-world conditions in an intended-use setting at the point of care. Implementing the RDT can eliminate treatment delays and may enhance disease control. [ABSTRACT FROM AUTHOR]

Newborn biochemical screening has been in place in many countries for over fifty years initially testing dried skin puncture whole blood spotted on collection paper (DBS) or urine for phenylalanine or phenylketones to identify phenylketonuria. Countries wishing to commence newborn screening need to consider which type of specimen will provide a satisfactory specimen and matrix for testing for disorders relevant to their population, is acceptable to parents and can be readily transported to the analytical or laboratory facility without significant degradation. Whilst DBSs have largely become the specimen of choice they may not be applicable to all cultures and infrastructures. The majority of disorders appropriate to be identified in the newborn period can be detected in DBSs taken shortly after birth. Some are also detectable in cord blood or urine, some are not. Most disorders have an ideal and often different time window of age for identification in relation to treatment for optimum outcome. When embarking on newborn screening for the first time or in expanding what is already in place, it is important that the disorders considered are evaluated against the Wilson and Jungner criteria for population screening. A brief overview of specimen types including urine, cord blood and DBSs with some of their advantages and limitations is provided in this review to assist in decision-making.

Objective: Examine differences in the detection of influenza by specimen and test type using paired nasal and nasopharyngeal swabs. Design: Prospective study Setting: Enrollment took place between January and March 2007 in a central Wisconsin population. Participants: Adult patients were screened and enrolled by trained research coordinators following medical encounters for acute respiratory illnesses of

A reversed-phase high-performance liquid chromatography (HPLC) method with fluorometric detection was developed for the routine determination of pyridoxal 5′-phosphate (PLP) and 4-pyridoxic acid (4-PA) in serum. Chlorite postcolumn derivatization was used to oxidize PLP to a more fluorescent carboxylic acid form. Sensitivity improved fourfold for PLP using chlorite postcolumn derivatization over traditional bisulfite postcolumn derivatization. The HPLC injection cycle was 15min, facilitating a throughput of 60 patient samples (72 injections that included standards and quality control (QC) samples) in 18.5h. Method precision was evaluated using three serum QC pools with PLP and 4-PA concentrations of 11.5–34.8nmol/L and 10.4–21.0nmol/L, respectively. Within-run (n=7) repeatabilities were 0.6–1.2% for PLP and 0.9–1.8% for 4-PA. Run-to-run (n=23) reproducibilities were 3.6–6.7% for PLP and 3.7–5.6% for 4-PA. Relative detection (3σ0) and quantitation (10σ0) limits were 0.3 and 0.9nmol/L, respectively, for both PLP and 4-PA using a 10-μl sample injection volume. Analytical recoveries ranged from 97 to 102%. Patient-matched serum and plasma specimens (n=25) were analyzed to evaluate specimen-type bias. Of the plasma types evaluated, heparinized plasma introduced the lowest relative bias for PLP (−5.3%) and minimal bias for 4-PA (−2.3%) compared with serum. Ethylenediaminetetraacetic acid (EDTA) plasma showed the lowest bias for 4-PA (0.7%) but a relatively high bias for PLP (13.0%) due to a chromatographic interference. Human serum samples from a nonrepresentative population subset (n=303) were commensurate with values published for other vitamin B6 HPLC methods. These values gave geometric means of 42.4nmol/L for PLP and 27.3nmol/L for 4-PA. Medians for PLP and 4-PA were 40.1 and 21.8nmol/L, respectively. The high sensitivity, precision, and throughput of this method, combined with its minimal serum specimen (150μl) and sample injection (10μl) volume requirements, make it well suited for routine clinical vitamin B6 analysis. [Copyright &y& Elsevier]

• Modified CDC-based assays can detect SARS-CoV-2 across a range of sample types. • SARS-CoV-2 N1 assay detection sensitivity was comparable between specimen types. • Of the specimen types detected using the N2 assay, CSF was the most sensitive. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused considerable disruption across the world, resulting in more than 235,000 deaths since December 2019. SARS-CoV-2 has a wide tropism and detection of the virus has been described in multiple specimen types, including various respiratory secretions, cerebrospinal fluid, and stool. To evaluate the accuracy and sensitivity of a laboratory modified CDCbased SARS-CoV-2 N1 and N2 assay across a range of sample types. Study Design We compared the matrix effect on the analytical sensitivity of SARS-CoV-2 detection by qRT-PCR in nasal swabs collected in viral transport medium (VTM), bronchoalveolar lavage (BAL), sputum, plasma, cerebral spinal fluid (CSF), stool, VTM, phosphate buffered saline (PBS), and Hanks' Balanced Salt Solution (HBSS). Initial limits of detection (LoD) were subsequently narrowed to confirm an LoD for each specimen type and target gene. LoDs were established using a modified CDC-based laboratory developed test and ranged from a mean CT cut-off of 33.8–35.7 (10–20 copies/reaction) for the N1 gene target, and 34.0–36.2 (1–10 copies/reaction) for N2. Alternatives to VTM such as PBS and HBSS had comparable LoDs. The N2 gene target was found to be most sensitive in CSF. A modified CDC-based laboratory developed test is able to detect SARSCoV- 2 accurately with similar sensitivity across all sample types tested. [ABSTRACT FROM AUTHOR]

Aims: As a proven and comprehensive molecular technique, metagenomic next-generation sequencing (mNGS) has shown its potential in the diagnosis of pathogens in patients with periprosthetic joint infection (PJI), using a single type of specimen. However, the optimal use of mNGS in the management of PJI has not been explored. In this study, we evaluated the diagnostic value of mNGS using three types of specimen with the aim of achieving a better choice of specimen for mNGS in these patients., Methods: In this prospective study, 177 specimens were collected from 59 revision arthroplasties, including periprosthetic tissues, synovial fluid, and prosthetic sonicate fluid. Each specimen was divided into two, one for mNGS and one for culture. The criteria of the Musculoskeletal Infection Society were used to define PJI (40 cases) and aseptic failure (19 cases)., Results: The sensitivity and specificity of mNGS in the diagnosis of PJI were 95% and 94.7%, respectively, for all types of specimen. The sensitivity and specificity were 65% and 100%, respectively, for periprosthetic tissues, 87.5% and 94.7%, respectively, for synovial fluid, and 92.5% and 94.7%, respectively, for prosthetic sonicate fluid. The mNGS of prosthetic sonicate fluid outperformed that for other types of specimen in the rates of detection of pathogens (84.6%), sequencing reads (> ten-fold) and the rate of genome coverage (> five-fold)., Conclusion: mNGS could serve as an accurate diagnostic tool in the detection of pathogens in patients with a PJI using three types of specimen. Due to its superior perfomance in identifying a pathogen, mNGS of prosthetic sonicate fluid provides the most value and may partly replace traditional tests such as bacteriological culture in these patients. Cite this article: Bone Joint J  2021;103-B(5):923-930.

Objective: NTRK mutations and clinicopathological factors in patients with lung cancer in northeast China were analyzed by next-generation sequencing (NGS), and references were provided for patients with NTRK mutations undergoing targeted therapy in northeast China., Methods: A total of 224 specimens in 173 patients with lung cancer were collected. This included 51 patients with matched tissue and whole blood samples,133 tissue samples, 84 whole blood samples, and 7 pleural effusion samples. NGS (520 genes) was used to detected NTRK mutations and clinicopathologic factors., Results: NTRK mutation was detected in eight patients (8/173, 4.6%), including four NTRK missense mutations (4/173, 2.3%), two NTRK fusion gene mutations (2/173, 1.2%), and two NTRK copy number deletions (2/173, 1.2%). Among the eight patients with NTRK mutations, four were associated with lung cancer driver gene mutations (3/4 EGFR, 1/4ALK); NTRK in two patients was inconsistent in tissue and paired whole blood testing; NTRK missense mutation was detected in one patient, and NTRK copy number deletion was detected in the other; and NTRK wild type was detected in two patients. There was no correlation between NTRK mutation and clinicopathologic factors (including gender, age, pathological type, smoking status, metastasis site)., Conclusion: NTRK mutation was only 4.6%, effective fusion gene mutation was 1.2%, and common driver gene mutation in lung cancer was evident in 50% of patients. The results of NTRK were inconsistent with matched tissues and whole blood. Therefore, patients with NTRK mutation should use a variety of specimen types and large target area sequencing (panel) analysis method to provide individualized treatment.

The COVID-19 outbreak has had a major impact on clinical microbiology laboratories in the past several months. This commentary covers current issues and challenges for the laboratory diagnosis of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the preanalytical stage, collecting the proper respiratory tract specimen at the right time from the right anatomic site is essential for a prompt and accurate molecular diagnosis of COVID-19. Appropriate measures are required to keep laboratory staff safe while producing reliable test results. In the analytic stage, real-time reverse transcription-PCR (RT-PCR) assays remain the molecular test of choice for the etiologic diagnosis of SARS-CoV-2 infection while antibody-based techniques are being introduced as supplemental tools. In the postanalytical stage, testing results should be carefully interpreted using both molecular and serological findings. Finally, random-access, integrated devices available at the point of care with scalable capacities will facilitate the rapid and accurate diagnosis and monitoring of SARS-CoV-2 infections and greatly assist in the control of this outbreak., (Copyright © 2020 Tang et al.)

We present the case of a 27-year-old immunocompetent man who progressively developed a generalized lymphadenopathy and B symptoms. Results of Epstein-Barr virus (EBV) serology were suggestive for a past infection, but the EBV viral load in whole blood was high. Also, core needle biopsy of the largest lymph node showed an image which could fit an EBV-driven reactive lymphoproliferation. Despite the absence of an immune disorder, all medical evidence points to an EBV-driven lymphoproliferative proces. In immunocompetent patients, it seems extremely uncommon to detect a high EBV viral load in the absence of serological evidence of an acute EBV infection or reactivation. We reviewed literature on this topic and on the selection of the appropriate sample type for EBV PCR, as this is known to be a critical point. Serological testing for the diagnosis of EBV infection is the gold standard in immunocompetent patients. Measuring EBV viral load is only recommended when dealing with immunocompromised patients. Although extremely rare, this case report shows that there is a place for EBV PCR in certain situations in immunocompetent patients. Besides, there is still no consensus regarding the specimen of choice for the determination of the EBV viral load. The preferred specimen type seems to depend on the patient's underlying condition.