Performance evaluation of influenza a rapid antigen test and PCR among nasopharyngeal and oropharyngeal samples.

Objectives: Rapid antigen test (RAT) and polymerase chain reaction (PCR) using nasopharyngeal (NP) or oropharyngeal (OP) swab specimens are the two main testing techniques used for laboratory diagnosis of influenza in clinical practice. However, performance variations have been observed not only between techniques, but also between different specimens. This study evaluated the differences in performance between specimens and testing techniques to identify the best combination in clinical practice. Methods: Both NP and OP samples from suspected influenza patients collected in the 2023/4-2023/5 Flu-season in Xiamen, China, were tested for RAT and quantitative PCR. The testing performance of the different specimens and testing techniques were recorded and evaluated. Results: Compared to PCR, RAT showed 58.9 % and 10.3 % sensitivity for NP and OP swabs, respectively. The Limit of Detection (LoD) was 28.71 the Median Tissue Culture Infectious Dose (TCID50)/mL. Compared with PCR using NP swabs, PCR with OP swabs showed 89.5 % sensitivity and 95.4 % specificity. Conclusions: There were no significant differences in performance between the specimens when PCR was used to test for influenza. However, a decrease in sensitivity was observed when the RAT was used, regardless of the specimen type. Therefore, to avoid false-negative results, PCR may be a better choice when OP swabs are used as specimens. In contrast, NP swabs should be the recommended specimens for RAT.

An overview of DNA methylation markers for early detection of gastric cancer: current status, challenges, and prospects.

Background: Gastric cancer (GC) is one of the most common malignancies, with a low 5-year survival rate. However, if diagnosed at an early stage, it can be cured by endoscopic treatment and has a good prognosis. While gastrointestinal X-ray and upper endoscopy are used as national GC screening methods in some GC high-risk countries, such as Japan and Korea, their radiation exposure, invasiveness, and high cost suggest that they are not the optimal tools for early detection of GC in many countries. Therefore, a cost-effective, and highly accurate method for GC early detection is urgently needed in clinical settings. DNA methylation plays a key role in cancer progression and metastasis and has been demonstrated as a promising marker for cancer early detection. Aims and methods: This review provides a comprehensive overview of the current status of DNA methylation markers associated with GC, the assays developed for GC early detection, challenges in methylation marker discovery and application, and the future prospects of utilizing methylation markers for early detection of GC. Through our analysis, we found that the currently reported DNA methylation markers related to GC are mainly in the early discovery stage. Most of them have only been evaluated in tissue samples. The majority of non-invasive assays developed based on blood lack standardized sampling protocols, pre-analytical procedures, and multicenter validation, and they exhibit insufficient sensitivity for early-stage GC detection. Meanwhile, the reported GC DNA methylation markers are generally considered pan-cancer markers. Conclusion: Therefore, future endeavors should focus on identifying additional methylation markers specific to GC and establishing non-invasive diagnostic assays that rely on these markers. These assays should undergo multicenter, large-scale prospective validation in diverse populations.

Comparative evaluation of mineral profiles in different blood specimens of dairy cows at different production phases.

Background: Evaluation of mineral profiles including essential and toxic elements in dairy cows provides fundamental information for bovine practitioners during regular herd supervision and monitoring. The present research was designed to investigate the variations of mineral profiles in different blood specimens of dairy cows at different lactation stages. Methods: This study was divided into two parts: the first included 32 cows, which were classified into four groups according to their lactation stages, and the second involved 10 cows at mid-lactation. The concentrations of copper (Cu), zinc (Zn), selenium (Se), manganese (Mn), barium (Ba), strontium (Sr), calcium (Ca), magnesium (Mg), total phosphorous (P), sulfur (S), cobalt (Co), silicon (Si), lithium (Li), nickel (Ni), thallium (Tl), boron (B), aluminum (Al), uranium (U), and arsenic (As) were measured in serum, ethylene diamine tetraacetic acid (EDTA) plasma, heparin plasma, and EDTA whole blood samples. Results: The concentrations of Cu, Zn, Fe, Mn, Ba, and Sr showed significant variations among the dairy cows of different lactation stages (p < 0.05). Strong regressions were determined between the mineral concentrations in individual and pooled samples (R 2 = 0.991, p = 0.000). In comparison to other blood sample types, the concentration of Cu, Ba, and Sr was higher in EDTA plasma (p < 0.000). In addition, the values of Zn, Se, Fe, and Mn were significantly increased in heparin and EDTA whole blood samples. Concentrations of Ca and Mg, and P were higher in EDTA plasma, and EDTA whole blood samples, respectively. Furthermore, the mean values of Si, Li, Ni, and Tl showed significant increases in EDTA plasma, while S values were higher in EDTA whole blood samples (p < 0.000). Concentrations of Al and U exhibited significant increases in serum samples (p < 0.000). Conclusion: Concentrations of Cu, Zn, Fe, Mn, Ba, and Sr undergo physiological variations among dairy cows at different lactation stages. Therefore, caution should be taken during assessment of these minerals. The concentrations of essential and toxic elements, as well as Ca, P, Mg, and S, varied among the different blood sample specimens, indicating their interpretations should be based on this regard. During dairy herd supervision, the use of pool sample, instead of individual ones, for determination of mineral status may be promising to minimize the costs of individual sample measurements. In general, EDTA plasma may be more suitable for measurements of Ca, Mg, P, and S. It seems that EDTA plasma and heparinized plasma are suited for the estimation of Se and Fe, respectively.

Point-of-Care Diagnostic Tools for Surveillance of SARS-CoV-2 Infections.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a recently emerged and highly contagious virus that causes coronavirus disease 2019 (COVID-19). As of August 24, 2021, there were more than 212 million confirmed COVID-19 cases and nearly 4.4 million deaths reported globally. Early diagnosis and isolation of infected individuals remains one of the most effective public health interventions to control SARS-CoV-2 spread and for effective clinical management of COVID-19 cases. Currently, SARS-CoV-2 infection is diagnosed presumptively based on clinical symptoms and confirmed by detecting the viral RNA in respiratory samples using reverse transcription polymerase chain reaction (RT-PCR). Standard RT-PCR protocols are time consuming, expensive, and technically demanding, which makes them a poor choice for large scale and point-of-care screening in resource-poor settings. Recently developed isothermal nucleic acid amplification tests (iNAAT), antigen and/or serological tests are cost-effective to scale COVID-19 testing at the point-of-care (PoC) and for surveillance activities. This review discusses the development of rapid PoC molecular tools for the detection and surveillance of SARS-CoV-2 infections.

Which sample type is better for Xpert MTB/RIF to diagnose adult and pediatric pulmonary tuberculosis?

OBJECTIVE: This review aimed to identify proper respiratory-related sample types for adult and pediatric pulmonary tuberculosis (PTB), respectively, by comparing performance of Xpert MTB/RIF when using bronchoalveolar lavage (BAL), induced sputum (IS), expectorated sputum (ES), nasopharyngeal aspirates (NPAs), and gastric aspiration (GA) as sample. METHODS: Articles were searched in Web of Science, PubMed, and Ovid from inception up to 29 June 2020. Pooled sensitivity and specificity were calculated, each with a 95% confidence interval (CI). Quality assessment and heterogeneity evaluation across included studies were performed. RESULTS: A total of 50 articles were included. The respective sensitivity and specificity were 87% (95% CI: 0.84-0.89), 91% (95% CI: 0.90-0.92) and 95% (95% CI: 0.93-0.97) in the adult BAL group; 90% (95% CI: 0.88-0.91), 98% (95% CI: 0.97-0.98) and 97% (95% CI: 0.95-0.99) in the adult ES group; 86% (95% CI: 0.84-0.89) and 97% (95% CI: 0.96-0.98) in the adult IS group. Xpert MTB/RIF showed the sensitivity and specificity of 14% (95% CI: 0.10-0.19) and 99% (95% CI: 0.97-1.00) in the pediatric ES group; 80% (95% CI: 0.72-0.87) and 94% (95% CI: 0.92-0.95) in the pediatric GA group; 67% (95% CI: 0.62-0.72) and 99% (95% CI: 0.98-0.99) in the pediatric IS group; and 54% (95% CI: 0.43-0.64) and 99% (95% CI: 0.97-0.99) in the pediatric NPA group. The heterogeneity across included studies was deemed acceptable. CONCLUSION: Considering diagnostic accuracy, cost and sampling process, ES was a better choice than other sample types for diagnosing adult PTB, especially HIV-associated PTB. GA might be more suitable than other sample types for diagnosing pediatric PTB. The actual choice of sample types should also consider the needs of specific situations.

Effects of blood sample handling procedures on measurable interleukin 6 in plasma and serum.

INTRODUCTION: Interleukin-6(IL-6) measurement is used as a biomarker in medical diagnosis, therapy, and prognosis in various diseases. However, several pre-analytical factors may yield a false IL-6 result. In this study, we set out to investigate the effects of corrected blood sample handling procedures on measurable IL-6. METHOD: EDTA plasma and serum samples were collected from 45 healthy individuals. The participants were divided into three groups to perform different handling procedures. Different centrifugal timing, storage temperature, and time were executed on the samples. The changed trends of IL-6 levels were analyzed. RESULTS: At baseline, while the paired plasma and serum IL-6 values had a good correlation, the plasma levels were higher than serum. In general, the unseparated EDTA plasma kept steady with time. With the increase in storage temperature and time, a more pronounced rise in unseparated serum IL-6 was observed. Nevertheless, the samples in Group 3 which centrifuged and separated immediately kept stable after a different temperature and longtime storage. CONCLUSION: Sample types, centrifugal timing, storage temperature, and time may affect the IL-6 levels. A standard blood sample handling procedure should be performed to ensure the accuracy and stability of IL-6 values.

A direct isothermal amplification system adapted for rapid SNP genotyping of multifarious sample types.

Genotyping of single nucleotide polymorphisms (SNPs) in point-of-care (POC) settings could be further improved through simplifying the treatment of samples. In this study, we devised an accurate, rapid and easy-to-use SNP detection system based on direct loop-mediated isothermal amplification (LAMP) without DNA extraction, known as Direct-LAMP. Samples from various sources (including whole blood, dried blood spot, buccal swab and saliva), treated with NaOH, can be used directly in amplification. The turnaround time was about 30 min from sample collection to provision of results. The accuracy was evaluated by assessing the polymorphisms of methylenetetrahydrofolate reductase (MTHFR) C677T and aldehyde dehydrogenase-2 (ALDH2) Glu504Lys, which are better known for their critical role in folate and ethanol metabolism, respectively. Completely consistent genotyping results reveal that Direct-LAMP is generally concordant with sequencing. This system can serve as a very promising platform in the fields of disease predisposition, drug metabolism and personalized medicine.

Establishing Statistical Equivalence of Data from Different Sampling Approaches for Assessment of Bacterial Phenotypic Antimicrobial Resistance.

To assess phenotypic bacterial antimicrobial resistance (AMR) in different strata (e.g., host populations, environmental areas, manure, or sewage effluents) for epidemiological purposes, isolates of target bacteria can be obtained from a stratum using various sample types. Also, different sample processing methods can be applied. The MIC of each target antimicrobial drug for each isolate is measured. Statistical equivalence testing of the MIC data for the isolates allows evaluation of whether different sample types or sample processing methods yield equivalent estimates of the bacterial antimicrobial susceptibility in the stratum. We demonstrate this approach on the antimicrobial susceptibility estimates for (i) nontyphoidal Salmonella spp. from ground or trimmed meat versus cecal content samples of cattle in processing plants in 2013-2014 and (ii) nontyphoidal Salmonella spp. from urine, fecal, and blood human samples in 2015 (U.S. National Antimicrobial Resistance Monitoring System data). We found that the sample types for cattle yielded nonequivalent susceptibility estimates for several antimicrobial drug classes and thus may gauge distinct subpopulations of salmonellae. The quinolone and fluoroquinolone susceptibility estimates for nontyphoidal salmonellae from human blood are nonequivalent to those from urine or feces, conjecturally due to the fluoroquinolone (ciprofloxacin) use to treat infections caused by nontyphoidal salmonellae. We also demonstrate statistical equivalence testing for comparing sample processing methods for fecal samples (culturing one versus multiple aliquots per sample) to assess AMR in fecal Escherichia coli These methods yield equivalent results, except for tetracyclines. Importantly, statistical equivalence testing provides the MIC difference at which the data from two sample types or sample processing methods differ statistically. Data users (e.g., microbiologists and epidemiologists) may then interpret practical relevance of the difference.IMPORTANCE Bacterial antimicrobial resistance (AMR) needs to be assessed in different populations or strata for the purposes of surveillance and determination of the efficacy of interventions to halt AMR dissemination. To assess phenotypic antimicrobial susceptibility, isolates of target bacteria can be obtained from a stratum using different sample types or employing different sample processing methods in the laboratory. The MIC of each target antimicrobial drug for each of the isolates is measured, yielding the MIC distribution across the isolates from each sample type or sample processing method. We describe statistical equivalence testing for the MIC data for evaluating whether two sample types or sample processing methods yield equivalent estimates of the bacterial phenotypic antimicrobial susceptibility in the stratum. This includes estimating the MIC difference at which the data from the two approaches differ statistically. Data users (e.g., microbiologists, epidemiologists, and public health professionals) can then interpret whether that present difference is practically relevant.

Reduction of preanalytical errors in clinical laboratory through multiple aspects and whole course intervention measures.

OBJECTIVE: Errors in preanalytical phase decrease the accuracy of reports from clinical laboratory department. Considering the disqualified rate of preanalytical sample in our hospital, we performed several intervention measures to improve the situation. METHODS: The disqualified sample types and major causes of errors in the preanalytical phase were investigated in clinical laboratory department from September 2008 to August 2009. In the following year, we utilized multiple measures to properly intervene the key points of whole sample collection process, and the preanalytical errors were reanalyzed trimonthly, then the disqualification rate of total, major disqualified sample types and different test groups were calculated to evaluate the effects of the intervention measures. RESULTS: The total disqualification rate in the preanalytical phase obtained from September 2008 to August 2009 was 1.36%, and the major types of disqualified samples were coagulation of anticoagulant sample, sample inadequacy, sample container error, sample information error and sample type error. After one year intervention through key points of whole preanalytical sample collection process, the total disqualification rate dropped to 0.94%, and the disqualification rate of coagulation of anticoagulant sample, sample inadequacy, sample container error, sample information error, and sample type error decreased by 20.45%, 28.00%, 25.00%, 76.92%, and 66.66%, respectively. As for test groups, the decreasing amplitude of biochemical, routine, immunological, microbiological and emergency test group was 47.36%, 33.33%, 20.00%, 50.00%, and 21.43%, respectively. CONCLUSIONS: The overall effect of the interventions is very good, and the disqualification rate of the main causes decreases to various degrees.

Bacterial Populations of Different Sample Types from Carcasses in the Dirty Area of a South African Poultry Abattoir.

Bacterial populations associated with three different sample types from carcasses in the dirty area of a South African poultry abattoir were compared. The three sample types from carcasses before and after scalding included neck skin only, feathers only, and a neck skin and feather combination. The neck skin of carcasses after defeathering was also sampled. Aerobic plate counts, Enterobacteriaceae counts, and Pseudomonas spp. counts were performed on all sample types, as well as on water, air, and equipment samples from the same area. The prevalence of potential pathogens was also investigated. Neck skins sampled before and after scalding consistently exhibited the lowest counts for all bacterial types, and feathers the highest. In most cases, the bacterial numbers of the neck skin samples from pre- and postscalded carcasses were significantly lower (P < 0.05) than those of feather samples and neck skin and feather combination samples. Scalding of carcasses resulted in a consistent decrease of bacterial populations, reflected by all three sample types. Neck skins sampled after defeathering, however, exhibited increased bacterial numbers compared to neck skins sampled postscalding, implicating the rubber fingers of the defeathering machine as contamination sources. These equipment surfaces exhibited aerobic plate counts as high as 7.7 log CFU/cm2. Potential pathogens were isolated from product as well as selected environmental samples. The prevalence of the potential pathogens was found to vary depending on the sample type.