An interlaboratory study on the detection method for Escherichia albertii in food using real time PCR assay and selective agars

Escherichia albertii is an emerging enteropathogen. Although E. albertii-specific detection and isolation methods have been developed, their efficiency on food samples have not yet been systematically studied. To establish a series of effective methods for detecting E. albertii in food, an interlaboratory study was conducted in 11 laboratories using enrichment with modified E. coli broth supplemented with cefixime and tellurite (CT-mEC), real-time PCR assay, and plating on four kinds of selective agars. This study focused on the detection efficiency of an E. albertii-specific real-time PCR assay (EA-rtPCR) and plating on deoxycholate hydrogen sulfide lactose agar (DHL), MacConkey agar (MAC), DHL supplemented with rhamnose and xylose (RX-DHL), and MAC supplemented with rhamnose and xylose (RX-MAC). Chicken and bean sprout samples were inoculated with E. albertii either at 17.7 CFU/25 g (low inoculation level) or 88.5 CFU/25 g (high inoculation level), and uninoculated samples were used as controls. The sensitivity of EA-rtPCR was 1.000 for chicken and bean sprout samples inoculated with E. albertii at low and high inoculation levels. The Ct values of bean sprout samples were higher than those of the chicken samples. Analysis of microbial distribution by 16S rRNA gene amplicon sequencing in enriched cultures of bean sprout samples showed that approximately >96 % of the population comprised unidentified genus of family Enterobacteriaceae and genus Acinetobacter in samples which E. albertii was not isolated. The sensitivity of the plating methods for chicken and bean sprout samples inoculated with a high inoculation level of E. albertii was 1.000 and 0.848-0.970, respectively. The sensitivity of the plating methods for chicken and bean sprout samples inoculated with a low inoculation level of E. albertii was 0.939-1.000 and 0.515-0.727, respectively. The E. albertii-positive rate in all colonies isolated in this study was 89-90 % in RX-DHL and RX-MAC, and 64 and 44 % in DHL and MAC, respectively. Therefore, the sensitivity of RX-supplemented agar was higher than that of the agars without these sugars. Using a combination of enrichment in CT-mEC and E. albertii isolation on selective agars supplemented with RX, E. albertii at an inoculation level of over 17.5 CFU/25 g of food was detected with a sensitivity of 1.000 and 0.667-0.727 in chicken and bean sprouts, respectively. Therefore, screening for E. albertii-specific genes using EA-rtPCR followed by isolation with RX-DHL or RX-MAC is an efficient method for E. albertii detection in food.

Variation in assessments of suitability and number of contributors for DNA mixtures

The interpretation of a DNA mixture (a sample that contains DNA from two or more people) depends on a laboratory/analyst's assessment of the suitability of the sample for comparison/analysis, and an assessment of the number of contributors (NoC) present in the sample. In this study, 134 participants from 67 forensic laboratories provided a total of 2272 assessments of 29 DNA mixtures (provided as electropherograms). The laboratories' responses were evaluated in terms of the variability of suitability assessments, and the accuracy and variability of NoC assessments. Policies and procedures related to suitability and NoC varied notably among labs. We observed notable variation in whether labs would assess a given mixture as suitable or not, predominantly due to differences in lab policies: if two labs following their standard operating procedures (SOPs) were given the same mixture, they agreed on whether the mixture was suitable for comparison 66% of the time. Differences in suitability assessments have a direct effect on variability in interpretations among labs, since mixtures assessed as not suitable would not result in reported interpretations. For labs following their SOPs, 79% of assessments of NoC were correct. When two different labs provided NoC responses, 63% of the time both labs were correct, and 7% of the time both labs were incorrect. Incorrect NoC assessments have been shown to affect statistical analyses in some cases, but do not necessarily imply inaccurate interpretations or conclusions. Most incorrect NoC estimates were overestimates, which previous research has shown have less of an effect on likelihood ratios than underestimates.

Interlaboratory prevalidation of a new in vitro transcriptional activation assay for the screening of (anti-)androgenic activity of chemicals using the UALH-hAR cell line

We report an interlaboratory evaluation of a recently developed androgen receptor (AR) transactivation assay using the UALH-hAR reporter cell line that stably expresses the luciferase gene under the transcriptional control of androgen receptor elements (AREs) with no glucocorticoid receptor (GR) crosstalk. Herein, a two-step prevalidation study involving three laboratories was conducted to assess performance criteria of the method such as transferability as well as robustness, sensitivity, and specificity. The first step consisted in the validation of the transfer of the cell line to participant laboratories through the testing of three reference chemicals: the AR agonist dihydrotestosterone, the AR antagonist hydroxyflutamide and the glucocorticoid dexamethasone. Secondly, a blinded study was conducted by screening a selection of ten chemicals, including four AR agonists, five AR antagonists, and one non-active chemical. All test compounds yielded the same activity profiles in all laboratories. The logEC₅₀ (agonist assay) or logIC₅₀ (antagonist assay) were in the same range, with intra-laboratory coefficients of variation (CVs) of 0.1-3.4% and interlaboratory CVs of 1-4%, indicating very good within- and between-laboratory reproducibility. Our results were consistent with literature and regulatory data (OECD TG458). Overall, this interlaboratory study demonstrated that the UALH-hAR assay is transferable, produces reliable, accurate and specific (anti)androgenic activity of chemicals, and can be considered for further regulatory validation.

Validation of PCR methods for confirmation and species identification of thermotolerant Campylobacter as part of EN ISO 10272 - Microbiology of the food chain - Horizontal method for detection and enumeration of Campylobacter spp

This article describes the outline and organisation of the validation of three multiplex PCR methods for species identification and/or confirmation of thermotolerant Campylobacter spp. The three PCR methods were validated against the reference method described in the EN ISO standard 10272:2017. The results of the PCR methods were compared against the reference method in a method comparison study and an interlaboratory study based on EN ISO 16140-6:2019. The performance, in terms of inclusivity and exclusivity, of each of the eight PCR targets were comparable to the performance of the reference method: close, equal, or better depending on the target. In total, all three PCR methods were concluded to be equally qualified as the reference method for molecular identification and/or confirmation of thermotolerant Campylobacter spp., C. jejuni, C. coli and C. lari isolated from the food chain and have been included in Amendment 1 of ISO 10272:2017.

Global interlaboratory assessments on PCBs, organochlorine pesticides and brominated flame retardants in various environmental matrices 2017/2019

In support of the United Nations Environment Programme (UNEP) global monitoring plan under the Stockholm Convention contributing laboratories were offered to take part in a series of interlaboratory assessments on persistent organic pollutants (POPs). The results of two rounds of these assessments are reported. The target compounds were polychlorinated biphenyls, organochlorine pesticides, polybrominated diphenylethers, one polybrominated biphenyl and hexabromocyclododecane diastereomers. The matrices distributed were a test solution, fish, sediment, human milk, and air extracts. The number of participants in each round was well over 100, showing the interest of laboratories worldwide. The results showed that many laboratories still struggle to obtain acceptable standard deviations of around 25% for their determinations. In particular for organochlorine pesticides serious improvement in quality is required. Acceptable results were obtained for the air extracts and for the determination of polybrominated diphenylethers in various matrices.

An interlaboratory study evaluating the interpretation of forensic glass evidence using refractive index measurements and elemental composition

Seventeen laboratories participated in three interlaboratory exercises to assess the performance of refractive index, micro X-ray Fluorescence Spectroscopy (μXRF), and Laser Induced Breakdown Spectroscopy (LIBS) data for the forensic comparison of glass samples. Glass fragments from automotive windshields were distributed to the participating labs as blind samples and participants were asked to compare the glass samples (known vs. questioned) and report their findings as they would in casework. For samples that originated from the same source, the overall correct association rate was greater than 92% for each of the three techniques (refractive index, μXRF, and LIBS). For samples that originated from different vehicles, an overall correct exclusion rate of 82%, 96%, and 87% was observed for refractive index, μXRF, and LIBS, respectively. Special attention was given to the reporting language used by practitioners as well as the use of verbal scales and/or databases to assign a significance to the evidence. Wide variations in the reported conclusions exist between different laboratories, demonstrating a need for the standardization of the reporting language used by practitioners. Moreover, few labs used a verbal scale and/or a database to provide a weight to the evidence. It is recommended that forensic practitioners strive to incorporate the use of a verbal scale and/or a background database, if available, to provide a measure of significance to glass forensic evidence (i.e., the strength of an association or exclusion).

Effect of the manufacturing process on Fiore Sardo PDO cheese microstructure by multi-frequency NMR relaxometry

The quality of Fiore Sardo cheese, a traditional Italian dairy product, was analyzed by means of Multi-frequency Nuclear Magnetic (NMR) relaxometry. Specifically, ten cheese wheels were purchased from different production chains, either industrial (N = 5) or artisanal (N = 5) samples. The former came from large scale productions and the latter were produced by shepherds in small quantities and in very small dairy factories. A preliminary interlaboratory proficiency testing of Time Domain - NMR (TD-NMR, 20 MHz) relaxometry by five laboratories, consistently showed that product quality is significantly different in terms of molecular mobility according to their production chain (i.e. industrial or artisanal). More detailed information about cheese microstructure was obtained by Multi-frequency Fast Field Cycling NMR (FFC-NMR) at lower magnetic fields (0.01-10 MHz). According to the interpretative model adopted to describe FFC-NMR data, industrially processed cheeses showed a higher para-casein hydration, higher protein protons to water protons ratio and a higher disorder (lower fractal dimension d_f) than artisanal products. It is suggested that differences between artisanal and industrial cheeses generate from the processing steps preceding cheese maturation, and are clearly reflected in the visual appearance of cheeses. This study shows that NMR relaxometry techniques can successfully discriminate Fiore Sardo cheese from different production chains, and paves the way for their implementation in quality control practices of dairy products.

Towards establishing indicative values for metabolites of organophosphate ester contaminants in human urine

In 2015, nine laboratories from Belgium, USA, Canada, China, and Australia participated in an interlaboratory exercise to quantify metabolites of organophosphate ester (OPE) contaminants in pooled human urine. Pooled human urine available as SRM 3673 (Organic contaminants in non-smokers' urine) was obtained from the U.S. National Institute of Standards and Technology and was analyzed for its content of OPE metabolites. Each participating laboratory received 10 mL sample and used its own validated method and standards to report the concentrations of the OPE metabolites of its choice. Four OPE metabolites were consistently measured by most laboratories and they were the following diesters: bis(1,3-dichloro-2-propyl) phosphate (BDCIPP), diphenyl phosphate (DPHP), bis(2-chloroethyl) phosphate (BCEP), and bis(1-chloro-2-propyl) phosphate (BCIPP). Concentrations of other OPE metabolites in SRM 3673 were also reported but are only considered as informative values since they were measured by three laboratories at most. All laboratories used liquid chromatography with tandem mass spectrometry (LC-MS/MS) with or without solid-phase extraction (SPE). This is the first study to report indicative values for OPE metabolites in a human urine Standard Reference Material. It is expected that these indicative values obtained for these four metabolites will be used as quality control to ensure compatibility of results in biomonitoring studies and by other researchers who validate their own methods for the quantification of OPE metabolites in human urine.

Interlaboratory studies on chlorinated paraffins: Evaluation of different methods for food matrices

Short-chained chlorinated paraffins (SCCP) and medium-chained chlorinated paraffins (MCCPs) are two of the main groups currently used to classify chlorinated paraffins (CPs). Since only SCCPs have been restricted by the Stockholm Convention, a robust but selective analysis with comparable results especially for SCCPs, but also for all other CPs is needed to ensure official controls to enforce future resulting food legislation. Failing that, expansion of the legislation towards total CP or to include MCCPs and other main groups needs to be considered. A survey taken amongst official and private laboratories in the EU and beyond revealed a large variety of methods currently in use or in planning stages for CP analysis. In June 2017, spiked samples of coconut fat were sent to 27 registered participants from 18 countries for an interlaboratory study. In July 2018, lard samples spiked with CPs, polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) were sent to 13 registered participants from 11 countries. In both cases, more than 55% of participants had a satisfactory overall performance (AZ²<3, σ = 25%). The greatest challenge seemed to be correct quantification of SCCP and MCCP mixtures, hinting at future problems with the through biodegradation much more complex food samples. Of the wide variety of methods being used, GC-MS based methods were favoured. Both HRMS and LRMS methods were able to perform satisfactorily. Identified influencing factors included choice of instrument, choice of standards and data processing strategy. These factors need to be further investigated in future interlaboratory studies.

Validation of EN ISO method 10273 - Detection of pathogenic Yersinia enterocolitica in foods

EN ISO 10273 method for the detection of pathogenic Yersinia enterocolitica in foods was validated in the project Mandate M/381 funded by European Commission. A total of 14 laboratories from five European countries participated in the interlaboratory study (ILS) organized during 2013 and 2014. Before the ILS, the method was revised by an international group of experts and the performance of the revised method was assessed in an ILS study. The results are published as a part of the standard EN ISO 10273 revision. The study included three rounds with different sample types; raw milk, iceberg lettuce and minced meat, inoculated with a low and high level of pathogenic Y. enterocolitica strains representing major pathogenic bioserotypes 4/O:3 and 2/O:9. The homogeneity and stability of the samples were verified before dispatching them to the laboratories. The results demonstrated the method sensitivity of 96% in raw milk, 97% in minced meat, and 98% in lettuce at high inoculation level of pathogenic Y. enterocolitica. The specificity was 100% in raw milk, 96% in minced meat, and 98% in lettuce. The level of detection, LOD50, varied between study rounds, being 9.4 CFU/25 ml in raw milk, 9.9 CFU/25 g in minced meat and 63 CFU/25 g in lettuce samples. During the study, confirmation by using real-time PCR method ISO/TS 18867 together with pyrazinamidase testing was also validated, as alternative to conventional biochemical confirmation. When comparing different isolation steps used in the revised method during the study rounds, PSB enrichment and plating on CIN after alkaline (KOH) treatment showed the highest sensitivity (52-92%) in raw milk and minced meat samples. In lettuce samples, however, ITC with KOH treatment before plating on CIN showed higher sensitivity (64% at low level; 82% at high level) than plating on CIN from PSB with KOH treatment (44% at low level; 74% at high level). Statistical analysis of different isolation steps supported the use of two enrichment media, PSB and ITC, in the revised method. Recovery of pathogenic Y. enterocolitica on CIN was most efficient after KOH treatment and, based on the analysis, plating on CIN agar without KOH treatment could be left as optional procedure in the method.

A reference high-pressure CO2 adsorption isotherm for ammonium ZSM-5 zeolite: results of an interlaboratory study

This paper reports the results of an international interlaboratory study led by the National Institute of Standards and Technology (NIST) on the measurement of high-pressure surface excess carbon dioxide adsorption isotherms on NIST Reference Material RM 8852 (ammonium ZSM-5 zeolite), at 293.15 K (20 °C) from 1 kPa up to 4.5 MPa. Eleven laboratories participated in this exercise and, for the first time, high-pressure adsorption reference data are reported using a reference material. An empirical reference equationn e x = d ( 1 + exp [ - ln ( P ) + a / b ] ) c , [n ex -surface excess uptake (mmol/g), P-equilibrium pressure (MPa), a = -6.22, b = 1.97, c = 4.73, and d = 3.87] along with the 95% uncertainty interval (U k = 2 = 0.075 mmol/g) were determined for the reference isotherm using a Bayesian, Markov Chain Monte Carlo method. Together, this zeolitic reference material and the associated adsorption data provide a means for laboratories to test and validate high-pressure adsorption equipment and measurements. Recommendations are provided for measuring reliable high-pressure adsorption isotherms using this material, including activation procedures, data processing methods to determine surface excess uptake, and the appropriate equation of state to be used.

Validation by an interlaboratory collaborative trial of EN ISO 21528 - microbiology of the food chain - horizontal methods for the detection and enumeration of Enterobacteriaceae

The methods for the detection and enumeration of Enterobacteriaceae, described in EN ISO 21528, parts 1 and 2, were validated by order of the European Commission under the mandate M/381. Fourteen laboratories from seven European countries participated in the collaborative trials, organized by The Netherlands Food and Consumer Product Safety Authority (Wageningen/Utrecht, The Netherlands). Five different matrices from different food categories were selected to be tested in the collaborative trials, in order to validate the method horizontally, according to ISO 16140. The matrices included meat, tiramisu, infant formula, liquid egg, smoked salmon (detection method only) and animal feed (enumeration method only). The raw meat and liquid egg were naturally contaminated and the other matrices were artificially contaminated with a cocktail of four different Enterobacteriaceae strains. The samples used in the trial were tested for homogeneity and stability before distribution. The method for detection of Enterobacteriaceae showed a specificity and sensitivity above 95% for all matrices. The method for the enumeration had a repeatability limit r of 0.37 (expressed as a difference between log₁₀-transformed test results) and a reproducibility limit R of 0.87 (expressed as a difference between log₁₀-transformed test results). The validation data were incorporated in the newly published ISO standards EN ISO 21528:2017- Microbiology of the food chain - Horizontal methods for the detection and enumeration of Enterobacteriaceae - Part 1: Detection method, and Part 2: Colony-count technique.

Laboratory performance study for passive sampling of nonpolar chemicals in water

Two laboratory performance studies with 21 and 11 participants were carried out for passive sampling of nonpolar chemicals in water, using silicone samplers that were deployed for 7 wk and 13 wk at 2 river sites in the Netherlands. Target analytes were polychlorinated biphenyls, polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs), hexachlorobutadiene, hexachlorobenzene, and a number of performance reference compounds (PRCs). Calculation of aqueous concentrations based on prescribed input values and a prescribed uptake model was also included. Between-laboratory coefficients of variation (CVs) in the analysis of target compounds were approximately 20% at concentrations of 100 ng g^-1 and approximately 100% at concentrations of 0.01 ng g^-1 , which was similar to previous results for the analysis of biota samples. The analysis of PRCs yielded water sampling rates with a between-laboratory CV of 18% to 30%. The sampling rate model showed a nearly perfect match with the consensus values of retained PRCs. The implications of the present study for future interlaboratory exercises are discussed. Environ Toxicol Chem 2017;36:1156-1161. © 2016 SETAC.

Interlaboratory evaluation of the assessment of arsenic bioaccumulation from field collected sediments using Hexagenia spp

Standardized bioaccumulation testing of aquatic organisms is essential to understanding the impact of historical contamination on the quality of water and sediment. A standardized 28-d laboratory bioaccumulation method with a freshwater burrowing mayfly, Hexagenia spp., has been developed and internally validated by the Ontario Ministry of the Environment and Climate Change (MOECC). An interlaboratory comparison was conducted to assess the precision of this method. Field-collected sediment contaminated with arsenic was chosen for the present study. Control and test sediments were subsampled and sent to 6 laboratories to perform the bioaccumulation test. One laboratory failed to meet the control survival criterion of ≥80%. When results of this laboratory are removed from the arsenic accumulation assessment, the mean interlaboratory variability (expressed as coefficient of variation) of the arsenic whole-body concentration is reduced from 44% to 24% in the test sediment-exposed Hexagenia spp. There was no significant interlaboratory difference between the Hexagenia spp. arsenic accumulations. While improved culturing and organism holding guidance may increase laboratory success, the MOECC Hexagenia spp. bioaccumulation test method has tight biological method precision when the control survival criterion is met. Environ Toxicol Chem 2016;35:2448-2455. © 2016 SETAC.

Interlaboratory analytical comparison of fatty acid concentrations in serum or plasma

BACKGROUND

There are a large number of clinical studies focusing on the measurement of individual fatty acids in serum or plasma; however, few studies have focused on the interlaboratory comparisons of these measurements. The National Institutes of Standards and Technology (NIST), in collaboration with the National Institutes of Health Office of Dietary Supplements (NIH-ODS) and the Centers for Disease Control and Prevention (CDC), has initiated a quality assurance program for assessing and improving the comparability of individual fatty acid measurements in serum and plasma.

METHODS

This is a performance-based study so participants are encouraged to use their laboratory's methods for the quantification of the individual fatty acids that they typically measure in the unknown serum or plasma samples along with a control material. The control materials used to date are SRM 1950 Metabolites in Human Plasma and SRM 2378 Fatty Acids in Frozen Human Serum.

RESULTS

To date, two studies of the Fatty Acid Quality Assurance Program (FAQAP) have been completed with 11 and 14 participants, respectively. The agreement among the laboratories for individual fatty acids was within 20% for 70% of the data submitted. Laboratories were also requested to run triplicate analyses for each unknown sample. The precision of the individual laboratory data was generally good, with relative standard deviations <20%.

CONCLUSIONS

The results from the first two exercises indicate the need for additional assessment of the comparability among laboratories doing these measurements. Future studies will be conducted with the goals of increasing the number of participating laboratories, increasing awareness of the need to use control materials, and improving the comparability among laboratories.

Interlaboratory study for nickel alloy 625 made by laser powder bed fusion to quantify mechanical property variability

Six different organizations participated in this interlaboratory study to quantify the variability in the tensile properties of Inconel 625 specimens manufactured using laser-powder-bed-fusion additive manufacturing machines. The tensile specimens were heat treated and tensile tests conducted until failure. The properties measured were yield strength, ultimate tensile strength, elastic modulus, and elongation. Statistical analysis revealed that between-participant variability for yield strength, ultimate tensile strength, and elastic modulus values were significantly higher (up to 4 times) than typical within-participant variations. Only between-participant and within-participant variability were both similar for elongation. A scanning electron microscope was used to examine one tensile specimen for fractography. The fracture surface does not have many secondary cracks or other features that would reduce the mechanical properties. In fact, the features largely consist of microvoid coalescence and are entirely consistent with ductile failure.

An interlaboratory study on efficient detection of Shiga toxin-producing Escherichia coli O26, O103, O111, O121, O145, and O157 in food using real-time PCR assay and chromogenic agar

To establish an efficient detection method for Shiga toxin (Stx)-producing Escherichia coli (STEC) O26, O103, O111, O121, O145, and O157 in food, an interlaboratory study using all the serogroups of detection targets was firstly conducted. We employed a series of tests including enrichment, real-time PCR assays, and concentration by immunomagnetic separation, followed by plating onto selective agar media (IMS-plating methods). This study was particularly focused on the efficiencies of real-time PCR assays in detecting stx and O-antigen genes of the six serogroups and of IMS-plating methods onto selective agar media including chromogenic agar. Ground beef and radish sprouts samples were inoculated with the six STEC serogroups either at 4-6CFU/25g (low levels) or at 22-29CFU/25g (high levels). The sensitivity of stx detection in ground beef at both levels of inoculation with all six STEC serogroups was 100%. The sensitivity of stx detection was also 100% in radish sprouts at high levels of inoculation with all six STEC serogroups, and 66.7%-91.7% at low levels of inoculation. The sensitivity of detection of O-antigen genes was 100% in both ground beef and radish sprouts at high inoculation levels, while at low inoculation levels, it was 95.8%-100% in ground beef and 66.7%-91.7% in radish sprouts. The sensitivity of detection with IMS-plating was either the same or lower than those of the real-time PCR assays targeting stx and O-antigen genes. The relationship between the results of IMS-plating methods and Ct values of real-time PCR assays were firstly analyzed in detail. Ct values in most samples that tested negative in the IMS-plating method were higher than the maximum Ct values in samples that tested positive in the IMS-plating method. This study indicates that all six STEC serogroups in food contaminated with more than 29CFU/25g were detected by real-time PCR assays targeting stx and O-antigen genes and IMS-plating onto selective agar media. Therefore, screening of stx and O-antigen genes followed by isolation of STECs by IMS-plating methods may be an efficient method to detect the six STEC serogroups.

Evaluation of microbial qPCR workflows using engineered Saccharomyces cerevisiae

AIMS

We describe the development and interlaboratory study of modified Saccharomyces cerevisiae as a candidate material to evaluate a full detection workflow including DNA extraction and quantitative polymerase chain reaction (qPCR).

METHODS AND RESULTS

S. cerevisiae NE095 was prepared by stable insertion of DNA sequence External RNA Control Consortium-00095 into S. cerevisiae BY4739 to convey selectivity. For the interlaboratory study, a binomial regression model was used to select three cell concentrations, high (4 × 10(7) cells ml(-1)), intermediate (4 × 10(5) cells ml(-1)) and low (4 × 10(3) cells ml(-1)), and the number of samples per concentration. Seven participants, including potential end users, had combined rates of positive qPCR detection (quantification cycle <37) of 100%, 40%, and 0% for high, intermediate, and low concentrations, respectively.

CONCLUSIONS

The NE095 strain was successfully detected by all participants, with the high concentration indicating a potential target concentration for a reference material.

SIGNIFICANCE AND IMPACT OF THE STUDY

The engineered yeast has potential to support measurement assurance for the analytical process of qPCR, encompassing the method, equipment, and operator, to increase confidence in results and better inform decision-making in areas of applied microbiology. This material can also support process assessment for other DNA-based detection technologies.

Round robin test on quantification of amyloid-β 1-42 in cerebrospinal fluid by mass spectrometry

INTRODUCTION

Cerebrospinal fluid (CSF) amyloid-β 1-42 (Aβ42) is an important biomarker for Alzheimer's disease, both in diagnostics and to monitor disease-modifying therapies. However, there is a great need for standardization of methods used for quantification. To overcome problems associated with immunoassays, liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as a critical orthogonal alternative.

METHODS

We compared results for CSF Aβ42 quantification in a round robin study performed in four laboratories using similar sample preparation methods and LC-MS instrumentation.

RESULTS

The LC-MS results showed excellent correlation between laboratories (r(2) >0.98), high analytical precision, and good correlation with enzyme-linked immunosorbent assay (r(2) >0.85). The use of a common reference sample further decreased interlaboratory variation.

DISCUSSION

Our results indicate that LC-MS is suitable for absolute quantification of Aβ42 in CSF and highlight the importance of developing a certified reference material.

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing(®), or Ion Torrent PGM(®). The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.