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The global use of pesticides is increasing; however, few studies have examined the exposure of current-use pesticide exposure in Inuit populations. Some current use pesticides are also capable of long-range transport, potentially increasing exposures to northern populations. The study aim was to analyse pesticide (chlorophenoxy, organophosphates, and pyrethroid pesticide) biomarker levels in pooled samples from an Inuit population in Nunavik, Quebec. Thirty pooled samples from the Qanuilirpitaa? 2017 survey (Q2017) from individuals aged 16–80 years were included. Creatinine-adjusted arithmetic (AM) were compared by sex, age, and region sub-groups, and geometric mean concentrations (GM) were compared to those in the Canadian Health Measures Survey (CHMS). Most analysed pesticide biomarkers were detected, and PNP (a metabolite of methyl and ethyl parathion), trans-DCCA (a metabolite of pyrethroids), and 3,5,6-TCP (a metabolite of chlorpyrifos) had the highest concentrations. Concentrations in Q2017 were largely similar to or less than CHMS concentrations. Although not significant, there was a general increase in 2,4-D (a chlorophenoxy biomarker), 3,5,6-TCP, 3-PBA (a metabolite of pyrethroids), and trans-DCCA with increasing age. Concentrations were also somewhat higher in females versus males, but these were not significant. Environmental exposures to current use pesticides were detected in Nunavik and concentrations were similar to or less than those in the general Canadian population. Regular monitoring of current use pesticide exposures is recommended given the increasing global use of pesticides. [ABSTRACT FROM AUTHOR]

The article "Coding genome of a novel potyvirus, hogweed virus Y (HogVY)" published in the Journal of Plant Pathology describes the discovery of a new virus, HogVY, in hogweed and cow parsley plants in the United Kingdom. The study used high throughput sequencing to identify the virus, which belongs to the genus Potyvirus. The research suggests that HogVY may be widespread in apiaceous weeds and has two known hosts in the Apiaceae family. The study was supported by various funding sources and researchers involved in the project. [Extracted from the article]

The global use of pesticides is increasing; however, few studies have examined the exposure of current-use pesticide exposure in Inuit populations. Some current use pesticides are also capable of long-range transport, potentially increasing exposures to northern populations. The study aim was to analyse pesticide (chlorophenoxy, organophosphates, and pyrethroid pesticide) biomarker levels in pooled samples from an Inuit population in Nunavik, Quebec. Thirty pooled samples from the Qanuilirpitaa? 2017 survey (Q2017) from individuals aged 16–80 years were included. Creatinine-adjusted arithmetic (AM) were compared by sex, age, and region sub-groups, and geometric mean concentrations (GM) were compared to those in the Canadian Health Measures Survey (CHMS). Most analysed pesticide biomarkers were detected, and PNP (a metabolite of methyl and ethyl parathion), trans-DCCA (a metabolite of pyrethroids), and 3,5,6-TCP (a metabolite of chlorpyrifos) had the highest concentrations. Concentrations in Q2017 were largely similar to or less than CHMS concentrations. Although not significant, there was a general increase in 2,4-D (a chlorophenoxy biomarker), 3,5,6-TCP, 3-PBA (a metabolite of pyrethroids), and trans-DCCA with increasing age. Concentrations were also somewhat higher in females versus males, but these were not significant. Environmental exposures to current use pesticides were detected in Nunavik and concentrations were similar to or less than those in the general Canadian population. Regular monitoring of current use pesticide exposures is recommended given the increasing global use of pesticides.

Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi. [ABSTRACT FROM AUTHOR]

Schizophrenia is a psychiatric syndrome that affects approximately 1 % of the world population and is among the top 10 reasons for disability. In this case-control study, we investigated the association between 15 insertion/deletion (Indel) polymorphisms and schizophrenia risk using pooled samples. In the present case-control study, 361 individuals with schizophrenia and 360 healthy individuals were included in the study. We examined the insertion/deletion polymorphisms in APOB, ADRA2B, PDCD6IP, LRPAP1, TLR2, DHFR, VEGF, HLA-G, TPA, DBH, UCP2, FADS2, MDM2, TP53 and SLC6A4 genes. Our results revealed that the Del allele of the HLA-G 14bp Indel polymorphism increased the risk of schizophrenia (OR=1.23, 95 % CI=1.01-1.52, p=0.045) and the Aluallele of the TPA Alu+ /Alu- polymorphism negatively associated with the schizophrenia risk (OR=0.67, 95 % CI=0.54- 0.82, p<0.001). [ABSTRACT FROM AUTHOR]

Abstract Background Tests have false positive or false negative results, which, if not properly accounted for, may provide misleading apparent prevalence estimates based on the observed rate of positive tests and not the true disease prevalence estimates. Methods to estimate the true prevalence of disease, adjusting for the sensitivity and the specificity of the diagnostic tests are available and can be applied, though, such procedures can be cumbersome to researchers with or without a solid statistical background. This manuscript introduces a web-based application that integrates statistical methods for Bayesian inference of true disease prevalence based on prior elicitation for the accuracy of the diagnostic tests. This tool allows practitioners to simultaneously analyse and visualize results while using interactive sliders and output prior/posterior plots. Methods - implementation Three methods for prevalence prior elicitation and four core families of Bayesian methods have been combined and incorporated in this web tool. |tPRiors| user interface has been developed with R and Shiny and may be freely accessed on-line. Results |tPRiors| allows researchers to use preloaded data or upload their own datasets and perform analysis on either single or multiple population groups clusters, allowing, if needed, for excess zero prevalence. The final report is exported in raw parts either as.rdata or.png files and can be further analysed. We utilize a real multiple-population and a toy single-population dataset to demonstrate the robustness and capabilities of |tPRiors|. Conclusions We expect |tPRiors| to be helpful for researchers interested in true disease prevalence estimation and who are keen on accounting for prior information. |tPRiors| acts both as a statistical tool and a simplified step-by-step statistical framework that facilitates the use of complex Bayesian methods. The application of |tPRiors| is expected to aid standardization of practices in the field of Bayesian modelling on subject and multiple group-based true prevalence estimation.

Background: Tests have false positive or false negative results, which, if not properly accounted for, may provide misleading apparent prevalence estimates based on the observed rate of positive tests and not the true disease prevalence estimates. Methods to estimate the true prevalence of disease, adjusting for the sensitivity and the specificity of the diagnostic tests are available and can be applied, though, such procedures can be cumbersome to researchers with or without a solid statistical background. This manuscript introduces a web-based application that integrates statistical methods for Bayesian inference of true disease prevalence based on prior elicitation for the accuracy of the diagnostic tests. This tool allows practitioners to simultaneously analyse and visualize results while using interactive sliders and output prior/posterior plots. Methods - implementation: Three methods for prevalence prior elicitation and four core families of Bayesian methods have been combined and incorporated in this web tool. |tPRiors| user interface has been developed with R and Shiny and may be freely accessed on-line. Results: |tPRiors| allows researchers to use preloaded data or upload their own datasets and perform analysis on either single or multiple population groups clusters, allowing, if needed, for excess zero prevalence. The final report is exported in raw parts either as.rdata or.png files and can be further analysed. We utilize a real multiple-population and a toy single-population dataset to demonstrate the robustness and capabilities of |tPRiors|. Conclusions: We expect |tPRiors| to be helpful for researchers interested in true disease prevalence estimation and who are keen on accounting for prior information. |tPRiors| acts both as a statistical tool and a simplified step-by-step statistical framework that facilitates the use of complex Bayesian methods. The application of |tPRiors| is expected to aid standardization of practices in the field of Bayesian modelling on subject and multiple group-based true prevalence estimation. [ABSTRACT FROM AUTHOR]

Background Screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) at pharyngeal, urogenital, and anorectal sites is recommended for men who have sex with men (MSM). Pooling samples is a promising technique, but no data are available when pooled screening also includes Mycoplasma genitalium (MG). The main objective of this study was to examine the sensitivity of pooled samples for detecting CT, NG, and MG in MSM using nucleic acid amplification versus single-site testing. Methods In this multicenter study, MSM with a positive result for CT, NG, or MG were recalled to the clinic for treatment and were asked to participate in this study. Separate samples were sent to a central virological department that proceeded to form the pooled samples. Testing was performed using the multiplex real-time polymerase chain reaction Allplex STI Essential Assay (Seegene, Seoul, Korea), which can simultaneously detect 7 pathogens. Results A total of 130 MSM with at least 1 positive test for CT, NG, or MG were included. A total of 25.4% had a coinfection. The sensitivities of pooled-sample testing were 94.8% for CT, 97.0% for NG, and 92.3% for MG. Pooling failed to detect 8 infections, but pooled-sample analysis missed detecting only samples with a low bacterial load (cycle threshold >35). Conclusions Pooling samples from MSM to detect CT, NG, and MG is as sensitive as individual-site testing for these 3 pathogens using the Allplex assay. Missed infections with a very low bacterial load could have a low impact on further transmission. Clinical Trials Registration. NCT03568695. [ABSTRACT FROM AUTHOR]

Introduction. Public and private health services worldwide have faced difficulties under the COVID-19 pandemic. High numbers of asymptomatic carriers difficulted the surveillance and tracing of infectious individuals. Also, diagnostic laboratories suffered shortage of reagents to perform on-time diagnosis. Pooling of clinical samples offers an alternative to overcome reagents unavailability and diagnosis of asymptomatic individuals. Methods. We performed pooling of 1937 clinical samples from asymptomatic people performing essential activities during the first wave of the COVID-19 pandemic in Yucatan, Mexico. Diagnosis by real time RT-PCR using the Berlin Method was performed in 229 pools. Results. The strategy successfully detected asymptomatic COVID-19 positive cases. A total of 27 pools were positive. Individuals performing essential activities as government administrative, food markets and police force were the most commonly positive. Conclusion. Pooling clinical samples is a strategy for the on-time isolation of infected individuals as well for saving laboratory resources. [ABSTRACT FROM AUTHOR]

Objective: To evaluate SARS-CoV-2 genome detection using pooled samples by RT-qPCR assay, compared to individual samples. Method: At first all samples were tested individually using two commercial methods targeting ORF1ab, NP and E genes. Then, four experimental groups of samples were pooled and evaluated using the same detection methods. Findings: Compared to the individual sample testing, the sample pooling conserved the sensitivity of the detection in all groups of pooled samples when the Ct value in single test was lower than 33. Conclusion: Specimen pooling may fail to detect positive samples with high Ct values. However, in scarcity of reagents or in population surveys, it could be considered as an alternative method in low prevalence settings. [ABSTRACT FROM AUTHOR]

Background: Control programs were implemented in several countries against bovine viral diarrhea (BVD), one of the most significant cattle diseases worldwide. Most of the programs rely on serological diagnostics in any phase of the program. For the detection of antibodies against BVD virus (BVDV), neutralization tests as well as a variety of (commercially available) ELISAs are used. Here, test systems applied in various laboratories were evaluated in the context of an international interlaboratory proficiency trial. A panel of standardized samples comprising five sera and five milk samples was sent to veterinary diagnostic laboratories (n=51) and test kit manufacturers (n=3). Results: The ring trial sample panel was investigated by nine commercially available antibody ELISAs as well as by neutralization tests against diverse BVDV-1, BVDV-2 and/or border disease virus (BDV) strains. The negative serum and milk sample as well as a serum collected after BVDV-2 infection were mostly correctly tested regardless of the applied test system. A serum sample obtained from an animal immunized with an inactivated BVDV-1 vaccine tested positive by neutralization tests or by total antibody or Erns-based ELISAs, while all applied NS3-based ELISAs gave negative results. A further serum, containing antibodies against the ovine BDV, reacted positive in all applied BVDV ELISAs, a differentiation between anti-BDV and anti-BVDV antibodies was only enabled by parallel application of neutralization tests against BVDV and BDV isolates. For the BVDV antibody-positive milk samples (n=4), which mimicked prevalences of 20% (n=2) or 50% (n=2), considerable differences in the number of positive results were observed, which mainly depended on the ELISA kit and the sample incubation protocols used. These 4 milk samples tested negative in 43.6%, 50.9%, 3.6% and 56.4%, respectively, of all investigations. Overall, negative results occurred more often, when a short sample incubation protocol instead of an over-night protocol was applied. Conclusions: While the seronegative samples were correctly evaluated in most cases, there were considerable differences in the number of correct evaluations for the seropositive samples, most notably when pooled milk samples were tested. Hence, thorough validation and careful selection of ELISA tests are necessary, especially when applied during surveillance programs in BVD-free regions. [ABSTRACT FROM AUTHOR]

As genetically resistant individuals, the "elite controllers" (ECs) of human immunodeficiency virus infection have been focused on as the keys to developing further functional treatments in medicine. In the livestock production field, identifying the ECs of bovine leukemia virus (BLV) infection in cattle is desired to stop BLV transmission chains on farms. Cattle carrying the bovine leukocyte antigen (BoLA)‐DRB3*009:02 allele (DRB3*009:02) have a strong possibility of being BLV ECs. Most of cattle carrying this allele maintain undetectable BLV proviral loads and do not shed virus even when infected. BLV ECs can act as transmission barriers when placed between uninfected and infected cattle in a barn. To identify cattle carrying DRB3*009:02 in large populations more easily, we developed a pooled testing system. It employs a highly sensitive, specific real‐time PCR assay and TaqMan MGB probes (DRB3*009:02‐TaqMan assay). Using this system, we determined the percentage of DRB3*009:02‐carrying cattle on Kyushu Island, Japan. Our pooled testing system detected cattle carrying the DRB3*009:02 allele from a DNA pool containing one DRB3*009:02‐positive animal and 29 cattle with other alleles. Its capacity is sufficient for herd‐level screening for DRB3*009:02‐carrying cattle. The DRB3*009:02‐TaqMan assay showed high‐discriminative sensitivity and specificity toward DRB3*009:02, making it suitable for identifying DRB3*009:02‐carrying cattle in post‐screening tests on individuals. We determined that the percentage of DRB3*009:02‐carrying cattle in Kyushu Island was 10.56%. With its ease of use and reliable detection, this new method strengthens the laboratory typing for DRB3*009:02‐carrying cattle. Thus, our findings support the use of BLV ECs in the field. [ABSTRACT FROM AUTHOR]

[Display omitted] • All 288 Schistosoma mansoni putative microsatellites were identified. • 27 of 52 published, simple, tri/tetramer microsatellites had ideal characteristics. • No physical characteristic predicted performance in a given parasite population. • 15–20 markers produced small standard deviations for population indices. • Diversity and differentiation were greater for a Kenyan sample than for a Brazilian sample. All Schistosoma mansoni tri- and tetranucleotide repeat microsatellites published as of December 2018 were identified. All 52 were evaluated for autosomal location, strength of amplification, scorability and behavior as single-copy loci by polyacrylamide and capillary gel electrophoresis. Of these, 27 were unique, autosomal, polymorphic, easily scored and single copy as assessed on pooled adult worm DNA from two different continental origins and adult worm clones. These microsatellites were distributed across all seven autosomal chromosomes. On laboratory strains their heterozygosity ranged from 0.22 to 0.77. Individual markers had 5–13 alleles, allelic richness of 2–10 and an effective allele number of 1.3–8.14. Those infected by Schistosoma mansoni carry many genetically distinct, sexually reproducing parasites, therefore, for an individual infection the complete allele frequency profile of their progeny consists of a pool of DNA from multiple diploid eggs. Using a set of 25 microsatellites, we calculated allele frequency profiles of eggs in fecal samples from people in two Brazilian communities separated by 6 km: Jenipapo (n = 80) and Volta do Rio (n = 38). There were no a priori characteristics that could predict the performance of markers in natural infections based on their performance with laboratory strains. Increasing marker number did not change accuracy for differentiation and diversity but did improve precision. Our data suggest that using a random set of 10–20 microsatellites appears to result in values that exhibit low standard deviations for diversity and differentiation indices. All identified microsatellites as well as PCR conditions, allele size, primer sequences and references for all tri- and tetramer microsatellites markers presented in this work are available at: https://sites.google.com/case.edu/cwru-and-fiocruz-wdrc/home. [ABSTRACT FROM AUTHOR]

Tilapia lake virus (TiLV) is a highly contagious novel orthomyxo‐like RNA virus that is negatively impacting tilapia production worldwide. To prevent TiLV from spreading globally, the infection status of source farms needs to be established prior to the movement of live tilapia to minimize the risk of horizontal transmission. However, testing individual fish for TiLV requires large sample sizes, when within‐farm prevalence is low and is costly, time‐consuming, and labour‐intensive. The objective of the present study was to evaluate the use of pool testing for TiLV detection and to estimate within‐farm prevalence based on the percentage of positive pooled samples. Pooled samples of liver and spleen were prepared by diluting different numbers of positive tissue samples with negative homogenate tissue samples. A tissue pool from 5 or 10 individual fish containing at least one TiLV‐positive sample was sufficient to yield a positive result except when cycle threshold (Ct) values were between 31 and the cut‐off value of 34. Additionally, our study characterized viral load in two farms after TiLV outbreaks. Bayesian modelling showed that within‐farm prevalence could be estimated from the percentage of positive pools of size 5 using prior information about pool sensitivity and specificity, and prevalence, and assuming random sampling of tilapia from infected ponds. Ninety‐five percent posterior intervals for prevalence were slightly wider than those obtained based on the results of individual samples. Findings in the present study corroborate the use of a pooling strategy for post‐outbreak surveillance of TiLV. [ABSTRACT FROM AUTHOR]

Purpose: The association of a few single nucleotide polymorphisms (SNPs) of gene involved in DNA repair pathways with the risk of age-related macular degeneration (AMD) have been studied. However, the contribution of SNPs of ataxia telangiectasia mutated gene (ATM; MIM: 706585) has not yet been evaluated. The aim of this study was to examine the relationship between the rs611646, rs609429, and rs228593 polymorphisms of the ATM with the risk of AMD. Materials and Methods: In the present study we used two pooled genomic DNA samples of 120 AMD patients and 118 healthy controls. PCR was carried out by specific primers using pooled samples, as template DNA. The allelic frequencies were estimated using measurement of band intensity on agarose gel electrophoresis. Results: Statistical analysis revealed that there was no significant association between the studied ATM polymorphisms and the risk of AMD. Conclusions: This study suggested that the rs611646, rs609429, and rs228593 of ATM1 is not predisposed polymorphisms for AMD. [ABSTRACT FROM AUTHOR]

There is increasing demand from governments and civil society for more data and indicators for smaller territories and/or with higher frequency to help formulate and evaluate policies. At the same time, there is increasing availability of new data sources created by technologies such as Big Data. Some indicators are regularly produced by official and public statistics organizations, while others are demanded but currently not available, leading to substantial data gaps for many topics of interest. In some cases, existing data may lack the quality needed for its use in decision-making. All this coincides with the trend of diminishing resources available to collect data via traditional surveys, limiting sample sizes and increasing difficulties in producing the desired information. Aiming to meet part of this demand, this article compares four small area estimation methods to produce state-level estimates for two selected indicators using two editions (2014 and 2015) of the Survey on the Use of Information and Communication Technologies in Brazilian Households: ICT Households. The empirical study results indicate that using both temporal aggregation by pooling together samples of two consecutive years, and a composite estimator which borrows strength across larger regions leads to improved estimation of the target state-level ICT indicators. [ABSTRACT FROM AUTHOR]

Neoehrlichia mikurensis is a tick‐borne pathogen widespread among ticks and rodents in Europe and Asia. A previous study on Ixodes ricinus ticks in Norway suggested that N. mikurensis was scarce or absent on the south‐west coast of Norway, but abundant elsewhere. The aim of this study was to further investigate the prevalence and distribution of N. mikurensis along the western seaboard of Norway in comparison with more eastern and northern areas. The second aim of the study was to examine seasonal variation of the bacterium in one specific location in the south‐eastern part of Norway. Questing I. ricinus were collected from 13 locations along the coast of Norway, from Brønnøysund in Nordland County to Spjærøy in Østfold County. In total, 11,113 nymphs in 1,113 pools and 718 individual adult ticks were analysed for N. mikurensis by real‐time PCR. The mean prevalence of N. mikurensis in adult ticks was 7.9% while the estimated pooled prevalence in nymphs was 3.5%. The prevalence ranged from 0% to 25.5%, with the highest prevalence in the southernmost and the northernmost locations. The pathogen was absent, or present only at low prevalence (<5%), at eight locations, all located in the west, from 58.9°N to 64.9°N. The prevalence of N. mikurensis was significantly different between counties (p <.0001). No significant seasonal variation of N. mikurensis prevalence was observed in the period May to October 2015. Our results confirm earlier findings of a low prevalence of N. mikurensis in the western seaboard of Norway. [ABSTRACT FROM AUTHOR]

Abstract Background Our group has recently provided a proof-of-principle for the examination of pooled stool samples using McMaster technique as a strategy for the rapid assessment of intensity of soil-transmitted helminth infections (STH, Ascaris lumbricoides, Trichuris trichiura and hookworm). In the present study we evaluated this pooling strategy for the assessment of intensity of both STH and Schistosoma mansoni infections using the Kato-Katz technique. Methods A cross-sectional survey was conducted in 360 children aged 5–18 years from six schools in Jimma Zone (southwest Ethiopia). We performed faecal egg counts (FECs) in both individual and pooled samples (pools sizes of 5, 10 and 20) to estimate the number of eggs per gram of stool (EPG) using the Kato-Katz technique. We also assessed the time to screen both individual and pooled samples. Results Except for hookworms, there was a significant correlation (correlation coefficient = 0.53–0.95) between the mean of individual FECs and the FECs of pooled samples for A. lumbricoides, T. trichiura and S. mansoni, regardless of the pool size. Mean FEC were 2,596 EPG, 125 EPG, 47 EPG, and 41 EPG for A. lumbricoides, T. trichiura, S. mansoni and hookworm, respectively. There was no significant difference in FECs between the examination of individual and pooled stool samples, except for hookworms. For this STH, pools of 10 resulted in a significant underestimation of infection intensity. The total time to obtain individual FECs was 65 h 5 min. For pooled FECs, this was 19 h 12 min for pools of 5, 14 h 39 min for pools of 10 and 12 h 42 min for pools of 20. Conclusions The results indicate that pooling of stool sample holds also promise as a rapid assessment of infections intensity for STH and S. mansoni using the Kato-Katz technique. In this setting, the time in the laboratory was reduced by 70 % when pools of 5 instead of individual stool samples were screened.

Campylobacter is considered an important foodborne pathogen, having a high impact on public health burden. Source allocation studies identified broiler meat as the most important food transmission vehicle of Campylobacter . In this regard, microbiological limits are under development in the EU and characterisation of microbial contamination seems to be an essential step towards implementing sampling schemes. The aim of this study was to analyse broiler batches processed at three conventional slaughterhouses in Germany for their Campylobacter load at the end of processing. Microbial data of positive and negative batches from the studied slaughterhouses were used to fit different statistical distributions (i.e., lognormal, Poisson-lognormal and negative binomial) by means of the maximum likelihood estimation method. Finally, the performance of microbiological criteria was assessed by calculating the probability of accepting batches using two microbiological limits recently discussed by the European Food Safety Authority (500 and 1000 cfu/g). Samples of broiler neck skin and caecal content (356 batches) were collected in three German slaughterhouses (A, B and C) for fresh meat production from conventionally reared broilers during the period from July 2013 to June 2016. Microbial analyses of five pooled neck skin samples and one pooled caecal sample per batch were performed. In this study, the prevalence of Campylobacter caecum positive broiler batches processed at slaughterhouses A, B and C was 42.7 (n = 117), 21.7 (n = 120) and 47.9% (n = 119), respectively. The Campylobacter mean count in neck skin samples of positive batches was highest in slaughterhouse A, with 2.9 ± 0.6 log 10 cfu/g compared to slaughterhouse B with 2.7 ± 0.7 log 10 cfu/g and slaughterhouse C with 2.7 ± 0.7 log 10 cfu/g. The results showed that distributions skewed to the right, thus indicating a high proportion of low microbial counts in the samples. Negative binomial regression provided a better fit at low contamination levels (<100 cfu/g), while the Poisson-lognormal distribution described both within- and between-batch variability better at higher microbial counts. The fitted statistical distributions were further used to evaluate the performance of different microbiological criteria based on an acceptance sampling approach in relation to the defective units based on different limits (mean counts) set at each slaughterhouse. Results obtained will help food business operators to evaluate the status of microbiological hygiene and safety in relation to Campylobacter contamination, also assisting them in setting their own limits of acceptance for process improvement under consideration of existing legal requirements. [ABSTRACT FROM AUTHOR]

Abstract: Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next‐generation sequencing (NGS) is a high‐throughput technology that has the potential to modernize vector surveillance. When combined with DNA barcoding, it is termed ‘metabarcoding.’ The aim of our study was to establish a metabarcoding protocol to characterize pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%. Nucleic acid extracted from both crude homogenate and supernatant was used to amplify a 269‐bp section of the mitochondrial cytochrome c oxidase subunit I (COI) locus. Additionally, a 67‐bp region of the RRV E2 gene was amplified from synthesized cDNA to screen for RRV. Amplicon sequencing was performed using an Illumina MiSeq, and bioinformatic analysis was performed using a DNA barcode database of Victorian mosquitoes. Metabarcoding successfully detected all mosquito species and RRV in every positive sample tested. The limits of species detection were also examined by screening a pool of 1000 individuals, successfully identifying the species and RRV from a single mosquito. The primers used for amplification, number of PCR cycles and total number of individuals present all have effects on the quantification of species in mixed bulk samples. Based on the results, a number of recommendations for future metabarcoding studies are presented. Overall, metabarcoding shows great promise for providing a new alternative approach to screening large insect surveillance trap catches. [ABSTRACT FROM AUTHOR]

Pooling individual samples for batch testing is a common procedure for reducing costs. The recent use of multidimensional array algorithms, due to the emergence of robotic pooling, is an innovative way of pooling. We show that the two-dimensional arraybased group tests can provide accurate estimates for the prevalence rate even for situations in which the traditional estimators, applied to one-dimensional arrays, are not valid. Hence, a computational script was developed to determine which prevalence rate estimate minimizes the sum of the squared deviations between the number of observed and expected rows and columns whose pooled sample had a positive test result.

Identifying single nucleotide polymorphism (SNPs) from pooled samples is critical for many studies and applications. SNPs determined by next-generation sequencing results may suffer from errors in both base calling and read mapping. Taking advantage of dual mononucleotide addition-based pyrosequencing, we present Epds, a method to efficiently identify SNPs from pooled DNA samples. On the basis of only five patterns of non-synchronistic extensions between the wild and mutant sequences using dual mononucleotide addition-based pyrosequencing, we employed an enumerative algorithm to infer the mutant locus and estimate the proportion of mutant sequence. According to the profiles resulting from three runs with distinct dual mononucleotide additions, Epds could recover the mutant bases. Results showed that our method had a false-positive rate of less than 3%. Series of simulations revealed that Epds outperformed the current method ( PSM) in many situations. Finally, experiments based on profiles produced by real sequencing proved that our method could be successfully applied for the identification of mutants from pooled samples. The software for implementing this method and the experimental data are available at . [ABSTRACT FROM AUTHOR]

Dioxin-like compounds (DLCs) are monitored in the U.S. population using data collected with the National Health and Nutrition Examination Survey (NHANES). Until recently, participants' serum samples have been analyzed individually, and summary statistics defining reference ranges by age, gender, and race/ethnicity have served as the background by which other biomonitoring data can be evaluated. In the most recent NHANES DLC data, 2005–2006 and 2007–2008, participants' sera have been physically pooled prior to laboratory analysis, introducing major challenges to their utility as a reference population: variability among individuals and relations with covariates are lost, and individual design effects cannot be applied. Further, the substantial drop in limits of detection (LODs) in pooled sample biennials prevents reliable comparisons to individual data, and has complicated estimates of change over time. In this study, we address the drawbacks introduced by pooled samples by generating U.S. population reference ranges based on individual-level data adjusted to 2005–2006 and 2007–2008 levels. Using publicly available data, multiple imputation (MI) generated four NHANES biennials (2001–2008) of individual DLC data; we then trended the change over time in each DLC by demographic stratum. NHANES 2003–2004 individuals were adjusted by the trended change over time. Population estimates of toxic equivalency (TEQ) concentrations were calculated using traditional MI survey analysis methods and reference tables provided for 2005–2006 and 2007–2008 by age, race, and gender. Demographic differences in TEQ concentrations and trended change are reported, e.g. TEQ continues to drop in young adults aged 20–39, but distributions appear stable in older adults 60 +; Mexican Americans have consistently lowest dioxins, furans, and PCBs, with non-Hispanic Blacks dropping to the same levels as non-Hispanic Whites in dioxins and PCBs and significantly below non-Hispanic Whites in furans by 2007–2008. Additionally, the ratio of 95th percentile to mean in DLC distributions was found to vary by age, between dioxins, furans, and PCBs, and across mean, making a simple ratio approach impractical for describing population concentrations using pooled samples. We discuss the practical implications of the pooled sample method, the performance of this trending solution in the context of other methods, and expected effects of distribution assumptions on variability and TEQ estimates, particularly in largely undetected congeners. These updated reference populations of individuals, along with information on trending, provide a common and valid basis for interpreting other individually sampled biomonitoring data. [ABSTRACT FROM AUTHOR]

Six major Shiga toxin producing Escherichia coli (STEC) serogroups: O26, O103, O145, O111, O121, and O45 have been declared as adulterants in federally inspected raw beef in the USA effective June 4th, 2012 in addition to the routinely tested STEC O157: H7. This study tests a real-time multiplex PCR assay and pooling of the samples to optimize the detection and quantification (prevalence and contamination) of six major non-O157 STEC, regardless of possessing Shiga toxins. To demonstrate the practicality, one large-scale slaughter plant (Plant LS) and one small-scale slaughter plant (Plant SS) located in the Mid-Western USA were sampled, in 2011, before the establishment of 2013 USDA laboratory protocols. Carcasses were sampled at consecutive intervention stations and beef trimmings were collected at the end of the fabrication process. Plant SS had marginally more contaminated samples than Plant LS (p-value 0.08). The post-hide removal wash, steam pasteurization, and lactic acid (≤5%) spray used in Plant LS seemed to reduce the six serogroups effectively, compared to the hot-water wash and 7-day chilling at Plant SS. Compared to the culture isolation methods, quantification of the non-O157 STEC using real-time PCR may be an efficient way to monitor the efficacy of slaughter line interventions. [ABSTRACT FROM AUTHOR]

Monitoring endoparasite burden (FEC) and treatment efficacy (FECR) is a key element of sustainable parasite control. However, the costs of the analysis often discourage their implementation by farmers and veterinary practitioners. Pooling samples is considered to be a good alternative to reduce time and monetary costs, but limited data are available on the use of pooled samples in small ruminants, especially for goats. In this study, data collected over the years in sheep and goat farms were analyzed, and results obtained from individual and pooled analysis were compared for the purposes of FEC and FECR assessment. A total of 801 individual and 134 pooled samples (composed of 3–12 individual samples) were included. For FECR testing, 2 pools of 5 samples each were created per trial and the same animals were sampled at day 0 (D0 – treatment day) and 14 days after (D14). Samples were analyzed by McMaster technique (limit of detection 20 EPG). Results from pooled and individual FEC were not significantly different (Wilcoxon signed-rank test) and correlation (Spearman's rank test) was high for all sub-categories, although agreement (Lin's concordance correlation) was often classified as poor. Results were not influenced by the pool size (<6 or ≥6). Interpretation of treatment efficacy between the two methods was comparable for all sheep trials, while it differed for goats in 4 out of 10 trials. Wilcoxon signed-rank test indicated a non significant difference between pooled and individual FECR. However, correlation and agreement between FECR were considerably better for sheep compared to goats, for which they were very limited, despite the correlation between FEC at D0 and D14 was always high. According to our results, pooled FECR can be a good option but the absence of 95 %CI represents a major drawbacks in the interpretation of results. Further studies on the topic for goats are needed. • Pooled and individual FEC and FECR results are not significantly different. • The pool size did not affect the results. • Lack of a 95 %CI is a major weakness of pooled samples, especially for FECRT. • The first data on pooled FECRT for goats are provided. [ABSTRACT FROM AUTHOR]

Schistosoma infection in snails can be monitored by microscopy or indirectly by sentinel mice. As both these approaches can miss infections, more sensitive tests are needed, particularly in low-level transmission settings. In this study, loop-mediated isothermal amplification (LAMP) technique, designed to detect a specific 28S ribosomal Schistosoma japonicum (Sj28S) gene with high sensitivity, was compared to microscopy using snail samples from 51 areas endemic for schistosomiasis in five Chinese provinces. In addition, the results were compared with those from polymerase chain reaction (PCR) by adding DNA sequencing as a reference. The testing of pooled snail samples with the LAMP assay showed that a dilution factor of 1/50, i.e., one infected snail plus 49 non-infected ones, would still result in a positive reaction after the recommended number of amplification cycles. Testing a total of 232 pooled samples, emanating from 4006 snail specimens, showed a rate of infection of 6.5%, while traditional microscopy found only 0.4% positive samples in the same materials. Parallel PCR analysis confirmed the diagnostic accuracy of the LAMP assay, with DNA sequencing even giving LAMP a slight lead. Microscopy and the LAMP test were carried out at local schistosomiasis-control stations, demonstrating that the potential of the latter assay to serve as a point-of-care (POC) test with results available within 60⁻90 min, while the more complicated PCR test had to be carried out at the National Institute of Parasitic Diseases (NIPD) in Shanghai, China. In conclusion, LAMP was found to be clearly superior to microscopy and as good as, or better than, PCR. As it can be used under field conditions and requires less time than other techniques, LAMP testing would improve and accelerate schistosomiasis control.

Venoms are evolutionary key adaptations that species employ for defense, predation or competition. However, the processes and forces that drive the evolution of venoms and their toxin components remain in many aspects understudied. In particular, the venoms of many smaller, neglected (mostly invertebrate) organisms are not characterized in detail, especially with modern methods. For the majority of these taxa, even their biology is only vaguely known. Modern evolutionary venomics addresses the question of how venoms evolve by applying a plethora of -omics methods. These recently became so sensitive and enhanced that smaller, neglected organisms are now more easily accessible to comparatively study their venoms. More knowledge about these taxa is essential to better understand venom evolution in general. The methodological core pillars of integrative evolutionary venomics are genomics, transcriptomics and proteomics, which are complemented by functional morphology and the field of protein synthesis and activity tests. This manuscript focuses on transcriptomics (or RNASeq) as one toolbox to describe venom evolution in smaller, neglected taxa. It provides a hands-on guide that discusses a generalized RNASeq workflow, which can be adapted, accordingly, to respective projects. For neglected and small taxa, generalized recommendations are difficult to give and conclusions need to be made individually from case to case. In the context of evolutionary venomics, this overview highlights critical points, but also promises of RNASeq analyses. Methodologically, these concern the impact of read processing, possible improvements by perfoming multiple and merged assemblies, and adequate quantification of expressed transcripts. Readers are guided to reappraise their hypotheses on venom evolution in smaller organisms and how robustly these are testable with the current transcriptomics toolbox. The complementary approach that combines particular proteomics but also genomics with transcriptomics is discussed as well. As recently shown, comparative proteomics is, for example, most important in preventing false positive identifications of possible toxin transcripts. Finally, future directions in transcriptomics, such as applying 3rd generation sequencing strategies to overcome difficulties by short read assemblies, are briefly addressed.

There are several arthropods that can transmit disease to humans. To make inferences about the rate of infection of these arthropods, it is common to collect a large sample of vectors, divide them into groups (called pools), and apply a test to detect infection. This paper presents an approximate likelihood point estimator to rate of infection for pools of different sizes, when the variability of these sizes is small and the infection rate is low. The performance of this estimator was evaluated in four simulated scenarios, created from real experiments selected in the literature. The new estimator performed well in three of these scenarios. As expected, the new estimator performed poorly in the scenario with great variability in the size of the pools for some values of the parameter space. [ABSTRACT FROM AUTHOR]

Background: Our group has recently provided a proof-of-principle for the examination of pooled stool samples using McMaster technique as a strategy for the rapid assessment of intensity of soil-transmitted helminth infections (STH, Ascaris lumbricoides, Trichuris trichiura and hookworm). In the present study we evaluated this pooling strategy for the assessment of intensity of both STH and Schistosoma mansoni infections using the Kato-Katz technique. Methods: A cross-sectional survey was conducted in 360 children aged 5-18 years from six schools in Jimma Zone (southwest Ethiopia). We performed faecal egg counts (FECs) in both individual and pooled samples (pools sizes of 5, 10 and 20) to estimate the number of eggs per gram of stool (EPG) using the Kato-Katz technique. We also assessed the time to screen both individual and pooled samples. Results: Except for hookworms, there was a significant correlation (correlation coefficient = 0.53-0.95) between the mean of individual FECs and the FECs of pooled samples for A. lumbricoides, T. trichiura and S. mansoni, regardless of the pool size. Mean FEC were 2,596 EPG, 125 EPG, 47 EPG, and 41 EPG for A. lumbricoides, T. trichiura, S. mansoni and hookworm, respectively. There was no significant difference in FECs between the examination of individual and pooled stool samples, except for hookworms. For this STH, pools of 10 resulted in a significant underestimation of infection intensity. The total time to obtain individual FECs was 65 h 5 min. For pooled FECs, this was 19 h 12 min for pools of 5, 14 h 39 min for pools of 10 and 12 h 42 min for pools of 20. Conclusions: The results indicate that pooling of stool sample holds also promise as a rapid assessment of infections intensity for STH and S. mansoni using the Kato-Katz technique. In this setting, the time in the laboratory was reduced by 70 % when pools of 5 instead of individual stool samples were screened. [ABSTRACT FROM AUTHOR]

Females of all seven living species of sea turtles are known to be polyandrous and show multiple paternity. The frequency of multiple paternity varies among species, and among populations of the same species. In the olive ridley sea turtle ( Lepidochelys olivacea ), multiple paternity levels correlate with the abundance of individuals in the mating system, being much higher in arribada rookeries than in solitary nesting sites. We used two highly polymorphic microsatellite markers (Cm84 and Or1) to assess the level of multiple paternity in an olive ridley solitary population nesting in the Gulf of Fonseca, Honduras. We found evidence of multiple paternity in 6 out of 8 clutches (75%), with a minimum number of two fathers in four clutches, and a minimum of three in the remaining two clutches. This high level of multiple paternity in a small solitary population suggests that some of the females nesting in Honduras may be coming from proximal Nicaraguan arribada nesting beaches. Historical evidences and recent satellite telemetry data support this hypothesis. In addition, we show that multiple paternity studies can be effectively performed in the absence of maternal samples, and that pooled DNA samples can be used with results comparable to individual hatchling sampling in multiple paternity analyses. [ABSTRACT FROM AUTHOR]

The Alberta Biomonitoring Program (ABP) was created in 2005 with the initial goal of establishing baseline levels of exposure to environmental chemicals in specific populations in the province of Alberta, Canada, and was later expanded to include multiple phases. The first two phases focused on evaluating exposure in pregnant women (Phase One, 2005) and children (Phase Two, 2004-2006) by analyzing residual serum specimens. Phase Three (2013-2016) employed active recruitment techniques to evaluate environmental exposures using a revised list of chemicals in paired serum pools from pregnant women and umbilical cord blood. These three phases of the program monitored a total of 226 chemicals in 285 pooled serum samples representing 31,529 individuals. Phase Four (2017-2020) of the ABP has taken a more targeted approach, focusing on the impact of the federal legalization of cannabis on the exposure of pregnant women in Alberta to cannabis, as well as tobacco and alcohol using residual prenatal screening serum specimens. Chemicals monitored in the first three phases include herbicides, neutral pesticides, metals, metalloids, and micronutrients, methylmercury, organochlorine pesticides, organophosphate pesticides, parabens, phthalate metabolites, perfluoroalkyl substances (PFAS), phenols, phytoestrogens, polybrominated compounds, polychlorinated biphenyls (PCBs), dioxins and furans, polycyclic aromatic hydrocarbons (PAHs), and tobacco biomarkers. Phase Four monitored six biomarkers of tobacco, alcohol, and cannabis. All serum samples were pooled. Mean concentrations and 95% confidence intervals (CIs) were calculated for the chemicals detected in ≥25% of the sample pools. cross the first three phases, the data from the ABP has provided baseline exposure levels for the chemicals in pregnant women, children, and newborns across the province. Comparison within and among the phases has highlighted differences in exposure levels with age, geography, seasonality, sample type, and time. The strategies employed throughout the program phases have been demonstrated to provide effective models for population biomonitoring. [ABSTRACT FROM AUTHOR]

Human biomonitoring of exposure to environmental chemicals is important. Individual monitoring is not viable because of low individual exposure level or insufficient volume of materials and the prohibitive cost of taking measurements from many subjects. Pooling of samples is an efficient and cost-effective way to collect data. Estimation is, however, complicated as individual values within each pool are not observed but are only known up to their average or weighted average. The distribution of such averages is intractable when the individual measurements are lognormally distributed, which is a common assumption. We propose to replace the intractable distribution of the pool averages by a Gaussian likelihood to obtain parameter estimates. If the pool size is large, this method produces statistically efficient estimates, but regardless of pool size, the method yields consistent estimates as the number of pools increases. An empirical Bayes (EB) Gaussian likelihood approach, as well as its Bayesian analog, is developed to pool information from various demographic groups by using a mixed-effect formulation. We also discuss methods to estimate the underlying mean-variance relationship and to select a good model for the means, which can be incorporated into the proposed EB or Bayes framework. By borrowing strength across groups, the EB estimator is more efficient than the individual group-specific estimator. Simulation results show that the EB Gaussian likelihood estimates outperform a previous method proposed for the National Health and Nutrition Examination Surveys with much smaller bias and better coverage in interval estimation, especially after correction of bias. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Abstract: Exact inference for the case when multiple independent progressively Type-II censored samples are pooled is considered. Two representations for the marginal distributions of the resulting pooled order statistics are given, a direct method and an iterative method. The coverage probabilities and expected widths of exact nonparametric confidence intervals for quantiles are compared for various scenarios with one or more independent samples. [Copyright &y& Elsevier]

Highlights: [•] Use of individual or pooled samples is important when designing sampling strategies. [•] Variation caused by e.g. chemical analysis or sample variation need to be considered. [•] Various solutions are offered using different numbers of individual/pooled samples. [•] Results allow the design of cost-efficient, statistically sound sampling strategies. [Copyright &y& Elsevier]

Abstract: The objective of this study was to evaluate the sensitivity of a commercially available real-time polymerase chain reaction (PCR) test for the detection of Tritrichomonas fetus in individual and pooled direct preputial samples. Two samples were collected and processed once a week from nine T. fetus–infected bulls (n = 121) and placed into either an InPouch TF or 2 mL of PBS. Preputial samples were also collected into both media and PBS from 1016 other bulls. All pouches were cultured and evaluated as per manufacturer's instructions. The prepuce samples collected directly into PBS were individually evaluated using real-time PCR by a commercial diagnostic laboratory. Direct preputial samples were then randomly divided for pooling into groups of 5 and 10 samples, ensuring that every pool had one sample from a known infected bull before testing using real-time PCR. Sensitivity was estimated for culture and real-time PCR of the 121 direct and culture-enriched individual samples from nine infected bulls. There were no differences (P = 0.12) among the sensitivity estimates for culture, 95.0% (95% confidence interval [CI]: 89.6%–97.7%); real-time PCR of culture-enriched samples, 95.9% (95% CI: 90.7–98.2); and direct preputial samples, 90.1% (95% CI: 83.5–94.2). There was also no significant difference (P = 0.08) between the sensitivity of real-time PCR for direct preputial samples in 110 pools of 5 (83.6%, 95% CI: 75.6–89.4) or 10 samples (77.3%, 95% CI: 68.6–84.1). The use of three sequential direct samples, collected in PBS at weekly intervals and tested by real-time PCR, increased the sensitivity to 100% for pools of 5 and 96% for pools of 10. In conclusion, direct preputial samples collected in PBS and tested by real-time PCR individually have comparable sensitivity to culture and real-time PCR in enriched samples. The use of pooled direct preputial samples appears to be relatively sensitive. However, this strategy requires repeated sampling to optimize sensitivity. Real-time PCR testing of preputial samples collected directly into PBS with the option of pooling would decrease the cost associated with screening bulls, and increase the feasibility of large epidemiological studies and active surveillance. [Copyright &y& Elsevier]

Abstract: The Baermann–Wetzel method is the recommended test for the diagnosis of lungworm infections. The objective of this study was to evaluate the use of pooled fecal samples for the diagnosis of protostrongylid infections in sheep flocks and to investigate the sensitivity of the pooled Baermann–Wetzel technique in relation to individual analysis, which is time consuming and expensive. Fecal samples were taken from 10 sheep flocks positive for protostrongylids located in northwestern Spain. Ten pools composed of 6 individual fecal samples, chosen at random from the entire flock sampling, were performed for each flock at the same time as individual analyses. Protostrongylid larvae were detected in 56 pools, with a 56% flock sensitivity. Flock sensitivity was positively associated with the within-flock prevalence (P <0.001), but not with the mean larvae output. A high sensitivity (78.3%) has been observed in flocks with medium or high prevalence, so pooled fecal samples can be used in those flocks that require an effective treatment regimen against these nematodes. [Copyright &y& Elsevier]

Molecular markers produced by next-generation sequencing ( NGS) technologies are revolutionizing genetic research. However, the costs of analysing large numbers of individual genomes remain prohibitive for most population genetics studies. Here, we present results based on mathematical derivations showing that, under many realistic experimental designs, NGS of DNA pools from diploid individuals allows to estimate the allele frequencies at single nucleotide polymorphisms ( SNPs) with at least the same accuracy as individual-based analyses, for considerably lower library construction and sequencing efforts. These findings remain true when taking into account the possibility of substantially unequal contributions of each individual to the final pool of sequence reads. We propose the intuitive notion of effective pool size to account for unequal pooling and derive a Bayesian hierarchical model to estimate this parameter directly from the data. We provide a user-friendly application assessing the accuracy of allele frequency estimation from both pool- and individual-based NGS population data under various sampling, sequencing depth and experimental error designs. We illustrate our findings with theoretical examples and real data sets corresponding to SNP loci obtained using restriction site-associated DNA ( RAD) sequencing in pool- and individual-based experiments carried out on the same population of the pine processionary moth ( Thaumetopoea pityocampa). NGS of DNA pools might not be optimal for all types of studies but provides a cost-effective approach for estimating allele frequencies for very large numbers of SNPs. It thus allows comparison of genome-wide patterns of genetic variation for large numbers of individuals in multiple populations. [ABSTRACT FROM AUTHOR]

Abstract: Strongyle parasites are ubiquitous in grazing horses. Of these, the bloodworm Strongylus vulgaris is regarded as most pathogenic. Increasing levels of anthelmintic resistance in strongyle parasites has led to recommendations of decreased treatment intensities, and there is now a pronounced need for reliable tools for detection of parasite burdens in general and S. vulgaris in particular. The only method currently available for diagnosing S. vulgaris in practice is the larval culture, which is laborious and time-consuming, so veterinary practitioners most often pool samples from several horses together in one culture to save time. Recently, molecular tools have been developed to detect S. vulgaris in faecal samples. The aim of this study was to compare the performance of a conventional polymerase chain reaction (PCR) assay with the traditional larval culture and furthermore test the performance of pooled versus individual PCR for farm screening purposes. Faecal samples were obtained from 331 horses on 18 different farms. Farm size ranged from 6 to 56 horses, and horses aged between 2 months and 31 years. Larval cultures and PCR were performed individually on all horses. In addition, PCR was performed on 66 faecal pools consisting of 3–5 horses each. Species-specific PCR primers previously developed were used for the PCR. PCR and larval culture detected S. vulgaris in 12.1 and 4.5% of individual horses, respectively. On the farm level, eight farms tested positive with the larval culture, while 13 and 11 farms were positive with the individual and pooled PCRs, respectively. The individual PCR method was statistically superior to the larval culture, while no statistical difference could be detected between pooled and individual PCR for farm screening. In conclusion, pooled PCR appears to be a useful tool for farm screening for S. vulgaris. [Copyright &y& Elsevier]

The article presents research which explored the different significant issues concerning the application of pooled sample in environmental chemical biomonitoring. Pooled samples are commonly used to offer effective and helpful alternatives to epidemiologic studies of biomarkers of exposure, gene microarray analyses as well as characterization of populations regarding environmental chemical exposures. The author addressed the bias and estimation issues related to the exposure of the U.S. population to polyfluoralkyl and perfluorooctanesulfonate compounds.

The article discusses a study of the correlation between real-time quantitative polymerase chain reaction (qPCR) threshold cycle (Ct) values and colony-forming units (CFU) on Herrold egg yolk medium (HEYM) for Mycobacterium avium subspecies paratuberculosis (MAP) in fresh and thawed pooled fecal and environmental samples. Results found an inverse correlation between HEYM culture and real-time qPCR for (MAP). Rapid, quantitative estimates of MAP load has been found with the use of real-time qPCR.

Biomonitoring involves the assessment of human or animal populations by measuring organic or biological compounds or their metabolites in the body fluids or tissues of individuals in those populations. Pooling samples before making analytical measurements can reduce the costs of biomonitoring by reducing the number of analyses. By proper choice of pooled-sample design, population means can be estimated without measuring individual samples. I present a statistical method for characterizing an entire population distribution of such compounds by exploiting the theoretic relationship between interindividual-sample variance and the variation between pooled samples. I use simulation experiments to determine an optimum pooled-sample design as a function of the number of subpopulations and the number of available samples. Using pooled samples to characterize populations is not only more cost-efficient, but also in some cases it can lead to more precise and less biased parameter estimation than that occurs with individual samples. [ABSTRACT FROM AUTHOR]

We tested the accuracy of molecular analyses for recovering the species richness and structure of pooled fungal communities of known composition. We constructed replicate pools of 2–20 species and analysed these pools by two separate pooling-DNA extraction procedures and three different molecular analyses (Automated Ribosomal Intergenic Spacer Analysis (ARISA), terminal restriction fragment length polymorphism (T-RFLP) and clone library-sequencing). None of the methods correctly described the known communities. Only clone library-sequencing with high sequencing per pool (∼100 clones) recovered reasonable estimates of richness. Frequency data were skewed with all procedures and analyses. These results indicate that the error introduced by pooling samples is significant and problematic for ecological studies of fungal communities. [ABSTRACT FROM AUTHOR]

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