Effect of pooled tracheal sample testing on the probability of Mycoplasma hyopneumoniae detection

Tracheal pooling for Mycoplasma hyopneumoniae (M. hyopneumoniae) DNA detection allows for decreased diagnostic cost, one of the main constraints in surveillance programs. The objectives of this study were to estimate the sensitivity of pooled-sample testing for the detection of M. hyopneumoniae in tracheal samples and to develop probability of M. hyopneumoniae detection estimates for tracheal samples pooled by 3, 5, and 10. A total of 48 M. hyopneumoniae PCR-positive field samples were pooled 3-, 5-, and 10-times using field M. hyopneumoniae DNA-negative samples and tested in triplicate. The sensitivity was estimated at 0.96 (95% credible interval [Cred. Int.]: 0.93, 0.98) for pools of 3, 0.95 (95% Cred. Int: 0.92, 0.98) for pools of 5, and 0.93 (95% Cred. Int.: 0.89, 0.96) for pools of 10. All pool sizes resulted in PCR-positive if the individual tracheal sample Ct value was < 33. Additionally, there was no significant decrease in the probability of detecting at least one M. hyopneumoniae-infected pig given any pool size (3, 5, or 10) of tracheal swabs. Furthermore, this manuscript applies the probability of detection estimates to various real-life diagnostic testing scenarios. Combining increased total animals sampled with pooling can be a cost-effective tool to maximize the performance of M. hyopneumoniae surveillance programs.

Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual samples

BACKGROUND

The pooled sample method is used in epigenomic research and expression analysis and is a cost-effective screening approach for small amounts of DNA. Evaluation of the pooled sample method in epigenomic studies is performed using the Illumina Infinium Methylation 450K BeadChip array; however, subsequent reports on the updated 850K array are lacking. A previous study demonstrated that the methylation levels obtained from individual samples were accurately replicated using pooled samples but did not address epigenome-wide association study (EWAS) statistics. The DNA quantification method, which is important for the homogeneous mixing of DNA in the pooled sample method, has since become fluorescence-based, and additional factors need to be considered including the resolution of batch effects of microarray chips and the heterogeneity of the cellular proportions from which the DNA samples are derived. In this study, four pooled samples were created from 44 individual samples, and EWAS statistics for differentially methylated positions (DMPs) and regions (DMRs) were conducted for individual samples and compared with the statistics obtained from the pooled samples.

RESULTS

The methylation levels could be reproduced fairly well in the pooled samples. This was the case for the entire dataset and when limited to the top 100 CpG sites, consistent with a previous study using the 450K BeadChip array. However, the statistical results of the EWAS for the DMP by individual samples were not replicated in pooled samples. Qualitative analyses highlighting methylation within an arbitrary candidate gene were replicable. Focusing on chr 20, the statistical results of EWAS for DMR from individual samples showed replicability in the pooled samples as long as they were limited to regions with a sufficient effect size.

CONCLUSIONS

The pooled sample method replicated the methylation values well and can be used for EWAS in DMR. This method is sample amount-effective and cost-effective and can be utilized for screening by carefully understanding the effective features and disadvantages of the pooled sample method and combining it with candidate gene analyses.

Monitoring temporal trends of dioxins, organochlorine pesticides and chlorinated paraffins in pooled serum samples collected from Northern Norwegian women: The MISA cohort study

The ubiquitous presence of legacy and emerging persistent organic pollutants (POPs) in the environmental matrices poses a potential hazard to the humans and creating public health concerns. The present study aimed to evaluate dioxins, dioxin-like polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and chlorinated paraffins (CPs) concentrations in serum of women (postpartum, pregnant and non-pregnant) from Northern Norway to better understand their exposure and contamination status as well as temporal trends across 2007-2009 (MISA 1) to 2019 (MISA 2). Sixty-two blood samples from the MISA 1 cohort and 38 samples from MISA 2 were randomly selected in this study (n = 100). Ninety samples from postpartum (MISA 1) and pregnant women (MISA 2) were randomly combined into 9 pools, with 9-11 individual samples contributing to each pool keeping the groups of pregnant and postpartum women. Remaining 10 samples from non-pregnant women (MISA 2) were allocated into separate group. Geometric mean, minimum and maximum were used to describe the serum concentrations of pooled POPs in MISA cohort. Mann-Whitney U test and independent sample t-test were applied for trend analysis of blood levels of POPs between MISA 1 and MISA 2. We found the serum concentrations of selected POPs in this study to be at lower range. Serum concentrations of dibenzo-p-dioxins (PCDDs) (p = 0.010), polychlorinated dibenzofurans (PCDFs) (p = 0.002), dioxins-like PCBs (p = 0.001), hexachlorobenzene (HCB) (p < 0.001) and p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE) (p = 0.002) were decreased between the studied time. In contrast, the serum concentrations of medium chain chlorinated paraffins showed an increasing trend between 2007 and 2009 and 2019 (p = 0.019). Our findings report a particular concern of emerging contaminant medium chain chlorinated paraffin exposure to humans. Future observational studies with repeated measurements of chlorinated paraffins in general populations worldwide and large sample size are warranted.

Robustness in quantifying the abundance of antimicrobial resistance genes in pooled faeces samples from batches of slaughter pigs using metagenomics analysis

OBJECTIVES

With the continued spread of antimicrobial resistance (AMR) in animals, it is important to assess its occurrence throughout a microbiome quantitatively in order to evaluate significantly affecting factors, e.g. antimicrobial usage. Metagenomics methods make it possible to measure the abundance of AMR genes in complex samples such as pooled faeces samples from batches of slaughter pigs. This study was performed to determine the random error in pooled samples from batches of pigs at slaughter and the measurement error from the metagenomics processes.

METHODS

In four farms, two pooled samples were obtained from a batch of slaughter pigs by two individual samplers, and each pooled sample was thereafter processed twice. Hierarchically clustered heatmaps were applied to evaluate dissimilarities between samples. The coefficient of variation was used to calculate the percentage difference between samples from the same farm.

RESULTS

Results of the analysis revealed that it was not possible to quantitatively separate the variation arising from sampling and metagenomics processes. They both contributed to the overall measurement error in batches of slaughter pigs.

CONCLUSION

Sampling of single pigs in 30 randomly selected pig pens within the farms provides a composition representative for frequently occurring AMR genes present within the farms, while rare genes were not dispersed in a similar manner. Aggregating the resistance abundance at gene family or antimicrobial class level will reduce the apparent variation originating from errors in sampling and metagenomics processing.

A descriptive survey of porcine epidemic diarrhea in pig populations in northern Vietnam

Porcine epidemic diarrhea (PED) virus (PEDV) is a globally emerging and re-emerging epizootic swine virus that causes massive economic losses in the swine industry, with high mortality in piglets. In Vietnam, PED first emerged in 2009 and has now developed to an endemic stage. This is the first cross-sectional survey performed to evaluate the proportion of PEDV-positive swine farms in Vietnam from January 2018 to February 2019. Fecal samples from 327 pig farms in northern Vietnam were collected and tested for PEDV infection by reverse transcription-loop-mediated isothermal amplification (RT-LAMP) method. The proportion of PEDV-positive farms was 30.9% and PEDV-positive farms were distributed throughout the study area. The highest proportion of PEDV-positive farms was 70% (7/10) among nucleus production type farms (P < 0.05). Higher proportions of PEDV-positive farms were found in the Northeast and Red River Delta areas, which are the major areas of pig production (P < 0.05). The proportion of PEDV-positive farms was higher among larger farms (P < 0.05). Our findings illustrate the high proportion of PEDV-positive farms in the Vietnamese pig population and will help to better understand the epidemiological dynamics of PED infection, to estimate impact, and establish and improve prevention and control measures.

Variability of urinary concentrations of phthalate metabolites during pregnancy in first morning voids and pooled samples

BACKGROUND

Because phthalates are quickly metabolized and excreted in urine, and human exposures tend to be episodic, phthalate metabolite concentrations measured in a maternal spot urine sample are only indicative of recent exposure.

OBJECTIVE

To examine temporal variability of pregnant women's phthalate exposure using multiple first morning voids (FMV) and pooled samples.

METHODS

We quantified 14 metabolites of eight phthalates in 577 urine samples collected from 188 pregnancies in the MARBLES (Markers of Autism Risk in Babies - Learning Early Signs) study. We calculated intraclass correlation coefficients (ICCs) using two samples of the same urine type (i.e., two FMVs or two pools) collected across the 2nd and 3rd trimesters. We also calculated ICCs and FMV/pool concentration ratios using two samples (i.e., two FMVs or one FMV and one pool) collected within the same trimester.

RESULTS

Overall, ICCs were higher in pooled samples (0.24-0.87) than in FMVs (0.08-0.69). Regardless of the sample type, ICCs tended to be higher for metabolites for which exposure sources are personal care products or indoor residential materials than those for which diet is an important exposure source. ICCs tended to increase and FMV/pool ratios tended to decrease with an increasing number of composite samples in the pools.

CONCLUSIONS

Our study helped determine the number of samples needed to capture moderate to high reproducibility of individual's average exposure to phthalates and the average exposure can be differently characterized depending on the number of samples in the pools.

Bronchoalveolar lavage fluid from both lungs in horses: Diagnostic reliability of cytology from pooled samples

Cytology of bronchoalveolar lavage fluid (BALF) from one lung may not predict findings in the contralateral lung of the same horse. The aim of this study was to determine whether a pooled BALF from both lungs was representative of corresponding individual samples. Fifty-one horses referred for poor performance and/or respiratory signs and for which a BALF was collected from both lungs, were included in the study. Cytology of pooled and individual BALF samples were performed using a masked protocol. Based on clinical signs and individual BALF cytologies, horses were classified as control (CTL), mild equine asthma (mEA), severe equine asthma (sEA) and/or exercise-induced pulmonary haemorrhage (EIPH). No significant difference was observed between pooled and individual BALF samples for all cell types (P>0.05). Correlations between pooled and individual BALF samples were good (r≥0.9) for neutrophil proportions and haemosiderophages/macrophages ratio, and moderate (r≥0.4) for metachromatic cell and eosinophil proportions. Similarly, intraclass correlation coefficient (ICC) were good (ICC≥0.9) for neutrophil proportions and haemosiderophages/macrophages ratio and substantial (ICC≥0.6) for metachromatic cell proportions. Based on threshold values for pooled samples as determined by receiver operating characteristic (ROC) analysis, categorical agreements were good (κ≥0.97) for diagnosis of mEA/sEA, and substantial (κ=0.74) for EIPH. Using a pooled BALF sample, only one horse was incorrectly classified as CTL instead of mEA and three horses were classified as EIPH instead of CTL. In conclusion, BALF cytology from pooled sample is representative of both individual lungs, and constitutes a valid method to diagnose EA.