Nutrient germination improves DNA recovery from industrial Bacillus subtilis endospores during qPCR enumeration assays

Growth-independent microbial enumeration methods such as quantitative PCR require the efficient extraction of genomic DNA from targeted cells. Bacillus endospores are popular inclusions in commercial products due to their hardiness and metabolic dormancy; however, this hardiness is known to render Bacillus endospores resistant to traditional DNA isolation techniques. Metagenomic studies have sought to address this resistance through nutrient-based germination of bacterial endospores in environmental samples. In the present study, we sought to apply this technique to the enumeration of microbial products using an industrial strain of Bacillus subtilis as a model organism. Germination was induced through incubation of axenic spore suspensions in an AGFK-based rich medium. Total spore count, dipicolinic acid release and OD₆₀₀ absorbance were monitored over time to track the progression of spore populations through the stages of germination and outgrowth. Aerobic plate counts and flow cytometry were used to monitor cell populations for proliferation during the incubation period. Finally, quantitative PCR with taxon-specific primers was used to examine DNA recovery as a function of time. Results show that customized germination protocols, once appropriately validated for the species and product matrix under consideration, can result in more efficient DNA extraction and thus lower limits of detection for qPCR assays targeting industrial Bacillus endospores in microbial products.

cDNA Display Mediated Immuno-PCR (cD-IPCR): A Novel PCR-based Antigen Detection Method

Immuno-PCR (IPCR) is a powerful method in antigen detection where a PCR-amplifiable DNA reporter is conjugated to a specific antibody or an aptamer for the target molecule. In the development and application of IPCR, successful conjugation of a protein (an antibody) with a reporter DNA becomes challenging. To address this issue, we recently demonstrated the feasibility of IPCR based on cDNA display, a 1:1 covalent complex of a polypeptide and its encoding cDNA at the single molecule level. The cDNA display molecule for IPCR is generated first by transcribing the DNA that encodes the detection antibody into an mRNA by in vitro transcription. A puromycin DNA linker is then ligated to the mRNA and then in vitro translation and reverse-transcription are performed to generate the cDNA display molecule. The molecule is then directly used in antigen detection and subsequent qPCR. This method can be applied to detect various antigens in biological samples, if sequences of their single-domain antibodies (VHHs) or peptide aptamers are known.

New bioluminescence pyrophosphate assay for high-sensitivity detection of food-borne pathogens

Traditional methods of identifying food-borne pathogens are time consuming and laborious, so innovative methods for their rapid identification must be developed. Testing for bioluminescence pyrophosphate is a convenient and fast method of detecting pathogens without complex equipment. However, the sensitivity of the method is not as high as that of other methods, and it has a very high detection limit. In this study, the method was optimized to improve its sensitivity. The shortcomings of the method were first identified and corrected using dATPαS instead of dATP for the polymerase chain reaction (PCR), therefore reducing the background signal. Also, when the DNA template extracted from the food-borne pathogens was purified, the new bioluminescence pyrophosphate assay had a limit of detection of <10 copy/μl or 10 colony-forming units/ml, and its sensitivity was higher than that of fluorescent real-time quantitative PCR. Moreover, a single copy of a food-borne pathogen could be detected when a single DNA template was included in the PCR. Salmonella was detected in and isolated from 60 samples of broiler chicken, and the accuracy of the results was verified using a culture method (GB 4789.4-2010). These results showed that the new bioluminescence pyrophosphate assay has the advantages of an intuitive detection process, convenient operation, and rapid measurements. Therefore, it can be used for the rapid detection of pathogenic bacteria and probiotics in various fields.

Dynamics of tumor-specific cfDNA in response to therapy in multiple myeloma patients

Objectives

Progress in multiple myeloma treatment allows patients to achieve deeper responses, for which the assessment of minimal residual disease (MRD) is critical. Typically, bone marrow samples are used for this purpose; however, this approach is site‐limited. Liquid biopsy represents a minimally invasive and more comprehensive technique that is not site‐limited, but equally challenging.

Methods

While majority of current data comes from short‐term studies, we present a long‐term study on blood‐based MRD monitoring using tumor‐specific cell‐free DNA detection by ASO‐qPCR. One hundred and twelve patients were enrolled into the study, but long‐term sampling and analysis were feasible only in 45 patients.

Results

We found a significant correlation of quantity of tumor‐specific cell‐free DNA levels with clinically meaningful events [induction therapy (P = .004); ASCT (P = .012)]. Moreover, length of cfDNA fragments is associated with better treatment response of patients.

Conclusions

These results support the concept of tumor‐specific cell‐free DNA as a prognostic marker.

High cases of submicroscopic Plasmodium falciparum infections in a suburban population of Lagos, Nigeria

BACKGROUND

Asymptomatic malaria parasites are significant sources of infections for onward malaria transmission. Conventional tools for malaria diagnosis such as microscopy and rapid diagnostic test kits (RDT) have relatively low sensitivity, hence the need for alternative tools for active screening of such low-density infections.

METHODS

This study tested var acidic terminal sequence-based (varATS) quantitative polymerase chain reaction (qPCR) for screening asymptomatic Plasmodium falciparum infections among dwellers of a sub-urban community in Lagos, Nigeria. Clinically healthy participants were screened for malaria using microscopy, RDT and varATS qPCR techniques. Participants were stratified into three age groups: 1-5, 6-14 and > 14 years old.

RESULTS

Of the 316 participants screened for asymptomatic malaria infection, 78 (24.68%) were positive by microscopy, 99 (31.33%) were positive by RDT and 112 (35.44%) by varATS qPCR. Participants aged 6-14 years had the highest prevalence of asymptomatic malaria, with geometric means of ~ 116 parasites/µL and ~ 6689 parasites/µL as detected by microscopy and varATS, respectively.

CONCLUSION

This study has revealed high prevalence of asymptomatic malaria in the study population, with varATS detecting additional sub-microscopic infections. The highest concentration of asymptomatic malaria was observed among school-age children between 6 and 14 years old. A large-scale screening to identify other potential hotspots of asymptomatic parasites in the country is recommended.

Assessment of differences between DNA content of cell-cultured and freely suspended oocysts of Cryptosporidium parvum and their suitability as DNA standards in qPCR

BACKGROUND

Although more modern methods are available, quantitative PCR (qPCR) is reproducible, sensitive and specific with instruments and expertise readily available in many laboratories. As such, the use of qPCR in Cryptosporidium research is well established and still widely used by researchers globally. This method depends upon the generation of standards at different concentrations to generate standard curves subsequently used for the quantification of DNA.

METHODS

We assessed four types of DNA template used to generate standard curves in drug screening studies involving Cryptosporidium spp.: (i) serially diluted Cryptosporidium parvum oocysts (106-1); (ii) diluted template DNA from pure oocysts (×10-×106 dilution of 106 oocyst DNA template); (iii) oocysts incubated in human ileocecal adenocarcinoma (HCT-8) cells (105-1 and 5 × 104-50); and (iv) diluted DNA template (5 × 104) from cell culture incubated parasites (×10-×1000).

RESULTS

Serial dilutions of both cell culture and pure oocyst suspension DNA template yielded better linearity than cell culture derived standards, with dilutions of 106 oocysts exhibiting similar quantification cycle (Cq) values to those obtained from DNA template dilutions of 106 oocysts. In contrast, cell culture incubated oocysts demonstrated significantly higher DNA content than equivalent freely suspended oocysts and diluted DNA template from both cell culture derived and freely suspended oocysts across numerous concentrations.

CONCLUSIONS

For many studies involving Cryptosporidium, only relative DNA content is required and as such, the superior linearity afforded by freely suspended oocysts and diluted DNA template (from either cell culture derived standards or freely suspended oocysts) will allow for more accurate relative quantification in each assay. Parasite division in the cell culture standards likely explains the higher DNA content found. These standards, therefore, have the potential to more accurately reflect DNA content in cell culture assays, and despite more modern methods available for absolute quantification, i.e. droplet digital PCR (ddPCR), the ubiquity of qPCR for the foreseeable future encourages further investigation into the reduced linearity observed in these standards such as varying oocyst seeding density, non-linear growth rates and assay efficiency.

(Non-)Sense of Milk Testing in Small Ruminant Lentivirus Control Programs in Goats. Comparative Analysis of Antibody Detection and Molecular Diagnosis in Blood and Milk

Small ruminant lentivirus (SRLV) control programs are mainly based on diagnostic tests performed on blood samples collected from sheep and goats. Since blood sampling is costly and stressful for the animals, we evaluated whether milk could be used as an inexpensive and easily collectable matrix for SRLV detection. We therefore compared SRLV detection via two commercial enzyme-linked immunosorbent assays (ELISAs) and quantitative polymerase chain reaction (qPCR) in blood and corresponding milk samples from 321 goats originating from eight different SRLV-infected farms in Flanders (Belgium). The IDscreen^® ELISA had a better relative sensitivity (97% vs 93%) and specificity (100% and 97%) than the Elitest^® ELISA for SRLV-specific antibody detection in milk compared to serum. The higher sensitivity correlates with a 10-fold higher analytical sensitivity of the IDscreen^® test. In contrast to the overall good ELISA results, qPCR on milk cell pellets lacked sensitivity (81%) and specificity (88%), compared to molecular detection in blood leucocyte pellets. Our results show that serology is more suitable than qPCR for SRLV diagnosis, and that milk may represent an interesting matrix for a preliminary evaluation of a herd’s infection status. Serum remains however the sample of choice for control programs where it is important to identify positive animals with the highest sensitivity.

Prevalence of Lawsonia intracellularis in pig herds in different European countries

Background

Lawsonia intracellularis causes large economic losses in the pig industry worldwide. Pigs suffer from reduced daily weight gain, poor feed conversion ratio and increased mortality. The number of affected animals and herds in Europe remains unknown. This study will provide an overview of the prevalence of Lawsonia intracellularis in herds with a history of diarrhoea in different European countries and thereby identify country specific differences.

Results

Out of the 144 herds sampled in Germany, Denmark, Spain, the Netherlands and the United Kingdom, 90.3% (79.2-100.0%) contained at least one positive faecal sample on quantitative polymerase chain reaction (qPCR). Of the 6450 nursery, growing and finishing pigs of the previously mentioned herds, 26.2% (15.9-41.5%) of the animals were tested positive in faecal samples. Enzyme linked immunosorbent assay (ELISA) results of 60 herds were 91.7% (70-100%) positive. The percentage of positive samples in these 1791 blood samples was 31.6% (20.3-51.0%). Herd prevalence did not differ significantly by qPCR or ELISA. Significant differences between the countries were found regarding: Within-herd prevalence- qPCR: Samples from Denmark were more often positive than samples of Spain or the United Kingdom. Within-herd prevalence- ELISA: Samples from Denmark were more often positive than samples from Spain and the Netherlands. Affected age category- qPCR: Nursery pigs in Denmark were more often positive and shed more genome equivalents than nursery pigs in the other countries. Concentration of detected genome equivalents- qPCR: The concentration of genome equivalents from Lawsonia intracellularis in herds in Denmark was higher compared to all other countries.

Conclusion

A widespread of Lawsonia intracellularis in the six European countries was confirmed, whereby a large part of the positive animals only excreted small amounts of genome equivalents. Country specific differences were found with Denmark in particular diagnosing more Lawsonia intracellularis then the other countries. Herd data collected in this study needs to be analysed to get more information about possible reasons for the differences found between the countries.

Real-Time Quantitative PCR Analysis of the Expression Pattern of the Hypoglycemic Polypeptide-P Gene in Momordica charantia

This study was designed to establish a real-time quantitative polymerase chain reaction (qPCR) method to rapidly and reliably analyze the hypoglycemic polypeptide-P gene expression pattern in Momordica charantia (MC) and to examine its expression changes in different MC accessions, harvesting seasons, and tissue types. The qPCR results were further verified by using Western blotting (WB). A total of 10 MCs with different accessions were collected and tested in this study. Among the tested accessions, RU5H showed the highest expression level of the polypeptide-P gene. The expression level of the polypeptide-P gene was not only season-related (with the highest in early July) but also tissue-related (with the highest in the seed tissue). In addition, the expression characteristic of the polypeptide-P gene was maturity-related, with the highest expression level in the tender MC. The WB results show that the transcription level of this gene shows an almost similar trend to the corresponding protein expression level. In conclusion, the established qPCR method can rapidly and effectively detect the expression levels of the polypeptide-P gene in MCs with different accessions; furthermore, various factors, including the accessions, harvesting seasons, and tissue types can affect the expression level.

Rapid molecular species identification of indigenous bats from Germany for surveillance purposes

Chiroptera form the second largest order of mammals and compromise >1200 species, of which only 51 species are abundant in Europe. As bats are important hosts involved in the emergence and spread of zoonotic infections, it is becoming more important to discriminate the different species of bats involved in the maintenance of causative agents. However, traditional taxonomic methods rely on morphological features and are challenging as they require long-lasting experience of an investigator and sometimes fail if the specimen is of poor condition. On the other hand, barcoding requires sequencing and is time consuming. Therefore, a versatile genetic approach for rapid species identification would be valuable. In this study, two mitochondrial loci, cytochrome b (cyt b) and cytochrome c oxidase subunit I (COI) were selected for the development of two multiplex qPCRs for differentiating four very abundant bat species in Germany using DNA extracted from the patagium or organ pools. Verification of the developed assays using a set of 1000 individual bat samples belonging to 20 different European species clearly showed that the multiplex qPCRs were able to determine the four most abundant species in this collection by a COI based qPCR. All other bat species which could not be covered by this approach could be easily identified by sequencing of the amplicon generated by broad-range qPCRs for cyt B and COI, respectively. Moreover, the double-check approach with cyt B and COI makes the identification of bats into species more reliable. The new multiplex PCRs allow a fast and easy genotyping of German bats and could be useful for screening approaches.

Quantitative PCR of INDELs to measure donor-derived cell-free DNA-a potential method to detect acute rejection in kidney transplantation: a pilot study

The quantification of donor‐derived cell‐free DNA (ddcfDNA) in recipient's plasma is a novel, but technically challenging noninvasive method to assist the diagnosis of acute rejection (AR). A quantitative real‐time PCR (qPCR) approach targeting insertion/deletion polymorphisms (INDEL) was adapted to measure ddcfNA in plasma samples from 29 kidney transplant recipients obtained at time of clinically indicated biopsies (eight patients with a histologically verified AR, nine with borderline rejection and 12 without evidence of rejection). Measured ddcfDNA levels of smaller INDEL amplicon targets differed significantly (P = 0.016, Kruskal–Wallis H test) between recipients with biopsy‐proven AR (median 5.24%; range 1.00–9.03), patients without (1.50%; 0.41–6.50) and patients with borderline AR (1.91%; 0.58–5.38). Similarly, pairwise testing by Mann–Whitney U‐tests revealed significant differences between recipients with AR and without AR (P = 0.012) as well as patients with AR and borderline histology (P = 0.015). Receiver operating characteristic (ROC) analysis revealed an area under the ROC curve for discriminating AR and non‐AR biopsies of 0.84 (95% CI: 0.66–1.00). The determined cutoff value of 2.7% ddcfDNA showed a sensitivity of 0.88 (95% CI: 0.63–1.00) and specificity of 0.81 (95% CI: 0.64–0.98). INDEL qPCR represents a novel method to quantify ddcfDNA on standard qPCR instruments within 6–8 h with high sensitivity and specificity to detect AR.

Soil Bacterial and Fungal Communities Exhibit Distinct Long-Term Responses to Disturbance in Temperate Forests

In Appalachian ecosystems, forest disturbance has long-term effects on microbially driven biogeochemical processes such as nitrogen (N) cycling. However, little is known regarding long-term responses of forest soil microbial communities to disturbance in the region. We used 16S and ITS sequencing to characterize soil bacterial (16S) and fungal (ITS) communities across forested watersheds with a range of past disturbance regimes and adjacent reference forests at the Coweeta Hydrologic Laboratory in the Appalachian mountains of North Carolina. Bacterial communities in previously disturbed forests exhibited consistent responses, including increased alpha diversity and increased abundance of copiotrophic (e.g., Proteobacteria) and N-cycling (e.g., Nitrospirae) bacterial phyla. Fungal community composition also showed disturbance effects, particularly in mycorrhizal taxa. However, disturbance did not affect fungal alpha diversity, and disturbance effects were not consistent at the fungal class level. Co-occurrence networks constructed for bacteria and fungi showed that disturbed communities were characterized by more connected and tightly clustered network topologies, indicating that disturbance alters not only community composition but also potential ecological interactions among taxa. Although bacteria and fungi displayed different long-term responses to forest disturbance, our results demonstrate clear responses of important bacterial and fungal functional groups (e.g., nitrifying bacteria and mycorrhizal fungi), and suggest that both microbial groups play key roles in the long-term alterations to biogeochemical processes observed following forest disturbance in the region.

Ciguatoxin Occurrence in Food-Web Components of a Cuban Coral Reef Ecosystem: Risk-Assessment Implications

In Cuba, ciguatera poisoning associated with fish consumption is the most commonly occurring non-bacterial seafood-borne illness. Risk management through fish market regulation has existed in Cuba for decades and consists of bans on selected species above a certain weight; however, the actual occurrence of ciguatoxins (CTXs) in seafood has never been verified. From this food safety risk management perspective, a study site locally known to be at risk for ciguatera was selected. Analysis of the epiphytic dinoflagellate community identified the microalga Gambierdiscus. Gambierdiscus species included six of the seven species known to be present in Cuba (G. caribaeus, G. belizeanus, G. carpenteri, G. carolinianus, G. silvae, and F. ruetzleri). CTX-like activity in invertebrates, herbivorous and carnivorous fishes were analyzed with a radioligand receptor-binding assay and, for selected samples, with the N2A cell cytotoxicity assay. CTX activity was found in 80% of the organisms sampled, with toxin values ranging from 2 to 8 ng CTX3C equivalents g⁻¹ tissue. Data analysis further confirmed CTXs trophic magnification. This study constitutes the first finding of CTX-like activity in marine organisms in Cuba and in herbivorous fish in the Caribbean. Elucidating the structure–activity relationship and toxicology of CTX from the Caribbean is needed before conclusions may be drawn about risk exposure in Cuba and the wider Caribbean.

Effect of temperature on growth, gene expression, and aflatoxin production by Aspergillus nomius isolated from Brazil nuts

Aspergillus nomius is a potent producer of aflatoxins B and G and is one of the most common species of fungi found in Brazil nuts. Temperature is considered a major abiotic factor that influences fungal colonization and aflatoxin production in nuts during pre- and post-harvest. Therefore, assessment of the response of aflatoxigenic species to different temperatures is important to add information about the understanding of aflatoxin production by Aspergillus nomius and may help in the development of new strategies to prevent aflatoxin contamination. The aim of this study was to evaluate the effect of temperature (25, 30, and 35 °C) on the radial growth, aflatoxin production (B and G), and aflatoxin gene expression of seven A. nomius strains isolated from Brazil nuts. The optimal temperature for growth was 30 °C and was also the best condition for the expression of the aflR, aflD, and aflQ genes. However, maximum production of aflatoxins B and G occurred at 25 °C. Interestingly, high expression of the structural gene aflQ was observed in the maximum aflatoxin production condition (25 °C). The present study demonstrates that temperature may influence aflatoxin production by A. nomius. The combination of molecular and physiological data aids the understanding of the aflatoxigenic species response to different temperatures and can assist in predicting the driving environmental factors that influence aflatoxin contamination of Brazil nuts.

Filtering maxRatio results with machine learning models increases quantitative PCR accuracy over the fit point method

With qPCR reaching thousands of reactions per run, assay validation needs automation. We applied support vector machine to qPCR analysis and we could identify reactions with 100% accuracy, dispensing them from further validation. We achieved a greatly reduced workload that could improve high-throughput qPCR analysis.

DNase I Chromatin Accessibility Analysis

Chromatin consists of compacted DNA in complex with proteins and contributes to the organization of DNA and its stability. Furthermore, chromatin plays key roles in regulating cellular processes such as DNA replication, transcription, DNA repair, and mitosis. Chromatin assumes more compact (inaccessible) or decondensed (accessible) conformations depending on the function that is being supported in the genome, either locally or globally. The activity of nucleases has been used previously to assess the accessibility of specific genomic regions in vitro, such as origins of replication at varying points in the cell cycle. Here, we provide an assay to determine the accessibility of specific human genomic regions (example used herein: Lamin B2 origin of DNA replication) by measuring the effect of DNase I nuclease on qPCR signal from the studied site. This assay provides a powerful method to interrogate the molecular mechanisms that regulate chromatin accessibility, and how these processes affect various cellular functions involving the human genome that require manipulation of chromatin conformation.

Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis

Single-cell transcriptional profiling has become a widespread tool in cell identification, particularly in the nervous system, based on the notion that genomic information determines cell identity. However, many cell-type classification studies are unconstrained by other cellular attributes (e.g., morphology, physiology). Here, we systematically test how accurately transcriptional profiling can assign cell identity to well-studied anatomically and functionally identified neurons in 2 small neuronal networks. While these neurons clearly possess distinct patterns of gene expression across cell types, their expression profiles are not sufficient to unambiguously confirm their identity. We suggest that true cell identity can only be determined by combining gene expression data with other cellular attributes such as innervation pattern, morphology, or physiology.

Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling—RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.

Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition

Alfalfa (Medicago sativa L.) silage (AS) is an important feedstuff in ruminant nutrition. However, its high non-protein nitrogen content often leads to poor ruminal nitrogen retention. Various pre-ensiling treatments differing with respect to dry matter concentrations, wilting intensities and sucrose addition have been previously shown to improve the quality and true protein preservation of AS, and have substantial effects on in vitro ruminal fermentation of the resulting silages. However, it is unknown how these pre-ensiling treatments affect the ruminal microbiota composition, and whether alterations in the microbiota explain previously observed differences in ruminal fermentation. Therefore, during AS incubation in a rumen simulation system, liquid and solid phases were sampled 2 and 7 days after first incubating AS, representing an early (ET) and late (LT) time point, respectively. Subsequently, DNA was extracted and qPCR (bacteria, archaea, and anaerobic fungi) and prokaryotic 16S rRNA gene amplicon sequence analyses were performed. At the ET, high dry matter concentration and sucrose addition increased concentrations of archaea in the liquid phase (P = 0.001) and anaerobic fungi in the solid phase (P < 0.001). At the LT, only sucrose addition increased archaeal concentration in the liquid phase (P = 0.014) and anaerobic fungal concentration in the solid phase (P < 0.001). Bacterial concentrations were not affected by pre-ensiling treatments. The prokaryotic phylogenetic diversity index decreased in the liquid phase from ET to LT (P = 0.034), whereas the solid phase was not affected (P = 0.060). This is suggestive of a general adaption of the microbiota to the soluble metabolites released from the incubated AS, particularly regarding the sucrose-treated AS. Redundancy analysis of the sequence data at the genus level indicated that sucrose addition (P = 0.001), time point (P = 0.001), and their interaction (P = 0.001) affected microbial community composition in both phases. In summary, of the pre-ensiling treatments tested sucrose addition had the largest effect on the microbiota, and together with sampling time point affected microbiota composition in both phases of the rumen simulation system. Thus, microbiota composition analysis helped to understand the ruminal fermentation patterns, but could not fully explain them.

A practical method for assessing infectious laryngotracheitis vaccine take in broilers following mass administration in water: Spatial and temporal variation in viral genome content of poultry dust after vaccination

Infectious laryngotracheitis is an important disease of chickens caused by infectious laryngotracheitis virus (ILTV). Outbreaks commonly occur in meat chicken flocks and mass vaccination with live attenuated vaccines, usually in water, is used to control the disease in these populations. Vaccination with live virus via water and nipple drinkers requires stringent adherence to protocols to ensure success, but vaccine administration monitoring is not currently assessed due to a lack of economically viable methods. Vaccinal ILTV has been shown to be detectable in dust in experimental studies and has potential as a method of assessing vaccination success. However, the pattern of vaccinal ILTV detection in dust following vaccination under commercial conditions has not been defined. We report the longitudinal profile of ILTV genome copies (GC) in poultry house dust collected on settle plates following vaccination of 8 flocks of commercial meat chickens on four farms. ILTV GC was enumerated using quantitative real-time polymerase chain reaction (qPCR). There was considerable variation between flocks in the levels of ILTV GC detected post vaccination and this variation was significantly associated with vaccine take measured in individual birds in a companion study. There was no effect of sampling location on ILTV GC in dust but the amount of dust collected was greater in locations closer to the exhaust fans in artificially ventilated houses. Results indicate that measurement of ILTV GC in single or pooled dust samples at 7-8 days post vaccination enables detection of poor vaccine takes and provides a practical means of monitoring ILT vaccination.

Effects of nebulized dexamethasone on the respiratory microbiota and mycobiota and relative equine herpesvirus-1, 2, 4, 5 in an equine model of asthma

Background

Prolonged exposure to environmental antigens or allergens elicits an immune response in both healthy horses and those with mild asthma. Corticosteroids often are used to treat lower airway inflammation.

Objective

To investigate the changes in equine herpesvirus (EHV)‐1,2,4,5 glycoprotein B gene expression and changes in respiratory bacterial and fungal communities after nebulized dexamethasone treatment of horses with asthma.

Animals

Horses with naturally occurring mild asthma (n = 16) and healthy control horses (n = 4).

Methods

Prospective, randomized, controlled, blinded clinical trial. Polymerase chain reaction amplification of EHV‐1,2,4,5 in bronchoalveolar lavage fluid, and 16S (microbiome) and ITS2 (mycobiome) genes with subsequent sequencing was performed on DNA extracted from nasal swabs and transendoscopic tracheal aspirates before and after 13 days treatment with nebulized dexamethasone (15 mg q24h) and saline (control).

Results

Nebulized dexamethasone treatment decreased microbial diversity; relative abundance of 8 genera in the upper respiratory tract were altered. For both the microbiota and the mycobiota, environment had a dominant effect over treatment. Alternaria, an opportunistic pathogen and allergen in humans recognized as a risk factor for asthma, asthma severity, and exacerbations, was increased with treatment. Treatment affected relative quantification of the equine gamma herpesviruses (EHV‐2 and ‐5); EHV‐2 DNA levels increased and those of EHV‐5 decreased.

Conclusions

Nebulized dexamethasone treatment affected the upper respiratory tract microbiota, but not the mycobiota, which was overwhelmed by the effect of a sustained dusty environment.

Challenges and standardization of microRNA profiling in serum and cerebrospinal fluid in dogs suffering from non-infectious inflammatory CNS disease

Non-infectious inflammatory (NII) central nervous system (CNS) conditions are primarily diagnosed by the demonstration of inflammatory changes in the cerebrospinal fluid (CSF). However, less-invasive methods and peripheral biomarkers are desired. Changes in circulating microRNA (miRNA), which are short non-coding regulatory RNAs, may serve as biomarkers of disease. The aim of this pilot study was to investigate selected miRNAs in serum and CSF, hypothesizing that the levels of specific miRNAs in serum correlate with their presence in CSF, and that changes in serum miRNAs levels may reflect CNS disease. We profiled serum and CSF samples using quantitative real-time PCR (qPCR) searching for selected and previously profiled miRNAs in serum (let-7a, let-7c, miR-15b, miR-16, miR-21, miR-23a, miR-24, miR-26a, miR-146a, miR-155, miR-181c and miR-221-3p) and in CSF (let-7c, miR-16, miR-21, miR-24, miR-146a, miR-155, miR-181c and miR-221-3p) from 13 dogs with NII CNS disease and six control dogs. We demonstrated the presence of several miRNAs in CSF (let-7c and miR-21 dominating) and serum (miR-23a and miR-21 dominating). However, we generally failed to reproduce consistent results in CSF samples due to several reasons: unacceptable PCR efficiency, a wide variation between cDNA replicates and/or no-amplification in qPCR suggesting very low levels of the investigated miRNAs in canine CSF. Serum samples performed better, and 10 miRNAs qPCR assays were qualified for analysis. We were nevertheless unable to detect a difference in the expression of miRNA levels between cases and controls. Moreover, we could not confirm the results of recent miRNA investigations of canine CNS diseases. We believe that these disagreements highlight the significant effect of methodological/analytical variation, rather than the incapacity of circulating miRNAs as biomarkers of CNS disease. A secondary aim was therefore to communicate methodological challenges in our study and to suggest recommendations for circulating miRNA profiling, including pre-, post- and analytical methods based on our experience, in order to reach reproducible and comparable results in veterinary miRNA research.

Effect of tetracycline treatment regimens on antibiotic resistance gene selection over time in nursery pigs

Background

The majority of antimicrobials given during the production of pigs are given to nursery pigs. The influence of antimicrobial use on the levels of antimicrobial resistant (AMR) genes is important to quantify to be able to assess the impact of resistance on the food chain and risk to human and animal health.

Results

This study investigated the response on the levels of nine AMR genes to five different treatment strategies with oxytetracycline, and the dynamics of gene abundance over time by following 1167 pigs from five different farms in Denmark.

The results showed no significant difference between treatments and an increase in abundance for the efflux pump encoding tet(A) gene and the genes encoding the ribosomal protection proteins tet(O) and tet(W) tetracycline resistant genes following treatment, while tet(M) showed no response to treatment. However, it was also observed that the levels of tet(O), tet(W), and ermB in some farms would drift more over time compared to a single treatment-course with antibiotic.

Conclusion

This study underlines the large variation in AMR levels under natural conditions and the need for increased investigation of the complex interactions of antimicrobial treatment and other environmental and managerial practices in swine production on AMR gene abundance.

Multiple gene expression profiling suggests epithelial dysfunction in polypoid chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disorder resulting from a complex gene-environment interaction. Although its aetiology remains elusive, numerous studies reported gene expression alterations of factors apparently implicated in all aspects of the inflammatory response. However, most investigations are limited, unconfirmed analyses of a single gene. Moreover, studies concerning multiple gene expression analyses, usually on inflammatory mediators (e.g. cytokines), show contrasting outcomes in part due to use of heterogeneous samples or methodologies with limited power. In this scenario, our goal was to simultaneously evaluate the expression of a panel of selected genes (AQP5, MUC5AC, CAV1, LTF, COX2, PGDS, TNFα, TGFβ1, MGB1) potentially involved in CRS inflammatory mechanisms. While most of the samples collected were excluded from the analysis because of poor quality RNA, we were able to demonstrate statistically significant downregulation of the AQP5, CAV1, LTF, MGB1 genes in a specific subset of polypoid CRS (patients without typical comorbidities), which might suggest relevant underlying epithelial dysfunction. Further studies are needed to enrich our knowledge on the pathogenesis of CRS. Forthcoming approaches might utilise next-generation RNA sequencing and comprehensive bioinformatics analyses to better characterise the transcriptome profiles of CRS endotypes.

A mathematical modeling approach to the quantification of lactic acid bacteria in vacuum-packaged samples of cooked meat: Combining the TaqMan-based quantitative PCR method with the plate-count method

The TaqMan-based quantitative Polymerase Chain Reaction (qPCR) method and the Plate Count (PC) method are both used in combination with primary and secondary mathematical modeling, to describe the growth curves of Leuconostoc mesenteroides and Weissella viridescens in vacuum-packaged meat products during storage under different isothermal conditions. Vacuum-Packaged Morcilla (VPM), a typical cooked blood sausage, is used as a representative meat product, with the aim of improving shelf-life prediction methods for those sorts of meat products. The standard curves constructed by qPCR showed good linearity between the cycle threshold (C_T) and log₁₀ CFU/g, demonstrating the high precision and the reproducible results of the qPCR method. The curves were used for the quantification of L. mesenteroides and W. viridescens in artificially inoculated VPM samples under isothermal storage (5, 8, 13 and 18 °C). Primally, both the qPCR and the PC methods were compared, and a linear regression analysis demonstrated a statistically significant linear correlation between the methods. Secondly, the Baranyi and Roberts model was fitted to the growth curve data to estimate the kinetic parameters of L. mesenteroides and W. viridescens under isothermal conditions, and secondary models were used to establish the dependence of the maximum specific growth rate on the temperature. The results proved that primary and secondary models were adequate for describing the growth curves of both methods in relation to both bacteria. In conclusion, the results of all the experiments proved that the qPCR method in combination with the PC method can be used to construct microbial growth kinetics and that primary and secondary mathematical modeling can be successfully applied to describe the growth of L. mesenteroides and W. viridescens in vacuum-packaged morcilla and, by extension, other cooked meat products with similar characteristics.

Evaluation and quantification of antimicrobial residues and antimicrobial resistance genes in two Italian swine farms

Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances in bacteria. The occurrence of ARGs in Italian swine farming - which has specific characteristics - was investigated in order to explore resistance spread dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.