Serum Metabolomic Profiles of Paratuberculosis Infected and Infectious Dairy Cattle by Ambient Mass Spectrometry

A Snapshot, Using a Multi-Omic Approach, of the Metabolic Cross-Talk and the Dynamics of the Resident Microbiota in Ripening Cheese Inoculated with Listeria innocua

Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in laboratory-controlled conditions, the present study evaluated the modulation of the resident microbiota and the changes of metabolite production directly in ripening raw milk cheese inoculated with Listeria innocua strains. Using a proxy of the pathogenic Listeria monocytogenes, we aimed to establish the key microbiota players and chemical signals that characterize Latteria raw milk cheese over 60 days of ripening time. The microbiota of both the control and Listeria-inoculated cheeses was analyzed using 16S rRNA targeted amplicon sequencing, while direct analysis in real time mass spectrometry (DART-HRMS) was applied to investigate the differences in the metabolic profiles of the cheeses. The diversity analysis showed the same microbial diversity trend in both the control cheese and the inoculated cheese, while the taxonomic analysis highlighted the most representative genera of bacteria in both the control and inoculated cheese: Lactobacillus and Streptococcus. On the other hand, the metabolic fingerprints revealed that the complex interactions between resident microbiota and L. innocua were governed by continuously changing chemical signals. Changes in the amounts of small organic acids, hydroxyl fatty acids, and antimicrobial compounds, including pyroglutamic acid, hydroxy-isocaproic acid, malic acid, phenyllactic acid, and lactic acid, were observed over time in the L. innocua-inoculated cheese. In cheese that was inoculated with L. innocua, Streptococcus was significantly correlated with the volatile compounds carboxylbenzaldheyde and cyclohexanecarboxylic acid, while Lactobacillus was positively correlated with some volatile and flavor compounds (cyclohexanecarboxylic acid, pyroxidal acid, aminobenzoic acid, and vanillic acid). Therefore, we determined the metabolic markers that characterize a raw milk cheese inoculated with L. innocua, the changes in these markers with the ripening time, and the positive correlation of flavor and volatile compounds with the resident microbiota. This multi-omics approach could suggest innovative food safety strategies based on the enhanced management of undesirable microorganisms by means of strain selection in raw matrices and the addition of specific antimicrobial metabolites to prevent the growth of undesirable microorganisms.

Empowering veterinary clinical diagnosis in industrial poultry production by ambient mass spectrometry and chemiometrics: a new approach for precise poultry farming

Untargeted metabolomic profiling, by ambient mass spectrometry and chemometric tools, has made a dramatic impact on human disease detection. In a similar vein, this study attempted the translation of this clinical human disease experience to farmed poultry for precise veterinary diagnosis. As a proof of principle, in this diagnostic/prognostic study, direct analysis in real-time high resolution mass spectrometry (DART-HRMS) was used in an untargeted manner to analyze fresh tissues (abdominal fat, leg skin, liver, and leg muscle) of pigmented and non-pigmented broilers to investigate the causes of lack of pigmentation in an industrial poultry farm. Afterwards, statistical analysis was applied to the DART-HRMS data to retrieve the molecular features that codified for 2 broiler groups, that is, properly pigmented and non-pigmented broilers. Higher abundance of oxidized lipids, high abundance of oxidized bile derivatives, and lower levels of tocopherol isomers (Vitamin E) and retinol (Vitamin A) were captured in nonpigmented than in pigmented broilers. In addition, conventional rapid analyses were used: 1) color parameters of the tissues of pigmented and non-pigmented broilers were measured to rationalize the color differences in abdominal fat, leg skin and leg muscle, and 2) macronutrients were determined in broiler leg muscle, to capture a detailed picture of the pathology and exclude other possible causes. In this study, the DART-HRMS system performed well in retrieving valuable chemical information from broilers that explained the differences between the 2 groups of broilers in absorption of xanthophylls and the subsequent lack of proper broiler pigmentation in affected broilers. The results suggest this technology could be useful in providing near real-time feedback to aid in veterinary decision-making in poultry farming.

Association of Mycobacterium avium paratuberculosis serostatus with age at first calving, calving interval, and milk production in dairy cows

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of bovine paratuberculosis, also known as Johne's disease. This infection is responsible for negative effects, ranging from reduction of milk production to reproductive compromise and increased susceptibility to other diseases such as mastitis. Contradictory information on the association between this infection and reproductive performance has been reported in dairy cows. The aim of this work was to investigate associations between individual cow MAP seropositivity and lifetime reproduction and production performance. The MAP serum ELISA (IDEXX MAP Ac) results from all the 13,071 adult cows present on 191 farms and corresponding birth- and calving-date records obtained from the National Association for Genetic Improvement of Dairy Cattle were used. Cows and farms were classified as positive or negative, based on ELISA results. Outcomes assessed were age at first calving (AFC), intercalving intervals (ICI) from first to fourth interval, and average milk production per day of productive cycle (Milk-305/ICI, a ratio between 305-d corrected milk production and the number of days of the respective calving interval). Multilevel mixed models were used to investigate the association of cow MAP status with AFC, ICI, and Milk-305/ICI. Three levels were considered in the models: "measurement occasion," the first level, was nested within cows and cows were nested within farms. The "measurement occasion" is the time point to which all the observed measures (between 2 successive parturitions, such as milk production and somatic cell count) were referred. Our results indicate that MAP-positive cows have a significantly lower 14-d mean AFC than MAP-negative cows. The overall average ICI in our study was 432.5 d (standard deviation: 94.6). The average ICI, from first to fourth, was not significantly affected by MAP seropositivity. No significant effect of MAP positivity was found on the overall ICI. In relation to Milk-305/ICI, MAP-positive cows did not produce significantly less milk than negative cows across their productive lifetime. We observed higher but nonsignificant Milk-305/ICI (kg/d) in MAP-positive cows. In our study, the proportion of MAP-positive cows within lactations remained similar across all lactations, suggesting that seropositivity did not increased drop-off rate.

Lateral-flow assays for bovine paratuberculosis diagnosis

Mycobacterium avium subsp. paratuberculosis (MAP) causes bovine paratuberculosis (PTB). PTB is responsible for significant economic losses in dairy herds around the word. PTB control programs that rely on testing and culling of test-positive cows have been developed. Current diagnostics, such as ELISA for detecting MAP antibodies in serum samples and PCR detecting MAP DNA in feces, have inadequate sensitivity for detecting subclinical animals. Innovative "omics" technologies such as next-generation sequencing (NGS) technology-based RNA-sequencing (RNA-Seq), proteomics and metabolomics can be used to find host biomarkers. The discovered biomarkers (RNA, microRNAs, proteins, metabolites) can then be used to develop new and more sensitive approaches for PTB diagnosis. Traditional approaches for measuring host antibodies and biomarkers, such as ELISAs, northern blotting, quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR), cDNA microarrays, and mass spectrometry are time-consuming, expensive, and sometimes exhibit poor sensitivity. With the rapid development of nanotechnology, low-cost monitoring devices for measuring antibodies against MAP proteins in point-of-care (POC) settings have been developed. Lateral flow assays (LFAs), in particular, are thought to be appropriate for the on-site detection of antibodies to MAP antigens and/or host biomarkers. This review aims to summarize LFAs that have recently been developed to accurately detect antibodies against MAP antigens, as well as the benefits that host biomarkers linked with MAP infection give to PTB diagnosis. The identification of these novel biomarkers could be the basis for the development of new LFAs. The dairy industry and producers are likely to benefit from reliable and rapid technologies capable of detecting MAP infection in situ to establish a quick and sensitive PTB diagnosis.

Pathological, microscopic, and molecular diagnosis of paratuberculosis/John's disease in naturally infected dromedary camel (Camelus dromedarius)

Background and Aim

Paratuberculosis (PTB) or John's disease is a chronic disease of ruminants impeding the reproduction and productivity of the livestock sector worldwide. Since there is a lack of pathological studies explaining the nature and development of the disease in camels, this study aimed to highlight the anatomopathological changes of PTB in camels, which may help in verifying and validating some diagnostic tests used to detect the etiology of the disease in camel tissues.

Materials and Methods

In August 2017, at Alselaa border's Veterinary Clinic of Al Dhafra Region, Western Abu Dhabi, UAE, one imported culled she-camel of 2 years old was subjected to clinical, microscopic, and anatomopathological investigations along with real-time quantitative polymerase chain reaction (q-PCR) to confirm the infection and correlate between clinical signs and pathological lesions of the PTB in dromedary camels.

Results

Clinically, typical clinical signs compliant with the pathognomonic gross and histologic lesions of PTB were seen in naturally infected dromedary camel. As presumptive diagnosis microscopically, acid-fast coccobacillus bacterium clumps were demonstrated in direct fecal smears as well as in scraped mucosal and crushed mesenteric lymph node films, and in histopathological sections prepared from a necropsied animal and stained by Ziehl-Neelsen stain. Free and intracellular acid-fast clump phagosomes were further confirmed as Mycobacterium avium subsp. paratuberculosis by q-PCR.

Conclusion

Clinical signs and pathological lesions of paratuberculosis in a dromedary camel were found to be similar to those of the other susceptible hosts.

Metabolomic changes in lactating multiparous naturally MAP-infected Holstein-Friesian dairy cows suggest changes in mitochondrial energy pathways

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative organism of Johne's Disease, a chronic intestinal infection of ruminants. Infected cows begin shedding MAP within the asymptomatic, subclinical stage of infection before clinical signs, such as weight loss, diarrhoea and reduced milk yields develop within the clinical stages of disease. Herein, we examine the milk metabolomic profiles of naturally MAP-infected Holstein-Friesian cows. The study used biobanked milk samples which were collected 73.4 ± 3.79 (early lactation) and 143 ± 3.79 (mean ± SE) (mid-lactation) days post-calving from 5 MAP-infected and 5 control multiparous cows. The milk metabolome was assessed using flow infusion electrospray high-resolution mass spectrometry (FIE-HRMS) for sensitive, non-targeted metabolite fingerprinting. Metabolite fingerprinting assessments using partial least squares discriminate analyses (PLS-DA) indicated that lactation stage was a larger source of variation than MAP status. Examining each lactation stage separately for changes associated to MAP-infection status identified 45 metabolites, 33 in early lactation and 12 in mid-lactation, but only 6 metabolites were targeted in both stages of lactation. Pathway enrichment analysis suggested that MAP affected the malate-aspartate shuffle during early lactation. Pearson's correlation analysis indicated relationships between milk lactose concentrations in mid-lactation and 6 metabolites that were tentatively linked to MAP-infection status. The targeted metabolites were suggestive of wider changes in the bioenergetic metabolism that appear to be an acceleration of the effects of progressing lactation in healthy cows. Additionally, milk lactose concentrations suggest that MAP reduces the availability of lactose derivatives.

Metabolomic changes in polyunsaturated fatty acids and eicosanoids as diagnostic biomarkers in Mycobacterium avium ssp. paratuberculosis (MAP)-inoculated Holstein-Friesian heifers

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative organism of Johne's disease, a chronic granulomatous enteritis of ruminants. We have previously used naturally MAP-infected heifer calves to document metabolomic changes occurring in MAP infections. Herein, we used experimentally MAP-inoculated heifer calves to identify biomarkers for MAP infections. At 2-weeks of age, 20 Holstein-Friesian (HF) calves were experimentally inoculated with MAP. These calves, along with 20 control calves, were sampled biweekly up to 13-months of age and then monthly up to 19-months of age. Sera were assessed using flow infusion electrospray high-resolution mass spectrometry (FIE-HRMS) on a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer for high throughput, sensitive, non-targeted metabolite fingerprinting. Partial least squares-discriminate analysis (PLS-DA) and hierarchical cluster analysis (HCA) discriminated between MAP-inoculated and control heifer calves. Out of 34 identified metabolites, six fatty acyls were able to differentiate between experimental groups throughout the study, including 8, 11, 14-eicosatrienoic acid and cis-8, 11, 14, 17-eicosatetraenoic acid which were also detected in our previous study and so further suggested their value as biomarkers for MAP infection. Pathway analysis highlighted the role of the alpha-linoleic acid and linoleic acid metabolism. Within these pathways, two broad types of response, with a rapid increase in some saturated fatty acids and some n-3 polyunsaturated fatty acids (PUFAs) and later n-6 PUFAs, became predominant. This could indicate an initial anti-inflammatory colonisation phase, followed by an inflammatory phase. This study demonstrates the validity of the metabolomic approach in studying MAP infections. Nevertheless, further work is required to define further key events, particularly at a cell-specific level.

Ambient mass spectrometry for rapid authentication of milk from Alpine or lowland forage

Metabolomics approaches, such as direct analysis in real time-high resolution mass spectrometry (DART-HRMS), allow characterising many polar and non-polar compounds useful as authentication biomarkers of dairy chains. By using both a partial least squares discriminant analysis (PLS-DA) and a linear discriminant analysis (LDA), this study aimed to assess the capability of DART-HRMS, coupled with a low-level data fusion, discriminate among milk samples from lowland (silages vs. hay) and Alpine (grazing; APS) systems and identify the most informative biomarkers associated with the main dietary forage. As confirmed also by the LDA performed against the test set, DART-HRMS analysis provided an accurate discrimination of Alpine samples; meanwhile, there was a limited capacity to correctly recognise silage- vs. hay-milks. Supervised multivariate statistics followed by metabolomics hierarchical cluster analysis allowed extrapolating the most significant metabolites. Lowland milk was characterised by a pool of energetic compounds, ketoacid derivates, amines and organic acids. Seven informative DART-HRMS molecular features, mainly monoacylglycerols, could strongly explain the metabolomic variation of Alpine grazing milk and contributed to its classification. The misclassification between the two lowland groups confirmed that the intensive dairy systems would be characterised by a small variation in milk composition.

Metabolomic changes in Mycobacterium avium subsp. paratuberculosis (MAP) challenged Holstein-Friesian cattle highlight the role of serum amino acids as indicators of immune system activation

INTRODUCTION

Paratuberculosis, commonly known as Johne's disease, is a chronic granulomatous infection of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Clinical signs, including reduced milk yields, weight loss and diarrhoea, are typically absent until 2 to 6 years post exposure.

OBJECTIVES

To identify metabolomic changes profiles of MAP challenged Holstein-Friesian (HF) cattle and correlate identified metabolites to haematological and immunological parameters.

METHODS

At approximately 6 weeks of age, calves (n = 9) were challenged with 3.8 × 10⁹ cells of MAP (clinical isolate CIT003) on 2 consecutive days. Additional unchallenged calves (n = 9) formed the control group. The study used biobanked serum from cattle sampled periodically from 3- to 33-months post challenge. The assessment of sera using flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) for high throughput, sensitive, non-targeted metabolite fingerprinting highlighted differences in metabolite levels between the two groups.

RESULTS

In total, 25 metabolites which were differentially accumulated in MAP challenged cattle were identified, including 20 which displayed correlation to haematology parameters, particularly monocyte levels.

CONCLUSION

The targeted metabolites suggest shifts in amino acid metabolism that could reflect immune system activation linked to MAP and as well as differences in phosphocholine levels which could reflect activation of the Th1 (tending towards pro-inflammatory) immune response. If verified by future work, selected metabolites could be used as biomarkers to diagnose and manage MAP infected cattle.

Metabolomic Changes in Naturally MAP-Infected Holstein-Friesian Heifers Indicate Immunologically Related Biochemical Reprogramming

Johne’s disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), causes weight loss, diarrhoea, and reduced milk yields in clinically infected cattle. Asymptomatic, subclinically infected cattle shed MAP bacteria but are frequently not detected by diagnostic tests. Herein, we compare the metabolite profiles of sera from subclinically infected Holstein–Friesian heifers and antibody binding to selected MAP antigens. The study used biobanked serum samples from 10 naturally MAP-infected and 10 control heifers, sampled monthly from ~1 to 19 months of age. Sera were assessed using flow infusion electrospray–high-resolution mass spectrometry (FIE–HRMS) on a Q Exactive hybrid quadrupole–Orbitrap mass spectrometer for high-throughput, sensitive, non-targeted metabolite fingerprinting. Partial least-squares discriminant analyses (PLS-DA) and hierarchical cluster analysis (HCA) of the data discriminated between naturally MAP-infected and control heifers. In total, 33 metabolites that differentially accumulated in naturally MAP-infected heifers compared to controls were identified. Five were significantly elevated within MAP-infected heifers throughout the study, i.e., leukotriene B4, bicyclo prostaglandin E2 (bicyclo PGE2), itaconic acid, 2-hydroxyglutaric acid and N6-acetyl-L-lysine. These findings highlight the potential of metabolomics in the identification of novel MAP diagnostic markers and particular biochemical pathways, which may provide insights into the bovine immune response to MAP.