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.

Authenticity assessment of ground black pepper by combining headspace gas-chromatography ion mobility spectrometry and machine learning

Currently, the authentication of ground black pepper is a major concern, creating a need for a rapid, highly sensitive and specific detection tool to prevent the introduction of adulterated batches into the food chain. To this aim, head space gas-chromatography ion mobility spectrometry (HS-GC-IMS), combined with machine learning, is tested in this initial, proof-of-concept study. A broad variety of authentic samples originating from eight countries and three continents were collected and spiked with a range of adulterants, both endogenous sub-products and an assortment of exogenous materials. The method is characterized by no sample preparation and requires 20 min for chromatographic separation and ion mobility data acquisition. After an explorative analysis of the data, those were submitted to two different machine learning algorithms (partial least squared discriminant analysis-PLS-DA and support vector machine-SVM). While the PLS-DA model did not provide fully satisfactory performances, the combination of HS-GC-IMS and SVM successfully classified the samples as authentic, exogenously-adulterated or endogenously-adulterated with an overall accuracy of 90 % and 96 % on withheld test set 1 and withheld test set 2, respectively (at a 95 % confidence level). Some limitations, expected to be mitigated by further research, were encountered in the correct classification of endogenously adulterated ground black pepper. Correct categorization of the ground black pepper samples was not adversely affected by the operator or the time span of data collection (the method development and model challenge were carried out by two operators over 6 months of the study, using ground black pepper harvested between 2015 and 2019). Therefore, HS-GC-IMS, coupled to an intelligent tool, is proposed to: (i) aid in industrial decision-making before utilization of a new batch of ground black pepper in the production chain; (ii) reduce the use of time-consuming conventional analyses and; (iii) increase the number of ground black pepper samples analyzed within an industrial quality control frame.

Thermal desorption direct analysis in real-time high-resolution mass spectrometry and machine learning allow the rapid authentication of ground black pepper and dried oregano: A proof-of-concept study

Thermal desorption direct analysis in real-time high-resolution mass spectrometry (TD-DART-HRMS) approaches have gained popularity for fast screening of a variety of samples. With rapid volatilization of the sample at increasing temperatures outside the mass spectrometer, this technique can provide a direct readout of the sample content with no sample preparation. In this study, TD-DART-HRMS's utility for establishing spice authenticity was examined. To this aim, we directly analyzed authentic (typical) and adulterated (atypical) samples of ground black pepper and dried oregano in positive and negative ion modes. We analyzed a set of authentic ground black pepper samples (n = 14) originating from Brazil, Sri Lanka, Madagascar, Ecuador, Vietnam, Costa Rica, Indonesia, Cambodia, and adulterated samples (n = 25) consisting of mixtures of ground black pepper with this spice's nonfunctional by-products (pinheads or spent) or with different exogenous materials (olive kernel, green lentils, black mustard seeds, red beans, gypsum plaster, garlic, papaya seeds, chili, green aniseed, or coriander seeds). TD-DART-HRMS facilitated the capture of informative fingerprinting of authentic dried oregano (n = 12) originating from Albania, Turkey, and Italy and those spiked (n = 12) with increasing percentages of olive leaves, sumac, strawberry tree leaves, myrtle, and rock rose. A predictive LASSO classifier was built, after merging by low-level data fusion, the positive and negative datasets for ground black pepper. Fusing multimodal data allowed retrieval of more comprehensive information from both datasets. The resultant classifier achieved on the withheld test set accuracy, sensitivity, and specificity of 100%, 75%, and 90%, respectively. On the contrary, the sole TD-(+)DART-HRMS spectra of the oregano samples allowed construction of a LASSO classifier that predicted the adulteration of the oregano with excellent statistical indicators. This classifier achieved, on the withheld test set, 100% each for accuracy, sensitivity, and specificity.

DART-HRMS allows the detection of toxic alkaloids in animal autopsy specimens and guides the selection of confirmatory methods in accidental plant poisoning

BACKGROUND

In cases of suspected animal poisonings or intoxications, there is the need for high-throughput, rapid and accurate analytical tools capable of giving rapid answers and, thus, speeding up the early stages of investigations. Conventional analyses are very precise, but do not meet the need for rapid answers capable of orienting the decisions and the choice of appropriate countermeasures. In this context, the use of ambient mass spectrometry (AMS) screening methods in toxicology laboratories could satisfy the requests of forensic toxicology veterinarians in a timely manner.

RESULTS

As a proof of principle, direct analysis in real time high resolution mass spectrometry (DART-HRMS) was applied to a veterinary forensic case in which 12 of a group of 27 sheep and goats died with an acute neurological onset. Because of evidence in the rumen contents, the veterinarians hypothesized an accidental intoxication after ingestion of vegetable materials. The DART-HRMS results showed abundant signals of the alkaloids calycanthine, folicanthidine and calycanthidine, both in the rumen content and at the liver level. The DART-HRMS phytochemical fingerprinting of detached Chimonanthus praecox seeds was also compared with those acquired from the autopsy specimens. Liver, rumen content and seed extracts were then subjected to LC-HRMS/MS analysis to gather additional insights and confirm the putative assignment of calycanthine anticipated by DART-HRMS. HPLC-HRMS/MS confirmed the presence of calycanthine in both rumen contents and liver specimens and allowed its quantification, ranging from 21.3 to 46.9 mg kg^-1 in the latter. This is the first report detailing the quantification of calycanthine in liver after a deadly intoxication event.

SIGNIFICANCE AND NOVELTY

Our study illustrates the potential of DART-HRMS to offer a rapid and complementary alternative to guide the selection of confirmatory chromatography-MSⁿ strategies in the analysis of autopsy specimens from animals with suspected alkaloid intoxication. This method offers the consequent saving of time and resources over those needed for other methods.

Seasonal Variation in Raw Milk VOC Profile within Intensive Feeding Systems

The study aimed to assess the seasonal variation in raw milk volatile organic compounds (VOCs) from three indoor feeding systems based on maize silage (n = 31), silages/hay (n = 19) or hay (n = 16). After headspace solid-phase microextraction (HS-SPME), VOC profiles were determined by gas chromatography (GC). Chemical and VOC (log₁₀ transformations of the peak areas) data were submitted to a two-way ANOVA to assess the feeding system (FS) and season (S) effects; an interactive principal component analysis (iPCA) was also performed. The interaction FS × S was never significant. The FS showed the highest (p < 0.05) protein and casein content for hay-milk samples, while it did not affect any VOCs. Winter milk had higher (p < 0.05) proportions of protein, casein, fat and some carboxylic acids, while summer milk was higher (p < 0.05) in urea and 2-pentanol and methyl aldehydes. The iPCA confirmed a seasonal spatial separation. Carboxylic acids might generate from incomplete esterification in the mammary gland and/or milk lipolytic activity, while aldehydes seemed to be correlated with endogenous lipid or amino acid oxidation and/or feed transfer. The outcomes suggested that VOCs could be an operative support to trace raw milk for further mild processing.

A multi-center validation study on the discrimination of Legionella pneumophila sg.1, Legionella pneumophila sg. 2-15 and Legionella non-pneumophila isolates from water by FT-IR spectroscopy

This study developed and validated a method, based on the coupling of Fourier-transform infrared spectroscopy (FT-IR) and machine learning, for the automated serotyping of Legionella pneumophila serogroup 1, Legionella pneumophila serogroups 2-15 as well as their successful discrimination from Legionella non-pneumophila. As Legionella presents significant intra- and inter-species heterogeneities, careful data validation strategies were applied to minimize late-stage performance variations of the method across a large microbial population. A total of 244 isolates were analyzed. In details, the method was validated with a multi-centric approach with isolates from Italian thermal and drinking water (n = 82) as well as with samples from German, Italian, French, and British collections (n = 162). Specifically, robustness of the method was verified over the time-span of 1 year with multiple operators and two different FT-IR instruments located in Italy and Germany. Moreover, different production procedures for the solid culture medium (in-house or commercial) and different culture conditions (with and without 2.5% CO₂) were tested. The method achieved an overall accuracy of 100, 98.5, and 93.9% on the Italian test set of Legionella, an independent batch of Legionella from multiple European culture collections, and an extra set of rare Legionella non-pneumophila, respectively.

Rapid, novel screening of toxicants in poison baits, and autopsy specimens by ambient mass spectrometry

Animal poisoning and dissemination of baits in the environment have public health and ethological implications, which can be followed by criminal sanctions for those responsible. The reference methods for the analysis of suspect baits and autopsy specimens are founded on chromatographic-based techniques. They are extremely robust and sensitive, but also very expensive and laborious. For this reason, we developed an ambient mass spectrometry (AMS) method able to screen for 40 toxicants including carbamates, organophosphate and chlorinated pesticides, coumarins, metaldehyde, and strychnine. Spiked samples were firstly purified and extracted by dispersive solid phase extraction (QuEChERS) and then analyzed by direct analysis in real time high-resolution mass spectrometry (DART-HRMS). To verify the performance of this new approach, 115 authentic baits (n = 59) and necropsy specimens (gastrointestinal content and liver, n = 56) were assessed by the official reference methods and combined QuEChERS-DART-HRMS. The agreement between the results allowed evaluation of the performances of the new screening method for a variety of analytes and calculation of the resultant statistical indicators (the new method had overall accuracy 89.57%, sensitivity of 88.24%, and a specificity of 91.49%). Taking into account only the baits, 96.61% of overall accuracy was achieved with 57/59 samples correctly identified (statistical sensitivity 97.50%, statistical specificity 94.74%). Successful identification of the bitter compound, denatonium benzoate, in all the samples that contained rodenticides (28/28) was also achieved. We believe initial screening of suspect poison baits could guide the choice of reference confirmatory methods, reduce the load in official laboratories, and help the early stages of investigations into cases of animal poisoning.