proteomes Review Applied Proteomics in ‘One Health’ Eleni I. Katsarou 1, Charalambos Billinis 1,2, Dimitrios Galamatis 3, George C. Fthenakis 1, George Th. Tsangaris 4 and Angeliki I. Katsafadou 2,* 1 Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; [email protected] (E.I.K.); [email protected] (C.B.); [email protected] (G.C.F.) 2 Faculty of Public and One Health, University of Thessaly, 43100 Karditsa, Greece 3 Hellenic Agricultural Organization DIMITRA (ELGO DIMITRA), 54248 Thessaloniki, Greece; [email protected] 4 Proteomics Research Unit, Biomedical Research Foundation of Academy of Athens, 11527 Athens, Greece; [email protected] * Correspondence: [email protected] Abstract: ‘One Health’ summarises the idea that human health and animal health are interdependent and bound to the health of ecosystems. The purpose of proteomics methodologies and studies is to determine proteins present in samples of interest and to quantify changes in protein expression during pathological conditions. The objectives of this paper are to review the application of proteomics technologies within the One Health concept and to appraise their role in the elucidation of diseases and situations relevant to One Health. The paper develops in three sections. Proteomics Applications in Zoonotic Infections part discusses proteomics applications in zoonotic infections and explores the use of proteomics for studying pathogenetic pathways, transmission dynamics, diagnostic biomarkers and novel vaccines in prion, viral, bacterial, protozoan and metazoan zoonotic infections. Proteomics Applications in Antibiotic Resistance part discusses proteomics applications in mechanisms of resistance development and discovery of novel treatments for antibiotic resistance. Proteomics Citation: Katsarou, E.I.; Billinis, C.; Applications in Food Safety part discusses the detection of allergens, exposure of adulteration, Galamatis, D.; Fthenakis, G.C.; identification of pathogens and toxins, study of product traits and characterisation of proteins in food Tsangaris, G.T.; Katsafadou, A.I. safety. Sensitive analysis of proteins, including low-abundant ones in complex biological samples, Applied Proteomics in ‘One Health’. will be achieved in the future, thus enabling implementation of targeted proteomics in clinical settings, Proteomes 2021, 9, 31. https:// shedding light on biomarker research and promoting the One Health concept. doi.org/10.3390/proteomes9030031 Keywords: antibiotic resistance; biomarker; food safety; foodomics; One Health; pathogenesis; Academic Editor: Rainer Cramer proteomics; veterinary; zoonotic infection Received: 14 April 2021 Accepted: 25 June 2021 Published: 30 June 2021 1. Introduction Publisher’s Note: MDPI stays neutral The concept of ‘One Health’ was developed at the start of the current century. One with regard to jurisdictional claims in Health is the notion that the health of people, animals and ecosystems are strongly inter- published maps and institutional affil- connected. The definition summarises the idea that human health and animal health are iations. interdependent and bound to the health of the ecosystems in which they exist. The areas of work in which a One Health approach is particularly relevant, include the control of zoonoses, limiting bacterial resistance to antimicrobial agents and food safety [1] (Figure1). Controlling zoonotic pathogens at their animal source is the most effective way of pro- Copyright: © 2021 by the authors. tecting humans from the respective infections; consequently, strategies to control zoonotic Licensee MDPI, Basel, Switzerland. pathogens must be developed to prevent animal and human diseases. Further, prevention This article is an open access article of antibiotic resistance development at the animal level reduces the chances of dissemina- distributed under the terms and tion of resistant strains to humans from animal sources. Indeed, the connection between conditions of the Creative Commons animal health, food of animal origin and human health is more than evident for public Attribution (CC BY) license (https:// opinion and consumers [2]. creativecommons.org/licenses/by/ 4.0/). Proteomes 2021, 9, 31. https://doi.org/10.3390/proteomes9030031 https://www.mdpi.com/journal/proteomes Proteomes 2021, 9, x FOR PEER REVIEW 2 of 39 Proteomes 2021, 9, 31 between animal health, food of animal origin and human health is more than evident2 of for 38 public opinion and consumers [2]. FigureFigure 1. 1. SummarySummary diagram diagram of of the the applications applications of of proteomics methodologies in One Health. TheThe proteome proteome contains contains all all proteins proteins in in a cell a cell or ortissue tissue at any at any one onetime, time, thus thus taking taking into accountinto account all post-translational all post-translational modifications. modifications. The proteome The proteome is dynamic is dynamic and andchanges changes de- pendingdepending on onvarious various physiological physiological and and pathological pathological conditions conditions in in the the tissues tissues of of an an organ- organ- ism.ism. The The purpose purpose of of proteomics proteomics methodologie methodologiess and and studies studies is is to determine the proteins present in a samplesample ofof interestinterest and and to to quantify quantify changes changes in in protein protein expression expression during during various vari- ouspathological pathological conditions conditions [3]. [3]. ProteomicsProteomics includesincludes aa variety variety of technologies,of technologies, which which aredivided are divided in two in major twogroups: major groups:the gel-dependent the gel-dependent and the and gel-independent the gel-independent methods methods [4–7]. [4–7]. Nevertheless, Nevertheless, in both in both ap- approaches,proaches, protein protein identification identification is is performed performed with with mass mass spectrometryspectrometry (MS)(MS) [[6].6]. In In gel- gel- dependentdependent approaches, after isolationisolation ofof thethe proteinsproteins byby two-dimensional two-dimensional gel gel electrophore- electropho- resissis (2-DE), (2-DE), proteins proteins are are identified identified mainly mainly by by MALDI-TOF MALDI-TOF MS/MS MS/MS (matrix-assisted(matrix-assisted laser desorption/ionisation-time of flight tandem mass spectrometry). In gel-independent ap- desorption/ionisation-time of flight tandem mass spectrometry). In gel-independent ap- proaches, the protein content of a sample is identified by MS [8]. Further, proteomics can be proaches, the protein content of a sample is identified by MS [8]. Further, proteomics can applied as bottom-up or top-down approaches [9]. In bottom-up proteomics, pure proteins be applied as bottom-up or top-down approaches [9]. In bottom-up proteomics, pure pro- or complex protein mixtures are subjected to proteolytic cleavage and the peptide products teins or complex protein mixtures are subjected to proteolytic cleavage and the peptide are analysed by MS. In a top-down approach, intact protein ions or large protein fragments products are analysed by MS. Ιn a top-down approach, intact protein ions or large protein are subjected to gas phase fragmentation for MS analysis. Finally, data processing and fragments are subjected to gas phase fragmentation for MS analysis. Finally, data pro- evaluation are performed with bioinformatics approaches [10,11]. Detailed descriptions of cessing and evaluation are performed with bioinformatics approaches [10,11]. Detailed proteomics techniques that can be used in such studies have been presented before [12,13] descriptions of proteomics techniques that can be used in such studies have been pre- and are beyond the scope of this paper. sented before [12,13] and are beyond the scope of this paper. The objectives of this paper are to review the application of proteomics technologies The objectives of this paper are to review the application of proteomics technologies within the One Health concept and to appraise the role of these methodologies in the withinelucidation the One of diseases Health concept and situations and to relevantappraise tothe the role One of Healththese methodologies approach. in the elu- cidation of diseases and situations relevant to the One Health approach. 2. Proteomics Applications in Zoonotic Infections Infections of animal origin that can be transmitted to humans are termed ‘zoonotic infections’ and pose worldwide risks to public health. Other infections that are mainly transmitted from person to person may also circulate in animals or have an animal reservoir, and may cause serious health emergencies (Table S1). These risks increase with global- Proteomes 2021, 9, 31 3 of 38 isation, climate change and changes in human behaviour, giving pathogens numerous opportunities to colonise new territories and evolve into new forms [1]. 2.1. Prion Zoonotic Diseases Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disor- ders characterised by the formation of amyloid aggregates, vacuolation of brain tissue and accumulation in the Central Nervous System (CNS) of a pathological conformer (PrPTSE) of the host-encoded cellular prion protein (PrPC). There are various human or animal prion diseases; the human diseases include kuru, Creutzfeldt–Jakob disease and variant Creutzfeldt–Jakob disease, Gerstmann–Straussler–Scheinker syndrome and fatal familial insomnia; the animal diseases include bovine spongiform encephalopathy, scrapie, chronic wasting disease,