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International audience ; In French Guiana, cutaneous leishmaniasis is highly endemic, whereas no autochthonous case of visceral leishmaniasis have been reported so far. However, due to its proximity to Brazil which is highly endemic for visceral leishmaniasis, and the high transboundary population flow, an epidemiological challenge could arise at any time. As an overseas department and region and the largest outermost region of the European Union, epidemiological surveillance of visceral leishmaniasis is of great importance. Our study aimed to investigate the presence of Leishmania spp. in domestic (dogs) and sylvatic (bats) animals from French Guiana. Over the 2008-2018 period, samples from 349 animals were collected. They included blood from 179 autochthonous dogs and 59 bats, spleen samples from 33 bats and, blood from 78 military working dogs (MWD) collected before their departure from continental France and at the end of their four-month stay in French Guiana. Samples were screened using real-time polymerase chain reaction (qPCR) assays targeting Leishmania DNA followed by sequencing of 18S rRNA, kDNA and ITS2 genes. L. infantum was detected in 2.3% (8/349) of animals with 1.7% (3/179) of autochthonous dogs, 5.1% (4/78) of MWD returning from French Guiana, whereas they were negative before their departure. One of them dates back to 2012. All these dogs were positive for serological tests. In addition, L. infantum DNA was detectable in one bat spleen sample, belonging to Carollia perspicillata species. We report here for the first time an infection with L. infantum in dogs and bat from French Guiana. Our results suggest the existence of potential reservoir and transmission cycle for visceral leishmaniasis, at least since 2012, which was unknown in this territory until now. Further studies are needed to determine how these animals were infected and which vectors are involved in the transmission in this area. PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.

International audience ; In French Guiana, cutaneous leishmaniasis is highly endemic, whereas no autochthonous case of visceral leishmaniasis have been reported so far. However, due to its proximity to Brazil which is highly endemic for visceral leishmaniasis, and the high transboundary population flow, an epidemiological challenge could arise at any time. As an overseas department and region and the largest outermost region of the European Union, epidemiological surveillance of visceral leishmaniasis is of great importance. Our study aimed to investigate the presence of Leishmania spp. in domestic (dogs) and sylvatic (bats) animals from French Guiana. Over the 2008-2018 period, samples from 349 animals were collected. They included blood from 179 autochthonous dogs and 59 bats, spleen samples from 33 bats and, blood from 78 military working dogs (MWD) collected before their departure from continental France and at the end of their four-month stay in French Guiana. Samples were screened using real-time polymerase chain reaction (qPCR) assays targeting Leishmania DNA followed by sequencing of 18S rRNA, kDNA and ITS2 genes. L. infantum was detected in 2.3% (8/349) of animals with 1.7% (3/179) of autochthonous dogs, 5.1% (4/78) of MWD returning from French Guiana, whereas they were negative before their departure. One of them dates back to 2012. All these dogs were positive for serological tests. In addition, L. infantum DNA was detectable in one bat spleen sample, belonging to Carollia perspicillata species. We report here for the first time an infection with L. infantum in dogs and bat from French Guiana. Our results suggest the existence of potential reservoir and transmission cycle for visceral leishmaniasis, at least since 2012, which was unknown in this territory until now. Further studies are needed to determine how these animals were infected and which vectors are involved in the transmission in this area. PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.

International audience ; In French Guiana, cutaneous leishmaniasis is highly endemic, whereas no autochthonous case of visceral leishmaniasis have been reported so far. However, due to its proximity to Brazil which is highly endemic for visceral leishmaniasis, and the high transboundary population flow, an epidemiological challenge could arise at any time. As an overseas department and region and the largest outermost region of the European Union, epidemiological surveillance of visceral leishmaniasis is of great importance. Our study aimed to investigate the presence of Leishmania spp. in domestic (dogs) and sylvatic (bats) animals from French Guiana. Over the 2008-2018 period, samples from 349 animals were collected. They included blood from 179 autochthonous dogs and 59 bats, spleen samples from 33 bats and, blood from 78 military working dogs (MWD) collected before their departure from continental France and at the end of their four-month stay in French Guiana. Samples were screened using real-time polymerase chain reaction (qPCR) assays targeting Leishmania DNA followed by sequencing of 18S rRNA, kDNA and ITS2 genes. L. infantum was detected in 2.3% (8/349) of animals with 1.7% (3/179) of autochthonous dogs, 5.1% (4/78) of MWD returning from French Guiana, whereas they were negative before their departure. One of them dates back to 2012. All these dogs were positive for serological tests. In addition, L. infantum DNA was detectable in one bat spleen sample, belonging to Carollia perspicillata species. We report here for the first time an infection with L. infantum in dogs and bat from French Guiana. Our results suggest the existence of potential reservoir and transmission cycle for visceral leishmaniasis, at least since 2012, which was unknown in this territory until now. Further studies are needed to determine how these animals were infected and which vectors are involved in the transmission in this area. PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.

International audience ; In French Guiana, cutaneous leishmaniasis is highly endemic, whereas no autochthonous case of visceral leishmaniasis have been reported so far. However, due to its proximity to Brazil which is highly endemic for visceral leishmaniasis, and the high transboundary population flow, an epidemiological challenge could arise at any time. As an overseas department and region and the largest outermost region of the European Union, epidemiological surveillance of visceral leishmaniasis is of great importance. Our study aimed to investigate the presence of Leishmania spp. in domestic (dogs) and sylvatic (bats) animals from French Guiana. Over the 2008-2018 period, samples from 349 animals were collected. They included blood from 179 autochthonous dogs and 59 bats, spleen samples from 33 bats and, blood from 78 military working dogs (MWD) collected before their departure from continental France and at the end of their four-month stay in French Guiana. Samples were screened using real-time polymerase chain reaction (qPCR) assays targeting Leishmania DNA followed by sequencing of 18S rRNA, kDNA and ITS2 genes. L. infantum was detected in 2.3% (8/349) of animals with 1.7% (3/179) of autochthonous dogs, 5.1% (4/78) of MWD returning from French Guiana, whereas they were negative before their departure. One of them dates back to 2012. All these dogs were positive for serological tests. In addition, L. infantum DNA was detectable in one bat spleen sample, belonging to Carollia perspicillata species. We report here for the first time an infection with L. infantum in dogs and bat from French Guiana. Our results suggest the existence of potential reservoir and transmission cycle for visceral leishmaniasis, at least since 2012, which was unknown in this territory until now. Further studies are needed to determine how these animals were infected and which vectors are involved in the transmission in this area. PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.

Although the veterinary profession remains a major actor in any individual or joint action on animal health, it has undoubtedly also become a major actor in public health policies. This significant success is based on several factors: veterinary training which includes public health issues, veterinary networks working with a parallel organisation including breeders and veterinary surgeons associations, integrated scientific and technical backing, and the development of epidemiosurveillance networks. All these aspects were tried and tested and proved their relevance, as shown in at least two recent actions: the fight against transmissible spongiform encephalopathies and the prevention of avian influenza. However, these advantages are burdened by weaknesses which must be overcome to face new health issues, such as the emergence of unknown diseases or the ree-mergence of known diseases. Some of the latter include high-risk major zoonoses, which could lead to epizootics, as well as epidemics or even pandemics. A non-exhaustive analysis of these weaknesses is given here. ; Si la profession vétérinaire reste un acteur important de toute action individuelle ou collective de santé animale, elle est devenue sans conteste un acteur majeur des politiques de santé publique. Des atouts ont permis des succès significatifs : la formation vétérinaire intégrant les problématiques de santé publique, le maillage vétérinaire jumelé à une organisation parallèle des fédérations d'éleveurs et de vétérinaires, un appui scientifique et technique intégré et le développement de réseaux d'épidémio-surveillance. Ils ont été mis à l'épreuve et ont pu démontrer leur pertinence, au moins dans deux actions récentes : la lutte contre les encéphalopathies spongiformes transmissibles et la prévention de l'influenza aviaire. Des faiblesses sont cependant à surmonter, afin de faire face aux nouveaux enjeux sanitaires que représentent l'émergence de maladies inconnues ou la ré-émergence de maladies connues : certaines de ces dernières sont des zoonoses majeures à risque élevé, pouvant être à l'origine non seulement d'épizooties, mais aussi d'épidémies, voire de pandémies. Une analyse non exhaustive de ces faiblesses est présentée.

Trypanosoma brucei gambiense causes human African trypanosomiasis (HAT). Between 1990 and 2015, almost 440000 cases were reported. Large-scale screening of populations at risk, drug donations, and efforts by national and international stakeholders have brought the epidemic under control with <2200 cases in 2016. The World Health Organization (WHO) has set the goals of gambiense-HAT elimination as a public health problem for 2020, and of interruption of transmission to humans for 2030. Latent human infections and possible animal reservoirs may challenge these goals. It remains largely unknown whether, and to what extend, they have an impact on gambiense-HAT transmission. We argue that a better understanding of the contribution of human and putative animal reservoirs to gambiense-HAT epidemiology is mandatory to inform elimination strategies. ; This work was supported by a grant from the Bill & Melinda Gates Foundation ( OPP1150674 ). KSR gratefully acknowledges funding of the NTD Modelling Consortium by the Bill & Melinda Gates Foundation in partnership with the Task Force for Global Health under grant number OPP1053230 . AML, BB, EM, GS, HI, MK, VJ, and VL are supported by TrypanoGen funded by the Wellcome Trust (grant number 099310/Z/12/Z ). NC acknowledges funding from the Bill & Melinda Gates Foundation under grant OPP1156227 . LMF is funded by Fundacao para a Ciencia e Tecnologia ( IF/01050/2014 ). FAO contribution to this study was provided in the framework of the Programme against African Trypanosomosis (PAAT), and supported by the Government of Italy (FAO Project 'Improving food security in sub-Saharan Africa by supporting the progressive reduction of tsetse-transmitted trypanosomosis in the framework of the NEPAD', codes GTFS/RAF/474/ITA and GCP/RAF/502/ITA). The funders had no role in design, decision to publish, or preparation of the manuscript. The views, opinions, assumptions or any other information set out in this article are solely those of the authors. ; Sí

Alien plant and animal hosts play an important role as vectors of dangerous pathogens. However, the knowledge on pathogens of many host species is still limited. To bridge this gap, we collated information on pathogens carried by 118 alien species in Europe in their native and secondary range. In Europe, these species are considered as invasive. Using the dataset we determined most prevailing pathogen groups and plant and animal hosts that carried the highest number of pathogens. The most numerous pathogens were bacteria Xylella fastidiosa (plants) and Rabies virus (animals). The principal pathogen groups among plant hosts were Arthropoda (phylum), Insecta (class) and Hemiptera (order), and among animal hosts – Platyhelminthes (phylum), Trematoda (class) and Plagiorchiida/Strongylida (order). In plants, the highest number of pathogens was recorded for Ambrosia artemisiifolia; in animals, Procyon lotor was the most infested species. Hosts introduced from North America carried the highest numbers of pathogen species; in addition, unintentionally introduced hosts carried more pathogens than those introduced intentionally. We revealed also that the level of infestation differs between the habitats in which the hosts occur. It should be also stressed that in all analyses the number of pathogens increased with the number of publications on the particular host' infestation. The highest number of publications was available for species useful for human, such as Crassostrea gigas. The results demonstrated that there are still significant gaps in the knowledge on the role of other hosts, including invasive ones (e.g., Sciurus niger) in pathogen transmission.

Denne PhD afhandling beskriver udviklingen af en matematisk model, der estimerer det kvantitative bidrag fra fire husdyrreservoirer til forekomsten af Salmonella infektioner hos mennesker i den Europæiske Union. Med henblik på at ekstrapolere resultaterne til lande, hvor datatilgængeligheden er mindre, præsenteres desuden en alternativ og mere udforskende metode baseret på ekspertvurderinger. Sidstnævnte skal ses som et første skridt på vejen til at kvantificere betydningen af forskellige smitteilder for human salmonellose i et mere globalt perspektiv. Human salmonellose i EU blev ved hjælp af en matematisk model tilskrevet udlandsrejse, fødevarebårne udbrud samt de fire husdyrreservoirer: svin, slagtekyllinger, kalkuner og konsumægsproducerende høner. Modellen inkluderede data fra 24 lande. Metoden kræver data vedr. Salmonella forekomst og serotypefordeling i husdyr, rapporterede infektioner hos mennesker, oplysninger om mulig erhvervelse af infektionen i udlandet (herfra benævnt "rejseinformation"), forekomst af fødevarebårne udbrud samt kilderne til disse, samt mængden af kød eller æg fra husdyrreservoirerne pr. land, som er til rådighed for forbrugerne i de enkelte lande. Datahåndtering, -analyse og -validering vurderedes at være af stor betydning for resultaternes kvalitet, og der blev derfor lagt vægt på at beskrive, hvad der kræves for at frembringe et datasæt med standardiserede oplysninger for alle lande (Manuskript I). Data om rapporterede Salmonella infektioner hos mennesker blev skaffet fra det Europæiske Center for Sygdomsforebyggelse og Kontrol (ECDC) via Den Europæiske Fødevaresikkerhedsautoritet (EFSA). Salmonella forekomsten i de fire husdyrarter blev indhentet fra de EU-dækkende baseline undersøgelser (BS) rapporteret af EFSA og blev, når det var nødvendigt, suppleret med oplysninger fra EU's Zoonoserapport (EUSR) ligeledes publiceret af EFSA. Oplysninger om fødevarebårne Salmonella udbrud blev også leveret af EFSA. Mængden af animalske fødevarer til rådighed til forbrug blev estimeret på baggrund af data om fødevareproduktion og samhandel indhentet fra det europæiske statistisk kontor, EUROSTAT. Disse data blev suppleret med oplysninger fra sammenslutningen af fjerkræslagterier i EU, AVEC. Der var visse begrænsninger i data, som for nogle lande inkluderede manglende deltagelse i en af baseline undersøgelserne, manglende indberetning af fødevarebårne udbrud eller rejseinformation, manglende indberetning af serotype specifikke data, manglende indberetning af case-baserede data og manglende tilgængelighed af data i EUROSTAT. For at standardisere de foreliggende oplysninger, blev det antaget, at human tilfælde uden rejseinformation var indenlandsk erhvervede, og human tilfælde uden specifik serotype information blev tildelt en serotype i forhold til serotypefordelinger observeret i det samme datasæt eller fra andre referencedata. Manglende EUROSTAT data blev estimeret baseret på tidligere år, og manglende baseline data blev, hvor det var muligt, erstattet af data fra EUSR. For nogle lande var datamængden og – kvaliteten for ringe til, at de kunne indgå i modellen uden at kompromittere validiteten af resultaterne. Det endelige datasæt omfattede Østrig, Belgien, Cypern, Tjekkiet, Danmark, Estland, Finland, Frankrig, Tyskland, Grækenland, Ungarn, Irland, Italien, Letland, Litauen, Luxembourg, Holland, Polen, Portugal, Slovakiet, Slovenien, Spanien, Sverige og Storbritannien. Tre lande blev inkluderet i den indledende analyse, men ikke i det endelige datasæt. Det var Bulgarien, hvor 100% af de humane tilfælde ikke havde oplysning om serotype; Rumænien, som kun deltog i én baseline undersøgelse og ikke havde andre relevante data, og desuden havde en stor andel human tilfælde uden serotypeoplysning; samt Norge, der ikke er en del af EU og ikke rapporterer til EUROSTAT (Manuskript I). Den Bayesiansk model, som blev anvendt til den matematiske analyse, sammenligner serotypefordelingen i mennesker med serotypefordelingen i husdyrreservoirerne. Modellen estimerer antallet af tilfælde af human salmonellose i de 24 lande fra hvert af disse reservoirer, samt fra rejser og udbrud baseret på de ovennævnte data (Manuskript II). Konsumægsproducerende høner (dvs. æg) blev anslået til at være den vigtigste kilde til salmonellose hos mennesker i EU med 48,1% (95% Credibility Interval (CI) 47,5 til 48,8%) af tilfældene, efterfulgt af svin (29,6%, 95% CI 28,9-30,3%). Kalkuner og slagtekyllinger blev estimeret til at være mindre betydningsfulde kilder og bidrog med hhv. 4,4% (95% CI 4,2-4,7%) og 3,7% (95% CI 3,4-4,0%) af tilfældene. I alt blev 10,2% af alle Salmonella tilfældene rapporteret som værende rejserelaterede, og 3,9% af tilfælde blev rapporteret som værende en del af et udbrud med ukendt kilde. S. Enteritidis var den hyppigste serotype og ansvarlig for 95,9% af de tilfælde som blev tilskrevet æg, 56,9% af tilfældene tilskrevet slagtekyllinger, 30,4% af de kalkunrelaterede tilfælde og 28,3% af de svinerelaterede tilfælde. Den vigtigste serotype i svin var S. Typhimurium, som udgjorde 63,1% af de svinerelaterede tilfælde. Landespecifikke resultater viste, at æg var den vigtigste kilde til salmonellose i 13 lande (Østrig, Tjekkiet, Estland, Tyskland, Grækenland, Ungarn, Letland, Litauen, Luxembourg, Slovenien, Slovakiet, Spanien og Storbritannien), mens svin var den store bidragyder i otte (Belgien, Cypern, Finland, Frankrig, Irland, Italien, Polen og Sverige). I Finland og Sverige kunne hovedparten af salmonellainfektionerne relateres til udlandsrejse. Rejse var også en vigtig kilde i Irland, Storbritannien og Danmark om end i lavere grad. I Holland var andelen af infektioner fra æg og svin omtrent det samme. I Danmark blev den vigtigste fødevarekilde estimeret at være kalkun, mens slagtekyllinger var den største kilde i Portugal (Manuskript II). Danske strategier for risikohåndtering af Salmonella i jord-til-bord kæden omfatter anvendelse af en såkaldt smittekilderegnskabsmodel, det estimerer bidraget fra de vigtigste animalske fødevarekilder til infektioner hos mennesker i Danmark. Det danske modelkoncept dannede grundlag for EU-modellen beskrevet i Manuskript II. Som en del af valideringsprocessen af EU-modellen, blev resultaterne for Danmark i EU-modellen sammenlignet med dem, der opnås under brug af den danske model i samme periode (Manuskript III). Den danske model pegede på svinekød (9,3% af tilfælde), som den vigtigste kilde til salmonellose i perioden, efterfulgt af æg (7,5% af tilfælde) og slagtekyllinger (4,7% af tilfælde), mens EU-modellen til sammenligning tilskrev 15,6% af tilfælde til svin, 15,1% til kalkuner, 10,5% til æg og 2,8% til slagtekyllinger. Andelen af rejserelaterede tilfælde var 30,6% i den danske model mod 18,2% i EU-modellen. Infektioner, der ikke kunne henføres til nogen bestemt kilde, svarede til 16,7% af tilfældene i den danske model og 14,1% i EU-modellen. De observerede uoverensstemmelser kan forklares ved forskelle i modellernes struktur og de grundlæggende antagelser: a) en andel af tilfældene uden rejseinformation tilskrives rejse i den danske model, hvilket baseres på proportionen af rejsetilfælde observeret for tilfælde med fuld rejseinformation; i EU-modellen antages det, at ingen rejseinformation er lig med ingen rejserelation, da mange lande ikke skelner mellem "nej til rejse" og "ingen rejseinformation", b) den danske model anvender Salmonella typefordelinger baseret på både serotypning, fagtypning og resistensbestemmelse, mens EU-modellen kun anvender serotypefordelinger, fordi mere detaljerede typningsdata ikke var til rådighed for de fleste lande og/eller kilder; dette giver en mere specifik fordeling af tilfælde til de rigtige kilder i den danske model; c) et større antal smittekilder i den danske model giver flere muligheder for specifik fordeling af tilfælde, hvilket formentlig resulterer i en mere korrekt fordeling af kilder; d) den danske model anvender officielle data om mængden af dansk producerede og importerede fødevarer til rådighed til forbrug, men tager i modsætning til EU-modellen ikke hensyn til den mængde, der importeres specifikt fra hvert land, hvilket resulterer i at bidrag fra lande med høje Salmonella forekomster underestimeres i den danske model (manuskript III). Alt taget betragtning, så rangerer de to modeller tre ud af de fire kilder i samme rækkefølge, og mens EU-modellen må anses for at være nyttig for lande, som ikke umiddelbart har den datadetaljeringsgrad som findes i Danmark, vil Danmark kunne drage større nytte af at anvende landespecifikke importdata frem for at anvende resultaterne fra EU-modellen. Det sidste kapitel beskriver en alternativ metode til at estimere kilder til human salmonellose for Tjekkiet, Bulgarien, Norge og Rumænien, hvoraf de tre sidstnævnte ikke var inkluderet i EU modellen pga. manglende data. Ved hjælp af clusteranalyser blev 28 lande grupperet efter nogle udvalgte variable, som karakteriserer landenes sociale og økonomiske status, den animalske husdyrproduktion samt kostvaner. Hvis data var tilgængelige, blev variable som afspejler forekomsten af Salmonella hos mennesker og husdyr også inddraget. Resultaterne af analyserne blev fremlagt et panel af eksperter med ekspertise indenfor fødevaresikkerhed, epidemiologi og risikomodellering. Disse blev bedt om at komme med estimater for den relative betydning af Salmonella smittekilder for de førnævnte lande, baseret på disses lighed med lande, for hvilke resultater allerede forelå dvs. på baggrund af resultater fra EU-modellen. Eksperterne blev også bedt om at evaluere metodens egnethed og anvendeligheden af resultaterne. Eksperternes individuelle estimater blev evalueret dels ved en sammenligning med de tjekkiske resultater, som var til rådighed fra EU-modellen, men også i forhold til estimaternes ensartethed og usikkerhedsintervallerne mellem de forskellige estimater fra samme ekspert og imellem eksperterne i panelet. Evalueringen resulterede i, at svarene fra fem ud af de syv respondenter blev bibeholdt i de endelige analyser. Selv om panelet angav estimater for Tjekkiet som ikke var identiske med dem fra EU-modellen, var der enighed om rækkefølgen af betydningen af de animalske kilder, og der var enighed i panelet om samme rækkefølge. Det vurderes derfor, at metoden med nogle justeringer, kan være nyttig til at prioritere målrettet Salmonella kontrol i lande uden tilstrækkelige data til en mere datadrevet fremgangsmåde. På sigt kan metoden måske bruges til at identificere "surrogatlande," hvorfra prævalensdata kan "lånes" og anvendes i en matematisk model baseret på sammenligning af Salmonella typer. Dette PhD projekt har fremlagt resultater for et Europæisk smittekilderegnskab for Salmonella, samt evalueret de anvendte metoder og fremkommet med løsninger til, hvordan man kan håndtere manglende eller utilstrækkelige data i lignende undersøgelser. Projektet har også opnået resultater, som kan lægge grunden for fremtidige forsøg på at udarbejde Salmonella smittekilderegnskaber i et mere globalt perspektiv. ; This thesis presents a mathematical modeling approach to estimate the contribution of four animal reservoirs of the food chain to the occurrence of salmonellosis cases in humans in the European Union. In addition, an alternative and more explorative approach based on expert elicitation is attempted in order to extrapolate results to countries with less data availability, as a first step to perform source attribution of Salmonella in a more global perspective. Cases of foodborne salmonellosis in humans were attributed to travel, outbreaks and four animal reservoirs, namely pigs, broilers, turkeys and laying hens, using a Bayesian model based on microbial subtyping in 24 countries of the European Union. The chosen approach is recognized as data intensive, requiring numbers for Salmonella occurrence in food-producing animals, reported human cases, information on possibility of infection abroad (from here on referred to as "travel information"), human cases originating from outbreaks with and without a confirmed source and amounts of the meat or eggs of each animal reservoir originating from each country and available for consumption in each country. Thus, special data management, analysis and validation was required to produce a dataset containing standardized information for all countries (Manuscript I). Data on reported human cases were provided by the European Centre for Disease Prevention and Control (ECDC) through the European Food Safety Authority (EFSA). Salmonella prevalences in animals were obtained from the EU-wide baseline studies (BS) conducted by EFSA and complemented where necessary with information found in the European Union Summary Report (EUSR), as published by EFSA. Information on outbreaks was also provided by EFSA. The amount of food available for consumption was calculated based on trade data obtained from the European Statistical Office (EUROSTAT) and complemented with information from the Association of Poultry Processors and Poultry Trade in the European Union Countries (AVEC). Common limitations included non-participation in all BS, non-reporting of outbreaks or travel information, non-reporting of serovar-specific information, non-reporting of case-based data and non-availability of trade data on EUROSTAT. In order to standardize the information available, cases without travel information were assumed to be domestic; cases without specific serovar information were redistributed according to serovar proportions observed in the same dataset or other reference documents; missing trade information was estimated based on previous years, and non-participation in a BS was supplied, where possible, with data from the EUSR. When the lack of original data was considered too extreme to the point of compromising the attribution results, countries were excluded. The resulting dataset comprised Austria, Belgium, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxembourg, the Netherlands, Poland, Portugal, Slovakia, Slovenia, Spain, Sweden and the United Kingdom. Three countries were included in the initial analysis, but were excluded from the final dataset. Those were: Bulgaria, which presented 100% of human cases without serovar detailing; Romania, which only participated in one BS and had not enough surrogate data to be retrieved from the EUSR, besides reporting a large parcel of cases without serovar information; and Norway, which is not part of the EU and does not report to EUROSTAT (Manuscript I). A Bayesian modeling approach which compares the occurrence of serovars in humans with the occurrence of the same serovars in animals of the food-chain was used to estimate the contribution of each of these reservoirs, travel and outbreaks to the number of human cases of salmonellosis in the 24 countries present in the dataset previously described (Manuscript II). Laying hens (i.e. eggs) were estimated to be the most important source of human salmonellosis at EU level, with 48.1% (95% Credibility Interval (CI) 47.5 – 48.8%) of cases, followed by pigs (29.6%, 95% CI 28.9-30.3%). Turkeys and broilers were estimated to be less important sources of Salmonella, contributing with 4.4% (95% CI 4.2-4.7%) and 3.7% (95% CI 3.4-4.0%), respectively. A total of 10.2% of all salmonellosis cases were reported as being travel-related, and 3.9% of cases were reported as being part of outbreaks with unknown source. S. Enteritidis was the most important serovar in the study, being responsible for 95.9% of cases attributed to laying hens, 56.9% of cases attributed to broilers, 30.4% of turkeys and 28.3% of cases attributed to pigs, for which the main serovar was S. Typhimurium (63.1% of cases attributed to this source). Country-specific results show laying hens as the most important source of salmonellosis in 13 countries (Austria, Czech Republic, Estonia, Germany, Greece, Hungary, Latvia, Lithuania, Luxembourg, Slovenia, Slovakia, Spain and the United Kingdom), whereas pigs were the larger animal contributor in eight (Belgium, Cyprus, Finland, France, Ireland, Italy, Poland and Sweden). In Finland and Sweden the majority of Salmonella infections were estimated to be travel-related. Travel was also an important source in Ireland, the UK and Denmark, although to a lower extent. In the Netherlands, the proportion of disease attributed to layers and pigs were similar. In Denmark, the most important food-animal source was estimated to be turkeys, and broilers were the major source in Portugal. (Manuscript II). Danish strategies for risk management of Salmonella in the farm-to-fork continuum include the routine application of a source attribution model to estimate the contribution of the major animal-food sources to human infections by Salmonella in Denmark. This model concept formed the basis for the model described in Manuscript II. As part of the validation process of the EU model, results for Denmark in the EU model were compared with the ones obtained using the Danish model in the same period (Manuscript III).The Danish model points to pork as the main animal source of human salmonellosis in the period (9.3% of cases), followed closely by table eggs (7.5% of cases) and broilers (4.7% of cases), while the EU model attributed 15.6% to pigs, 15.1% to turkeys, 10.5% to eggs and 2.8% to broilers. Travel-related cases constitute 30.6% in the Danish model and only 18.2% in the EU model. Cases that could not be attributed to any source corresponded to 16.7% in the Danish model and 14.1% in the European model. Discrepancies in numbers are explained by differences in model structure and basic assumptions: a) cases with no travel information in the Danish model are redistributed according to proportions observed in cases with full information; in the EU model, as some countries did not provide any information regarding travel prior to sickness, it had to be assumed that no information means no travel; b) the Danish model uses data subtyped to phage-type level, while the EU model only uses serovar level, as phage-type data in humans and animals was not sufficiently available; this allows the more specific allocation of cases to the right sources; c) the larger number of sources in the Danish model allows more options for specific allocation of cases, presumably resulting in a more correct distribution of cases among sources; d) the Danish model uses official data on amount of domestic and imported food items available for consumption in the country, but does not as opposed to the EU model take into account the amount imported from each country specifically, which results in an underestimation of the contribution from high prevalence countries as compared to the EU model (Manuscript III). All facts considered, the two models rank three out of the four sources in a similar order and, while the EU model is considered useful for countries which cannot readily attain the level of detailing found in Denmark for monitoring and surveillance data, Denmark would benefit more from applying country-specific data than to adopt the results of the EU model. The last chapter presents an alternative approach to obtain results for the Czech Republic, Bulgaria, Norway and Romania, the last three of which were excluded from the EU-model due to insufficient data. Using clustering techniques, 28 countries were grouped according to variables used to characterize them as to social and economic status, animal production characteristics and food consumption patterns. Where available, variables reflecting the occurrence of Salmonella enterica in humans and animals were also used. The results of the analyses were delivered to a panel of experts composed by foodborne disease epidemiologists and risk modelers, which were asked to provide attribution estimates for the aforementioned countries, based on their similarity to countries for which results were previously obtained. Experts were also asked to evaluate the method concerning its utility and applicability of results. Individual estimates were evaluated based on comparison with the Czech results, for which results based on the microbial subtyping model were available, but also in relation to uniformity of guesses and uncertainty intervals among different estimates from the same expert and among all experts in the panel. This evaluation resulted in five out of the seven respondents being maintained in the panel. Although the Czech Republic values obtained did not match the ones observed in the EU study, the order of importance of the animal sources was in agreement between the two studies and there was also a consensus in the panel concerning that order. It is, therefore, believed that with some adjustments, this method may be useful for prioritizing targeted actions for Salmonella control in countries without sufficient data for a traditional approach. Further on, this method may be used to identify "surrogate countries" from where animal prevalence data can be "borrowed" and applied in the traditional microbial subtyping approach in the aforementioned Member States. This PhD project has provided results for a European "source of infection account" for Salmonella, and has at the same time been evaluating the approaches attempted, raising questions and proposing solutions on how to deal with the lack of good-quality data for such studies. The project has also achieved results that may lay the groundwork for future attempts to develop Salmonella source attribution estimates in a more global perspective.

Understanding pathogen exchange among human, wildlife, and livestock populations, and the varying ecological and cultural contexts in which this exchange takes place, is a major challenge. The present review contextualizes the risk factors that result from human interactions with livestock, companion animals, animal exhibits, wildlife through nature-based tourism, and wildlife through consumption. Given their phylogenetic relatedness to humans, primates are emphasized in this discussion; primates serve as reservoirs for several human pathogens, and some human pathogens can decimate wild primate populations. Anthropologists must play a central role in understanding cultural variation in attitudes toward other species as well as perceived risks when interacting with animals. I argue that the remediation of emerging infectious diseases will be accomplished primarily through human behavioral changes rather than through efforts in pathogen discovery. Given the history of human interactions with wildlife, candid discussions on zoonotic diseases will be increasingly important for our combined survival.

After the 2017 Ebola virus (EBOV) outbreak in Likati, a district in northern Democratic Republic of the Congo, we sampled small mammals from the location where the primary case-patient presumably acquired the infection. None tested positive for EBOV RNA or antibodies against EBOV, highlighting the ongoing challenge in detecting animal reservoirs for EBOV.

International audience ; After the 2017 Ebola virus (EBOV) outbreak in Likati, a district in northern Democratic Republic of the Congo, we sampled small mammals from the location where the primary case-patient presumably acquired the infection. None tested positive for EBOV RNA or antibodies against EBOV, highlighting the ongoing challenge in detecting animal reservoirs for EBOV.

International audience ; After the 2017 Ebola virus (EBOV) outbreak in Likati, a district in northern Democratic Republic of the Congo, we sampled small mammals from the location where the primary case-patient presumably acquired the infection. None tested positive for EBOV RNA or antibodies against EBOV, highlighting the ongoing challenge in detecting animal reservoirs for EBOV.

International audience ; After the 2017 Ebola virus (EBOV) outbreak in Likati, a district in northern Democratic Republic of the Congo, we sampled small mammals from the location where the primary case-patient presumably acquired the infection. None tested positive for EBOV RNA or antibodies against EBOV, highlighting the ongoing challenge in detecting animal reservoirs for EBOV.