Double-crested cormorants have steadily increased in the Mississippi Delta. This bird serves as a definitive host for digenetic trematodes, many of which infect fish. To identify these digeneans in cormorants and determine the impact these infections have on wild fish in the Mississippi Delta, two surveys were done. Cormorants were collected for two years in the Mississippi Delta. At necropsy trematodes were collected and identified morphologically and molecularly as: Austrodiplostomum ostrowskiae, Hysteromorpha triloba, Drepanocephalus spathans, Ascocotyle longa and Pseudopsilostoma varium. Additionally, 14 fish species were collected from a Mississippi Delta lake. Fish were examined for parasites and Posthodiplostomum minimum metacercariae were found in multiple organs in 6/14 fish species. The 18S gene sequences of these metacercariae were identical to published P. minimum sequences, whereas the cytochrome oxidase I (COI) sequences matched published COI sequences for Posthodiplostomum sp. 3, 5 and 8, suggesting subspecies of Posthodiplostomum in this fish population.

La dynamique globale des systèmes parasites-hôte (SPH) ‘trématode digènes - coque Cerastoderma edule’ a été étudiée simultanément à Merja Zerga (Maroc) et dans le Bassin d’Arcachon (France). La dynamique de populations de la coque a montré une variabilité intra et inter-site et a été expliquée essentiellement par la température, la prédation, la compétition et la dynamique sédimentaire. Dans les deux lagunes, le recrutement s’opère à une température de 19°C avec un décalage temporel en relation avec les positions latitudinales des sites (avril-mai à Merja Zerga et juin-juillet à Arcachon). Les taux de croissance restent comparables pour les deux populations de coque (K=1,5 an-1) mais les performances de croissance sont plus élevées à Arcachon (F’=3,3) qu’à Merja Zerga (F’=3,1). La production était plus élevée à Merja Zerga (36-65 g poids sec.m-2.an-1). P/B est faible sur les deux sites et légèrement plus élevée à Arguin (1,1-1,5 contre 1,0-1,1 an-1). Les deux sites présentent deux riches communautés parasitaires regroupant à Merja Zerga (11 espèces) et à Arguin (13 espèces), respectivement, 69% et 81% de la richesse parasitaire (digènes) connue des coques. Les communautés parasitaires restent comparables et l’éloignement géographique et climatique n’a eu qu’un faible retentissement sur la structure des peuplements parasitaires. La comparaison latitudinale de la structure et de la dynamique des SPH a permis de relativiser l’importance de la température dans la dynamique de l’hôte et des parasites, du moins dans cet intervalle climatique. A Merja Zerga, la température ne semble pas être un facteur limitant de l’infestation contrairement aux sites plus au nord. Mais finalement, les niveaux d’infestation des coques adultes sont similaires. Les échinostomatidés et les gymnophalidés ont été les plus contributives dans la mortalité parasito- dépendante observée. L’impact des parasites digènes en situation normale se traduit par une augmentation de E/B, cependant plus marqué à Merja Zerga. Cette différence d’effet dénote d’un gradient positif de virulence en allant du nord vers le sud. La présence d’herbiers, la situation ‘intertidal versus subtidal’ et la densité des coques ont un effet modéré sur l’infestation parasitaire. / The global dynamics of the parasites-host systems (PHS) ‘digenean trematodes – cockle Cerastoderma edule’ was simultaneously studied in Merja Zerga (Morocco) and Arcachon Bay (France). Cockle population dynamics exhibited an intra- and inter-site variability mostly explained by temperature, predation, competition and sedimentary dynamics. In both lagoons, recruitment occurred at 19° C, with a temporal delay due to latitudinal position (April-May at Merja Zerga, and June-July at Arcachon). Growth rates were similar in both cockle populations (K=1.5 an-1) but growth performances were higher at Arcachon (F’=3.3) than at Merja Zerga (F’=3.1). Production was higher at Merja Zerga (36-65 g dry weight.m-2.yr-1). P/B was low in both sites and slighly higher at Arguin (1.1-1.5 contre 1.0-1.1 yr-1). Both sites exhibited rich parasite communities with 11 species at Merja Zerga and 13 species at Arguin, corresponding to 69 and 81% of the identified cockle parasite species richness (digeneans). Great distances and climate differences did not alter the structure of parasite communities. Structure and dynamics of PHS related to latitude showed the moderate effect of temperature, within this climate range. At Merja Zerga, temperature was not a limiting factor for parasite infestation, in contrast with what happens in northern countries. But eventually, parasite loads in adult cockles were similar in both sites. Echinostomatids and gymnophallids were the most contributive families explaining parasite- dependent mortality. Digenean impact on cockle resulted in an increasing of E/B, with a higher effect at Merja Zerga. This difference could be linked to a higher virulence in southern sites. The presence of seagrass beds, the position between subtidal and intertidal and the cockle density remained secondary factors in controlling parasite infestation.

Les interactions hôte – parasites sont des systèmes qui affectent probablement la totalité des êtres vivants et constituent un facteur clé dans la compréhension de la dynamique des maladies infectieuses. On a abordé cette problématique en utilisant le système Fasciola hepatica/Lymnaeidae dans sur l'île de Cuba. Cette thèse utilise une approche basée sur différentes disciplines de la biologie comme l’écologie des populations (distribution et abondances de mollusques hôtes intermédiaires), l'écologie parasitaire (données de prévalences naturelles de parasites chez les hôtes), la génétique des populations en utilisant des marqueurs microsatellites (tant pour le parasite que pour les mollusques hôtes), et des études de susceptibilité et compatibilité douve/limnée.En ce qui concerne la diversité génétique du parasite, une très haute diversité et une forte probabilité d’allofécondation ont été observées. En revanche, on n’a pas trouvé de différentiation significatives entre souches. Les taux d’infection chez le bétail sont très élevés.Pour ce qui est de la biologie des populations des limnées hôtes, on a cartographié la distribution des deux espèces présentes à Cuba : Galba cubensis qui est très répandue et Pseudosuccinea columella qui n'est présente que dans la partie centre-occidentale. Nous avons mis en évidence des différences concernant les types d’habitats préférés pour chaque espèce : G. cubensis est plus plastique écologiquement et se retrouve beaucoup plus dans les sites anthropisés.L'étude des compatibilités douve/mollusque a révélé l’existence de populations avec une résistance naturelle à l’infection par F. hepatica chez la limnée P. columella. Ces populations sont génétiquement différenciées des populations sensibles. La plupart des populations sensibles sont monomorphes avec le même haplotype très répandu. Par contre, on a observé une diversité génétique plus importante chez G. cubensis qui suggère un temps évolutif plus ancien à Cuba. L’échantillonnage fait dans une aire de où la fasciolose sévit fortement chez le bétail a révélé un très faible taux d’infection naturel chez les limnées, mais avec de fortes variations d'intensités. Différentes combinaisons douve/limnée sympatriques et allopatriques testées expérimentalement ont montré une compatibilité supérieure de G. cubensis qui suggère une meilleure adaptation aux souches de F. hepatica cubaines.Les résultats obtenus montrent que la compréhension de la dynamique des maladies infectieuses ainsi que leur contrôle doivent s’appuyer sur des connaissances très solides de la biologie, écologie, génétique et évolution des systèmes hôtes – parasites. / Host – parasite interactions are biological systems that probably affect every living being. It also constitute a key factor in the understanding of infectious diseases. This subject has been studied using the Fasciola hepatica/Lymnaeidae system in the insular environment of Cuba. This thesis makes a biological multidisciplinary approach through population ecology (distribution and abundance of intermediary hosts snails), infection rates estimations of parasites in their hosts, population genetics using microsatellites markers (for both parasite and snails hosts), and studies of susceptibility and compatibility fluke/snail.The genetic diversity of the parasite is characterized by high values of diversity as well as probability of cross fertilization. However, we failed to detect significant differences between the strains but a highly infection rate is shared in cattle.Regarding the lymnaeid snails, the distribution of the two occurring species is mapped showing that Galba cubensis is widely distributed while Pseudosuccinea columella only exists in central-western Cuba. Both snail species differ in preferred habitat types and G. cubensis displays a higher ecological plasticity commonly observed in heavily human-transformed sites.Differences in host-parasite compatibilities have been revealed. It has been noted the existence of some populations of P. columella with a natural resistance to F. hepatica infection which display a marked differentiation of their population genetic structure compared to susceptible populations. Most susceptible populations are monomorphic with a very common haplotype in Cuba. Conversely, we observed a higher diversity in G. cubensis indicating a larger evolutionary time in Cuba. The sampling conducted in a fasciolosis endemic area revealed very low prevalences in the snail populations. However, strong variation in parasite mean intensity within individuals supports the high infection rates observed in cattle. Different sympatric and allopatric fluke/snail combinations were experimentally tested in which G. cubensis proved to be more compatible and suggest a better adaptation to the circulating F. hepatica in Cuba.Our results show that the understanding of infectious diseases’ dynamics and their effective control must strictly rely in a full knowledge of the biology, ecology, genetics and evolution of host – parasite systems.

The dusky grouper Epinephelus marginatus (Lowe 1834), is a protogynous sequential hermaphrodite and is considered to be one of the most important fish species in the Mediterranean Sea. It is a K-strategist, being slow growing and late maturing, and this, coupled with its reproductive biology and relatively sedentary behaviour, has made it extremely sensitive to overexploitation, leading it to be classified by the IUCN as an endangered fish species. Wild dusky grouper have suffered from disease outbreaks in the past decade, leading to mass mortalities across the Mediterranean Sea, including Libyan coastal waters. These mortalities have mostly been attributed to Nodavirus infections. In Europe and Brazil, efforts are in place to culture this fish for commercial grow-out and stock enhancement programmes. In Libya, the dusky grouper is consumed regularly and is considered a prime-eating fish. Its importance for the Libyan internal market, as well as its potential for export, makes it an ideal candidate for future Libyan aquaculture activities. Given the scarce literature regarding the dusky grouper in Libya, this study aimed first to assess dusky grouper fisheries, spawning seasons and to identify the main threats that the fishing sector poses for wild stocks. Second this study aimed to determine the health status of wild dusky grouper offered at a local fish market in the capital Tripoli, in order to identify pathogens, pathologies or other health issues that might pose a hazard to cultured populations but also to remaining wild dusky grouper stocks. To achieve these aims, twelve field surveys spanning the period of 2013-2015 were conducted. From these surveys, it was established that the dusky grouper is captured throughout the year, including the spawning season. Fish sizes offered for sale ranged between 20-92 cm total length (TL), with the fish being sold from local fishing grounds around Tripoli, but also from as far as Benghazi, 1300 km to the east of Tripoli. The dusky grouper is principally caught in artisanal fisheries and by spearfishing, with approximately 300 spear-fishermen serving one particular fish market in Tripoli that was a focus in this study, and with dusky grouper being one of their main targets. Over the period of the survey, 267 landed dusky grouper were inspected for visible lesions prior to sampling. A total of 50 dusky grouper with sizes ranging from 27- 66 cm TL including the gonads from a further five fish measuring 66-92 cm TL that were sampled separately and examined to assess the stage of sexual maturity and to look for the presence of parasitic infections mainly affecting the gills, skin and gonads. The spawning season was found to extend from May to early September, with females ranging between 39-68 cm TL, males measuring 57-92 cm TL, and transient fish measuring 58-68 cm TL. From otolith readings of 8 fish, the youngest fish was a 3 year old juvenile of 28 cm TL and the oldest was an 8-9 year old 56 cm TL female. Whilst the highest prevalence of parasitic infection was found to be monogenean infection of the gills, with 100% prevalence, followed by gnathiid isopods infecting the oral cavity with 92% prevalence, it was the nematode Philometra sp. infecting post-spawning ovaries at 52% prevalence, that gave the highest apparent pathological impact. Necrosis potentially attributed to Philometra sp. in one particular ovary, was at a level likely to have caused complete parasitic castration, while others showed varying levels of probable functional reduction. The pathologies described need further investigation, especially in relation to possible synergies between Philometra sp. and bacteria in causing the necrosis. From the 267 inspected dusky grouper, 55 fish ranging in size from 42-92 cm TL were observed to be affected by external skin lesions of unknown aetiology. Twenty-six of these fish were sampled, having lesions at various stages of severity, and 5 further unaffected fish were used for histological assessment of the skin as negative controls. Histopathologically, the lesions comprised a multifocal, unilateral or bilateral dermatitis, involving the epidermis, superficial dermis and scale pockets, and sometimes, in severe cases, the hypodermis. Severe lesions had marked epidermal spongiosis progressing to ulceration. Healing was observed in some fish. Bacteria and fungi could be isolated from severe lesions, although they were not seen histopathologically in early-stage lesions. By contrast, metazoan parasite eggs were observed in the dermis and epidermis of some fish with mild and moderate dermatitis. Unidentified gravid digenean trematodes, carrying similar eggs, were also seen within the blood vessels of the deep and superficial dermis. The newly described condition was termed dusky grouper dermatitis (DGD). DGD’s geographical distribution along the Libyan coastline was investigated using a novel application of the social media network Facebook. Using Facebook, it was possible to document skin lesions of dusky grouper in Libyan waters from images attached to the entries of spear-fishermen. Thirty two Facebook accounts and 8 Facebook groups posting from 23 Libyan coastal cities provided a retrospective observational dataset comprising a total of 382 images of dusky grouper caught by spearfishing from December 2011-December 2015. Skin lesions were observable on 57 / 362 fish, for which images were of sufficient quality for analysis, giving a minimal prevalence for lesions of 15.75%. Only dusky grouper exceeding an estimated 40 cm total length exhibited lesions. The ability to collect useful data about the occurrence and geographical distribution of pathological conditions affecting wild fish using social media networks, demonstrates their potential utility as a tool to support epidemiological studies and monitor the health of populations of aquatic animals. The gravid digenean trematode described from mild lesions of five fish was identified using reconstruction through histological sectioning as belonging to the Family Aporocotylidae Odhner, 1912. This is the first description of a blood fluke from the dusky grouper, as well as from dermal blood vessels. The parasite was relatively long; the longest section of the parasite that could be measured was 1500 µm and 20-80 µm in width, while the total length of the parasite was estimated at 1500-2000 µm. Minute tegumental spines, possibly covering only a few parts of the parasite, were seen from some cross-sections. The parasite had one post-testicular ovary, which might overlap the testis, a pre-ovarian ascending uterus, and a post-ovarian descending uterus. It also possessed an oesophagus surrounded by oesophageal glandular cells and a pre-ovarian and pre-testicular extension of the vitelline cells, mostly at the level of the ascending uterus. The parasite was observed to be intra-vascular, the uterine lumen varies in size to accommodate between 1-7 eggs. The uterine eggs were embryonated and observed to span several stages of maturation. Eggs were also found in the dermal blood vessels, in the dermis, and in the epidermis, with the latter appearing to provide a potential route of egress of eggs into the environment. The extra-uterine eggs were 23.5 to 37.52 µm long and contained a ciliated miracidium. The eggs seemed to elicit a mixed inflammatory reaction, with degranulation of eosinophilic granular cells attached to the external surface of some of the eggs within the blood vessels but also the dermis. From observations made in the current study, this parasite appears to be a new species, most closely allied to none of the currently described Aporocotylidae genera. / In summary, the present study has demonstrated that the dusky grouper is extensively fished in Libya without discrimination to sizes and season, by both artisanal and spearfishing, with the latter as one of the main fishing methods, posing treats to the spawning potential and conservation of dusky grouper in Libya. The philometrid infecting the ovaries has a potential to reduce fecundity or to result in parasitic castration of wild broodstock. Gill-infecting monogeneans might represent a hazard for all stages of dusky grouper production. Dusky grouper dermatitis is a skin lesion, although there are no indications that infections may result in mortalities. Under culture conditions, however, this might change due to increase bacterial loads, which might lead to secondary bacterial infection. The presence of skin lesions would undoubtedly reduce the market value of whole fish. These findings are important for existing wild stocks, and for future plans regarding the aquaculture of dusky grouper. Future studies need to focus on the pathology of DGD, describing the disease process and aetiology using laboratory techniques such as TEM and virology as well as using morphology and molecular-based tools to describe the blood fluke and to determine their potential role in the initiation the disease. The novel approach to disease surveillance using social media Facebook posts could be further expanded by attracting citizen scientists, for future research assessing disease in wild fish, for sightings of mortality events and/or the appearance of disease outbreaks, or, for mapping marine mammal stranding’s and/or turtle nesting activity.