Report of the ICES Working Group on Marine Mammal Ecology (WGMME)

131 pages.-- This work is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0)Five terms of reference (ToRs) were addressed at the working group. The first three terms of reference were standing ones. Under ToR A, new information on cetacean and seal population abundance, distribution, and population/stock structure, was reviewed, including information on vagrancy in cetacean and pinniped species. For cetaceans, coverage from the latest SCANS-IV survey (summer 2022) was presented as well as the results of recent regional/national surveys, particularly those in the Bay of Biscay and around the Iberian Peninsula. Updates on population estimates and distribution were provided for particular species studies, such as some coastal bottlenose dolphin populations. For seals, latest monitoring results were given for harbour, grey, and Baltic and Saimaa ringed seals. In addition, where possible, local long-term trends were illustrated for those species, based on earlier efforts by WGMME to assemble these data into a seal database. For both species’ groups, recent records of vagrant species were summarised. Under ToR B, cetacean and seal management frameworks in the North Atlantic were discussed, with an overview of the EU Maritime Spatial Planning Directive, and examples from the United Kingdom, Spain and the Faroe Islands of national management frameworks regarding marine mammals.ToR C provided an overview of new published information with regards to anthropogenic threats to marine mammal populations following on from the review by WGMME in 2015 (ICES, 2015) and subsequent updates. These were considered under the following headings: cumulative effects, fishery interactions, chemical pollution including marine debris, underwater noise, ship strikes and other physical trauma, tourism disturbance, climate change, and new pathogens (including avian influenza). ToR D focused upon bycatch. In support of WGBYC, this ToR aimed to contribute to the Roadmap for ICES PETS bycatch advice. ToR E involved liaison with other WGs. The Chairs of the newly-formed WGJCDP introduced to WGMME members, the Joint Cetacean Database Programme, which is to be hosted by the ICES Data Centre. The scope to collect information on other marine species besides cetaceans was discussed. A meeting with another newly formed ICES working group, on Marine Protected Areas, was planned but was deferred at the request of that group. On behalf of the working group, the Chairs would like to thank The Swedish Museum of Natural History for hosting the meetingN

Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises

Abstract A type of monophasic group B Salmonella enterica with the antigenic formula 4,12:a:- (“Fulica-like”) has been described as associated with harbour porpoises (Phocoena phocoena), most frequently recovered from lung samples. In the present study, lung tissue samples from 47 porpoises found along the Swedish coast or as bycatch in fishing nets were analysed, two of which were positive for S. enterica. Pneumonia due to the infection was considered the likely cause of death for one of the two animals. The recovered isolates were whole genome sequenced and found to belong to sequence type (ST) 416 and to be closely related to ST416/ST417 porpoise isolates from UK waters as determined by core-genome MLST. Serovars Bispebjerg, Fulica and Abortusequi were identified as distantly related to the porpoise isolates, but no close relatives from other host species were found. All ST416/417 isolates had extensive loss of function mutations in key Salmonella pathogenicity islands, but carried accessory genetic elements associated with extraintestinal infection such as iron uptake systems. Gene ontology and pathway analysis revealed reduced secondary metabolic capabilities and loss of function in terms of signalling and response to environmental cues, consistent with adaptation for the extraintestinal niche. A classification system based on machine learning identified ST416/417 as more invasive than classical gastrointestinal serovars. Genome analysis results are thus consistent with ST416/417 as a host-adapted and extraintestinal clonal population of S. enterica, which while found in porpoises without associated pathology can also cause severe opportunistic infections

Overcoming species barriers: an outbreak of Lagovirus europaeus GI.2/RHDV2 in an isolated population of mountain hares (Lepus timidus)

Abstract Background Prior to 2010, the lagoviruses that cause rabbit hemorrhagic disease (RHD) in European rabbits (Oryctolagus cuniculus) and European brown hare syndrome (EBHS) in hares (Lepus spp.) were generally genus-specific. However, in 2010, rabbit hemorrhagic disease virus 2 (RHDV2), also known as Lagovirus europaeus GI.2, emerged and had the distinguishing ability to cause disease in both rabbits and certain hare species. The mountain hare (Lepus timidus) is native to Sweden and is susceptible to European brown hare syndrome virus (EBHSV), also called Lagovirus europaeus GII.1. While most mountain hare populations are found on the mainland, isolated populations also exist on islands. Here we investigate a mortality event in mountain hares on the small island of Hallands Väderö where other leporid species, including rabbits, are absent. Results Post-mortem and microscopic examination of three mountain hare carcasses collected from early November 2016 to mid-March 2017 revealed acute hepatic necrosis consistent with pathogenic lagovirus infection. Using immunohistochemistry, lagoviral capsid antigen was visualized within lesions, both in hepatocytes and macrophages. Genotyping and immunotyping of the virus independently confirmed infection with L. europaeus GI.2, not GII.1. Phylogenetic analyses of the vp60 gene grouped mountain hare strains together with a rabbit strain from an outbreak of GI.2 in July 2016, collected approximately 50 km away on the mainland. Conclusions This is the first documented infection of GI.2 in mountain hares and further expands the host range of GI.2. Lesions and tissue distribution mimic those of GII.1 in mountain hares. The virus was most likely initially introduced from a concurrent, large-scale GI.2 outbreak in rabbits on the adjacent mainland, providing another example of how readily this virus can spread. The mortality event in mountain hares lasted for at least 4.5 months in the absence of rabbits, which would have required virus circulation among mountain hares, environmental persistence and/or multiple introductions. This marks the fourth Lepus species that can succumb to GI.2 infection, suggesting that susceptibility to GI.2 may be common in Lepus species. Measures to minimize the spread of GI.2 to vulnerable Lepus populations therefore are prudent

Summary of semi-quantitative amyloid scores in subadult and adult Herring gulls (<i>Larus argentatus</i>).

<p>For more information on collection regions refer to text, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.g001" target="_blank">Fig 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.t001" target="_blank">Table 1</a>.</p

Post mortem findings and their relation to AA amyloidosis in free-ranging Herring gulls (<i>Larus argentatus</i>)

<div><p>Since the late 1990s, high mortality and declining populations have been reported among sea birds including Herring gulls (<i>Larus argentatus</i>) from the Baltic Sea area in Northern Europe. Repeated BoNT type C/D botulism outbreaks have occurred, but it remains unclear whether this is the sole and primary cause of mortality. Thiamine deficiency has also been suggested as a causal or contributing factor. With this study, we aimed to investigate gross and microscopic pathology in Herring gulls from affected breeding sites in Sweden in search of contributing diseases. Herring gulls from Iceland served as controls. Necropsies and histopathology were performed on 75 birds, of which 12 showed signs of disease at the time of necropsy. Parasites of various classes and tissues were commonly observed independent of host age, e.g. oesophageal capillariosis and nematode infection in the proventriculus and gizzard with severe inflammation, air sac larid pentastomes and bursal trematodiasis in pre-fledglings. Gross and microscopic findings are described. Notably, amyloidosis was diagnosed in 93 and 33% of the adult birds from Sweden and Iceland, respectively (<i>p</i><0.001), with more pronounced deposits in Swedish birds (<i>p</i><0.001). Gastrointestinal deposits were observed in the walls of arteries or arterioles, and occasionally in villi near the mucosal surface. Amyloid was identified within the intestinal lumen in one severely affected gull suggesting the possibility of oral seeding and the existence of a primed state as previously described in some mammals and chickens. This could speculatively explain the high occurrence and previously reported rapid onset of amyloidosis upon inflammation or captivity in Herring gulls. Amyloid-induced malabsorbtion is also a possibility. The Herring gull SAA/AA protein sequence was shown to be highly conserved but differed at the N-terminus from other avian species.</p></div

Summarized bird characteristics of the 75 Herring gulls <i>(Larus argentatus</i>) included in the study.

<p>For collection regions also refer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.g001" target="_blank">Fig 1</a>.</p

N-terminal amino acid sequence of Herring gull (<i>Larus argentatus</i>) protein AA compared with the same region of protein AA of some birds and mammals.

<p>Identical amino acid residues are shown in red.</p

Microscopic parasite findings in Herring gulls (<i>Larus argentatus</i>).

<p>(A) Nematode infection in the gizzard with disruption of the koilin layer, focal necroses and lymphoplasmacytic inflammation (bird no. 12, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s001" target="_blank">S1 Table</a>). H&E, bar 100 μm. (B) Trematodiasis (<i>Ichtyocotylarus platycephalus</i> (Creplin, 1825) of the bursa of Fabricius. Lymphocyte and heterophilic granulocyte infiltration and effacement of lymphoid follicles can be observed adjacent to rostral parasite structures (bird no. 6, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s001" target="_blank">S1 Table</a>). H&E, bar 100 μm. (C–D) Oesophageal mucosa infected by <i>Capillaria</i> sp. Parasite eggs are present in the mucosa and in the lumen in association with inflammatory cells and necrotic debris (bird no. 11, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s002" target="_blank">S2 Table</a>). H&E, bar 100 μm (C), 50 μm (D). (E) Proventricular mucosa with a trematode present in a submucosal gland. Note compression of glandular epithelium and absence of an inflammatory reaction (bird no. 6, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s002" target="_blank">S2 Table</a>). H&E, bar 50 μm. (F) Jejunal villi with large numbers of parasite larvae (bird no. 17, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s002" target="_blank">S2 Table</a>). H&E, bar 50 μm.</p

Microscopic amyloid findings in Herring gulls (<i>Larus argentatus</i>).

<p>(A) Amyloid deposits mainly in arterial adventitia of the spleen (bird no. 27, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s002" target="_blank">S2 Table</a>, amyloid score 1). Congo red, crossed polars, bar 50 μm. (B) Massive diffuse amyloid infiltration throughout the splenic parenchyma (bird no. 6, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s002" target="_blank">S2 Table</a>, amyloid score 4). Congo red, bar 100 μm. (C) Small, localized deposits around some kidney tubules and in walls of small arteries. (bird no. 33, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s002" target="_blank">S2 Table</a>, amyloid score 3). Congo red, bar 200 μm. (D) Diffusely spread amyloid deposits interstitially in the kidney. Note glomeruli virtually free of amyloid (bird no. 9, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s002" target="_blank">S2 Table</a>, amyloid score 4). Congo red, bar 100 μm. (E) Pronounced but patchy and mainly interstitial deposits of amyloid in the myocardium (bird no. 11, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s002" target="_blank">S2 Table</a>, amyloid score 4). Congo red, crossed polars, bar 100 μm. (F) Brain was free of amyloid in all birds except for the choroid plexus, which is outside the blood-brain barrier. Amyloid is present in vessel walls (bird no. 9, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193265#pone.0193265.s002" target="_blank">S2 Table</a>, amyloid score 4). Congo red, bar 50 μm.</p