Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii Circulation in a Dairy Farm and Sources of Milk Contamination.

Even though dairy cows are known carriers of Arcobacter species and raw or minimally processed foods are recognized as the main sources of human Arcobacter infections in industrialized countries, data on Arcobacter excretion patterns in cows and in milk are scant. This study aimed to identify potentially pathogenic Arcobacter species in a dairy herd and to investigate the routes of Arcobacter transmission among animals and the potential sources of cattle infection and milk contamination. A strategy of sampling the same 50 dairy animals, feed, water, and milk every month for a 10-month period, as well as the sampling of quarter milk, animal teats, the milking environment, and animals living on the farm (pigeons and cats), was used to evaluate, by pulsed-field gel electrophoresis (PFGE), the characteristic patterns in animals, their living environment, and the raw milk they produced. Of the 463 samples collected, 105 (22.6%) were positive for Arcobacter spp. by culture examination. All the matrices except quarter milk and pigeon gut samples were positive, with prevalences ranging from 15 to 83% depending on the sample. Only three Arcobacter species, Arcobacter cryaerophilus (54.2%), A. butzleri (34.2%), and A. skirrowii (32.3%), were detected. PFGE analysis of 370 isolates from positive samples provided strong evidence of Arcobacter circulation in the herd: cattle likely acquire the microorganisms by orofecal transmission, either by direct contact or from the environment, or both. Water appears to be a major source of animal infection. Raw milk produced by the farm and collected from a bulk tank was frequently contaminated (80%) by A. butzleri; our PFGE findings excluded primary contamination of milk, whereas teats and milking machine surfaces could be sources of Arcobacter milk contamination.

"Till death do us apart": The common destiny of brown hare and its parasite community.

Although parasites may threaten individual hosts' survival and reproduction, their role as an essential part of ecosystem functioning and biodiversity has been recognized. In Northern Italy, the hare population has evidently declined since 2008. This paper aims to assess the relationship between host demographic trends and helminth parasite community diversity in a two-year survey in Northern Italy to evaluate the impact of parasites on hosts and confirm the hypothesis that endangered host populations are poor in parasites. In 2013 and 2015 the viscera of 54 and 61 hares legally hunted in agro-ecosystems of the Po Plain were collected. This area is characterized by heavy anthropic pressure: more than 60% of the landscape is represented by agricultural or urbanized territories. No intestinal cestodes were detected. Trichuris sp. and Micipsella numidica were collected in 2015 only; Trichostrongylus retortaeformis, Taenia pisiformis cysticercosis and bronchopulmonary lesions caused by small strongyles were observed in both years. The richness and evenness appeared increased in the second year of the survey, although lower than those obtained by literature data from similar populations examined in the last two decades of 1900. The dominant helminth, T. retortaeformis, was more abundant in individuals with higher weight, while pathological findings were mostly unrelated to this nematode infection; this is consistent with a reduced action, even no harm, of the parasites on the individual host or population level. Our results suggest that the conservation of hosts, environment, and parasites cannot be achieved separately and that parasites and wildlife hosts' destinies are intimately linked, confirming the complexity of ecosystems and the need to contemplate parasite biodiversity in conservation strategies.

Helminth biocoenosis of Lepus europaeus meridiei (Hilzheimer, 1906) from Pianosa island, Italy.

Pianosa is a 10 km2 Italian island in the Tyrrhenian Sea which is part of the Tuscan Archipelago National Park. In this island lives a brown hare population which, according to the literature, belongs to the ancestral taxon Lepus europaeus meridei that offers a unique opportunity to observe how the parasite biocoenosis shapes in condition of isolation, limited space availability and high population density. The aim of this work is to describe the helminth component community of a non-managed, isolated, and dense hare population, evaluating host-parasite relationship and parasite community structure. All 26 analyzed hares (13 males and 13 females) were in good physical conditions, and all of them harboured exclusively the nematode Protostrongylus oryctolagi only. This is the first report of this lungworm species in Italy. The estimated overall abundance was 48.15 worms per examined hare (range 3-258, median 50) and the parasites were unevenly distributed across host population, with few hosts having most parasites (aggregated or overdispersed distribution). No significant relationship was detected between the number of isolated parasites and hare sex and weigh. The effect of the isolation of Pianosa's hare population seems to have acted reducing parasite richness, while the high host density is probably the cause of the high prevalence and abundance of the single helminth species collected. In conclusion, despite the low impact of parasites confirmed also by the overdispersed parasite distribution, the low diversity of the studied parasite community sounds a warning for the management of the hare population and the whole Pianosa's ecosystem.

Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library.

Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.

First microsatellite loci of red mullet (Mullus barbatus) and their application to genetic structure analysis of Adriatic shared stock.

In order to study the genetic structure of the Adriatic shared stock of red mullet (Mullus barbatus), we developed a set of dinucleotide microsatellite markers. A dinucleotide-enriched genomic library was obtained, and 6 polymorphic dinucleotide loci were successfully optimized. The markers showed high expected heterozygosity (from 0.68 to 0.92) and allele number (from 12 to 33); thus they appear to be suitable for detecting genetic differences in the population of red mullet. Four Adriatic samples were subsequently analyzed for microsatellite variation, and the results showed subtle but statistically significant genetic differentiation, indicating that the Adriatic red mullet may group into local, genetically isolated populations. No correlation between geographic distance and genetic differentiation was observed. In addition, the evidence of recent bottlenecks in the Adriatic samples indicates that the observed population subdivision might reflect random local allelic variations, generated by reproductive success, survival rates, or fishing pressure.

Mitochondrial DNA sequence variation suggests the lack of genetic heterogeneity in the Adriatic and Ionian stocks of Sardina pilchardus.

A genetic stock structure analysis of 11 sardine samples from the Adriatic Sea and Ionian neighboring area was carried out through sequence variation analysis of a 307-bp cytochrome b gene fragment in order to identify self-recruiting units in the Adriatic Sardina pilchardus stock. The overall lack of genetic subdivision among samples detected by analysis of molecular variance, pairwise Phi(st) values, and the exact test of population differentiation indicates this sardine stock is part of a larger self-recruiting population whose boundaries are larger than the investigated area. This conclusion is in agreement with preliminary allozymic and mitochondrial DNA restriction fragment length polymorphism data, but contradicts the previous identification of 2 subpopulations of sardines in the Adriatic Sea argued on morphologic differences, which could be rather attributed to different hydrographic or ecologic conditions occurring in different areas of the Adriatic Sea. The reduced gene flow observed between Adriatic-Ionian and Spanish sardine geographic samples (P < 0.001) suggests that reproductively isolated populations of sardines may occur in the Mediterranean Sea.

First detection of Arcobacter sp. in Eurasian collared doves (Streptopelia decaocto).

Data about the presence of Arcobacter in wild birds are currently lacking. In this study cloacal swabs from 95 collared doves (Streptopelia decaocto), submitted to the Department of Veterinary Medical Sciences (Bologna, Italy) between 2011 and 2013 from various urban and suburban areas of the Emilia-Romagna region (Northern Italy), were tested for the presence of Arcobacter sp. by a rRNA 23S nested Polymerase Chain Reaction (PCR). Eighteen out of 95 (19%) samples showed the expected PCR product. Further cultural and molecular studies are needed to assess the Arcobacter prevalence in wild birds and elucidate their potential epidemiological role as source of animal and human infections.

Temporal Variation of Faecal Shedding of Escherichia coli 0157:H7 in A Dairy Herd Producing Raw Milk for Direct Human Consumption.

The objective of this study was to analyse over time the evolution of E. coli O157:H7 faecal shedding in a dairy herd producing raw milk for direct human consumption. The study was performed between October 2012 and September 2013 in an average size Italian dairy farm where animals are housed inside the barn all over the year. The farm housed about 140 animals during the study - 70 cows and 70 calves and heifers. Twenty-six animals were randomly selected from both the cows and young animals group, and faecal sampling was performed rectally six times two months apart in each animal. Eleven animals were culled during the study and a total of 285 faecal samples were collected. At each faecal sampling, three trough water samples and two trough feed samples were also collected for a total of 36 water samples and 24 feed samples. Samples were analysed by real time polymerase chain reaction (RT-PCR) and culture. Overall, 16 (5.6%) faecal samples were positive for E. coli O157 by RT-PCR. Cultural examination found 9 (3.1%) samples positive for E. coli O157; all the isolates were positive for stx1, stx 2 and eae genes. One (4.1%) feed sample was positive for E. coli O157 by RT-PCR; none of the water samples was positive for E. coli O157. The model highlighted a general significant reduction of the number of positive samples observed during the study from the first to the sixth sampling (P=0.000) and a positive relation between the presence of positive samples and average environmental temperature (P=0.003). The results of the study showed that in an Italian dairy farm housing animals all year, faecal shedding of E. coli O157 followed the same temporal trend reported for other types of farming. The enhanced faecal shedding during warmer months may have a significant impact on environmental contamination and the safety of raw milk and its byproducts.

Restriction fragment length analysis of the cytochrome b gene and muscle fatty acid composition differentiate the cryptic flatfish species Solea solea and Solea aegyptiaca.

Overlapping external morphometric characters easily confound the flatfishes Solea aegyptiaca and Solea solea (Soleidae) in areas of the Mediterranean Sea where both species live in sympatry. This leads to uncertainties in the fisheries and marketing of the species, in addition to misinterpretations in biogeography and conservation studies. This paper describes a simple restriction fragment length-based diagnostic test that differentiates S. solea from S. aegyptiaca, as well as from other species of the Soleidae family. Furthermore, the two species living in sympatry in the Gulf of Kavala (North Aegean Sea, Greece) present significant qualitative differences in muscle fatty acid composition, a property that can also be used to distinguish the two cryptic species.

Gene-associated markers provide tools for tackling illegal fishing and false eco-certification.

Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.

Comparative analysis of AFLPs and SSRs efficiency in resolving population genetic structure of Mediterranean Solea vulgaris.

The performance of different molecular markers in the assessment of population structure was tested using samples of Solea vulgaris collected in the Mediterranean within and outside the hypothetical dispersal ability of the species. A total of 172 individuals belonging to four population samples were analysed using 15 microsatellites [simple sequence repeats (SSRs)] and 153 amplified fragment length polymorphisms (AFLPs). Considering the global qualitative patterns, we found a correlation between SSRs and AFLPs in detecting genetic differentiation among samples. However, on a small geographical scale, AFLPs were able to discriminate individuals from neighbouring populations whereas SSRs were not, and the percentage of individuals correctly assigned to their population of origin was higher with AFLPs than with SSRs. The high number of loci analysed with the AFLP technique could increase the probability to include outlier loci in the analysis; however, the neutrality test performed on our data set did not show evidence of selection acting on the S. vulgaris samples. Even if the choice of the molecular marker depends mainly on the biological question to be addressed, the higher power of discrimination and the comparative technical ease of obtaining data from AFLPs with respect to SSRs suggest the use of AFLPs for many population genetics studies.