1,721,024 research outputs found
PANGENOME ANALYSIS AND ANTIMICROBIAL RESISTOME OF Salmonella enterica SEROVARS TYPHIMURIUM AND 1,4,[5],12:I:- SEQUENCE TYPE 34
No full textSalmonella enterica serovar 1,4,[5],12:i:- has recently emerged in food-borne epidemics of
multi-drug resistance (MDR) strains associated to several outbreaks in Europe (EU) as well
as in other continents. The existence of a European clone, associated to Multi-Locus
Sequence Types ST34 and to R-Type ASSuT, has been described. The aim of the present
study was to investigate the geographical structure and antimicrobial resistance gene
patterns of a set of Salmonella serovars Typhimurium and 1,4,[5],12:i:- genomes belonging to
ST34. A core genome gene-by-gene approach was performed on 1,254 publicly available S.
1,4,[5],12:i:- and S. Typhimurium genomes belonging to ST34 and including 148 newly
sequenced genomes of Italian S. 1,4,[5],12:i:- isolates collected from humans, swine and pork
meat between 2012 and 2014. Strains gathered in several clusters irrespectively of the year
and of the source of isolation. Three subclades, STY-, WE- and NA-clade, accounting for
roughly the 60% of the genomes were identified as significantly associated to Italian, United
Kingdom and North American origin, respectively (Fisher’s exact test; P<0.0001). The AMR
patterns of all genomes were predicted by in silico identification of antimicrobial resistance
associated genes (ARGs) from ResFinder database. Almost all genomes (96.5%) were
positive for at least one ARG, whereas a limited number (45) did not show any positive match
for ARGs in Resfinder database. The 63% of all ST34 isolates and the 66% of Italian ones
were predicted to harbour the R-Type ASSuT. Within the 1,254 ST34 tested genomes, 55
different ARGs of the ResFinder database were found. The number of fluoroquinolone
detected ARGs was 67 with qnrB gene as the most prevalent one (46). Aminoglycosides
ARGs were detected 2,352 times with aph(3'')-Ib and aph(6)-Id genes as the most reported
(925 and 963 respectively). Beta-lactam ARGs were rarely detected with the exception of
blaTEM-1B (960). Sulfonamides ARGs were frequently detected (1,090) with sul2 (1,006) as
the most identified. The frequency of detection of tetracycline ARGs was high (1,226) with
tetB (1,137) as the most represented. In relation to the country of origin, Italian genomes and
non-Italian genomes showed similar percentages of the most abundant ARGs (around 70-
80% for aph(3'')-Ib, aph(6)-Id and blaTEM-1B genes and around 80-90% for tetB gene).
However, in relation to the other ARGs, a lower percentage of ARGs was observed in Italian
genomes with the exception of floR2 (7% Italian vs 5 % non-Italian genomes) and mcr genes
(5 Italian genomes vs 0 non-Italian genomes). Regarding the 5 Italian S. 1,4,[5],12:i:-
genomes found positive for mcr genes, three isolates and one isolate harboured mcr-1 and
mcr-5 genes respectively and were collected from pigs between 2012 and 2014; one isolate
carried mcr-4 and was collected from human in 2007. In conclusion, the identification of most
prevalent ARGs might be useful to identify key genetic biomarkers of antimicrobial resistance
in S. Typhimurium and S. 1,4,[5],12:i:-. Moreover, the identification of geographically
segregated clades in combination with their antimimicrobial resistome gave first insights to
uncover the evolution and potential routes of spread of antimicrobial resistance genes from
country to countr
29th National Congress of the Italian Association of Veterinary Food Hygienists (AIVI), Bari, 11-13 September 2019
No full textThis abstract book contains the abstracts presented at the 28th National Congress of the Italian Association of Veterinary Food Hygienists (AIVI) | Bari, 11-13 September 201
Salmonella detection and aerobic colony count in deep-frozen carcasses of house sparrow (Passer domesticus) and starling (Sturnus vulgaris) intended for human consumption
Full text linkWild birds are potential vehicles of zoonotic pathogen transmission to humans. The zoonotic concern increases for small wild birds like house sparrows (Passer domesticus) and starlings (Sturnus vulgaris) which are hunted in developing countries and commercialised in Italy for human consumption. From June to October 2011, 330 house sparrows and 140 starlings were hunted and slaughtered. Deepfrozen carcasses were transported to Italy and stored for 6-8 months at -18°C. Aerobic colony count and Salmonella detection in carcasses were assessed following standard microbiological methods (ISO 4833:2003 and ISO 6579:2004, respectively). Carcasses of house sparrows showed higher levels of aerobic bacteria in comparison to starling carcasses (5.7 vs 3.2 log10 CFU/g). Moreover, 7 out of 11 lots of carcasses of house sparrows were positive for Salmonella. Among the 18 isolates of Salmonella, 14 were S. Typhimurium, 2 were S. Enteritidis, and 2 were not distinguishable. All of them were susceptible to antibiotics. All tested carcasses of starling were Salmonella negative. Deep-freezing was not efficient as a decontamination technique on carcasses of house sparrows
Transcriptome analysis of brain, intestine and hypopharyngeal glands of Apis mellifera using the Oxford Nanopore third generation sequencing technology
No full textIntroduction
Apis mellifera plays a crucial role in biodiversity and ecological balance. So far, honey bee transcriptome and its modifications induced by stress or pathogens have been poorly studied. Thus, the characterization of the transcriptional profiles of key organs in response to biotic and abiotic factors could fill these gaps and provide new knowledge.
Materials and Methods
Honey bees from four apiaries in Northern Italy were collected and immediately frozen in liquid nitrogen. Brain, hypopharyngeal glands, and intestine were excised and total RNA was extracted from four pools of each tissue (1 pool = 3 bees from a single apiary). Twelve tissue-specific cDNA libraries were constructed and sequenced using the Nanopore Mk1C. State-of-the-art software were used for raw data analysis, reads alignment, and splicing isoforms detection.
Results
About 27 million sequences per tissue were obtained. A total of 55,651 isoforms were identified, of which 21,501 were expressed in at least one of target tissues. Out of these, 6,719 transcripts were annotated, while 10,071 were identified as novel transcripts. The brain showed the highest number of transcripts (14,689), followed by the intestine (8,953) and hypopharyngeal glands (5,227). The analysis of differential expression among the tissues highlighted 2,371 differentially expressed transcripts (DETs), of which 1,236 with known biological function and 715 novel transcripts. The most abundant DETs were those 'activated' exclusively in the brain (some opsins, crucial for vision, and a gene with a fundamental role in longevity) or intestine (genes involved in apoptosis). Several DETs were moderately, but differentially, expressed in all the target organs. As an example, Glutathione S-transferase theta-3 and peroxiredoxin 6 genes, involved in oxidative stress response, were significantly more ‘activated’ in the intestine and hypopharyngeal glands.
Discussion and Conclusion
The present study, carried out within the RC IZS VE 09/20 project and funded by the Ministry of Health, has improved the knowledge of the transcriptome of three key organs of A. mellifera and investigated its complexity by identifying new transcripts. Therefore, it represents a valuable basis for further molecular investigations into honey bee response to environmental stress
Impacts on production performances and costs from the development of antibiotic-free poultry farming, a case study in Italy
No full text
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Depression and Microbiome—Study on the Relation and Contiguity between Dogs and Humans
Full text linkBehavioral studies demonstrate that not only humans, but all other animals including dogs, can suffer from depression. A quantitative molecular evaluation of fatty acids in human and animal platelets has already evidenced similarities between people suffering from depression and German Shepherds, suggesting that domestication has led dogs to be similar to humans. In order to verify whether humans and dogs suffering from similar pathologies also share similar microorganisms at the intestinal level, in this study the gut-microbiota composition of 12 German Shepherds was compared to that of 15 dogs belonging to mixed breeds which do not suffer from depression. Moreover, the relation between the microbiota of the German Shepherd’s group and that of patients with depression has been investigated. The results indicate that the German Shepherd’s gut-microbiota has a different composition compared to other dog breeds and is characterized by microbial groups identified in humans with depression, highlighting the existence of a “core” microbiota associated with depression
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