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Conservation, characterization and exploitation of agrobiodiversity are key factors to guarantee food security and face future challenges such as climate changes. These issues are the subject of a series of international agreements, such as the Convention of Biological Diversity, with its Nagoya Protocol, and the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) adopted in 2001 and entered into force in 2004. Italy ratified the Treaty in 2004 and instituted a long-lasting program, RGV-FAO, to implement it. CREA is one of the three organizations involved in the RGV-FAO Program, together with the National Research Council (CNR) and Reti Semi Rurali. CREA maintains a total of 40,186 accessions including cereals, vegetables, fruits, forages, industrial crops, forest and woody crops, medicinal and aromatic plants, and their wild relatives. Accessions are conserved using different ex situ conservation systems (seeds, in vivo plants, vegetative organs and in vitro plantlets), and characterized using genetic, morpho-phenological and/or biochemical methods. Herein, we will present the CREA long-lasting program RGV-FAO with some examples of the use of plant genetic resources in breeding programs, including molecular approaches. Some critical issues related to access and benefit sharing in PGRFA, such as the Nagoya Protocol and the Digital Sequence Information, will be discussed, highlighting their potential impact on food security and on the advancement of knowledge. [ABSTRACT FROM AUTHOR]

Human papillomaviruses (HPVs) commonly infect the anogenital mucosa; most infections are transient, but a fraction of those caused by high-risk (HR) types persist and may lead to anogenital cancer. The epidemiology of HPV genotypes in anal infections in groups at different risk for anal cancer has not been well described in Italy. This retrospective study reports the results of HPV DNA testing and complete genotyping performed on anal swabs from 691 female and male patients attending proctology clinics in Rome during 2012–2021; one-third had repeated testing. Cumulative HPV positivity in 1212 anal swabs was approximately 60%, was not age related, and showed an increasing trend over the study period. HPV rates differed significantly by sex and HIV status: HIV-negative women had the lowest (43.6%) and HIV-positive men the highest (83.5%) HPV prevalence. HIV-positive men had more oncogenic HPV genotypes detected, more multiple infections, and the highest frequency of persistent infections. Two-thirds of all infections were vaccine-preventable. This study found that anal HPV infection rates are still elevated and even increasing in groups at low and high risk of developing anal cancer. Prevention programs need to be improved to reduce rates of anal infection in young women and men. [ABSTRACT FROM AUTHOR]

Rotavirus H (RVH) has been detected in humans, pigs and bats. Recently, RVH infections were reported in different porcine farms worldwide, suggesting epidemiological relevance. However, to date, the genome information of RVH strains has been limited due to the scarcity of deposited sequences. This study aimed to characterize the VP7, VP4, VP6 and NSP4 genes of RVHs from 27 symptomatic pigs, in Italy, between 2017 and 2021. RVH genes were amplified via RT-PCR using specific primers, and the amplicons were sequenced. By coupling the data generated in this study with the sequences available in the databases, we elaborated a classification scheme useful to genotype the VP7, VP4, VP6 and NSP4 genes. The nucleotide identity and phylogenetic analyses unveiled an impressive genetic heterogeneity and allowed the classification of the Italian RVH strains into 12G (VP7), 6P (VP4), 8I (VP6) and 8E (NSP4) genotypes, of which 6I, 5E and the totality of the G and P genotypes were of novel identification. Our data highlight the high genetic variability of the RVH strains circulating in pigs and underline the importance of a robust classification system to track the epidemiology of RVHs. [ABSTRACT FROM AUTHOR]

Background: Awareness about the importance of implementing DPYD pharmacogenetics in clinical practice to prevent severe side effects related to the use of fluoropyrimidines has been raised over the years. Since 2012 at the National Cancer Institute, CRO-Aviano (Italy), a diagnostic DPYD genotyping service was set up. Purpose: This study aims to describe the evolution of DPYD diagnostic activity at our center over the last 10 years as a case example of a successful introduction of pharmacogenetic testing in clinical practice. Methods: Data related to the diagnostic activity of in-and out-patients referred to our service between January 2012 and December 2022 were retrieved from the hospital database. Results: DPYD diagnostic activity at our center has greatly evolved over the years, shifting gradually from a post-toxicity to a pre-treatment approach. Development of pharmacogenetic guidelines by national and international consortia, genotyping, and IT technology evolution have impacted DPYD testing uptake in the clinics. Our participation in a large prospective implementation study (Ubiquitous Pharmacogenomics) increased health practitioners' and patients' awareness of pharmacogenetic matters and provided additional standardized infrastructures for genotyping and reporting. Nationwide test reimbursement together with recommendations by regulatory agencies in Europe and Italy in 2020 definitely changed the clinical practice guidelines of fluoropyrimidines prescription. A dramatic increase in the number of pre-treatment DPYD genotyping and in the coverage of new fluoropyrimidine prescriptions was noticed by the last year of observation (2022). Conclusion: The long path to a successful DPYD testing implementation in the clinical practice of a National Cancer Center in Italy demonstrated that the development of pharmacogenetic guidelines and genotyping infrastructure standardization as well as capillary training and education activity for all the potential stakeholders are fundamental. However, only national health politics of test reimbursement and clear recommendations by drug regulatory agencies will definitely move the field forward. [ABSTRACT FROM AUTHOR]

Toxoplasma gondii and Neospora caninum are apicomplexan protozoa of major concern in livestock and T. gondii is also considered one of the major threats and a public health concern. These protozoa have a wide range of intermediate hosts, including birds. The present work aimed to assess the prevalence of these cyst-forming parasites in migratory and sedentary birds of prey. The skeletal muscle and myocardium of 159 birds of prey from Central Italy, belonging to 19 species and recovered across 6 Wildlife Recovery Centers/Care structures along the Italian migratory route, were collected specifically for molecular (PCR) and for histopathological analysis to detect T. gondii and N. caninum. For the molecular analysis, genomic DNA was extracted. The DNA was tested by sequence typing, targeting GRA6, 529 bp repeated element, B1, PK1, BTUB, SAG2, alt.SAG2, and APICO genes for T. gondii and to end-point PCR targeting NC5 gene for N. caninum. Thirty-seven out of the one hundred and fifty-nine analyzed samples tested positive for T. gondii with a prevalence of 23.27% and nine for N. caninum, with a prevalence of 5.66%. Thirty-two sequences were obtained from the thirty-seven isolates of T. gondii. Among these, 26 presented alleles compatible with type I strain in 1 or more loci, 4 with type II strain and 2 consisted of atypical strains. Toxoplasma gondii genetic variability in birds of prey confirms previous findings of wildlife as reservoirs of atypical strains. Results from the histology showed few protozoal tissue cysts in skeletal muscle (n. 4) and hearts (n. 2). [ABSTRACT FROM AUTHOR]

Toxoplasma gondii is one of the most common protozoan parasites and is widely present in all warm-blooded animals. Although clinical disease is uncommon, some species, including ring-tailed lemurs (Lemur catta), have been found to develop acute and lethal toxoplasmosis. The aim of this study was to describe the pathologic, immunohistochemical, serological, and molecular findings of an outbreak of fatal toxoplasmosis in three captive ring-tailed lemurs in Central Italy in 2009. The animals died acutely within few days. The necropsy was immediately performed; necrotic lesions in the spleen, liver, and kidney, as well as interstitial pneumonia, were found histologically. All animals had high titers of anti–T. gondii-specific antibodies (1:1280 IgM and 1:640 IgG) according to a modified agglutination test (MAT) and immunohistochemistry showed scattered tachyzoites in the target organs. Diagnosis was confirmed by PCR and clonal type II was identified. In addition, the seven co-habiting lemurs were seronegative. This paper reports the first outbreak of acute disseminated toxoplasmosis in captive ring-tailed lemurs in Italy. These findings confirm the high susceptibility of this endangered species to toxoplasma infection, which may be considered a further threat to captive population viability. [ABSTRACT FROM AUTHOR]

Small ruminant lentiviruses (SRLV) belong to the Retroviridae family and can cause various diseases. One of the most impacting diseases is visna-maedi, a complex disease characterized by long latencies and chronic progressive inflammatory events affecting the nervous system, lungs, mammary gland, and articular joints. A single nucleotide polymorphism (rs408593969, c.103G>A, missense mutation E35K) in the ovine transmembrane protein gene 154 (TMEM154) was identified as protective against small ruminant lentivirus infection in different herds worldwide. However, there is evidence in the scientific literature of a breed-specificity of this protective effect and, furthermore, there are still limited studies regarding the association between the animal genotype and the infecting virus genotype. Thus, the aim of this study was to further investigate the association between the animal genotype for the suggested protective mutation and the infecting virus genotype, in three different sheep breeds reared in northern Italy. The results obtained only partially confirmed the data available in the literature, as the protective effect was confirmed only for SRLV genotype A clusters, while other genotypes (namely B and E) infected AA and GA animals. Further studies with an experimental infection of specific virus genotypes in hosts with specific genotypes are required to confirm the larger number of cases the results obtained in this study. [ABSTRACT FROM AUTHOR]

On the River Ticino in northern Italy, a small number of captive Eurasian otters Lutra lutra, belonging to the European breeding programme for self-sustaining captive populations, were reintroduced in 1997, after the species had been declared locally extinct in the 1980s. We surveyed for otter signs in 2008, 2010, 2016–2017 and 2018, confirming the presence of what is probably a small population. To assess the abundance and viability of the population, we genotyped fresh spraints collected during the last two surveys, using 11 microsatellite markers, and modelled the population trend using Vortex. A minimum of six individuals were identified from 25 faecal samples. The analysis of mitochondrial DNA determined that the reintroduced otters share a transversion that is characteristic of the Asiatic subspecies Lutra lutra barang, confirming the contribution of the Asiatic subspecies to the genetic pool of the captive-bred founder population. Population size was consistent with the release of three pairs of otters and all models implied that the number of founders was too small to ensure the long-term survival of the population. Stochastic factors are therefore likely to threaten the success of this reintroduction. [ABSTRACT FROM AUTHOR]

Toxoplasmosis, caused by the protozoan parasite Toxoplasma gondii, is a widespread zoonosis capable to affect a wide range of warm‐blooded vertebrates. In the past two decades, T. gondii emerged as a significant aquatic pathogen with some pathogenic atypical genotypes isolated and characterized from stranded marine mammals. In contrast, no information is available for mammals in freshwater environment. Although otters are considered highly susceptible to T. gondii infection, to date molecular evidence of T. gondii in Eurasian otter (Lutra lutra) does not exist. We report the first molecular evidence of T. gondii in a free‐ranging Eurasian otter from southern Italy and characterized the present strain as a genotype type II variant, with all loci type II except PK1 (locus sequence corresponding to type II variant B), B1 (locus sequence corresponding to type II/X A) and C29‐2 (locus with SNPs). Our results indicate circulation of a type II variant in freshwater environment which suggests potential risk of transmission to animals and humans. The finding of a potential pathogenic strain is of great concern for future conservation programmes of the critically endangered Eurasian otter in southern Italy. [ABSTRACT FROM AUTHOR]

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Background: Fluconazole-resistant Candida parapsilosis is a matter of concern., Objectives: To describe fluconazole-resistant C. parapsilosis genotypes circulating across hospitals in Spain and Rome and to study their azole-resistance profile associated with ERG11p substitutions., Patients/methods: We selected fluconazole-resistant C. parapsilosis isolates (n = 528 from 2019 to 2023; MIC ≥8 mg/L according to EUCAST) from patients admitted to 13 hospitals located in five Spanish cities and Rome. Additionally, we tested voriconazole, posaconazole, isavuconazole, amphotericin B, micafungin, anidulafungin and ibrexafungerp susceptibility., Results: Of the 53 genotypes found, 49 harboured the Y132F substitution, five of which were dominating city-specific genotypes involving almost half the isolates. Another genotype involved isolates harbouring the G458S substitution. Finally, we found two genotypes with the wild-type ERG11 gene sequence and one with the R398I substitution. All isolates were fully susceptible/wild-type to amphotericin B, anidulafungin, micafungin and ibrexafungerp. The azole-resistance patterns found were: voriconazole-resistant (74.1%) or voriconazole-intermediate (25.2%), posaconazole-resistant (10%) and isavuconazole non-wild-type (47.5%). Fluconazole-resistant and voriconazole non-wild-type isolates were likely to harbour substitution Y132F if posaconazole was wild type; however, if posaconazole was non-wild type, substitution G458S was indicated if isavuconazole MIC was >0.125 mg/L or substitution Y132F if isavuconazole MIC was ≤0.125 mg/L., Conclusions: We detected a recent clonal spread of fluconazole-resistant C. parapsilosis across some cities in Spain, mostly driven by dominating city-specific genotypes, which involved a large number of isolates harbouring the Y132F ERG11p substitution. Isolates harbouring substitution Y132F can be suspected because they are non-susceptible to voriconazole and rarely posaconazole-resistant., (© 2024 Wiley-VCH GmbH. Published by John Wiley & Sons Ltd.)

Norovirus (NoV) is an enteric virus with foodborne transmission. Bivalve shellfish are a main source of infections and outbreaks. In Italy a voluntary based monitoring plan to check the safety of bivalve shellfish was set up at provincial level. This study describes the occurrence and distribution of NoV in the Northern Adriatic Sea and in the Ligurian Sea. From October 2018 to September 2020, 807 bivalve shellfish samples ( n  = 205 oysters, n  = 182 mussels, n  = 348 clams, n  = 72 other bivalve shellfish) were tested by One-Step Retrotranscription Real-time polymerase chain reaction for NoV GI and GII and quantified according to the ISO 15216-2:2013 and ISO 15216-1:2017. Positive samples were further analyzed to determine genotype by sequencing of the ORF1/ORF2 junction of the viral genome. A total of 126 samples were positive for NoV, mussels, and oysters had the highest probability of being positive and positive samples were found mainly in the colder season. Of these samples, 46% were NoV GII, 13% NoV GI, and 40% carried both genogroups. Thirty-seven samples were typeable (GI n  = 12 and GII n  = 25) with GI samples belonging to four genotypes and GII samples belonging to five genotypes. GII.3 genotype was the most prevalent, followed by GII.4, particularly Sydney 2012 subtype, a leading cause of infections worldwide, was found in three oysters' and three clams' samples. The phylogenetic analysis revealed a high heterogeneity among the species that are scattered in several clusters. Considering the low infectious dose the overall presence of NoV in edible shellfish, particular those to be eaten raw or undercooked, is moderately high. The presence of genotypes frequently involved in human infections strengthens the need for ongoing monitoring, which should be extended at national level.

Toxoplasma gondii is a widespread protozoan parasite (phylum Apicomplexa), which causes a zoonotic parasitic disease, known as toxoplasmosis. The aim of this study was to evaluate the occurrence and genotypes of T. gondii in wild boars of southern Italy and thus to assess the risk of infection for consumers. The boars were inspected during the hunting season within the regional project 'Wild Boar Emergency Plan in Campania', and molecular analyses were performed on 338 boars analysing a total number of 884 matrices (263 brains, 310 hearts and 311 masseter muscles). Toxoplasma gondii was detected in 134 out of 338 boars (39.6%). No significant statistical difference between genders was found (χ2 = 0.15 p =.70). The prevalence was 47.1%, 39.3% and 39.2% in piglets, yearlings and adults, respectively (χ2 = 0.41; p =.81). The highest prevalence of T. gondii was found in masseter muscles (74/311, 23.8%), followed by the heart (70/310, 22.6%) and brain (58/263, 22.0%), respectively. Microsatellite (MS) analysis of 11 samples revealed eleven T. gondii genotypes (nine atypical, one belonging to type II one to type III). Most of the genotypes found were thus atypical and may be virulent in humans. Hierarchical clustering analysis showed the presence of three distinct clusters, with the majority of atypical genotypes in the GII‐GIII cluster. The high prevalence of infection in masseters highlights the potential risk for public health, considering that this muscle is commonly used to prepare raw meat products ('guanciale' and sausages), which may be a source of T. gondii infection in humans. Wild boars may act as an interface role between wildlife, livestock and humans. Our data highlight the urgent need to minimize the risk of infection for animals and humans by setting up a surveillance programme and preventive strategies in a One Health approach to wildlife species. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus is one of the most important pathogens causing mastitis in cattle, and it is responsible for economic losses in dairy herds worldwide. The PCR amplification of the 16S-23S rRNA intergenic spacer (ribosomal spacer PCR, RS-PCR) allows a rapid classification of the strains in genotypes and genotypic clusters (CL), which are characterized by different epidemiological and clinical properties. Both RS-PCR and multi-locus sequence typing (MLST) were performed on strains isolated from bovine bulk tank milk (BTM) collected from dairy herds located in the Lombardy region (northern Italy), to outline the distribution of Staph. aureus genotypes in this geographical area. Out of 844 examined samples, 398 were positive for Staph. aureus , with a variable count (cfu/mL) Up to 8 colonies from each sample were genotyped. A total of 1,101 Staph. aureus strains were analyzed with RS-PCR, and only a selection of them (n = 86), in relation to their frequency and geographical origin, underwent MLST. This study revealed 8 major genotypic clusters (CLB, CLC, CLR, CLS, CLI, CLF, CLAO, and CLZ), of which Staph. aureus CLB (29.3%) was the most common. Samples of BTM positive for CLB had a Staph. aureus cfu/mL count significantly higher than the non-CLB positive ones. Our MLST analysis showed genotypes already known as bovine-associated in literature, such as clonal complexes CC8, CC97, and CC151. The same selection of 86 strains was also analyzed for the presence of the adlb gene, which was recently proposed as a possible marker of contagiousness. Most Staph. aureus belonging to CLB or CC8 carried the adlb gene (85%), whereas this gene was detected in only 9% of non-CLB strains (CLAA, CLBI, CLBJ, CLS). In conclusion, the present study confirms that Staph. aureus CLB, which is recognized as a contagious genotype, is a particularly relevant agent of intramammary infection in dairy cows in Lombardy, and indirectly supports the idea that adlb can be a possible marker of contagiousness of isolates. [ABSTRACT FROM AUTHOR]

Blastocystis is a ubiquitous protozoan with a wide range of hosts. In humans, its presence has been associated with gastrointestinal disorders, although its role as a pathogen still needs to be elucidated. Until now, 17 Blastocystis subtypes (STs) have been identified, with ST1–ST4 the most commonly found in humans. Among domestic animals, the same STs reported in humans have been detected in dogs. An epidemiological survey on dog kennels was carried out to evaluate the prevalence of Blastocystis and the STs involved. Overall, 99 faecal samples were collected from the rescue shelters. Blastocystis detection was performed through conventional barcoding PCR targeting the 1800-bp SSU-rDNA, followed by sequencing and phylogenetic analysis. Blastocystis DNA was found in 21 faecal samples (21.2%), and all samples were successfully sequenced and identified as ST3 in a unique monophyletic group. The presence of Blastocystis was reported for the first time in dogs from Italy, with the identification of ST3, the subtype most commonly found in humans. [ABSTRACT FROM AUTHOR]

• SEZ strains from clinical samples of Italian horses showed high genetic variability. • 16S–23S ISR typing detected all types, mainly A1 and 30.5% multi-products. • 16S rRNA gene sequencing showed V1-V5 regions are the most important for typing. • 16S rRNA gene sequencing detected three genetic subgroups of equine SEZ. Streptococcus equi subsp. zooepidemicus (SEZ) is an opportunistic and zoonotic pathogen of horses. In this study, genetic intraspecies variability of SEZ obtained mainly from respiratory and genital samples of horses was investigated by analysis of the 16S–23S rRNA intergenic spacer region (ISR) and of the 16S rRNA gene. 16S–23S ISR rRNA type A1 was predominant, although a high rate of multiple products (30.5%) was obtained. Phylogenetic analysis of the 16S rRNA gene detected three genogroups (I, II and III). 16S rRNA variable regions V1 and V2 are the most important regions for evaluating SEZ intraspecies variability, but at least V1-V5 regions should be considered to avoid mistakes. Analysis of all 16S rRNA sequences available in databases assigned human SEZ to groups I and III but not to group II. These results show a high genetic variability in SEZ collected from different specimens of horses from various regions of Italy. [ABSTRACT FROM AUTHOR]

Extended-spectrum β-lactamase (ESBL)- and plasmid mediated AmpC-type cephalosporinase (pAmpC)-producing Escherichia coli (ESBL/pAmpC E. coli) in food-producing animals is a major public health concern. This study aimed at quantifying ESBL/pAmpC-E. coli occurrence and transfer in Italy’s broiler production pyramid. Three production chains of an integrated broiler company were investigated. Cloacal swabs were taken from parent stock chickens and offspring broiler flocks in four fattening farms per chain. Carcasses from sampled broiler flocks were collected at slaughterhouse. Samples were processed on selective media, and E. coli colonies were screened for ESBL/pAmpC production. ESBL/pAmpC genes and E. coli phylogroups were determined by PCR and sequencing. Average pairwise overlap of ESBL/pAmpC E. coli gene and phylogroup occurrences between subsequent production stages was estimated using the proportional similarity index, modelling uncertainty in a Monte Carlo simulation setting. In total, 820 samples were processed, from which 513 ESBL/pAmpC E. coli isolates were obtained. We found a high prevalence (92.5%, 95%CI 72.1–98.3%) in day-old parent stock chicks, in which blaCMY-2 predominated; prevalence then dropped to 20% (12.9–29.6%) at laying phase. In fattening broilers, prevalence was 69.2% (53.6–81.3%) at the start of production, 54.2% (38.9–68.6%) at slaughter time, and 61.3% (48.1–72.9%) in carcasses. Significantly decreasing and increasing trends for respectively blaCMY-2 and blaCTX-M-1 gene occurrences were found across subsequent production stages. ESBL/pAmpC E. coli genetic background appeared complex and bla-gene/phylogroup associations indicated clonal and horizontal transmission. Modelling revealed that the average transfer of ESBL/pAmpC E. coli genes between subsequent production stages was 47.7% (42.3–53.4%). We concluded that ESBL/pAmpC E. coli in the broiler production pyramid is prevalent, with substantial transfer between subsequent production levels. [ABSTRACT FROM AUTHOR]

Mild cognitive impairment (MCI) generally evolves in a gradually progressive decline in memory and non-memory cognitive domains that may eventually decay to dementia. This process might be preventable by improving early detection of the MCI syndrome followed by proper and timely interventions. The aim of this work was providing helpful indications for a standardized early diagnosis of MCI, mainly focusing on the Italian elderly population. We reviewed here MCI epidemiology and classification, as well as the most recent advancements in early detection of the patient with MCI in the Italian scenario. Specialist centers in connection with general practitioners (GPs) have been established across the country and designated as Centers for Cognitive Disorders and Dementia (CDCD). CDCDs are dedicated to the diagnosis and management of patients for all forms of dementia across all the complex staging spectrum. New tools were made available by the advancements of imaging techniques and of the research on biomarkers, leading to novel approaches based on the combination of imaging and biomarker detection, to improve accuracy and effectiveness in the early diagnosis of MCI. Moreover, patient genotyping, alone or in combination with other techniques, was also revealed as a promising method in evaluating and preventing MCI progression. We recommend the introduction of all these novel tools in the diagnostic practice of the specialist centers and that further efforts and resources are spent into the research of the most effective techniques and biomarkers to be introduced as first-level tests into the practice of early diagnosis of MCI. [ABSTRACT FROM AUTHOR]

Highlights • This is the first surveillance study to report representative data from Sicily on food and environmental contamination by human enteric viruses. • Human bocavirus detection in bivalve molluscs is reported, suggesting an assessment of their transmission risk by food. • Enteric viruses are widely found in aquatic environments and on vegetables; this information is essential to develop risk management decisions. Abstract Objectives Enteric viruses are responsible for foodborne and waterborne infections affecting a large number of people. Data on food and water viral contamination in the south of Italy (Sicily) are scarce and fragmentary. The aim of this study was to evaluate the presence of viral contamination in food, water samples, and surface swabs collected in Sicily Methods The survey was conducted on 108 shellfish, 23 water samples (seawater, pipe water, and torrent water), 52 vegetables, one peach and 17 berries, 11 gastronomic preparations containing fish products and/or raw vegetables, and 28 surface swabs. Hepatitis A virus (HAV), genogroup GI, GII, and GIV norovirus (NoV), enterovirus (EV), rotavirus (RoV), hepatitis E virus (HEV), adenovirus (AdV), and bocavirus (BoV) were detected by nested (RT) PCR, real-time PCR, and sequence analysis. Results The most frequently detected viruses in shellfish were HAV (13%), NoV (18.5%), and EV (7.4%). Bocavirus was found in 3.7%, HEV in 0.9%, and AdV in 1.9% of the molluscs. Of the 23 water samples, 21.7% were positive for GII NoV and 4.3% for RoV and HEV genotype 3. Of the 70 vegetable samples, 2.9% were positive for NoV GI (GI.5 and GI.6), 2.9% for EV, and 1.4% for HEV. In the gastronomic preparations, only one EV (9%) was detected. No enteric viruses were detected in the berries, fruit, or swabs analyzed. Conclusions Molecular surveillance of water and food samples clearly demonstrated that human pathogenic viruses are widely found in aquatic environments and on vegetables, and confirmed the role of vegetables and bivalve molluscs as the main reservoirs. [ABSTRACT FROM AUTHOR]

For over three centuries, thoroughbred (TB) horses have been selected exclusively for traits enhancing racing performances. Officially the TB origins can be genetically traced back along the male line due to the crossbreeding among 50 English royal mares and four Arab oriental stallions in 1700s. Because of the TB population is tightly controlled, possible loss of genetic variability should be carefully evaluated for breed conservation and management programme. To this aim FTA® cards of 10032 TB foals over a 14-year new-born campaign period were collected for genetic variability evaluation using 16 microsatellite markers. Total number of allele was 118 with a mean value of 7.37 alleles per locus; Polymorphic information content (PIC) values were above the informative threshold (PIC >0.5) for all microsatellites except for HTG4 and HMS2 whereas no significant differences were showed between the mean expected (He) and observed heterozygosity (Ho) values (0.674 vs. 0.675, respectively). Hardy–Weinberg proportion exhibited no statistically significant deviation from equilibrium (p <.05) for all loci; the inbreeding coefficient mean was close to zero suggesting very low probability of autozygosity. The number of genotypes observed (Ng) was calculated for each microsatellite and the most representative was found at the HMS2 locus (LL, frequency 0.557). Parentage testing was also investigated reporting a combined probability of identity (PI) for the 16 loci of 4.1 × 10−14 while the probability of exclusion (PE) exceeded 99% in all cases. Overall data reported a reasonable level of informativeness which genuinely reflect the narrower genetic structure of the Thoroughbred population. Thoroughbred population from Italy did not show any significant evidence for close inbreeding; a moderate level of genetic diversity was found at some loci yet still adequate for parentage and identity verification. Appropriate management programme could be placed to introduce new genetic variability in the Italian Thoroughbred population. [ABSTRACT FROM AUTHOR]

Toxoplasma gondii is an apicomplexan parasite that in Europe is genetically characterized by three main clonal genotypes, with a lesser prevalence of atypical patterns. Data on the genotypes of T. gondii circulating both in wildlife and livestock in Northern Italy are scarce. In the present study skeletal muscle samples of cattle ( Bos taurus ), swine ( Sus scrofa domesticus ), fox ( Vulpes vulpes ), roe deer ( Capreolus capreolus ) and wild boar ( Sus scrofa ) were genotyped by using a nested PCR of 6 loci (alt.SAG2, GRA6, 5′SAG2, BTUB, C22-8 and SAG1) and in silico RFLP. High prevalence of genotype I and non-canonical genotypes were observed in this study, with some differences in the population structure of the parasite between livestock and wildlife. Genetic variability of T. gondii in Europe could be more variable than previously thought, with possible implication for public health. [ABSTRACT FROM AUTHOR]

Objective: Attacks on humans by dogs in a pack, though uncommon, do happen, and result in severe, sometimes fatal, injuries. We describe the role that canine genetic markers played during the investigation of a fatal dog-pack attack involving a 50-year-old male truck driver in a parking lot in Tuscany (Italy). Using canine specific STR genetic markers, the local authorities, in the course of their investigations, reconstructed the genetic relationships between the dogs that caused the deadly aggression and other dogs belonging to the owner of the parking who, at the moment of the aggression, was located in another region of Italy. Results: From a Bayesian clustering algorithm, the most likely number of clusters was two. The average relatedness among the dogs responsible for the aggression was higher than the average relatedness among the other dogs or between the two groups. Taken together, all these results indicate that the two groups of dogs are clearly distinct. Genetic relationships showed that the two groups of dogs were not related. It was therefore unlikely that the murderous dogs belonged to the owner of the parking lot who, on grounds of this and additional evidence, was eventually acquitted. [ABSTRACT FROM AUTHOR]

In accordance with the goal of the World Health Organization Regional Office for Europe, the Italian National Measles and Rubella Elimination Plan aimed to interrupt indigenous measles transmission in Italy by the end of 2015. However, from 2013 to 2015, Italy experienced high measles burden with 4902 measles cases (49.3% laboratory-confirmed) reported to the enhanced measles surveillance system (cumulative incidence in the triennium reference period: 2.4/100,000 population). The measles elimination goal was not reached. Laboratory surveillance of measles circulating genotypes is performed by the Measles and Rubella National Reference Laboratory (NRL) at the Italian National Institute of Health (Istituto Superiore di Sanità − ISS), in Rome. Samples received from 1 January 2013–31 December 2015 were analysed. Those positive for measles genome by molecular tests were sequenced and phylogenetically analysed. Phylogenetic analysis performed by NRL identified that genotypes D4 and D8 were endemic and co-circulated in 2011–2013: study results show that genotype D4 disappeared during 2013. Sporadic cases were associated to genotype B3 during 2011–2013, which became endemic in Italy during 2014 and co-circulated with D8 until 2015. Sporadic cases were found belonging to genotypes D9 and H1 all over the period in exam. Similar trend has been observed in European WHO Region. [ABSTRACT FROM AUTHOR]

Genotyping of bacteria is critical for diagnosis, treatment, and epidemiological surveillance. Coxiella burnetii, the etiological agent of Q fever, has been recognized to have a potential for bioterrorism purposes. Because few serosurveys have been conducted in Italy, there is still limited information about the distribution of this pathogen in natural conditions. In this paper, we describe the genotyping of C. burnetii strains by multispacer sequence typing (MST) detected in cattle and goat farms in the Abruzzi region of Italy. Biological samples (milk, aborted fetus) positive for C. burnetii DNA were sequenced in the spacer regions and compared with those already publicly available (). The MST profile of C. burnetii detected in milk samples demonstrated the presence of a new allele, whereas the C. burnetii spacer sequences from fetus and milk goat samples displayed a new allelic combination. The results suggest the circulation of novel genotypes of C. burnetii in Italy. [ABSTRACT FROM AUTHOR]

Simple Summary: In this study, serological and molecular assays in 55 pigs in Sicily were conducted in order to investigate Leptospira spp. prevalence and to carry out strain characterization. A seropositivity rate of 16.4% was determined; 3.64% of kidney samples tested positive for pathogenic Leptospiral DNA. Obtained data showed that Leptospira infection is common among pigs in southern Italy, confirming the importance of Leptospiral infection in pigs and reaffirming the potential role of these animals as a source of infection for humans (occupational risk) and other animals. Our study delivers a comprehensive overview based on up-to-date data to deepen the knowledge of swine leptospiral infections, characterize new potential emerging strains, and reinforce control measures able to reduce the infection risk in swine herds. Leptospirosis is a re-emerging zoonosis of worldwide significance; a wide spectrum of wild and domestic animal species act as natural or accidental hosts. Swine can act as maintenance or accidental hosts of pathogenic Leptospira spp. This study aimed at investigation of Leptospira spp. prevalence and diversity in slaughtered pigs in southern Italy (Sicily). In total, 55 samples of kidneys and blood were collected. Microscopic agglutination test and real-time PCR were performed to detect pathogenic and intermediately pathogenic Leptospira. Partial rpoB gene sequencing and multi-locus sequence typing (MLST) were performed to characterize Leptospira species. The analysis showed a seropositivity rate of 16.4%, with Australis representing the most frequently identified serogroup (63.64%); Pomona and Sejroe were detected with a prevalence of 27.27% and 9.09%, respectively. Pathogenic Leptospiral DNA was detected in 2 kidney samples (3.64%). Leptospira were identified through MLST as L. borgpetersenii serovar Tarassovi (serogroup Tarassovi). Obtained data confirmed the presence of Leptospira infection among pigs in southern Italy, suggesting that management of these animals may be considered an occupational risk for humans. [ABSTRACT FROM AUTHOR]

Abstract: Background: The prevalence of infections with human papillomavirus (HPV) specific genotypes differs by age and areas. Knowledge of these differences will help predicting how prophylactic HPV vaccination and screening program could best be integrated. Objectives: To investigate variations in the HPV distribution between areas and ages in Italy and the impact of vaccination on HPV prevalence. Study design: 37,367 women aged 25–60 years who attended cervical screening in eight different areas in Northern and Central Italy were tested for HPV infection with the high-risk hybrid capture (hr-HC2) assay. hr-HC2 positive samples were genotyped by an intensive integrated strategy. Results: hr-HPV types were detected in 79.1% of HC2 positive women. HPV16 was the most frequent type, followed by HPV31, HPV18 and HPV56. A statistically significant variability in HPV type distribution between centres (overall p <0.001) was observed. No significant overall difference in the HPV type distribution was observed in the age groups 25–34, 35–44 and 45–60 years. Considering cross-protection, overall 57.6% (95%CI 56.0–59.3) of all infections by hr-HPV types was preventable by vaccination with the bivalent vaccine and 49% (95%CI 46.9–51.1) with the quadrivalent vaccine. The variability between centres was statistically significant with both bivalent ( , p <0.0001) and quadrivalent vaccine ( , p <0.0001). Conclusions: We observed differences in HPV genotype distribution according to centres but not to age. Results suggest that the higher proportion of HPV16/18 related high grade CIN in younger women could be the result of faster progression and not of earlier infection by these types. [Copyright &y& Elsevier]

Purpose: Treatment with statins requires close monitoring of serum creatine kinase (CK) levels to prevent myopathy, a common and potentially serious dose-dependent adverse effect of these drugs. We have investigated the correlation between elevated CK levels and polymorphisms in the genes encoding transporters involved in statin disposition. Methods: Patients with and without statin-induced elevated serum CK levels were genotyped for polymorphisms in SLCO1B1 ( SLCO1B1 A388G and SLCO1B1 T521C), ABCB1 ( ABCB1 C1236T and ABCB1 C3435T) and ABCG2 ( ABCG2 C421A). Results: Patients carrying SLCO1B1 T521C or ABCB1 C1236T single nucleotide polymorphisms (SNPs) had an odds ratio (OR) for statin-induced elevated serum CK levels of 8.86 ( p < 0.01) and 4.67 ( p < 0.05), respectively, while patients carrying the SLCO1B1 A388G SNP had an OR of 0.24 ( p < 0.05). An arbitrary score based on genotype combination discriminated patients with and without CK elevation at a specificity of 97 % and a sensitivity of 39 %. Conclusion: Genotyping of the SLCO1B1, ABCB1 and ABCG2 genes deserves consideration as a clinical approach to improve statin safety while concomitantly reducing the burden of blood tests for CK measurements. [ABSTRACT FROM AUTHOR]

Highlights: [•] Surveillance for HAstV in Italy identified the circulation of HAstV-4. [•] Italian HAstV-4 strains belong to three distinct genetic lineages (4a–4c). [•] A possible recombination among type-1 and some type-4 HAstVs have been observed. [•] Puzzled pathways of evolution for the various lineages have been observed. [ABSTRACT FROM AUTHOR]

Highlights: [•] Molecular characterization of 113 genotypes intercepting Italian and abroad almond varieties. [•] A total of 9 polymorphic SSR loci were employed detecting 159 alleles. [•] Data represent the first overview of genetic diversity among Italian almond cultivars using molecular markers. [•] STRUCTURE analysis allowed to identify admixture among different gene pools. [ABSTRACT FROM AUTHOR]

Highlights: [•] We examined genetic diversity and geographic distribution of Brucella melitensis and Brucella abortus in Italy. [•] MLVA-16 distinguished 56 genotypes for B. melitensis, most isolates were in the West Mediterranean lineage. [•] MLVA-16 distinguished 32 genotypes for B. abortus but 77.8% of isolates had the same MLVA-11 genotype. [•] One B. melitensis from human had an identical genotype as a sheep isolate suggesting a possible epidemiological link. [•] Isolates with genotypes not typically found in Italy were readily identified. [ABSTRACT FROM AUTHOR]

Objectives To assess the prevalence of hepatitis C virus (HCV) NS3/4A protease inhibitor (PI) resistance mutations in HCV genotype 1-infected PI-naive individuals in Italy. Patients and methods One hundred and twelve patients infected with HCV genotype 1a or 1b (based on Versant HCV Genotype 2.0 or 5′UTR/core sequencing) and never treated with any HCV PI were evaluated. The whole NS3 region was analysed by population sequencing and mutations related to resistance to linear and macrocyclic PIs were recorded. Results Forty-six HCV-monoinfected and 66 HCV/HIV-coinfected subjects were studied. Complete NS3 sequence information was obtained for 109 (97.3%) samples: 67 subtype 1a and 42 subtype 1b. Subtype assignment by NS3 sequencing was concordant in 100.0% and 83.9% of cases with the original 5′UTR sequencing and Versant result, respectively. At least one mutation related to PI resistance was detected in 21 (19.3%) isolates. However, 11 of these had only Q80K, expected to confer resistance to one investigational macrocyclic compound, and were detected only in subtype 1a. Boceprevir and telaprevir resistance-related mutations were detected in 10 (9.2%) isolates and included V36L, T54S and V55A. Only one isolate harboured two mutations (V36L and T54S). There was no association between HCV PI resistance and HIV coinfection or exposure to HIV PIs. Conclusions A minority of untreated HCV genotype 1 patients in Italy harbour a virus population carrying HCV PI resistance-related mutations. The clinical implications of this finding warrant further analysis. [ABSTRACT FROM PUBLISHER]

Abstract: Use of rifampicin (RIF) in combination with colistin (COL) has been proposed for the treatment of multidrug-resistant Acinetobacter baumannii infections owing to in vitro synergism. The aim of the present study was to evaluate the molecular epidemiology and mechanisms of RIF resistance in 57 clinical isolates of A. baumannii in two tertiary care hospitals in Naples (Italy) from 2006 to 2010. Amongst the collection, 36 isolates showed high RIF minimum inhibitory concentrations (MICs) (256mg/L to ≥512mg/L), 16 showed intermediate MICs (8–16mg/L) and 5 had low MICs (4mg/L). Of the 36 isolates with elevated RIF MICs, 35 were assigned to sequence type ST2 and 1 to ST78. Amongst the 57 isolates, 35 carried at least one mutation in rpoB, including H535L in 9 isolates and double mutations D525N and P544L in 7 isolates, whilst 22 showed no rpoB mutations. Treatment with the efflux pump inhibitor phenyl-arginine-β-naphthylamide (PAβN) of resistant isolates with no mutations in rpoB and different RIF MICs reduced the MIC by >10-fold and restored the synergism between RIF and COL in time–kill studies, whilst it had no effect on strains carrying rpoB mutations. In conclusion, the emergence of elevated RIF MICs in A. baumannii isolates from our geographical area was mostly caused by mutations in rpoB; low to intermediate RIF MICs were also caused by altered membrane permeability to the drug. The phenomenon was contributed by the selection of two prevalent clones both assigned to ST2 genotype. These data may have implications for the correct identification of cases with A. baumannii infection that would not benefit from addition of RIF to COL. [Copyright &y& Elsevier]

Abstract: This study reports the occurrence of Toxoplasma gondii in the brain of three striped dolphins (Stenella ceoruleoalba) found stranded on the Ligurian Sea coast of Italy between 2007 and 2008. These animals showed a severe, subacute to chronic, non-purulent, multifocal meningo-encephalitis, with the cerebral parenchyma of two dolphins harbouring protozoan cysts and zoites immunohistochemically linked to T. gondii. Molecular, phylogenetic and mutation scanning analyses showed the occurrence of Type II and of an atypical Type II T. gondii isolates in one and two dolphins, respectively. In spite of the different molecular patterns characterizing the above T. gondii genotypes, the brain lesions observed in the three animals showed common microscopic features, with no remarkable differences among them. The role of T. gondii in causing the meningo-encephalitis is herein discussed. [Copyright &y& Elsevier]

Abstract: Group A human rotavirus (HRV) strains with a bovine-like (G6) major outer capsid protein VP7 were first detected in Palermo, Italy, in the late 1980s, and subsequently worldwide. During a 25-year rotavirus surveillance period, additional HRV G6 strains, associated with either a P[9] or P[14] VP4 genotype, have been detected sporadically, but repeatedly, in Palermo. Whether these G6 HRVs were transmitted to humans directly from an animal reservoir or could have circulated at low prevalence in susceptible individuals is uncertain. Upon sequence analyses of the VP7, VP4, VP6, NSP4 and NSP5 gene segments, all the Italian HRV strains displayed a conserved genotype constellation, G6-P[9]/[14]-I2-E2-H3. Intra-genotypic lineages and/or sub-lineages were observed among the various HRV strains, with some lineage/sublineage combinations being retained over time. Interestingly, two epidemiologically unrelated G6P[9] viruses, collected in the same rotavirus season, were found to have a clonal origin. In conclusion, our results indicate not only diverse origin of animal derived G6 HRVs in Palermo but also suggest human-to-human transmission of certain strains. [Copyright &y& Elsevier]

Abstract: We genotyped celiac disease (CD)–associated haplotypes DQ2.5, DQ8, DQ2.2, and DQ7 in 1005 CD patients from North Eastern Italy using a Tag–single nucleotide polymorphism (SNPs) approach and real time PCR platform, checking the accuracy and reliability of the method and comparing it to traditional PCR-SSP. Only 14 of 2010 chromosomes analyzed (0.7%) showed discrepancies between the Tag-SNPs real-time polymerase chain reaction (PCR) method and the PCR–single-strand polymorphism (SSP) technique, indicating a high sensitivity and specificity (ranging from 0.987 to 1 and from 0.998 to 0.999, respectively) for tagging with respect to corresponding human leukocyte antigen (HLA) alleles identified by PCR-SSP. Moreover, the overall cost of the Tag-SNPs HLA typing method was low (3 to 4 €/sample instead of 35 to 70 €/sample with commercial kits), making it suitable for mass screenings. Hence, we believe that the Tag-SNPs HLA typing could be used to complement or replace classic HLA typing in at high-risk groups, for research purposes and eventually in population screening programs. [Copyright &y& Elsevier]

Abstract: A total of 47 stool samples were collected at the same stud farm from young foals with rotavirus diarrhoea and from their stud mares. Illness involved foals during three consecutive winter seasons. Infection in the farm appeared firstly in January–February 2008. After vanishing in the warm seasons, cases reappeared in March 2009 and 2010. Determination of the rotavirus G- and P-types was carried out using nested RT-PCR in samples collected in 2009 and 2010. A total of 19 of 47 samples resulted positive for rotavirus. The G type was determined in 19/47 samples, whereas the P genotype was determined in 17/47 samples. All equine strains presented a G14 VP7 in combination with a P[12] VP4, suggesting persistence of the same viral strain in the stud farm, during at least two consecutive winter periods. Sequence analysis of the genes encoding the outer capsid rotavirus proteins VP7 and VP4 revealed that the virus had a close relationship between strains recently isolated in the rest of Europe. [Copyright &y& Elsevier]

Objectives Infections caused by multidrug-resistant (MDR) Acinetobacter baumannii are a challenging problem worldwide. Here, the molecular epidemiology and the genetic basis of antibiotic resistance in 111 MDR A. baumannii strains isolated from June 2005 to March 2009 from infected patients in 10 intensive care units (ICUs) in central Italy were investigated. Methods Epidemiological typing was performed by random amplification of polymorphic DNA, PCR-based sequence grouping and macrorestriction analysis. MICs of antibiotics were determined by the broth microdilution method. Genes for OXA carbapenemases, metallo-β-lactamases and the CarO porin were searched for by PCR. Results Molecular genotyping identified one predominant A. baumannii lineage, related to the international clonal lineage II, accounting for 95.6% of isolates. Isolates referable to this lineage were recovered from all ICUs surveyed and were resistant to nearly all classes of antimicrobials, with the exception of tigecycline and colistin. A high percentage (60.5%) of A. baumannii isolates showed elevated resistance to imipenem (MICs ≥ 128 mg/L), concomitant with resistance to meropenem. Carbapenem resistance was associated with the presence of either blaOXA-58-like (22.8%) or blaOXA-23-like (71.1%) carbapenemase genes. Molecular typing showed that the epidemic lineage encoding OXA-23 emerged in 2007 and displaced a genetically related clone encoding OXA-58 that had been responsible for previous ICU outbreaks in the same region. Conclusions Emergence of the OXA-23 epidemic lineage could result from selective advantage conferred by the blaOXA-23-like determinant, which provides increased resistance to carbapenems. [ABSTRACT FROM PUBLISHER]

By screening faecal samples collected over four consecutive years (2002-2005) from hospitalized children with diarrhoea in Palermo, Italy, astroviruses (HAstVs) were detected in 3.95% of the patients. The predominant type circulating was HAstV-1 but, in 2002, only HAstV-2 and -4 were identified. Interestingly, the HAstVs-2 detected appeared to be consistently different in 5' end of their open reading frame 2 from the previously described subtypes. These novel type 2 strains were included in a new 2c lineage based on the phylogenetic analysis and the presence of nine peculiar substitutions. [ABSTRACT FROM AUTHOR]

Abstract: A survey for methicillin-resistant Staphylococcus aureus (MRSA) in finishing pig holdings was carried out in Italy in 2008. MRSA isolates were characterised by spa-, MLST-, SCCmec- and antimicrobial susceptibility typing. A prevalence of 38% (45/118, 95% CI 29.4–46.9%) positive holdings was observed. Eleven different spa-types were found among 102 MRSA isolates, clustering in lineages associated with farm animals (ST398, ST9, ST(CC)97 in 36 holdings) and humans (ST1, 7 holdings). Nine (7.6%) holdings were positive for two, three or four different and unrelated spa-types in various combinations. ST398 was the most prevalent lineage (33 positive holdings). The most prevalent spa-type was t899 (ST398), detected in 22 positive holdings. Three novel spa-types (t4794 of ST9; t4795 of ST97; t4838 of ST398) were detected. Ten holdings were positive for spa-type t1730, that proved to be a new single-locus variant of ST97, within the CC97 (ST1476). The most prevalent SCCmec was Type V (79 isolates), while Type IVb was found in 10 isolates. None of the isolates was positive for Panton-Valentine Leukocidin, while most of the t127 and t1730 isolates, one t4794, one t4795, and one t2922 were positive for LukE-LukD genes. All 64 antimicrobial susceptibility tested isolates were resistant to tetracyclines, with high resistance rates to trimethoprim (68.8%), erythromycin (60.9%), and ciprofloxacin (35.4%). All t127, ST1 isolates were resistant to tetracycline–ciprofloxacin–erythromycin. This survey provides the first report of MRSA ST1 and ST(CC)97 among pigs and the first report of MRSA ST9 from pigs in Europe. The presence of human-associated CA-MRSA (t127, ST1, SCCmec type V) in 6% holdings surveyed can represent an additional MRSA reservoir for infections in humans. [Copyright &y& Elsevier]

Abstract: The adiponectin (adiponectin, C1Q and collagen domain containing) encoded by ADIPOQ is an adipokine that modulates several biological processes such as lipogenesis, gluconeogenesis, fatty acid oxidation, glucose uptake and insulin sensitivity. An objective of this study was to identify SNPs in the ADIPOQ gene both in cosmopolitan and local pig breeds reared in Italy and in Meishan samples. Resequencing of ADIPOQ gene regions in 16 pigs of 12 breeds revealed only two SNPs (EU489740:g.1611G>A synonymous and EU489740:g.1735G>A missense mutations) already reported. The g.1735G>A polymorphism was genotyped by PCR-RFLP in 510 pigs from 11 breeds reared in Italy (Italian Large White, Italian Duroc, Italian Landrace, Belgian Landrace, Hampshire, Pietrain, Calabrese, Casertana, Cinta Senese, Mora Romagnola and Nero Siciliano) and from Chinese Meishan breed. The Italian local breeds were homozygous for the g.1735G allele while the Meishan samples resulted homozygous for the g.1735A allele. The polymorphism segregates in the cosmopolitan breeds, except for Hampshire, and the rarer g.1735A allele showed the highest frequency in Italian Duroc (0.12). Association analysis of g.1735G>A polymorphism with estimated breeding values (EBVs) for average daily gain (ADG), feed:gain ratio (FGR), weight of neck and loin (lean cuts, LC), weight of ham (H) and backfat thickness (BFT) were performed in Italian Duroc heavy pigs. The GA vs GG pigs showed higher least square means for ADG (P =0.003) and LC (P =0.036) EBVs and lower value for FGR EBV (P =0.033). [Copyright &y& Elsevier]

The association between isolate genotype, defined as in the international spoligotype database SpolDB4, and extrapulmonary tuberculosis was determined among 1009 patients in a population-based, 4-year survey performed in Tuscany, Italy. Extrapulmonary disease occurred in 24.2% of patients. A statistically significant association with extrapulmonary disease was found for the BOVIS (adjusted OR 3.2; 95% CI  1.2–8.1) and for the Central Asian (CAS) lineages (adjusted OR 2.3; 95% CI  1.0–5.1). These findings support the view that Mycobacterium tuberculosis strains within individual genotypic lineages might have evolved unique pathogenic characteristics that are capable of influencing the clinical outcome of the infection. [ABSTRACT FROM AUTHOR]

Abstract: Amino acid polymorphisms of the prion protein gene influence sheep susceptibility to classical and atypical scrapie. Substitutions at codons 136, 154 and 171 play an important role in classical scrapie. Codon 141 leucine to phenylalanine mutation (AFRQ) has been recognized as an increased risk factor for atypical scrapie. In addition a rare allele with lysine at codon 171 (ARK) has been detected in Mediterranean sheep breeds. The presence of ARK poses two problems: the determination of its frequency and its possible interference with genotyping output of routine methods lacking specific detection capacity for ARK. The aim of our work was the development of a routine genotyping method with the capacity to identify ARK and AFRQ in addition to the normally detected alleles and to determine the frequencies of all these alleles in 5 main Italian breeds: Sarda (n =2494), Bergamasca (n =2686), Appenninica (n =297), Comisana (n =361) and Massese (n =402). A multiplex primer extension assay targeting the six single nucleotide polymorphisms of interest was developed. Allele frequencies revealed a very low level of ARR in Bergamasca (6.91%) as opposed to the other breeds, very diverse levels of AFRQ ranging from absence in Comisana to 10.70% in Massese and a restricted presence of ARK. This allele has only been detected in Bargamasca with a significant 3.67% and marginally in Appenninica (0.34%). These results underline the need for adequate routine methods for genotyping of breeds with alleles that can interfere with typing of important codons such as the case of ARK for codon 171. [Copyright &y& Elsevier]

In animals, botulism is commonly sustained by botulinum neurotoxin C, D or their mosaic variants, which are produced by anaerobic bacteria included in Clostridium botulinum group III. In this study, a WGS has been applied to a large collection of C. botulinum group III field strains in order to expand the knowledge on these BoNT-producing Clostridia and to evaluate the potentiality of this method for epidemiological investigations. Sixty field strains were submitted to WGS, and the results were analyzed with respect to epidemiological information and compared to published sequences. The strains were isolated from biological or environmental samples collected in animal botulism outbreaks which occurred in Italy from 2007 to 2016. The new sequenced strains belonged to subspecific groups, some of which were already defined, while others were newly characterized, peculiar to Italian strains and contained genomic features not yet observed. This included, in particular, two new flicC types (VI and VII) and new plasmids which widen the known plasmidome of the species. The extensive genome exploration shown in this study improves the C. botulinum and related species classification scheme, enriching it with new strains of rare genotypes and permitting the highest grade of discrimination among strains for forensic and epidemiological applications. [ABSTRACT FROM AUTHOR]

The systematics and taxonomy of Ascaris lumbricoides and Ascaris suum , two of the world's most widespread nematodes, still represent a highly debated scientific issue. Two different transmission scenarios have been described according to endemicity: separated host-specific transmission cycles in endemic regions, and a single pool of infection shared by humans and pigs in non-endemic regions. The swine roundworm A. suum is now recognized as an important cause of human ascariasis also in endemic areas such as China, where cross-infections and hybridization have also been reported, as well as in non-endemic regions like Italy. This study aimed to investigate the molecular epidemiology of human and pig ascariasis in three countries representing different epidemiological scenarios: Italy as a non-endemic country, Colombia as an endemic country, and Slovakia as a non-endemic country, but with a poor socio-economic context linked to some focal populations of Roma settlements. A total of 237 nematodes were analysed: 46 from Colombia (13 from humans, 33 from pigs), 114 from Slovakia (20 from humans, 94 from pigs) and 77 from Italy (17 from humans and 60 from pigs). Genotyping by PCR-RFLP of nuclear (ITS) and sequencing of mitochondrial (cox1) target regions were performed. ITS genotypes were used to estimate the Hardy-Weinberg (HW) equilibrium according to hosts and country of origin. The partial cox1 sequences were used to analyse genetic polymorphisms according to hosts and country of origin, as well as to infer the network of haplotypes, their evolutionary relationships and geographical distribution. 110 quality cox1 sequences were obtained. Haplotype network revealed three main groups corresponding to clade A, B and C. Clade C included most of the human cases from Italy, while those from Slovakia and Colombia were grouped in clade B. Ascaris from Italian and Colombian pigs showed HW equilibrium at the ITS marker, while disequilibrium was found in A. lumbricoides from Slovak pigs, which suggest a high unexpected amount of roundworms of human origin circulating also in pigs. This study updates and extends the current understanding of Ascaris species and genotypes circulating in different epidemiological scenarios, with particular attention to the inclusion of human-derived Ascaris in the phylogenetic cluster C. Despite the evidence of HW equilibrium in the ITS in pig-derived Italian samples, the amount of genetic variation seems to support the existence of two closely related species. • Haplotype network of Ascaris cox 1 confirmed the presence of three clades. • Ascaris from Italian and Colombian pigs showed to be in Hardy-Weinberg equilibrium. • Hardy-Weinberg disequilibrium was found in Ascaris from Slovak pigs. • Significant genetic variation within populations Ascaris based on geography was found. [ABSTRACT FROM AUTHOR]

Aims: To determine the variability of the prion protein gene ( PRNP) in goats from Northern and Southern Italy. Methods and results: Genomic DNA isolated from goat blood was polymerase chain reaction (PCR)-amplified for the coding region of the PRNP gene and then sequenced. In total, 13 polymorphic sites were identified: G37V, T110P, G127S, M137I, I142M, I142T, H143R, R154H, P168Q, T194P, R211Q, Q222K and S240P (substitutions I142T and T194P are novel) giving rise to 14 haplotypes. Clear frequency differences between Northern and Southern breeds were found and confirmed by genetic distance analysis. Conclusions: Differences in allele distribution were found between Northern and Southern goats, in particular regarding the M142 and K222 alleles, possibly associated to scrapie resistance; philogeographical analysis supported the idea that Northern and Southern breeds may be considered as separate clusters. Significance and impact of the study: In Italy only limited studies have been carried out on caprine PRNP genotype distribution; this study is important to fill this lack of information. Moreover the finding of significant differences among allele distributions in Northern and Southern goats, especially if involved in modulating resistance/susceptibility, need to be carefully considered for the feasibility of selection plans for resistance to scrapie. [ABSTRACT FROM AUTHOR]

Abstract: DNA molecular techniques were used in a forensic investigation involving the poaching of wildlife in a national park of Italy. A poacher, after having snared a wild boar (Sus scrofa) sow, knifed it to death. The animal was retrieved by conservation officers at the scene before the poacher could remove the carcass. Subsequently, the suspect denied the charges. During a search of his home, a bloodstained knife was confiscated. A method to identify the species from the DNA extracted from the stains revealed the blood to be that of the non-domestic form of Sus scrofa. Further DNA typing for individual identity using species-specific single tandem repeats or microsatellites (STRs) showed that the DNA on the knife matched that of the poached boar. Based upon the forensic evidence obtained, the suspect was convicted of poaching and of cruelty to animals. [Copyright &y& Elsevier]

Malaria due to Plasmodium vivax is globally widespread and is associated with substantial morbidity. The parasite was previously prevalent in temperate areas from which it has been eradicated, however there is a risk of re-introduction because of increased international travel and migration. Following the occurrence of an autochthonous case of P. vivax malaria in Italy after decades of malaria eradication, we applied a molecular approach to compare parasites involved in the introduced case and to determine whether a highly polymorphic gene marker could be useful to tag a P. vivax isolate geographically. To this end, the sequence encompassing the interspecies conserved blocks 5 and 6 of the gene encoding for merozoite surface protein 1 (msp-1) was determined in 16 P. vivax isolates from different regions, and analysed along with 24 pvmsp-1 sequences downloaded from published data. Results have shown that: (i) parasites from the introduced case and the putative source of infection identified following epidemiological investigation, although very similar, differed in three nucleotide substitutions, of which one non synonymous; ii) some geographical isolates looked tightly clustered (e.g. Korean and Punjab isolates), but others were less so. [Copyright &y& Elsevier]

Conclusions: Our data reinforces the need to monitor the molecular epidemiology of CR A. baumannii and its associated antimicrobial resistance genes at national level., Background: Carbapenem-resistant (CR) Acinetobacter baumannii has been increasingly recognized as a major cause of health care-associated infections in critically ill patients and hospital outbreaks., Results: CR A. baumannii isolates assigned to international clonal lineage II (ICL II) and to ST78 clonal lineages were responsible for several epidemics in Italian hospitals during 2002-2018. Molecular analysis of carbapenem resistance showed the presence of OXA-58 CHDL in A. baumannii isolates assigned to ICL II and ST78 clonal lineage, which was replaced by OXA-23 CHDL in A. baumannii isolates assigned to ICL II since 2007 in several hospitals. CR A. baumannii was mainly responsible for respiratory tract infections and at a lesser extent for sepsis in intensive care unit patients., Methods: A narrative review of literature was conducted, searching PubMed database for articles on CR Acinetobacter spp. isolates from Italy published between January 2010 and December 2019.

Objective: To evaluate partial HPV16/18 genotyping as a possible biomarker to select women attending HPV-based cervical cancer screening at higher risk to be referred to colposcopy., Design: Population-based cohort study., Setting: Organised cervical cancer screening programmes (Italy)., Population: Women with high-risk HPV infection (period: 2015-2019)., Methods: We analysed the association between partial HPV16/18 genotyping, cytology triage and histologically confirmed diagnosis of high-grade cervical intraepithelial neoplasia (CIN3 + ) lesions., Main Outcome Measures: Detection rate (DR) and positive predictive value (PPV) for histologically confirmed CIN3 + (any episode in the 2 years after baseline); sensitivity for CIN3 + and number of colposcopies needed for lesion detection., Results: The study included 145 437 women screened with HPV testing by the clinically validated COBAS 4800 HPV assay (Roche). Overall, 9601 (6.6%) women were HPV + at baseline; HPV16 and HPV18 were present in 1865 and 594 samples, respectively. The cumulative (baseline plus 1-year repeat) cytology positivity was 42.8% and high-grade cytology was significantly higher (P < 0.0001) among women with HPV16 infection at baseline (15.2%). The cumulative CIN3 + DR for women with HPV16, HPV18 and other HPV-type infections was 9.8%, 3.4% and 1.8%, respectively., Conclusions: Partial HPV16 genotyping may play a role in triage, whereas HPV18 seems to behave much more similarly to the other HPV types and does not provide additional stratification. HPV16 genotyping combined with high-grade cytology can be envisaged as a triage biomarker in cervical screening to maximise CIN3 + detection while minimising colposcopy at baseline or 1-year repeat., Tweetable Abstract: HPV16 genotyping combined with high-grade cytology can be used as triage biomarker for CIN3 + in HPV-positive women., (© 2020 The Authors. BJOG: An International Journal of Obstetrics and Gynaecology published by John Wiley & Sons Ltd.)