Adriano Di Pasquale

IZS Istituto Zooprofilattico Sperimentale | IZS · Bioinformatics Unit

Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for serious respiratory infections in humans. Even in the absence of respiratory symptoms, gastrointestinal (GI) signs were commonly reported in adults and children. Thus, oral–fecal transmission was suspected as a possible route of infection. The objective o...

Background Genomic data-based machine learning tools are promising for real-time surveillance activities performing source attribution of foodborne bacteria such as Listeria monocytogenes. Given the heterogeneity of machine learning practices, our aim was to identify those influencing the source prediction performance of the usual holdout method co...

Background Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases’ prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and dem...

The Istituti Zooprofilattici Sperimentali (IZSs) are public health institutes dealing with the aetiology and path-ogenesis of infectious diseases of domestic and wild animals. During Coronavirus Disease 2019 epidemic, the Italian Ministry of Health appointed the IZSs to carry out diagnostic tests for the detection of SARS-CoV-2 in human samples. In...

Hepatitis E virus (HEV) is a zoonotic pathogen, causing infectious hepatitis in man. Pigs and wild boars are the natural asymptomatic reservoirs, while the disease in humans could be either asymptomatic or evolve in hepatitis. In Europe, an increasing number of human infections from HEV have been reported over the last few years. The main route of...

Human orthopneumovirus (HRSV) is a virus belonging to the Pneumovirus genus that causes lower respiratory tract infections (LRTI) in infants worldwide. In Tunisia, thousands of infants hospitalized for LRTI are found to be positive for HRSV but no whole genome sequences of HRSV strains circulating in this country are available thus far. In this stu...

Abstract Campylobacter jejuni is considered as the main pathogen in human food‐borne outbreaks worldwide. Over the past years, several studies have reported antimicrobial resistance (AMR) in C. jejuni strains. In Europe, the official monitoring of AMR comprises the testing of Campylobacter spp. from food‐producing animals because this microorganism...

Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes listeriosis, a serious foodborne illness. In the nature-to-human transmission route, Lm can prosper in various ecological niches. Soil and decaying organic matter are its primary reservoirs. Certain clonal complexes (CCs) are over-represented in food production and represent a challe...

Background Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles. Method...

Background Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases’ prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and dem...

Streptococcus suis is a pathogen associated with severe diseases in pigs and humans. Human infections have a zoonotic origin in pigs. To assess circulating strains, we characterized the serotypes, sequence types, and antimicrobial susceptibility of 78 S. suis isolates from diseased farmed pigs in Italy during 2017-2019. Almost 60% of infections wer...

Background Faced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise’ (IZSAM) in Teramo (Italy) is in charge of the SARS-Co...

Background Faced to the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise’ (IZSAM) in Teramo (Italy) supports the genomic surveill...

A total of 66 Listeria monocytogenes (Lm) isolated from 2013 to 2018 in a small-scale meat processing plant and a dairy facility of Central Italy were studied. Whole Genome Sequencing and bioinformatics analysis were used to assess the genetic relationships between the strains and investigate persistence and virulence abilities. The biofilm forming...

Background Klebsiella pneumoniae (Kp) is a Gram-negative hospital-acquired pathogen. Kp also poses a potential food safety hazard, since a significant increase of multidrug-resistant (MDR) Kp was observed in foods. The purpose of this study was to characterize MDR Kp strains in order to evaluate the presence of beta-lactams, quinolones and aminogly...

Background Food is the main source of Listeria monocytogenes (Lm) infection. Lm is a highly heterogeneous species composed of hypervirulent and hypovirulent clones. Understanding the distribution of Lm clonal complexes (CCs) in different food categories has strong implications for risk assessment. The aim of this work was to analyse collection of L...

Hepatitis E virus (HEV) is an emergent zoonotic pathogen, causing worldwide acute and chronic hepatitis in humans. HEV comprises eight genotypes and several subtypes. HEV genotypes 3 and 4 (HEV3 and HEV4) are zoonotic. In Italy, the most part of HEV infections (80%) is due to autochthonous HEV3 circulation of the virus, and the key role played by w...

The advent of “omics” is transforming Biological Sciences. Next Generation Sequencing (NGS) in Food Safety represents a challenge for Clinical Microbiology and Public Health. A new professional profile which combines different domains represents a strategic lever to increase competitiveness in this field. The Erasmus+ project Learning Genomics for...

Soil is a central habitat in the transmission routes of L. monocytogenes from the farm environment to foodstuff. Little information is available on the genetic feautures underlying its fitness in this complex habitat. The aim of this study was to investigate genome characteristics linked to fitness in soil. Soil survival was assessed in a large col...

In this report, the draft genome sequence of Listeria monocytogenes serovar 1/2a strain IZSAM_Lm_14-16064, isolated in Italy from a cooked ham, is announced. The genome is similar to that of a clinical strain isolated in 2014.

The genus Brucella includes several genetically monomorphic species but with different phenotypic and virulence characteristics. In this study, proteins of two Brucella species, B. melitensis type strain 16 M and B. ovis REO198 were compared by proteomics approach, in order to explain the phenotypic and pathophysiological differences among Brucella...

The current pandemic is caused by a novel coronavirus (CoV) called SARS-CoV-2 (species Severe acute respiratory syndrome-related coronavirus, subgenus Sarbecovirus, genus Betacoronavirus, family Coronaviridae). In Italy, up to the 2nd of April 2020, overall 139,422 confirmed cases and 17,669 deaths have been notified, while 26,491 people have recov...

Abstract The ‘learning‐by‐doing’ EU‐FORA fellowship programme in the development of risk assessment tools based on molecular typing and WGS of Campylobacter jejuni genome was structured into two main activities: the primary one focused on training on risk assessment methodology and the secondary one in starting and enhancing the cooperation between...

Here, we report the genome sequence of Listeriamonocytogenes serovar 1/2a strain IZSAM_Lm_15_17439_A144, isolated in Italy from a patient during a Listeria monocytogenes outbreak in 2008. This strain showed 98.9% sequence identity to a strain isolated in Canada in the same year.

We report the whole-genome sequence of a Listeria monocytogenes strain isolated from a child in central Italy. Interestingly, the sequence showed a difference of only 13 single-nucleotide polymorphisms (SNPs) from a strain responsible for a severe listeriosis outbreak that occurred between January 2015 and March 2016 in the same region.

Il documento presenta un progetto sperimentale il cui scopo è quello di realizzare un sistema di navigazione sul benessere animale durante il trasporto in armonia con il regolamento europeo (EC) 1/2005. Il prototipo realizzato è costituito da componenti hardware e software. Una unità a bordo installata sui camion raccoglie e trasmette informazioni...

The authors present an experimental project that aims to establish an effective navigation system in accordance with European Council Regulation 1/2005 concerning animal welfare during transport. The prototype created during the project consists of both hardware and software components. An onboard unit is installed at truck level. It collects and t...

Transport can be a significant stress factor for livestock and can result in poor animal welfare and economic losses. Quality management measures are actively employed in fields different from animal welfare and could be applied to improve the welfare of animals and reduce the consequent losses during road transportation and related activities Trai...

Animal welfare protection during long journeys is mandatory according to European Union regulations designed to ensure that animals are transported in accordance with animal welfare requirements and to provide control bodies with a regulatory tool to react promptly in cases of non-compliance and to ensure a safe network between products, animals an...

Many available services have been designed for a single-channel world, Web and Internet typically. In a real world scenario, an ever-growing number of users take advantage of different kinds of communication channels and devices. In this paper, we propose a methodology to formalize the re-design process of these services to support multi-channel ac...

The DRT* is an order preserving Scalable Distributed Data Struc- tures with an almost constant amortized upper bound costs for ex- act searches and insertions. The result is based on the correction techinque the DRT* uses when a given request produces an ad- dress error. This technique mainly consists in exchanging infor- mation among servers about...

In this paper we revise some of the most relevant aspects concerning the quality of service in wireless networks, providing, along the research issues we are currently pursuing, both the state-of-the-art and our recent achievements. More specifically, first of all we focus on network survivability, that is the ability of the network of maintaining...

The RP s is an order preserving Scalable Distributed Data Structure (SDDS) ables to manage exact searches and insertions with a cost of O log f 2 n messages in the worst case, where n is the final number of servers and f is a large value. Unfortunately, the RP s presents the same logarithmic costs for both the operations in the amortized case. On t...

We investigate the servers allocation problem in a network of worksta- tions, a first step toward the analysis of more realistic scenarios for Scalable and Distributed Data Structures. Unlike the previous frameworks, we con- sider the cost of the messages exchanged among the sites in terms of time or length of the paths traversed in the network. Th...

In this paper we analyze the amortized cost of inserts and exact searches in a DRT*, an order preserving scalable distributed data structure able to manage both mono-dimensional and multi-dimensional data. We show that by adding to the DRT* strategy a correction algorithm after split operations, a sequence of m requests of intermixed exact-searches...

Scalable Distributed Data Structures (SDDS) are access methods specifically designed to satisfy the high performance requirements of a distributed computing environment made up by a collection of computers connected through a high speed network. In this paper we propose an order preserving SDDS with a worst-case constant cost for exact-search queri...

SDDSs (Scalable Distributed Data Structures) are access methods specifically designed to satisfy the high performance requirements of a distributed computing environment made up by a collection of computers connected through a high speed network. In this paper we present and discuss performances of ADST, a new order preserving SDDS with a worst-cas...

This paper reviews literature on scalable data structures for searching in a distributed computing environment. Starting with a system where one server manages a file of a given size that is accessed by a specific number of clients at a specific rate, a scalable distributed data structures (SDDS) can efficiently manage a file that is n times bigger...

In this paper we consider the dictionary problem in the scalable distributed data structure paradigm introduced by Litwin, Neimat and Schneider and analyze costs for insert and exact searches in an amortized framework. We show that both for the 1-dimensional and the k- dimensional case insert and exact searches have an amortized almost constant cos...

The performance of a database management system (DBMS) is fundamentally dependent on the access methods and query processing techniques available to the system. Traditionally, relational DBMSs have relied on well-known access methods, such as the ubiquitous B + -tree, hashing with chaining, and, in some cases, linear hashing [52]. Object-oriented a...