Principles for Good Practice in the Conduct of Non-interventional Studies: The View of Industry Researchers.

This reflection paper presents a consolidated view of EFPIA on the need for principles for good practice in the generation and use of non-interventional studies (NIS), including overarching principles such as the registration of hypothesis evaluating treatment effect (HETE) studies. We first define NIS and the important adjacencies to clinical trials and relationship with real-world evidence (RWE). We then outline the principles for good practice with respect to appropriate research design, study protocol, fit-for-purpose variables and data quality, analytical methods, bias reduction, transparency in conduct and use, privacy management and ethics review.

Identification and Characterisation of pST1023 A Mosaic, Multidrug-Resistant and Mobilisable IncR Plasmid.

We report the identification and characterisation of a mosaic, multidrug-resistant and mobilisable IncR plasmid (pST1023) detected in ST1023, a monophasic variant 4,[5],12:i: strain of widespread pandemic lineage, reported as a Southern European clone. pST1023 contains exogenous DNA regions, principally gained from pSLT-derivatives and IncI1 plasmids. Acquisition from IncI1 included and and these conferred the ability to be mobilisable in the presence of a helper plasmid, as we demonstrated with the conjugative plasmids pST1007-1D (IncFII) or pVC1035 (IncC).

Clinical and epidemiological aspects of sporotrichosis: an overview of the cases reported in Europe and in Italy.

Sporotrichosis is a fungal infection occurring worldwide, especially in tropical and sub-tropical areas. We present a brief review of clinical and epidemiological aspects of sporotrichosis, as well as its treatment. Sporotrichosis is rarely reported in Europe and the European Centre of Disease Control does not track its infection rate.

Antimicrobial resistance gene shuffling and a three-element mobilisation system in the monophasic Salmonella typhimurium strain ST1030.

In this study we describe the genetic elements and the antimicrobial resistance units (RUs) harboured by the Salmonella Typhimurium monophasic variant 1,4,[5],12:i:- strain ST1030. Of the three identified RUs two were chromosomal, RU1 (IS26-bla-IS26-strAB-sul2- IS26) and RU2 (IS26-tetR(B)-tetA(B)-ΔIS26), and one, RU3 (a sul3-associated class 1 integron with cassette array dfrA12-orfF-aadA2-cmlA1-aadA1), was embedded in a Tn21-derived element harboured by the conjugative I1 plasmid pST1030-1A. IS26 elements mediated the antimicrobial resistance gene (ARG) shuffling and this gave rise to pST1030-1A derivatives with different sets of ARGs.

Infection caused by Sporothrix schenckii: an autochthonous case in Bari, Southern Italy.

An autochthonous case of lymphocutaneous sporotrichosis caused by Sporothrix schenckii is reported. The patient developed skin lesions localized along the lymphatics that appeared after he suffered an injury while collecting wicker canes in marshy water. The fungus was identified as Sporothrix schenckii by MALDI-TOF and sequencing.

Evaluation of Antibiotic Resistance of Strains Isolated in Bari, Southern Italy, in 2017-2018 by Phenotypic and Genotyping Methods.

antibiotic resistance is a constantly evolving process and local surveillance is warranted to guide clinicians in the choice of therapy. Antibiotic susceptibility testing was performed by E-test on 92 strains, and resistance to clarithromycin and levofloxacin was also evaluated using a commercially available genotyping method. In naïve patients the resistance to clarithromycin, levofloxacin, and metronidazole was 37.

Genomics: Novel Insights on Candidate Antibiotic Resistance and Virulence Genes in an Emerging Opportunistic Pathogen.

Coagulase Negative Staphylococci (CoNS) are becoming increasingly recognized as an important cause of human and animal infections. Notwithstanding their clinical relevance, annotation of genes potentially involved in pathogenicity and/or antibiotic resistance in the CoNS species (SAR) is currently very limited. In the current work we describe the genome of a novel methicillin resistant isolate of SAR, which we named Bari, and present a comprehensive analysis of predicted antibiotic resistance profiles and virulence determinants for all the 22 currently available SAR genomes.

Helicobacter pylori: Survival in cultivable and non-cultivable form in artificially contaminated Mytilus galloprovincialis.

Several studies report the presence of Helicobacter pylori (H. pylori) in seawater either free or attached to planktonic organism. After considering the role played by plankton in the food chain of most aquatic ecosystems and the possible role that seafood products can assume in the transmission of H.

Helicobacter pylori infection: association with dietary habits and socioeconomic conditions.

Introduction: Few studies have investigated factors possibly related to the source of Helicobacter pylori infection in humans.

Materials And Methods: This was a retrospective study including a population of 201 H.pylori positive patients and 259 H.

A case report of esophageal actinomycosis in an immunocompetent patient and review of the literature.

Actinomycosis is a rare, chronic and slowly progressive granulomatous disease caused by Actinomyces spp., a Gram-positive anaerobic bacterium that rarely affects the esophagus. Although this infection is uncommon, it has been reported in both immunocompromised and immunocompetent individuals.

IS26 mediated antimicrobial resistance gene shuffling from the chromosome to a mosaic conjugative FII plasmid.

In the present study we report the identification of a sul3-associated class 1 integron containing the dfrA12-orfF-aadA2-cmlA1-aadA1-qacH array embedded in a Tn21-derived element that is part of a conjugative FII plasmid named pST1007-1A. The plasmid was identified in the Salmonella Typhimurium strain ST1007, a member of a clinically relevant clonal MDR lineage diffuse in Italy. ST1007 exhibited resistance to ampicillin, chloramphenicol, streptomycin, sulphamethoxazole, tetracycline and trimethoprim encoded by bla, cmlA1, (aadA1, aadA2, strAB), (sul2, sul3), tet(B) and dfrA12 genes, respectively.

Carbapenemases-producing Klebsiella pneumoniae in hospitals of two regions of Southern Italy.

Carbapenem-resistant Klebsiella pneumoniae infections are reported with increasing frequency elsewhere in the world, representing a worrying phenomenon for global health. In Italy, there are hotspot data on the diffusion and type of carbapenemase-producing Enterobacteriaceae and K. pneumoniae in particular, with very few data coming from Apulia and Basilicata, two regions of Southern Italy.

Update on Acanthamoeba jacobsi genotype T15, including full-length 18S rDNA molecular phylogeny.

Free-living amoebae of the genus Acanthamoeba are worldwide present in natural and artificial environments, and are also clinically important, as causative agents of diseases in humans and other animals. Acanthamoeba comprises several species, historically assigned to one of the three groups based on their cyst morphology, but presently recognized as at least 20 genotypes (T1-T20) on the basis of their nuclear 18S ribosomal RNA (rRNA) gene (18S rDNA) sequences. While strain identification may usually be achieved targeting short (<500 bp) 18S ribosomal DNA (rDNA) fragments, the use of full-length gene sequences (>2200 bp) is necessary for correct genotype description and reliable molecular phylogenetic inference.

A novel group of IncQ1 plasmids conferring multidrug resistance.

The IncQ is a group of non-conjugative but mobilisable plasmids that are found and stably maintained in a wide range of bacteria contributing to the spread of antimicrobial resistance genes and to the insurgence of multidrug resistant bacteria. Here we report the identification, in clinical Salmonella Typhimurium strains, of an IncQ1 plasmid (pNUC) which confers resistance to sulfamethoxazole, streptomycin and tetracycline through the presence of sul2, strAB and tetA genes, respectively. pNUC was detected in five multidrug resistant S.

Helicobacter pylori DNA isolation in the stool: an essential pre-requisite for bacterial noninvasive molecular analysis.

Purpose: Real-time polymerase chain reaction (RT-PCR) is a widely used technique for bacterial and viral infection diagnosis. Herein, we report our preliminary experience in retrieving H. pylori genetic sequences in stools and analyzing genotypic clarithromycin resistance by RT-PCR (noninvasive), with the aim of comparing this procedure with that performed on biopsy samples (invasive).

Fusariosis in a Patient with Acute Myeloid Leukemia: A Case Report and Review of the Literature.

Fusarium spp. causes infections mostly in patients with prolonged neutropenia. We describe the case of a disseminated Fusarium solani infection in a patient with acute myeloid leukemia which never reached complete remission during its clinical course.

Human papilloma virus (HPV) genotypes prevalence in a region of South Italy (Apulia).

Introduction: Since human papillomavirus (HPV) is the central casual factor in cervical cancer, understanding the epidemiology and geographical area distribution of the most prevalent HPV genotypes constitutes an important step towards development of strategies of prevention.

Aim: The aim of this study was to investigate the prevalence of HPV infection and to determine HPV types distribution among 822 HPV positive women and some sexual male partners in Apulia (Italy).

Methods: HPV DNA detection and genotyping was performed by nested-PCR for the L1 region and reverse line blot hybridization allowing the specific detection of 24 HPV genotyping both high risk (HR) and low risk (LR).

Colistin-associated Acute Kidney Injury in Severely Ill Patients: A Step Toward a Better Renal Care? A Prospective Cohort Study.

Background: Critically ill patients with severe sepsis or septic shock may need relatively high colistin daily doses for efficacy against multidrug-resistant and extensively drug-resistant gram-negative rods. However, acute kidney injury (AKI) may represent a major dose-limiting adverse effect of colistin. We sought to determine AKI occurrence and to identify factors influencing AKI risk in severely ill patients receiving colistin according to a recently proposed dosing strategy.

Diffusion and persistence of multidrug resistant Salmonella Typhimurium strains phage type DT120 in southern Italy.

Sixty-two multidrug resistant Salmonella enterica serovar Typhimurium strains isolated from 255 clinical strains collected in Southern Italy in 2006-2008 were characterised for antimicrobial resistance genes, pulsotype, and phage type. Most strains (83.9%) were resistant to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (ACSSuT) encoded in 88.

Comparison of two methods for the detection of verotoxin producing E.coli in human faecal samples during an outbreak of HUS in Apulia, Southern Italy.

This study evaluated the diagnostic performances of an ELISA method and a molecular method for the detection of verotoxin in faecal samples during an outbreak of haemolytic-uraemic syndrome (HUS) occurring in Apulia, Southern Italy. Two of the 16 faecal samples were positive for verotoxin when analysed by ELISA and resulted PCR positive for stx1, stx2, eaeA and serogroup O26. The other 14 faecal samples resulted negative with both tests.

Isolation and molecular characterization of free-living amoebae from different water sources in Italy.

Free-living amoebae (FLA) are protozoa ubiquitous in Nature, isolated from a variety of environments worldwide. In addition to their natural distribution, some species have been found to be pathogenic to humans. In the present study a survey was conducted in order to evaluate the presence and to characterize at molecular level the isolates of amoebic organisms collected from different water sources in Italy.

Alternaria is an Infrequent Cause of Keratitis: A Case Report and Review of the Literature.

Objective: To report a case of fungal keratitis caused by Alternaria in a 49-year-old female who developed an acute onset of eye infection after ocular trauma caused by an olive leaf.

Methods: The clinical presentation, microbiological diagnosis, and therapeutic approaches are reported.

Results: The patient was referred to our university hospital clinic with corneal abscess in her left eye.

Genotypic heterogeneity based on 18S-rRNA gene sequences among Acanthamoeba isolates from clinical samples in Italy.

Acanthamoeba keratitis (AK) is an ocular disease caused by members of a genus of free-living amoebae and it is associated predominantly with contact lens (CL) use. This study reports 55 cases of AK diagnosed in Italy. Genotype identification was carried out by PCR assay followed by sequence analysis of the 18S rRNA gene using the genus specific primers JDP1 and JDP2.