Investigating transmission patterns among preterm neonates during an outbreak of necrotizing enterocolitis related to Clostridium butyricum using whole-genome sequencing.

BACKGROUND: Necrotizing enterocolitis is the most severe life-threatening acquired gastrointestinal disorder among preterm neonates. We describe here an outbreak of Clostridium butyricum-related necrotizing enterocolitis in preterm neonates that occurred in three different neonatal centres, in southeast France. METHODS: We defined a confirmed case of C. butyricum-related necrotizing enterocolitis in preterm neonates by the presence of clinical signs according to modified Bell criteria and C. butyricum identified from stool samples using real-time polymerase chain reaction or culture. A phylogenetic analysis of the isolated strains by whole-genome sequencing was also performed. RESULTS: Between 5th and 27th January 2022, we identified 10 confirmed cases of C. butyricum-related necrotizing enterocolitis, including five from Neonatal Centre 1, four from Neonatal Centre 2, and one from Neonatal Centre 3. The attack rate of necrotizing enterocolitis in Neonatal Centre 1 was 7.1% (5/70). The positivity rate of C. butyricum detected from stool samples was higher during the outbreak period (37/276; 13.4%) than outside this period (7/369; 1.9%), while systematic screening was maintained (P<0.001). Phylogenetic analysis showed a clonality between strains inside four clusters. Two clusters included neonates hospitalized in different neonatal centres, suggesting the transmission of C. butyricum strains during the transfer of neonates between neonatal centres. CONCLUSIONS: This outbreak of C. butyricum-related necrotizing enterocolitis confirms a cross-transmission between preterm neonates, including twin or triplet siblings, and involving necrotizing enterocolitis cases together with asymptomatic carriers. After three months of follow-up, no further cases were identified following the implementation of contact precautions with sporicidal agents.

Three-dimensional facial swelling evaluation of piezo-electric vs conventional drilling bur surgery of impacted lower third molar: a randomized clinical trial.

BACKGROUND: Among the post-surgical complications of lower wisdom teeth surgery, swelling is considered by patients one of the most impairing, with both social and biological influences and impacting patients' quality of life. Aim of the study was to evaluate the swelling following the osteotomy when performed with drilling burs versus piezo-electric instruments in the mandibular impacted third molar extraction, using a facial reconstruction software. MATERIALS AND METHODS: A randomized, split-mouth, single-blind study was conducted on patients, ranging between 18 and 40 years of age, requiring lower third molars extraction and referred at the Oral Surgery Unit of the School of Dentistry of the University of Messina. Twenty-two patients were recruited during an 8 months period according to the following criteria: good general health conditions; bilateral, symmetrical, impacted third molars; no use of medication that would influence or alter wound healing; no temporomandibular joint disorder history; no smoking. All patients underwent bilateral surgical removal. For each patient, a facial scan was obtained prior to the surgical procedures. The two extractions were conducted performing, in a randomized way, osteotomy with rotatory burs or use of piezo surgical instruments. Facial scans were repeated at 3 and 7 days after the surgical procedures. Volumetric differences were calculated via superimposition using a dedicated software. The data obtained were processed using paired t-test. RESULTS: The results obtained from our study showed no significant differences between two groups regarding post-operative swelling. To the best of our knowledge, this study represents the first experience of using an objective method that can be reproducible on the collection of patients' clinical parameters. CONCLUSIONS: The 3D digital analysis, in the evaluation of facial swelling, is a technique of simple application, objective, reproducible, reliable, decreasing the variables of error. Based on these data, it is possible to conclude that piezo surgery is a safe way for performing the osteotomies during third molar surgery. However, regarding the post-operative swelling, it does not show an advantage over classical rotary instruments. TRIAL REGISTRATION: Registered on ClinicalTrials.gov (ID: NCT05488028, on 04/08/2022). Approved by Ethical Committee of Messina: (ID 01-2020, on 27/04/2020).

Simplified Histologic Mucosal Healing Scheme (SHMHS) for inflammatory bowel disease: a nationwide multicenter study of performance and applicability.

BACKGROUND: Assessment of mucosal healing is important for the management of patients with inflammatory bowel disease (IBD), but endoscopy can miss microscopic disease areas that may relapse. Histological assessment is informative, but no single scoring system is widely adopted. We previously proposed an eight-item histological scheme for the easy, fast reporting of disease activity in the intestine. The aim of the present study was to evaluate the performance of our Simplified Histologic Mucosal Healing Scheme (SHMHS). METHODS: Between April and May 2021 pathologists and gastroenterologists in Italy were invited to contribute to this multicenter study by providing data on single endoscopic-histological examinations for their IBD patients undergoing treatment. Disease activity was expressed using SHMHS (maximum score, 8) and either Simple Endoscopic Score for Crohn's Disease (categorized into grades 0-3) or Mayo Endoscopic Subscore (range 0-3). RESULTS: Thirty hospitals provided data on 597 patients (291 Crohn's disease; 306 ulcerative colitis). The mean SHMHS score was 2.96 (SD = 2.42) and 66.8% of cases had active disease (score ≥ 2). The mean endoscopic score was 1.23 (SD = 1.05), with 67.8% having active disease (score ≥ 1). Histologic and endoscopic scores correlated (Spearman's ρ = 0.76), and scores for individual SHMHS items associated directly with endoscopic scores (chi-square p < 0.001, all comparisons). Between IBD types, scores for SHMHS items reflected differences in presentation, with cryptitis more common and erosions/ulcerations less common in Crohn's disease, and the distal colon more affected in ulcerative colitis. CONCLUSIONS: SHMHS captures the main histological features of IBD. Routine adoption may simplify pathologist workload while ensuring accurate reporting for clinical decision making.

Use of Narrow-Diameter Implants in Completely Edentulous Patients as a Prosthetic Option: A Systematic Review of the Literature.

OBJECTIVE: The objective of the present review is to assess the implant survival, marginal bone loss, and biomechanical features of narrow-diameter implants (2.5-3.5 mm) supporting or retaining full-arch fixed or removable restorations. MATERIALS AND METHODS: Three operators screened the literature (PubMed, Cochrane Library, and Google Scholar) and performed a hand search on the main journals that focus on implantology until 24 March 2019. Only articles that considered full-arch restorations supported or retained by narrow-diameter implants (2.5-3.5 mm) were considered if they have a minimum of 10 patients and a mean follow-up of at least 6 months. The outcome variables were survival of implants and marginal bone loss. The review was performed according to the PRISMA statements. Risk of bias assessment was evaluated. Failure rates were analyzed using random effect Poisson regression models to obtain the summary estimate of 5-year survival rate and marginal bone loss. RESULTS: A total of nine papers were finally selected, reporting a high survival rate of the implants. Eight studies focused only on the mandible while one study reported data from both mandible and maxilla. All studies reported on removable restorations; none focused on fixed rehabilitations. The estimated survival rate for 5 years of follow-up was calculated to be 92.25% for the implants. The estimated marginal bone loss after 5 years was calculated to be 1.40 mm. No study reported implant fractures. CONCLUSIONS: With the limitations of the present study, there is evidence that 2.5-3.5 mm narrow-diameter implants retaining a removable restoration can be a successful treatment in fully edentulous patients. No data on fixed restorations was available.

Halobacillus ihumii sp. nov., a new bacterium isolated from stool of healthy children living in Mali.

Strain Marseille-Q1234T is a new species from the genus Halobacillus that was isolated in 2019 from a stool sample in a healthy Malian child <5 years old. Cells are Gram-positive and strictly halophilic bacilli. Strain Marseille-Q1234T exhibits 98.46% 16S rRNA gene sequence similarity to Halobacillus naozhouensis strain JSM 071068T (NR_116505.1), the phylogenetically closely related species with standing in nomenclature. Based on the phenotypic and phylogenetic evidence, OrthoANI values and results of the biochemical tests, the new species is named Halobacillus ihumii sp. nov., for which strain Marseille-Q1234T (= CSURQ1234) is proposed as the type strain.

Natural antibodies and their relationship with total immunoglobulins and acquired antibody response in goat kid (Capra hircus, L. 1758) serum.

Natural antibodies (NAb) are antibodies that can bind to a particular antigen without any apparent antigenic stimulation. In this paper, a careful analysis has been carried out on NAb levels in goat kid serum; possible correlations with the total immunoglobulin (tot-Ig) levels and specific antibody (SpAb) response were considered. Twenty randomly chosen kids were submitted to a first blood sampling (day 0). After 60 and 100 days, new blood samplings were carried out in the same animals. On day 0, after blood collection, all animals were immunized with a commercial vaccine; the immunization was repeated 30 days apart. Some exogenous antigens were tested to verify their immunoreactivity to NAb. Among them, the synthetic hapten 2,4,6-trinitrophenyl (TNP) conjugated with bovine serum albumin, resulted as the antigen with the higher immunoreactivity to NAb. Tot-Ig levels increased over time (p < 0.001). On the contrary, NAb levels, both IgG- and IgM-isotypes, significantly decreased during the experimental period (p < 0.001 and <0.05, respectively). Linear regression analyses showed a high correlation between IgM-NAb and tot-IgM levels (p < 0.001) at all the evaluated sampling times. However, a significant correlation between IgG-NAb and IgM-NAb was found only at the 1st (p < 0.01) and at the 2nd sampling (p < 0.05). No significant correlations were found between SpAb response and the other assessed humoral immune parameters. The obtained results are discussed in the light of the possible use of NAb assessment for the evaluation of the immune system activity in goat.

Assessment of Clinical Meaningfulness of Endpoints in the Generation Program by the Insights to Model Alzheimer's Progression in Real Life (iMAP) Study.

We are launching the Insights to Model Alzheimer's Progression in Real Life study in parallel with the Alzheimer Prevention Initiative Generation Program. This is a 5-year, multinational, prospective, longitudinal, non-interventional cohort study that will collect data across the spectrum of Alzheimer's disease. The primary objective is to assess the ability of the Alzheimer's Prevention Initiative Cognitive Composite Test Score and Repeatable Battery for the Assessment of Neuropsychological Status to predict clinically meaningful outcomes such as diagnosis of mild cognitive impairment or dementia due to Alzheimer's disease, and change in Clinical Dementia Rating - Global Score. This study is the first large-scale, prospective effort to establish the clinical meaningfulness of cognitive test scores that track longitudinal decline in preclinical Alzheimer's disease. This study is also expected to contribute to our understanding of the relationships among outcomes in different stages of Alzheimer's disease as well as models of individual trajectories during the course of the disease.

The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.

Diatom diazotroph associations (DDAs) are a widespread marine planktonic symbiosis between several diatom genera and di-nitrogen (N2)-fixing bacteria. Combining single cell confocal microscopy observations and molecular genetic approaches on individual field collected cells, we determined the phylogenetic diversity, distribution and evolution of the DDAs. Confocal analyses coupled with 3-D imaging re-evaluated the cellular location of DDA symbionts. DDA diversity was resolved by paired gene sequencing (18S rRNA and rbcL genes, 16S rRNA and nifH genes). A survey using the newly acquired sequences against public databases found sequences with high similarity (99-100%) to either host (18S rRNA) or symbiont (16S rRNA) in atypical regions for DDAs (high latitudes, anoxic basin and copepod gut). Concatenated phylogenies were congruent for the host and cyanobacteria sequences and implied co-evolution. Time-calibrated trees dated the appearance of N2 fixing planktonic symbiosis from 100-50Mya and were consistent with the symbiont cellular location: symbioses with internal partners are more ancient. An ancestral state reconstruction traced the evolution of traits in DDAs and highlight that the adaptive radiation to the marine environment was likely facilitated by the symbiosis. Our results present the evolutionary nature of DDAs and provide new genetic and phenotypic information for these biogeochemically relevant populations.

The hypervirulent Coxiella burnetii Guiana strain compared in silico, in vitro and in vivo to the Nine Mile and the German strain.

OBJECTIVE: Q fever epidemic outbreaks have been reported in French Guiana and in The Netherlands. To determine whether the C. burnetii strains involved in these epidemics had a peculiar virulence pattern, we compared the pathogenicity of the Guiana and the German strain (a clone of The Netherlands strain), in silico, in vitro, and in vivo versus the Nine Mile strain. METHOD: The pan-genomes of the Guiana (Cb175), German (Z3055), and the referent Nine Mile (RSA 493) C. burnetii strains were compared. In vitro, the growth rate and the morphological presentation were compared. In vivo (SCID and Balb/c mice), weight loss, histological lesions, C. burnetii bacterial load in deep organs, and serological response were reported according to each C. burnetii strain studied. RESULTS: The Guiana strain had 77 times more missing genes and 12 times more unique genes than the German strain. The Guiana strain presented as large cell variants (LCVs) and led to the most pronounced fatality rate in SCID mice (100% at 4 weeks). The German strain presented as small cell variants (SCVs), and had an intermediate fatality rate (75% at 4 weeks). Both the Guiana and the German strains led to a significant higher serological response at 2 and 4 weeks post infection (p <0.05). CONCLUSION: The Guiana strain was the most virulent strain, followed by the German strain and the referent Nine Mile strain. Unique and missing genes could be implicated but further investigations are necessary to specify their role.

Prejudices towards people with intellectual disabilities: reliability and validity of the Italian Modern and Classical Prejudices Scale.

BACKGROUND: Prejudices and negative attitudes towards intellectual disabilities (IDs) may hinder social inclusion of ID individuals, limiting their well-being. This study investigated the psychometric characteristics of the Italian Modern and Classical Prejudices Scale (MCPS-IT) towards people with ID and the effects of gender, age and socio-economic status (SES) on prejudices. METHOD: The MCPS-IT was administered to 474 adults (69% women, age range 18-70 years, M = 33.13) in conjunction with a questionnaire evaluating socio-demographic information (SES), the contact and the education about ID people and the social dominance orientation. RESULTS: Results confirmed that Italian MCPS has a two-factor structure that measures in a reliable and valid way prejudice towards people with ID. Multivariate analyses of variance confirmed a weak gender difference in both scales and age differences in modern scale. No SES differences were found. CONCLUSION: The Italian MCPS represents a valid scale that can be used to monitor the social context of people with ID.

Volcanoes in Italy and the role of muon radiography.

Cosmic-ray muon radiography (muography), an imaging technique that can provide measurements of rock densities within the top few 100 m of a volcanic cone, has now achieved a spatial resolution of the order of 10 m in optimal detection conditions. Muography provides images of the top region of a volcano edifice with a resolution that is considerably better than that typically achieved with other conventional methods (i.e. gravimetric). We expect such precise measurements, to provide us with information on anomalies in the rock density distribution, which can be affected by dense lava conduits, low-density magma supply paths or the compression with the depth of the overlying soil. The MUon RAdiography of VESuvius (MURAVES) project is now in its final phase of construction and deployment. Up to four muon hodoscopes, each with a surface of roughly 1 m2, will be installed on the slope of Vesuvius and take data for at least 12 months. We will use the muographic profiles, combined with data from gravimetric and seismic measurement campaigns, to determine the stratigraphy of the lava plug at the bottom of the Vesuvius crater, in order to infer potential eruption pathways. While the MURAVES project unfolds, others are using emulsion detectors on Stromboli to study the lava conduits at the top of the volcano. These measurements are ongoing: they have completed two measurement campaigns and are now performing the first data analysis.This article is part of the Theo Murphy meeting issue 'Cosmic-ray muography'.

A baseline tool for predicting response to peginterferon alfa-2a in HBeAg-positive patients with chronic hepatitis B.

BACKGROUND: Peginterferon induces off-treatment responses in approximately one-third of patients with hepatitis B e antigen (HBeAg)-positive chronic hepatitis B. AIM: To develop an easy-to-use baseline prediction score to identify hepatitis B virus (HBV) genotype B-/C-infected HBeAg-positive Asian patients likely to respond to peginterferon alfa-2a. METHODS: Generalised additive models, multiple logistic regression (MLR) analysis and internal validation methods were applied to data from 647 HBeAg-positive patients from China, Hong Kong and Taiwan to develop a scoring system to predict response 24 weeks after completing a 48-week course of peginterferon alfa-2a. RESULTS: Five baseline factors (age, sex, alanine aminotransferase ratio, hepatitis B surface antigen (HBsAg) level and HBV DNA level) were retained in the final MLR for HBeAg seroconversion and used to develop a scoring system from 0 to 7. Among patients with scores of 0-1, 2-3, 4 or ≥5, HBeAg seroconversion was achieved in 6.4% (6/94), 23.0% (61/265), 36.4% (67/184) and 54.8% (57/104), respectively, and a combined response (HBeAg seroconversion plus HBV DNA <2000 IU/mL) in 5.3% (5/94), 12.8% (34/265), 25.0% (46/184) and 36.5% (38/104), respectively. Among patients with scores of 0-1, 2-3, 4 or ≥5, 57.0% (53/93), 12.3% (31/253), 3.4% (6/178) and 1.0% (1/100) had HBsAg ≥20 000 IU/mL at treatment Week 12; only 3/91 (3.3%) with HBsAg ≥20 000 IU/mL experienced a combined response at 24 weeks post-treatment (negative predictive value = 97% [88/91]). CONCLUSION: A pre-treatment scoring system using readily available baseline characteristics identifies HBeAg-positive Asian patients likely to experience sustained HBeAg seroconversion after treatment with peginterferon alfa-2a.

The Alzheimer's Prevention Initiative Generation Program: Evaluating CNP520 Efficacy in the Prevention of Alzheimer's Disease.

Alzheimer's disease pathology begins decades before the onset of clinical symptoms. This provides an opportunity for interventional clinical trials to potentially delay or prevent the onset of cognitive impairment or dementia. CNP520 (a beta-site-amyloid precursor protein-cleaving enzyme inhibitor) is in clinical development for the treatment of preclinical Alzheimer's disease under the Alzheimer's Prevention Initiative Generation Program. The Alzheimer's Prevention Initiative is a public-private partnership intended to accelerate the evaluation of Alzheimer's disease prevention therapies. The Generation Program comprises two pivotal phase II/III studies with similar designs to assess the efficacy and safety of investigational treatments in a cognitively unimpaired population at increased risk for developing Alzheimer's disease based on age and apolipoprotein E (APOE) genotype (i.e., presence of the APOE ε4 allele). The program has been designed to maximize benefit to Alzheimer's disease research. Generation Study 1 (NCT02565511) and Generation Study 2 (NCT03131453) are currently enrolling; their key features are presented here.

Draft genome sequence of a human-associated isolate of Haloferax alexandrinus strain Arc-hr, an extremely halophilic archaea.

We report the draft genome sequence of Haloferax alexandrinus strain Arc-hr (CSUR P798), isolated from the human gut of a 10-year-old Amazonian individual. Its 3 893 626 bp genome exhibits a 66.00% GC content. The genome of the strain Arc-hr contains 37 genes identified as ORFans, seven genes associated to halocin and 11 genes associated with polyketide synthases or nonribosomal peptide synthetases.

Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient.

Butyricimonas phoceensis strain AT9 (= CSUR 1981 = DSM 100664) was isolated from a stool sample from a morbidly obese French patient living in Marseille using the culturomics approach. The genome of this Gram-negative-staining, anaerobic and non-spore forming rod bacillus is 4 736 949 bp long and contains 3947 protein-coding genes. Genomic analysis identified 173 genes as ORFans (4.5%) and 1650 orthologous proteins (42%) not shared with the closest phylogenetic species, Butyricimonas virosa. Its major fatty acid was the branched acid iso-C15:0 (62.3%).

The molecular characterization by SSRs reveals a new South Italian kinship and the origin of the cultivar Uva di Troia.

Vitis vinifera L. varieties were spread through cuttings following historic migrations of people, trades, or after biological crises due to pests outbreaks. Some today's varieties could be more than a 1000 years old and, although over the centuries these varieties generated most of the remaining cultivars, their origin could be impossible to track back. The Italian grapevine biodiversity is one of most important, most likely due to its strategic position in the middle of the Mediterranean sea. Unravelling of its structure is challenging because of its complexity and the lack of historical documentation. In this paper molecular data are compared with historical documentations. Simple Sequence Repeats fingerprinting are molecular markers best suited to investigate genetic relationships and identify pedigrees. South-Italian germplasm was studied with 54 nuclear microsatellites. A family was identified, consisting of two parents and three siblings and further genetically characterized with six nuclear and five chloroplast microsatellites and described with ampelographic and phylometric analysis. Although these latter were not informative for the kinship identification. The common Bombino bianco was the female parent and the previously unknown Uva rosa antica was the male parent. Bombino nero, Impigno and the popular Uva di Troia, all typical of the south-east Italy, were the offspring. Further research showed that the Uva rosa antica was a synonym of Quagliano and Bouteillan noir, both minor varieties. Quagliano was considered to be autochthonous of some alpine valleys in the north-west of Italy and Bouteillan noir is a neglected variety of Vancluse in France. This finding uncovers the intricate nature of Italian grape cultivars, considered peculiar of an area, but possibly being the remains of ancient latin founding varieties. Consequently, intriguing new hypotheses are discussed and some conclusions are drawn, based on the peculiar geographical origin of the parents, on the distribution of the offspring, on the chance of a single, and perhaps intentional, crossing event.

Noncontiguous finished genome sequence and description of Bacillus andreraoultii strain SIT1(T) sp. nov.

Bacillus andreraoultii strain SIT1(T) (= CSUR P1162 = DSM 29078) is the type strain of B. andreraoultii sp. nov. This bacterium was isolated from the stool of a 2-year-old Nigerian boy with a severe form of kwashiorkor. Bacillus andreraoultii is an aerobic, Gram-positive rod. We describe here the features of this bacterium, together with the complete genome sequencing and annotation. The 4 092 130 bp long genome contains 3718 protein-coding and 116 RNA genes.

High-quality genome sequencing and description of Dermabacter indicis sp. nov.

Strain FF11(T) was isolated from the wound on a researcher's finger who had been bitten by a fish (Protopterus annectens) in Senegal. Analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry did not provide any identification, but the 16S rRNA sequence exhibited 97.9% identity with Dermabacter hominis. Phenotypic and genomic analyses demonstrated that strain FF11(T) is Gram-positive, facultatively anaerobic, nonmotile and non-spore forming; it exhibited a genome of 2 222 902 bp encoding 2074 protein-coding and 50 RNA genes, with a 63.2% G+C content. We consequently proposed the creation of Dermabacter indicis strain FF11(T).

Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5.

Paenibacillus ihumii sp. nov. strain AT5 (= CSUR 1981 = DSM 100664) is the type strain of P. ihumii. This bacterium was isolated from a stool sample from a morbidly obese French patient using the culturomics approach. The genome of this Gram-negative, facultative anaerobic, motile and spore-forming bacillus is 5 924 686 bp long. Genomic analysis identified 253 (5%) of 3812 genes as ORFans and at least 2599 (50.03%) of 5194 orthologous proteins not shared with the closest phylogenetic species.