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As part of an interdisciplinary research project, the performance response of sows and their litters to the probiotic strain Enterococcus faecium NCIMB 10415, as well as some health characteristics of the piglets, were studied. Gestating sows (n = 26) were randomly allotted into 2 groups. The probiotic was administered by dietary supplementation to 1 group of sows and their respective litters (probiotic group), whereas the second group (control group) received no probiotic supplementation. The duration of the treatment was nearly 17 wk for sows (d 90 ante partum until d 28 postpartum) and 6 wk for piglets (d 15 to 56). Body weight and feed consumption were recorded weekly. The frequency of 4 toxin and 5 adhesion genes of putative pathogenic Escherichia coli was monitored weekly (d 7 to 35) by multiplex PCR assays, and fecal consistency of weaned piglets was studied daily. Probiotic treatment of lactating sows led to an overall preweaning mortality of 16.2% compared with 22.3% in the control group (P = 0.44). Animal losses during the first 3 d of the suckling period were decreased in the probiotic group (P = 0.09). For piglets (n = 153), which were weaned at 28 d, there were no overall treatment differences in BW gain, feed intake, or feed efficiency. Probiotic supplementation, however, led to nearly a 40% reduction (P = 0.012). The actual percentage of piglets with postweaning diarrhea in the probiotic group was 21% compared with 38% in the control group (P = 0.05). The study on virulence factors of dominant fecal E. coli isolates revealed a high diversity with varying frequency and distribution of each single pathogenicity gene. The 440 isolates carried 29 different pathogenicity gene combinations as well as each of the 9 pathogenicity genes alone. Altogether, isolates with more than 2 pathogenicity genes were quite rare ([less than or equal to] 10%), and up until d 28 isolates without any pathogenicity gene occurred most frequently. Depending on the time of sampling, one-third or more of all isolates contained est2 or est1b as single gene or in combination with other pathogenicity genes. Key words: Enterococcus faecium NCIMB 10415, diarrhea, pathogenicity genes, performance, pig, probiotics

Considering that caries around restorations is a serious problem in dentistry, and some restorative materials with fluoride may be important in inhibiting these lesions, tins research is aimed at performing an in vitro evaluation of the cariostatic action of some esthetic restorative materials. Standardized cavities were prepared in the center of either intact blocks of bovine enamel or with bovine teeth containing early artificial carious lesions. The specimens were restored with a high viscosity glass ionomer cement (Molar Ketac), a resin-modified glass ionomer cement (Vitremer), a polyacid-modified resin composite (Dyract AP) and a conventional resin composite (Z-250). In addition to the restored specimens, four corresponding control groups were evaluated. All groups, except for two control groups, were subjected to a demineralization/remineralization cycling model for 14 days, simulating a situation of severe cariogenic challenge. The blocks were then longitudinally sectioned through the restorations. Mineral loss was evaluated in these specimens using the Knoop microhardness profiles in longitudinal sections at three different distances of the cavities and at eight distinct depths in relation to the external enamel surface. Statistical analysis of the results showed significant differences (p<0.05) among the groups, although none of the study materials completely inhibited creation of the lesions. Vitremer demonstrated the best cariostatic action in intact bovine enamel. Ketac Molar, in intact or demineralized enamel, and Vitremer, in demineralized enamel, presented intermediate cariostatic potential. Z-250 and Dyract AP did not demonstrate any cariostatic effect. The data suggests that glass ionomer cements demonstrated better cariostatic action compared to the other restorative materials. [ABSTRACT FROM AUTHOR]

The intestinal bacterium Enterococcus faecium NCIMB 10415 ( E. faecium SF68) has been used for more than a decade as a probiotic strain in animal nutrition as well as in the prevention and treatment of diarrhoea in humans. Beneficial effects have been shown in feeding and clinical trials. However, the strain has no selective growth markers and monitoring in the intestinal tract is impossible by cultivation. Using specific nucleotide sequences, in this study a probe for colony hybridization was constructed in order to quantify this probiotic strain in feed and intestinal and faecal samples from piglets and sows. The probiotic strain showed almost constant amounts in sow faeces (1.8·10 5 cfu/g wet weight), while contents in digesta and piglet faeces varied on a lower level depending on gut section and piglet age. The ratio of specific probiotic counts and total enterococci was much lower than in sow faeces however the strain could be detected reliably in faeces already on the 14th day of life. The application of the colony hybridization method enables for the first time the selective detection of the widely used probiotic E. faecium NCIMB 10415 strain among total Enterococcus spp. counts of digesta, faeces and feed. It is now possible to monitor the presence of the probiotic in the intestinal tract and faeces. Results of this study have implications for the proposed modes of action of probiotics in animal nutrition. [ABSTRACT FROM AUTHOR]

Determines the effects of sustained submaximal physical exercise on the distribution of neutrophils in the blood and on stimulated hydrogen peroxide generation by isolated neutrophils. Materials and methods; Results; Discussion.

Presents information on a field experiment performed to investigate the interrelationships among components of bulb yield of nine genotypes of onion at the Sokoine University of Agriculture in Morogo, Tanzania. Materials and methods; Results and discussion.

Introduction: The specificity of HIV-1 DNA genotypic resistance tests (GRTs) is hampered by the detection of the APOBEC-context drug resistance mutations (AC DRMs), usually harboured by replication-incompetent proviruses. We sought factors associated with defective sequences in the HIV-1 pol region. In addition, AC DRMs and their link with defective sequences were investigated., Methods: We included ART-treated patients with viral suppression or plasma viral load (VL) lower than 200 copies/mL, who underwent HIV-1 DNA genotyping, with successful sequencing of protease (PR), reverse transcriptase (RT) and integrase (IN) regions. Sequencing was performed using either the Sanger method or the Sentosa® NGS approach with a 20% cut-off. All hypermutated sequences and/or those containing at least one stop codon were considered defective., Results: A total of 613 HIV-1 DNA GRTs were analysed. Defective sequences were identified for 186 samples (30.3%) including 65 PR sequences, 92 RT sequences and 65 IN sequences. No association, including HIV-1 DNA levels, was found with the detection of defective pol sequences. A total of 226 AC DRMs were recorded in all sequences. Most of these mutations (78%) were harboured by defective sequences. AC DRMs did not emerge in the plasma viral population, and likely do not impact the virological response to ART., Conclusions: Defectives pol sequences were not associated with HIV-1 DNA levels and harboured most of the AC DRMs. Such mutations likely have no clinical impact, and should not be reported in routine practice. Consensus guidelines for reporting HIV-1 DNA GRTs are needed, especially for the assessment and management of AC DRMs., (© The Author(s) 2025. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Stable-isotope resolved metabolomics (SIRM) is a powerful approach for characterizing metabolic states in cells and organisms. By incorporating isotopes, such as 13 C, into substrates, researchers can trace reaction rates across specific metabolic pathways. Integrating metabolomics data with gene expression profiles further enriches the analysis, as we demonstrated in our prior study on glioblastoma metabolic symbiosis. However, the bioinformatics tools for analyzing tracer metabolomics data have been limited. In this protocol, we encourage the researchers to use SIRM and transcriptomics data and to perform the downstream analysis using our software tool DIMet. Indeed, DIMet is the first comprehensive tool designed for the differential analysis of tracer metabolomics data, alongside its integration with transcriptomics data. DIMet facilitates the analysis of stable-isotope labeling and metabolic abundances, offering a streamlined approach to infer metabolic changes without requiring complex flux analysis. Its pathway-based "metabologram" visualizations effectively integrate metabolomics and transcriptomics data, offering a versatile platform capable of analyzing corrected tracer datasets across diverse systems, organisms, and isotopes. We provide detailed steps for sample preparation and data analysis using DIMet through its intuitive, web-based Galaxy interface. To showcase DIMet's capabilities, we analyzed LDHA/B knockout glioblastoma cell lines compared to controls. Accessible to all researchers through Galaxy, DIMet is free, user-friendly, and open source, making it a valuable resource for advancing metabolic research. Key features • Glioblastoma tumor spheroids in vitro replicate tumors' three-dimensional structure and natural nutrient, metabolite, and gas gradients, providing a more realistic model of tumor biology. • Joint analysis of tracer metabolomics and transcriptomics datasets provides deeper insights into the metabolic states of cells. • DIMet is a web-based tool for differential analysis and seamless integration of metabolomics and transcriptomics data, making it accessible and user-friendly. • DIMet enables researchers to infer metabolic changes, offering intuitive and visually appealing "metabologram" outputs, surpassing conventional visual representations commonly used in the field., Competing Interests: Competing interestsThere are no conflicts of interest or competing interests., (©Copyright : © 2025 The Authors; This is an open access article under the CC BY-NC license.)

Carbapenem-resistant Pseudomonas aeruginosa is a global public health concern. IMP-13 is a carbapenemase that was described for the first time in 2001 but is often underestimated due to poor hydrolysis of carbapenems and a lack of molecular detection. The aim of this study was to characterize the genetic support of bla IMP-13 in P. aeruginosa and to assess the ability of mobile genetic elements to disseminate this resistance. A retrospective analysis conducted between 2010 and 2020 revealed eight multiresistant P. aeruginosa isolates by their production of the carbapenemase IMP-13 in Bordeaux. Additionally, three of the studied isolates exhibited high-level resistance to imipenem and imipenem-relebactam that was linked to an insertion sequence in the oprD gene. Successful mating was achieved, and transconjugants and parental clinical isolate genomes were sequenced. All clinical isolates were found to be ST621 strains. The data revealed that bla IMP-13 was carried on an Integrative and Conjugative Element (ICEclc-like) of 88,589 bp with a 62% GC content harboring 85 CDSs, and was inserted at the tRNA Gly locus PA0729.1. The ICE was identical in the eight studied clinical isolates and in all the ST621 strains found in the databases. The conjugation rate was low, at approximately 10 -8 transconjugants per donor and ICE transfer appeared to mobilize some adjacent parental genes located immediately downstream of the ICE. In conclusion, these results suggest that even if the spread of bla IMP-13 is mainly due to an epidemic ST621 clone, the mobilization of a bla IMP-13 -carrying ICEclc-like element is possible and should not be underestimated., Competing Interests: Declaration of competing interest None declared., (Copyright © 2024. Published by Elsevier Ltd.)

FeS clusters are prosthetic groups present in all organisms. Proteins with FeS centers are involved in most cellular processes. ISC and SUF are machineries necessary for the formation and insertion of FeS in proteins. Recently, a phylogenetic analysis on more than 10,000 genomes of prokaryotes have uncovered two new systems, MIS and SMS, which were proposed to be ancestral to ISC and SUF. SMS is composed of SmsBC, two homologs of SufBC(D), the scaffolding complex of SUF. In this review, we will specifically focus on the current knowledge of the SUF system and on the new perspectives given by the recent discovery of its ancestor, the SMS system., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests. Ollagnier Sandrine reports was provided by National Centre for Scientific Research. Ollagnier Sandrine reports a relationship with National Centre for Scientific Research that includes: employment, funding grants, and non-financial support. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Antimicrobial resistance (AMR) is a public health threat worldwide. Next-generation sequencing (NGS) has opened unprecedented opportunities to accelerate AMR mechanism discovery and diagnostics. Here, we present an integrative approach to investigate trimethoprim (TMP) resistance in the key pathogen Streptococcus pneumoniae . We explored a collection of 662 S . pneumoniae genomes by conducting a genome-wide association study (GWAS), followed by functional validation using resistance reconstruction experiments, combined with machine learning (ML) approaches to predict TMP minimum inhibitory concentration (MIC). Our study showed that multiple additive mutations in the folA and sulA loci are responsible for TMP non-susceptibility in S. pneumoniae and can be used as key features to build ML models for digital MIC prediction, reaching an average accuracy within ±1 twofold dilution factor of 86.3%. Our roadmap of in silico analysis-wet-lab validation-diagnostic tool building could be adapted to explore AMR in other combinations of bacteria-antibiotic., Importance: In the age of next-generation sequencing (NGS), while data-driven methods such as genome-wide association study (GWAS) and machine learning (ML) excel at finding patterns, functional validation can be challenging due to the high numbers of candidate variants. We designed an integrative approach combining a GWAS on S. pneumoniae clinical isolates, followed by whole-genome transformation coupled with NGS to functionally characterize a large set of GWAS candidates. Our study validated several phenotypic folA mutations beyond the standard Ile100Leu mutation, and showed that the overexpression of the sulA locus produces trimethoprim (TMP) resistance in Streptococcus pneumoniae . These validated loci, when used to build ML models, were found to be the best inputs for predicting TMP minimal inhibitory concentrations. Integrative approaches can bridge the genotype-phenotype gap by biological insights that can be incorporated in ML models for accurate prediction of drug susceptibility., Competing Interests: The authors declare no conflict of interest.

Objectives: We aimed to assess the frequency, management, and burden of enterococcal-related vascular graft infection., Patients and Methods: From 2008 to 2021, data regarding all episodes of vascular graft infections initially managed or secondarily referred to our referral center were prospectively collected. We described the history and management of the infection, depending on the type of prosthesis used., Results: The frequency of enterococcal-related vascular graft infections was 29/249 (12 %). Most of them were early infections (22/29, 76 %). Infections were polymicrobial (26/29, 90 %), mostly associated with Enterobacterales. Among patients with positive blood cultures, 7/8 (88 %) involved enterococci. Patients with enterococcal-related vascular graft infections were mainly (22/29, 76 %) treated with an association of antibiotics. Mortality and relapse occurred in 28 % and 7 % respectively of the cases., Conclusions: Enterococcal-related vascular graft infections occurred in patients with comorbidities, during the early period following surgery and were more frequent in cases of intra-cavitary prosthesis. Their potential virulence needs to be considered, especially in polymicrobial infections., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Ticks are notable vectors of diseases affecting both humans and animals, with Hyalomma anatolicum being of particular significance due to its wide distribution and capability to transmit a variety of pathogens, including Theileriaannulata and Crimean-Congo haemorrhagic fever virus. This study aimed to investigate the inhibitory effects of H. anatolicum salivary gland extract (HaSGE) and the identification of its key component on the complement system of the host's innate immune defense. We demonstrated that HaSGE exerts a dose-dependent inhibition on the complement activation in a host-specific manner. Mechanistic studies revealed that HaSGE interferes with deposition and cleavage of complement proteins C3 and C5, thus preventing the formation of the membrane attack complex. Further, we identified a serine protease inhibitor, Hyalomma anatolicum serpin-1 (HAMpin-1), from the HaSGE through proteomic analysis and characterized its structure, function, and interaction with complement proteins. HAMpin-1 exhibited potent inhibitory activity against chymotrypsin and cathepsin-G, and notably, it is the first serpin from ticks shown to inhibit the classical and lectin pathways of the complement system. The expression of HAMpin-1 was highest in the salivary glands, suggesting its crucial role in blood feeding and immune evasion. Our findings revealed one of the potential mechanisms used by H. anatolicum to modulate host immune responses at the interface, offering new insights into tick-host interactions., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Motivation: Many diseases, such as cancer, are characterized by an alteration of cellular metabolism allowing cells to adapt to changes in the microenvironment. Stable isotope-resolved metabolomics (SIRM) and downstream data analyses are widely used techniques for unraveling cells' metabolic activity to understand the altered functioning of metabolic pathways in the diseased state. While a number of bioinformatic solutions exist for the differential analysis of SIRM data, there is currently no available resource providing a comprehensive toolbox., Results: In this work, we present DIMet, a one-stop comprehensive tool for differential analysis of targeted tracer data. DIMet accepts metabolite total abundances, isotopologue contributions, and isotopic mean enrichment, and supports differential comparison (pairwise and multi-group), time-series analyses, and labeling profile comparison. Moreover, it integrates transcriptomics and targeted metabolomics data through network-based metabolograms. We illustrate the use of DIMet in real SIRM datasets obtained from Glioblastoma P3 cell-line samples. DIMet is open-source, and is readily available for routine downstream analysis of isotope-labeled targeted metabolomics data, as it can be used both in the command line interface or as a complete toolkit in the public Galaxy Europe and Workfow4Metabolomics web platforms., Availability and Implementation: DIMet is freely available at https://github.com/cbib/DIMet, and through https://usegalaxy.eu and https://workflow4metabolomics.usegalaxy.fr. All the datasets are available at Zenodo https://zenodo.org/records/10925786., (© The Author(s) 2024. Published by Oxford University Press.)