ENOVAT: the European Network for Optimization of Veterinary Antimicrobial Treatment.

The global antimicrobial resistance crisis has been the driver of several international strategies on antimicrobial stewardship. For their implementation at the field level, the veterinary sector encounters several specific challenges and in particular: (i) a shortage of experts in key disciplines related to antimicrobial stewardship, (ii) a lack of evidence-based antimicrobial treatment guidelines, and (iii) inferior diagnostic tests available compared to human medicine. The present white paper describes how the COST Action ENOVAT (the European Network for Optimization of Veterinary Antimicrobial Treatment, CA18217), comprising 332 persons from 51 countries, worked towards solutions to these challenges. Initially, surveys were conducted to explore the present state in Europe in terms of existing antimicrobial use guidelines and microbiology practices performed. Concurrently, various research activities were launched to optimize diagnostics, including development of epidemiological cut-offs, clinical breakpoints and matrix-assisted laser desorption ionization time of flight mass spectrometry interpretive criteria. Also, guidelines drafting groups working towards evidence-based antimicrobial treatment guidelines for six conditions in food-producing and companion animals were established. The processes and outcomes, also in terms of capacity building, are summarized in this white paper where emphasis is placed on sustainability of the activities. Although several ENOVAT initiatives and spin-off projects will continue beyond the Action, we recommend that a new European veterinary research agenda is launched focusing on research and funding leading to long-term impacts on veterinary antimicrobial use.

Antimicrobial resistance is an urgent global public health threat that is amplified by over- and misuse of antimicrobials. As a result of antimicrobial resistance, antibiotics and other antimicrobial medicines become ineffective and infections become difficult or impossible to treat. This goes for human infections, but also for infections in animals. In a recently finished European project called ENOVAT we tried to tackle the problem of antimicrobial resistance in animals. We focused on two topics. First we optimized and harmonized diagnostics of bacterial infections in the laboratory, and second we developed evidence-based treatment guidelines to support veterinary practitioners on how and when to use antibiotics in the best way. Improved diagnostics and new treatment guidelines can help veterinary practitioners to a more sensible antibiotic choice and with that less over- and misuse of antimicrobials. This article summarizes the process and progress of the work done in the ENOVAT project. Emphasis is also put on how the project benefitted from a unique consortium encompassing 332 professionals with diverse backgrounds, from 51 countries.

Functional Assessment of >18 Years Old Patients at Internal Medicine Ward-Relationship with In-Hospital and 30-Day Mortality.

Objective: To evaluate the connection between the items included in the AVD-DezIs score (a questionnaire about basic and instrumental activities of daily living and other topics related to social and personal life) and in-hospital and 30-day mortality after discharge. Methods: Prospective cohort study of hospitalizations in the Internal Medicine ward from 2014 to 2020, including >18 years old patients with a fully completed AVD-DezIs. To identify in-hospital and 30 days mortality, univariate and multivariate logistic models were applied, including random effects if justified. Results: A total of 19,771 episodes of hospitalization were included. In the univariate analysis, except for the presence of isolation and financial insufficiency, all the items were predictors of mortality in-hospital or within 30 days after discharge. In multivariate analysis, older age, male sex, longer hospital stay, higher Charlson score, deficiency in all four activities of daily living, deficiency in meal preparation and housekeeping, presence of pain/depression, immobility, and malnutrition are associated with a higher probability of in-hospital death whereas older age, male gender, higher Charlson score, longer length of hospital stay, deficiency in personal hygiene, ambulation, and eating habits, as well as the presence of incontinence and malnutrition, are associated with a higher probability of 30 days after discharge death. Discussion/Conclusion: Except for isolation and financial insufficiency, all items were individually associated with the outcomes. When they are considered in conjunction and taking into account sex, age, comorbidities and length of stay, the predictive ability of in-hospital and 30 days mortality differed.

A catalog of small proteins from the global microbiome.

Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.

Estimation of Hamiltonian Parameters from Thermal States.

We upper bound and lower bound the optimal precision with which one can estimate an unknown Hamiltonian parameter via measurements of Gibbs thermal states with a known temperature. The bounds depend on the uncertainty in the Hamiltonian term that contains the parameter and on the term's degree of noncommutativity with the full Hamiltonian: higher uncertainty and commuting operators lead to better precision. We apply the bounds to show that there exist entangled thermal states such that the parameter can be estimated with an error that decreases faster than 1/sqrt[n], beating the standard quantum limit. This result governs Hamiltonians where an unknown scalar parameter (e.g., a component of a magnetic field) is coupled locally and identically to n qubit sensors. In the high-temperature regime, our bounds allow for pinpointing the optimal estimation error, up to a constant prefactor. Our bounds generalize to joint estimations of multiple parameters. In this setting, we recover the high-temperature sample scaling derived previously via techniques based on quantum state discrimination and coding theory. In an application, we show that noncommuting conserved quantities hinder the estimation of chemical potentials.

Spontaneously Hypertensive Rats Present Exacerbated Focal Stroke Behavioral Outcomes.

This study aimed to analyze the effects of systemic arterial hypertension (SAH) in a model of permanent ischemic stroke (focal ischemia due to thermocoagulation of pial vessels) on sensorimotor function (cylinder test and patch removal test), behavioral tasks (novelty habituation memory open field task) and cerebral infarct size in adult male spontaneously hypertensive rats (SHR) and normotensive Wistar Kyoto rats (WKY) for 42 days after the occurrence of a stroke. We observed that the stroke caused asymmetry in the front paws and delayed adhesive removal. These effects were spontaneously reduced in WKY rats, but not in SHR. Short- and long-term novelty habituation memories were abolished by stroke in WYK and SHR. On the 3rd day after stroke, the size of the focal cerebral infarct was the same in WKY and SHR. However, on the 7th day, the infarct size decreased in WKY rats, but not SHR. These results suggested that SAH impairment of sensorimotor recovery in rats subjected to cerebral ischemia could be related to augmented focal cerebral infarct size. Moreover, the behavioral tasks used in this study were unaffected by Systemic Arterial Hypertension. Our results highlight the need for animal models of comorbidities in stroke research.

Local recurrence after endoscopic submucosal dissection of gastric neoplastic lesions: special attention should be given also to safety margins.

INTRODUCTION: The incidence of local recurrence following gastric endoscopic submucosal dissection (ESD) remains a clinical concern. We aimed to evaluate the impact of narrow safety margin (< 1 mm) on the recurrence rate. METHODS: A retrospective cohort study was conducted across two centers. Cases of R0-ESD with subsequent recurrence were compared to matched controls in a 1:2 ratio in a case-cohort analysis. RESULTS: Over a median period of 25 months (IQR 14-43), a recurrence rate of 3% (95%CI 1.7-4.3) was observed, predominantly (13/21) following R0 resections with favourable histology. Endoscopic retreatment was feasible in 18 of 21 recurrences. The proportion of R0-cases where the safety margin in both horizontal (HM) and vertical (VM) margin exceeded 1 mm was similarly distributed in the recurrence and non-recurrence group, representing nearly 20% of cases. However, cases with HM less than 1 mm, despite VM greater than 1 mm, nearly doubled in the recurrence group (7.7% vs. 3.9%), and tripled when both margins were under 1 mm (23.1% vs. 7.7%). Despite this trend, statistical significance was not achieved (p = 0.05). In the overall cohort, the only independent risk factor significantly associated with local recurrence was the presence of residual tumor at the HM (HM1) or not assessable HM (HMx) (OR 16.5 (95%CI 4.4-61.7), and OR 11.7 (95%CI 1.1-124.1), respectively). CONCLUSIONS: While not common or typically challenging to manage, recurrence post-ESD warrants attention and justifies rigorous post-procedural surveillance, especially in patients with HM1, HMx, and probably also in those with R0 resections but narrow safety margin.

Erratum: Lower Bounds on Quantum Annealing Times [Phys. Rev. Lett. 130, 140601 (2023)].

This corrects the article DOI: 10.1103/PhysRevLett.130.140601.

Predictors of Outcomes in Gastric Neuroendocrine Tumors: A Retrospective Cohort.

Introduction/Aim: Gastric neuroendocrine tumors (GNETs) frequently have an indolent clinical course, despite their metastatic potential. The aim of the study was to identify prognostic factors associated with overall survival and risk of metastases and to evaluate the impact of serial measurements of chromogranin A (CgA). Methods: The authors performed a retrospective cohort study including consecutive patients with GNET diagnosed between 2010 and 2019, with a minimum follow-up of 1 year. Univariate and multivariate analyses were performed. Results: We included 132 patients with GNET (type I, 113 patients; type II, 1 patient; type III, 14 patients; type IV, 2 patients; not classifiable, 2 patients), with 61% being female and a mean age at diagnosis of 66 years. During the follow-up period (median 66 months), 3 (2.3%) patients died due to metastatic disease (1 patient with type III and 2 patients with type IV). Male gender (p = 0.030), type III/IV (p < 0.001), Ki-67 index >20% (p < 0.001), grade 2/3 (p < 0.001), invasion beyond the submucosa (p < 0.001), and presence of metastases (p < 0.001) were identified as risk factors for mortality in the univariate analysis. Metastasis developed in 7 patients (5.3%). Multivariable analysis revealed that Ki-67 >20% (p = 0.016) was an independent risk factor for metastasis. Overall, CgA showed a sensitivity of 20% for detection of recurrence and a specificity of 79% (sensitivity of 8% and specificity of 71% in type I GNETs). Conclusion: Identification of risk factors for the presence of metastases and for mortality in these groups of patients can help in individualizing the therapeutic strategy. CgA seems to be a weak marker for monitoring patients with GNET.

Introdução/Objetivo: Os tumores neuroendócrinos gástricos (TNEs-G) têm frequentemente um curso indolente, apesar do seu potencial metastático. O objetivo deste trabalho foi identificar fatores de prognóstico associados à sobrevida global e à metastização nos doentes com TNEs-G e avaliar o impacto da análise seriada de cromogranina A (CgA). Methods: Estudo retrospectivo incluindo doentes consecutivos admitidos por TNE-G entre 2010 e 2019, com um follow-up mínimo de 1 ano. Foi realizada análise univariada e multivariada. Results: Foram incluídos 132 doentes com TNE-G (Tipo I, 113 doentes; Tipo II, 1 doente; Tipo III, 14 doentes; Tipo IV, 2 doentes; Não classificável, 2 doentes), sendo 61% mulheres, com idade média de 66 anos. Durante o periodo de follow-up (mediana 66 meses), 3 (2.3%) doentes faleceram por doença metastática (1 doente com Tipo III e 2 com Tipo IV). O sexo masculino (p = 0,030), tipo III/IV (p < 0,001), Ki-67 index >20% (p < 0,001), Grau 2/3 (p < 0,001), invasão além da submucosa (p < 0,001) e presença de metástases (p < 0,001) foram identificados como fatores de risco para mortalidade na análise univariada. Sete doentes desenvolveram metástases (5,3%). A análise multivariáda revelou que o Ki-67 >20% (p = 0,016) era um factor de risco independente para metastização.Globalmente, a CgA mostrou uma sensibilidade de detecção de recorrência de 20% e uma especificidade de 79% (sensibilidade de 8% e especificidade de 71% em em TNEs-G do Tipo I). Conclusão: A identificação dos fatores de risco para a presença de metástases e para a mortalidade neste grupo de pacientes pode ajudar a individualizar a estratégia terapêutica. A CgA parece ser um marcador fraco para a monitorização de doentes com TNEs-G.

Modeling transmission of avian influenza viruses at the human-animal-environment interface in Cuba.

Introduction: The increasing geographical spread of highly pathogenic avian influenza viruses (HPAIVs) is of global concern due to the underlying zoonotic and pandemic potential of the virus and its economic impact. An integrated One Health model was developed to estimate the likelihood of Avian Influenza (AI) introduction and transmission in Cuba, which will help inform and strengthen risk-based surveillance activities. Materials and methods: The spatial resolution used for the model was the smallest administrative district ("Consejo Popular"). The model was parameterised for transmission from wild birds to poultry and pigs (commercial and backyard) and then to humans. The model includes parameters such as risk factors for the introduction and transmission of AI into Cuba, animal and human population densities; contact intensity and a transmission parameter (ß). Results: Areas with a higher risk of AI transmission were identified for each species and type of production system. Some variability was observed in the distribution of areas estimated to have a higher probability of AI introduction and transmission. In particular, the south-western and eastern regions of Cuba were highlighted as areas with the highest risk of transmission. Discussion: These results are potentially useful for refining existing criteria for the selection of farms for active surveillance, which could improve the ability to detect positive cases. The model results could contribute to the design of an integrated One Health risk-based surveillance system for AI in Cuba. In addition, the model identified geographical regions of particular importance where resources could be targeted to strengthen biosecurity and early warning surveillance.

Discovery of antimicrobial peptides in the global microbiome with machine learning.

Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and 87,920 prokaryotic genomes from environmental and host-associated habitats to create the AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, few of which match existing databases. AMPSphere provides insights into the evolutionary origins of peptides, including by duplication or gene truncation of longer sequences, and we observed that AMP production varies by habitat. To validate our predictions, we synthesized and tested 100 AMPs against clinically relevant drug-resistant pathogens and human gut commensals both in vitro and in vivo. A total of 79 peptides were active, with 63 targeting pathogens. These active AMPs exhibited antibacterial activity by disrupting bacterial membranes. In conclusion, our approach identified nearly one million prokaryotic AMP sequences, an open-access resource for antibiotic discovery.

A scoping review on associations between paratuberculosis and productivity in cattle.

Paratuberculosis (PTB), or Johne's disease, is a disease with worldwide distribution caused by Mycobacterium avium subsp. paratuberculosis (MAP) that leads to chronic enteritis, primarily in ruminants. Even subclinical infection significantly reduces the animals' performance, and consequences of the disease lead to high economic losses for the cattle industry. To estimate the economic burden of bovine PTB and to evaluate the benefits of a potential control program, accurate estimates of the production effects associated with the disease are required. Therefore, the aim of this scoping review was to provide a comprehensive overview of associations between MAP infection and production parameters in cattle. The studies were collected from three electronic databases. Of the total 1,605 identified studies, 1,432 did not meet the set criteria in the title and abstract screening and a further 106 were excluded during full-text review. Finally, data on 34 different production parameters were extracted from 67 publications. Results show that the magnitude of reported performance losses varies depending on several factors, such as the type of diagnostic test applied, disease status or number of lactations. Studies reported a reduction in milk yield, changes in milk quality (e.g., higher somatic cell count, lower amount of produced milk fat and protein), reduced fertility (e.g., prolonged calving interval and service period, higher abortion rate and calving difficulties), reduced weaning weight, slaughter weight and slaughter value, or a higher risk for mastitis. Results from the studies included in our review show a median decrease of milk yield per infected cow of -452 kg/lactation for raw and -405 kg/lactation for modeled data. Similarly, the amount of produced milk protein fell by a median of -14.41 kg/lactation for modeled data and the amount of produced milk fat by a median of -13.13 kg/lactation. The reviewed studies revealed a prolonged calving interval by around 30 days and a 1.5 to 3 times higher likeliness of culling per lactation in PTB positive animals. Results from this scoping review provide evidence-based inputs for the development of economic models aiming at the estimation of the costs and benefits associated with different disease control scenarios for PTB.

Limits on the evolutionary rates of biological traits.

This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These rate limits link the variability in a population to evolutionary rates. In particular, high variances in the fitness of a population and of a quantitative trait allow for fast changes in the trait's average. In contrast, low variability makes a trait less susceptible to random changes due to genetic drift. The results in this article generalize Fisher's fundamental theorem of natural selection to dynamics that allow for mutations and genetic drift, via trade-off relations that constrain the evolutionary rates of arbitrary traits. The rate limits can be used to probe questions in various evolutionary biology and ecology settings. They apply, for instance, to trait dynamics within or across species or to the evolution of bacteria strains. They apply to any quantitative trait, e.g., from species' weights to the lengths of DNA strands.

Proximalization of Arterial Inflow for the Treatment of Limb Ischemia in a Transposed Femoral Arteriovenous Fistula-A Case Report.

INTRODUCTION: Femoral vein transposition is one of the final resorts for vascular access in patients with exhaustion of upper limb venous patrimony and central venous occlusive disease. Its major pitfalls include hemodialysis access-induced distal ischemia and infection. Surgical procedures may be warranted to preserve vascular access if ischemia develops. Several techniques are reported in the literature for femoral vein transposition. CASE REPORT: We expose an endoscopic femoral vein harvesting as an alternative to the single thigh incision in order to avoid its associated complications. In the setting of ischemia, proximalization of arterial inflow was used to manage femoral vein transposition associated limb ischemia. CONCLUSION: This case report aims to expose the aforementioned unreported surgical techniques for lower limb arteriovenous fistula, its advantages, and pitfalls, as well as considerations on its future use.

Stool Glycoproteomics Signatures of Pre-Cancerous Lesions and Colorectal Cancer.

Colorectal cancer (CRC) screening relies primarily on stool analysis to identify occult blood. However, its sensitivity for detecting precancerous lesions is limited, requiring the development of new tools to improve CRC screening. Carcinogenesis involves significant alterations in mucosal epithelium glycocalyx that decisively contribute to disease progression. Building on this knowledge, we examined patient series comprehending premalignant lesions, colorectal tumors, and healthy controls for the T-antigen-a short-chain O-glycosylation of proteins considered a surrogate marker of malignancy in multiple solid cancers. We found the T-antigen in the secretions of dysplastic lesions as well as in cancer. In CRC, T-antigen expression was associated with the presence of distant metastases. In parallel, we analyzed a broad number of stools from individuals who underwent colonoscopy, which showed high T expressions in high-grade dysplasia and carcinomas. Employing mass spectrometry-based lectin-affinity enrichment, we identified a total of 262 proteins, 67% of which potentially exhibited altered glycosylation patterns associated with cancer and advanced pre-cancerous lesions. Also, we found that the stool (glyco)proteome of pre-cancerous lesions is enriched for protein species involved in key biological processes linked to humoral and innate immune responses. This study offers a thorough analysis of the stool glycoproteome, laying the groundwork for harnessing glycosylation alterations to improve non-invasive cancer detection.

Aberrantly Glycosylated GLUT1 as a Poor Prognosis Marker in Aggressive Bladder Cancer.

Muscle-invasive bladder cancer (MIBC) remains a pressing health concern due to conventional treatment failure and significant molecular heterogeneity, hampering the development of novel targeted therapeutics. In our quest for novel targetable markers, recent glycoproteomics and bioinformatics data have pinpointed (glucose transporter 1) GLUT1 as a potential biomarker due to its increased expression in tumours compared to healthy tissues. This study explores this hypothesis in more detail, with emphasis on GLUT1 glycosylation patterns and cancer specificity. Immunohistochemistry analysis across a diverse set of human bladder tumours representing all disease stages revealed increasing GLUT1 expression with lesion severity, extending to metastasis, while remaining undetectable in healthy urothelium. In line with this, GLUT1 emerged as a marker of reduced overall survival. Revisiting nanoLC-EThcD-MS/MS data targeting immature O-glycosylation on muscle-invasive tumours identified GLUT1 as a carrier of short glycosylation associated with invasive disease. Precise glycosite mapping uncovered significant heterogeneity between patient samples, but also common glycopatterns that could provide the molecular basis for targeted solutions. Immature O-glycosylation conferred cancer specificity to GLUT1, laying the molecular groundwork for enhanced targeted therapeutics in bladder cancer. Future studies should focus on a comprehensive mapping of GLUT1 glycosites for highly specific cancer-targeted therapy development for bladder cancer.

Review state-of-the-art of output-based methodological approaches for substantiating freedom from infection.

A wide variety of control and surveillance programmes that are designed and implemented based on country-specific conditions exists for infectious cattle diseases that are not regulated. This heterogeneity renders difficult the comparison of probabilities of freedom from infection estimated from collected surveillance data. The objectives of this review were to outline the methodological and epidemiological considerations for the estimation of probabilities of freedom from infection from surveillance information and review state-of-the-art methods estimating the probabilities of freedom from infection from heterogeneous surveillance data. Substantiating freedom from infection consists in quantifying the evidence of absence from the absence of evidence. The quantification usually consists in estimating the probability of observing no positive test result, in a given sample, assuming that the infection is present at a chosen (low) prevalence, called the design prevalence. The usual surveillance outputs are the sensitivity of surveillance and the probability of freedom from infection. A variety of factors influencing the choice of a method are presented; disease prevalence context, performance of the tests used, risk factors of infection, structure of the surveillance programme and frequency of testing. The existing methods for estimating the probability of freedom from infection are scenario trees, Bayesian belief networks, simulation methods, Bayesian prevalence estimation methods and the STOC free model. Scenario trees analysis is the current reference method for proving freedom from infection and is widely used in countries that claim freedom. Bayesian belief networks and simulation methods are considered extensions of scenario trees. They can be applied to more complex surveillance schemes and represent complex infection dynamics. Bayesian prevalence estimation methods and the STOC free model allow freedom from infection estimation at the herd-level from longitudinal surveillance data, considering risk factor information and the structure of the population. Comparison of surveillance outputs from heterogeneous surveillance programmes for estimating the probability of freedom from infection is a difficult task. This paper is a 'guide towards substantiating freedom from infection' that describes both all assumptions-limitations and available methods that can be applied in different settings.

A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer.

Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer. Here we focus on transfers detected through comparison of individual gene trees to the species tree, assessing the distribution of gene-exchanging prokaryotes across over a million environmental sequencing samples. By analysing detected horizontal gene transfer events, we show distinct functional profiles for recent versus old events. Although most genes transferred are part of the accessory genome, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We find that co-occurring, interacting and high-abundance species tend to exchange more genes. Finally, we show that host-associated specialist species are most likely to exchange genes with other host-associated specialist species, whereas species found across different habitats have similar gene exchange rates irrespective of their preferred habitat. Our study covers an unprecedented scale of integrated horizontal gene transfer and environmental information, highlighting broad eco-evolutionary trends.