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Abstract Background Genomic epidemiology has helped reconstruct the global and regional movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is still a lack of understanding of SARS-CoV-2 spread in some of the world’s least developed countries (LDCs). Methods To begin to address this disparity, we studied the transmission dynamics of the virus in Bangladesh during the country’s first COVID-19 wave by analysing case reports and whole-genome sequences from all eight divisions of the country. Results We detected > 50 virus introductions to the country during the period, including during a period of national lockdown. Additionally, through discrete phylogeographic analyses, we identified that geographical distance and population -density and/or -size influenced virus spatial dispersal in Bangladesh. Conclusions Overall, this study expands our knowledge of SARS-CoV-2 genomic epidemiology in Bangladesh, shedding light on crucial transmission characteristics within the country, while also acknowledging resemblances and differences to patterns observed in other nations.

Chicken meat (broiler) production is a rapidly growing livestock sector in India, and one dominated by contract farming. Studies have reported high levels of antibiotic use in Indian broiler farms which is concerning given this is one of the driving forces for the development of antibiotic resistance. This study used the economic lens of agency theory to examine strategic decisions which occur during contract broiler production and their potential impact on antibiotic use, using West Bengal as a case study. Agency theory focuses on the informational asymmetry and opportunism between service providers and seekers and the subsequent agency cost needed to avoid aberrant outcomes. Interviews were conducted with key informants (n = 6) and stakeholders (n = 20) associated with broiler production, and broiler farmers (17 contract and four non-contract), using online and face-to-face interviews. Data were analysed descriptively using manifest content analysis and interpretatively using reflexive thematic analysis. Contract farming in West Bengal exists within a series of inter-dependent relationships, many of which contain information asymmetry and can be subject to opportunism. Positioning contract companies as principals seeking labour from agents, we see how out-sourcing of production to distal farms led to antibiotics being used as a risk mitigation strategy. This was further compounded by concerns about the Mycoplasma status of breeding stock, and a perception that broiler day old chicks were infected, resulting in use of antibiotics belonging to classes deemed critically important for human health. While antibiotic use decisions were predominately made by contract companies, they were dependent on the decisions farmers and breeding companies made concerning biosecurity and production practices. In turn, farmers' decisions were shaped by factors such as access to financial and social capital. Thus, efforts to reduce antibiotic use in West Bengal's broilers must not just focus on changing the prescribing behavior of individuals but more broadly consider the environment within which contracting exists.

Introduction and aim: Hepatocellular carcinoma (HCC) is the third most frequent cancer of digestive tract tumors in Peru, with a high mortality rate of 17.7 per 100,000 inhabitants. A significant number of HCC cases in Peru do not follow the classic clinical epidemiology of the disease described in other parts of the world. Those patients present with a distinct transcriptome profile and a singular tumor process, suggesting a particular type of hepatocarcinogenesis in a portion of the Peruvian population. Our aim was to understand the clinical and biologic involvement of the epigenetic profile (methylation) and gene expression (transcriptome) of HCC in Peruvian patients. Methods: HCC and liver transcriptome and DNA methylation profiles were evaluated in 74 Peruvian patients. Results: When grouped by age, there was greater DNA methylation in younger patients with HCC but no differences with respect to the transcriptomic profile. A high prevalence of the hepatitis B virus (HBV) (>90%) was also observed in the younger patients with HCC. Enrichment analyses in both molecular profiles pinpointed PRC2 as an important molecular effector of that liver tumor process in Peruvian patients. Conclusion: HCC in Peruvian patients has a unique molecular profile, associated with the presence of HBV, as well as overall DNA hypermethylation related to undifferentiated liver cells or cellular reprogramming. Resumen: Introducción: En Perú, el carcinoma hepatocelular (CHC) ocupa el tercer lugar en incidencia entre los tumores del sistema digestivo, y tiene una alta tasa de mortalidad, 17.7 por 100 000 habitantes. La mayoría de los casos reportados no presentan la epidemiología clínica clásica del CHC observado en otras partes del mundo. Además, se ha identificado que estos pacientes presentan un perfil transcriptómico distinto y un proceso tumoral singular, sugiriendo un proceso particular de hepatocarcinogénesis en una fracción de la población peruana. Objetivo: El presente estudio busca comprender la implicancia clínica y biológica del perfil epigenético (metilación) y de expresión de los genes (transcriptómico) del CHC en los pacientes peruanos. Métodos: Se evaluó el perfil de transcriptómico y de metilación de ADN de hígado y CHC en 74 pacientes peruanos. Resultados: El agrupamiento por edades mostró una mayor metilación del ADN en los pacientes jóvenes con CHC, en contraste no se observaron diferencias en el perfil transcriptómico. Adicionalmente, también se evidenció una alta prevalencia del virus de la hepatitis B (VHB) (>90%) en los pacientes jóvenes con CHC. El análisis de enriquecimiento en ambos perfiles moleculares demostró que PRC2 es posiblemente uno de los principales actores moleculares en este proceso tumoral hepático en pacientes peruanos. Conclusión: El CHC peruano presenta un perfil molecular único, asociado a la presencia del VHB, y con una hipermetilación global del ADN asociado a células hepáticas indiferenciadas o a una reprogramación celular.

Antimicrobial resistance has emerged as a significant health problem worldwide, including in Bangladesh, where chickens are an important protein source for human nutrition. One of the factors accelerating the development of antimicrobial resistance is the inappropriate use of antimicrobials on commercial chicken farms. A cross-sectional study was conducted in 2019 on 140 commercial chicken farms in the Chattogram district of Bangladesh to investigate the association between antimicrobial use and resistance in Escherichia coli and Salmonella spp. cultured from cloacal swabs of chickens and from the poultry shed environment. All E. coli and Salmonella spp. isolates were resistant to multiple antimicrobial classes, including those categorized as “Highest Priority Critically Important Antimicrobials” for human medicine. Notably, resistance was observed in E. coli isolates from farms that did not use these antimicrobial classes in the current production cycle. For example, although quinolones were not used on 43.9% of E. coli positive farms, 95.7% of these farms had quinolone-resistant E. coli isolates. The results of the path analysis revealed that there was a “direct effect” of the frequency of antimicrobial usage on “high” resistance, with resistance increasing when antimicrobials were administered more frequently (β = 0.28, p = 0.002). There was a “direct effect” of the purpose of antimicrobial use on “low” resistance, with resistance marginally decreasing when antimicrobials were administered solely for therapeutic use (β = −0.17, p = 0.062), but increasing when they were used prophylactically. Overall, the study results could be used to educate farmers on better practices for antimicrobial administration, and to guide government agencies to update policies on antimicrobial use and resistance surveillance in the poultry sector of Bangladesh.

Abstract Background Angioimmunoblastic T-cell lymphoma (AITL) is a malignancy with very poor survival outcome, in urgent need of more specific therapeutic strategies. The drivers of malignancy in this disease are CD4+ follicular helper T cells (Tfh). The metabolism of these malignant Tfh cells was not yet elucidated. Therefore, we decided to identify their metabolic requirements with the objective to propose a novel therapeutic option. Methods To reveal the prominent metabolic pathways used by the AITL lymphoma cells, we relied on metabolomic and proteomic analysis of murine AITL (mAITL) T cells isolated from our established mAITL model. We confirmed these results using AITL patient and healthy T cell expression data. Results Strikingly, the mAITL Tfh cells were highly dependent on the second branch of the Kennedy pathway, the choline lipid pathway, responsible for the production of the major membrane constituent phosphatidylcholine. Moreover, gene expression data from Tfh cells isolated from AITL patient tumors, confirmed the upregulation of the choline lipid pathway. Several enzymes involved in this pathway such as choline kinase, catalyzing the first step in the phosphatidylcholine pathway, are upregulated in multiple tumors other than AITL. Here we showed that treatment of our mAITL preclinical mouse model with a fatty acid oxydation inhibitor, significantly increased their survival and even reverted the exhausted CD8 T cells in the tumor into potent cytotoxic anti-tumor cells. Specific inhibition of Chokα confirmed the importance of the phosphatidylcholine production pathway in neoplastic CD4 + T cells, nearly eradicating mAITL Tfh cells from the tumors. Finally, the same inhibitor induced in human AITL lymphoma biopsies cell death of the majority of the hAITL PD-1high neoplastic cells. Conclusion Our results suggest that interfering with choline metabolism in AITL reveals a specific metabolic vulnerability and might represent a new therapeutic strategy for these patients.

Neuro-ophthalmological changes have been reported after prolonged exposure to microgravity; however, the pathophysiology remains unclear. Furthermore, several countermeasures have been suggested to counteract the side effects of microgravity. The objectives of the present study were twofold: (1) to assess the neuro-ophthalmological impact of 60 days of head-down bed rest (HDBR) and (2) to determine the potential effects of an antioxidant cocktail. In this case, 20 healthy male subjects completed a 60-day HDBR and were randomly allocated into two groups: a control condition without an antioxidant cocktail (CON) and a condition with an antioxidant cocktail (NUT). The retinal nerve fibre layer thickness (RNFLT) and central retinal thickness (CRT) were assessed with spectral domain optical coherence tomography. The optic nerve sheath diameter (ONSD) was measured by ocular ultrasonography and used to assess indirect changes in the intracranial pressure (ICP). The intraocular pressure (IOP) was assessed by Goldmann applanation tonometry. The CRT tended to be reduced after HDBR. The ONSD was increased at the end and after HDBR. The IOP tended to decrease after HDBR. Finally, the antioxidant cocktail had minor impacts on the ophthalmological changes induced by HDBR. It is worth noting that two participants presented peripapillary edema.

Recent highly pathogenic avian influenza A(H5N1) outbreaks in two Korean cat shelters highlight the need to enhance surveillance for cross-species viral transmission into animal populations kept by humans for non-agricultural or non-conventional livestock farming purposes from a One Health perspective.

Background: The poultry industry in India, estimated to be worth about one trillion INR, was severely affected by the COVID-19 pandemic. This study was conducted in Gujarat, India to unpack the processes through which COVID-19-related factors affected the poultry production and distribution network and explore the impacts on the relevant actors. Methods: An exploratory qualitative study was conducted among 34 poultry stakeholders using semi-structured interviews. The data were thematically analyzed by adopting an interpretative phenomenological approach. Results: Convincing evidence emerged that the lockdown and the pandemic significantly impacted the production, distribution, and consumption of poultry products. Movement restrictions during the first lockdown disrupted the supply of inputs and the distribution of poultry and poultry products. Between March and June 2020, rumors contributed to a substantial decrease in the consumption of poultry products. Consumption picked up following the reopening after the lockdown and the prices and availability of poultry products. The profits, however, failed to compensate for the losses that had been incurred. Conclusions: The experience and impacts of the first COVID-19 lockdown on the poultry industry unraveled several short- and medium-term challenges in the poultry sector in India that need to be addressed to make it more resilient to similar shocks.

Optic Atrophy (OA) can be associated with the development of microcystic macular edema (MME) in the perifoveal retinal inner nuclear layer (INL). We aimed here to retrospectively determine the prevalence of MME in patients with non-glaucomatous OA in our tertiary ophthalmology department between 2015 and 2020. We then examined how MME affected the thicknesses of the different retinal layers and the differences in demographic and clinical characteristics between those patients who developed MME and those who did not. A total of 643 eyes (429 patients) were included (mean age 45.9 ± 17.8 years, 52% female). MME developed in 95 (15%) eyes and across all etiologies of OA except for toxic/nutritional causes, but the prevalence of MME varied between the different etiologies. The development of MME was associated with thinning of the ganglion cell layer (11.0 vs. 9.6 μm; p = 0.001) and the retinal nerve fiber layer (10.1 vs. 9.15 μm; p = 0.024), with INL thickening in the 3- and 6-mm diameter areas of the central fovea. Patients developing MME had significantly worse distance best-corrected visual acuity than those not developing MME (0.62 vs. 0.38 logMAR; p = 0.002). Overall, the presence of MME in OA cannot be used to guide the diagnostic work-up of OA.

The rapid intensification of poultry production raises important concerns about the associated risks of zoonotic infections. Here, we introduce EPINEST (EPIdemic NEtwork Simulation in poultry Transportation systems): an agent-based modelling framework designed to simulate pathogen transmission within realistic poultry production and distribution networks. We provide example applications to broiler production in Bangladesh, but the modular structure of the model allows for easy parameterization to suit specific countries and system configurations. Moreover, the framework enables the replication of a wide range of eco-epidemiological scenarios by incorporating diverse pathogen life-history traits, modes of transmission and interactions between multiple strains and/or pathogens. EPINEST was developed in the context of an interdisciplinary multi-centre study conducted in Bangladesh, India, Vietnam and Sri Lanka, and will facilitate the investigation of the spreading patterns of various health hazards such as avian influenza, Campylobacter, Salmonella and antimicrobial resistance in these countries. Furthermore, this modelling framework holds potential for broader application in veterinary epidemiology and One Health research, extending its relevance beyond poultry to encompass other livestock species and disease systems.

Background Follicular lymphoma (FL), the most common indolent non-Hodgkin’s Lymphoma, is a heterogeneous disease and a paradigm of the contribution of immune tumor microenvironment to disease onset, progression, and therapy resistance. Patient-derived models are scarce and fail to reproduce immune phenotypes and therapeutic responses.Methods To capture disease heterogeneity and microenvironment cues, we developed a patient-derived lymphoma spheroid (FL-PDLS) model culturing FL cells from lymph nodes (LN) with an optimized cytokine cocktail that mimics LN stimuli and maintains tumor cell viability.Results FL-PDLS, mainly composed of tumor B cells (60% on average) and autologous T cells (13% CD4 and 3% CD8 on average, respectively), rapidly organizes into patient-specific three-dimensional (3D) structures of three different morphotypes according to 3D imaging analysis. RNAseq analysis indicates that FL-PDLS reproduces FL hallmarks with the overexpression of cell cycle, BCR, or mTOR signaling related gene sets. FL-PDLS also recapitulates the exhausted immune phenotype typical of FL-LN, including expression of BTLA, TIGIT, PD-1, TIM-3, CD39 and CD73 on CD3+ T cells. These features render FL-PDLS an amenable system for immunotherapy testing. With this aim, we demonstrate that the combination of obinutuzumab (anti-CD20) and nivolumab (anti-PD1) reduces tumor load in a significant proportion of FL-PDLS. Interestingly, B cell depletion inversely correlates with the percentage of CD8+ cells positive for PD-1 and TIM-3.Conclusions In summary, FL-PDLS is a robust patient-derived 3D system that can be used as a tool to mimic FL pathology and to test novel immunotherapeutic approaches in a context of personalized medicine.

The seasonality of African swine fever (ASF) outbreaks in domestic pigs differs between temperate and subtropical/tropical regions. We hypothesise that variations in the importance of wild boar-to-farm and farm-to-farm transmission routes shape these contrasting patterns, and we emphasise the implications for effective ASF control.

In 2021, the world marked 10 years free from rinderpest. The United Nations Food and Agriculture Organization and World Organisation for Animal Health have since made great strides in consolidating, sequencing, and destroying stocks of rinderpest virus–containing material, currently kept by only 14 known institutions. This progress must continue.

Abstract A cross-sectional study was conducted with 144 small-scale poultry farmers across 42 Bangladeshi villages to explore risk factors associated with avian influenza H5 and H9 seropositivity on backyard chicken farms. Using mixed-effects logistic regression with village as random effect, we identified crow abundance in garbage dumping places and presence of migratory wild birds within villages to be associated with higher odds of H5 and H9 seropositivity. At farm-level, garbage around poultry houses was also associated with higher odds of H5 and H9 seropositivity. In addition, specific trading practices (such as, purchase of chickens from live bird markets (LBM) and neighboring farms to raise them on their own farms, frequency of visits to LBM, purchase of poultry at LBM for consumption) and contact of backyard chickens with other animals (such as, feeding of different poultry species together, using pond water as drinking source for poultry, access of feral and wild animals to poultry houses) were associated with higher odds of H5 or H9 seropositivity. Resource-constrained small-scale poultry farmers should be able to address risk factors identified in this study without requiring large investments into poultry management, thereby reducing the likelihood of avian influenza virus transmission and ultimately occurrence of avian influenza outbreaks.

Chicken meat (broiler) production is a rapidly growing livestock sector in India, and one dominated by contract farming. Studies have reported high levels of antibiotic use in Indian broiler farms which is concerning given this is one of the driving forces for the development of antibiotic resistance. This study used the economic lens of agency theory to examine strategic decisions which occur during contract broiler production and their potential impact on antibiotic use, using West Bengal as a case study. Agency theory focuses on the informational asymmetry and opportunism between service providers and seekers and the subsequent agency cost needed to avoid aberrant outcomes. Interviews were conducted with key informants (n = 6) and stakeholders (n = 20) associated with broiler production, and broiler farmers (17 contract and four non-contract), using online and face-to-face interviews. Data were analysed descriptively using manifest content analysis and interpretatively using reflexive thematic analysis. Contract farming in West Bengal exists within a series of inter-dependent relationships, many of which contain information asymmetry and can be subject to opportunism. Positioning contract companies as principals seeking labour from agents, we see how out-sourcing of production to distal farms led to antibiotics being used as a risk mitigation strategy. This was further compounded by concerns about the Mycoplasma status of breeding stock, and a perception that broiler day old chicks were infected, resulting in use of antibiotics belonging to classes deemed critically important for human health. While antibiotic use decisions were predominately made by contract companies, they were dependent on the decisions farmers and breeding companies made concerning biosecurity and production practices. In turn, farmers' decisions were shaped by factors such as access to financial and social capital. Thus, efforts to reduce antibiotic use in West Bengal's broilers must not just focus on changing the prescribing behavior of individuals but more broadly consider the environment within which contracting exists. [ABSTRACT FROM AUTHOR]

Limited genomic sampling in many high-incidence countries has impeded studies of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of virus genetic diversity. We investigated SARS-CoV-2 transmission dynamics in Gujarat, India, during the state’s first epidemic wave to shed light on spread of the virus in one of the regions hardest hit by the pandemic. By integrating case data and 434 whole-genome sequences sampled across 20 districts, we reconstructed the epidemic dynamics and spatial spread of SARS-CoV-2 in Gujarat. Our findings indicate global and regional connectivity and population density were major drivers of the Gujarat outbreak. We detected >100 virus lineage introductions, most of which appear to be associated with international travel. Within Gujarat, virus dissemination occurred predominantly from densely populated regions to geographically proximate locations that had low population density, suggesting that urban centers contributed disproportionately to virus spread.