Emerging role of microglia in the developing dopaminergic system: Perturbation by early life stress

Early life stress correlates with a higher prevalence of neurological disorders, including autism, attention-deficit/hyperactivity disorder, schizophrenia, depression, and Parkinson's disease. These conditions, primarily involving abnormal development and damage of the dopaminergic system, pose significant public health challenges. Microglia, as the primary immune cells in the brain, are crucial in regulating neuronal circuit development and survival. From the embryonic stage to adulthood, microglia exhibit stage-specific gene expression profiles, transcriptome characteristics, and functional phenotypes, enhancing the susceptibility to early life stress. However, the role of microglia in mediating dopaminergic system disorders under early life stress conditions remains poorly understood. This review presents an up-to-date overview of preclinical studies elucidating the impact of early life stress on microglia, leading to dopaminergic system disorders, along with the underlying mechanisms and therapeutic potential for neurodegenerative and neurodevelopmental conditions. Impaired microglial activity damages dopaminergic neurons by diminishing neurotrophic support (e.g., insulin-like growth factor-1) and hinders dopaminergic axon growth through defective phagocytosis and synaptic pruning. Furthermore, blunted microglial immunoreactivity suppresses striatal dopaminergic circuit development and reduces neuronal transmission. Furthermore, inflammation and oxidative stress induced by activated microglia can directly damage dopaminergic neurons, inhibiting dopamine synthesis, reuptake, and receptor activity. Enhanced microglial phagocytosis inhibits dopamine axon extension. These long-lasting effects of microglial perturbations may be driven by early life stress-induced epigenetic reprogramming of microglia. Indirectly, early life stress may influence microglial function through various pathways, such as astrocytic activation, the hypothalamic-pituitary-adrenal axis, the gut-brain axis, and maternal immune signaling. Finally, various therapeutic strategies and molecular mechanisms for targeting microglia to restore the dopaminergic system were summarized and discussed. These strategies include classical antidepressants and antipsychotics, antibiotics and anti-inflammatory agents, and herbal-derived medicine. Further investigations combining pharmacological interventions and genetic strategies are essential to elucidate the causal role of microglial phenotypic and functional perturbations in the dopaminergic system disrupted by early life stress.

Chitosan alleviates symptoms of Parkinson's disease by reducing acetate levels, which decreases inflammation and promotes repair of the intestinal barrier and blood-brain barrier

JOURNAL/nrgr/04.03/01300535-202601000-00041/figure1/v/2025-06-09T151831Z/r/image-tiff Studies have shown that chitosan protects against neurodegenerative diseases. However, the precise mechanism remains poorly understood. In this study, we administered chitosan intragastrically to an MPTP-induced mouse model of Parkinson's disease and found that it effectively reduced dopamine neuron injury, neurotransmitter dopamine release, and motor symptoms. These neuroprotective effects of chitosan were related to bacterial metabolites, specifically short-chain fatty acids, and chitosan administration altered intestinal microbial diversity and decreased short-chain fatty acid production in the gut. Furthermore, chitosan effectively reduced damage to the intestinal barrier and the blood-brain barrier. Finally, we demonstrated that chitosan improved intestinal barrier function and alleviated inflammation in both the peripheral nervous system and the central nervous system by reducing acetate levels. Based on these findings, we suggest a molecular mechanism by which chitosan decreases inflammation through reducing acetate levels and repairing the intestinal and blood-brain barriers, thereby alleviating symptoms of Parkinson's disease.

Respiratory syncytial virus vaccination in older adults and patients with chronic disorders: A position paper from the Portuguese Society of Pulmonology, the Portuguese Association of General and Family Medicine, the Portuguese Society of Cardiology, the Portuguese Society of Infectious Diseases and Clinical Microbiology, the Portuguese Society of Endocrinology, Diabetes and Metabolism, and the Portuguese Society of Internal Medicine

BACKGROUND

Respiratory syncytial virus (RSV) is an important cause of lower respiratory tract infection, hospitalisation and death in adults.

METHODS

Based on evidence regarding the impact of RSV on adult populations at risk for severe infection and the efficacy and safety of RSV vaccines, the Portuguese Society of Pulmonology, the Portuguese Association of General and Family Medicine, the Portuguese Society of Cardiology, the Portuguese Society of Infectious Diseases and Clinical Microbiology, the Portuguese Society of Endocrinology, Diabetes and Metabolism, and the Portuguese Society of Internal Medicine endorses this position paper with recommendations to prevent RSV-associated disease and its complications in adults through vaccination.

CONCLUSION

The RSV vaccine is recommended for people aged ≥50 years with risk factors (chronic obstructive pulmonary disease, asthma, heart failure, coronary artery disease, diabetes, chronic kidney disease, chronic liver disease, immunocompromise, frailty, dementia, and residence in a nursing home) and all persons aged ≥60 years. If it cannot be made available to this population, then the vaccine should be prioritised for individuals aged ≥75 years and those aged ≥50 years with risk factors. The vaccine should preferably be given between September and November and can be co-administered with the influenza vaccine. Ongoing studies on RSV vaccines may justify extending these recommendations in the future.

C. P. Long-term cognitive and autonomic effects of COVID-19 in young adults: a cross-sectional study at 28 months

OBJECTIVES

The COVID-19 pandemic, caused by SARS-CoV-2, has had profound global impacts since its emergence in late 2019. Whilst acute symptoms are well-documented, increasing evidence suggests long-term consequences extending beyond the acute phase. This study aimed to investigate the long-term cognitive and autonomic effects of COVID-19 in young adults.

MATERIALS AND METHODS

We conducted a cross-sectional study comparing young adults with a history of COVID-19 (n = 34) to matched controls (n = 34). Cognitive function was assessed using the Sternberg Task, Stroop Task, and Go/No-Go Task (GNG). Autonomic function was evaluated using heart rate variability (HRV) parameters.

RESULTS

The average time interval between COVID-19 infection and testing was 28.2 months. The COVID-19 group showed significantly increased reaction time in the 2-item absent condition (p = 0.044) and errors in the 4-item present condition (p = 0.012) of the Sternberg Task and increased neutral response time (p = 0.028) and the normalized time for completing the task (p = 0.022) in the Stroop Task. No significant differences were found in the GNG Task. HRV parameters did not differ significantly between groups, although trends toward higher overall HRV were observed in the COVID-19 group.

CONCLUSION

Young adults who had COVID-19 infection approximately 28 months ago show minimal long-term impact on cognitive function and autonomic regulation. However, subtle cognitive inefficiencies persist, particularly in working memory and executive function tasks. These findings suggest a generally favorable long-term prognosis for young adults following mild to moderate COVID-19 but highlight the need for further investigation into persistent subtle cognitive effects and autonomic effects.

Unraveling cysteinyl leukotrienes and their receptors in inflammation through the brain-gut-lung axis

Cysteinyl leukotrienes (CysLTs), as potent lipid inflammatory mediators, play a pivotal role in systemic multi-organ inflammation and inter-organ communication through interactions with their receptors (CysLTRs). However, However, the function of CysLT3R is unclear and lacks a network of cross-organ metabolite interactions, and the clinical use of leukotriene receptor antagonists (LTRAs) has certain limitations. This review systematically synthesizes existing evidence and proposes future directions by clarifying receptor subtype specificity, optimizing targeted therapies, exploring CysLTs' applications in neuroimmunology, and elucidating the dual roles of CysLTs in chronic inflammation. It is indicated that CysLTs activate eosinophils, mast cells, and airway tuft cells, driving type 2 immune responses and mucus secretion in the lungs, thereby exacerbating respiratory diseases such as asthma. In the nervous system, CysLTs aggravate neurodegenerative disorders like cerebral ischemia and Alzheimer's disease by disrupting the blood-brain barrier, promoting glial activation, and inducing neuronal damage. In the gut, CysLTs regulate anti-helminth immunity via the tuft cell-ILC2 pathway and collaborate with prostaglandin D2 (PGD2) to modulate bile excretion and mucosal protection. Furthermore, CysLTs mediate communication through the gut-lung and gut-brain axes via metabolites such as succinate, contributing to cross-organ inflammatory regulation. In conclusion, this review highlights the complex roles of CysLTs in chronic inflammation, providing a theoretical foundation for precise intervention in multi-organ inflammatory diseases, which provides a theoretical framework for precision interventions in multi-organ inflammatory diseases and inspires interdisciplinary breakthroughs.

Vaccine effectiveness dynamics against influenza and SARS-CoV-2 in community-tested patients in France 2023-2024

The epidemiology of respiratory viruses and vaccine effectiveness (VE) in the community are not well described. This study assessed VE against a positive test of influenza (VEf) and SARS-CoV-2 (VECov). Data from networks of community-based laboratories in France were collected during standard of care in the 2023-2024 epidemic season (n = 511,083 multiplex RT-PCR tests). Patients' demographics and symptoms were reported in addition to viral sequencing results. The test-negative design was used to estimate VEf and VECov by time since vaccination and calendar week. Adjusted VEf by age, sex, presence of symptoms, PCR technique, and week of testing, was 47.6% (95% CI: 44.3-50.7%). VEf was lower in patients ≥65 years (42.0%; 95% CI: 36.6-46.9%) than in 18-64 years (52.9%; 95% CI: 48.6-56.8%). The adjusted VEf against type A influenza, which represented 98% of typed viruses, was 51% (45%-56.6%) for patients vaccinated 15 days to 3 months before testing, and 35.5% (24.2%-45.3%) for those vaccinated 3-6 months before testing. For VECov, the adjusted estimate in patients vaccinated 15 days to 3 months prior to testing was 40.6% (7.2%-58.6%) at week 39, 24.8% (4.0%-38.8%) at week 45, and dropped systematically through the epidemic season as the JN.1 variant became dominant. This study showed moderate VEf and VECov against infection in the community and highlighted the impact of time since vaccination and age for both estimates, and the new variant emergence on VECov. These findings should be considered in future vaccination campaigns.

Protection acquired upon intraperitoneal group a Streptococcus immunization is independent of concurrent adaptive immune responses but relies on macrophages and IFN-γ

Group A Streptococcus (GAS; Streptococcus pyogenes) is an important bacterial pathogen causing over 700 million superficial infections and around 500.000 deaths due to invasive disease or severe post-infection sequelae yearly. In spite of this major impact on society, there is currently no vaccine available against this bacterium. GAS strains can be separated into >250 distinct emm (M)-types, and protective immunity against GAS is believed to in part be dependent on type-specific antibodies. Here, we analyse the nature of protective immunity generated against GAS in a model of intraperitoneal immunization in mice. We demonstrate that multiple immunizations are required for the ability to survive a subsequent lethal challenge, and although significant levels of GAS-specific antibodies are produced, these are redundant for protection. Instead, our data show that the immunization-dependent protection in this model is induced in the absence of B and T cells and is accompanied by the induction of an altered acute cytokine profile upon subsequent infection, noticeable e.g. by the absence of classical pro-inflammatory cytokines and increased IFN-γ production. Further, the ability of immunized mice to survive a lethal infection is dependent on macrophages and the macrophage-activating cytokine IFN-γ. To our knowledge these findings are the first to suggest that GAS may have the ability to induce forms of trained innate immunity. Taken together, the current study proposes a novel role for the innate immune system in response to GAS infections that potentially could be leveraged for future development of effective vaccines.

Origin, pathogenicity, and transmissibility of a human isolated influenza A(H10N3) virus from China

Subtype H10 viruses are known to infect humans in Africa, Oceania, and Asia. In 2021, 2022, and recently in April 2024, a novel H10N3 subtype avian influenza virus was found cause human infection with severe pneumonia. Herein, we comprehensively studied the phylogenetic evolution and biological characteristics of the newly emerged influenza A(H10N3) virus. We found that the human isolated H10N3 virus was generated in early 2019 in domestic poultry. The viruses bound to salic acid α2, 3 receptors, indicating their insufficient ability to infect humans. Although a low pathogenic avian influenza virus, the human isolated H10N3 virus exhibited robust pathogenicity in both BALB/c and C57BL/6 mice, with MLD50 1000 times higher than a homologous environmental isolate. The human isolated H10N3 also showed respiratory droplet transmissibility in ferrets. Considering the continuous circulation in avian populations and repeated transmission to humans, strengthened surveillance of H10 subtype viruses in poultry should be put into effect.

The microbiota-derived bile acid taurodeoxycholic acid improves hepatic cholesterol levels in mice with cancer cachexia

Alterations in bile acid profile and pathways contribute to hepatic inflammation in cancer cachexia, a syndrome worsening the prognosis of cancer patients. As the gut microbiota impinges on host metabolism through bile acids, the current study aimed to explore the functional contribution of gut microbial dysbiosis to bile acid dysmetabolism and associated disorders in cancer cachexia. Using three mouse models of cancer cachexia (the C26, MC38 and HCT116 models), we evidenced a reduction in the hepatic levels of several secondary bile acids, mainly taurodeoxycholic (TDCA). This reduction in hepatic TDCA occurred before the appearance of cachexia. Longitudinal analysis of the gut microbiota pinpointed an ASV, identified as Xylanibacter rodentium, as a bacterium potentially involved in the reduced production of TDCA. Coherently, stable isotope-based experiments highlighted a robust decrease in the microbial 7α-dehydroxylation (7α-DH) activity with no changes in the bile salt hydrolase (BSH) activity in cachectic mice. This approach also highlighted a reduced microbial 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 12α-hydroxysteroid dehydrogenase (12α-HSDH) activities in these mice. The contribution of the lower production of TDCA to cancer cachexia was explored in vitro and in vivo. In vitro, TDCA prevented myotube atrophy, whereas in vivo hepatic whole transcriptome analysis revealed that TDCA administration to cachectic mice improved the unfolded protein response and cholesterol homeostasis pathways. Coherently, TDCA administration reversed hepatic cholesterol accumulation in these mice. Altogether, this work highlights the contribution of the gut microbiota to bile acid dysmetabolism and the therapeutic interest of the secondary bile acid TDCA for hepatic cholesterol homeostasis in the context of cancer cachexia. Such discovery may prove instrumental in the understanding of other metabolic diseases characterized by microbial dysbiosis. More broadly, our work demonstrates the interest and relevance of microbial activity measurements using stable isotopes, an approach currently underused in the microbiome field.

The natural immune molecules urinary Tamm-Horsfall protein and pentraxin 3 as predictors for recurrent urinary tract infection severity: a single-center self-control study

OBJECTIVE

The innate immune defense plays a pivotal role in protecting the urinary tract from uropathogenic invasion and maintaining immune homeostasis. Dysregulation of the innate immune system can result in recurrent urinary tract infections (RUTI) due to heightened susceptibility to uropathogens. Despite this, predicting the risk of recurrence and the degree of immune compromise in patients who have had one urinary tract infection remains challenging. Also identifying which patients are more susceptible to developing pyelonephritis rather than the more local disease of cystitis is imperfect, although delayed diagnosis of a UTI is a good indicator for developing pyelonephritis. This study aims to assess the potential of urinary Tamm-Horsfall protein (THP) and Pentraxin 3 (PTX3) as predictors of RUTI symptom severity and recurrence, while also evaluating the efficacy of the Chinese herbal formulation Tailin Formula (TLF) as a clinical therapeutic intervention for RUTI.

METHODS

A single-center cohort study was conducted involving 142 participants, consisting of 31 healthy individuals (non-RUTI group, n = 31) and 111 patients with RUTI. The RUTI patients were divided into two groups: one group received continuous low-dose antibiotic therapy (CLAT group, n = 55), and the other group received herbal preparations (Tailin formula) (TLF group, n = 56). All patients received consistent lifestyle guidance. Descriptive analysis was performed on the RUTI cohort.

RESULTS

Urinary THP levels were significantly lower in RUTI patients (TLF and CLAT groups) compared to the non-RUTI, whereas PTX3 levels showed a tendency toward elevation. After treatment, urinary THP levels were markedly higher in the TLF group (27.43 ± 7.07) compared to pretreatment levels (10.00 ± 2.79), while levels remained lower in the CLAT group (8.91 ± 2.23) than in the TLF group. Urinary PTX3 levels decreased post-treatment in both groups after treatment than before (CLAT: 0.30 ± 0.13 vs. 1.04 ± 0.38; TLF: 0.29 ± 0.12 vs. 1.15 ± 0.36). Additionally, THP was negatively correlated with renal tubular injury markers NAG/Cr and β2-MG in RUTI patients (r = -0.5041 and -0.6169, respectively), while PTX3 showed a positive correlation with NAG/Cr and β2-MG (r = 0.28 and 0.498, respectively). Notably, as RUTI symptoms improved and recurrence rates decreased, urinary THP levels increased, while PTX3 levels decreased.

CONCLUSION

This study suggests that urinary THP and PTX3 are likely involved in the pathogenesis of RUTI. These biomarkers may serve as valuable predictors for assessing symptom severity, recurrence risk, and therapeutic efficacy in patients with RUTI at risk of disease progression.

The canine blood-brain barrier in health and disease: focus on brain protection

This review examines the role of the canine blood-brain barrier (BBB) in health and disease, focusing on the impact of the multidrug resistance (MDR) transporter P-glycoprotein (P-gp) encoded by the ABCB1/MDR1 gene. The BBB is critical in maintaining central nervous system homeostasis and brain protection against xenobiotics and environmental drugs that may be circulating in the blood stream. We revise key anatomical, histological and functional aspects of the canine BBB and examine the role of the ABCB1/MDR1 gene mutation in specific dog breeds that exhibit reduced P-gp activity and disrupted drug brain pharmacokinetics. The review also covers factors that may disrupt the canine BBB, including the actions of aging, canine cognitive dysfunction, epilepsy, inflammation, infection, traumatic brain injury, among others. We highlight the critical importance of this barrier in maintaining central nervous system homeostasis and protecting against xenobiotics and conclude that a number of neurological-related diseases may increase vulnerability of the BBB in the canine species and discuss its profound impacts on canine health.

Neutralizing antibody levels as a key factor in determining the immunogenic efficacy of the novel PEDV alpha coronavirus vaccine

Porcine epidemic diarrhea virus (PEDV) causes significant global agricultural losses. Despite commercial inactivated and live attenuated vaccines, persistent outbreaks underscore the need for more effective solutions. Here, we isolated a novel Chinese PEDV variant, PEDV ShXXY2-2023, with amino acid substitutions in key neutralizing epitopes (N-terminal domain, receptor-binding domain, and CO-26K equivalent epitope) compared to vaccine strains. An inactivated ShXXY2-2023 vaccine induced higher neutralizing antibodies and superior cross-protection versus commercial vaccines. Vaccinated sows conferred enhanced protection to offspring, improving piglet survival post-challenge. Maternal serum neutralizing antibody titers correlated strongly with piglet survival; titers of 1:377-1:774 at one week prepartum yielded >80% protective efficacy. These findings emphasize neutralizing antibodies' critical role in PEDV prevention and position ShXXY2-2023 as a promising vaccine candidate, with broader implications for coronavirus vaccine development.

Impact of gut microbiota in chronic kidney disease: natural polyphenols as beneficial regulators

Chronic kidney disease (CKD) poses a severe health risk with high morbidity and mortality, profoundly affecting patient quality of life and survival. Despite advancements in research, the pathophysiology of CKD remains incompletely understood. Growing evidence links CKD with shifts in gut microbiota function and composition. Natural compounds, particularly polyphenols, have shown promise in CKD treatment due to their antioxidant and anti-inflammatory properties and their ability to modulate gut microbiota. This review discusses recent progress in uncovering the connections between gut microbiota and CKD, including microbiota changes across different kidney diseases. We also examine metabolite alterations,such as trimethylamine-N-oxide, tryptophan derivatives, branched-chain amino acids, short-chain fatty acids, and bile acids,which contribute to CKD progression. Further, we outline the mechanisms through which polyphenols exert therapeutic effects on CKD, focusing on signaling pathways like nuclear factor kappa-B (NF-κB), mitogen-activated protein kinase (MAPK), mammalian target of rapamycin (mTOR), NOD-like receptor thermal protein domain associated protein 3 (NLRP3), phosphatidylin-ositol-3-kinase (PI3K)/protein kinase B (Akt), and toll like receptors (TLR), as well as their impact on gut microbiota. Lastly, we consider how dietary polyphenols could be harnessed as bioactive drugs to slow CKD progression. Future research should prioritize multi-omics approaches to identify patients who would benefit from polyphenolic interventions, enabling personalized treatment strategies to enhance therapeutic efficacy.

Transcriptomic insights into Mycobacterium orygis infection-associated pulmonary granulomas reveal multicellular immune networks and tuberculosis biomarkers in cattle

Mycobacterium orygis, a member of the Mycobacterium tuberculosis complex (MTBC), has emerged as a significant contributor to tuberculosis (TB) in cattle, wildlife, and humans. However, understanding about its pathogenesis and severity is limited, compounded by the lack of reliable TB biomarkers in cattle. This study delves into the comparative pathology and transcriptomic landscape of pulmonary granulomas in cattle naturally infected with M. orygis, using high-throughput RNA sequencing. Histopathological analysis revealed extensive, multistage granulomatous, necrotic, and cavitary lesions, indicative of severe lung pathology induced by M. orygis. Transcriptomic profiling highlighted numerous differentially expressed genes and dysregulated pathways related to immune response modulation and extracellular matrix remodelling. Additionally, cell type enrichment analysis provided insights into the multicellularity of the granulomatous niche, emphasising complex cell-cell interactions within TB granulomas. Via comparative transcriptomics leveraging publicly available bovine and human TB omics datasets, 14 key immunomodulators (SOD2, IL1α/β, IL15, IL18, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, CCL8/MCP-2, CCL20/MIP-3α, CXCL2/MIP-2, CXCL10/IP-10, CXCL11, and IFN-γ) were identified as potential biomarkers for active TB in cattle. These findings significantly advance our understanding of M. orygis pathogenesis in bovine TB and highlight potential targets for the development of diagnostic tools for managing and controlling the disease.

Fusobacterium nucleatum upregulates the immune inhibitory receptor PD-L1 in colorectal cancer cells via the activation of ALPK1

Fusobacterium nucleatum is a Gram-negative oncobacterium that is associated with colorectal cancer. The molecular mechanisms utilized by F. nucleatum to promote colorectal tumor development have largely focused on adhesin-mediated binding to the tumor tissue and on the pro-inflammatory capacity of F. nucleatum. However, the exact manner in which F. nucleatum promotes inflammation in the tumor microenvironment and subsequent tumor promotion remains underexplored. Here, we show that both living F. nucleatum and sterile F. nucleatum-conditioned medium promote CXCL8 release from the intestinal adenocarcinoma HT-29 cell line. We determined that the observed pro-inflammatory effect was ALPK1-dependent in both HEK293 and HT-29 cells and that the released F. nucleatum molecule had characteristics that match those of the pro-inflammatory ALPK1 ligand ADP-heptose or related heptose phosphates. In addition, we determined that not only F. nucleatum promoted an ALPK1-dependent pro-inflammatory environment but also other Fusobacterium species such as F. varium, F. necrophorum and F. gonidiaformans generated similar effects, indicating that ADP-heptose or related heptose phosphate secretion is a conserved feature of the Fusobacterium genus. By performing transcriptional analysis of ADP-heptose stimulated HT-29 cells, we found several inflammatory and cancer-related pathways to be differentially regulated, including DNA mismatch repair genes and the immune inhibitory receptor PD-L1. Finally, we show that stimulation of HT-29 cells with F. nucleatum resulted in an ALPK1-dependent upregulation of PD-L1. These results aid in our understanding of the mechanisms by which F. nucleatum can affect tumor development and therapy and pave the way for future therapeutic approaches.

Bacterial metabolism in the host and its association with virulence

The host restricted pathogens are competently dependent on their respective host for nutritional requirements. The bacterial metabolic pathways are surprisingly varied and remarkably flexible that in turn help them to successfully overcome competition and colonise their host. The metabolic adaptation plays pivotal role in bacterial pathogenesis. The understanding of host-pathogen metabolic crosstalk needs to be prioritized to decipher host-pathogen interactions. The review focuses on various aspects of host pathogen interactions that majorly involves adaptation of bacterial metabolism to counteract immune mechanisms by rectifying metabolic cues that provides pathogen the idea of different anatomical sites and the local physiology of the host. The key set of metabolites that are recognized as centre of competition between host and its pathogens are also briefly discussed. The factors that control the timely expression of virulence of bacterial pathogens is poorly understood. The perspective presented herein will facilitate us with a broader view of molecular mechanisms that modulates the expression of virulence factors in bacterial pathogens. The knowledge of crosslinked metabolic pathways of bacteria and their host will serve to develop novel potential therapeutics.

Targeted insertion of heterogenous DNA using Cas9-gRNA ribonucleoprotein-mediated gene editing in Ganoderma lucidum

Gene editing is emerging as a powerful tool for introducing novel functionalities in mushrooms. While CRISPR/Cas9-induced double-strand breaks (DSBs) typically rely on non-homologous end joining (NHEJ) for gene disruption, precise insertion of heterologous DNA in mushrooms is less explored. Here, we evaluated the efficacy of inserting donor DNAs (8-1008 bp) with or without homologous arms at Cas9-gRNA RNP-induced DSBs. Co-transformation of donor DNAs with RNP targeting the pyrG gene in Ganoderma lucidum yielded 184 transformants without homologous arms and 781 with 300-bp homologous arms (HR_donor DNAs). Restriction analysis and sequencing identified 122 hR_donor DNA transformants with complete donor DNA sequences, achieving 15.6% HDR efficiency (122/781), contrasting with 8 instances via NHEJ from the 184 transformants. These findings highlight the viability of HDR for precise genomic editing in mushrooms, enabling targeted modifications to enhance functionalities.

Serum metabolomic characteristics of COVID-19 patients co-infection with echovirus

Currently, the Omicron variant of the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate globally. In our multiplex respiratory pathogen detection, we identified numerous instances of co-infection with Echovirus (ECHO) among Coronavirus Disease 2019 (COVID-19) patients, which exacerbated the clinical symptoms of these patients. Such co-infections are likely to impact the subsequent medical treatment. To date, there are no reports on the pathogenic mechanisms related to COVID-19 co-infected with ECHO. Therefore, this study employed the TM Widely-Targeted metabolomics approach to analyze the serum metabolomes of COVID-19 patients with single SARS-CoV-2 infection (COVID-19), COVID-19 patients co-infected with ECHO (COVID-19  +  ECHO), and healthy individuals (Control) recruited from routine physical examinations during the same period. Concurrent clinical laboratory tests were performed on the patients to reveal the differences in metabolomic characteristics between the COVID-19 patients and the COVID-19  +  ECHO patients, as well as to explore potential metabolic pathways that may exacerbate disease progression. Our findings indicate that both clinical examination indicators and the pathways enriched by differential metabolites confirm that patients with dual infection exhibit higher inflammatory and immune responses compared to those with single COVID-19 infections. This difference is likely reflected through abnormalities in the glycerophospholipid metabolic pathway, with the metabolite Sn-Glycero-3-Phosphocholine playing a crucial role in this process. Finally, we established a diagnostic model based on logistic regression using five differential metabolites, which accurately differentiates between the dual infection population and the single COVID-19 infection population (AUC = 0.828).

A promising endeavor against human cytomegalovirus: Predominant epitopes-based recombinant subunit vaccine RHEcIE1/pp65/pp150

Human cytomegalovirus (HCMV) is widespread in the population, typically remaining latent. However, it can cause severe morbidity and mortality in transplant patients and immunodeficient individuals. Currently, there is no approved vaccine against HCMV. This study used immunoinformatics methods to predict the predominant T and B-cell epitopes of three key HCMV proteins, including phosphoprotein 65 (pp65), pp150, and immediate-early protein 1 (IE1). Subsequently, we synthesized a recombinant subunit vaccine (RHEcIE1/pp65/pp150) from Escherichia coli, comprising RHEc-1 and RHEc-2. We observed that the RHEcIE1/pp65/pp150 vaccine exhibited high safety and immunogenicity in mice, enhancing a significant upregulation of CD80, CD86, CD40, and MHCII on dendritic cells and macrophages. Additionally, the vaccine activated innate immune responses through the NF-κB signalling pathway, triggering CD4+ and CD8+T cells to secrete tumour necrosis factor (TNF)-α, interferon (IFN)-γ, and interleukin (IL)-2, directing the T-cell response towards Th1. Moreover, it stimulated CD4+T cells to secrete IL-4, IL-6, and IL-10, promoting B-cell immunity. Furthermore, the RHEcIE1/pp65/pp150 vaccine induced the formation of abundant memory cells and high levels of neutralizing antibody titres, conducive to providing long-lasting protection. Taken together, the RHEcIE1/pp65/pp150 vaccine is a promising endeavour against HCMV, and these findings contribute valuable insights to the development of HCMV vaccine candidates.

Chronic Wasting Disease Research in North America: A systematic review highlighting species-wise and interdisciplinary research trends

Chronic Wasting Disease (CWD) research has experienced significant growth, spanning diverse disciplines such as genetics, immunology, modelling, and behaviour. To gain a broad understanding of the changes in CWD research focusing cervids, we analysed temporal trends in study location, species, genus investigated, infection types, and population type since the discovery of CWD in 1980s. Our findings indicate that Colorado, USA, published the highest number of articles, followed by Wisconsin, and publication numbers correlated with reported CWD cases in states/provinces. Odocoileus emerged as the most studied genus. Wild populations are studied more commonly than captive populations. Keyword analysis of transmission types shows the discovery of novel transmission modes in the recent past. We also used a novel approach to categorize studies into five themes: field-based, lab-based, math/analytics/modelling-based, management-based, and human dimensions. Overall, most studies captured had a lab-based component. The interdisciplinary or transdisciplinary nature of major disciplines and evolving trends in keywords, particularly the increased reliance on genetics/genomics, accentuate the beginning of using genomics to under and tackle CWD at a fundamental scale. Encapsulated in our analysis, these dynamic changes offer valuable insights for navigating CWD through scientifically informed proactive management decisions in conjunction with existing surveillance efforts not only for the commonly studied species but also for potentially susceptible species.

Fusobacterium nucleatum-driven CX3CR1+ PD-L1+ phagocytes route to tumor tissues and reshape tumor microenvironment

The intracellular bacterium Fusobacterium nucleatum (Fn) mediates tumorigenesis and progression in colorectal cancer (CRC). However, the origin of intratumoral Fn and the role of Fn-infected immunocytes in the tumor microenvironment remain unclear. Here, we observed that Fn-infected neutrophils/macrophages (PMNs/MΦs), especially PMNs, accumulate in tumor tissues and fecal Fn abundance correlates positively with an abundance of blood PD-L1+ PMNs in CRC patients. Moreover, Fn accumulates in tumor tissues of tumor-bearing mice via intragingival infection and intravenous injection. Mechanistically, Fn can survive inside PMNs by reducing intracellular ROS levels and producing H2S. Specifically, the lysozyme inhibitor Fn1792 as a novel virulence factor of Fn suppressed apoptosis of phagocytes by inducing CX3CR1 expression. Furthermore, Fn-driven CX3CR1+PD-L1+ phagocytes transfer intracellular Fn to tumor cells, which recruit PMNs/MΦs through the CXCL2/8-CXCR2 and CCL5/CCR5 axes. Consequently, CX3CR1+PD-L1+ PMNs infiltration promotes CRC metastasis and weakens the efficacy of immunotherapy. Treatment with the doxycycline eradicated intracellular Fn, thereby reducing the CX3CR1+PD-L1+ PMNs populations and slowing Fn-promoted tumor growth and metastasis in mice. These results suggest phagocytes as Fn-presenting cells use mutualistic strategies to home to tumor tissues and induce immunosuppression, and treatment with ROS-enhanced antibiotics can inhibit Fn-positive tumor progression.

PCV20 for the prevention of invasive pneumococcal disease in the Mexican pediatric population: A cost-effectiveness analysis

The introduction of a pneumococcal conjugate vaccine (PCV) covering 13 serotypes (PCV13) into the Mexican pediatric national immunization program (NIP) has substantially reduced the burden of pneumococcal disease (PD) since 2010. This study aimed to estimate the impact of replacing either PCV13 or 15valent PCV (PCV15) with 20-valent PCV (PCV20) in the Mexican pediatric NIP. A decision-analytic Markov model was developed to compare the cost-effectiveness of PCV20 versus lower-valent vaccines from a Mexican public health sector (payer) perspective over 10 years. Epidemiological and cost inputs were sourced from Mexican data. Direct and indirect vaccine effects were estimated using PCV13 clinical effectiveness, 7-valent PCV efficacy studies, and PCV13 impact data in Mexico. The estimated disease and cost impact of PCV20 was compared with PCV13 and PCV15, all under a 2 + 1 dosing schedule. A discount rate of 5% per annum was applied to costs and health outcomes. Model robustness was evaluated through sensitivity analyses, including deterministic sensitivity analysis (DSA), probabilistic sensitivity analysis (PSA), and additional scenario assessments. PCV20 was estimated to provide considerably more health benefits than both comparators by averting more cases of PD compared with both PCV13 and PCV15, as well as a total cost saving of over 10 billion Mexican pesos. The DSA, PSA, and scenario assessments confirmed minimal deviation from the base case. Therefore, the introduction of PCV20 (2 + 1) into the Mexican pediatric NIP is expected to reduce the burden of PD and medical costs compared with lower-valent alternatives.

Control measures for neglected tropical diseases: vaccine updates

INTRODUCTION

Infectious diseases like neglected tropical diseases (NTDs) have seen a rapid surge in recent times, threatening public health. These diseases impose a significant global health burden, affecting individuals, particularly in tropical locations characterized by low-income populations. The comprehensive compilation of NTDs includes an array of bacterial, viral, and parasitic infections. The prioritization of 20-NTD action plans in 2020 was undertaken by the WHO to acknowledge their importance. Infections such as leishmaniasis, schistosomiasis, and human African trypanosomiasis exhibit high rates of mortality. This highlights the pressing need for collaborative initiatives aimed at addressing these diseases and minimizing their detrimental impact on susceptible populations.

AREAS COVERED

The etiology, types of NTDs, and management strategies, particularly vaccinations are discussed. The limitations of the available vaccines and the scope of development of novel formulations are also covered.

EXPERT OPINION

The emergence of vaccines for NTDs poses significant challenges, mostly arising from the complex developmental phases of diverse diseases, inadequate resources for research, minimal involvement from the pharmaceutical industry, and the wide spectrum of infections, impeding vaccine development. Advancements in technology have improved vaccine quality, which could lead to the development of personalized vaccines tailored to individual susceptibility to specific NTD pathogens.

Human gut commensal Alistipes timonensis modulates the host lipidome and delivers anti-inflammatory outer membrane vesicles to suppress colitis in an Il10-deficient mouse model

Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD is understudied, and the underlying molecular mechanisms remain unknown. In this study, colonization of Il10-deficient mice with Alistipes timonensis DSM 27924 delays colitis development. Colonization does not significantly alter the gut microbiome composition, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are detected in the plasma of colonized mice, carrying potentially immunomodulatory metabolites into the host circulatory system. Fractions of A. timonensis OMVs suppress LPS-induced Il6, Il1b, and Tnfa expression in vitro in murine macrophages. We detect putative bioactive lipids in the OMVs, including immunomodulatory sulfonolipids (SoLs) in the active fraction, which are also increased in the blood of colonized mice. Treating Il10-deficient mice with purified SoL B, a representative SoL, suppresses colitis development, suggesting its contribution to the anti-inflammatory phenotype observed with A. timonensis colonization. Thus, A. timonensis OMVs represent a potential mechanism for Alistipes-mediated delay of colitis in Il10-deficient mice via delivery of immunomodulatory lipids and modulation of the host plasma lipidome.

The T-type voltage-gated Ca2+ channel CaV3.1 involves in the disruption of respiratory epithelial barrier induced by Pasteurella multocida toxin

Pasteurella multocida toxin (PMT) is an exotoxin produced by several members of the zoonotic respiratory pathogen P. multocida. The role of PMT in disrupting the mammalian respiratory barrier remains to be elucidated. In this study, we showed that inoculation of recombinantly expressed PMT increased the permeability of the respiratory epithelial barrier in mouse and respiratory cell models. This was evidenced by a decreased expression of tight junctions (ZO-1, occludin) and adherens junctions (β-catenin, E-cadherin), as well as enhanced cytoskeletal rearrangement. In mechanism, we demonstrated that PMT inoculation induced cytoplasmic Ca2+ inflow, leading to an imbalance of cellular Ca2+ homoeostasis and endoplasmic reticulum stress. This process further stimulated the RhoA/ROCK signalling, promoting cytoskeletal rearrangement and reducing the expression of tight junctions and adherens junctions. Notably, the T-type voltage-gated Ca2+ channel CaV3.1 was found to participate in PMT-induced cytoplasmic Ca2+ inflow. Knocking out CaV3.1 significantly reduced the cytotoxicity induced by PMT on swine respiratory epithelial cells and mitigated cytoplasmic Ca2+ inflow stimulated by PMT. These findings suggest CaV3.1 contributes to PMT-induced respiratory epithelial barrier disruption.

Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection

An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1 but had positive correlations with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effects of ART on virome and cytokine profiles in HIV-1-infected individuals.

Rapid surge of reassortant A(H1N1) influenza viruses in Danish swine and their zoonotic potential

In 2018, a single detection of a novel reassortant swine influenza A virus (swIAV) was made in Denmark. The hemagglutinin (HA) of the virus was from the H1N1 pandemic 2009 (H1N1pdm09) lineage and the neuraminidase (NA) from the H1N1 Eurasian avian-like swine lineage (H1N1av). By 2022, the novel reassortant virus (H1pdm09N1av) constituted 27% of swIAVs identified through the Danish passive swIAV surveillance program. Sequencing detected two H1pdm09N1av genotypes; Genotype 1 contained an entire internal gene cassette of H1N1pdm09 origin, Genotype 2 differed by carrying an NS gene segment of H1N1av origin. The internal gene cassette of Genotype 2 became increasingly dominant, not only in the H1pdm09N1av population, but also in other Danish enzootic swIAV subtypes. Phylogenetic analysis of the HA genes from H1pdm09N1av viruses revealed a monophyletic source, a higher substitution rate compared to other H1N1pdm09 viruses and genetic differences with human seasonal and other swine adapted H1N1pdm09 viruses. Correspondingly, H1pdm09N1av viruses were antigenically distinct from human H1N1pdm09 vaccine viruses. Both H1pdm09N1av genotypes transmitted between ferrets by direct contact, but only Genotype 1 was capable of efficient aerosol transmission. The rapid spread of H1pdm09N1av viruses in Danish swine herds is concerning for swine and human health. Their zoonotic threat is highlighted by the limited pre-existing immunity observed in the human population, aerosol transmission in ferrets and the finding that the internal gene cassette of Genotype 2 was present in the first two zoonotic influenza infections ever detected in Denmark.

Salmonella utilizes L-arabinose to silence virulence gene expression for accelerated pathogen growth within the host

Carbon source is an important nutrient for bacteria to sustain growth and often acts as a signal that modulates virulence expression. L-arabinose is produced by plants and plays an important role in regulating the global gene expression of bacteria. Previously, we have shown that L-arabinose induces a more severe systemic infection in Salmonella-infected mice with normal microbiota, but does not affect the disease progression in mice with microbiota depleted by antibiotic treatment. The underlying mechanism remains elusive. In this study, we demonstrate that L-arabinose represses the expression of Salmonella type III secretion system 1 (T3SS-1) genes by negatively regulating the activity of the cyclic 3' 5'-AMP (cAMP)-cAMP receptor protein (CRP) complex. The cAMP-CRP complex can activate ribosome-associated inhibitor A, encoded by yfiA, to maintain the stability of HilD, a key transcriptional regulator of T3SS-1. L-arabinose supplementation promotes Salmonella initial bloom in the antibiotic-pretreated mouse gut and ultimately compensates for reduced virulence within the host. These results decipher the molecular mechanism by which cAMP-CRP directs regulatory changes of virulence in response to L-arabinose in Salmonella. It further implies that Salmonella exploits L-arabinose both as a nutrient and a regulatory signal to maintain a balance between growth and virulence within the host.

Biofilm-associated proteins: from the gut biofilms to neurodegeneration

Human microbiota form a biofilm with substantial consequences for health and disease. Numerous studies have indicated that microbial communities produce functional amyloids as part of their biofilm extracellular scaffolds. The overlooked interplay between bacterial amyloids and the host may have detrimental consequences for the host, including neurodegeneration. This work gives an overview of the biofilm-associated amyloids expressed by the gut microbiota and their potential role in neurodegeneration. It discusses the biofilm-associated proteins (BAPs) of the gut microbiota, maps the amyloidogenic domains of these proteins, and analyzes the presence of bap genes within accessory genomes linked with transposable elements. Furthermore, the evidence supporting the existence of amyloids in the gut are presented. Finally, it explores the potential interactions between BAPs and α-synuclein, extending the literature on amyloid cross-kingdom interactions. Based on these findings, this study propose that BAP amyloids act as transmissible catalysts, facilitating the misfolding, accumulation, and spread of α-synuclein aggregates. This review contributes to the understanding of complex interactions among the microbiota, transmissible elements, and host, which is crucial for developing novel therapeutic approaches to combat microbiota-related diseases and improve overall health outcomes.

Lessons for medical countermeasure development from unforeseen outbreaks

The unanticipated emergence of the COVID-19 pandemic and the rapid spread of the mpox epidemic in 2022 and 2024 brought unforeseen challenges to public health. While distinct in nature, these outbreaks share some similarities and offer valuable insights into responding to novel virus dissemination in vulnerable populations. In light of these two experiences, we aim to discern the prioritization of medical countermeasures (MCM) among antivirals, antibodies, and vaccines. Comparative analysis of MCMs reveals that while antivirals serve essential roles as therapeutic tools, monoclonal antibodies can be used for both prevention and treatment, and vaccines remain of paramount importance for controlling epidemics as mass or targeted prophylaxis. Variability in production processes, administration methods, logistics, and costs distinguish these countermeasures. Vaccines, by inducing long-lasting immunity and ideally promoting herd effects, exhibit substantial advantages over other options. To enhance future pandemic readiness, proactive measures must include ready-to-use vaccine platforms with regulatory approval and manufacturing capacities, as well as prototype vaccines for representative pathogens and preexisting protocols to evaluate their efficacies and side effects. The comparison underscores the challenges of social acceptance and equity, particularly in vaccine production and distribution. As the world faces unknown agents, the three major types of MCMs do not have equal and symmetrical effects in terms of epidemic control. Thus, a vaccine-oriented strategy with a community-centered approach, proves essential for effective pandemic preparedness, encouraging continued innovation in vaccinology.

Engineered bacteria as an orally administered anti-viral treatment and immunization system

The emergence of new viral pathogens necessitates innovative antiviral therapies and vaccines. Traditional approaches, such as monoclonal antibodies and vaccines, are often hindered by resistance, limited effectiveness, and high costs. Here, we develop an engineered probiotic-based antiviral platform using Escherichia coli Nissle 1917 (EcN), capable of providing both mucosal and systemic immunity via oral administration. EcN was engineered to display anti-spike nanobodies or express the Spike-Receptor Binding Domain on its surface. Our findings reveal that EcN with nanobodies effectively inhibits the interaction between spike protein-expressing pseudoviruses and the ACE2 receptor. Furthermore, we observed the translocation of nanobodies to distant organs, facilitated by outer membrane vesicles (OMVs). The oral administration of EcN expressing spike proteins induced a robust immune response characterized by the production of both IgG and IgA, antibodies that blocked the pseudovirus-ACE2 interaction. While SARS-CoV-2 served as a model, this versatile probiotic platform holds potential for developing customizable biotherapeutics against a wide range of emerging pathogens such as influenza virus or respiratory syncytial virus (RSV) by engineering EcN to express viral surface protein or neutralizing nanobodies demonstrating its versatility as a next-generation mucosal vaccine strategy.

Gut microbiota and derived metabolites mediate obstructive sleep apnea induced atherosclerosis

Obstructive sleep apnea (OSA) is characterized by intermittent hypoxia/hypercapnia (IHC), affects predominantly obese individuals, and increases atherosclerosis risk. Since we and others have implicated gut microbiota and metabolites in atherogenesis, we dissected their contributions to OSA-induced atherosclerosis. Atherosclerotic lesions were compared between conventionally-reared specific pathogen free (SPF) and germ-free (GF) Apoe-/- mice following a high fat high cholesterol diet (HFHC), with and without IHC conditions. The fecal microbiota and metabolome were profiled using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry (LC-MS/MS) respectively. Phenotypic data showed that HFHC significantly increased atherosclerosis as compared to regular chow (RC) in both aorta and pulmonary artery (PA) of SPF mice. IHC exacerbated lesions in addition to HFHC. Differential abundance analysis of gut microbiota identified an enrichment of Akkermansiaceae and a depletion of Muribaculaceae (formerly S24-7) family members in the HFHC-IHC group. LC-MS/MS showed a dysregulation of bile acid profiles with taurocholic acid, taurodeoxycholic acid, and 12-ketodeoxycholic acid enriched in the HFHC-IHC group, long-chain N-acyl amides, and phosphatidylcholines. Interestingly, GF Apoe-/- mice markedly reduced atherosclerotic formation relative to SPF Apoe-/- mice in the aorta under HFHC/IHC conditions. In contrast, microbial colonization did not show a significant impact on the atherosclerotic progression in PA. In summary, this research demonstrated that (1) IHC acts cooperatively with HFHC to induce atherosclerosis; (2) gut microbiota modulate atherogenesis, induced by HFHC/IHC, in the aorta not in PA; (3) different analytical methods suggest that a specific imbalance between Akkermansiaceae and Muribaculaceae bacterial families mediate OSA-induced atherosclerosis; and (4) derived bile acids, such as deoxycholic acid and lithocholic acid, regulate atherosclerosis in OSA. The knowledge obtained provides novel insights into the potential therapeutic approaches to prevent and treat OSA-induced atherosclerosis.

Role of gut microbiome in suppression of cancers

The pathogenesis of cancer is closely related to the disruption of homeostasis in the human body. The gut microbiome plays crucial roles in maintaining the homeostasis of its host throughout lifespan. In recent years, a large number of studies have shown that dysbiosis of the gut microbiome is involved in the entire process of cancer initiation, development, and prognosis by influencing the host immune system and metabolism. Some specific intestinal bacteria promote the occurrence and development of cancers under certain conditions. Conversely, some other specific intestinal bacteria suppress the oncogenesis and progression of cancers, including inhibiting the occurrence of cancers, delaying the progression of cancers and boosting the therapeutic effect on cancers. The promoting effects of the gut microbiome on cancers have been comprehensively discussed in the previous review. This article will review the latest advances in the roles and mechanisms of gut microbiome in cancer suppression, providing a new perspective for developing strategies of cancer prevention and treatment.

Comparative genomics of Salmonella enterica serovars Paratyphi A, Typhi and Typhimurium reveals distinct profiles of their pangenome, mobile genetic elements, antimicrobial resistance and defense systems repertoire

Salmonella enterica (S. enterica) is a highly ubiquitous and diverse animal and human pathogen. Distinct S. enterica serovars may present varying host-specificity and cause different diseases. While the human-restricted serovars S. Typhi (STY) and S. Paratyphi A (SPA) cause in humans a systemic life-threatening enteric fever, the host-generalist serovar, S. Typhimurium (STM) causes in immunocompetent individuals a self-limited gastroenteritis. Here, we have performed whole-genome sequencing and hybrid assembly of new SPA and STY typhoidal strains and took a comparative genomics approach to examine their phylogeny, pangenome structure and accessory genome content in comparison to the reference non-typhoidal serovar, STM. Our results identified previously uncharacterized lineages of SPA and refined the presence and distribution of core pseudogenes in typhoidal serovars. Pangenome analysis showed that while these serovars have a relatively similar core-genome size, the accessory genome of STM is more than four times larger than those of typhoidal Salmonellae and that STY and SPA display a more closed pangenome than STM. Unexpectedly, we demonstrate that STY and SPA present distinct differences in their pangenome composition, with a noticeable lower number of prophages, conjugative elements and antimicrobial genes per genome in SPA vs. STY. These results suggest that although SPA and STY are closely related at the DNA level, share a similar lifestyle and cause a symptomatic-indistinguishable disease, their genomic evolution and accessory genomes are markedly different. Moreover, these results may provide genomic explanation to phenotypic and epidemiological differences in antimicrobial resistance profiles associated with these serovars globally.

Meta-analysis of shotgun sequencing of gut microbiota in obese children with MASLD or MASH

Alterations in the gut microbiome affect the development and severity of metabolic dysfunction-associated steatotic liver disease (MASLD) or metabolic dysfunction-associated steatohepatitis (MASH). We analyzed microbiomes of obese children with and without MASLD, MASH, and healthy controls. Electronic databases were searched for studies on the gut microbiome in children with obesity with/without MASLD or MASH, providing shotgun-metagenomic-sequencing data. Nine studies and an additionally recruited cohort were included. Fecal microbiomes of children with MASLD (n = 153) and MASH (n = 70) were significantly different in alpha- and beta-diversity (p < 0.001) compared to obese (n = 58) and healthy (n = 132). Species Faecalibacterium_prausnitzii and Prevotella_copri are differentially abundant between obese, MASLD and MASH groups. XGBoost and random forest-models accurately predict MASLD over obesity with an AUROC of 87% and MASH over MASLD with 89%. Pathway-abundance-based models accurately predict MASLD over obesity with an AUROC of 81% and MASH over MASLD with 88%. The composition of the gut microbiome is altered with increasing hepatic fibrosis and concomitant species-abundance increase of Prevotella_copri (p = 0.0082). Machine-learning models discriminate pediatric from adult MASH with an AUROC of 97%. The gut microbial composition is increasingly altered in children with the progression of MASLD toward MASH. This can be utilized as a fecal biomarker and highlights the impact of diet on the gut microbiome for disease intervention.

Structural and functional analysis reveals the catalytic mechanism and substrate binding mode of the broad-spectrum endolysin Ply2741

The emergence of antibiotic-resistant bacteria has attracted interest in the field of endolysins. Here, we analyzed the diversity of Streptococcus endolysins and identified a new endolysin, Ply2741, that exhibited broad-spectrum bactericidal activity. Our results demonstrated that Ply2741 could effectively eradicate multidrug-resistant gram-positive pathogens in vitro and in vivo. Structural analysis revealed that the bactericidal activity of Ply2741 depends on the classic "Cys-His-Asn" catalytic triad. Site-directed mutagenesis results further identified that the conserved residue Gln29, located near the catalytic triad, also contributes to the lytic activity of Ply2741. Furthermore, the key residues (R189 and W250) in the Ply2741 cell wall binding domain (CBD) responsible for binding to peptidoglycan were revealed by molecular docking and fluorescence-activated cell sorting (FACS) analysis. Ply2741 demonstrates a broad lytic spectrum, with significant bactericidal activity against Enterococcus, Staphylococcus, and Streptococcus and species. To the best of our knowledge, we found that residue Gln29 participated in the lytic activity of endolysin for the first time. Additionally, we systematically elucidate the binding mode and key residues of the Ply2741CBD. This study proposes Ply2741 as a potential antibiotic substitute and provides a structural basis for the modification and design of endolysins.

Pathogenicity and virulence of lumpy skin disease virus: A comprehensive update

Lumpy skin disease (LSD), which was confined to the Africa for many decades, has expanded its geographical distribution to numerous countries across Asia and Europe in recent years. The LSD virus (LSDV) is a relatively poorly studied virus. Its 151 Kb genome encodes 156 open reading frames (ORF); however, the exact number of the proteins encoded by the viral genome and their specific functions remain largely unknown. Arthropod vectors primarily transmit the LSDV mechanically, but the precise nature of these vectors in different regions and their role in transmission is not fully understood. Homologous live-attenuated vaccines prepared using LSDV have proven to be highly efficacious compared to heterologous vaccines based on sheep pox virus or goatpox virus, in protecting cattle against LSD. This review offers the latest insights into the molecular biology and transmission of LSDV and discusses the safety and efficacy of available vaccines, along with the challenges faced in controlling and eradicating the disease in endemic regions.

Outcomes of peripherally inserted central catheter vs conventional central venous catheters in hematological cancer patients: a systematic review and meta-analysis

OBJECTIVE

This review aimed to examine if there is any difference in the risk of thrombosis and central line-associated bloodstream infection (CLABSI) with the use of peripherally inserted central catheter (PICC) and conventional central venous catheters (CVC) in hematological cancer patients.

METHODS

We searched the online databases of PubMed, CENTRAL, Scopus, Web of Science, and Embase for all types of studies comparing the risk of thrombosis and CLABSI between PICC and CVC. The search ended on 23rd September 2024.

RESULTS

Eight studies were included. One was a randomized trial while others were observational studies. Meta-analysis showed no statistically significant difference in the risk of thrombosis between PICC and CVC (OR: 1.69 95% CI: 0.75, 3.82 I2 = 78%). However, these results were not stable on sensitivity analysis. The exclusion of two studies indicated a higher risk of thrombosis with PICC. Pooled analysis showed that the risk of CLABSI was significantly lower with PICC as compared to CVC (OR: 0.52 95% CI: 0.40, 0.66 I2 = 0%). Results of subgroup analysis based on study design and diagnosis showed conflicting results.

CONCLUSIONS

There is conflicting evidence on the risk of thrombosis between PICC and CVC when used for hematological cancer patients. There could be a tendency of higher risk of thrombosis with PICC which needs to be confirmed by further studies. However, the use of PICC may reduce the risk of CLABSI in such patients. The quality of evidence is low owing to the predominance of observational studies with high inter-study heterogeneity.

Scarless excision of an insertion sequence in the OmpK36 promoter restores meropenem susceptibility in a non-carbapenemase-producing Klebsiella pneumoniae

Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant global health challenge due to its limited treatment options and high mortality rates. Meanwhile, the prevalence of non-carbapenemase-producing CRKP (NC-CRKP) strains is increasing, but their resistance mechanisms remain less understood compared to those of carbapenemase-producing CRKP (CP-CRKP). In this study, KP-469, an NC-CRKP strain, was found to lack the major porins OmpK35 and Ompk36 but possessed OmpK37, coexisting with ESBL resistance genes CTX-M and SHV. Membrane porin coding sequence alignment revealed a minor deletion in Ompk35 and a 768 bp insertion sequence in the promoter region (IS-PR) of Ompk36, located between the -10 region and the ribosome-binding site (RBS). In the KO-469 strain with scarless excision of IS-PR and the constructed pHSG396-promoter-Ompk36 strain that incorporated wild-type Ompk36 promoter into KP-469, the transcription levels of Ompk36 were significantly higher than that in KP-469 strain, and His-tag antibody quantification further confirmed the regular expression of Ompk36 in KO-469. These results demonstrated that IS-PR markedly reduced the transcriptional and translational efficiency of Ompk36 in the KP-469 strain, leading to decreased permeability to meropenem. Moreover, the restored susceptibility to meropenem in the KO-469 strain was validated by in vitro antimicrobial susceptibility tests and an in vivo intraperitoneal infection model constructed in neutrophil-depleted mice. The novel carbapenem resistance mechanism of NC-CRKP caused by the insertion sequence in the OmpK36 promoter will facilitate the development of antibacterial regimens for treating NC-CRKP infections.

PMA1-containing extracellular vesicles of Candida albicans triggers immune responses and colitis progression

Candida albicans (C. albicans) exhibits aberrant changes in patients with colitis, and it has been reported to dominate the colonic mucosal immune response. Here, we found that PMA1 expression was significantly increased in C. albicans from patients with IBD compared to that in healthy controls. A Crispr-Cas9-based fungal strain editing system was then used to knock out PMA1 expression in C. albicans. Compared to WT-C.a, ΔPMA1-C.a could not aggravate colitis. Proteomic analysis showed that PMA1 was transported by extracellular vesicles (EVs) of C. albicans. PMA1-containing EVs aggravated colitis, modulated the migration of cDC2 from the lamina propria to mesenteric lymph nodes, and induced TH17 cell differentiation. Moreover, the adaptor protein CARD9 was critical in PMA1-containing EV-induced colitis, and CARD9-deficient DCs did not induce TH17 cell differentiation or IL-17A production. Mechanically, CARD9 combines with the glycolytic protein GAPDH (aa2-146 domain) through its CARD region. CARD9 deficiency led to decreased enzyme activity of GAPDH and decreased glycolysis of DCs. These findings indicate that PMA1 is a potential virulence factor responsible for the pathogenesis of C. albicans colitis.

Bacteriophage-driven DNA inversions shape bacterial functionality and long-term co-existence in Bacteroides fragilis

Bacterial genomic DNA inversions, which govern molecular phase-variations, provide the bacteria with functional plasticity and phenotypic diversity. These targeted rearrangements enable bacteria to respond to environmental challenges, such as bacteriophage predation, evading immune detection or gut colonization. This study investigated the short- and long-term effects of the lytic phage Barc2635 on the functional plasticity of Bacteroides fragilis, a gut commensal. Germ-free mice were colonized with B. fragilis and exposed to Barc2635 to identify genomic alterations driving phenotypic changes. Phage exposure triggered dynamic and prolonged bacterial responses, including significant shifts in phase-variable regions (PVRs), particularly in promoter orientations of polysaccharide biosynthesis loci. These shifts coincided with increased entropy in PVR inversion ratios, reflecting heightened genomic variability. In contrast, B. fragilis in control mice exhibited stable genomic configurations after gut adaptation. The phase-variable Type 1 restriction-modification system, which affects broad gene expression patterns, showed variability in both groups. However, phage-exposed bacteria displayed more restrained variability, suggesting phage-derived selection pressures. Our findings reveal that B. fragilis employs DNA inversions to adapt rapidly to phage exposure and colonization, highlighting a potential mechanism by which genomic variability contributes to its response to phage. This study demonstrates gut bacterial genomic and phenotypic plasticity upon exposure to the mammalian host and to bacteriophages.

All-cause healthcare resource utilization and costs among community-managed adults with long-COVID in France, 2020-2023

BACKGROUND

The clinical and economic burden of long COVID is poorly understood. We aim to assess all-cause healthcare resource utilization (HCRU) and costs in the primary care setting among adults with long COVID in France.

METHODS

A retrospective cohort study using the electronic healthcare records (EHRs) of confirmed and/or probable COVID-19 patients from The Health Improvement Network (THIN) data between March 2020 and December 2022 was conducted. Long COVID was identified per World Health Organization (WHO) definition as suggestive symptoms present ≥3 months following acute SARS-CoV-2 infection. Patients' characteristics, HCRU, direct healthcare and indirect costs (National Health Insurance-based prices) were summarized. Costs between patients with previous SARS-CoV-2 infection who developed long COVID, patients with previous SARS-CoV-2 infection who did not develop long COVID (COVID only), and contemporaneous controls without SARS-CoV-2 infection were compared (Non-COVID).

RESULTS

Long COVID developed among 30,122 (11.6%) adults; mean (SD) age was 50 (17) years, 63.6% were female and 27.5% had a Charlson Comorbidity Index score >2. During the post-infection follow-up (mean = 13 months), 97.3% of patients had general practitioner consultations (GP) and 62.4% had nursing care. Costs were highest during the first post-diagnosis year with per patient per year costs of €2,443 (total cost of €52 million), including costs for GP (€208) and specialist (€170) consultations, outpatient procedures (€413), retail pharmacy use (€595), biological testing (€147), and medical device usage (€172). Patients with long COVID had additional costs of €163 and €176 when compared to patients in the COVID only and Non-COVID cohorts, respectively.

LIMITATIONS

Since the THIN database is generated from GP EHRs, there is the possibility of measurement/documentation errors and missing values which could compromise the validity and accuracy of certain results.

CONCLUSION

Long COVID was associated with non-negligible HCRU, direct and indirect costs to the French healthcare system. These findings reinforce the importance of optimizing long-term resource allocation for patients infected with SARS-CoV-2.

Association of live microbes intake and risk of all-cause, cardiovascular disease, and cancer-related mortality in patients with chronic kidney disease

BACKGROUND

Chronic kidney disease (CKD) is a prevalent chronic, non-communicable disease. The long-term health effects of dietary live microbes, primarily probiotics, on CKD patients remain insufficiently understood. This study aims to investigate the association between dietary intake of live microbes and long-term health outcomes among individuals with CKD.

METHODS

Utilizing the National Health and Nutrition Examination Survey (NHANES) database, Cox regression analysis assessed the association between medium and high categories dietary live microbe intake and health outcomes (all-cause, cardiovascular disease [CVD], and cancer-related mortality) in CKD patients.

RESULTS

A total of 3,646 CKD patients were enrolled. During the follow-up period, 1,593 all-cause mortality events were recorded, including 478 CVD deaths and 268 cancer deaths. In the fully adjusted model, compared to CKD patients in the lowest quartile (quartile 1) of live microbes intake, those in quartiles 3 and 4 exhibited a 20% and 26% reduced risk of all-cause mortality, with hazard ratios (HR) of 0.80 (95% confidence interval, CI: 0.69, 0.94) and 0.74 (95% CI: 0.62, 0.90), respectively. Additionally, compared to those with low live microbe intake (quartile 1), higher live microbe intake in quartile 4 was associated with a 37% reduction in the risk of CVD mortality for CKD patients, with an HR of 0.63 (95% CI: 0.45, 0.88). Consistent results were observed in subgroup and sensitivity analyses. A significant negative association was observed between live microbe intake and the risk of all-cause mortality as well as CVD mortality in the CKD population, with a p-value for trend < 0.05.

CONCLUSION

Our study indicated that high dietary live microbe intake could mitigate the risk of all-cause and CVD mortality in CKD patients. These findings support the inclusion of live microbes in dietary recommendations, highlighting their significant roles in CKD.

Development of a Caco-2-based intestinal mucosal model to study intestinal barrier properties and bacteria-mucus interactions

The intestinal mucosal barrier is a dynamic system that allows nutrient uptake, stimulates healthy microbe-host interactions, and prevents invasion by pathogens. The mucosa consists of epithelial cells connected by cellular junctions that regulate the passage of nutrients covered by a mucus layer that plays an important role in host-microbiome interactions. Mimicking the intestinal mucosa for in vitro assays, particularly the generation of a mucus layer, has proven to be challenging. The intestinal cell-line Caco-2 is widely used in academic and industrial laboratories due to its capacity to polarize, form an apical brush border, and reproducibly grow into confluent cell layers in different culture systems. However, under normal culture conditions, Caco-2 cultures lack a mucus layer. Here, we demonstrate for the first time that Caco-2 cultures can form a robust mucus layer when cultured under air-liquid interface (ALI) conditions on Transwell inserts with addition of vasointestinal peptide (VIP) in the basolateral compartment. We demonstrate that unique gene clusters are regulated in response to ALI and VIP single stimuli, but the ALI-VIP combination treatment resulted in a significant upregulation of multiple mucin genes and proteins, including secreted MUC2 and transmembrane mucins MUC13 and MUC17. Expression of tight junction proteins was significantly altered in the ALI-VIP condition, leading to increased permeability to small molecules. Commensal Lactiplantibacillus plantarum bacteria closely associated with the Caco-2 mucus layer and differentially colonized the surface of the ALI cultures. Pathogenic Salmonella enterica were capable of invading beyond the mucus layer and brush border. In conclusion, Caco-2 ALI-VIP cultures provide an accessible and straightforward way to culture an in vitro intestinal mucosal model with improved biomimetic features. This novel in vitro intestinal model can facilitate studies into mucus and epithelial barrier functions and in-depth molecular characterization of pathogenic and commensal microbe-mucus interactions.

High-throughput single-cell analysis reveals Omp38-specific monoclonal antibodies that protect against Acinetobacter baumannii infection

Infections caused by Acinetobacter baumannii (A. baumannii) have emerged as a global public health concern because of high pathogenicity of this bacterium. Monoclonal antibodies (mAbs) have a lower likelihood of promoting drug resistance and offer targeted treatment, thereby reducing potential adverse effects; however, the therapeutic potential of mAbs targeting A. baumannii has not been fully characterized. In this study, mAbs against the outer membrane proteins (OMPs) of A. baumannii were isolated in a high-throughput manner. The ability of Omp38-specific mAbs to bind to A. baumannii strains from diverse sources was confirmed via enzyme-linked immunosorbent assay (ELISA). Intravenous administration of the Omp38-specific mAbs significantly improved the survival rate and reduced the bacterial load in a mouse model of lethal A. baumannii infection. Flow cytometry and ELISA confirmed that immune cell infiltration and cytokine production, respectively, decreased in a mouse model of sublethal A. baumannii infection. In addition, analysis of the Omp38-mAb C3 binding conformation revealed the potential mechanism of broad-spectrum binding activity of this mAb against A. baumannii. Taken together, these findings indicate that mAbs against Omp38 facilitate bacterial clearance from host, minimize inflammatory mediator release and reduce host damage, highlighting the potential of Omp38-specific mAbs in the clinical treatment of A. baumannii infection.

Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology

The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson's Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.

From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy

The integration of fecal microbiota transplantation (FMT) with immune checkpoint inhibitors (ICIs) presents a promising approach for enhancing cancer treatment efficacy and overcoming therapeutic resistance. This review critically examines the controversial effects of FMT on ICIs outcomes and elucidates the underlying mechanisms. We investigate how FMT modulates gut microbiota composition, microbial metabolite profiles, and the tumor microenvironment, thereby influencing ICIs effectiveness. Key factors influencing FMT efficacy, including donor selection criteria, recipient characteristics, and administration protocols, are comprehensively discussed. The review delineates strategies for optimizing FMT formulations and systematically monitoring post-transplant microbiome dynamics. Through a comprehensive synthesis of evidence from clinical trials and preclinical studies, we elucidate the potential benefits and challenges of combining FMT with ICIs across diverse cancer types. While some studies report improved outcomes, others indicate no benefit or potential adverse effects, emphasizing the complexity of host-microbiome interactions in cancer immunotherapy. We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. This comprehensive review seeks to guide future research endeavors and clinical applications of FMT-ICIs combination therapy, with the potential to improve cancer patient outcomes while ensuring both safety and efficacy. As this rapidly evolving field advances, maintaining a judicious balance between openness to innovation and cautious scrutiny is crucial for realizing the full potential of microbiome modulation in cancer immunotherapy.

Circulation characteristics of bat coronaviruses linked to bat ecological factors in Korea, 2021-2022

Considering that bat ecology alterations may be linked with pathogen spillover, research on bat coronaviruses, particularly on the infection and transmission pattern among bats in relation with their ecology, is essential. We captured bats distributed in Korea from 2021 to 2022, examined coronaviruses in oral swabs, feces, urine, and ectoparasites, and were able to detect alphacoronavirus. We investigated coronaviruses, but noted no substantial differences in the body condition index in the coronavirus-positive bats. Binary logistic regression analysis revealed that bat ecological factors that were significantly associated with coronavirus-positive were roost type, sample type, and bat species. Coronavirus-positive ectoparasite cases suggested additional study on the potential role of them as the viral transmission vectors or fomites. Reinfection of a different coronavirus in recaptured bats was evident, suggesting the possibility that coronavirus circulation can evade the potential protective immunity acquired from previous coronavirus infections. The present findings provide comprehensive information on the coronaviruses transmission dynamics within bat populations linked with bat ecology.

The response to desiccation in Acinetobacter baumannii

The long-term resistance to desiccation on abiotic surfaces is a key determinant of the adaptive success of Acinetobacter baumannii as a healthcare-associated bacterial pathogen. Here, the cellular and molecular mechanisms enabling A. baumannii to resist desiccation and persist on abiotic surfaces were investigated. Experiments were set up to mimic the A. baumannii response to air-drying that would occur when bacterial cells contaminate fomites in hospitals. Resistance to desiccation and transition to the "viable but nonculturable" (VBNC) state were determined in the laboratory-adapted strain ATCC 19606T and the epidemic strain ACICU. Culturability, membrane integrity, metabolic activity, virulence, and gene expression profile were compared between the two strains at different stages of desiccation. Upon desiccation, ATCC 19606T and ACICU cells lose culturability and membrane integrity, lower their metabolism, and enter the VBNC state. However, desiccated A. baumannii cells fully recover culturability and virulence in an insect infection model following rehydration in physiological buffers or human biological fluids. Transcriptome and chemical analyses of A. baumannii cells during desiccation unveiled the production of protective metabolites (L-cysteine and L-glutamate) and decreased energetic metabolism consequent to activation of the glyoxylate shunt (GS) pathway, as confirmed by reduced resuscitation efficiency of aceA mutants, lacking the key enzyme of the GS pathway. VBNC cell formation and extensive metabolic reprogramming provide a biological basis for the response of A. baumannii to desiccation, with implications on environmental control measures aimed at preventing the transmission of A. baumannii infection in hospitals.

The stems and leaves of Panax notoginseng reduce the abundance of antibiotic resistance genes by regulating intestinal microbiota in Duzang pigs

In order to study the distribution characteristics of intestinal microbiota and antibiotic resistance genes (ARGs) in Duzang pigs after adding stems and leaves of Panax notoginseng to the feed, the characteristics of intestinal microbiota were explored by metagenomic sequencing, and 14 ARGs and 2 integrase genes were detected by qPCR. The results showed that the addition of stems and leaves of P. notoginseng increased the relative abundance of Firmicutes, Lactobacillus and Pediococcus in the cecum of Duzang pigs. A total of 10 ARGs and 2 integrase genes were detected in the cecal contents of pigs. The addition of stems and leaves of P. notoginseng reduced the relative abundance of total ARGs, ermB, tetO and tetW in the cecum of Duzang pigs. The results of network analysis showed that multiple genera were potential hosts of ARGs. The addition of stems and leaves of P. notoginseng may reduce the relative abundance of ARGs by reducing the relative abundance of genera such as Corynebacterium and Flavonifractor, thereby reducing the risk of ARGs spread. This study provides a theoretical basis for the rational use of stems and leaves of P. notoginseng to control ARGs.