Tissue Compartmentalization Research Articles

FC07 Transcriptomic profiling across tissues and machine learning reveal molecular endotypes of psoriasis phenotypes and signatures of disease severity during biologic therapy

Abstract Despite advances in understanding the pathogenesis of psoriasis, important knowledge gaps exist including (i) whether molecular endotypes of stable plaque psoriasis underlie distinct clinical phenotypes (e.g. subjects with specific comorbidities) and (ii) the positive drivers and negative molecular regulators of disease severity across tissue compartments. We performed a comprehensive RNA-seq study of skin and blood samples (n = 718) from deeply phenotyped discovery (n = 89) and refinement (n = 57) psoriasis cohorts, during targeted treatment with a TNF inhibitor (adalimumab) or an interleukin (IL)-12/23 inhibitor (ustekinumab). As gene expression is controlled by multiple factors across different cell types, network analysis of bulk RNAseq data across large numbers of clinical samples takes into account the underlying latent factors and modules that result in the coordination of gene expression and can more accurately reflect the relationship between transcriptional signatures and clinical phenotypes compared with analysis of individual genes. Using two complementary methods for dimensionality reduction, weighted gene correlation network analysis (WGCNA) and Independent Component Analysis (ICA), we defined distinct but interconnected gene modules and factors within skin and blood that were significantly positively or negatively associated with disease severity as measured by Psoriasis Area Severity Index (PASI). To understand which modules and factors in lesional psoriasis skin contribute to the prediction of disease severity, we applied Gaussian process regression followed by SHAP (SHapley Additive exPlanations). This analysis highlighted 2 principal gene modules [cytokine signalling (267 genes) and Wnt signalling (207 genes)] that explained ∼50% of the variance of PASI during clinical response to both adalimumab and ustekinumab. We derived a further gene signature (14 genes), linked to body mass index in nonlesional skin at baseline, that in lesional skin was significantly negatively associated with PASI. Notably, PASI-associated signatures in blood were only seen following exposure to adalimumab whereas ustekinumab PASI-associated signatures were confined to skin. These highly drug-specific tissue compartmentalization effects indicate a differential systemic impact of adalimumab compared with ustekinumab, in line with differences in side-effect profiles. In contrast, a gene signature in blood closely linked to HLA-C*06:02 status was independent of disease severity (PASI). The systematic nature of the dataset across skin and blood and its integration with key clinical features and outcomes to therapy provides a comprehensive and global perspective of psoriasis that are not apparent from previous studies. Specifically, our findings delineate, across skin and blood, distinct gene-environmental and genetic effects on the psoriasis transcriptome linked to clinical phenotypes and disease severity endotypes.

HIV-1 exploits LBPA-dependent intraepithelial trafficking for productive infection of human intestinal mucosa.

The gastrointestinal tract is a prominent portal of entry for HIV-1 during sexual or perinatal transmission, as well as a major site of HIV-1 persistence and replication. Elucidation of underlying mechanisms of intestinal HIV-1 infection are thus needed for the advancement of HIV-1 curative therapies. Here, we present a human 2D intestinal immuno-organoid system to model HIV-1 disease that recapitulates tissue compartmentalization and epithelial-immune cellular interactions. Our data demonstrate that apical exposure of intestinal epithelium to HIV-1 results in viral internalization, with subsequent basolateral shedding of replication-competent viruses, in a manner that is impervious to antiretroviral treatment. Incorporation of subepithelial dendritic cells resulted in HIV-1 luminal sampling and amplification of residual viral replication of lab-adapted and transmitted-founder (T/F) HIV-1 variants. Markedly, intraepithelial viral capture ensued an altered distribution of specialized endosomal pathways alongside durable sequestration of infectious HIV-1 within lysobisphosphatidic acid (LPBA)-rich vesicles. Therapeutic neutralization of LBPA-dependent trafficking limited productive HIV-1 infection, and thereby demonstrated the pivotal role of intraepithelial multivesicular endosomes as niches for virulent HIV-1 within the intestinal mucosa. Our study showcases the application of primary human 2D immune-competent organoid cultures in uncovering mechanisms of intestinal HIV-1 disease as well as a platform for preclinical antiviral drug discovery.

Integrated insights into the cytological, histochemical, and cell wall composition features of Espinosa nothofagi (Hymenoptera) gall tissues: implications for functionality.

Many insect-induced galls are considered complex structures due to their tissue compartmentalization and multiple roles performed by them. The current study investigates the complex interaction between Nothofagus obliqua host plant and the hymenopteran gall-inducer Espinosa nothofagi, focusing on cell wall properties and cytological features. The E. nothofagi galls present an inner cortex with nutritive and storage tissues, as well as outer cortex with epidermis, chlorenchyma, and water-storing parenchyma. The water-storing parenchyma cells are rich in pectins, heteromannans, and xyloglucans in their walls, and have large vacuoles. Homogalacturonans contribute to water retention, and periplasmic spaces function as additional water reservoirs. Nutritive storage cell walls support nutrient storage, with plasmodesmata facilitating nutrient mobilization crucial for larval nutrition. Their primary and sometimes thick secondary cell walls support structural integrity and act as a carbon reserve. The absent labeling of non-cellulosic epitopes indicates a predominantly cellulosic nature in nutritive cell walls, facilitating larval access to lipid, protein, and reducing sugar-rich contents. The nutritive tissue, with functional chloroplasts and high metabolism-related organelles, displays signs of self-sufficiency, emphasizing its role in larval nutrition and cellular maintenance. Overall, the intricate cell wall composition in E. nothofagi galls showcases adaptations for water storage, nutrient mobilization, and larval nutrition, contributing significantly to our understanding of plant-insect interactions.

Differential Expression of Branched-Chain Aminotransferase in the Rat Ocular Tissues.

Branched-chain amino acids (BCAAs) play vital roles in metabolic and physiological processes, with their catabolism initiated by two branched-chain aminotransferase isozymes: cytosolic (BCATc) and mitochondrial (BCATm). These enzymes have tissue and cell-specific compartmentalization and are believed to shuttle metabolites between cells and tissues. Although their expression and localization have been established in most tissues, ocular tissues remain unknown. In this study, we used immunohistochemical analyses to investigate the expression and localization of BCAT enzymes in the normal eye tissues. As expected, BCATc was highly expressed in the neuronal cells of the retina, particularly in the ganglion cell layers, inner nuclear layer, and plexiform layer, with little to no expression in Müller cells. BCATc was also present in the cornea, retinal pigment epithelium (RPE), choroid, ciliary body, and iris but not in the lens. In contrast, BCATm was expressed across all ocular tissues, with strong expression in the Muller cells of the retina, the endothelial and epithelial layers of the cornea, the choroid and iris, and the epithelial cells at the lens's front. The extensive expression and distribution of BCAT isozymes in the ocular tissue, suggests that BCAA transamination is widespread in the eye, potentially aiding in metabolite transport between ocular tissues. The findings provide new insights into the physiological role of BCATs in the eye, particularly within the neuronal retina.

Spatial adaptation of eosinophils and their emerging roles in homeostasis, infection and disease.

Eosinophils are bone marrow-derived granulocytes that are traditionally associated with type 2 immune responses, such as those that occur during parasite infections and allergy. Emerging evidence demonstrates the remarkable functional plasticity of this elusive cell type and its pleiotropic functions in diverse settings. Eosinophils broadly contribute to tissue homeostasis, host defence and immune regulation, predominantly at mucosal sites. The scope of their activities primarily reflects the breadth of their portfolio of secreted mediators, which range from cytotoxic cationic proteins and reactive oxygen species to multiple cytokines, chemokines and lipid mediators. Here, we comprehensively review basic eosinophil biology that is directly related to their activities in homeostasis, protective immunity, regeneration and cancer. We examine how dysregulation of these functions contributes to the physiopathology of a broad range of inflammatory diseases. Furthermore, we discuss recent findings regarding the tissue compartmentalization and adaptation of eosinophils, shedding light on the factors that likely drive their functional diversification within tissues.

Deciphering pathophysiological mechanisms underlying cystathionine beta-synthase-deficient homocystinuria using targeted metabolomics, liver proteomics, sphingolipidomics and analysis of mitochondrial function

BackgroundCystathionine β-synthase (CBS)-deficient homocystinuria (HCU) is an inherited disorder of sulfur amino acid metabolism with varying severity and organ complications, and a limited knowledge about underlying pathophysiological processes. Here we aimed at getting an in-depth insight into disease mechanisms using a transgenic mouse model of HCU (I278T). MethodsWe assessed metabolic, proteomic and sphingolipidomic changes, and mitochondrial function in tissues and body fluids of I278T mice and WT controls. Furthermore, we evaluated the efficacy of methionine-restricted diet (MRD) in I278T mice. ResultsIn WT mice, we observed a distinct tissue/body fluid compartmentalization of metabolites with up to six-orders of magnitude differences in concentrations among various organs. The I278T mice exhibited the anticipated metabolic imbalance with signs of an increased production of hydrogen sulfide and disturbed persulfidation of free aminothiols. HCU resulted in a significant dysregulation of liver proteome affecting biological oxidations, conjugation of compounds, and metabolism of amino acids, vitamins, cofactors and lipids. Liver sphingolipidomics indicated upregulation of the pro-proliferative sphingosine-1-phosphate signaling pathway. Liver mitochondrial function of HCU mice did not seem to be impaired compared to controls. MRD in I278T mice improved metabolic balance in all tissues and substantially reduced dysregulation of liver proteome. ConclusionThe study highlights distinct tissue compartmentalization of sulfur-related metabolites in normal mice, extensive metabolome, proteome and sphingolipidome disruptions in I278T mice, and the efficacy of MRD to alleviate some of the HCU-related biochemical abnormalities.

Differences in boundary behavior in the 3D vertex and Voronoi models.

An important open question in the modeling of biological tissues is how to identify the right scale for coarse-graining, or equivalently, the right number of degrees of freedom. For confluent biological tissues, both vertex and Voronoi models, which differ only in their representation of the degrees of freedom, have effectively been used to predict behavior, including fluid-solid transitions and cell tissue compartmentalization, which are important for biological function. However, recent work in 2D has hinted that there may be differences between the two models in systems with heterotypic interfaces between two tissue types, and there is a burgeoning interest in 3D tissue models. Therefore, we compare the geometric structure and dynamic sorting behavior in mixtures of two cell types in both 3D vertex and Voronoi models. We find that while the cell shape indices exhibit similar trends in both models, the registration between cell centers and cell orientation at the boundary are significantly different between the two models. We demonstrate that these macroscopic differences are caused by changes to the cusp-like restoring forces introduced by the different representations of the degrees of freedom at the boundary, and that the Voronoi model is more strongly constrained by forces that are an artifact of the way the degrees of freedom are represented. This suggests that vertex models may be more appropriate for 3D simulations of tissues with heterotypic contacts.

Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection.

The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we sequenced saliva and nasal samples collected daily from vaccinated and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both unvaccinated and vaccinated individuals appeared largely stochastic; however, in rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of viral variants between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.IMPORTANCEWe detail the within-host evolutionary dynamics of SARS-CoV-2 during acute infection in 31 individuals using daily longitudinal sampling. We characterized patterns of mutational accumulation for unvaccinated and vaccinated individuals, and observed that temporal variant dynamics in both groups were largely stochastic. Comparison of paired nasal and saliva samples also revealed significant genetic compartmentalization between tissue environments in multiple individuals. Our results demonstrate how selection, genetic drift, and spatial compartmentalization all play important roles in shaping the within-host evolution of SARS-CoV-2 populations during acute infection.

A fully convolutional neural network for comprehensive compartmentalization of abdominal adipose tissue compartments in MRI

BackgroundExisting literature has highlighted structural, physiological, and pathological disparities among abdominal adipose tissue (AAT) sub-depots. Accurate separation and quantification of these sub-depots are crucial for advancing our understanding of obesity and its comorbidities. However, the absence of clear boundaries between the sub-depots in medical imaging data has challenged their separation, particularly for internal adipose tissue (IAT) sub-depots. To date, the quantification of AAT sub-depots remains challenging, marked by a time-consuming, costly, and complex process. PurposeTo implement and evaluate a convolutional neural network to enable granular assessment of AAT by compartmentalization of subcutaneous adipose tissue (SAT) into superficial subcutaneous (SSAT) and deep subcutaneous (DSAT) adipose tissue, and IAT into intraperitoneal (IPAT), retroperitoneal (RPAT), and paraspinal (PSAT) adipose tissue. Material and methodsMRI datasets were retrospectively collected from Singapore Preconception Study for Long-Term Maternal and Child Outcomes (S-PRESTO: 389 women aged 31.4 ± 3.9 years) and Singapore Adult Metabolism Study (SAMS: 50 men aged 28.7 ± 5.7 years). For all datasets, ground truth segmentation masks were created through manual segmentation. A Res-Net based 3D-UNet was trained and evaluated via 5-fold cross-validation on S-PRESTO data (N = 300). The model's final performance was assessed on a hold-out (N = 89) and an external test set (N = 50, SAMS). ResultsThe proposed method enabled reliable segmentation of individual AAT sub-depots in 3D MRI volumes with high mean Dice similarity scores of 98.3%, 97.2%, 96.5%, 96.3%, and 95.9% for SSAT, DSAT, IPAT, RPAT, and PSAT respectively. ConclusionConvolutional neural networks can accurately sub-divide abdominal SAT into SSAT and DSAT, and abdominal IAT into IPAT, RPAT, and PSAT with high accuracy. The presented method has the potential to significantly contribute to advancements in the field of obesity imaging and precision medicine.

Rapid In Vitro Screening of Prunus Genotypes for Resistance to Armillaria Root Rot Using Roots of Young Rootstocks

Armillaria root rot (ARR), caused by Armillaria species and Desarmillaria tabescens, is a severe disease that affects stone fruit trees in the United States. One strategy to mitigate the impact of this disease is to develop ARR-resistant rootstocks. However, current techniques to screen Prunus species for resistance to ARR are time-consuming, labor-intensive, and may not fully replicate field conditions. To address these limitations, we developed a new rapid in vitro screening assay, which uses roots of 2-year-old Prunus rootstock genotypes. We screened 12 Prunus genotypes against Armillaria mellea, Armillaria solidipes, and Desarmillaria tabescens in vitro. Freshly excavated root segments were placed next to or on top of fungal cultures. After 21 days, the circumferential percentage and horizontal length of the fungal colonization and the ability of the fungus to enter through root periderm were evaluated. The root tissue surrounding the infection was also evaluated to assess any response reactions against the ARR pathogens. Our results showed that inoculated root tissues displayed signs of fungal infection, and infection and host responses varied among the Prunus genotypes. Host responses similar to those observed in the field, such as compartmentalization of infected tissue with barrier zones, necrophylactic periderm formation, and callus formation on root surfaces, were observed and were more evident in less susceptible genotypes. In conclusion, our newly developed assay, which uses freshly excavated roots from 2-year-old rootstocks, can rapidly screen Prunus genotypes for resistance to ARR.

Inter-host Genetic Variability of Severe Acute Respiratory Syndrome Coronavirus 2 and its Implication in Biomedicine: A Bioinformatics Approach

Abstract Background: Genomic sequencing data from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have provided important information on the emergence of variants of interest. Some research has focused on determining intra-host variability and evolution, and others have focused on viral genetic variability in different tissues, as well as implications for virus infectivity and pathogenicity. However, the inter-host variability of SARS-CoV-2 in respiratory compartments and its implications has not yet been explained. To determine a possible pattern of tissue-specific inter-host variability at different levels of the respiratory system associating this information with clinically important characteristics. Methods: In this work, we analyzed the inter-host variability of SARS-CoV-2 using the Shannon entropy method with genomic data from NCBI database. Fifty-seven SARS-CoV-2 viral genomic sequences were included in the study. Oronasopharyngeal (n = 30) and tracheal aspirate (n = 27) sample sequences were analyzed by bioinformatics methods to determine the viral variability. Results: Different patterns of variability were observed in SARS-CoV-2 in the respiratory tract, which may indicate tissue compartmentalization phenomena. Genetic changes found in the N y S gene could affect the detection and spread of the virus. The overall analysis of the viral genomes identifies the variants of worldwide distribution. The viral diversity found in the different parts of the respiratory tract was high and uniformly distributed throughout the genome. Conclusions: Tracking inter-host variations in SARS-CoV-2 could help to understand the effects of viral evolution, provide information for diagnosis, drug, and vaccine design.

Temporal intra-host variability of mpox virus genomes in multiple body tissues.

Whole-genome sequencing (WGS) has been widely used for the genomic characterization and the phylogenesis of mpox virus (MPXV) 2022 multi-country outbreak. To date, no evidence has been reported on intra-host evolution within samples collected over time from a single patient with long-term infection. Fifty-one samples were collected from five patients at different time points post-symptom onset. All samples were confirmed as MPXV DNA positive, amplified by a multiplexed PCR amplicon, and sequenced by WGS. Complete MPXV genomes were assembled by reference mapping and then aligned to perform phylogenetic and hierarchical clustering analysis. Large intra-host variability was observed among the MPXV genomes sequenced from samples of two immunocompromised with advanced HIV-1 infection patients with prolonged MPXV shedding. Overall, 20 nucleotide mutations were identified in the 32 genomes from HIV patients, differently distributed in samples collected from different tissues and at different time points. No sequence compartmentalization nor variation was observed in the three patients with rapid viral clearance. MPXV exhibits adaptation to changing environments within the infected host and consequently demonstrates tissue compartmentalization. Further studies are needed to elucidate the role of this adaptation in forming a pool of genetic variability and contributing to viral persistence and its clinical implications.

Spatially resolved characterization of tissue metabolic compartments in fasted and high-fat diet livers.

Cells adapt their metabolism to physiological stimuli, and metabolic heterogeneity exists between cell types, within tissues, and subcellular compartments. The liver plays an essential role in maintaining whole-body metabolic homeostasis and is structurally defined by metabolic zones. These zones are well-understood on the transcriptomic level, but have not been comprehensively characterized on the metabolomic level. Mass spectrometry imaging (MSI) can be used to map hundreds of metabolites directly from a tissue section, offering an important advance to investigate metabolic heterogeneity in tissues compared to extraction-based metabolomics methods that analyze tissue metabolite profiles in bulk. We established a workflow for the preparation of tissue specimens for matrix-assisted laser desorption/ionization (MALDI) MSI that can be implemented to achieve broad coverage of central carbon, nucleotide, and lipid metabolism pathways. Herein, we used this approach to visualize the effect of nutrient stress and excess on liver metabolism. Our data revealed a highly organized metabolic tissue compartmentalization in livers, which becomes disrupted under high fat diet. Fasting caused changes in the abundance of several metabolites, including increased levels of fatty acids and TCA intermediates while fatty livers had higher levels of purine and pentose phosphate-related metabolites, which generate reducing equivalents to counteract oxidative stress. This spatially conserved approach allowed the visualization of liver metabolic compartmentalization at 30 μm pixel resolution and can be applied more broadly to yield new insights into metabolic heterogeneity in vivo.

A phenological trick and cell wall bricks toward adaptive strategies of Mimosa tenuiflora-Lopesia mimosae interaction in Caatinga environment

Caatinga environment tends to impose constraints on the phenology and development of the host plants and their associated galls. Phenological synchronism in Mimosa tenuiflora-Lopesia mimosae system, and anatomical, cytometric, and immunocytochemical analyzes reveal strategies of the gall survivorship in Caatinga. As phenological strategies, the peak of young galls synchronizes with leaf sprouting in the rainy season, and the reproductive phase is concomitant to gall senescence in the dry season. As structural strategies, the reorganization and the compartmentalization of gall tissues assist gall development in response to environmental constraints, and the predominance of periclinal cell elongation determined the gall bivalve shape. The distribution of pectins, glycoproteins, and hemicelluloses modulate cell walls toward favoring gall resistance to drought stress. The homogalacturonans confer high porosity to the cell walls of the typical nutritive tissue. The galactans and arabinans confer flexibility to the cell walls of the common storage tissue favoring tolerance to drought. The xylogalacturonans and heteromannans in the cell walls of the typical nutritive tissue are associated with nutritive reserves directed to the galling insect. The phenological synchronism, modulation of leaf tissues and cell wall components confer water and nutritional resources to the Lopesia mimosae microenvironment, the gall.

Chlorine inhalation toxicology‐on‐a‐chip

Accidental or environmental exposures to chlorine (Cl2 ) gas represent a major health threat. In particular, inhalation toxicology of Cl2 is an area of active research that focuses on investigating the deleterious effects of Cl2 on the human respiratory system and developing effective countermeasures to mitigate the risk of Cl2 -induced lung injury. While traditional cell culture models have gained widespread use as a simple and convenient research tool for in vitro investigation of Cl2 toxicity, they have limited capacity to recapitulate the complexity of native human lung tissues and thus largely fail to generate accurate predictions on pulmonary responses to Cl2 . Here we present two distinct microengineered biomimetic models that reconstruct the small airway and alveolar regions of the human lung for experimental studies of respiratory toxicity of Cl2 in the distal lung, which remains an outstanding question in inhalation toxicology of Cl2 . Our microengineered small airway model is composed of two microfabricated 3D chambers separated by a semipermeable membrane. The design of this microdevice makes it possible to mimic tissue compartmentalization in native airways by permitting long-term co-culture of primary human small airway epithelial cells, primary human pulmonary microvascular endothelial cells, and lung fibroblasts in a physiological 3D microenvironment to engineer fully differentiated airway epithelium directly exposed to air and supported by vascularized, perfusable 3D stromal tissues. The alveolar model, which is constructed in the same device, uses primary human type II pneumocytes harvested from iPSC-derived human alveolar organoids, some of which are transdifferentiated into type I alveolar epithelial cells during the course of controlled microfluidic culture in our device. In this study, these models were capable of producing human lung tissues that exhibited differentiated phenotype and functional capacity that could be maintained for extended periods (over 1 month). Notably, our data revealed the potential of the underlying pulmonary vasculature to accelerate and promote differentiation and maturation of lung epithelial cells during air-liquid interface culture. Using the lung-on-a-chip systems in conjunction with an in-house Cl2 exposure system, we conducted a preliminary study in which the devices were exposed to various concentrations of Cl2 gas (10, 50, 100 and 300 ppm) for 15 min. Our preliminary data showed the deleterious potential of Cl2 to induce acute injury of both small airway and alveolar tissues in a dose-dependent manner. Studies are underway for more extensive screening of Cl2 toxicity and in-depth analysis of lung injury in our models at the molecular, cellular, and tissue levels. We believe that the microengineered systems developed in this work represent an important advance in our ability to model acute respiratory responses to toxic gases and may provide a potentially powerful in vitro platform to study biochemical threats and develop medical countermeasures against them.

Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness.

The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates, and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to superspreading. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant of concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be simply explained by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.

Complexity of Human Cytomegalovirus Infection in South African HIV-Exposed Infants with Pneumonia.

Human cytomegalovirus (HCMV) can cause significant end-organ diseases such as pneumonia in HIV-exposed infants. Complex viral factors may influence pathogenesis including: a large genome with a sizeable coding capacity, numerous gene regions of hypervariability, multiple-strain infections, and tissue compartmentalization of strains. We used a whole genome sequencing approach to assess the complexity of infection by comparing high-throughput sequencing data obtained from respiratory and blood specimens of HIV-exposed infants with severe HCMV pneumonia with those of lung transplant recipients and patients with hematological disorders. There were significantly more specimens from HIV-exposed infants showing multiple HCMV strain infection. Some genotypes, such as UL73 G4B and UL74 G4, were significantly more prevalent in HIV-exposed infants with severe HCMV pneumonia. Some genotypes were predominant in the respiratory specimens of several patients. However, the predominance was not statistically significant, precluding firm conclusions on anatomical compartmentalization in the lung.

Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution.

BackgroundThe global effort to vaccinate people against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during an ongoing pandemic has raised questions about how vaccine breakthrough infections compare with infections in immunologically naive individuals and the potential for vaccinated individuals to transmit the virus.MethodsWe examined viral dynamics and infectious virus shedding through daily longitudinal sampling in 23 adults infected with SARS-CoV-2 at varying stages of vaccination, including 6 fully vaccinated individuals.ResultsThe durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases.ConclusionsVaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.

SIV Evolutionary Dynamics in Cynomolgus Macaques during SIV-Mycobacterium tuberculosis Co-Infection.

Co-infection with Mycobacterium tuberculosis (Mtb) and human immunodeficiency virus (HIV) is a worldwide public health concern, leading to worse clinical outcomes caused by both pathogens. We used a non-human primate model of simian immunodeficiency virus (SIV)-Mtb co-infection, in which latent Mtb infection was established prior to SIVmac251 infection. The evolutionary dynamics of SIV env was evaluated from samples in plasma, lymph nodes, and lungs (including granulomas) of SIV-Mtb co-infected and SIV only control animals. While the diversity of the challenge virus was low and overall viral diversity remained relatively low over 6–9 weeks, changes in viral diversity and divergence were observed, including evidence for tissue compartmentalization. Overall, viral diversity was highest in SIV-Mtb animals that did not develop clinical Mtb reactivation compared to animals with Mtb reactivation. Among lung granulomas, viral diversity was positively correlated with the frequency of CD4+ T cells and negatively correlated with the frequency of CD8+ T cells. SIV diversity was highest in the thoracic lymph nodes compared to other sites, suggesting that lymphatic drainage from the lungs in co-infected animals provides an advantageous environment for SIV replication. This is the first assessment of SIV diversity across tissue compartments during SIV-Mtb co-infection after established Mtb latency.

Tissue compartmentalization enables Salmonella persistence during chemotherapy

Antimicrobial chemotherapy can fail to eradicate the pathogen, even in the absence of antimicrobial resistance. Persisting pathogens can subsequently cause relapsing diseases. In vitro studies suggest various mechanisms of antibiotic persistence, but their invivo relevance remains unclear because of the difficulty of studying scarce pathogen survivors in complex host tissues. Here, we localized and characterized rare surviving Salmonella in mouse spleen using high-resolution whole-organ tomography. Chemotherapy cleared >99.5% of the Salmonella but was inefficient against a small Salmonella subset in the white pulp. Previous models could not explain these findings: drug exposure was adequate, Salmonella continued to replicate, and host stresses induced only limited Salmonella drug tolerance. Instead, antimicrobial clearance required support of Salmonella-killing neutrophils and monocytes, and the density of such cells was lower in the white pulp than in other spleen compartments containing higher Salmonella loads. Neutrophil densities declined further during treatment in response to receding Salmonella loads, resulting in insufficient support for Salmonella clearance from the white pulp and eradication failure. However, adjunctive therapies sustaining inflammatory support enabled effective clearance. These results identify uneven Salmonella tissue colonization and spatiotemporal inflammation dynamics as main causes of Salmonella persistence and establish a powerful approach to investigate scarce but impactful pathogen subsets in complex host environments.