Biology subjects

David, S. C.

Publications and source records attributed to David, S. C..

10 recordsLinked to original sources

bioRxiv2025

Harnessing Alpine Lake Bacteria for the Development of Synthetic Communities with Broad-Spectrum Antiviral Activity

In aquatic ecosystems, phagotrophic protists and bacteriophages are major biological factors shaping bacterial populations. However, the extreme environmental conditions and low nutrient concentrations in alpine lakes limit the abundance of protists. Thus, bacteriophages may represent the main biological factor shaping bacterial communities in these ecosystems. We hypothesized that alpine lake bacteria populations harbor diverse antiviral strategies against bacteriophages that could be used to fight against other viral pathogens. To evaluate the presence of bacteria with broad-spectrum antiviral activity in high altitude Swiss lakes, we developed a sampling campaign in 24 alpine lakes in Switzerland. We assessed the decay of two human viruses (echovirus 11 and influenza A virus) in lakewater and characterized the microbial abundance and metabolic diversity in the collected samples. In addition, we obtained a collection of 223 bacterial isolates and selected bacteriophage resistant bacteria to build synthetic communities with enhanced antiviral activity against the two tested human viruses, and one plant virus of commercial significance (Potato Virus X). This confirmed our hypothesis and drew for the first time a relation between bacteriophage resistance and viral inactivation. Our findings emphasize the importance of alpine lakes as hotspots of microbial diversity with unexplored biotechnological applications.

microbiology↗

bioRxiv2024

Comparative Characterization of Bronchial and Nasal Mucus Reveals Key Determinants of Influenza A Virus Inhibition

Differentiated primary human respiratory epithelial cells grown at air-liquid interface have become a widely used cell culture model of the human conducting airways. These cultures contain secretory cells such as goblet and club cells, which produce and secrete mucus. Here, we characterize the composition of mucus harvested from airway cultures of nasal and bronchial origin. We find that despite inter-donor variability, the salt, sugar, lipid, and protein content and composition are very similar between nasal and bronchial mucus. However, subtle differences in the abundance of individual components in nasal versus bronchial mucus can influence its antimicrobial properties: The ability of mucus to neutralize influenza A virus varies with the anatomical origin of the airway cultures and correlates with the abundance of triglycerides and sialylated glycoproteins and glycolipids. ImportanceRespiratory mucus plays an important role during the transmission and infection process of microbes in the human respiratory tract. In case of influenza A virus, mucus stabilizes virions in infectious respiratory particles and droplets but hampers virus particles before they reach the respiratory epithelium through its physicochemical properties and the presence of sialylated decoy receptors. However, it is thus far not well understood which components of mucus mediate protection and inhibition. Our study now provides a comprehensive analysis of bronchial and nasal mucus from primary human airway cultures that can be used as a resource for future experimental designs and interpretations.

microbiology↗

bioRxiv2024

Dependence of aerosol-borne influenza A virus infectivity on relative humidity and aerosol composition

We describe a novel biosafety aerosol chamber equipped with state-of-the-art instrumentation for bubble-bursting aerosol generation, size distribution measurement, and condensation-growth collection to minimize sampling artifacts when measuring virus infectivity in aerosol particles. Using this facility, we investigated the effect of relative humidity (RH) in very clean air without trace gases (except [~]400 ppm CO2) on the preservation of influenza A virus (IAV) infectivity in saline aerosol particles. We characterized infectivity in terms of 99%-inactivation time, t99, a metric we consider most relevant to airborne virus transmission. The viruses remained infectious for a long time, namely t99 > 5 h, if RH < 30% and the particles effloresced. Under intermediate conditions of humidity (40% < RH < 70%), the loss of infectivity was the most rapid (t99 {approx} 15-20 min, and up to t99 {approx} 35 min at 95% RH). This is more than an order of magnitude faster than suggested by many previous studies of aerosol-borne IAV, possibly due to the use of matrices containing organic molecules, such as proteins, with protective effects for the virus. We tested this hypothesis by adding sucrose to our aerosolization medium and, indeed, observed protection of IAV at intermediate RH (55 %). Interestingly, the t99 of our measurements are also systematically lower than those in 1-L droplet measurements of organic-free saline solutions, which cannot be explained by particle size effects alone.

microbiology↗

bioRxiv2024

Impact of Organic Compounds on the Stability of Influenza A Virus in deposited 1-ul droplets

The composition of respiratory fluids influences the stability of viruses in exhaled aerosol particles and droplets, though the role of respiratory organics in modulating virus stability remains poorly understood. This study investigates the effect of organic compounds on the stability of influenza A virus (IAV) in deposited droplets. We compare the infectivity loss of IAV at different relative humidities (RH) over the course of one hour in 1-l droplets consisting of phosphate-buffered saline (without organics), synthetic lung fluid, or nasal mucus (both containing organics). We show that IAV stability increases with increasing organic:salt ratios. Among the various organic species, proteins are identified as the most protective component, with smaller proteins stabilizing IAV more efficiently at the same mass concentration. Organics act by both increasing the efflorescence RH and shortening the drying period until efflorescence at a given RH. This research advances our mechanistic understanding of how organics stabilize exhaled viruses and thus influence their inactivation in respiratory droplets.

microbiology↗

bioRxiv2024

Stability of influenza A virus in droplets and aerosols is heightened by the presence of commensal respiratory bacteria.

Aerosol transmission remains a major challenge for the control of respiratory viruses, particularly for those that cause recurrent epidemics, like influenza A virus (IAV). These viruses are rarely expelled alone, but instead are embedded in a consortium of microorganisms that populate the respiratory tract. The impact of microbial communities and inter-pathogen interactions upon the stability of transmitted viruses is well-characterised for pathogens of the gut, but is particularly under-studied in the respiratory niche. Here, we assessed whether the presence of 5 different species of common commensal respiratory bacteria could influence the stability of IAV within droplets deposited on surfaces and within airborne aerosol particles at typical indoor air humidity. It was found that bacterial presence within stationary droplets, either a mixed community or individual strains, resulted in 10- to 100-fold more infectious IAV remaining after 1 hour. Bacterial viability was not required for this viral stabilisation, though maintained bacterial morphology seemed to be essential. Additionally, non-respiratory bacteria tested here had little stabilising effect, indicating this phenomenon was respiratory-specific. The protective bacteria stabilised IAV in droplets via induction of early efflorescence due to flattened droplet morphology during drying. Even when no efflorescence occurred at high humidity or the bacteria-induced changes in droplet morphology were abolished by aerosolization instead of deposition on a well-plate, the bacteria remained protective. This indicates an additional stabilisation mechanism that is currently unknown. Notably, respiratory bacteria at equivalent density offered varying degrees of protection in droplets, with the Gram-positive species Staphylococcus aureus and Streptococcus pneumoniae being the most robustly stabilising. This suggests that the composition of an individuals respiratory microbiota could be a previously un-considered host-specific factor influencing the efficacy of expelled viral spread. Identifying novel host-specific factors such as the commensal microbiota that can influence viral stability in the environment will further increase our understanding of individual transmission risks, and will provide novel opportunities to limit the spread of respiratory infections within our populations. SynopsisOur findings have significant environmental and health relevance, as they identify the host respiratory microbiota as a novel factor potentially contributing to environmental viral stability within indoor environments.

microbiology↗

bioRxiv2023

Salt-mediated inactivation of influenza A virus in 1-ul droplets exhibits exponential dependence on NaCl molality

Influenza A virus (IAV) spreads through exhaled aerosol particles and larger droplets. Estimating the stability of IAV is challenging and depends on factors such as the respiratory matrix and drying kinetics. Here, we combine kinetic experiments on millimeter-sized saline droplets with a biophysical aerosol model to quantify the impact of NaCl on IAV stability. We show that IAV inactivation is determined by NaCl concentration, which increases during water evaporation and then decreases again when efflorescence occurs. When drying in air with relative humidity RH = 30%, inactivation follows an inverted sigmoidal curve, with inactivation occurring most rapidly when the NaCl concentration exceeds 20 molal immediately prior to efflorescence. Efflorescence reduces the NaCl molality to saturated conditions, resulting in a significantly reduced inactivation rate. We demonstrate that the inactivation rate k depends exponentially on NaCl molality, and after the solution reaches equilibrium, the inactivation proceeds at a first-order rate. Introducing sucrose, an organic co-solute, attenuates IAV inactivation via two mechanisms, firstly by decreasing the NaCl molality during the drying phase, and secondly by a protective effect against the NaCl-induced inactivation. For both pure saline and sucrose-containing droplets, our biophysical model ResAM accurately simulates the inactivation when NaCl molality is used as the only inactivating factor. This study highlights the role of NaCl molality in IAV inactivation and provides a mechanistic basis for the observed inactivation rates. SYNOPSIS: This work quantifies the dependence of influenza A virus stability on salt molality in drying droplets and furthers the understanding of airborne virus transmission.SYNOPSIS: This work quantifies the dependence of influenza A virus stability on salt molality in drying droplets and furthers the understanding of airborne virus transmission.

microbiology↗

bioRxiv2023

The early communication stages between serine proteases and enterovirus capsids in the race for viral disintegration

Enteroviruses are human pathogens known to challenge water safety1,2. Among the microbial stressors found in water, bacterial serine proteases contribute to the control of enterovirus persistence3. However, the structural interactions accounting for the susceptibility of enteroviruses to proteases remains unexplained. Here, we describe the molecular mechanisms involved in the recruitment of serine proteases to viral capsids. Among the virus types used, coxsackievirus A9 (CVA9), but not CVB5 and echovirus 11 (E11), was inactivated by Subtilisin A in a host-independent manner, while Bovine Pancreatic Trypsin (BPT) only reduced CVA9 infectivity in a host-dependent manner. Predictive interaction models of each protease with capsid protomers indicate the main targets as internal disordered protein (IDP) segments exposed either on the 5-fold vertex (DE loop VP1) or at the 5/2-fold intersection (C-terminal end VP1) of viral capsids. We further show that a functional binding protease/capsid depends on both the strength and the evolution over time of protease-VP1 complexes, and lastly on the local adaptation of proteases on surrounding viral regions. Finally, we identified three residues on CVA9 capsid that trigger cleavage by Subtilisin A, one of which acts as a sensor residue contributing to enzyme recognition on the DE loop. Overall, this study describes an important biological mechanism involved in enteroviruses biocontrol.

microbiology↗

bioRxiv2022

Inactivation of Influenza A virus by pH conditions encountered in expiratory aerosol particles results from localized conformational changes within Haemagglutinin and Matrix 1 proteins.

Multiple respiratory viruses including Influenza A virus (IAV) can be transmitted via expiratory aerosol particles, and aerosol pH was recently identified as a major factor influencing airborne virus infectivity. For indoor air, small exhaled aerosols undergo rapid acidification to pH [~]4. IAV is known to be sensitive to mildly acidic conditions encountered within host endosomes, however, it is unknown whether the same mechanisms could mediate viral inactivation within the more acidic aerosol micro-environment. Here, we identified that transient exposure to pH 4 caused IAV inactivation by a two-stage process, with an initial sharp decline in infectious titers that was mainly attributed to premature attainment of the post-fusion conformation of viral protein haemagglutinin (HA). Changes to HA were observed by hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) as early as 10 seconds post-exposure to acidic conditions. In addition, virion integrity was partially but irreversibly affected by acidic conditions. This was attributed to a progressive unfolding of the internal matrix protein 1 (M1), and aligned with a more gradual decline in viral infectivity with time. In contrast, no acid-mediated changes to the genome or lipid envelope were detected. Our HDX-MS data are in agreement with other more labor-intensive structural analysis techniques such as X-ray crystallography, highlighting the usefulness of whole-virus HDX-MS for multiplexed protein analyses, even within enveloped viruses such as IAV. Improved understanding of respiratory virus fate within exhaled aerosols constitutes a global public health priority, and information gained here could aid development of novel strategies to control the airborne persistence of seasonal and/or pandemic influenza in the future.

microbiology↗

bioRxiv2022

Observed Kinetics of Enterovirus Inactivation by Free Chlorine Is Host Cell-Dependent

The virucidal efficacy of disinfectants is typically assessed by infectivity assay utilizing a single type of host cell. Enteroviruses infect multiple host cells via different entry routes, and each entry route may be impaired to a varying extent by a given disinfectant. Yet, it is not known how the choice of host cells for titration affects the observed inactivation kinetics. Here, we evaluated the inactivation kinetics of echovirus 11 (E11) by free chlorine, ultraviolet (UV) irradiation, and heat, using three different host cells (BGMK, RD, and A549). E11 inactivation by free chlorine occurred at a two-fold greater rate when enumerated on BGMK cells compared to RD and A549 cells. Conversely, a comparable inactivation rate was observed for UV and heat independent of the host cell used. Host cell-dependent inactivation kinetics by free chlorine were also observed for echovirus 7, 9 and 13, and coxsackievirus A9, confirming that this phenomenon is not serotype-specific. Inactivation of E11 was partly caused by a loss in host cell attachment, which was most pronounced for BGMK cells, and which may be promoted by a lack of CD55 attachment receptors on this cell type. Additionally, BGMK cells lack a key subunit of the uncoating receptor, {beta}2M, which may further contribute to the differential inactivation kinetic for this cell type. Consequently, inactivation kinetics of enteroviruses should be assessed using host cells with different receptor profiles. This will yield a more complete understanding of the inactivating power of disinfectants targeting the viral attachment and/or uncoating. Graphic for Table of Contents (TOC) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/509468v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@148461eorg.highwire.dtl.DTLVardef@1f3667corg.highwire.dtl.DTLVardef@cd75a3org.highwire.dtl.DTLVardef@e65616_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2019

In Vivo Dual RNA-Seq Analysis Reveals the Basis for Differential Tissue Tropism of Clinical Isolates of Streptococcus pneumoniae

Streptococcus pneumoniae is a genetically diverse human-adapted pathogen commonly carried asymptomatically in the nasopharynx. We have recently shown that a single nucleotide polymorphism (SNP) in the raffinose pathway regulatory gene rafR accounts for a significant difference in the capacity of clonally-related strains to cause localised versus systemic infection. Here we have used dual RNA-seq to show that this SNP extensively impacts both bacterial and host transcriptomes in infected lungs. It affects expression of bacterial genes encoding multiple sugar transporters, and fine-tunes carbohydrate metabolism, along with extensive rewiring of host transcriptional responses to infection, particularly expression of genes encoding cytokine and chemokine ligands and receptors. The dual RNA-seq data predicted a crucial role for differential neutrophil recruitment in the distinct virulence profiles of the infecting strains and single cell analysis revealed that while reduced expression of the RafR regulon driven by a single rafR SNP provides a clear advantage for pneumococci to colonize the ear, in the lung it leads to massive recruitment of neutrophils and bacterial clearance. Importantly, the observed disease outcomes were confirmed by in vivo neutrophil depletion showing that early detection of bacteria by the host in the lung environment is crucial for effective clearance. Thus, dual RNA-seq provides a powerful tool for understanding complex host-pathogen interactions and revealed how a single bacterial SNP can drive differential disease outcomes.

microbiology↗