Nema, V. | Search bioRxiv

bioRxiv2024

Exploring respiratory viral pathogens and bacteriome from symptomatic SARS-CoV-2-negative and positive individuals

In the COVID pandemic era, increased mortality was seen despite some unknown etiologies other than SARS-CoV2 viral infection. Vaccination targeted to SARS-CoV2 was successful due to infection caused by pathogens of viral origin based on symptomatology. Hence, it is essential to detect other viral and bacterial infections throughout the initial wave of the COVID-19 disease outbreak, particularly in those suffering from a symptomatic respiratory infection with SARS-CoV-2-negative status. This study was planned to explore the presence of bacterial and other respiratory viruses in symptomatic patients with SARS-CoV2-positive or negative status. The study selected128 patients samples out of 200 patients samples (100 at each time point) collected for routine SARS-CoV-2 detection schedule in December 2020 and June 2021. Considering the seasonal changes responsible for the occurrence of respiratory pathogens, we finalized 64 SARS-CoV-2 tested patients with 32 SARS-CoV-2-negatives and 32 SARS-CoV-2-positives from each collection time to examine them further using real-time PCR for the presence of other viral species and bacterial infection analyzing 16S rRNA metagenome supporting to cause respiratory infections. Along with various symptoms, we observed the co-infection of adenovirus and influenza B(Victoria) virus to two SARS-CoV-2-positive samples. The SARS-CoV-2-negative but symptomatic patient showed Rhinovirus (7/64 i.e. 10.9%) and Influenza (A/H3N2) infection in 4 patients out of 64 patients (6.25%). Additionally, one SARS-CoV-2-negative patient enrolled in June 2021 showed PIV-3 infection. Influenza A/H3N2 and Adenovirus were the cause of symptoms in SARS-CoV-2-negative samples significantly. Thus, the overall viral infections are considerably higher among SARS-CoV-2-negative patients (37.5% Vs 6.25%) compared to SARS-CoV-2-positive patients representing respiratory illness probably due to the abundance of the viral entity as well as competition benefit of SARS-CoV-2 in altering the imperviousness of the host. Simultaneously, 16S rRNA ribosomal RNA metagenomenext-generation sequencing (NGS) data from the same set of samples indicated a higher frequency of Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota, fusobacteriota, Patescibacteria, and Campilobacterotaphyla out of 15 phyla, 240 species from positive and 16 phyla, 274 species from negative samples. Exploring co-infecting respiratory viruses and bacterial populations becomes significant in understanding the mechanisms associated with multiple infecting pathogens from symptomatic COVID-positive and negative individuals for initiating proper antimicrobial therapy. Author SummaryFrequent transfer of SARS-CoV-2 events has resulted in the emergence of other viral infections along with several evolutionarily separate viral lineages in the global SARS-CoV-2 population, presenting significant viral variants in various regions worldwide. This variation also raises the possibility of reassortment and the creation of novel variants of SARS-CoV-2, as demonstrated by the COVID pandemic in all the waves, which may still be able to cause illness and spread among people. Still unclear, though, are the molecular processes that led to the adaption of other viral and bacterial pathogens in humans when a human SARS-CoV-2 virus was introduced. In this study, we identified the presence of various other viral infections and bacterial content in symptomatic COVID-19-positive and negative patients, as evidenced by the data obtained using next-generation sequencing of 16S rRNA metagenome and real-time PCR detection technologies. Symptoms might have been induced by bacterial content and various viral entities other than the SARS-CoV-2 viral infection in the COVID-negative population, indicating its importance in detecting and initiating appropriate therapy to recover from all other infections.

microbiology↗

bioRxiv2022

The role of thioredoxin proteins in Mycobacterium tuberculosis probed by proteome-wide target profiling

Mycobacterium tuberculosis encounters diverse microenvironments as it attempts to establish itself within its human host. The bacterium survives oxidative assault (ROS and RNS) when it is inside the host macrophages. Redox sensory and regulation processes therefore assume significant importance, as these are essential processes for M. tuberculosis to survive under these hostile conditions. The thioredoxin system that maintains balance between the thiol/dithiol couple plays a key role in maintaining redox homeostasis in M. tuberculosis. The most explored function of the thioredoxin system is elimination of toxic molecules such as free radicals, while very little is known about its role in other metabolic processes. In the present study, we aimed to reduce the knowledge gap about the thioredoxin system in M. tuberculosis. We attempted to capture targets of all the thioredoxins (viz., TrxB and TrxC) and a thioredoxin-like protein, NrdH in M. tuberculosis under aerobic and hypoxic conditions by performing thioredoxin trapping chromatography followed by mass spectrometry. Targets were classified using the PANTHER classification system and most enriched processes were figured out using Gene Ontology analysis. We found that TrxC captured the maximum number of targets in both the physiological conditions. Also, we suggest that the thioredoxin system might play an important role in hypoxic conditions by targeting proteins responsible to sense and maintain hypoxic conditions. Furthermore, our studies establish a link between TrxB and iron-sulfur cluster biogenesis in M. tuberculosis. Ultimately, these findings open a novel avenue to target the thioredoxin system for screening new anti-mycobacterial drug targets. ImportanceTuberculosis (TB), an infectious disease caused by bacteria M. tuberculosis, is the leading cause of death in the list of infectious diseases. Worldwide 1.7 billion people are estimated to be infected with TB, containing active and latent cases. An alarming situation is that M. tuberculosis has developed resistance against one or many of the first line drugs leading to emergence of drug resistant or multidrug resistant TB. Novel drugs targeting the drug resistant bacteria is an urgent need to cure the disease. Our study provides the framework to identify new drug targets. The significance of our study is to understand the thioredoxin system in more details by identifying their target proteins, which might facilitate development of new anti-tubercular drugs.

biochemistry↗