Innate Immune Response and Pathogen Dynamics

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Immunological Responses and Immune Defense Mechanisms".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 3370

Editor


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Guest Editor
Department of Biomedicine Neurosciences and Advanced Diagnostic, University of Palermo, 90133 Palermo, Italy
Interests: NKT cells; gamma delta cells; autoimmunity; complement; natural killer; phagocytosis; DNA extracellular traps release

Special Issue Information

Dear Colleagues,

The innate immune response is the body's immediate and non-specific defense against a variety of pathogens. It is the first line of defense that is activated upon pathogen invasion and it also plays a crucial role in activating the adaptive immune response. The dynamics between the innate immune system and pathogens are complex, involving various cellular components and mechanisms such as complement activities in response to pathogens, NK activation in response to microbes, neutrophil phagocytosis, NETosis by neutrophils, monocytes/macrophages, CD4-CD8-NK, eosinophils, etc.

Pathogenic bacteria such as Streptococcus pneumoniae and Escherichia coli are recognized by the innate immune system through pattern recognition receptors (PRRs), which detect conserved microbial structures known as pathogen-associated molecular patterns (PAMPs). This recognition triggers the complement system and phagocytosis by neutrophils and macrophages. Viruses like influenza and HIV are targeted by NK cells, which can recognize and kill virus-infected cells without prior sensitization. NK cells are also involved in the production of cytokines that help shape the adaptive immune response. Parasitic infections, such as those caused by Plasmodium species (malaria), are also met with an innate immune response. Eosinophils and macrophages are particularly effective against parasitic infections, utilizing mechanisms such as phagocytosis and the release of toxic granules. The innate immune system also interacts with the commensal microbiota, which can influence immune responses and contribute to host defense against pathogens. This interaction is crucial for maintaining immune homeostasis.

This Special Issue delves into the multifaceted aspects of innate immunity, focusing on how it interacts with and responds to different types of pathogens. We are hoping that many contributors will enjoy this topic and share their findings and insights into the intricate dynamics between the innate immune system and a wide range of pathogens.

Prof. Dr. Guido Sireci
Guest Editor

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Keywords

  • complement
  • natural killer
  • phagocytosis
  • DNA extracellular traps release

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Published Papers (3 papers)

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Research

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20 pages, 9565 KB  
Article
Temporally Resolved Single-Cell RNA Sequencing Reveals Pathogenesis and Immune Responses in Intracerebral Bacille Calmette–Guérin (BCG) Infection
by Shiqi Xie, Huiling Wang, Shaoqiong Huang, Yawen He, Ying Zhang, Shuqi Yang, Xuejiao Huang, Yang Ren, Xiao-Yong Fan, Zhidong Hu and Feng Li
Pathogens 2026, 15(5), 531; https://doi.org/10.3390/pathogens15050531 - 14 May 2026
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Abstract
Background: In some children with immunodeficiency, Bacille Calmette–Guérin (BCG) vaccination can lead to dissemination and severe infection, including severe intracranial infection, called disseminated BCG disease (BCGosis), which is characterized by high rates of disability and mortality. However, the specific routes by which BCG [...] Read more.
Background: In some children with immunodeficiency, Bacille Calmette–Guérin (BCG) vaccination can lead to dissemination and severe infection, including severe intracranial infection, called disseminated BCG disease (BCGosis), which is characterized by high rates of disability and mortality. However, the specific routes by which BCG crosses CNS barriers and the patterns of temporal remodeling of the CNS immune microenvironment during infection have yet to be fully elucidated. Methods: Mice were infected with BCG through tail vein injection to construct an intracerebral mycobacterial infection mouse model, wherein the brain was collected and analyzed using single-cell RNA sequencing. We profiled temporal transcriptomic changes in cell populations, pathways, and cell–cell communication associated with anti-mycobacterial activity and inflammation-induced disturbance of physiological brain activities. Results: After BCG was injected via tail vein, histopathological images and cultured colonies of brain tissue confirmed successful brain infection. Then, whole-brain tissue was dissected for 10× Genomics single-cell sequencing, and we acquired 15 cell types. Dysfunction and inflammatory responses were observed in endothelial and ependymal cells. Infection induced dynamic state transitions in microglia, enabling their differentiation into disease-related and interferon-responsive states. Along with peripheral immune cells, microglia formed temporally structured communication networks that mediated early events such as chemokine recruitment and inflammatory storms, and facilitated late-stage immune checkpoint upregulation. Conclusions: This study proposes BCSFB as a possible pathway of mycobacteria invasion and reveals the temporality of immune response processes in the pathogenesis of intracerebral mycobacterial infection. Full article
(This article belongs to the Special Issue Innate Immune Response and Pathogen Dynamics)
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21 pages, 8378 KB  
Article
Physalin F Promotes AFG3L2-Mediated Degradation of VISA/MAVS to Suppress Innate Immune Response to RNA Virus
by Xiao-Nan Gao, Hong-Bing Shu and Mi Li
Pathogens 2026, 15(1), 74; https://doi.org/10.3390/pathogens15010074 - 9 Jan 2026
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Abstract
Upon RNA virus infection, viral RNA is sensed by the RIG-I-like receptors (RLRs), which signal through the adaptor protein VISA/MAVS to induce an innate antiviral response. How the VISA-mediated innate antiviral response is regulated and whether it can be targeted for drug development [...] Read more.
Upon RNA virus infection, viral RNA is sensed by the RIG-I-like receptors (RLRs), which signal through the adaptor protein VISA/MAVS to induce an innate antiviral response. How the VISA-mediated innate antiviral response is regulated and whether it can be targeted for drug development against diseases caused by RNA virus infection needs to be further investigated. Here we report that physalin F, a natural secosteroid isolated from Physalis angulata L., inhibits innate immune response to RNA virus. Mechanistically, physalin F binds to and promotes the activation of the mitochondrial m-AAA protease AFG3L2, which subsequently mediates the degradation of VISA. Knockdown of AFG3L2 promotes RLR-mediated innate antiviral signaling, whereas physalin F inhibits innate immune response to RNA virus both in cells and mice. Our study discovers physalin F as an inhibitor of VISA-mediated innate antiviral response as well as a candidate compound for the treatment of related diseases. More importantly, our findings suggest that AFG3L2 constitutively mediates degradation of VISA under physiological conditions, which represents a novel negative regulatory mechanism of RLR-mediated innate antiviral response. Full article
(This article belongs to the Special Issue Innate Immune Response and Pathogen Dynamics)
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Review

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20 pages, 360 KB  
Review
Alterations in the Immune Response in Individuals with Latent Tuberculosis Infection
by Anna Starshinova, Adilya Sabirova, Igor Kudryavtsev, Artem Rubinstein, Arthur Aquino, Leonid P. Churilov, Ekaterina Belyaeva, Anastasia Kulpina, Raul A. Sharipov, Ravil K. Tukfatullin, Nikolay Nikolenko and Dmitry Kudlay
Pathogens 2026, 15(1), 14; https://doi.org/10.3390/pathogens15010014 - 22 Dec 2025
Cited by 1 | Viewed by 1356
Abstract
Latent tuberculosis infection (LTBI) represents a biologically active yet clinically asymptomatic stage of Mycobacterium tuberculosis (Mtb) persistence. This condition is characterized by subtle immunometabolic alterations reflecting the host–pathogen equilibrium. Understanding the mechanisms and biomarkers associated with the preclinical phase of LTBI is crucial [...] Read more.
Latent tuberculosis infection (LTBI) represents a biologically active yet clinically asymptomatic stage of Mycobacterium tuberculosis (Mtb) persistence. This condition is characterized by subtle immunometabolic alterations reflecting the host–pathogen equilibrium. Understanding the mechanisms and biomarkers associated with the preclinical phase of LTBI is crucial for preventing progression to active tuberculosis (ATB). Recent advances have identified multiple immunological, transcriptomic, metabolic, and imaging-based approaches that enable stratification of individuals at increased risk of LTBI reactivation. Quantitative assays such as IGRA, multiplex and T-cell activation marker (TAM) tests, as well as interferon-related transcriptional signatures, demonstrate predictive potential when combined with functional assays (MGIA) and metabolic imaging (PET/CT). Experimental primate models faithfully reproduce the spectrum from latency to reactivation, allowing for validation of biomarkers and vaccine or immunomodulatory strategies. The review also highlights the particular challenges of multidrug-resistant LTBI (MDR-LTBI), where standard chemoprophylaxis is less effective and immune control plays a decisive role. The preclinical phase of LTBI constitutes a key point in the TB control cascade. Integrating immunological, transcriptomic, and radiological data into risk-based screening algorithms could substantially improve early detection and targeted prevention. Translating research-derived signatures into clinically applicable, standardized, and cost-effective diagnostic tools requires coordinated international efforts, technological transfer, and policy-level support to reduce TB reactivation and transmission, including MDR-TB. Full article
(This article belongs to the Special Issue Innate Immune Response and Pathogen Dynamics)
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