Coinfections in the lung: How viral infection creates a favorable environment for bacterial and fungal infections

Immunotherapy with nebulized pattern recognition receptor agonists restores severe immune paralysis and improves outcomes in mice with influenza-associated pulmonary aspergillosis

Influenza-associated pulmonary aspergillosis (IAPA) is a potentially deadly superinfection in patients with influenza pneumonia, especially those with severe disease, underlying immunosuppression, corticosteroid therapy, or requiring intensive care support. Given the high mortality of IAPA, adjunct immunomodulatory strategies remain a critical unmet need. Previously, the desensitization of pattern recognition pathways has been described as a hallmark of IAPA pathogenesis and a predictor of mortality in IAPA patients. Therefore, we studied the impact of nebulized Toll-like receptor 2/6/9 agonists Pam2 CSK4 (Pam2) and CpG oligodeoxynucleotides (ODNs) on infection outcomes and pulmonary immunopathology in a corticosteroid-immunosuppressed murine IAPA model. Mice with IAPA receiving mock therapy showed rapidly progressing disease and a paralyzed immune response to secondary Aspergillus fumigatus infection. Nebulized Pam2ODN was well tolerated and significantly prolonged event-free survival. Specifically, dual-dose Pam2ODN therapy before and after A. fumigatus infection led to 81% survival and full recovery of all survivors. Additionally, transcriptional analysis of lung tissue homogenates revealed induction of pattern recognition receptor signaling and several key effector cytokine pathways after Pam2ODN therapy. Moreover, transcriptional and flow cytometric analyses suggested increased frequencies of macrophages, natural killer cells, and T cells in the lungs of Pam2ODN-treated mice. Collectively, immunomodulatory treatment with nebulized Pam2ODN strongly improved morbidity and mortality outcomes and alleviated paralyzed antifungal immunity in an otherwise lethal IAPA model. These findings suggest that Pam2ODN might be a promising candidate for locally delivered immunomodulatory therapy to improve outcomes of virus-associated mold infections such as IAPA.IMPORTANCEThe COVID-19 pandemic has highlighted the significant healthcare burden, morbidity, and mortality caused by secondary fungal pneumonias. Given the heightened prevalence of severe viral pneumonias, such as influenza, and poor outcomes of secondary mold pneumonias, adjunct immunotherapies are needed to prevent and treat secondary infections. We herein demonstrate severely paralyzed immunity to secondary Aspergillus fumigatus infection in a corticosteroid-immunosuppressed mouse model of influenza-associated pulmonary aspergillosis (IAPA), partially due to dysregulated pathogen-sensing pathways. To overcome immune paralysis and IAPA progression, we used a dyad of nebulized immunomodulators (Toll-like receptor agonists). Nebulized immunotherapy significantly improved morbidity and mortality compared to mock therapy, increased frequencies of mature mononuclear phagocytes and natural killer cells in the lung, and stimulated antimicrobial signaling. Collectively, this proof-of-concept study demonstrates the feasibility and efficacy of locally delivered immunomodulatory therapy to alleviate virus-induced immune dysregulation in the lung and improve outcomes of post-viral mold pneumonias such as IAPA.

Recent developments in Aspergillus fumigatus research: diversity, drugs, and disease

SUMMARYAdvances in modern medical therapies for many previously intractable human diseases have improved patient outcomes. However, successful disease treatment outcomes are often prevented due to invasive fungal infections caused by the environmental mold Aspergillus fumigatus. As contemporary antifungal therapies have not experienced the same robust advances as other medical therapies, defining mechanisms of A. fumigatus disease initiation and progression remains a critical research priority. To this end, the World Health Organization recently identified A. fumigatus as a research priority human fungal pathogen and the Centers for Disease Control has highlighted the emergence of triazole-resistant A. fumigatus isolates. The expansion in the diversity of host populations susceptible to aspergillosis and the complex and dynamic A. fumigatus genotypic and phenotypic diversity call for a reinvigorated assessment of aspergillosis pathobiological and drug-susceptibility mechanisms. Here, we summarize recent advancements in the field and discuss challenges in our understanding of A. fumigatus heterogeneity and its pathogenesis in diverse host populations.

Nuclear receptor 4A1 is critical for neutrophil-dependent pulmonary immunity to Klebsiella pneumoniae infection

Introduction

Bacterial pneumonia is a burdensome, costly disease and increasingly challenging to treat due to antibiotic resistance. Complex host-pathogen interactions regulate protective immunity. Neutrophils play a central role in pulmonary bacterial immunity, and mechanistic understanding of neutrophil functions in bacterial pneumonia has potential clinical and fundamental application. Nuclear receptor 4a1 (Nr4a1), a member of the nuclear orphan receptor family, has been described to regulate inflammation and immune development in a cell type-specific manner, but its role in pulmonary host defense is not well understood.

Methods

Wild-type (WT) and Nr4a1-/- mice, as well as bone marrow chimeric and Gr-1+ antibody depleted mice, were infected with Klebsiella pneumoniae and assessed for bacterial burden in the lung and spleen, gene transcription, protein levels, histology and cellular abundance by flow cytometry in the lung. WT and Nr4a1-/- neutrophils were exposed to live Klebsiella pneumoniae to quantify bacterial killing, as well as bulk RNA sequencing to assess transcriptomic differences.

Results

Nr4a1-deficient mice are highly susceptible to Klebsiella pneumoniae pneumonia, which was mediated by Nr4a1 expression in immune cells. Gr-1+ antibody depletion ameliorated the Nr4a1-dependent phenotype. Ex vivo, Nr4a1-deficient neutrophils had impaired bactericidal capacity, and transcriptomic analysis identified an Nr4a1-dependent host defense program in neutrophils.

Discussion

Neutrophil Nr4a1 expression is critical for defense against K. pneumoniae infection by regulating the neutrophil transcriptome. These findings suggest targeting Nr4a1 signaling pathways in neutrophils may be useful for bacterial pneumonia treatment.

Developing a Coccidioides posadasii and SARS-CoV-2 Co-infection Model in the K18-hACE2 Transgenic Mouse

BACKGROUND

Early reports showed that patients with COVID-19 had recrudescence of previously resolved coccidioidomycosis (Valley fever, VF), and there were indications that coinfection had more severe outcomes. We therefore investigated serial infection of Coccidioides posadasii and SARS-CoV-2 in a K18-hACE2 mouse model to assess disease outcomes.

METHODS

In our model, we challenged K18-hACE2 mice sequentially with a sub-lethal dose of SARS-CoV-2 and 24 hours later with low virulence strain of Coccidioides posadasii, and vice versa, compared to mice that only received a single infection challenge. We performed survival and pathogenesis mouse studies as well as looked at the systemic immune response differences between treatment groups.

RESULTS

Here we show that co-infected groups have a more severe disease progression as well as a decrease in survival. Importantly, results differ depending on the SARS-CoV-2 variant (WA-1, Delta, or Omicron) and infection timing (SARS-CoV-2 first, C. posadasii second or vice versa). We find that groups that are infected with the virus first had a decrease in survival, increased morbidity and weight loss, increased fungal and viral burdens, differences in immune responses, and the amount and size of fungal spherules. We also find that groups coinfected with C. posadasii first have a decrease fungal burden and inflammatory responses.

CONCLUSIONS

This is the first in vivo model investigation of a coinfection of SARS-CoV-2 and Coccidioides. Because of the potential for increased severity of disease in a coinfection, we suggest populations that live in areas of high coccidioidomycosis endemicity may experience higher incidence of complicated disease progression with COVID-19.

Determinant of 30-Day Mortality of Pulmonary Legionellosis: Do Coinfections Matter?

We retrospectively reviewed 64 cases of cancer with pulmonary legionellosis (Legionella pneumophila in 73%). Nearly all patients received Legionella-active antibiotics, yet 30-day mortality was 23%. Independent predictors of 30-day mortality were hyponatremia, bilateral lung involvement, and Sequential Organ Failure Assessment score ≥5. Lung coinfections were common (31%) but did not significantly increase mortality.

Integrating genetic and immune factors to uncover pathogenetic mechanisms of viral-associated pulmonary aspergillosis

Invasive pulmonary aspergillosis is a severe fungal infection primarily affecting immunocompromised patients. Individuals with severe viral infections have recently been identified as vulnerable to developing invasive fungal infections. Both influenza-associated pulmonary aspergillosis (IAPA) and COVID-19-associated pulmonary aspergillosis (CAPA) are linked to high mortality rates, emphasizing the urgent need for an improved understanding of disease pathogenesis to unveil new molecular targets with diagnostic and therapeutic potential. The recent establishment of animal models replicating the co-infection context has offered crucial insights into the mechanisms that underlie susceptibility to disease. However, the development and progression of human viral-fungal co-infections exhibit a significant degree of interindividual variability, even among patients with similar clinical conditions. This observation implies a significant role for host genetics, but information regarding the genetic basis for viral-fungal co-infections is currently limited. In this review, we discuss how genetic factors known to affect either antiviral or antifungal immunity could potentially reveal pathogenetic mechanisms that predispose to IAPA or CAPA and influence the overall disease course. These insights are anticipated to foster further research in both pre-clinical models and human patients, aiming to elucidate the complex pathophysiology of viral-associated pulmonary aspergillosis and contributing to the identification of new diagnostic and therapeutic targets to improve the management of these co-infections.

Invasive pulmonary aspergillosis following human metapneumovirus infection in solid-organ transplant recipients: Another virus to add to the list

There is increasing recognition that respiratory viral infections such as influenza, respiratory syncytial virus, parainfluenza virus, adenovirus, and SARS-CoV-2 can promote the development of invasive fungal pulmonary coinfections, particularly invasive aspergillosis, both in immunocompetent and immunocompromised patients. To date, there are no case reports exploring the role of human metapneumovirus as a risk factor for fungal coinfection. Below, we describe the case of a 63-year-old woman who received a kidney transplant and developed invasive pulmonary aspergillosis after a human metapneumovirus infection and discuss the possible phenomena that could favor this association.

Fungal pathogens and COVID-19

COVID-19 pandemic highlighted the complications of secondary fungal infections that occurred globally in severe cases of coronavirus disease managed in the intensive care units. Furthermore, varied underlying host factors, such as preexisting immunosuppression, the use of immunomodulatory agents, and invasive procedures predisposing lung tissues to fungal colonization and proliferation, caused increased susceptibility to fungal infections in COVID-19 patient populations. These invasive fungal infections directly impact the overall length of hospitalization and mortality. The most commonly reported fungal infections in patients with COVID-19 include aspergillosis, invasive candidiasis, and mucormycosis. An overall worldwide increase in the prevalence of candidiasis and aspergillosis was observed in COVID-19 patients , whereas outbreaks of mucormycosis were mainly recorded from India. Diagnostic challenges and limited antifungal treatment options make secondary fungal infections among COVID-19 patients more burdensome, which results in improper management and increased mortality.

Co-infection of mice with SARS-CoV-2 and Mycobacterium tuberculosis limits early viral replication but does not affect mycobacterial loads

Viral co-infections have been implicated in worsening tuberculosis (TB) and during the COVID-19 pandemic, the global rate of TB-related deaths has increased for the first time in over a decade. We and others have previously shown that a resolved prior or concurrent influenza A virus infection in Mycobacterium tuberculosis (Mtb)-infected mice resulted in increased pulmonary bacterial burden, partly through type I interferon (IFN-I)-dependent mechanisms. Here we investigated whether SARS-CoV-2 (SCV2) co-infection could also negatively affect bacterial control of Mtb. Importantly, we found that K18-hACE2 transgenic mice infected with SCV2 one month before, or months after aerosol Mtb exposure did not display exacerbated Mtb infection-associated pathology, weight loss, nor did they have increased pulmonary bacterial loads. However, pre-existing Mtb infection at the time of exposure to the ancestral SCV2 strain in infected K18-hACE2 transgenic mice or the beta variant (B.1.351) in WT C57Bl/6 mice significantly limited early SCV2 replication in the lung. Mtb-driven protection against SCV2 increased with higher bacterial doses and did not require IFN-I, TLR2 or TLR9 signaling. These data suggest that SCV2 co-infection does not exacerbate Mtb infection in mice, but rather the inflammatory response generated by Mtb infection in the lungs at the time of SCV2 exposure restricts viral replication.