Biology subjects

Nutter, N. A.

Publications and source records attributed to Nutter, N. A..

3 recordsLinked to original sources

bioRxiv2026

Influenza A Virus Coinfection Alters Streptococcus pneumoniae Gene Expression during Upper Respiratory Tract Colonization

Streptococcus pneumoniae (Spn) asymptomatically colonizes the upper respiratory tract (URT), a niche from which it can transmit to another host or cause invasive disease in the same host. The in vivo transcriptional adaptations that Spn undergoes during nasopharyngeal colonization, particularly during influenza A virus (IAV) coinfection, are poorly understood. Here, we leveraged an established infant mouse model of colonization, shedding, and transmission to perform genome-wide transcriptomic profiling of Spn during mono- and during IAV coinfection. Compared with broth-grown controls, pneumococci isolated from the URT exhibited distinct transcriptional programs, with over 200 genes differentially expressed across time points. Genes involved in carbohydrate uptake and metabolism, glycan degradation, amino sugar and nucleotide sugar metabolism, and amino acid biosynthesis were consistently enriched during colonization, highlighting metabolic adaptation to the nasopharyngeal niche. In contrast, IAV coinfection induced a markedly distinct transcriptional signature, including upregulation of branched-chain amino acid biosynthesis, bacteriocin production, and phosphate acquisition systems. Notably, the pilus islet-1 locus was upregulated during Spn-IAV coinfection. Functional studies demonstrated that while the pilus was dispensable for colonization under mono- and coinfection conditions, it promoted high-shedding events and enhanced inflammatory responses during IAV coinfection. However, reduced inflammation and reduced high shedding events from pups inoculated with a pilus-deficient mutant did not alter transmission frequency in the infant mouse model. Collectively, our findings define the in vivo transcriptional landscape of Spn during URT colonization and reveal distinct bacterial adaptations during viral coinfection, providing insight into mechanisms that influence pneumococcal persistence, inflammation, and transmission.

microbiology↗

bioRxiv2026

DksA-Dependent Stringent Stress Response Drives Virulence and Gastrointestinal Persistence of Klebsiella pneumoniae

Successful gastrointestinal colonization (GI) by bacterial pathogens requires adaptation to nutrient competition and host-derived stresses in the gut, with adaptation via the bacterial stringent stress response playing a critical role. Epidemiological data suggest that the GI tract serves as a reservoir from where K. pneumoniae can spread and cause invasive disease or transmit to another host. DksA is a conserved stringent response transcriptional regulator that was identified in an in vivo transposon mutagenesis screen as an important K. pneumoniae gut determinant. However, its role in K. pneumoniae pathogenesis and gut colonization remains uncharacterized. Here, we demonstrate that DksA is required for survival against membrane-targeting antibiotics, consistent with a role in cell envelope stress tolerance. In addition, DksA positively regulates capsule biosynthesis gene expression and hypermucoviscosity and is essential for robust biofilm formation. Using a murine model, we show that DksA functions as a determinant of GI colonization independently of the resident gut microbiota. Furthermore, we demonstrate that DksA is important for environmental survival and transmission by regulating RpoS, thereby providing a mechanistic link between the stringent stress response, environmental survival, and subsequent transmission. Together, these findings establish DksA as a central integrator of the stringent response, coordinating membrane stress resistance, virulence traits, and gastrointestinal colonization in K. pneumoniae. ImportanceK. pneumoniae, a pathobiont, is responsible for multidrug-resistant infections and poses a major threat in hospital settings as well as community-acquired invasive infections. The bacterium tightly coordinates its virulence-associated traits to adapt to diverse environmental conditions and survive; however, the regulatory mechanisms remain poorly understood. In this study, we demonstrated that the conserved stringent response regulator DksA contributes to bacterial membrane stability, thereby affecting antibiotic resistance, inherent virulence, and persistence traits of K. pneumoniae. Additionally, DksA was identified as required for gut colonization, environmental survival through dysregulation of RpoS, and transmission to a naive host. These results enhance our overall understanding of the K. pneumoniae stringent response and will provide new avenues for controlling K. pneumoniae infections.

microbiology↗

bioRxiv2025

Divergent roles for complement components C3 and C4 in controlling Klebsiella pneumoniae gut colonization and systemic dissemination

Klebsiella pneumoniae is an escalating public health threat driven by the emergence of antibiotic-resistant and hyper-encapsulated strains that spread systemically from the gut. The immune defenses preventing gut colonization and dissemination remain poorly defined. Herein, we uncover distinct and context-dependent roles for complement proteins C3 and C4 in host defense following K. pneumoniae infection. Following gut colonization, C3 and C4 levels rise significantly. In addition to inducing alternative pathway-mediated C3b deposition on K. pneumoniae grown under gut-relevant conditions, C3 is critical for recruiting myeloid cells to the gut, promoting local opsonophagocytosis, and preventing lethal systemic spread. Depletion of systemic C3 reveals mucosal-derived C3 controls K. pneumoniae GI colonization, whereas systemic C3 is essential for limiting fatal dissemination. In contrast, C4 is dispensable for controlling GI colonization, dissemination, and myeloid recruitment under conditions of natural acquisition. However, C4 becomes critical for controlling GI burden and systemic disease following antibiotic-induced dysbiosis and supercolonization with antibiotic-resistant K. pneumoniae. Notably, mice deficient in CD21/35--a receptor for cleaved C3 and C4 fragments important for B cell activation and antigen retention--exhibit a defect similar to C4-/- mice, with significantly increased GI burden under antibiotic-induced supercolonization, suggesting distinct complement-dependent pathways are involved in mucosal protection. Collectively, these findings reveal a dual-layered immune strategy: C3-driven opsonophagocytosis is critical for controlling colonization and dissemination under baseline conditions, while C4 and CD21/35 become indispensable following antibiotic-induced supercolonization. This work advances our understanding of complement-dependent mucosal immune protection and identifies potential targets for preventing gut-to-bloodstream transition of this pathogen.

immunology↗