Tools for noninvasive detection of bacterial pathogens are needed but are not currently available for clinical use. We have previously shown that para-aminobenzoic acid (PABA) rapidly accumulates in a wide range of pathogenic bacteria, motivating the development of related PET radiotracers. In this study, 11C-PABA PET imaging was used to accurately detect and monitor infections due to pyogenic bacteria in multiple clinically relevant animal models. 11C-PABA PET imaging selectively detected infections in muscle, intervertebral discs, and methicillin-resistant Staphylococcus aureus–infected orthopedic implants. In what we believe to be first-in-human studies in healthy participants, 11C-PABA was safe, well-tolerated, and had a favorable biodistribution, with low background activity in the lungs, muscles, and brain. 11C-PABA has the potential for clinical translation to detect and localize a broad range of bacteria.
Alvaro A. Ordonez, Matthew F.L. Parker, Robert J. Miller, Donika Plyku, Camilo A. Ruiz-Bedoya, Elizabeth W. Tucker, Justin M. Luu, Dustin A. Dikeman, Wojciech G. Lesniak, Daniel P. Holt, Robert F. Dannals, Lloyd S. Miller, Steven P. Rowe, David M. Wilson, Sanjay K. Jain
BACKGROUND. Adenoviral (Ad)-vectored vaccines are typically administered via intramuscular injection to humans, incapable of inducing respiratory mucosal immunity. However, aerosol delivery of Ad-vectored vaccines remains poorly characterized and its ability to induce mucosal immunity in humans is unknown. This phase 1b trial was to evaluate the safety and immunogenicity of human serotype-5 Ad-vectored tuberculosis (TB) vaccine (AdHu5Ag85A) delivered to humans via inhaled aerosol or intramuscular injection. METHODS. 31 healthy, previously BCG-vaccinated adults were enrolled. AdHu5Ag85A was administered by single-dose aerosol using Aeroneb® Solo Nebulizer or by intramuscular (IM) injection. The study consisted of the low dose (LD) aerosol, high dose (HD) aerosol and IM groups. The adverse events were assessed at various times post-vaccination. Immunogenicity data were collected from the peripheral blood and bronchoalveolar lavage samples at baseline and select timepoints post-vaccination. RESULTS. The nebulized aerosol droplets were <5.39µm in size. Both LD and HD of AdHu5Ag85A administered by aerosol inhalation and IM injection were safe and well-tolerated. Both aerosol doses, particularly LD, but not IM, vaccination markedly induced airway tissue-resident memory CD4 and CD8 T cells of polyfunctionality. While as expected, IM vaccination induced Ag85A-specific T cell responses in the blood, the LD aerosol vaccination also elicited such T cells in the blood. Furthermore, the LD aerosol vaccination induced persisting transcriptional changes in alveolar macrophages. CONCLUSIONS. Inhaled aerosol delivery of Ad-vectored vaccine is a safe and superior way to elicit respiratory mucosal immunity. This study warrants further development of aerosol vaccine strategies against respiratory pathogens including TB and COVID-19. TRIAL REGISTRATION. This trial is registered with ClinicalTrial.gov, NCT# 02337270. FUNDING. The Canadian Institutes for Health Research and the Natural Sciences and Engineering Research Council of Canada.
Mangalakumari Jeyanathan, Dominik K. Fritz, Sam Afkhami, Emilio Aguirre, Karen J. Howie, Anna Zganiacz, Anna Dvorkin-Gheva, Michael R. Thompson, Richard Silver, Ruth P. Cusack, Brian D. Lichty, Paul M. O'Byrne, Martin Kolb, Maria Fe C. Medina, Myrna B. Dolovich, Imran Satia, Gail M Gauvreau, Zhou Xing, Fiona Smaill
A hallmark of chronic bacterial infections is the long-term persistence of 1 or more pathogen species at the compromised site. Repeated detection of the same bacterial species can suggest that a single strain or lineage is continually present. However, infection with multiple strains of a given species, strain acquisition and loss, and changes in strain relative abundance can occur. Detecting strain-level changes and their effects on disease is challenging because most methods require labor-intensive isolate-by-isolate analyses, and thus, only a few cells from large infecting populations can be examined. Here, we present a population-level method for enumerating and measuring the relative abundance of strains called population multi-locus sequence typing (PopMLST). The method exploits PCR amplification of strain-identifying polymorphic loci, next-generation sequencing to measure allelic variants, and informatic methods to determine whether variants arise from sequencing errors or low-abundance strains. These features enable PopMLST to simultaneously interrogate hundreds of bacterial cells that are cultured en masse from patient samples or are present in DNA directly extracted from clinical specimens without ex vivo culture. This method could be used to detect epidemic or super-infecting strains, facilitate understanding of strain dynamics during chronic infections, and enable studies that link strain changes to clinical outcomes.
Sarah J. Morgan, Samantha L. Durfey, Sumedha Ravishankar, Peter Jorth, Wendy Ni, Duncan T. Skerrett, Moira L. Aitken, Edward F. McKone, Stephen J. Salipante, Matthew C. Radey, Pradeep K. Singh
Acute respiratory distress syndrome (ARDS) is a life-threatening syndrome of respiratory failure and diffuse alveolar damage that results from dysregulated local and systemic immune activation, causing pulmonary vascular, parenchymal and alveolar damage. SARS-CoV-2 infection has become the dominant cause of ARDS worldwide, and emerging evidence implicates neutrophils and their cytotoxic arsenal of effector functions as central drivers of immune-mediated lung injury in COVID-19 ARDS. However, a key outstanding question is whether COVID-19 drives a unique program of neutrophil activation or effector functions that contributes to the severe pathogenesis of this pandemic illness, and whether this unique neutrophil response can be targeted to attenuate disease. Using a combination of high-dimensional single cell analysis and ex vivo functional assays of neutrophils from patients with COVID-19 ARDS compared to non-COVID ARDS (caused by bacterial pneumonia), we identified a functionally distinct landscape of neutrophil activation in COVID-19 ARDS that was intrinsically programmed during SARS-CoV-2 infection. Furthermore, neutrophils in COVID-19 ARDS were functionally primed to produce high amounts of neutrophil extracellular traps (NETs). Surprisingly, this unique pathological program of neutrophil priming escaped conventional therapy with dexamethasone, thereby revealing a promising target for adjunctive immunotherapy in severe COVID-19.
Rachita Panda, Fernanda V.S. Castanheira, Jared M. Schlechte, Bas G.J. Surewaard, Hanjoo Brian Shim, Amanda Z. Zucoloto, Zdenka Slavikova, Bryan G. Yipp, Paul Kubes, Braedon McDonald
Nonphlogistic migration of macrophages contributes to the clearance of pathogens and apoptotic cells: critical steps for the resolution of inflammation and return to homeostasis. Angiotensin-(1-7) [Ang-(1-7)] is an heptapeptide of the Renin-Angiotensin system that acts through Mas receptor (MasR). Ang-(1-7) has recently emerged as a novel pro-resolving mediator, yet Ang-(1-7) resolution mechanisms are not fully determined. Herein, Ang-(1-7) stimulated migration of human and murine monocytes/macrophages in a MasR, CCR2 and MEK/ERK1/2-dependent manner. Pleural injection of Ang-(1-7) promoted nonphlogistic mononuclear cell influx alongside increased levels of CCL2, IL-10 and macrophage polarization towards a regulatory phenotype. Ang-(1-7) induction of CCL2 and mononuclear cell migration was also dependent on MasR and MEK/ERK. Noteworthy, MasR was upregulated during resolution phase of inflammation and their pharmacological inhibition or genetic deficiency impaired mononuclear cell recruitment during self-resolving models of LPS pleurisy and E. coli peritonitis. Inhibition/absence of MasR was associated with reduced CCL2 levels, impaired phagocytosis of bacteria, efferocytosis and delayed resolution of inflammation. In summary, we have uncovered a novel pro-resolving feature of Ang-(1-7), namely the recruitment of mononuclear cells favoring efferocytosis, phagocytosis and resolution of inflammation. Mechanistically, cell migration was dependent on MasR, CCR2 and the MEK/ERK pathway.
Isabella Zaidan, Luciana P. Tavares, Michelle A. Sugimoto, Kátia M. Lima, Graziele L. Negreiros-Lima, Lívia C.R. Teixeira, Thais C. Miranda, Bruno V.S. Valiate, Allysson Cramer, Juliana Priscila Vago, Gabriel H. Campolina-Silva, Jéssica A.M. Souza, Laís C. Grossi, Vanessa Pinho, Maria Jose Campagnole-Santos, Robson A .S. Santos, Mauro M. Teixeira, Izabela Galvão, Lirlândia P. Sousa
Isolation guidelines for severe acute respiratory syndrome–cornavirus-2 (SARS-CoV-2) are largely derived from data collected prior to emergence of the delta variant. We followed a cohort of ambulatory patients with post-vaccination breakthrough SARS-CoV-2 infections with longitudinal collection of nasal swabs for SARS-CoV-2 viral load quantification, whole genome sequencing, and viral culture. All delta variant infections (10/10, 100%) in our cohort were symptomatic, compared with 64% (9/14) of non-delta variant infections. Symptomatic delta variant breakthrough infections were characterized by higher initial viral load, longer duration of virologic shedding by PCR, greater likelihood of replication-competent virus at early stages of infection, and longer duration of culturable virus compared to non-delta variants. The duration of time since vaccination was also correlated with both duration of PCR positivity and duration of detection of replication-competent virus. Nonetheless, no individuals with symptomatic delta variant infections had replication-competent virus by day 10 after symptom onset or 24 hours after resolution of symptoms. These data support current US Center for Disease Control isolation guidelines and reinforce the importance of prompt testing and isolation among symptomatic individuals with delta variant breakthrough infections. Additional data are needed to evaluate these relationships among asymptomatic and more severe delta variant breakthrough infections.
Mark J. Siedner, Julie Boucau, Rebecca F. Gilbert, Rockib Uddin, Jonathan Luu, Sebastien Haneuse, Tammy Vyas, Zahra Reynolds, Surabhi Iyer, Grace C. Chamberlin, Robert H. Goldstein, Crystal M. North, Chana A. Sacks, James Regan, James P. Flynn, Manish C. Choudhary, Jatin M. Vyas, Amy K. Barczak, Jacob E. Lemieux, Jonathan Z. Li
BACKGROUND. While most children experience mild COVID-19, high-risk children with underlying conditions may develop severe disease, requiring interventions. Kinetics of antibodies transferred via COVID-19 convalescent plasma early in disease, have not been characterized. METHODS. In this study (NCT04377672), high-risk children were prospectively enrolled to receive high-titer COVID-19 convalescent plasma (>1:320 anti-spike IgG; Euroimmun). Passive transfer of antibodies and endogenous antibody production were serially evaluated for up to 2 months after transfusion. Commercial and research ELISA assays, virus neutralization assays, high-throughput phage-display assay utilizing a coronavirus epitope library and pharmacokinetic analyses were performed. RESULTS. Fourteen high-risk children (median age 7.5 years) received high-titer COVID-19 convalescent plasma, nine children within five days (range 2-7) of symptom onset and five children within 4 days (range 3-5) after exposure to SARS-CoV-2. There were no serious adverse events related to transfusion. Antibodies to SARS-CoV-2 were transferred from the donor to the recipient, but antibody titers declined by 14-21 days with a 15.1-day t½ for spike protein IgG. Donor plasma had significant neutralization capacity which was transferred to the recipient. However, as early as 30 minutes post-transfusion, recipient plasma had low neutralization capacity. CONCLUSIONS. Convalescent plasma transfused to high-risk children appears to be safe with expected antibody kinetics, regardless of weight or age. However, current use of convalescent plasma in high-risk children achieves low neutralizing capacity.
Oren Gordon, Mary Katherine Brosnan, Steve Yoon, Dawoon Jung, Kirsten Littlefield, Abhinaya Ganesan, Christopher A. Caputo, Maggie Li, William R. Morgenlander, Stephanie N. Henson, Alvaro A. Ordonez, Patricia De Jesus, Elizabeth W. Tucker, Nadine Peart Akindele, Zexu Ma, Jo Wilson, Camilo A. Ruiz-Bedoya, M. Elizabeth M. Younger, Evan M. Bloch, Shmuel Shoham, David Sullivan, Aaron A.R. Tobian, Kenneth R. Cooke, Ben Larman, Jogarao V.S. Gobburu, Arturo Casadevall, Andrew Pekosz, Howard M. Lederman, Sabra L. Klein, Sanjay K. Jain
Identification and analysis of fungal communities commonly rely on internal transcribed spacer (ITS)-based amplicon sequencing. There is no gold standard to infer and classify fungal constituents since methodologies have been adapted from analyses of bacterial communities. To achieve high resolution inference of fungal constituents, we customized a DADA2-based pipeline using a mix of eleven medically relevant fungi. While DADA2 allowed the discrimination of ITS1 sequences differing by single nucleotides, quality filtering, sequencing bias, and database selection were identified as key variables determining the accuracy of sample inference. Due to species-specific differences in sequencing quality, default filtering settings removed most reads that originated from Aspergillus species, Saccharomyces cerevisiae, and Candida glabrata. By fine-tuning the quality filtering process, we achieved an improved representation of the fungal communities. By adapting a wobble nucleotide in the ITS1 forward primer region, we further increased the yield of S. saccharomyces and C. glabrata sequences. Finally, we showed that a BLAST-based algorithm based on the UNITE+INSD or the NCBI NT database achieved a higher reliability in species-level taxonomic annotation than the naïve Bayesian classifier implemented in DADA2. These steps optimized a robust fungal ITS1 sequencing pipeline that, in most instances, enabled species level-assignment of community members.
Thierry Rolling, Bing Zhai, John Frame, Tobias M. Hohl, Ying Taur
Superficial cutaneous Staphylococcus aureus (S. aureus) infection in humans can lead to soft tissue infection, an important cause of morbidity and mortality. IL-17A production by skin TCRγδ+ cells in response to IL-1 and IL-23 produced by epithelial and immune cells is important for restraining S. aureus skin infection. How S. aureus evades this cutaneous innate immune response to establish infection is not clear. Here we show that mechanical injury of mouse skin by tape stripping predisposed mice to superficial skin infection with S. aureus. Topical application of S. aureus to tape-stripped skin caused cutaneous influx of basophils and increased Il4 expression. This basophil-derived IL-4 inhibited cutaneous IL-17A production by TCRγδ+ cells and promoted S. aureus infection of tape-stripped skin. We demonstrate that IL-4 acted on multiple checkpoints that suppress the cutaneous IL-17A response. It reduced Il1 and Il23 expression by keratinocytes, inhibited IL-1+IL-23–driven IL-17A production by TCRγδ+ cells, and impaired IL-17A–driven induction of neutrophil-attracting chemokines by keratinocytes. IL-4 receptor blockade is shown to promote Il17a expression and enhance bacterial clearance in tape-stripped mouse skin exposed to S. aureus, suggesting that it could serve as a therapeutic approach to prevent skin and soft tissue infection.
Juan-Manuel Leyva-Castillo, Mrinmoy Das, Jennifer Kane, Maria Strakosha, Sonal Singh, Daniel Sen Hoi Wong, Alexander R. Horswill, Hajime Karasuyama, Frank Brombacher, Lloyd S. Miller, Raif S. Geha
Severe respiratory coronavirus 2 (SARS-CoV-2) promotes an imbalanced host response which underlies the development and severity of COVID-19. Infections with viruses are known to modulate transposable elements (TEs) which can exert downstream effects by modulating host gene expression, innate immune sensing, or activities encoded by their protein products. We investigated the impact of SARS-CoV-2 infection on TE expression using RNA-seq data from cell lines and from primary patient samples. Using a bioinformatic tool, Telescope, we showed that SARS-CoV-2 infection led to up- or down-regulation of TE transcripts, a subset of which differed from cells infected with SARS, MERS, RSV, HPIV3 or IAV. Differential expression of key retroelements specifically identified distinct virus families such as coronaviridae, with unique retroelement expression subdividing viral species. Analysis of ChIP-seq data shows that TEs differentially expressed in SARS-CoV-2 infection are enriched for binding sites for TFs involved in immune responses and for pioneer transcription factors. In COVID-19 patient samples, there was a significant TE overexpression in bronchoalveolar lavage fluid and downregulation in peripheral blood mononuclear cells. Thus, while the host gene transcriptome is altered by infection with SARS-CoV-2, the retrotranscriptome may contain the most distinctive features of the cellular response to SARS-CoV-2 infection.
Jez L. Marston, Matthew Greenig, Manvendra Singh, Matthew L. Bendall, Rodrigo R.R. Duarte, Cédric Feschotte, Luis P. Iñiguez, Douglas F. Nixon
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