Sasha E. Larsen

Background: Phage nebulization is an attractive administration strategy for pulmonary infections, including tuberculosis (TB). Yet, it requires penetration into and activity in airway linings and secretions.Methods: We assessed activity of a three-phage combination (Fred313cpm-1Δ33, Muddy_HRM_N00157-2 and Fionnbharth_CG_REM-1) against M. tuberculosis in fresh sputum samples from 35 untreated pulmonary TB patients in Cape Town, South Africa. We also evaluated clinical M. tuberculosis isolates for phage susceptibility and assessed patient serum for presence of phage-specific antibodies and neutralizing activity.Results: Sputum incubation for 24 hours with single phage and phage combination significantly increased time to culture positivity (TTP) compared to the control. For the combination at approximately 108 PFU/mL, the median proportional TTP increase was 4·0% (IQR 0·1–8·2%; p=0·003). Incubation with rifampicin (0·1μg/mL) had no effect. Most clinical isolates were susceptible to all phages (23/34, 68%) and 31/34 (91%) were susceptible to two of the three phages. We found phage-specific IgG in serum samples of a subset of TB patients but no phage-neutralizing effect was observed.Interpretation: Individual phages and the three-phage combination reduced viable mycobacterial load in sputum from pulmonary TB patients. The three-phage combination covered most clinical isolates. No neutralising antibodies were detected. These findings support testing of nebulized phage treatment for pulmonary tuberculosis in clinical trials.

Phage therapy offers promise to combat antimicrobial resistance, including drug-resistant tuberculosis (TB). Understanding phage activity against Mycobacterium tuberculosis (Mtb) adapted to physiologic microenvironments, such as hypoxia and acidity in granulomas, is essential since these conditions induce non-replicating states. We evaluated a phage combination against Mtb under hypoxic, acidic (pH 5.5), and stationary-phase conditions in vitro . In planktonic Mtb growth conditions, phage concentrations increased around day seven followed by a significant reduction in Mtb H37Rv load, which was maintained over 31 days. Phage addition prevented regrowth was observed with rifampicin and isoniazid alone. Individual phage stability was differentially affected by acidic media conditions, resulting in variability of antimycobacterial activity. In hypoxic conditions and stationary growth experiments, phage titers remained stable over time with no change in mycobacterial load compared to controls. Model-based predictions were able to adequately capture phage-mycobacterial interactions with and without rifampicin. The lack of antimycobacterial activity in assays with non-replicating mycobacteria suggest that phages need actively replicating mycobacteria to exert lytic activity. Stable phage concentrations in assays with non-replicating mycobacteria suggests low grade phage replication in these conditions. Established models can support future study design through simulations of different experimental scenarios.

COVID-19 continues causing substantial mortality despite existing FDA-approved COVID-19 vaccines. An effective COVID-19 vaccine providing durable immunity with minimal reactogenicity is needed. CVXGA1, a PIV5-based intranasal COVID-19 vaccine expressing the Spike (S) protein of SARS-CoV-2, was evaluated in this phase 1 study in adults and teens. CVXGA1 was well tolerated without serious adverse events (AEs) or fever reported. Solicited local and systemic AEs were mostly mild. CVXGA1 elicited S-specific serum and mucosal antibodies and CD8 ⁺ cytotoxic T lymphocyte responses in all groups. Significantly lower rates of symptomatic COVID-19 infection were reported in groups receiving high-dose CVXGA1 (HD) compared to that in the group receiving low-dose CVXGA1 (LD) during the SARS-CoV-2 delta and omicron waves. The data indicate that CVXGA1 is a potentially effective intranasal COVID-19 vaccine that is immunogenic with minimal reactogenicity.

In contrast to natural nontuberculous mycobacterial (NTM) exposures or infections whose pathology is founded on a slow-replicating organism, the aerosol infection in a mouse model can cause an elevated proliferation of bacterial growth in the lungs. Chronic aerosol and systemic infections can be treated with anti-mycobacterial drugs, which could also reflect a prior exposure, but these procedures are lengthy and less representative of natural exposures. The goal of this protocol is to develop a less invasive mouse model of NTM exposure-like conditions that are more translational. Here, we describe a method to intradermally challenge preclinical mice through ear tissue using Mycobacterium avium (M. avium) to mimic an exposure and enable immune responses to the bacteria without obvious disease. In this article, we describe the intradermal ear injection method and confirm the presence of sustained and contained mycobacterial infection, which provides further opportunities to interrogate the immune responses in this in vivo model.

The global tuberculosis (TB) epidemic affected 10 million people and caused 1.3 million deaths in 2022 alone. Multidrug-resistant TB is successfully treated in less than 60% of cases by long, expensive, and aggressive treatments. Mycobacteriophages, viruses that can infect bacteria such as Mycobacterium tuberculosis —the species responsible for TB—have the potential to redefine TB prevention and treatments. However, the development of phage-based products necessitates the assessment of numerous parameters, including virulence and adsorption, to ensure their performance and quality. In this work, we characterized the virulence of three different mycobacteriophages (Fionnbharth, Muddy, and D29), alone and as cocktails, against a TB model host ( Mycobacterium smegmatis ) under planktonic and early-stage biofilm growth conditions. Phage D29 and cocktails containing D29 had the highest virulence under all conditions. Interestingly, phages Fionnbharth and Muddy and their combination showed higher virulence against early-stage biofilm than against the planktonic phenotype. Adsorption assays indicated that all three phages had lower adsorption efficiencies on the early-stage biofilm phenotype than on the planktonic one, suggesting a reduced availability of receptors in the former. Given that, despite these lower adsorption efficiencies, the virulence of the phages and phage cocktails was either unchanged or higher against the early-stage biofilm, this phenotype must display properties that are favorable to other steps of the infection process. These results inform us on the dynamics of mycobacteriophage infections, both alone and in cocktail formulations, under different host growth conditions, serving as a basis for the development of phage products targeting mycobacteria biofilms. IMPORTANCE: This study provides a systematic investigation of the virulence of three mycobacteriophages, Fionnbharth, Muddy, and D29, and their combinations as cocktails against Mycobacterium smegmatis . We also included considerations on the hydrodynamic conditions (shaking and not shaking) and host phenotype (planktonic and early-onset biofilm cultures) during the infection process and adsorption of the phage to the host. We showed that virulence was strongly affected by phenotype and that higher virulence shown against the early-onset biofilm phenotype was not linked to faster adsorption to the host. We also showed that phage D29 and cocktails containing this phage had the highest virulence. These results are important as they provide a framework for a better evaluation and development of phage-based treatment against mycobacterial infections.

Tuberculosis (TB) is again the deadliest infectious disease globally, and more efficacious vaccines are needed to reduce this mortality. Successful subunit TB vaccines need antigens and adjuvants that are immunogenic, inexpensive, and accessible. Here we evaluated the potential of synthetically produced Monophosphoryl lipid A (SyMLP), a TLR4-agonist, formulated in an oil-in-water emulsion (EmT4™) in combination with selected fusion proteins, to drive an effective vaccine-mediated immunogenic response in C57BL/6 mice against Mycobacterium tuberculosis (M.tb) HN878 and H37Rv challenge. We first observed that EmT4™ enhances activation of C57BL/6 bone-marrow derived macrophages and dendritic cells measured by CD40, CD86, and MHCII expression by flow cytometry. EmT4™ did not induce safety signals in a scaled tolerability study. In immunogenicity studies, mice immunized 3 times 3 weeks apart with ID93 antigen + EmT4™ produced a significantly higher magnitude of circulating proinflammatory cytokines and ID93-specific immunoglobulin G (IgG) antibodies pre- and post-challenge with M.tb than saline control animals. Ex vivo ID93 restimulated splenocytes and lung cells elicited significant polyfunctional CD4+ T-helper 1 responses. Importantly, ID93 + EmT4™ immunizations significantly reduced bacterial burden in C57BL/6 mice 4 weeks post-challenge. Interestingly, EmT4™ paired with a next generation protein fusion ID91 also afforded prophylactic protection against M.tb HN878 challenge in both young (6 to 8 wk) and aged (20 mo) immunocompromised Beige mice. These protection and immunogenicity findings suggest that synthetically derived EmT4™ adjuvant is not only suitable to help backfill the preclinical TB vaccine candidate pipeline but is also suitable for the needs of the global community.

Background: Maternal immunization provides vaccine-specific immunity to the infant via breast milk. Multiple studies have reported the presence of SARS-CoV-2 antibodies in human breast milk (HBM) from infected and/or vaccinated women. However, there is limited information on the analytical performance, consistency, and quality of the methods used. Standardized and rigorous assays are needed to meet clinical study endpoints and for comparisons across studies. Methods: We optimized high-throughput multiplex immunoassays for quantification of SARS-CoV-2 immunoglobulin (Ig)G and IgA in HBM and determined antibody levels in HBM samples from 236 SARS-CoV-2 vaccinated (infected and non-infected) and 50 pre-pandemic (unexposed) lactating women. Additionally, SARS-CoV-2 neutralizing activity was examined in a subset of 75 SARS-CoV-2 HBM from vaccinated (infected and non-infected) women using live virus focus reduction neutralization and pseudovirus assays. Concordance between SARS-CoV-2 binding and live virus neutralization outcomes was examined. Results: The multiplex SARS-CoV-2 assays had adequate analytical sensitivity, repeatability, precision, and assay linearity and were reliable for quantification of IgG and IgA in HBM. Positivity thresholds for Spike- and Nucleocapsid-specific IgG and IgA were established; IgG discriminated positive/negative SARS-CoV-2-immune HBM with high sensitivity and specificity, while IgA reactivity overlapped. A strong correlation was observed between live SARS-CoV-2 and pseudovirus neutralization activity. HBM Spike IgA and neutralization titers were highly correlated. Conclusions: SARS-CoV-2 binding and neutralizing antibody activity in HBM was determined using standardized and rigorous assays. HBM positivity cutoff values for SARS-CoV-2 vaccination and infection were established. The methods and approach described here could be applied to other pathogens and mucosal secretions.

It is unclear whether human progression to active tuberculosis disease (TB) risk signatures are viable endpoint criteria for evaluations of treatments in development. TB is the deadliest infectious disease globally and more efficacious vaccines are needed to reduce this mortality. However, the immune correlates of protection for either preventing infection with Mycobacterium tuberculosis or preventing TB disease have yet to be completely defined, making the advancement of candidate vaccines through the pipeline slow, costly, and fraught with risk. Human-derived correlate of risk (COR) gene signatures, which identify an individual’s risk of progressing to active TB disease, provide an opportunity for evaluating new therapies for TB with clear and defined endpoints. Though prospective clinical trials with longitudinal sampling are prohibitively expensive, the characterization of COR gene signatures is practical with preclinical models. Using a 3Rs (replacement, reduction, and refinement) approach we reanalyzed heterogeneous publicly available transcriptional data sets to determine whether a specific set of COR signatures are viable endpoints in the preclinical pipeline. We selected RISK6, Sweeney3, and BATF2 human-derived blood-based RNA biosignatures because they require relatively few genes and have been carefully evaluated across several clinical cohorts. These data suggest that in certain experimental designs and in several tissue types, human COR signatures correlate with disease progression as measured by the bacterial burden in the preclinical TB model pipeline. We observed the best performance when the model most closely reflected human infection or disease conditions. Human-derived COR signatures offer an opportunity for high-throughput preclinical endpoint criteria of vaccine and drug therapy evaluations. IMPORTANCE: Understanding the strengths or limitations of back-translating human-derived correlate of risk (COR) RNA signatures into the preclinical pipeline may help streamline down-selection of therapeutic vaccine and drug candidates and better align preclinical models with proposed clinical trial efficacy endpoints.

The global tuberculosis (TB) epidemic affected 10 million people and caused 1.3 million deaths in 2022 alone. Multidrug-resistant TB is successfully treated in less than 60% of cases by long, expensive and aggressive treatments. Mycobacteriophages, viruses that can infect bacteria such as Mycobacterium tuberculosis —the species responsible for TB, have the potential to redefine TB prevention and treatments. However, the development of phage-based products necessitates the assessment of numerous parameters, including virulence and adsorption, to ensure their performance and quality. In this work, we characterized the virulence of three different mycobacteriophages (Fionnbharth, Muddy and D29), alone and as cocktails, against a TB model host ( Mycobacterium smegmatis ) under planktonic and early-stage biofilm growth conditions. Phage D29 and cocktails containing D29 had the highest virulence under all conditions. Interestingly, phages Fionnbharth and Muddy and their combination showed higher virulence against early-stage biofilm than against the planktonic phenotype. Adsorption assays indicated that all three phages had lower adsorption efficiencies on the early-stage biofilm phenotype than on the planktonic one, suggesting a reduced availability of receptors in the former. Given that, despite these lower adsorption efficiencies, the virulence of the phages and phage cocktails was either unchanged or higher against the early-stage biofilm, this phenotype must display properties that are favorable to other steps of the infection process. These results inform us on the dynamics of mycobacteriophage infections, alone and in cocktail formulations, under different host growth conditions, and serve as a basis for the development of phage products targeting mycobacteria biofilms.

It is not clear whether human progression to active tuberculosis disease (TB) risk signatures are viable endpoint criteria for evaluations of treatments in clinical or preclinical development. TB is the deadliest infectious disease globally and more efficacious vaccines are needed to reduce this mortality. However, the immune correlates of protection for either preventing infection with Mycobacterium tuberculosis or preventing TB disease have yet to be completely defined, making the advancement of candidate vaccines through the pipeline slow, costly, and fraught with risk. Human-derived correlate of risk (COR) gene signatures, which identify an individual’s risk to progressing to active TB disease, provide an opportunity for evaluating new therapies for TB with clear and defined endpoints. Though prospective clinical trials with longitudinal sampling are prohibitively expensive, characterization of COR gene signatures is practical with preclinical models. Using a 3Rs (Replacement, Reduction and Refinement) approach we reanalyzed heterogeneous publicly available transcriptional datasets to determine whether a specific set of COR signatures are viable endpoints in the preclinical pipeline. We selected RISK6, Sweeney3 and BATF2 human-derived blood-based RNA biosignatures because they require relatively few genes to assign a score and have been carefully evaluated across several clinical cohorts. Excitingly, these data provide proof-of-concept that human COR signatures seem to have high fidelity across several tissue types in the preclinical TB model pipeline and show best performance when the model most closely reflected human infection or disease conditions. Human-derived COR signatures offer an opportunity for high-throughput preclinical endpoint criteria of vaccine and drug therapy evaluations. One Sentence Summary: Human-derived biosignatures of tuberculosis disease progression were evaluated for their predictive fidelity across preclinical species and derived tissues using available public data sets.