Integrated Signaling Pathways Mediate Bordetella Immunomodulation, Persistence, and Transmission

Perspectives on the future of host-microbe biology from the Council on Microbial Sciences of the American Society for Microbiology

Host-microbe biology (HMB) stands on the cusp of redefinition, challenging conventional paradigms to instead embrace a more holistic understanding of the microbial sciences. The American Society for Microbiology (ASM) Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the future of the HMB field and innovations needed to advance the microbial sciences. The retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their profound influence on humans, animals, and environmental health, as well as the need to broaden perspectives to fully embrace the complexity of these interactions. To advance HMB research, microbial scientists would benefit from enhancing interdisciplinary and transdisciplinary research to utilize expertise in diverse fields, integrate different disciplines, and promote equity and accessibility within HMB. Data integration will be pivotal in shaping the future of HMB research by bringing together varied scientific perspectives, new and innovative techniques, and 'omics approaches. ASM can empower under-resourced groups with the goal of ensuring that the benefits of cutting-edge research reach every corner of the scientific community. Thus, ASM will be poised to steer HMB toward a future that champions inclusivity, innovation, and accessible scientific progress.

Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection

Bordetella spp. are respiratory pathogens equipped with immune evasion mechanisms. We previously characterized a Bordetella bronchiseptica mutant (RB50ΔbtrS) that fails to suppress host responses, leading to rapid clearance and long-lasting immunity against reinfection. This work revealed eosinophils as an exclusive requirement for RB50ΔbtrS clearance. We also show that RB50ΔbtrS promotes eosinophil-mediated B/T cell recruitment and inducible bronchus-associated lymphoid tissue (iBALT) formation, with eosinophils being present throughout iBALT for Th17 and immunoglobulin A (IgA) responses. Finally, we provide evidence that XCL1 is critical for iBALT formation but not maintenance, proposing a novel role for eosinophils as facilitators of adaptive immunity against B. bronchiseptica. RB50ΔbtrS being incapable of suppressing eosinophil effector functions illuminates active, bacterial targeting of eosinophils to achieve successful persistence and reinfection. Overall, our discoveries contribute to understanding cellular mechanisms for use in future vaccines and therapies against Bordetella spp. and extension to other mucosal pathogens.

Bordetella spp. utilize the type 3 secretion system to manipulate the VIP/VPAC2 signaling and promote colonization and persistence of the three classical Bordetella in the lower respiratory tract

Introduction

Bordetella are respiratory pathogens comprised of three classical Bordetella species: B. pertussis, B. parapertussis, and B. bronchiseptica. With recent surges in Bordetella spp. cases and antibiotics becoming less effective to combat infectious diseases, there is an imperative need for novel antimicrobial therapies. Our goal is to investigate the possible targets of host immunomodulatory mechanisms that can be exploited to promote clearance of Bordetella spp. infections. Vasoactive intestinal peptide (VIP) is a neuropeptide that promotes Th2 anti-inflammatory responses through VPAC1 and VPAC2 receptor binding and activation of downstream signaling cascades.

Methods

We used classical growth in vitro assays to evaluate the effects of VIP on Bordetella spp. growth and survival. Using the three classical Bordetella spp. in combination with different mouse strains we were able to evaluate the role of VIP/VPAC2 signaling in the infectious dose 50 and infection dynamics. Finally using the B. bronchiseptica murine model we determine the suitability of VPAC2 antagonists as possible therapy for Bordetella spp. infections.

Results

Under the hypothesis that inhibition of VIP/VPAC2 signaling would promote clearance, we found that VPAC2-/- mice, lacking a functional VIP/VPAC2 axis, hinder the ability of the bacteria to colonize the lungs, resulting in decreased bacterial burden by all three classical Bordetella species. Moreover, treatment with VPAC2 antagonists decrease lung pathology, suggesting its potential use to prevent lung damage and dysfunction caused by infection. Our results indicate that the ability of Bordetella spp. to manipulate VIP/VPAC signaling pathway appears to be mediated by the type 3 secretion system (T3SS), suggesting that this might serve as a therapeutical target for other gram-negative bacteria.

Conclusion

Taken together, our findings uncover a novel mechanism of bacteria-host crosstalk that could provide a target for the future treatment for whooping cough as well as other infectious diseases caused primarily by persistent mucosal infections.

Generating enhanced mucosal immunity against Bordetella pertussis: current challenges and new directions

Bordetella pertussis (Bp) is the highly transmissible etiologic agent of pertussis, a severe respiratory disease that causes particularly high morbidity and mortality in infants and young children. Commonly known as "whooping cough," pertussis is one of the least controlled vaccine-preventable diseases worldwide with several countries experiencing recent periods of resurgence despite broad immunization coverage. While current acellular vaccines prevent severe disease in most cases, the immunity they confer wanes rapidly and does not prevent sub clinical infection or transmission of the bacterium to new and vulnerable hosts. The recent resurgence has prompted new efforts to generate robust immunity to Bp in the upper respiratory mucosa, from which colonization and transmission originate. Problematically, these initiatives have been partially hindered by research limitations in both human and animal models as well as potent immunomodulation by Bp. Here, we consider our incomplete understanding of the complex host-pathogen dynamics occurring in the upper airway to propose new directions and methods that may address critical gaps in research. We also consider recent evidence that supports the development of novel vaccines specifically designed to generate robust mucosal immune responses capable of limiting upper respiratory colonization to finally halt the ongoing circulation of Bordetella pertussis.

Deep longitudinal multi-omics analysis of Bordetella pertussis cultivated in bioreactors highlights medium starvations and transitory metabolisms, associated to vaccine antigen biosynthesis variations and global virulence regulation

Bordetella pertussis is the bacterial causative agent of whooping cough, a serious respiratory illness. An extensive knowledge on its virulence regulation and metabolism is a key factor to ensure pertussis vaccine manufacturing process robustness. The aim of this study was to refine our comprehension of B. pertussis physiology during in vitro cultures in bioreactors. A longitudinal multi-omics analysis was carried out over 26 h small-scale cultures of B. pertussis. Cultures were performed in batch mode and under culture conditions intending to mimic industrial processes. Putative cysteine and proline starvations were, respectively, observed at the beginning of the exponential phase (from 4 to 8 h) and during the exponential phase (18 h 45 min). As revealed by multi-omics analyses, the proline starvation induced major molecular changes, including a transient metabolism with internal stock consumption. In the meantime, growth and specific total PT, PRN, and Fim2 antigen productions were negatively affected. Interestingly, the master virulence-regulating two-component system of B. pertussis (BvgASR) was not evidenced as the sole virulence regulator in this in vitro growth condition. Indeed, novel intermediate regulators were identified as putatively involved in the expression of some virulence-activated genes (vags). Such longitudinal multi-omics analysis applied to B. pertussis culture process emerges as a powerful tool for characterization and incremental optimization of vaccine antigen production.

Conquering the host: Bordetella spp. and Pseudomonas aeruginosa molecular regulators in lung infection

When bacteria sense cues from the host environment, stress responses are activated. Two component systems, sigma factors, small RNAs, ppGpp stringent response, and chaperones start coordinate the expression of virulence factors or immunomodulators to allow bacteria to respond. Although, some of these are well studied, such as the two-component systems, the contribution of other regulators, such as sigma factors or ppGpp, is increasingly gaining attention. Pseudomonas aeruginosa is the gold standard pathogen for studying the molecular mechanisms to sense and respond to environmental cues. Bordetella spp., on the other hand, is a microbial model for studying host-pathogen interactions at the molecular level. These two pathogens have the ability to colonize the lungs of patients with chronic diseases, suggesting that they have the potential to share a niche and interact. However, the molecular networks that facilitate adaptation of Bordetella spp. to cues are unclear. Here, we offer a side-by-side comparison of what is known about these diverse molecular mechanisms that bacteria utilize to counteract host immune responses, while highlighting the relatively unexplored interactions between them.

Bbvac: A Live Vaccine Candidate That Provides Long-Lasting Anamnestic and Th17-Mediated Immunity against the Three Classical Bordetella spp

Acute pathogens such as Bordetella pertussis can cause severe disease but are ultimately cleared by the immune response. This has led to the accepted paradigm that convalescent immunity is optimal and therefore broadly accepted as the “gold standard” against which vaccine candidates should be compared. However, successful pathogens like B. pertussis have evolved multiple mechanisms for suppressing and evading host immunity, raising the possibility that disruption of these mechanisms could result in substantially stronger or better immunity. Current acellular B. pertussis vaccines, delivered in a 5-dose regimen, induce only short-term immunity against disease and even less against colonization and transmission. Importantly, they provide modest protection against other Bordetella species that cause substantial human disease. A universal vaccine that protects against the three classical Bordetella spp. could decrease the burden of whooping cough-like disease in humans and other animals. Our recent work demonstrated that Bordetella spp. suppress host inflammatory responses and that disrupting the regulation of immunosuppressive mechanisms can allow the host to generate substantially stronger sterilizing immunity against the three classical Bordetella spp. Here, we identify immune parameters impacted by Bordetella species immunomodulation, including the generation of robust Th17 and B cell memory responses. Disrupting immunomodulation augmented the immune response, providing strong protection against the prototypes of all three classical Bordetella spp. as well as recent clinical isolates. Importantly, the protection in mice lasted for at least 15 months and was associated with recruitment of high numbers of B and T cells in the lungs as well as enhanced Th17 mucosal responses and persistently high titers of antibodies. These findings demonstrate that disrupting bacterial immunomodulatory pathways can generate much stronger and more protective immune responses to infection, with important implications for the development of better vaccines.

IMPORTANCE Infectious diseases are a major cause of morbidity and mortality in the United States, accounting for over 40 million hospitalizations since 1998. Therefore, novel vaccine strategies are imperative, which can be improved with a better understanding of the mechanisms that bacteria utilize to suppress host immunity, a key mechanism for establishing colonization. Bordetella spp., the causative agents of whooping cough, suppress host immunity, which allows for persistent colonization. We discovered a regulator of a bacterial immunosuppressive pathway, which, when mutated in Bordetella spp., allows for rapid clearance of infection and subsequent generation of protective immunity for at least 15 months. After infection with the mutant strain, mice exhibited sterilizing immunity against the three classical Bordetella spp., suggesting that the immune response can be both stronger and cross-protective. This work presents a strategy for vaccine development that can be applied to other immunomodulatory pathogens.

Pathogenicity and virulence of Bordetella pertussis and its adaptation to its strictly human host

The highly contagious whooping cough agent Bordetella pertussis has evolved as a human-restricted pathogen from a progenitor which also gave rise to Bordetella parapertussis and Bordetella bronchiseptica. While the latter colonizes a broad range of mammals and is able to survive in the environment, B. pertussis has lost its ability to survive outside its host through massive genome decay. Instead, it has become a highly successful human pathogen by the acquisition of tightly regulated virulence factors and evolutionary adaptation of its metabolism to its particular niche. By the deployment of an arsenal of highly sophisticated virulence factors it overcomes many of the innate immune defenses. It also interferes with vaccine-induced adaptive immunity by various mechanisms. Here, we review data from invitro, human and animal models to illustrate the mechanisms of adaptation to the human respiratory tract and provide evidence of ongoing evolutionary adaptation as a highly successful human pathogen.

Evaluation of bioremediation and detoxification potentiality for papermaking black liquor by a new isolated thermophilic and alkali-tolerant Serratia sp. AXJ-M

There is a great need for efficiently treating papermaking black liquor because it can seriously pollute both soil and water ecosystems. In this study, the Plackett-Burman (PB) experimental design combined with response surface methodology (RSM) was used for improving the biodegradation efficiency of lignin by a new isolated thermophilic and alkali-tolerant strain Serratia sp. AXJ-M, and the results showed that a biodegradation efficiency of 70.5% was achieved under optimal culture conditions. The bacterium with ligninolytic activities significantly decreased target the parameters (color 80%, lignin 60%, phenol 95%, BOD 80% and COD 80%). The control and treated samples were analyzed by gas chromatography-mass spectrometer (GC-MS), which showed that the concentrations of a majority of low-molecular-weight compounds were decreased after biological treatment. Furthermore, toxicological, genotoxicity and phytotoxicity studies have supported the detoxification by the bacterium of black liquor. Finally, the genome sequence of the thermophilic, alkali-tolerant and lignin-degrading bacterium AXJ-M was completed, and the genetic basis of the thermophilic and alkali-resistant properties of AXJ-M was preliminarily revealed. The dyp-type peroxidase was first reported to have the potential to catalyze lignin degradation structurally. These findings suggest that Serratia sp. AXJ-M may be potentially useful for bioremediation applications for papermaking black liquor.

"NETs and EETs, a Whole Web of Mess"

Neutrophils and eosinophils are granulocytes that have very distinct functions. Neutrophils are first responders to external threats, and they use different mechanisms to control pathogens. Phagocytosis, reactive oxygen species, and neutrophil extracellular traps (NETs) are some of the mechanisms that neutrophils utilize to fight pathogens. Although there is some controversy as to whether NETs are in fact beneficial or detrimental to the host, it mainly depends on the biological context. NETs can contribute to disease pathogenesis in certain types of diseases, while they are also undeniably critical components of the innate immune response. On the contrary, the role of eosinophils during host immune responses remains to be better elucidated. Eosinophils play an important role during helminthic infections and allergic responses. Eosinophils can function as effector cells in viral respiratory infections, gut bacterial infections, and as modulators of immune responses by driving the balance between Th1 and Th2 responses. In particular, eosinophils have biological activities that appear to be quite similar to those of neutrophils. Both possess bactericidal activity, can activate proinflammatory responses, can modulate adaptive immune responses, can form extracellular traps, and can be beneficial or detrimental to the host according to the underlying pathology. In this review we compare these two cell types with a focus on highlighting their numerous similarities related to extracellular traps.

Disrupting Bordetella Immunosuppression Reveals a Role for Eosinophils in Coordinating the Adaptive Immune Response in the Respiratory Tract

Recent findings revealed pivotal roles for eosinophils in protection against parasitic and viral infections, as well as modulation of adaptive immune responses in the gastric mucosa. However, the known effects of eosinophils within the respiratory tract remain predominantly pathological, associated with allergy and asthma. Simulating natural respiratory infections in mice, we examined how efficient and well-adapted pathogens can block eosinophil functions that contribute to the immune response. Bordetella bronchiseptica, a natural pathogen of the mouse, uses the sigma factor btrS to regulate expression of mechanisms that interfere with eosinophil recruitment and function. When btrS is disrupted, immunomodulators are dysregulated, and eosinophils are recruited to the lungs, suggesting they may contribute to much more efficient generation of adaptive immunity induced by this mutant. Eosinophil-deficient mice failed to produce pro-inflammatory cytokines, to recruit lymphocytes, to organize lymphoid aggregates that resemble Bronchus Associated Lymphoid Tissue (BALT), to generate an effective antibody response, and to clear bacterial infection from the respiratory tract. Importantly, the failure of eosinophil-deficient mice to produce these lymphoid aggregates indicates that eosinophils can mediate the generation of an effective lymphoid response in the lungs. These data demonstrate that efficient respiratory pathogens can block eosinophil recruitment, to inhibit the generation of robust adaptive immune responses. They also suggest that some post-infection sequelae involving eosinophils, such as allergy and asthma, might be a consequence of bacterial mechanisms that manipulate their accumulation and/or function within the respiratory tract.

Characterization and genome functional analysis of an efficient nitrile-degrading bacterium, Rhodococcus rhodochrous BX2, to lay the foundation for potential bioaugmentation for remediation of nitrile-contaminated environments

Nitriles are a class of extremely toxic chemicals with extensive applications, and these compounds pose potential risks to humans and ecosystems. The activated sludge isolate Rhodococcus rhodochrous BX2 efficiently metabolizes aliphatic nitriles. However, the molecular underpinnings of the degradation mechanism of aliphatic nitriles by BX2 remain unknown, and the metabolic fate of aliphatic nitriles also has not been elucidated. Here, strain BX2 was capable of completely mineralizing three aliphatic nitriles. Bioinformatic analysis yielded a deeper insight into the genetic basis of BX2 for efficient degradation of aliphatic nitriles and adaptation to harsh environments. Transcriptional, enzyme activity and metabolite analyses confirmed that the intracellular inducible nitrile hydratase/amidase pathway is the preferred metabolic pathway. Our findings provide an in-depth understanding of the environmental fate of aliphatic nitriles and, most importantly, offer a new perspective on the potential applications of the genus Rhodococcus in bioremediation and the development of degradation enzyme resources.

Enhancement of immune response against Bordetella spp. by disrupting immunomodulation

Well-adapted pathogens must evade clearance by the host immune system and the study of how they do this has revealed myriad complex strategies and mechanisms. Classical bordetellae are very closely related subspecies that are known to modulate adaptive immunity in a variety of ways, permitting them to either persist for life or repeatedly infect the same host. Exploring the hypothesis that exposure to immune cells would cause bordetellae to induce expression of important immunomodulatory mechanisms, we identified a putative regulator of an immunomodulatory pathway. The deletion of btrS in B. bronchiseptica did not affect colonization or initial growth in the respiratory tract of mice, its natural host, but did increase activation of the inflammasome pathway, and recruitment of inflammatory cells. The mutant lacking btrS recruited many more B and T cells into the lungs, where they rapidly formed highly organized and distinctive Bronchial Associated Lymphoid Tissue (BALT) not induced by any wild type Bordetella species, and a much more rapid and strong antibody response than observed with any of these species. Immunity induced by the mutant was measurably more robust in all respiratory organs, providing completely sterilizing immunity that protected against challenge infections for many months. Moreover, the mutant induced sterilizing immunity against infection with other classical bordetellae, including B. pertussis and B. parapertussis, something the current vaccines do not provide. These findings reveal profound immunomodulation by bordetellae and demonstrate that by disrupting it much more robust protective immunity can be generated, providing a pathway to greatly improve vaccines and preventive treatments against these important pathogens.

Immunomodulation as a Novel Strategy for Prevention and Treatment of Bordetella spp. Infections

Well-adapted pathogens have evolved to survive the many challenges of a robust immune response. Defending against all host antimicrobials simultaneously would be exceedingly difficult, if not impossible, so many co-evolved organisms utilize immunomodulatory tools to subvert, distract, and/or evade the host immune response. Bordetella spp. present many examples of the diversity of immunomodulators and an exceptional experimental system in which to study them. Recent advances in this experimental system suggest strategies for interventions that tweak immunity to disrupt bacterial immunomodulation, engaging more effective host immunity to better prevent and treat infections. Here we review advances in the understanding of respiratory pathogens, with special focus on Bordetella spp., and prospects for the use of immune-stimulatory interventions in the prevention and treatment of infection.

Computational Health Engineering Applied to Model Infectious Diseases and Antimicrobial Resistance Spread

Infectious diseases are the primary cause of mortality worldwide. The dangers of infectious disease are compounded with antimicrobial resistance, which remains the greatest concern for human health. Although novel approaches are under investigation, the World Health Organization predicts that by 2050, septicaemia caused by antimicrobial resistant bacteria could result in 10 million deaths per year. One of the main challenges in medical microbiology is to develop novel experimental approaches, which enable a better understanding of bacterial infections and antimicrobial resistance. After the introduction of whole genome sequencing, there was a great improvement in bacterial detection and identification, which also enabled the characterization of virulence factors and antimicrobial resistance genes. Today, the use of in silico experiments jointly with computational and machine learning offer an in depth understanding of systems biology, allowing us to use this knowledge for the prevention, prediction, and control of infectious disease. Herein, the aim of this review is to discuss the latest advances in human health engineering and their applicability in the control of infectious diseases. An in-depth knowledge of host–pathogen–protein interactions, combined with a better understanding of a host’s immune response and bacterial fitness, are key determinants for halting infectious diseases and antimicrobial resistance dissemination.

Superior B. pertussis Specific CD4+ T-Cell Immunity Imprinted by Natural Infection

Pertussis remains endemic in vaccinated populations due to waning of vaccine-induced immunity and insufficient interruption of transmission. Correlates of long-term protection against whooping cough remain elusive but increasing evidence from experimental models indicates that the priming of particular lineages of B. pertussis (Bp) specific CD4+ T cells is essential to control bacterial load. Critical hallmarks of these protective CD4+ T cell lineages in animals are suggested to be their differentiation profile as Th1 and Th17 cells and their tissue residency. These features seem optimally primed by previous infection but insufficiently or only partially by current vaccines. In this review, evidence is sought indicating whether infection also drives such superior Bp specific CD4+ T cell lineages in humans. We highlight key features of effector immunity downstream of Th1 and Th17 cell cytokines that explain clearing of primary Bp infections in naïve hosts, and effective prevention of infection in convalescent hosts during secondary challenge. Outstanding questions are put forward that need answers before correlates of human Bp infection-primed CD4+ T cell immunity can be used as benchmark for the development of improved pertussis vaccines.