bims-bac4me Biomed News
on Microbiome and trained immunity
Issue of 2023‒11‒26
34 papers selected by
Chun-Chi Chang, University Hospital Zurich

  1. Am J Physiol Lung Cell Mol Physiol. 2023 Nov 22.
      Cell-free hemoglobin (CFH) is elevated in the airspace of patients with acute respiratory distress syndrome (ARDS) and is sufficient to cause acute lung injury in a murine model. However, the pathways through which CFH causes lung injury are not well understood. Toll-like receptor 4 (TLR4) is a mediator of inflammation after detection of damage- and pathogen-associated molecular patterns. We hypothesized that TLR4 signaling mediates the pro-inflammatory effects of CFH in the airspace. After intra-tracheal CFH, BALBc mice deficient in TLR4 had reduced inflammatory cell influx into the airspace (bronchoalveolar lavage [BAL] cell counts, median TLR4KO:0.8x104/mL [IQR 0.4-1.2x104/mL], wild-type (WT): 3.0x104/mL [2.2-4.0x104/mL], p<0.001) and attenuated lung permeability (BAL protein, TLR4KO: 289mg/mL [236-320], WT: 488mg/mL [422-536], p<0.001). These mice also had attenuated production of IL-1β, IL-6, and TNF-α in the airspace. C57Bl/6 mice lacking TLR4 on myeloid cells only (LysM.Cre+/-TLR4fl/fl) had reduced cytokine production in the airspace after CFH, without attenuation of lung permeability. In vitro studies confirm that WT primary murine alveolar macrophages exposed to CFH (0.01-1mg/mL) had dose-dependent increases in IL-6, IL-1 b, CXCL-1, TNF-a, and IL-10 (p<0.001). Murine MH-S alveolar-like macrophages show TLR4-dependent expression of IL-1b, IL-6, and CXCL-1 in response to CFH. Primary alveolar macrophages from mice lacking TLR4 adaptor proteins MyD88 or TRIF revealed that MyD88KO macrophages had 71-96% reduction in CFH-dependent pro-inflammatory cytokine production (p<0.001), whereas macrophages from TRIFKO mice had variable changes in cytokine responses. These data demonstrate that myeloid TLR4 signaling through MyD88 is a key regulator of airspace inflammation in response to CFH.
    Keywords:  TLR4; acute lung injury; cell-free hemoglobin; inflammation; macrophages
  2. Ann Allergy Asthma Immunol. 2023 Nov 17. pii: S1081-1206(23)01454-0. [Epub ahead of print]
    Keywords:  AERD; Biologic; CRSwNP; allergic rhinitis; aspirin-exacerbated respiratory disease; atopic dermatitis; comorbidities; eosinophilic esophagitis; type 2 inflammation; urticaria
  3. J Immunol. 2023 Nov 20. pii: ji2300151. [Epub ahead of print]
      Staphylococcus aureus is a significant cause of morbidity and mortality in pulmonary infections. Patients with autosomal-dominant hyper-IgE syndrome due to STAT3 deficiency are particularly susceptible to acquiring staphylococcal pneumonia associated with lung tissue destruction. Because macrophages are involved in both pathogen defense and inflammation, we investigated the impact of murine myeloid STAT3 deficiency on the macrophage phenotype in vitro and on pathogen clearance and inflammation during murine staphylococcal pneumonia. Murine bone marrow-derived macrophages (BMDM) from STAT3 LysMCre+ knockout or Cre- wild-type littermate controls were challenged with S. aureus, LPS, IL-4, or vehicle control in vitro. Pro- and anti-inflammatory responses as well as polarization and activation markers were analyzed. Mice were infected intratracheally with S. aureus, bronchoalveolar lavage and lungs were harvested, and immunohistofluorescence was performed on lung sections. S. aureus infection of STAT3-deficient BMDM led to an increased proinflammatory cytokine release and to enhanced upregulation of costimulatory MHC class II and CD86. Murine myeloid STAT3 deficiency did not affect pathogen clearance in vitro or in vivo. Matrix metalloproteinase 9 was upregulated in Staphylococcus-treated STAT3-deficient BMDM and in lung tissues of STAT3 knockout mice infected with S. aureus. Moreover, the expression of miR-155 was increased. The enhanced inflammatory responses and upregulation of matrix metalloproteinase 9 and miR-155 expression in murine STAT3-deficient as compared with wild-type macrophages during S. aureus infections may contribute to tissue damage as observed in STAT3-deficient patients during staphylococcal pneumonia.
  4. Cell Rep. 2023 Nov 22. pii: S2211-1247(23)01470-5. [Epub ahead of print]42(12): 113458
      Innate immune memory, also called "trained immunity," is a functional state of myeloid cells enabling enhanced immune responses. This phenomenon is important for host defense, but also plays a role in various immune-mediated conditions. We show that exogenously administered sphingolipids and inhibition of sphingolipid metabolizing enzymes modulate trained immunity. In particular, we reveal that acid ceramidase, an enzyme that converts ceramide to sphingosine, is a potent regulator of trained immunity. We show that acid ceramidase regulates the transcription of histone-modifying enzymes, resulting in profound changes in histone 3 lysine 27 acetylation and histone 3 lysine 4 trimethylation. We confirm our findings by identifying single-nucleotide polymorphisms in the region of ASAH1, the gene encoding acid ceramidase, that are associated with the trained immunity cytokine response. Our findings reveal an immunomodulatory effect of sphingolipids and identify acid ceramidase as a relevant therapeutic target to modulate trained immunity responses in innate immune-driven disorders.
    Keywords:  CP: Immunology; acid ceramidase; epigenetics; immune memory; innate immunity; lipid metabolism; monocytes; nanobiologics; sphingolipids; trained immunity
  5. J Clin Med. 2023 Nov 20. pii: 7184. [Epub ahead of print]12(22):
      The process of microbiome development arguably begins before birth. Vertical transmission of bacteria from the mother to the infant is a keystone event in microbiome development. Subsequent to birth, the developing microbiome is vulnerable to influence from a wide range of factors. Additionally, the microbiome can influence the health and development of the host infant. This intricate interaction of the gastrointestinal microbiome and the host has been described as both symbiotic and dysbiotic. Defining these terms, a symbiotic microbiome is where the microbiome and host provide mutual benefit to each other. A pathogenic microbiome, or more precisely a gastrointestinal microbiome associated with disease, is increasing described as dysbiotic. This review seeks to investigate the factors that contribute to evolving a disease-causing or 'dysbiotic' microbiome. This review covers the development of the gastrointestinal microbiome in infants, the interaction of the microbiome with the host, and its contribution to host immunity and investigates specific features of the gastrointestinal microbiome that are associated with disease.
    Keywords:  childhood; dysbiosis; infant; inflammatory disease; microbiome
  6. Nutrients. 2023 Nov 09. pii: 4728. [Epub ahead of print]15(22):
      Multiple studies have confirmed that Lactiplantibacillus plantarum has beneficial effects in respiratory diseases, including respiratory tract infections, asthma, and chronic obstructive pulmonary disease. However, the role of L. plantarum lysates in respiratory diseases is unclear. Staphylococcus aureus infects the lungs of mice, recruits immune cells, and induces structural changes in alveoli. Lung diseases can be further aggravated by inflammatory cytokines such as CCL2 and interleukin (IL)-6. In in vivo studies, L. plantarum K8 nanoparticles (K8NPs) restored lung function and prevented lung damage caused by S. aureus infection. They inhibited the S. aureus infection and the infiltration of immune cells and prevented the increase in goblet cell numbers in the lungs of S. aureus-infected mice. K8NPs suppressed the expression of CCL2 and IL-6, which were increased by the combination treatment of tumor necrosis factor alpha and interferon gamma (TI), in a dose-dependent manner. In in vitro studies, the anti-inflammatory effect of K8NPs in TI-treated A549 cells and TI-injected mice occurred through the reduction in activated mitogen-activated protein kinases and nuclear factor kappa-B. These findings suggest that the efficacy of K8NPs in controlling respiratory inflammation and infection can be used to develop functional materials that can prevent or alleviate respiratory diseases.
    Keywords:  Lactiplantibacillus plantarum K8; Staphylococcus aureus; lung infection; lung inflammation; lysates; probiotics nanoparticles
  7. J Innate Immun. 2023 Nov 21.
      Introduction A role for innate immune memory in protection during COVID-19 infection or vaccination has been recently reported. However, no study so far has shown whether SARS-CoV-2 can train innate immune cells. The aim of this study was to investigate whether this virus can induce trained immunity in human monocytes. Methods Monocytes were exposed to inactivated (i)SARS-CoV-2 for 24 hours, followed by a resting period in medium only and a secondary stimulation on day 6 after which, the cytokine/chemokine and transcriptomic profiles were determined. Results Compared to untrained cells, the iSARS-CoV-2-trained monocytes secreted significantly higher levels of IL-6, TNF-α, CXCL10, CXCL9 and CXCL11 upon restimulation. Transcriptome analysis of iSARS-CoV-2 trained monocytes revealed increased expression of several inflammatory genes. As epigenetic and metabolic modifications are hallmarks of trained immunity, we analyzed the expression of genes related to these processes. Findings indicate that indeed SARS-CoV-2-trained monocytes show changes in the expression of genes involved in metabolic pathways including the tricarboxylic acid (TCA) cycle, amino acid metabolism and the expression of several epigenetic regulator genes. Using epigenetic inhibitors that block histone methyl and acetyl transferases, we observed that the capacity of monocytes to be trained by iSARS-CoV-2 was abolished. Conclusion Overall, our findings indicate that iSARS-CoV-2 can induce properties associated with trained immunity in human monocytes. These results contribute to the knowledge required for improving vaccination strategies to prevent infectious diseases.
  8. FASEB J. 2023 Dec;37(12): e23316
      Alveolar inflammation is a hallmark of acute lung injury (ALI), and its clinical correlate is acute respiratory distress syndrome-and it is as a result of interactions between alveolar type II cells (ATII) and alveolar macrophages (AM). In the setting of acute injury, the microenvironment of the intra-alveolar space is determined in part by metabolites and cytokines and is known to shape the AM phenotype. In response to ALI, increased glycolysis is observed in AT II cells, mediated by the transcription factor hypoxia-inducible factor (HIF) 1α, which has been shown to decrease inflammation. We hypothesized that in acute lung injury, lactate, the end product of glycolysis, produced by ATII cells shifts AMs toward an anti-inflammatory phenotype, thus mitigating ALI. We found that local intratracheal delivery of lactate improved ALI in two different mouse models. Lactate shifted cytokine expression of murine AMs toward increased IL-10, while decreasing IL-1 and IL-6 expression. Mice with ATII-specific deletion of Hif1a and mice treated with an inhibitor of lactate dehydrogenase displayed exacerbated ALI and increased inflammation with decreased levels of lactate in the bronchoalveolar lavage fluid; however, all those parameters improved with intratracheal lactate. When exposed to LPS (to recapitulate an inflammatory stimulus as it occurs in ALI), human primary AMs co-cultured with alveolar epithelial cells had reduced inflammatory responses. Taken together, these studies reveal an innate protective pathway, in which lactate produced by ATII cells shifts AMs toward an anti-inflammatory phenotype and dampens excessive inflammation in ALI.
    Keywords:  acute lung injury; acute respiratory distress syndrome; alveolar epithelium; alveolar macrophage; glycolysis; hypoxia-inducible factor; lactate
  9. J Innate Immun. 2023 Nov 23.
      Background Innate immune cells play a crucial role in responding to microbial infections, but their improper activation can also drive inflammatory disease. For this reason, their activation state is governed by a multitude of factors, including the metabolic state of the cell and, more specifically, the individual metabolites which accumulate intra- and extra-cellularly. This relationship is bidirectional, as innate immune cell activation by pathogen-associated molecular patterns (PAMPs) causes critical changes in cellular metabolism. Summary In this review we describe the emergence of various 'immunometabolites'. We outline the general characteristics of these immunometabolites, the conditions under which they accumulate, and their subsequent impact on immune cells. We delve into well-studied metabolites of recent years, such as succinate and itaconate, as well as newly emerging immunometabolites, such as methylglyoxal. Key Messages We hope that this review may be used as a framework for further studies dissecting the mechanisms by which immunometabolites regulate the immune system, and provide an outlook to harnessing these mechanisms in the treatment of inflammatory diseases.
  10. Microbiome. 2023 Nov 23. 11(1): 260
      BACKGROUND: The modulation of immune responses by probiotics is crucial for local and systemic immunity. Recent studies have suggested a correlation between gut microbiota and lung immunity, known as the gut-lung axis. However, the evidence and mechanisms underlying this axis remain elusive.RESULTS: In this study, we screened various Lactobacillus (L.) strains for their ability to augment type I interferon (IFN-I) signaling using an IFN-α/β reporter cell line. We identified L. paracasei (MI29) from the feces of healthy volunteers, which showed enhanced IFN-I signaling in vitro. Oral administration of the MI29 strain to wild-type B6 mice for 2 weeks resulted in increased expression of IFN-stimulated genes and pro-inflammatory cytokines in the lungs. We found that MI29-treated mice had significantly increased numbers of CD11c+PDCA-1+ plasmacytoid dendritic cells and Ly6Chi monocytes in the lungs compared with control groups. Pre-treatment with MI29 for 2 weeks resulted in less weight loss and lower viral loads in the lung after a sub-lethal dose of influenza virus infection. Interestingly, IFNAR1-/- mice did not show enhanced viral resistance in response to oral MI29 administration. Furthermore, metabolic profiles of MI29-treated mice revealed changes in fatty acid metabolism, with MI29-derived fatty acids contributing to host defense in a Gpr40/120-dependent manner.
    CONCLUSIONS: These findings suggest that the newly isolated MI29 strain can activate host defense immunity and prevent infections caused by the influenza virus through the gut-lung axis. Video Abstract.
    Keywords:  Gut microbiota; IFN-I; Influenza; Lactobacillus paracasei
  11. Trends Microbiol. 2023 Nov 18. pii: S0966-842X(23)00300-1. [Epub ahead of print]
      Invasive fungal infections pose a major threat to human health. Bacterial and protozoan pathogens secrete protein effectors that overcome innate immune barriers to promote microbial colonization, yet few such molecules have been identified in human fungal pathogens. Recent studies have begun to reveal these long-sought effectors and have illuminated how they subvert key cellular pathways, including apoptosis, myeloid cell polarization, Toll-like receptor signaling, and phagosome action. Thus, despite lacking the specialized secretion systems of bacteria and parasites, it is increasingly clear that fungi independently evolved effectors targeting pathways often subverted by other classes of pathogens. These findings demonstrate the remarkable power of convergent evolution to enable diverse microbes to infect humans while also setting the stage for detailed dissection of fungal disease mechanisms.
    Keywords:  apoptosis; dendritic cell; fungal pathogen; phagosome trafficking; secreted effector; type 2 immunity
  12. Cell. 2023 Nov 22. pii: S0092-8674(23)01164-9. [Epub ahead of print]186(24): 5375-5393.e25
      Itch is an unpleasant sensation that evokes a desire to scratch. The skin barrier is constantly exposed to microbes and their products. However, the role of microbes in itch generation is unknown. Here, we show that Staphylococcus aureus, a bacterial pathogen associated with itchy skin diseases, directly activates pruriceptor sensory neurons to drive itch. Epicutaneous S. aureus exposure causes robust itch and scratch-induced damage. By testing multiple isogenic bacterial mutants for virulence factors, we identify the S. aureus serine protease V8 as a critical mediator in evoking spontaneous itch and alloknesis. V8 cleaves proteinase-activated receptor 1 (PAR1) on mouse and human sensory neurons. Targeting PAR1 through genetic deficiency, small interfering RNA (siRNA) knockdown, or pharmacological blockade decreases itch and skin damage caused by V8 and S. aureus exposure. Thus, we identify a mechanism of action for a pruritogenic bacterial factor and demonstrate the potential of inhibiting V8-PAR1 signaling to treat itch.
    Keywords:  PAR1; Staphylococcus aureus; V8 protease; itch; microbe; proteinase-activated receptor; pruriceptor
  13. Nature. 2023 Nov 22.
      All nucleated cells express major histocompatibility complex I and interferon-γ (IFNγ) receptor1, but an epithelial cell-specific function of IFNγ signalling or antigen presentation by means of major histocompatibility complex I has not been explored. We show here that on sensing IFNγ, colonic epithelial cells productively present pathogen and self-derived antigens to cognate intra-epithelial T cells, which are critically located at the epithelial barrier. Antigen presentation by the epithelial cells confers extracellular ATPase expression in cognate intra-epithelial T cells, which limits the accumulation of extracellular adenosine triphosphate and consequent activation of the NLRP3 inflammasome in tissue macrophages. By contrast, antigen presentation by the tissue macrophages alongside inflammasome-associated interleukin-1α and interleukin-1β production promotes a pathogenic transformation of CD4+ T cells into granulocyte-macrophage colony-stimulating-factor (GM-CSF)-producing T cells in vivo, which promotes colitis and colorectal cancer. Taken together, our study unravels critical checkpoints requiring IFNγ sensing and antigen presentation by epithelial cells that control the development of pathogenic CD4+ T cell responses in vivo.
  14. J Infect Dis. 2023 Nov 24. pii: jiad498. [Epub ahead of print]
      BACKGROUND: Clinical outcomes in bacterial bloodstream infections (BSI) are influenced by multiple factors, including bacterial species, host immunity, and antibiotic therapy. However, the mechanisms by which such factors influence outcomes and their potential biomarkers are poorly understood. We aimed to identify bacterial- and antibiotic-specific host transcriptional signatures in patients with bacterial BSI.METHODS: RNA-Seq was performed on blood from patients with BSI due to prototypic Gram-negative vs. Gram-positive pathogens: Escherichia coli (n = 30) or Klebsiella pneumoniae (n = 28) vs. methicillin-susceptible Staphylococcus aureus [MSSA] (n = 24) or methicillin-resistant S. aureus (MRSA) (n = 58). Patients were matched by age, gender, and race.
    RESULTS: No significant host transcriptome differences were detected in patients with E. coli versus K. pneumoniae BSI, so these were considered together as Gram-negative BSI. Relative to S. aureus BSI, patients with Gram-negative BSI had increased activation of the classical complement system. However, the most significant signal was a reduction in host transcriptional signatures involving mitochondrial energy transduction and oxidative burst in MRSA vs. MSSA. This attenuated host transcriptional signature remained after controlling for antibiotic therapy.
    CONCLUSIONS: Given importance of immune cellular energetics and reactive oxygen species in eliminating hematogenous or intracellular MRSA, these findings may offer insights into its persistence relative to other bacterial BSI.
    Keywords:  Escherichia coli; Klebsiella pneumoniae; Staphylococcus aureus; bacteremia; transcriptome
  15. Am Fam Physician. 2023 11;108(5): 509-510
  16. Nature. 2023 Nov 22.
      Inflammatory caspases are key enzymes in mammalian innate immunity that control the processing and release of interleukin-1 (IL-1)-family cytokines1,2. Despite the biological importance, the structural basis for inflammatory caspase-mediated cytokine processing has remained unclear. To date, catalytic cleavage of IL-1-family members, including pro-IL-1β and pro-IL-18, has been attributed primarily to caspase-1 activities within canonical inflammasomes3. Here we demonstrate that the lipopolysaccharide receptor caspase-4 from humans and other mammalian species (except rodents) can cleave pro-IL-18 with an efficiency similar to pro-IL-1β and pro-IL-18 cleavage by the prototypical IL-1-converting enzyme caspase-1. This ability of caspase-4 to cleave pro-IL-18, combined with its previously defined ability to cleave and activate the lytic pore-forming protein gasdermin D (GSDMD)4,5, enables human cells to bypass the need for canonical inflammasomes and caspase-1 for IL-18 release. The structure of the caspase-4-pro-IL-18 complex determined using cryogenic electron microscopy reveals that pro-lL-18 interacts with caspase-4 through two distinct interfaces: a protease exosite and an interface at the caspase-4 active site involving residues in the pro-domain of pro-IL-18, including the tetrapeptide caspase-recognition sequence6. The mechanisms revealed for cytokine substrate capture and cleavage differ from those observed for the caspase substrate GSDMD7,8. These findings provide a structural framework for the discussion of caspase activities in health and disease.
  17. Neonatal Netw. 2023 Nov 01. 42(6): 342-347
      The newborn who requires intensive care hospitalization is forced into an external environment that can negatively impact the developing microbiome. The NICU nurse has a unique role that affects, and may even protect, the development of the newborn microbiome through daily nursing care. The purpose of this article is to inform neonatal nurses regarding common nursing interventions that can positively or negatively impact the developing microbiome. Evidence-based practices are presented and bundled to describe their impact the neonatal microbiome.
    Keywords:  GI; antibiotic stewardship; feeding; human milk oligosaccharides; microbiome; probiotics; quality improvement; skin-to-skin care; vernix caseosa
  18. J Invertebr Pathol. 2023 Nov 18. pii: S0022-2011(23)00139-8. [Epub ahead of print] 108022
      β-glucans (βGs) are carbohydrate polymers linked by β-1,3, 1,4 or 1,6 bonds; they have been used to protect against potential pathogens and prevent lethal diseases. The immune system possesses several receptors that identify a wide range of structures and trigger cellular and humoral mechanisms. However, the mechanisms by which βGs activate the immune system of invertebrate organisms have not been fully clarified. This review is focused on evaluating the effect of βGs on innate immune system in invertebrates. βGs stimulate different cellular and humoral mechanisms, such as phagocytosis, oxygen species production, extracellular trap formation, proPO system, and antimicrobial peptide synthesis, moreover, βGs increase survival rate and decrease pathogen load in several species.
  19. Int J Mol Sci. 2023 Nov 10. pii: 16169. [Epub ahead of print]24(22):
      The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
    Keywords:  TTFL; biological clock; cellular timekeeping; circadian rhythm; evolution; metabolic oscillations; microbiome; peroxiredoxins
  20. STAR Protoc. 2023 Nov 18. pii: S2666-1667(23)00704-9. [Epub ahead of print]4(4): 102737
      Population-level dynamics of host-pathogen interactions can be characterized using quantitative live-cell imaging. Here, we present a protocol for infecting macrophages with the fungal pathogen Candida albicans in vitro and quantitative live-cell imaging of immune and pathogen responses. We describe steps for detailed image analysis and provide resources for quantification of phagocytosis and pathogen escape, as well as macrophage membrane permeabilization and viability. This protocol is modifiable for applications with a range of pathogens, immune cell types, and host-pathogen mechanisms. For complete details on the use and execution of this protocol, please refer to Olivier et al.1.
    Keywords:  Immunology; Microbiology; Microscopy; Model Organisms
  21. Int J Mol Sci. 2023 Nov 14. pii: 16308. [Epub ahead of print]24(22):
      Methicillin-sensitive Staphylococcus (S.) aureus (MSSA) bacteremia remains a global challenge, despite the availability of antibiotics. Primary treatments include β-lactam agents such as cefazolin and flucloxacillin. Ongoing discussions have focused on the potential synergistic effects of combining these agents with rifampicin or fosfomycin to combat infections associated with biofilm formation. Managing staphylococcal infections is challenging due to antibacterial resistance, biofilms, and S. aureus's ability to invade and replicate within host cells. Intracellular invasion shields the bacteria from antibacterial agents and the immune system, often leading to incomplete bacterial clearance and chronic infections. Additionally, S. aureus can assume a dormant phenotype, known as the small colony variant (SCV), further complicating eradication and promoting persistence. This study investigated the impact of antibiotic combinations on the persistence of S. aureus 6850 and its stable small colony variant (SCV strain JB1) focusing on intracellular survival and biofilm formation. The results from the wild-type strain 6850 demonstrate that β-lactams combined with RIF effectively eliminated biofilms and intracellular bacteria but tend to select for SCVs in planktonic culture and host cells. Higher antibiotic concentrations were associated with an increase in the zeta potential of S. aureus, suggesting reduced membrane permeability to antimicrobials. When using the stable SCV mutant strain JB1, antibiotic combinations with rifampicin successfully cleared planktonic bacteria and biofilms but failed to eradicate intracellular bacteria. Given these findings, it is reasonable to report that β-lactams combined with rifampicin represent the optimal treatment for MSSA bacteremia. However, caution is warranted when employing this treatment over an extended period, as it may elevate the risk of selecting for small colony variants (SCVs) and, consequently, promoting bacterial persistence.
    Keywords:  Staphylococcus aureus; bacteremia; bacterial persistence; cefazolin; flucloxacillin; fosfomycin; rifampicin; small colony variants
  22. Antibiotics (Basel). 2023 Nov 11. pii: 1617. [Epub ahead of print]12(11):
      BACKGROUND: The microbiome of newborn infants during the first 1000 days, influenced early on by their mothers' microbiome health, mode of delivery and breast feeding, orchestrates the education and programming of the infant's immune system and determines in large part the general health of the infant for years.METHODS: PubMed was reviewed for maternal infant microbiome health and microbiota therapy in this setting with prebiotics, probiotics, vaginal seeding and fecal microbiota transplantation (FMT).
    RESULTS: A healthy nonobese mother, vaginal delivery and strict breast feeding contribute to microbiome health in a newborn and young infant. With reduced microbiome diversity (dysbiosis) during pregnancy, cesarean delivery, prematurity, and formula feeding contribute to dysbiosis in the newborn. Microbiota therapy is an important approach to repair dysbiosis in pregnant women and their infants. Currently available probiotics can have favorable metabolic effects on mothers and infants, but these effects are variable. In research settings, reversal of infant dysbiosis can be achieved via vaginal seeding or FMT. Next generation probiotics in development should replace current probiotics and FMT.
    CONCLUSIONS: The most critical phase of human microbiome development is in the first 2-3 years of life. Preventing and treating dysbiosis during pregnancy and early life can have a profound effect on an infant's later health.
    Keywords:  fecal microbiota transplantation; hygiene theory; microbiome in infants; microbiome in pregnancy; prebiotics; probiotics; vaginal seeding
  23. Clin Microbiol Rev. 2023 Nov 20. e0014822
      SUMMARYMethicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of severe and often fatal infections. MRSA epidemics have occurred in waves, whereby a previously successful lineage has been replaced by a more fit and better adapted lineage. Selection pressures in both hospital and community settings are not uniform across the globe, which has resulted in geographically distinct epidemiology. This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. While the important role of antibiotic resistance will be mentioned throughout, factors which influence the capacity of S. aureus to colonize and cause disease within a host will be the primary focus of this review. We show that while MRSA possesses a diverse arsenal of toxins including alpha-toxin, the success of a lineage involves more than just producing toxins that damage the host. Success is often attributed to the acquisition or loss of genetic elements involved in colonization and niche adaptation such as the arginine catabolic mobile element, as well as the activity of regulatory systems, and shift metabolism accordingly (e.g., the accessory genome regulator, agr). Understanding exactly how specific MRSA clones cause prolonged epidemics may reveal targets for therapies, whereby both core (e.g., the alpha toxin) and acquired virulence factors (e.g., the Panton-Valentine leukocidin) may be nullified using anti-virulence strategies.
    Keywords:  gene regulation; metabolism; methicillin-resistant Staphylococcus aureus; mobile genetic elements; superantigens; toxins; virulence
  24. NPJ Biofilms Microbiomes. 2023 Nov 20. 9(1): 87
      Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice (HMbmice). Like the community structure in conventional mice, HMbmice vaginal microbiota clustered into community state types but, uniquely, HMbmice communities were frequently dominated by Lactobacillus or Enterobacteriaceae. Compared to conventional mice, HMbmice were less susceptible to uterine ascension by urogenital pathobionts group B Streptococcus (GBS) and Prevotella bivia. Although Escherichia and Lactobacillus both correlated with the absence of uterine GBS, vaginal pre-inoculation with exogenous HMbmouse-derived E. coli, but not Ligilactobacillus murinus, reduced vaginal GBS burden. Overall, HMbmice serve as a useful model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.
  25. Nature. 2023 Nov 22.
      The canonical (caspase-1) and noncanonical (comprising caspases 4, 5 and 11; hereafter, caspase-4/5/11) inflammasomes both cleave gasdermin D (GSDMD) to induce pyroptosis1,2. Whereas caspase-1 processes IL-1β and IL-18 for maturation3-6, no cytokine target has been firmly established for lipopolysaccharide-activated caspase-4/5/117-9. Here we show that activated human caspase-4, but not mouse caspase-11, directly and efficiently processes IL-18 in vitro and during bacterial infections. Caspase-4 cleaves the same tetrapeptide site in pro-IL-18 as caspase-1. The crystal structure of the caspase-4-pro-IL-18 complex reveals a two-site (binary) substrate-recognition mechanism; the catalytic pocket engages the tetrapeptide, and a unique exosite that critically recognizes GSDMD10 similarly binds to a specific structure formed jointly by the propeptide and post-cleavage-site sequences in pro-IL-18. This binary recognition is also used by caspase-5 as well as caspase-1 to process pro-IL-18. In caspase-11, a structural deviation around the exosite underlies its inability to target pro-IL-18, which is restored by rationally designed mutations. The structure of pro-IL-18 features autoinhibitory interactions between the propeptide and the post-cleavage-site region, preventing recognition by the IL-18Rα receptor. Cleavage by caspase-1, -4 or -5 induces substantial conformational changes of IL-18 to generate two critical receptor-binding sites. Our study establishes IL-18 as a target of lipopolysaccharide-activated caspase-4/5. The finding is paradigm shifting in the understanding of noncanonical-inflammasome-mediated defences and also the function of IL-18 in immunity and disease.
  26. Cell. 2023 Nov 22. pii: S0092-8674(23)01178-9. [Epub ahead of print]186(24): 5201-5202
      Itch exacerbates infection and inflammation-associated skin pathology. In this issue of Cell, Deng et al. identify a V8 protease released by Staphylococcus aureus triggering itch via neuronal protease-activated receptor 1. In so doing, they uncover profound consequences of microbial neurosensory modulation and the ensuing scratch-induced tissue damage that potentiates infection.
  27. Eur Respir Rev. 2023 Dec 31. pii: 230080. [Epub ahead of print]32(170):
      BACKGROUND: Autoimmune pulmonary alveolar proteinosis (aPAP) results from impaired macrophage-mediated clearance of alveolar surfactant lipoproteins. Whole lung lavage has been the first-line treatment but recent reports suggest the efficacy of granulocyte-macrophage colony-stimulating factor (GM-CSF). We aimed to review the efficacy and safety of nebulised GM-CSF in aPAP.METHODS: We conducted a systematic review and meta-analysis searching Embase, CINAHL, MEDLINE and Cochrane Collaborative databases (1946-1 April 2022). Studies included patients aged >18 years with aPAP receiving nebulised GM-CSF treatment and a comparator cohort. Exclusion criteria included secondary or congenital pulmonary alveolar proteinosis, GM-CSF allergy, active infection or other serious medical conditions. The protocol was prospectively registered with PROSPERO (CRD42021231328). Outcomes assessed were St George's Respiratory Questionnaire (SGRQ), 6-min walk test (6MWT), gas exchange (diffusing capacity of the lung for carbon monoxide (D LCO) % predicted) and arterial-alveolar oxygen gradient.
    RESULTS: Six studies were identified for review and three for meta-analysis, revealing that SGRQ score (mean difference -8.09, 95% CI -11.88- -4.3, p<0.0001), functional capacity (6MWT) (mean difference 21.72 m, 95% CI -2.76-46.19 m, p=0.08), gas diffusion (D LCO % predicted) (mean difference 5.09%, 95% CI 2.05-8.13%, p=0.001) and arterial-alveolar oxygen gradient (mean difference -4.36 mmHg, 95% CI -7.19- -1.52 mmHg, p=0.003) all significantly improved in GM-CSF-treated patients with minor statistical heterogeneity (I2=0%). No serious trial-related adverse events were reported.
    CONCLUSIONS: Patients with aPAP treated with inhaled GM-CSF demonstrated significant improvements in symptoms, dyspnoea scores, lung function, gas exchange and radiology indices after treatment with nebulised GM-CSF of varying duration. There is an important need to review comparative effectiveness and patient choice in key clinical outcomes between the current standard of care, whole lung lavage, with the noninvasive treatment of nebulised GM-CSF in aPAP.
  28. Scand J Gastroenterol. 2023 Nov 24. 1-10
      OBJECTIVES: The early life microbiome has been linked to inflammatory diseases in adulthood and a role for the microbiome in bile duct inflammation is supported by both human and murine studies. We utilized the NOD.c3c4 mouse model that develops a spontaneous immune-driven biliary disease with a known contribution of the microbiome to evaluate the temporal effects of the early life microbiome.MATERIALS AND METHODS: Germ-free (GF) NOD.c3c4 mice were conventionalized into a specific pathogen free environment at birth (conventionally raised, CONV-R) or at weaning (germ-free raised, GF-R) and compared with age and gender-matched GF and conventional (CONV) NOD.c3c4 mice. At 9 weeks of age, liver pathology was assessed by conventional histology and flow cytometry immunophenotyping.
    RESULTS: Neonatal exposure to microbes (CONV-R) increased biliary inflammation to similar levels as regular conventional NOD.c3c4 mice, while delayed exposure to microbes (GF-R) restrained the biliary inflammation. Neutrophil infiltration was increased in all conventionalized mice compared to GF. An immunophenotype in the liver similar to CONV was restored in both CONV-R and GF-R compared to GF mice displaying a proportional increase of B cells and reduction of T cells in the liver.
    CONCLUSIONS: Microbial exposure during early life has a temporal impact on biliary tract inflammation in the NOD.c3c4 mouse model suggesting that age-sensitive interaction with commensal microbes have long-lasting effects on biliary immunity that can be of importance for human cholangiopathies.
    Keywords:  Microbiota; NOD.c3c4; cholangitis; dysbiosis; germ-free
  29. Cancer Immunol Res. 2023 Nov 21.
      Immune cells in the tumor niche robustly influence disease progression. Remarkably, in cancer, developmental pathways are re-enacted. Many parallels between immune regulation of embryonic development and immune regulation of tumor progression can be drawn, with evidence clearly supporting an immune-suppressive microenvironment in both situations. In these ecosystems, metabolic and bioenergetic circuits guide and regulate immune cell differentiation, plasticity, and functional properties of suppressive and inflammatory immune subsets. As such, there is an emerging pattern of intersection across the dynamic process of ontogeny and the ever-evolving tumor neighborhood. In this article, we focus on the convergence of immune programming during ontogeny and in the tumor microenvironment. Exemplifying dysregulation of Hedgehog (Hh) activity, a key player during ontogeny, we highlight a critical convergence of these fields and the metabolic axis of the nutrient sensing hexosamine biosynthetic pathway (HBP) that integrates glucose, glutamine, amino acids, acetyl CoA, and uridine-5'-triphosphate (UTP), culminating in the synthesis of UDP-GlcNAc, a metabolite that functions as a metabolic and bioenergetic sensor. We discuss an emerging pattern of immune regulation, orchestrated by O-GlcNAcylation of key transcriptional regulators, spurring suppressive activity of dysfunctional immune cells in the tumor microenvironment.
  30. Rev Esp Quimioter. 2023 Nov;36 Suppl 1 68-70
      The world of infectious diseases, for various reasons, before and after the COVID-19 pandemic, capture the attention of the scientific community, either due to the epidemiological data of various microbial agents that are emerging, due to the implementation with successful results of new diagnostic strategies or due to the appearance of new therapeutic options, which encourage healthcare workers to continue on the front line. Topics such as antimicrobial resistance, S. aureus bacteremia, clostridioides difficile, short treatments for tuberculosis, prosthetic joint infection or invasive fungal infections are included. In this article, we want to highlight, among many others, seven recently published articles that deserve our attention, full of useful information to keep us updated.
  31. Int J Mol Sci. 2023 Nov 07. pii: 16042. [Epub ahead of print]24(22):
      Bronchial asthma is a heterogeneous disease characterized by persistent respiratory system inflammation, airway hyperreactivity, and airflow obstruction. Airway remodeling, defined as changes in airway wall structure such as extensive epithelial damage, airway smooth muscle hypertrophy, collagen deposition, and subepithelial fibrosis, is a key feature of asthma. Lung fibrosis is a common occurrence in the pathogenesis of fatal and long-term asthma, and it is associated with disease severity and resistance to therapy. It can thus be regarded as an irreversible consequence of asthma-induced airway inflammation and remodeling. Asthma heterogeneity presents several diagnostic challenges, particularly in distinguishing between chronic asthma and other pulmonary diseases characterized by disruption of normal lung architecture and functions, such as chronic obstructive pulmonary disease. The search for instruments that can predict the development of irreversible structural changes in the lungs, such as chronic components of airway remodeling and fibrosis, is particularly difficult. To overcome these challenges, significant efforts are being directed toward the discovery and investigation of molecular characteristics and biomarkers capable of distinguishing between different types of asthma as well as between asthma and other pulmonary disorders with similar structural characteristics. The main features of bronchial asthma etiology, pathogenesis, and morphological characteristics as well as asthma-associated airway remodeling and lung fibrosis as successive stages of one process will be discussed in this review. The most common murine models and biomarkers of asthma progression and post-asthmatic fibrosis will also be covered. The molecular mechanisms and key cellular players of the asthmatic process described and systematized in this review are intended to help in the search for new molecular markers and promising therapeutic targets for asthma prediction and therapy.
    Keywords:  airway remodeling; asthma; biomarkers; in vivo models; lung fibrosis