Commensal microbes provide first line defense against Listeria monocytogenes infection

A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria

Extracellular electron transfer (EET) describes microbial bioelectrochemical processes in which electrons are transferred from the cytosol to the exterior of the cell1. Mineral-respiring bacteria use elaborate haem-based electron transfer mechanisms2-4 but the existence and mechanistic basis of other EETs remain largely unknown. Here we show that the food-borne pathogen Listeria monocytogenes uses a distinctive flavin-based EET mechanism to deliver electrons to iron or an electrode. By performing a forward genetic screen to identify L. monocytogenes mutants with diminished extracellular ferric iron reductase activity, we identified an eight-gene locus that is responsible for EET. This locus encodes a specialized NADH dehydrogenase that segregates EET from aerobic respiration by channelling electrons to a discrete membrane-localized quinone pool. Other proteins facilitate the assembly of an abundant extracellular flavoprotein that, in conjunction with free-molecule flavin shuttles, mediates electron transfer to extracellular acceptors. This system thus establishes a simple electron conduit that is compatible with the single-membrane structure of the Gram-positive cell. Activation of EET supports growth on non-fermentable carbon sources, and an EET mutant exhibited a competitive defect within the mouse gastrointestinal tract. Orthologues of the genes responsible for EET are present in hundreds of species across the Firmicutes phylum, including multiple pathogens and commensal members of the intestinal microbiota, and correlate with EET activity in assayed strains. These findings suggest a greater prevalence of EET-based growth capabilities and establish a previously underappreciated relevance for electrogenic bacteria across diverse environments, including host-associated microbial communities and infectious disease.

Carbapenems and alternative β-lactams for the treatment of infections due to extended-spectrum β-lactamase-producing Enterobacteriaceae: What impact on intestinal colonisation resistance?

The ongoing pandemic of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) is responsible for a global rise in carbapenem consumption that may hasten the dissemination of carbapenemase-producing Enterobacteriaceae (CPE). Hence, carbapenem sparing through the use of alternative β-lactams is increasingly considered as a potential option in patients with ESBL-E infections. However, at the individual level, this strategy implies an in-depth understanding of how carbapenems and their alternatives impair the gut microbiota, especially the anaerobic bacteria and the colonisation resistance (CR) that it confers. In this review, we sought to appraise the impact of carbapenems and their main alternatives for ESBL-E infections (namely β-lactam/β-lactamase inhibitor combinations, cephamycins and temocillin) on the gut ecosystem and the resulting hazard for acquisition of CPE. Although limited, the available evidence challenges our perception of the ecological side effects of these antimicrobials and highlights knowledge gaps regarding antibiotic-induced alterations in intestinal CR. These alterations may depend not only on anti-anaerobic properties but also on a panel of parameters with marked interindividual variability, such as baseline characteristics of the gut microbiota or the degree of biliary excretion for the considered drug. In the current context of ESBL-E dissemination and increasing opportunities for carbapenem-sparing initiatives, large, comparative, high-quality studies based on new-generation sequencing tools are more than ever warranted to better define the positioning of alternative β-lactams in antimicrobial stewardship programmes.

Advancing risk assessment: mechanistic dose-response modelling of Listeria monocytogenes infection in human populations

The utility of characterizing the effects of strain variation and individual/subgroup susceptibility on dose-response outcomes has motivated the search for new approaches beyond the popular use of the exponential dose-response model for listeriosis. While descriptive models can account for such variation, they have limited power to extrapolate beyond the details of particular outbreaks. By contrast, this study exhibits dose-response relationships from a mechanistic basis, quantifying key biological factors involved in pathogen-host dynamics. An efficient computational algorithm and geometric interpretation of the infection pathway are developed to connect dose-response relationships with the underlying bistable dynamics of the model. Relying on in vitro experiments as well as outbreak data, we estimate plausible parameters for the human context. Despite the presence of uncertainty in such parameters, sensitivity analysis reveals that the host response is most influenced by the pathogen-immune system interaction. In particular, we show how variation in this interaction across a subgroup of the population dictates the shape of dose-response curves. Finally, in terms of future experimentation, our model results provide guidelines and highlight vital aspects of the interplay between immune cells and particular strains of Listeria monocytogenes that should be examined.

Culturing the human microbiota and culturomics

The gut microbiota has an important role in the maintenance of human health and in disease pathogenesis. This importance was realized through the advent of omics technologies and their application to improve our knowledge of the gut microbial ecosystem. In particular, the use of metagenomics has revealed the diversity of the gut microbiota, but it has also highlighted that the majority of bacteria in the gut remain uncultured. Culturomics was developed to culture and identify unknown bacteria that inhabit the human gut as a part of the rebirth of culture techniques in microbiology. Consisting of multiple culture conditions combined with the rapid identification of bacteria, the culturomic approach has enabled the culture of hundreds of new microorganisms that are associated with humans, providing exciting new perspectives on host-bacteria relationships. In this Review, we discuss why and how culturomics was developed. We describe how culturomics has extended our understanding of bacterial diversity and then explore how culturomics can be applied to the study of the human microbiota and the potential implications for human health.

Growth, detection and virulence of Listeria monocytogenes in the presence of other microorganisms: microbial interactions from species to strain level

Like with all food microorganisms, many basic aspects of L. monocytogenes life are likely to be influenced by its interactions with bacteria living in close proximity. This pathogenic bacterium is a major concern both for the food industry and health organizations since it is ubiquitous and able to withstand harsh environmental conditions. Due to the ubiquity of Listeria monocytogenes, various strains may contaminate foods at different stages of the supply chain. Consequently, simultaneous exposure of consumers to multiple strains is also possible. In this context even strain-to-strain interactions of L. monocytogenes play a significant role in fundamental processes for the life of the pathogen, such as growth or virulence, and subsequently compromise food safety, affect the evolution of a potential infection, or even introduce bias in the detection by classical enrichment techniques. This article summarizes the impact of microbial interactions on the growth and detection of L. monocytogenes primarily in foods and food-associated environments. Furthermore it provides an overview of L. monocytogenes virulence in the presence of other microorganisms.

MicroRNA-146a Deficiency Protects against Listeria monocytogenes Infection by Modulating the Gut Microbiota

The gut microbiota and microRNAs play important roles in the defense against infection. However, the role of miR-146a in L. monocytogenes infection and gut microbiota remains unclear. We tried to determine whether miR-146a controlled L. monocytogenes infection by regulating the gut microbiota. Wild-type and miR-146a-deficient mice or macrophages were used to characterize the impact of miR-146a on animal survival, cell death, bacterial clearance, and gut microbiota following L. monocytogenes challenge. We found that L. monocytogenes infection induced miR-146a expression both in vitro and in vivo. When compared to wild-type mice, miR-146a-deficient mice were more resistant to L. monocytogenes infection. MiR-146a deficiency in macrophages resulted in reduced invasion and intracellular survival of L. monocytogenes. High-throughput sequencing of 16S rRNA revealed that the gut microbiota composition differed between miR-146a-deficient and wild-type mice. Relative to wild-type mice, miR-146a-deficient mice had decreased levels of the Proteobacteria phylum, Prevotellaceae family, and Parasutterella genus, and significantly increased short-chain fatty acid producing bacteria, including the genera Alistipes, Blautia, Coprococcus_1, and Ruminococcus_1. Wild-type mice co-housed with miR-146a-deficient mice had increased resistance to L. monocytogenes, indicating that miR-146a deficiency guides the gut microbiota to alleviate infection. Together, these results suggest that miR-146a deficiency protects against L. monocytogenes infection by regulating the gut microbiota.

A Comparison of Oral and Intravenous Mouse Models of Listeriosis

Listeria monocytogenes is one of several enteric microbes that is acquired orally, invades the gastric mucosa, and then disseminates to peripheral tissues to cause systemic disease in humans. Intravenous (i.v.) inoculation of mice with L. monocytogenes has been the most widely-used small animal model of listeriosis over the past few decades. The infection is highly reproducible and has been invaluable in deciphering mechanisms of adaptive immunity in vivo, particularly CD8⁺ T cell responses to intracellular pathogens. However, the i.v. model completely bypasses the gut phase of the infection. Recent advances in generating both humanized mice and murinized bacteria, as well as the development of a foodborne route of transmission has reignited interest in studying oral models of listeriosis. In this review, we analyze previously published reports to highlight both the similarities and differences in tissue colonization and host response to infection using either oral or i.v. inoculation.

Listeria monocytogenes: towards a complete picture of its physiology and pathogenesis

Listeria monocytogenes is a food-borne pathogen responsible for a disease called listeriosis, which is potentially lethal in immunocompromised individuals. This bacterium, first used as a model to study cell-mediated immunity, has emerged over the past 20 years as a paradigm in infection biology, cell biology and fundamental microbiology. In this Review, we highlight recent advances in the understanding of human listeriosis and L. monocytogenes biology. We describe unsuspected modes of hijacking host cell biology, ranging from changes in organelle morphology to direct effects on host transcription via a new class of bacterial effectors called nucleomodulins. We then discuss advances in understanding infection in vivo, including the discovery of tissue-specific virulence factors and the 'arms race' among bacteria competing for a niche in the microbiota. Finally, we describe the complexity of bacterial regulation and physiology, incorporating new insights into the mechanisms of action of a series of riboregulators that are critical for efficient metabolic regulation, antibiotic resistance and interspecies competition.

Multifaceted Defense against Listeria monocytogenes in the Gastro-Intestinal Lumen

Listeria monocytogenes is a foodborne pathogen that can cause febrile gastroenteritis in healthy subjects and systemic infections in immunocompromised individuals. Despite the high prevalence of L. monocytogenes in the environment and frequent contamination of uncooked meat and poultry products, infections with this pathogen are relatively uncommon, suggesting that protective defenses in the general population are effective. In the mammalian gastrointestinal tract, a variety of defense mechanisms prevent L. monocytogenes growth, epithelial penetration and systemic dissemination. Among these defenses, colonization resistance mediated by the gut microbiota is crucial in protection against a range of intestinal pathogens, including L. monocytogenes. Here we review defined mechanisms of defense against L. monocytogenes in the lumen of the gastro-intestinal tract, with particular emphasis on protection conferred by the autochthonous microbiota. We suggest that selected probiotic species derived from the microbiota may be developed for eventual clinical use to enhance resistance against L. monocytogenes infections.

Comparison between Listeria sensu stricto and Listeria sensu lato strains identifies novel determinants involved in infection

The human pathogen L. monocytogenes and the animal pathogen L. ivanovii, together with four other species isolated from symptom-free animals, form the “Listeria sensu stricto” clade. The members of the second clade, “Listeria sensu lato”, are believed to be solely environmental bacteria without the ability to colonize mammalian hosts. To identify novel determinants that contribute to infection by L. monocytogenes, the causative agent of the foodborne disease listeriosis, we performed a genome comparison of the two clades and found 151 candidate genes that are conserved in the Listeria sensu stricto species. Two factors were investigated further in vitro and in vivo. A mutant lacking an ATP-binding cassette transporter exhibited defective adhesion and invasion of human Caco-2 cells. Using a mouse model of foodborne L. monocytogenes infection, a reduced number of the mutant strain compared to the parental strain was observed in the small intestine and the liver. Another mutant with a defective 1,2-propanediol degradation pathway showed reduced persistence in the stool of infected mice, suggesting a role of 1,2-propanediol as a carbon and energy source of listeriae during infection. These findings reveal the relevance of novel factors for the colonization process of L. monocytogenes.

Protective Microbiota: From Localized to Long-Reaching Co-Immunity

Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity,” where an organism is protected by both its own immune system and components of its microbiota.

Analyzing the innate immunity of NIH hairless mice and the impact of gut microbial polymorphisms on Listeria monocytogenes infection

Spontaneous mutant hairless (HL) mice are often used to study hair growth and hair follicle development, and they often exhibit immune dysfunctions. Listeria monocytogenes, an important food-borne bacterium, has been used in animal models to study immune responses to infection. Herein, we analyzed the innate immunity of HL mice and the impact of gut microbial polymorphisms on L. monocytogenes infection. Compared to NIH mice, NIH HL mice were more susceptible to L. monocytogenes, as weight losses, mortality, bacterial load, and histopathological lesions were more severe; the decrease in monocytes may be an important underlying reason. The degree of spleen damage was reduced after co-housing, indicating that the host guides the gut microbiota to alleviate infection. High-throughput pyrosequencing of 16S rRNA demonstrated that gut microbiota composition differed between NIH HL and NIH mice. Infection with L. monocytogenes induced an increase in the number of bacteria belonging to the Rikenellaceae family and Gammaproteobacteria class, and decreased bacteria belonging to the Clostridiales class and Lachnospiraceae family. A substantial reduction in Clostridiales bacteria in infected HL mice may cause a serious infection. The Mycoplasma genus was present only in NIH HL mice and was, thus, considered a biomarker. The results of this study improve our understanding of the use of NIH HL mice as a good animal model of innate immune dysfunction.

The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens

The human gastrointestinal tract hosts a diverse network of microorganisms, collectively known as the microbiota that plays an important role in health and disease. For instance, the intestinal microbiota can prevent invading microbes from colonizing the gastrointestinal tract, a phenomenon known as colonization resistance. Perturbations to the microbiota, such as antibiotic administration, can alter microbial composition and result in the loss of colonization resistance. Consequently, the host may be rendered susceptible to colonization by a pathogen. This is a particularly relevant concern in the hospital setting, where antibiotic use and antibiotic-resistant pathogen exposure are more frequent. Many nosocomial infections arise from gastrointestinal colonization. Due to their resistance to antibiotics, treatment is often very challenging. However, recent studies have demonstrated that manipulating the commensal microbiota can prevent and treat various infections in the intestine. In this review, we discuss the members of the microbiota, as well as the mechanisms, that govern colonization resistance against specific pathogens. We also review the effects of antibiotics on the microbiota, as well as the unique epidemiology of immunocompromised patients that renders them a particularly high-risk population to intestinal nosocomial infections.