Antibody-mediated cross-linking of gut bacteria hinders the spread of antibiotic resistance

The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected for by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a multiscale model of the interaction between antibiotic use and resistance spread in a host population, focusing on an important aspect of within-host immunity. Antibodies secreted in the gut enchain bacteria upon division, yielding clonal clusters of bacteria. We demonstrate that immunity-driven bacteria clustering can hinder the spread of a novel resistant bacterial strain in a host population. We quantify this effect both in the case where resistance pre-exists and in the case where acquiring a new resistance mutation is necessary for the bacteria to spread. We further show that the reduction of spread by clustering can be countered when immune hosts are silent carriers, and are less likely to get treated, and/or have more contacts. We demonstrate the robustness of our findings to including stochastic within-host bacterial growth, a fitness cost of resistance, and its compensation. Our results highlight the importance of interactions between immunity and the spread of antibiotic resistance, and argue in the favor of vaccine-based strategies to combat antibiotic resistance.Comment: 49 pages, 11 figure

Modélisation biophysique des dynamiques d'une population bactérienne et de la réponse immunitaire dans les intestins

The first part of this thesis focuses on the colonization dynamics of a bacterial population in early infection of the gut. The aim is to infer biologically relevant parameters from indirect data. We discuss the optimal observable to characterize the variability in genetic tags distributions. In a first one-population model, biological arguments and inconsistencies between several experimental observables lead to the study of a second model with two-subpopulations replicating at different rates. As expected, this model allows for broader possibilities in observables combination, even though no clear conclusion can be drawn as to a data set on Salmonella in mice. The second part concerns the mechanisms that make the immune response effective. The main effector of the immune system in the gut, IgA (an antibody), enchains daughter bacteria in clonal clusters upon replication. Our model predicting the ensuing reduction of diversity in the bacterial population contributes to evidence this phenomenon, called “enchained growth”. Inside the host, the interplay of cluster growth and fragmentation results in preferentially trapping faster-growing and potentially noxious bacteria away from the epithelium, which could be a way for the immune system to regulate the microbiota composition. At the scale of the hosts population, in the context of evolution of antibiotic resistance, if bacteria are transmitted via clonal clusters, the probability to transmit a resistant bacteria is reduced in immune populations. Thus we use statistical physics tools to identify some generic mechanisms in biology.La première partie de cette thèse porte sur les dynamiques de colonisation d'une population bactérienne au début d'une infection intestinale. Le but est de déduire des paramètres biologiquement pertinents de données indirectes. Un modèle simple est étudié, et l'on discute de l'observable optimale pour caractériser la variabilité d'une distribution d'étiquettes génétiques. Des arguments biologiques et des incohérences entre des observables expérimentales avec le premier modèle motivent l'étude d'un second, où deux sous-populations se répliquent à des taux différents, mais on ne peut pas conclure clairement sur le jeu de données utilisé. La seconde partie porte sur les mécanismes de la réponse immunitaire. Le principal effecteur du système immunitaire adaptatif dans l'intestin, l'IgA (un anticorps), enchaîne les bactéries-filles en agrégats clonaux lors de la réplication. Nous avons contribué à prouver ce phénomène par un modèle qui prédit la réduction de la diversité bactérienne qui en découle. Au sein de l'hôte, l'interaction entre la croissance et la fragmentation des agrégats a pour conséquence le piégeage préférentiel des bactéries à croissance rapide, ce qui pourrait permettre au système immunitaire de réguler la composition du microbiote. A l'échelle de la population-hôte, et dans le contexte de l'évolution d'une résistance aux antibiotiques, si les bactéries sont transmises sous forme d'amas clonaux, alors la probabilité de transmettre une bactérie résistante est réduite dans une population immunisée. Ainsi, des outils de physique statistique nous permettent d'identifier des mécanismes génériques en biologie

Enchained growth and cluster dislocation: A possible mechanism for microbiota homeostasis

Immunoglobulin A is a class of antibodies produced by the adaptive immune system and secreted into the gut lumen to fight pathogenic bacteria. We recently demonstrated that the main physical effect of these antibodies is to enchain daughter bacteria, i.e. to cross-link bacteria into clusters as they divide, preventing them from interacting with epithelial cells, thus protecting the host. These links between bacteria may break over time. We study several models using analytical and numerical calculations. We obtain the resulting distribution of chain sizes, that we compare with experimental data. We study the rate of increase in the number of free bacteria as a function of the replication rate of bacteria. Our models show robustly that at higher replication rates, bacteria replicate before the link between daughter bacteria breaks, leading to growing cluster sizes. On the contrary at low growth rates two daughter bacteria have a high probability to break apart. Thus the gut could produce IgA against all the bacteria it has encountered, but the most affected bacteria would be the fast replicating ones, that are more likely to destabilize the microbiota. Linking the effect of the immune effectors (here the clustering) with a property directly relevant to the potential bacterial pathogeneicity (here the replication rate) could avoid to make complex decisions about which bacteria to produce effectors against.ISSN:1553-734XISSN:1553-735

Treatment policy for localized oral cancer

This paper analyzes the results of treatment for disseminated oral cancer (T1N0M0). The combined (surgery and radiotherapy) treatment group demonstrated the best 5-year overall and relapse-free survival rates (96.6 and 92.3 %, respectively). In the surgery group only, these rates were lower, amounting to 79.2 and 68.7 %, respectively. The medical therapy group was noted to have the lowest 5-year overall and relapse-free survival rates (81.8 and 45.5 %, respectively)

Bacterial c-di-GMP has a key role in establishing host–microbe symbiosis

Most microbes evolve faster than their hosts and should therefore driveevolution of host–microbe interactions. However, relatively little is knownabout the characteristics that define the adaptive path of microbes to hostassociation. Here we identified microbial traits that mediate adaptation tohosts by experimentally evolving the free-living bacterium Pseudomonaslurida with the nematode Caenorhabditis elegans as its host. After tenpassages, we repeatedly observed the evolution of beneficial host-specialistbacteria, with improved persistence in the nematode being associatedwith increased biofilm formation. Whole-genome sequencing revealedmutations that uniformly upregulate the bacterial second messenger,cyclic diguanylate (c-di-GMP). We subsequently generated mutants withupregulated c-di-GMP in different Pseudomonas strains and species, whichconsistently increased host association. Comparison of pseudomonadgenomes from various environments revealed that c-di-GMP underliesadaptation to a variety of hosts, from plants to humans. This study indicatesthat c-di-GMP is fundamental for establishing host association

Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota

Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. In this study, we used genetically barcoded Bacteroides thetaiotaomicron (B. theta) strains to quantify population bottlenecks experienced by a B. theta population during colonization of the mouse gut. As expected, this reveals an inverse relationship between microbiota complexity and the probability that an individual wildtype B. theta clone will colonize the gut. The polysaccharide capsule of B. theta is important for resistance against attacks from other bacteria, phage, and the host immune system, and correspondingly acapsular B. theta loses in competitive colonization against the wildtype strain. Surprisingly, the acapsular strain did not show a colonization defect in mice with a low-complexity microbiota, as we found that acapsular strains have an indistinguishable colonization probability to the wildtype strain on single-strain colonization. This discrepancy could be resolved by tracking in vivo growth dynamics of both strains: acapsular B.theta shows a longer lag phase in the gut lumen as well as a slightly slower net growth rate. Therefore, as long as there is no niche competitor for the acapsular strain, this has only a small influence on colonization probability. However, the presence of a strong niche competitor (i.e., wildtype B. theta, SPF microbiota) rapidly excludes the acapsular strain during competitive colonization. Correspondingly, the acapsular strain shows a similarly low colonization probability in the context of a co-colonization with the wildtype strain or a complete microbiota. In summary, neutral tagging and detailed analysis of bacterial growth kinetics can therefore quantify the mechanisms of colonization resistance in differently-colonized animals

Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota

Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. However, we remain largely blind to the quantitative effects of processes determining colonization success. In this study, we used genetically-barcoded Bacteroides thetaiotaomicron ( B.theta ) strains in combination with mathematical modeling to quantify population bottlenecks experienced by B.theta during gut colonization. Integrating population bottlenecks sizes with careful quantification of net growth rates in vivo and in vitro allows us to build models describing the events during intestinal colonization in the context of gnotobiotic and complex microbiotas. Using these models, we estimated the decrease in niche size for B.theta colonization with increasing microbiota complexity. In addition, our system can be applied to mechanistically dissect colonization defects of mutant strains. As a proof of concept, we demonstrated that the competitive disadvantage of a B.theta mutant lacking capsular polysaccharide is due to a combination of an increased lag-phase before growth initiation in the gut, combined with an increased clearance rate. Crucially, the requirement for the B.theta capsule depended strongly on microbiota composition, suggesting that the dominant role may be protection from bacterial or phage aggression rather than from host-induced bactericidal mechanisms

Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota

Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. In this study, we used genetically barcoded Bacteroides thetaiotaomicron (B. theta) strains to quantify population bottlenecks experienced by a B. theta population during colonization of the mouse gut. As expected, this reveals an inverse relationship between microbiota complexity and the probability that an individual wildtype B. theta clone will colonize the gut. The polysaccharide capsule of B. theta is important for resistance against attacks from other bacteria, phage, and the host immune system, and correspondingly acapsular B. theta loses in competitive colonization against the wildtype strain. Surprisingly, the acapsular strain did not show a colonization defect in mice with a low-complexity microbiota, as we found that acapsular strains have an indistinguishable colonization probability to the wildtype strain on single-strain colonization. This discrepancy could be resolved by tracking in vivo growth dynamics of both strains: acapsular B .theta shows a longer lag-phase in the gut lumen as well as a slightly slower net growth rate. Therefore, as long as there is no niche competitor for the acapsular strain, this has only a small influence on colonization probability. However, the presence of a strong niche competitor (i.e., wildtype B. theta, SPF microbiota) rapidly excludes the acapsular strain during competitive colonization. Correspondingly, the acapsular strain shows a similarly low colonization probability in the context of a co-colonization with the wildtype strain or a complete microbiota. In summary, neutral tagging and detailed analysis of bacterial growth kinetics can therefore quantify the mechanisms of colonization resistance in differently-colonized animals.ISSN:2050-084

mTOR inhibitors for the treatment of severe congenital hyperinsulinism:perspectives on limited therapeutic success

Context: Congenital hyperinsulinism (CHI) is the most common cause of persistent hypoglycemia in neonates and infants. In medically unresponsive CHI, subtotal pancreatectomy is performed to achieve euglycemia with consequent diabetes in later life. Sirolimus, a mammalian target of rapamycin (mTOR) inhibitor, has been reported to obviate the need for pancreatectomy, but experience is limited. Objective: We have investigated the efficacy and adverse effect profile of mTOR inhibitors in the treatment of severe CHI. Design, Setting, and Patients: This was an observational review of 10 severe CHI patients treated with mTOR inhibitors, in France and the United Kingdom, with the intention of achieving glycemic control without pancreatectomy. Safety information was recorded. Main Outcome Measure(s): We examined whether mTOR inhibitors achieved glycemic control, fasting tolerance, and weaning of supportive medical therapy. Results: mTOR inhibition achieved euglycemia, fasting tolerance, and reduced medical therapy in only three patients (30%). Triglyceride levels were elevated in five patients (50%). One child required a blood transfusion for anemia, four had stomatitis, two had sepsis, one developed varicella zoster, and two patients developed gut dysmotility in association with exocrine pancreatic insufficiency. In silico analysis of transcriptome arrays from CHI patients revealed no significant association between mTOR signaling and disease. Pancreatic tissue from two patients who did not respond to sirolimus showed no reduction in cell proliferation, further suggesting that mTOR signaling did not down-regulate proliferation in the CHI pancreas. Conclusion: mTOR inhibitor treatment is associated with very limited success and must be used with caution in children with severe CHI. </jats:sec

High-avidity IgA protects the intestine by enchaining growing bacteria

Vaccine-induced high-avidity IgA can protect against bacterial enteropathogens by directly neutralizing virulence factors or by poorly defined mechanisms that physically impede bacterial interactions with the gut tissues ('immune exclusion'). IgA-mediated cross-linking clumps bacteria in the gut lumen and is critical for protection against infection by non-typhoidal Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium). However, classical agglutination, which was thought to drive this process, is efficient only at high pathogen densities (≥10; 8; non-motile bacteria per gram). In typical infections, much lower densities (10; 0; -10; 7; colony-forming units per gram) of rapidly dividing bacteria are present in the gut lumen. Here we show that a different physical process drives formation of clumps in vivo: IgA-mediated cross-linking enchains daughter cells, preventing their separation after division, and clumping is therefore dependent on growth. Enchained growth is effective at all realistic pathogen densities, and accelerates pathogen clearance from the gut lumen. Furthermore, IgA enchains plasmid-donor and -recipient clones into separate clumps, impeding conjugative plasmid transfer in vivo. Enchained growth is therefore a mechanism by which IgA can disarm and clear potentially invasive species from the intestinal lumen without requiring high pathogen densities, inflammation or bacterial killing. Furthermore, our results reveal an untapped potential for oral vaccines in combating the spread of antimicrobial resistance