Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut

From microbiome composition to functional engineering, one step at a time

SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

Antibiotic perturbations to the gut microbiome

Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.

Differences in carbon metabolic capacity fuel co-existence and plasmid transfer between Salmonella strains in the mouse gut

Antibiotic resistance plasmids can be disseminated between different Enterobacteriaceae in the gut. Here, we investigate how closely related Enterobacteriaceae populations with similar nutrient needs can co-bloom in the same gut and thereby facilitate plasmid transfer. Using different strains of Salmonella Typhimurium (S.Tm SL1344 and ATCC14028) and mouse models of Salmonellosis, we show that the bloom of one strain (i.e., recipient) from very low numbers in a gut pre-occupied by the other strain (i.e., donor) depends on strain-specific utilization of a distinct carbon source, galactitol or arabinose. Galactitol-dependent growth of the recipient S.Tm strain promotes plasmid transfer between non-isogenic strains and between E. coli and S.Tm. In mice stably colonized by a defined microbiota (OligoMM12), galactitol supplementation similarly facilitates co-existence of two S.Tm strains and promotes plasmid transfer. Our work reveals a metabolic strategy used by Enterobacteriaceae to expand in a pre-occupied gut and provides promising therapeutic targets for resistance plasmids spread.

Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion

Plasmids are the main vector by which antibiotic resistance is transferred between bacterial cells within surface-associated communities. In this study, we ask whether there is an optimal time to administer antibiotics to minimize plasmid spread in new bacterial genotypes during community expansion across surfaces. We address this question using consortia of Pseudomonas stutzeri strains, where one is an antibiotic resistance-encoding plasmid donor and the other a potential recipient. We allowed the strains to co-expand across a surface and administered antibiotics at different times. We find that plasmid transfer and transconjugant proliferation have unimodal relationships with the timing of antibiotic administration, where they reach maxima at intermediate times. These unimodal relationships result from the interplay between the probabilities of plasmid transfer and loss. Our study provides mechanistic insights into the transfer and proliferation of antibiotic resistance-encoding plasmids within microbial communities and identifies the timing of antibiotic administration as an important determinant.

Determinants of persistent Salmonella infections

Persistent bacterial infections constitute an enormous challenge for public health. Amongst infections with other bacteria, infections with typhoidal and nontyphoidal Salmonella enterica serovars can result in long-term infections of the human and animal host. Persistent infections that are asymptomatic are difficult to identify and thus can serve as a silent reservoir for transmission. Symptomatic persistent infections are often difficult to treat as they harbor a combination of antibiotic-tolerant and antibiotic-resistant bacteria and boost the spread of genetic antibiotic resistance. In the last couple of years, the field has made some major progress in understanding the role of persisters, their reservoirs as well as their interplay with host factors in persistent Salmonella infections.

Untangling Cellular Host-Pathogen Encounters at Infection Bottlenecks

Bacterial pathogens can invade the tissue and establish a protected intracellular niche at the site of invasion that can spread locally (e.g., microcolonies) or to systemic sites (e.g., granulomas). Invasion of the tissue and establishment of intracellular infection are rare events that are difficult to study in the in vivo setting but have critical clinical consequences, such as long-term carriage, reinfections, and emergence of antibiotic resistance. Here, I discuss Salmonella interactions with its host macrophage during early stages of infection and their critical role in determining infection outcome. The dynamics of host-pathogen interactions entail highly heterogenous host immunity, bacterial virulence, and metabolic cross talk, requiring in vivo analysis at single-cell resolution. I discuss models and single-cell approaches that provide a global understanding of the establishment of a protected intracellular niche within the tissue and the host-pathogen landscape at infection bottlenecks during early stages of infection. Studying cellular host-pathogen interactions in vivo can improve our knowledge of the trajectory of infection between the initial inoculation with a dose of pathogens and the appearance of symptoms of disease.

Factors and Mechanisms Influencing Conjugation In Vivo in the Gastrointestinal Tract Environment: A Review

The emergence and spread of antibiotic resistance genes (ARGs) have imposed a serious threat on global public health. Horizontal gene transfer (HGT) via plasmids is mainly responsible for the spread of ARGs, and conjugation plays an important role in HGT. The conjugation process is very active in vivo and its effect on the spreading of ARGs may be underestimated. In this review, factors affecting conjugation in vivo, especially in the intestinal environment, are summarized. In addition, the potential mechanisms affecting conjugation in vivo are summarized from the perspectives of bacterial colonization and the conjugation process.

The Mobilizable Plasmid P3 of Salmonella enterica Serovar Typhimurium SL1344 Depends on the P2 Plasmid for Conjugative Transfer into a Broad Range of Bacteria In Vitro and In Vivo

The global rise of drug-resistant bacteria is of great concern. Conjugative transfer of antibiotic resistance plasmids contributes to the emerging resistance crisis. Despite substantial progress in understanding the molecular basis of conjugation in vitro, the in vivo dynamics of intra- and interspecies conjugative plasmid transfer are much less understood. In this study, we focused on the streptomycin resistance-encoding mobilizable plasmid pRSF1010^SL1344 (P3) of Salmonella enterica serovar Typhimurium strain SL1344. We show that P3 is mobilized by interacting with the conjugation machinery of the conjugative plasmid pCol1B9^SL1344 (P2) of SL1344. Thereby, P3 can be transferred into a broad range of relevant environmental and clinical bacterial isolates in vitro and in vivo. Our data suggest that S. Typhimurium persisters in host tissues can serve as P3 reservoirs and foster transfer of both P2 and P3 once they reseed the gut lumen. This adds to our understanding of resistance plasmid transfer in ecologically relevant niches, including the mammalian gut. IMPORTANCE S. Typhimurium is a globally abundant bacterial species that rapidly occupies new niches and survives unstable environmental conditions. As an enteric pathogen, S. Typhimurium interacts with a broad range of bacterial species residing in the mammalian gut. High abundance of bacteria in the gut lumen facilitates conjugation and spread of plasmid-carried antibiotic resistance genes. By studying the transfer dynamics of the P3 plasmid in vitro and in vivo, we illustrate the impact of S. Typhimurium-mediated antibiotic resistance spread via conjugation to relevant environmental and clinical bacterial isolates. Plasmids are among the most critical vehicles driving antibiotic resistance spread. Further understanding of the dynamics and drivers of antibiotic resistance transfer is needed to develop effective solutions for slowing down the emerging threat of multidrug-resistant bacterial pathogens.

Studying antibiotic persistence in vivo using the model organism Salmonella Typhimurium

Antibiotic persistence permits a subpopulation of susceptible bacteria to survive lethal concentrations of bactericidal antibiotics. This prolongs antibiotic therapy, promotes the evolution of antibiotic-resistant pathogen strains and can select for pathogen virulence within infected hosts. Here, we review the literature exploring antibiotic persistence in vivo, and describe the consequences of recalcitrant subpopulations, with a focus on studies using the model pathogen Salmonella Typhimurium. In vitro studies have established a concise set of features distinguishing true persisters from other forms of bacterial recalcitrance to bactericidal antibiotics. We discuss how animal infection models are useful for exploring these features in vivo, and describe how technical challenges can sometimes prevent the conclusive identification of true antibiotic persistence within infected hosts. We propose using two complementary working definitions for studying antibiotic persistence in vivo: the strict definition for studying the mechanisms of persister formation, and an operative definition for functional studies assessing the links between invasive virulence and persistence as well as the consequences for horizontal gene transfer, or the emergence of antibiotic-resistant mutants. This operative definition will enable further study of how antibiotic persisters arise in vivo, and of how surviving populations contribute to diverse downstream effects such as pathogen transmission, horizontal gene transfer and the evolution of virulence and antibiotic resistance. Ultimately, such studies will help to improve therapeutic control of antibiotic- recalcitrant populations.

In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome

Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.

Toxin-Antitoxin Systems: A Key Role on Persister Formation in Salmonella enterica Serovar Typhimurium

The toxin and antitoxin modules in bacteria consist of a toxin molecule that has activity to inhibit various cellular processes and its cognate antitoxin that neutralizes the toxin. This system is considered taking part in the formation of persister cells, which are a subpopulation of recalcitrant cells able to survive antimicrobial treatment without any resistance mechanisms. Importantly, persisters have been associated with long-term infections and treatment failures in healthcare settings. It is a public health concern since persisters can be involved in the evolution and dissemination of antimicrobial resistance amidst the aggravating spread of multidrug-resistant bacteria and insufficient novel antimicrobial therapy to tackle this issue. Salmonella enterica serovar Typhimurium is one of the most prevalent Salmonella serotypes in the world and is a leading cause of food-borne salmonellosis. S. Typhimurium has been known to cause persistent infection and a wealth of investigations on Salmonella persisters indicates that toxin and antitoxin modules play a role in mediating the phenotypic switch of persisters, rendering its survival ability in the presence of antimicrobial agents. In this review, we discuss findings regarding mechanisms that underly persistence in S. Typhimurium, especially the involvement of toxin and antitoxin modules.

Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium

Intestinal inflammation fuels the transmission of Salmonella Typhimurium (S.Tm). However, a substantial fitness cost is associated with virulence expression. Mutations inactivating transcriptional virulence regulators generate attenuated variants profiting from inflammation without enduring virulence cost. Such variants interfere with the transmission of fully virulent clones. Horizontal transfer of functional regulatory genes (HGT) into attenuated variants could nevertheless favor virulence evolution. To address this hypothesis, we cloned hilD, coding for the master regulator of virulence, into a conjugative plasmid that is highly transferrable during intestinal colonization. The resulting mobile hilD allele allows virulence to emerge from avirulent populations, and to be restored in attenuated mutants competing against virulent clones within-host. However, mutations inactivating the mobile hilD allele quickly arise. The stability of virulence mediated by HGT is strongly limited by its cost, which depends on the hilD expression level, and by the timing of transmission. We conclude that robust evolution of costly virulence expression requires additional selective forces such as narrow population bottlenecks during transmission.

Salmonella Typhimurium virulence is costly and can be lost by mutation during infection. Bakkeren et al. show that virulence restoration via horizontal gene transfer is only transient while transmission bottlenecks promote long-term virulence stability.