Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans.

Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module, feature a DinG helicase instead of a nuclease, and form ribonucleoprotein complexes of unknown biological functions. Type IV-A3 systems are carried by conjugative plasmids that often harbor antibiotic-resistance genes and their CRISPR array contents suggest a role in mediating inter-plasmid conflicts, but this function remains unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system co-opts the type I-E adaptation machinery from its host, Klebsiella pneumoniae (K.

Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro.

Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains.

Antibiotic-degrading resistance changes bacterial community structure via species-specific responses.

Some bacterial resistance mechanisms degrade antibiotics, potentially protecting neighbouring susceptible cells from antibiotic exposure. We do not yet understand how such effects influence bacterial communities of more than two species, which are typical in nature. Here, we used experimental multispecies communities to test the effects of clinically important pOXA-48-plasmid-encoded resistance on community-level responses to antibiotics.

Host-specific plasmid evolution explains the variable spread of clinical antibiotic-resistance plasmids.

Antibiotic resistance encoded on plasmids is a pressing global health problem. Predicting which plasmids spread in the long term remains very challenging, even though some key parameters influencing plasmid stability have been identified, such as plasmid growth costs and horizontal transfer rates. Here, we show these parameters evolve in a strain-specific way among clinical plasmids and bacteria, and this occurs rapidly enough to alter the relative likelihoods of different bacterium-plasmid combinations spreading.

Community composition of bacteria isolated from Swiss banknotes varies depending on collection environment.

Humans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear.

Estimating plasmid conjugation rates: A new computational tool and a critical comparison of methods.

Plasmids are important vectors for the spread of genes among diverse populations of bacteria. However, there is no standard method to determine the rate at which they spread horizontally via conjugation. Here, we compare commonly used methods on simulated and experimental data, and show that the resulting conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations.

Rapid decline of adaptation of to soil biotic environment.

Interactions between microbes can both constrain and enhance their adaptation to the environment. However, most studies to date have employed simplified microbial communities and environmental conditions. We determined how the presence of a commercial potting compost microbial community affected adaptation of the soil bacterium SBW25 in potting compost.

Exposure to lysed bacteria can promote or inhibit growth of neighboring live bacteria depending on local abiotic conditions.

Microbial death is extremely common in nature, yet the ecological role of dead bacteria is unclear. Dead cells are assumed to provide nutrients to surrounding microbes, but may also affect them in other ways. We found that adding lysate prepared from dead bacteria to cultures of Escherichia coli in nutrient-rich conditions suppressed their final population density.

Collateral Sensitivity Interactions between Antibiotics Depend on Local Abiotic Conditions.

Mutations conferring resistance to one antibiotic can increase (cross-resistance) or decrease (collateral sensitivity) resistance to others. Antibiotic combinations displaying collateral sensitivity could be used in treatments that slow resistance evolution. However, lab-to-clinic translation requires understanding whether collateral effects are robust across different environmental conditions.

Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota.

Background And Objectives: Slowing the spread of antimicrobial resistance is urgent if we are to continue treating infectious diseases successfully. There is increasing evidence microbial interactions between and within species are significant drivers of resistance. On one hand, cross-protection by resistant genotypes can shelter susceptible microbes from the adverse effects of antibiotics, reducing the advantage of resistance.

Evolution of honey resistance in experimental populations of bacteria depends on the type of honey and has no major side effects for antibiotic susceptibility.

With rising antibiotic resistance, alternative treatments for communicable diseases are increasingly relevant. One possible alternative for some types of infections is honey, used in wound care since before 2000 BCE and more recently in licensed, medical-grade products. However, it is unclear whether medical application of honey results in the evolution of bacterial honey resistance and whether this has collateral effects on other bacterial traits such as antibiotic resistance.

Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples.

Biological invasions can alter ecosystem stability and function, and predicting what happens when a new species or strain arrives remains a major challenge in ecology. In the mammalian gastrointestinal tract, susceptibility of the resident microbial community to invasion by pathogens has important implications for host health. However, at the community level, it is unclear whether susceptibility to invasion depends mostly on resident community composition (which microbes are present), or also on local abiotic conditions (such as nutrient status).

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics.

In light of their adverse impacts on resident microbial communities, it is widely predicted that broad-spectrum antibiotics can promote the spread of resistance by releasing resistant strains from competition with other strains and species. We investigated the competitive suppression of a resistant strain of Escherichia coli inoculated into human-associated communities in the presence and absence of the broad and narrow spectrum antibiotics rifampicin and polymyxin B, respectively. We found strong evidence of community-level suppression of the resistant strain in the absence of antibiotics and, despite large changes in community composition and abundance following rifampicin exposure, suppression of the invading resistant strain was maintained in both antibiotic treatments.

Using ecological coexistence theory to understand antibiotic resistance and microbial competition.

Tackling antibiotic resistance necessitates deep understanding of how resource competition within and between species modulates the fitness of resistant microbes. Recent advances in ecological coexistence theory offer a powerful framework to probe the mechanisms regulating intra- and interspecific competition, but the significance of this body of theory to the problem of antibiotic resistance has been largely overlooked. In this Perspective, we draw on emerging ecological theory to illustrate how changes in resource niche overlap can be equally important as changes in competitive ability for understanding costs of resistance and the persistence of resistant pathogens in microbial communities.

Fitness benefits to bacteria of carrying prophages and prophage-encoded antibiotic-resistance genes peak in different environments.

Understanding the role of horizontal gene transfer (HGT) in adaptation is a key challenge in evolutionary biology. In microbes, an important mechanism of HGT is prophage acquisition (phage genomes integrated into bacterial chromosomes). Prophages can influence bacterial fitness via the transfer of beneficial genes (including antibiotic-resistance genes, ARGs), protection from superinfecting phages, or switching to a lytic lifecycle that releases free phages infectious to competitors.

Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris murisinfection.

Studies of controlled lab animals and natural populations represent two insightful extremes of microbiota research. We bridged these two approaches by transferring lab-bred female C57BL/6 mice from a conventional mouse facility to an acclimation room and then to an outdoor enclosure, to investigate how the gut microbiota changes with environment. Mice residing under constant conditions served as controls.

Measuring Coevolutionary Dynamics in Species-Rich Communities.

Identifying different types of coevolutionary dynamics is important for understanding biodiversity and infectious disease. Past work has often focused on pairs of interacting species, but observations of extant communities suggest that coevolution in nature occurs in networks of antagonism and mutualism. We discuss challenges for measuring coevolutionary dynamics in species-rich communities, and we suggest ways that established approaches used for two-species interactions can be applied.

Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples.

Countering the rise of antibiotic-resistant pathogens requires improved understanding of how resistance emerges and spreads in individual species, which are often embedded in complex microbial communities such as the human gut microbiome. Interactions with other microorganisms in such communities might suppress growth and resistance evolution of individual species (e.g.

Associations between sensitivity to antibiotics, disinfectants and heavy metals in natural, clinical and laboratory isolates of Escherichia coli.

Bacteria in nature often encounter non-antibiotic antibacterials (NAAs), such as disinfectants and heavy metals, and they can evolve resistance via mechanisms that are also involved in antibiotic resistance. Understanding whether susceptibility to different types of antibacterials is non-randomly associated across natural and clinical bacteria is therefore important for predicting the spread of resistance, yet there is no consensus about the extent of such associations or underlying mechanisms. We tested for associations between susceptibility phenotypes of 93 natural and clinical Escherichia coli isolates to various NAAs and antibiotics.

Impact of bile salts on coevolutionary dynamics between the gut bacterium Escherichia coli and its lytic phage PP01.

Although host and parasites are typically embedded in complex abiotic and biotic environments our understanding of how environmental variation impacts on host-parasite interactions, including antagonistic coevolution (AC) is poorly understood. Nonetheless, previous studies using bacteria and bacteriophages have shown that variation in just one abiotic parameter can have profound effects not only on the type of AC dynamics observed but also the time-frames over which AC interactions can persist. Here, we investigated the effect of an important component of the abiotic human gut environment, bile salts, on AC dynamics between the bacterium Escherichia coli and the lytic phage PP01 in an in vitro model system.

Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis.

Transition bias, an overabundance of transitions relative to transversions, has been widely reported among studies of the rates and spectra of spontaneous mutations. However, demonstrating the role of transition bias in adaptive evolution remains challenging. In particular, it is unclear whether such biases direct the evolution of bacterial pathogens adapting to treatment.

Coevolutionary dynamics shape the structure of bacteria-phage infection networks.

Coevolution-reciprocal evolutionary change among interacting species driven by natural selection-is thought to be an important force in shaping biodiversity. This ongoing process takes place within tangled networks of species interactions. In microbial communities, evolutionary change between hosts and parasites occurs at the same time scale as ecological change.

Resistance Gene Carriage Predicts Growth of Natural and Clinical Isolates in the Absence of Antibiotics.

Bacterial pathogens that carry antibiotic resistance alleles sometimes pay a cost in the form of impaired growth in antibiotic-free conditions. This cost of resistance is expected to be a key parameter for understanding how resistance spreads and persists in pathogen populations. Analysis of individual resistance alleles from laboratory evolution and natural isolates has shown they are typically costly, but these costs are highly variable and influenced by genetic variation at other loci.