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Bacterial defences: mechanisms, evolution and antimicrobial resistance

NATURE REVIEWS MICROBIOLOGY (2023)

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Bacteria elicit a phage tolerance response subsequent to infection of their neighbors

Elhanan Tzipilevich et al.

Summary: When bacteria sense infection of their neighbors, a temporary phage tolerance response is triggered, which is primarily executed by the stress-response RNA polymerase sigma factor sigma(X) (SigX). This response activates the dlt operon, encoding enzymes that hinder phage binding and infection, allowing uninfected bacteria to form a protective shield against phage spread.

EMBO JOURNAL (2022)

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Review Biochemistry & Molecular Biology

Challenges and opportunities for cheat therapy in the control of bacterial infections

James Gurney et al.

Summary: The article discusses how bacterial pathogens communicate and cooperate within groups to make us sick, and introduces two cheat therapy methods. These methods, including genetic engineering and chemical induction, can reduce pathogen burden and disease severity, but also face challenges of instability in efficacy.

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Article Multidisciplinary Sciences

Emergence of methicillin resistance predates the clinical use of antibiotics

Jesper Larsen et al.

Summary: This study reveals that methicillin-resistant Staphylococcus aureus (MRSA) strains were present in European hedgehogs before the discovery of antibiotics and have spread among hedgehog populations and between hedgehogs and secondary hosts. The study also shows that the hedgehog dermatophyte Trichophyton erinacei produces two beta-lactam antibiotics that give an advantage to MRSA strains. These findings emphasize the importance of understanding and managing antibiotic resistance in both wild animals and different ecosystems.

NATURE (2022)

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Article Multidisciplinary Sciences

Bacterial gasdermins reveal an ancient mechanism of cell death

Alex G. Johnson et al.

Summary: Gasdermin proteins play important roles in immune regulation and induction of cell death in human cells by forming membrane pores. Similar proteins encoded by bacteria have been found to defend against phages and execute cell death.

SCIENCE (2022)

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Article Biochemistry & Molecular Biology

Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?

Eduardo P. C. Rocha et al.

Summary: Prokaryotes possess mobile genetic elements that enable horizontal gene transfer between cells. These elements contain defense systems to filter, control, or inactivate other elements. The abundance of defense systems in these mobile genetic elements sheds new light on their role as tools of intragenomic conflict.

PLOS BIOLOGY (2022)

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Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism

See-Yeun Ting et al.

Summary: Pseudomonas aeruginosa shows a coordinated defense against bacterial threats by activating conserved interbacterial antagonism resistance clusters, similar to eukaryotic innate immunity.

ELIFE (2022)

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Review Microbiology

Interactions between bacterial and phage communities in natural environments

Anne Chevallereau et al.

Summary: This review explores the composition and evolution of phage communities and their roles in controlling the population and evolutionary dynamics of bacterial communities. The study emphasizes the need for greater ecological realism in laboratory studies to better understand the complexity of microbial communities thriving in natural environments.

NATURE REVIEWS MICROBIOLOGY (2022)

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Bacterial motility: machinery and mechanisms

Navish Wadhwa et al.

Summary: Bacteria have developed different mechanisms for motility to utilize resources and environments. They can swim in aqueous media through rotation of helical filaments, or move over solid surfaces using various mechanisms such as twitching, gliding, and sliding. Recent technological advances have improved our understanding of the molecular machinery behind bacterial motility.

NATURE REVIEWS MICROBIOLOGY (2022)

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Bacterial DNA excision repair pathways

Katherine J. Wozniak et al.

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NATURE REVIEWS MICROBIOLOGY (2022)

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Bacterial species rarely work together

Jacob D. Palmer et al.

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Michael Hunter et al.

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RtcB2-PrfH Operon Protects E. coli ATCC25922 Strain from Colicin E3 Toxin

Tinashe P. Maviza et al.

Summary: Bacterial species have evolved to protect themselves by using antibiotics and toxins to fight off rival species. A recent study found that a specific toxin called colicin E3 ribotoxin can damage the translational apparatus of bacteria, but competing bacteria may have evolved counter-conflict mechanisms to prevent their demise. The study also showed that the RtcB2-PrfH module can confer resistance to colicin E3 toxicity in E. coli cells.

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Fast bacterial growth reduces antibiotic accumulation and efficacy

Urszula Lapinska et al.

Summary: Phenotypic variations in microbial cells, driven by differences in drug transport rates, play a crucial role in the resistance of microbial pathogens to pharmacotherapies. This study used microfluidics-based single-cell microscopy and fluorescent antibiotic probes to identify phenotypic variants that avoid antibiotic accumulation. Surprisingly, fast growing variants were found to avoid macrolide accumulation and survive treatment without genetic mutations, contrary to current consensus. These fast growing variants also showed higher expression of ribosomal promoters, facilitating essential cellular processes and reducing macrolide accumulation. This new knowledge can be used to develop strategies to overcome antibiotic treatment failures.

ELIFE (2022)

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Article Microbiology

An expanded arsenal of immune systems that protect bacteria from phages

Adi Millman et al.

Summary: This study reports the discovery of 21 bacterial defense systems against phages. These systems contain domains involved in eukaryotic antiviral immunity and are widely distributed in microbial genomes. These findings contribute to our understanding of the defense mechanisms bacteria use against phage infection.

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The evolution of spectrum in antibiotics and bacteriocins

Jacob D. Palmera et al.

Summary: A key property of many antibiotics is their broad-spectrum activity, which allows them to kill or inhibit a wide range of microbial species. However, some bacteria also produce narrow-spectrum toxins to specifically target their conspecifics. An evolutionary model suggests that broad-spectrum toxins are favored when a strain is highly abundant and can overpower both its key competitor and other species. The analysis of a toxin regulation and spectrum database supports this prediction, showing a strong association between broad-spectrum toxins and density-dependent regulation.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome

Christopher N. Vassallo et al.

Summary: The study identified numerous new candidate defense systems in E. coli using an experimental selection scheme, demonstrating that intact prophages and mobile genetic elements are primary reservoirs and distributors of defense systems.

NATURE MICROBIOLOGY (2022)

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Bacterial origins of human cell-autonomous innate immune mechanisms

Tanita Wein et al.

Summary: This paper describes the elements of antiviral immunity that are conserved from bacteria to humans and presents possible evolutionary scenarios to explain this conservation.

NATURE REVIEWS IMMUNOLOGY (2022)

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The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution

Joao Botelho et al.

Summary: Mobile genetic elements (MGEs) play a key role in the spread of antibiotic resistance, with the coevolution between bacteria and MGEs shaping their transfer and stability. Despite the abundance of ICEs, the dynamics of ICE-bacterium coevolution remain largely unexplored. Both conjugative plasmids and ICEs are transferred via type IV secretion systems, but the immunity to segregational loss in ICEs results in different evolutionary paths for ICE-bacterium associations compared to plasmid-bacterium associations.

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Prokaryotic viperins produce diverse antiviral molecules

Aude Bernheim et al.

Summary: Eukaryotic viperins originated from a clade of bacterial and archaeal proteins that protect against phage infection. These proteins produce modified ribonucleotides to combat viruses. Prokaryotic viperins can inhibit T7 phage infection by blocking viral polymerase-dependent transcription.

NATURE (2021)

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Predatory bacteria as living antibiotics-where are we now?

Robert J. Atterbury et al.

Summary: Antimicrobial resistance (AMR) is a global health and economic crisis. There is a critical need for new therapies to treat Gram-negative infections due to limited antibiotics in development to meet current and anticipated needs. Predatory bacteria, such as Bdellovibrio bacteriovorus, are being researched as potential alternatives to antibiotics.

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Roderich Roemhild et al.

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Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion

Jordan Vacheron et al.

Summary: This study investigates the mechanisms by which environmentally important Pseudomonas bacteria perform kin interference competition through the use of R-tailocins. The findings demonstrate the deadly impact of cellular self-sacrifice coupled with deployment of phage tail-like weaponry on closely-related bacterial competitors, highlighting the importance of microscale assessment in microbial competitions.

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Bacterial defense islands limit viral attack

Sean Meaden et al.

SCIENCE (2021)

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Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages

Fatima Aysha Hussain et al.

Summary: In marine Vibrio, phage resistance evolves rapidly and leads to differential susceptibility among bacterial strains. This resistance is cumulative, with each bacterial genome carrying multiple defense elements. The fast evolution of these elements decouples phage resistance from other genomic features.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Droplet printing reveals the importance of micron-scale structure for bacterial ecology

Ravinash Krishna Kumar et al.

Summary: The spatial arrangement of bacterial strains and species within microbial communities is considered crucial for their ecology. Krishna Kumar et al. use a droplet-based printing method to arrange different bacterial genotypes across a sub-millimetre array, and show that micron-scale changes in spatial distributions can drive major shifts in ecology.

NATURE COMMUNICATIONS (2021)

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Article Biochemistry & Molecular Biology

Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics

Lucas A. Meirelles et al.

Summary: Bacterial opportunistic pathogens with intrinsic antibiotic resistance can be driven by their evolutionary history as environmental chemical warfare microbes. Self-produced antibiotics by these pathogens can dramatically modulate the efficacy of clinical antibiotics and the evolution of antibiotic resistance for themselves and other members of clinically relevant polymicrobial communities.

PLOS BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Ecological rules for the assembly of microbiome communities

Katharine Z. Coyte et al.

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PLOS BIOLOGY (2021)

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Article Biology

Integron activity accelerates the evolution of antibiotic resistance

Celia Souque et al.

Summary: Integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity.

ELIFE (2021)

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Human commensal gut Proteobacteria withstand type VI secretion attacks through immunity protein-independent mechanisms

Nicolas Flaugnatti et al.

Summary: The study reveals mechanisms by which certain bacteria are protected from Vibrio cholerae's T6SS attacks, including through superior T6SS weaponry and molecular armors made of membrane-tethered capsular polysaccharides of diverse Klebsiella isolates. Meanwhile, the pathogen efficiently depletes representative genera of Proteobacteria in vitro, while members of the Enterobacter cloacae complex and several Klebsiella species remain unaffected.

NATURE COMMUNICATIONS (2021)

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Bacterial predation transforms the landscape and community assembly of biofilms

Benjamin R. Wucher et al.

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CURRENT BIOLOGY (2021)

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Modular Design of Membrane-Active Antibiotics: From Macromolecular Antimicrobials to Small Scorpionlike Peptidomimetics

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The metabolic network of the last bacterial common ancestor

Joana C. Xavier et al.

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The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins

Alexander Martin Geller et al.

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NATURE COMMUNICATIONS (2021)

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Matrix-trapped viruses can prevent invasion of bacterial biofilms by colonizing cells

Matthew C. Bond et al.

Summary: Bacteriophages can be trapped in the biofilm matrix, remaining viable and able to kill susceptible cells, even if colonizing cells are present prior to phage exposure. Colonizing cells gain phage protection by being enveloped in curli-producing clusters of resident biofilm cells if they are present on the biofilm long enough before phage exposure.

ELIFE (2021)

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High potency of sequential therapy with only β-lactam antibiotics

Aditi Batra et al.

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The evolution of strategy in bacterial warfare via the regulation of bacteriocins and antibiotics

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The stringent response and physiological roles of (pp)pGpp in bacteria

Sophie E. Irving et al.

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Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host

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Vibrio cholerae motility exerts drag force to impede attack by the bacterial predator Bdellovibrio bacteriovorus

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Sensor histidine kinase is a β-lactam receptor and induces resistance to β-lactam antibiotics

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Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli

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Remarkable Mechanisms in Microbes to Resist Phage Infections

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Natural antimicrobial peptides from bacteria: characteristics and potential applications to fight against antibiotic resistance

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Heterogeneity in Pseudomonas aeruginosa Biofilms Includes Expression of Ribosome Hibernation Factors in the Antibiotic-Tolerant Subpopulation and Hypoxia-Induced Stress Response in the Metabolically Active Population

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Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli LsoA and RnlA toxins

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Evidence for Induction of Integron-Based Antibiotic Resistance by the SOS Response in a Clinical Setting

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Shiga toxin in enterohemorrhagic E.coli: regulation and novel anti-virulence strategies

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Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes

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Contribution of bacterial outer membrane vesicles to innate bacterial defense

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BMC MICROBIOLOGY (2011)

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Escherichia coli rnlA and rnlB Compose a Novel Toxin-Antitoxin System

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Activation of the SoxR Regulon in Streptomyces coelicolor by the Extracellular Form of the Pigmented Antibiotic Actinorhodin

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Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

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Genetic Response to Bacteriophage Infection in Lactococcus lactis Reveals a Four-Strand Approach Involving Induction of Membrane Stress Proteins, D-Alanylation of the Cell Wall, Maintenance of Proton Motive Force, and Energy Conservation

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Genomic island variability facilitates Prochlorococcus-virus coexistence

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Predator-Prey Chemical Warfare Determines the Expression of Biocontrol Genes by Rhizosphere-Associated Pseudomonas fluorescens

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A Transcriptional Scream Early Response of E. coli Prey to Predatory Invasion by Bdellovibrio

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Antagonistic coevolution accelerates molecular evolution

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A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria

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Impact of recombination on bacterial evolution

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Protozoan-Induced Regulation of Cyclic Lipopeptide Biosynthesis Is an Effective Predation Defense Mechanism for Pseudomonas fluorescens

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The natural history of antibiotics

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Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within Gram-negative bacteria

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Bacterial Attraction and Quorum Sensing Inhibition in Caenorhabditis elegans Exudates

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Social evolution in micro-organisms and a Trojan horse approach to medical intervention strategies

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ramR mutations involved in efflux-mediated multidrug resistance in Salmonella enterica serovar Typhimurium

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agr-mediated dispersal of Staphylococcus aureus biofilms

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Quorum-sensing regulation of the production of blp bacteriocins in Streptococcus thermophilus

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Evolutionary theory of bacterial quorum sensing: when is a signal not a signal?

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Evolution and ecology of antibiotic resistance genes

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Initiation of actinorhodin export in Streptomyces coelicolor

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Cooperation and conflict in microbial biofilms

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The emergence of antibiotic resistance by mutation

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Characterizing the flagellar filament and the role of motility in bacterial prey-penetration by Bdellovibrio bacteriovorus

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Escherichia coli K1's capsule is a barrier to bacteriophage T7

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High motility reduces grazing mortality of planktonic bacteria

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Dynamics and spatial distribution of β-lactamase expression in Pseudomonas aeruginosa biofilms

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Bacterial persistence as a phenotypic switch

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Protozoan predation, diversifying selection, and the evolution of antigenic diversity in Salmonella

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Quorum sensing controls biofilm formation in Vibrio cholerae

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Stress-induced mutagenesis in bacteria

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Guanine nucleotides guanosine 5′-diphosphate 3′-diphosphate and GTP co-operatively regulate the production of an antibiotic bacilysin in Bacillus subtilis

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The importance of efflux pumps in bacterial antibiotic resistance

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Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors

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The role of integrons in antibiotic resistance gene capture

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Bacteriocin diversity: ecological and evolutionary perspectives

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The pyocins of Pseudomonas aeruginosa

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Chemical warfare between microbes promotes biodiversity

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

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The TolC protein of Escherichia coli serves as a cell-surface receptor for the newly characterized TLS bacteriophage

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Microbial fermentation-derived inhibitors of efflux-pump-mediated drug resistance

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FARMACO (2001)

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The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage

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MOLECULAR MICROBIOLOGY (2000)

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