Role of CRISPR-Cas System as a New Approach in Fighting the Antimicrobial Resistance of Bacterial and Viral Pathogens DOI Creative Commons
Heba Mohammed Refat M. Selim, Fatma Alzahraa M. Gomaa, Mohammad Y. Alshahrani

et al.

Infectious Diseases & Immunity, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

Abstract The clustered regularly interspaced short palindromic repeat (CRISPR)-Caspase (Cas) system acts as a natural defense of bacteria against invasion by mobile genetic elements, such plasmids, transposons, and bacteriophages. review discusses the different classes types CRISPR-Cas systems in terms principles their action, limitations, future perspectives. Also, role new arsenal fighting multidrug-resistant pathogens clinically relevant pathogenic viruses up-to-date clinical trials have been discussed highlighted. Moreover, utilization mode, regulation, link to quorum sensing for targeting cell chromosome or antimicrobial-resistant gene(s) some pathogens, including Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa discussed. information provided this can act platform researchers use smart antimicrobial agent combating infections caused life-threatening particularly those with limited therapeutic options.

Language: Английский

Timescales and genetic linkage explain the variable impact of defense systems on horizontal gene transfer DOI Creative Commons
Yang Liu, João Botelho, Jaime Iranzo

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 29, 2024

Abstract Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange beneficial accessory genes, could consequently impede rapid adaptation in microbial populations. Here, we study how impact horizontal gene transfer (HGT) short and long terms. By combining comparative genomics phylogeny-aware statistical methods, quantified association between presence 7 widespread abundance genomes 196 bacterial 1 archaeal species. We also calculated differences rates gain loss lineages that possess lack each system. Our results show on HGT is highly taxon- system-dependent. CRISPR-Cas stands out as system most often associates with decrease number reduced acquisition. Timescale analysis reveals must persist lineage relatively time exert an appreciable negative HGT. In contrast, at evolutionary times, systems, MGE, tend be positively correlated. Based these given high turnover experienced propose inhibitory effect masked recent co-transfer events involving MGE.

Language: Английский

Citations

4
Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer DOI Creative Commons
Yang Liu, João Botelho, Jaime Iranzo

et al.

Genome Research, Journal Year: 2025, Volume and Issue: unknown, P. gr.279300.124 - gr.279300.124

Published: Jan. 10, 2025

Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange beneficial accessory genes, could consequently impede rapid adaptation in microbial populations. Here, we study how impact horizontal gene transfer (HGT) short and long terms. By combining comparative genomics phylogeny-aware statistical methods, quantified association between presence 7 widespread abundance genomes 196 bacterial 1 archaeal species. We also calculated differences rates gain loss lineages that possess lack each system. Our results show on HGT is highly taxon- system-dependent, most cases not statistically significant. Timescale analysis reveals must persist lineage relatively time exert an appreciable negative HGT. In contrast, shorter evolutionary timescales, frequent co-acquisition net positive latter with Given high turnover experienced systems, propose inhibitory effect masked their strong linkage MGE. These findings help explain contradictory conclusions previous research pointing at mobility within-host retention times as key factors determine genome plasticity.

Language: Английский

Citations

0
Invasive bacteriophages between a bell and a hammer: a comprehensive review of pharmacokinetics and bacterial defense systems DOI Creative Commons

Mohammed F Hamdi,

Alyaa Abdulhussein Alsaedi,

Alaa Qasim Hayder

et al.

Discover Life, Journal Year: 2025, Volume and Issue: 55(1)

Published: April 3, 2025

Language: Английский

Citations

0
Dynamics of CRISPR-mediated virus–host interactions in the human gut microbiome DOI Creative Commons

Adrián López-Beltrán,

João Botelho, Jaime Iranzo

et al.

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying interactions among bacteria, plasmids, phages. Here, we used longitudinal metagenomic data from 130 healthy diseased individuals study how interplay parasites immunity reflects on dynamics human gut microbiome. Based coordinated 80 000 loci their targets, show that effectively modulates bacteriophage abundances gut. Acquisition typically leads a decrease abundance lytic phages but does not necessarily cause complete disappearance. Much smaller effects observed for lysogenic plasmids. Conversely, phage-CRISPR shape bacterial microdiversity producing weak selective sweeps benefit immune host lineages. We also distal (and chronologically older) regions CRISPR arrays enriched spacers potentially functional target crass-like local prophages. This suggests exposure reactivated prophages other endemic viruses is pressure drives maintenance long-lasting memory.

Language: Английский

Citations

3
Characterization of a novel phage SPX1 and biological control for biofilm of Shewanella in shrimp and food contact surfaces DOI
Xi Liu,

Zixin Ming,

Yifeng Ding

et al.

International Journal of Food Microbiology, Journal Year: 2024, Volume and Issue: 426, P. 110911 - 110911

Published: Sept. 10, 2024

Language: Английский

Citations

3
From Forgotten Cure to Modern Medicine: The Resurgence of Bacteriophage Therapy DOI Creative Commons

Tasnime Abdo Ahmad,

Samar El Houjeiry,

Souha S. Kanj

et al.

Journal of Global Antimicrobial Resistance, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

Language: Английский

Citations

2
Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host DOI Creative Commons
Thomas Ipoutcha,

Ιason Τsarmpopoulos,

Géraldine Gourgues

et al.

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(11)

Published: Nov. 18, 2024

Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are bacterial defences that target bacteriophages and mobile genetic elements. How these evolve in novel host environments remains largely unknown. We studied the evolution of CRISPR-Cas system

Language: Английский

Citations

2
Evolution of the CRISPR-Cas9 defence system following a bacterial host shift DOI Open Access
Thomas Ipoutcha,

Ιason Τsarmpopoulos,

Géraldine Gourgues

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 14, 2023

Abstract CRISPR-Cas systems are bacterial defences that target bacteriophages and mobile genetic elements. How these evolve in novel host environments remains, however, unknown. We studied the evolution of system Mycoplasma gallisepticum , a pathogen poultry jumped into passerine ∼30 years ago. Over decade following shift, all isolates displayed functional were found not only to harbour completely new sets spacers, but DNA protospacer adjacent motif (PAM) recognised by main effector MgCas9 was also different. These changes diversity specificity consistent with change community phages elements infecting M. as it colonised host. In we detected gradual rise displaying non-functional MgCas9. After 12 years, circulating harboured inactive forms only. This loss function comes at time when is known have evolved widespread resistance, which turn drove increasing virulence through antagonistic coevolution. Such striking concordance inactivated resistance suggests inactivation necessary for enabling adaptive responses host-driven selection. highlight need consider both selection pressures on bacteria understanding key factors driving emergence pathogenic bacterium Data summary The authors confirm supporting data protocols been provided within article or supplementary files available online version this article. GenBank accession numbers publicly genomes listed Table S3. Sequences CRISPR locus other strains Impact statement minimal involved many diseases affecting humans wide animals. paper, report Type II bird pathogen, an jump from its original house finch early 90’s. Instances pathogens documented subsequently adapt rare, well case unique model evaluate effect any dramatic environmental defence systems. First, performed silico analyses extended set 98 better understand CRISPR-Cas9 several evolutionary events leading drastic divergence spacer present arrays, progressive after Second, using vitro vivo assays, demonstrated PI domain, recognition has led major system, modification recognized PAM radical may implications rapid adaptation Together, our results experiences, complex interplay between

Language: Английский

Citations

4
Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome DOI Creative Commons

Adrián López-Beltrán,

João Botelho, Jaime Iranzo

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 23, 2024

Abstract Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying interactions among bacteria, plasmids, phages. Here, we used longitudinal metagenomic data from 130 healthy diseased individuals study how interplay parasites immunity reflects on dynamics human gut microbiome. Based coordinated 80,000 loci their targets, show that effectively modulates bacteriophage abundances gut. Acquisition typically leads a decrease abundance lytic phages, but does not necessarily cause complete disappearance. Much smaller effects observed for lysogenic phages plasmids. Conversely, phage-CRISPR shape bacterial microdiversity producing weak selective sweeps benefit immune host lineages. Interestingly, distal (and chronologically older) regions CRISPR arrays enriched spacers potentially functional target crass-like local prophages. This suggests exposure reactivated prophages other endemic viruses is pressure drives maintenance long-lasting memory.

Language: Английский

Citations

1
Salicaceae endophyte inoculation alters stomatal patterning and improves the intrinsic water-use efficiency ofPopulus trichocarpaafter a water-deficit DOI Creative Commons
Matthew Hendrickson, Darshi Banan, Robert Tournay

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 12, 2024

ABSTRACT Microorganisms may enhance plant resilience to water stress by influencing their hosts’ physiology and anatomy at the leaf-level. Bacterial yeast endophytes, isolated from wild poplar willow, can improve intrinsic water-use efficiency ( iWUE ) of cultivated Populus under water-deficits lowering stomatal conductance g sw ). However, relevance underlying this reduction remains unclear. We hypothesized endophyte inoculation could change host anatomy, would relate decreases in . subjected Salicaceae endophyte-inoculated uninoculated trichocarpa well-watered water-deficit treatments greenhouse studies. examined changes individual traits related composition these parameters, termed patterning, leaf gas-exchange light saturation. After a water-deficit, improved saturation preserving carbon assimilation A net , but were independent soil-moisture status. Drops corresponded shifts patterning. Inoculated plants had smaller, more compact stomata greater anatomical maximum smax relative control. endophytes alter density size, increasing Future efforts quantify colonization draw direct relationships between microbes traits. HIGHLIGHT Poplars inoculated with specific bacteria leaves containing many, tiny pores trees without microbes; small, dense efficiency.

Language: Английский

Citations

1