Role of CRISPR/cas System in the Development of Bacteriophage Resistance

Szczepankowska, Agnieszka K.

doi:10.1016/b978-0-12-394621-8.00011-x

Cited by 30 publications

(25 citation statements)

References 109 publications

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“…Integrated phages (prophages), which represent a sizable fraction of bacterial chromosomes, are major contributors to differences among individuals within a bacterial species8. Although acquisition of phage DNA can increase the fitness of host bacteria under certain environmental conditions, the replication and maintenance of these nucleotide sequences could be a burden9. Overall, predation by phages presents a serious challenge to bacterial survival; hence, bacteria have evolved numerous mechanisms to resist phage infection9.…”

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confidence: 99%

The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii

Zeng

Zhang

et al. 2017

Sci Rep

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Cronobacter sakazakii is an important foodborne pathogens causing rare but life-threatening diseases in neonates and infants. CRISPR-Cas system is a new prokaryotic defense system that provides adaptive immunity against phages, latter play an vital role on the evolution and pathogenicity of host bacteria. In this study, we found that genome sizes of C. sakazakii strains had a significant positive correlation with total genome sizes of prophages. Prophages contributed to 16.57% of the genetic diversity (pan genome) of C. sakazakii, some of which maybe the potential virulence factors. Subtype I-E CRISPR-Cas system and five types of CRISPR arrays were found in the conserved site of C. sakazakii strains. CRISPR1 and CRISPR2 loci with high variable spacers were active and showed potential protection against phage attacks. The number of spacers from two active CRISPR loci in clinical strains was significant less than that of foodborne strains, it maybe a reason why clinical strains were found to have more prophages than foodborne strains. The frequently gain/loss of prophages and spacers in CRISPR loci is likely to drive the quick evolution of C. sakazakii. Our study provides a new insight into the co-evolution of phages and C. sakazakii.

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confidence: 99%

The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii

Zeng

Zhang

et al. 2017

Sci Rep

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“…Creating ⌬mazG mutants of M. tuberculosis and evaluating the ability of phAE901/ ⌽ 2 GFP13 to form plaques on them could reveal another host system that mycobacteriophage can commandeer. Bacteria utilize a wide variety of systems to prevent phage infection, including restriction-modification (R-M) systems, abortive infection systems (Abis), and clustered regularly interspaced short palindromic repeat (CRISPR) systems (44)(45)(46), but few such systems have been characterized in mycobacteria. Our novel DS6A fluorophages allow us to start evaluating if these systems operate in NTM.…”

Section: Discussionmentioning

confidence: 99%

Fluorescent Reporter DS6A Mycobacteriophages Reveal Unique Variations in Infectibility and Phage Production in Mycobacteria

et al. 2016

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Mycobacteriophage DS6A is unique among the more than 8,000 isolated mycobacteriophages due to its ability to form plaques exclusively on mycobacteria belonging to the Mycobacterium tuberculosis complex (MTBC). Speculation surrounding this specificity has led to unsupported assertions in published studies and patents that nontuberculous mycobacteria (NTM) are wholly resistant to DS6A infection. In this study, we identified two independent nonessential regions in the DS6A genome and replaced them with an mVenus-expressing plasmid to generate fluorescent reporter phages ⌽ 2 GFP12 and ⌽ 2 GFP13. We show that even though DS6A is able to form plaques only on MTBC bacteria, infection of various NTM results in mVenus expression in transduced cells. The efficiency of DS6A in delivering DNA varied between NTM species. Additionally, we saw a striking difference in the efficiency of DNA delivery between the closely related members of the Mycobacterium abscessus complex, M. abscessus and Mycobacterium massiliense. We also demonstrated that TM4 and DS6A, two phages that do not form plaques on M. massiliense, differ in their ability to deliver DNA, suggesting that there is a phage-specific restriction between mycobacterial species. Phylogenetic analysis reveals that the DS6A genome has a characteristically mosaic structure but provided few insights into the basis for the specificity for MTBC hosts. This study demonstrates that the inability of the MTBC-specific phage DS6A to form plaques on NTM is more complex than previously thought. Moreover, the DS6A-derived fluorophages provide important new tools for the study of mycobacterial biology. IMPORTANCEThe coevolution of bacteria and their infecting phages involves a constant arms race for bacteria to prevent phage infection and phage to overcome these preventions. Although a diverse array of phage defense systems is well characterized in bacteria, very few phage restriction systems are known in mycobacteria. The DS6A mycobacteriophage is unique in the mycobacterial world in that it forms plaques only on members of the Mycobacterium tuberculosis complex. However, the novel DS6A reporter phages developed in this work demonstrate that DS6A can infect nontuberculous mycobacteria at various efficiencies. By comparing the abilities of DS6A and another phage, TM4, to infect and form plaques on various mycobacterial species, we can begin to discern new phage restriction systems employed within the genus. The standard treatment for a drug-susceptible Mycobacterium tuberculosis infection is four drugs (rifampin, isoniazid, pyrazinamide, and ethambutol) for 2 months, followed by 4 months of two drugs (rifampin and isoniazid). One of the key aspects of successfully treating tuberculosis is ensuring that the infecting strain is susceptible to each of the antibiotics given; therefore, quickly diagnosing antibiotic resistance is important for successful patient outcome as well as for lowering the incidence of the generation of drug-resistant mutants from improper antibiotic administra...

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“…CRISPR arrays are in most cases adjacent to cas genes that encode a set of functionally very diverse proteins. These proteins carry functional domains typical of helicase, polymerase, nuclease, and polynucleotide-binding proteins (Makarova et al, 2011) and are essential to CRISPR-Cas system activity (Barrangou et al, 2007; Brouns et al, 2008; Szczepankowska, 2012). cas genes and the proteins they encode are diverse but usually highly conserved within a given CRISPR-Cas type, and thus represent an important criterion of CRISPR-Cas system classification.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the type II-A CRISPR-Cas system of Streptococcus agalactiae reveals distinctive features according to genetic lineages

et al. 2015

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CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) are found in 90% of archaea and about 40% of bacteria. In this original system, CRISPR arrays comprise short, almost unique sequences called spacers that are interspersed with conserved palindromic repeats. These systems play a role in adaptive immunity and participate to fight non-self DNA such as integrative and conjugative elements, plasmids, and phages. In Streptococcus agalactiae, a bacterium implicated in colonization and infections in humans since the 1960s, two CRISPR-Cas systems have been described. A type II-A system, characterized by proteins Cas9, Cas1, Cas2, and Csn2, is ubiquitous, and a type I–C system, with the Cas8c signature protein, is present in about 20% of the isolates. Unlike type I–C, which appears to be non-functional, type II-A appears fully functional. Here we studied type II-A CRISPR-cas loci from 126 human isolates of S. agalactiae belonging to different clonal complexes that represent the diversity of the species and that have been implicated in colonization or infection. The CRISPR-cas locus was analyzed both at spacer and repeat levels. Major distinctive features were identified according to the phylogenetic lineages previously defined by multilocus sequence typing, especially for the sequence type (ST) 17, which is considered hypervirulent. Among other idiosyncrasies, ST-17 shows a significantly lower number of spacers in comparison with other lineages. This characteristic could reflect the peculiar virulence or colonization specificities of this lineage.

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Role of CRISPR/cas System in the Development of Bacteriophage Resistance

Cited by 30 publications

References 109 publications

The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii

The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii

Fluorescent Reporter DS6A Mycobacteriophages Reveal Unique Variations in Infectibility and Phage Production in Mycobacteria

Analysis of the type II-A CRISPR-Cas system of Streptococcus agalactiae reveals distinctive features according to genetic lineages

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