Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies

Karimi, Zahra; Ahmadi, Ali; Najafi, Ali; Ranjbar, Reza

doi:10.2174/1874285801812010059

Cited by 36 publications

(27 citation statements)

References 80 publications

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“…Although the characteristics of CRISPR/Cas systems in Kp are still not fully understood, they are mainly distributed mainly in ST15 isolates [23], including in Brazil [3], suggesting that this is a clonal feature. Additionally, CRISPR/Cas sequence analyses have been used as a complementary bacterial typing tool, and for evolutionary and epidemiological studies [24].…”

Section: Resultsmentioning

confidence: 99%

Emergence of mgrB locus deletion mediating polymyxin resistance in pandemic KPC-producing Klebsiella pneumoniae ST15 lineage

Longo

Fontana

Sousa

et al. 2021

Journal of Medical Microbiology

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Klebsiella pneumoniae causes a diversity of infections in both healthcare and community settings. This pathogen is showing an increased ability to accumulate antimicrobial resistance and virulence genes, making it a public health concern. Here we describe the whole-genome sequence characteristics of an ST15 colistin-resistant K. pneumoniae isolate obtained from a blood culture of a 79-year-old female patient admitted to a university hospital in Brazil. Kp14U04 was resistant to most clinically useful antimicrobial agents, remaining susceptible only to aminoglycosides and fosfomycin. The colistin resistance in this isolate was due to a ~1.3 kb deletion containing four genes, namely mgrB, yebO, yobH and the transcriptional regulator kdgR. The study isolate presented a variety of antimicrobial resistance genes, including the carbapenemase-encoding gene bla KPC-2, the extended-spectrum beta-lactamase (ESBL)-encoding gene bla SHV-28 and the beta-lactamase-encoding gene bla OXA-1. Additionally, Kp14U04 harboured a multiple stress resistance protein, efflux systems and regulators, heavy metal resistance and virulence genes, plasmids, prophage-related sequences and genomic islands. These features revealed the high potential of this isolate to resist antimicrobial therapy, survive in adverse environments, cause infections and overcome host defence mechanisms.

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Section: Resultsmentioning

confidence: 99%

Emergence of mgrB locus deletion mediating polymyxin resistance in pandemic KPC-producing Klebsiella pneumoniae ST15 lineage

Longo

Fontana

Sousa

et al. 2021

Journal of Medical Microbiology

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“…Table 6). The CRISPR-Cas system; consisting of the CRISPR array and cas gene is a versatile system in bacteria that procures immunity against exogenous DNA (Karimi et. al., 2018).…”

Section: Crispr-cas Systemmentioning

confidence: 99%

Whole genome analysis and characterization of Salmonella enterica subsp. enterica serovar Typhimurium strain UPM 260 for mediated genetic manipulation

Ns¹,

Nm²,

Ar³

et al. 2020

Preprint

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Background Salmonella enterica serovar Typhimurium persists as one of the most frequent food-borne zoonoses, causing a major public health concern worldwide. Furthermore, Salmonella infection has a large economic impact. Globally, the main sources of infection for humans include the consumption of contaminated poultry meat and eggs. In animals however, Salmonella transmission usually occurs horizontally from infected birds and contaminated environments. Hence, to delve further on how the impact of this disease can be lessened, an epidemiological study needs to be performed. It is vital to determine the genomic sequences of microorganisms to understand their biology and functional characterization. Thus, we determined the whole-genome sequence and virulence profile of S. enterica serovar Typhimurium strain UPM 260 isolated from Perak, Malaysia. Whole genome sequencing (WGS) using paired-end sequencing generated 107 contigs with a total genome size of 4.9 Mbp and 52% G+C content. The contigs were annotated for phylogenetic and functional analysis. Results Through the analysis, it is revealed that the genome were resistant to a number of antimicrobial drug classes including aminoglycoside, fluoroquinolone, tetracycline and phenicol. Also found in UPM 260 genome were three intact prophages (Fels-1, Gifsy-2 and one unique prophage, mEp390). The genome housed four types of restriction-modification systems (RMS) and Type I-E subtype of CRISPR-Cas system. Two metal resistance operons (mer and cop) and six pathogenicity islands (SPIs) were also discovered in UPM 260 genome. The SPIs contributed mostly to the bacterial virulence properties since 1054 CDS were reported to be homologous to the virulence factors in the database VFDB. Conclusion This study benefits us specifically in the field of genome engineering where gene-based genetic manipulations can be applied in reducing the prevalence and pathogenicity in Salmonella.

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“…Conversely, some reports demonstrate a positive correlation between the CRISPR and pathogenicity owing to virulence genes regulation 9 . S. enterica possesses type I–E CRISPR system with two CRISPR arrays, CRISPR1 and CRISPR2 10 , separated by ~16 kb 11 . Many proto-spacers of this were traced on the chromosome instead of its general target - phages and plasmids 12 .…”

Section: Introductionmentioning

confidence: 99%

The Phylogenomics of CRISPR-Cas System inSalmonella: an evolutionary race with housekeeping genes

Kushwaha¹,

Lahiri

Abdella

et al. 2020

Preprint

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AbstractSalmonellae display intricate evolutionary patterns comprising over 2500 serovars having diverse pathogenic profiles. The acquisition/exchange of various virulence factors influence the evolutionary framework. To gain insights into evolution of Salmonella as a pathogen in association with the CRISPR-Cas genes we performed phylogenetic surveillance across strains of 22 Salmonella serovars. The strains assorted into two main clades, pertaining to the differences in their CRISPR1-leader and cas operon. Considering Salmonella enterica subsp. enterica serovar Typhimurium and serovar Typhi as signature serovars, we classified the clades as CRISPR1-STM/cas-STM and CRISPR1-STY/cas-STY, respectively. Serovars of the two clades displayed better relatedness, concerning CRISPR-1 leader and cas operon, across genera than between themselves. This signifies the acquisition of CRISPR1/Cas region a horizontal gene transfer event owing to the presence of mobile genetic elements flanking CRISPR1 array. The CRISPR2 tree does not show such relation. Spacer mapping of the two CRISPR arrays suggests the construct to be canonical, with only 8.8% spacer conservation among the serovars. As opposed to broad-host-range serovars, the host-specific serovars harbor fewer spacers. All typhoidal serovars have CRISPR1-STY/cas-STY system. Comparison of CRISPR and cas phenograms with that of multilocus sequence typing (MLST) suggests differential evolution of CRISPR/Cas system implying supplementary roles beyond immunity.

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Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies

Cited by 36 publications

References 80 publications

Emergence of mgrB locus deletion mediating polymyxin resistance in pandemic KPC-producing Klebsiella pneumoniae ST15 lineage

Emergence of mgrB locus deletion mediating polymyxin resistance in pandemic KPC-producing Klebsiella pneumoniae ST15 lineage

Whole genome analysis and characterization of Salmonella enterica subsp. enterica serovar Typhimurium strain UPM 260 for mediated genetic manipulation

The Phylogenomics of CRISPR-Cas System inSalmonella: an evolutionary race with housekeeping genes

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