Analysis of the structures of confirmed and questionable CRISPR loci in 325 <i>Staphylococcus</i> genomes

Zhang, Mengmeng; Bi, Chun-xia; Wang, Mengyuan; Fu, Hengxia; Mu, Zhengrong; Zhu, Yue; Zhang, Yan

doi:10.1002/jobm.201900124

Cited by 8 publications

(5 citation statements)

References 40 publications

(45 reference statements)

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“…In this study, the minority spacers targeted plasmids and phage, indicating that Enterococcus has been less subjected to plasmids and phage invasion. The proportion of targeting exogenous genetic elements was lower than the reported in Staphylococcus (12.1%) (Zhang et al, 2019). The lower proportion of spacer sequences of Enterococcus matching with plasmids or phages in this study may be related to the limited number of plasmids or phages already sequenced and included in the Nucleotide database.…”

Section: Figurecontrasting

confidence: 73%

Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains

et al. 2023

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Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign mobile genetic elements, such as plasmids and phages. This study aims to analyze the gene structure and to explore the function of the CRISPR system in the Enterococcus genome, especially with regard to drug resistance. The whole genome information of 110 enterococci was downloaded from the NCBI database to analyze the distribution and the structure of the CRISPR-Cas system including the Cas gene, repeat sequences, and spacer sequence of the CRISPR-Cas system by bioinformatics methods, and to find drug resistance-related genes and analyze the relationship between them and the CRISPR-Cas system. Multilocus sequence typing (MLST) of enterococci was performed against the reference MLST database. Information on the drug resistance of Enterococcus was retrieved from the CARD database, and its relationship to the presence or absence of CRISPR was statistically analyzed. Among the 110 Enterococcus strains, 39 strains (35.45%) contained a complete CRISPR-Cas system, 87 CRISPR arrays were identified, and 62 strains contained Cas gene clusters. The CRISPR system in the Enterococcus genome was mainly type II-A (59.68%), followed by type II-C (33.87%). The phylogenetic analysis of the cas1 gene sequence was basically consistent with the typing of the CRISPR-Cas system. Of the 74 strains included in the study for MLST typing, only 19 (25.68%) were related to CRISPR-Cas typing, while the majority of the strains (74.32%) of MLST typing were associated with the untyped CRISPR system. Additionally, the CRISPR-Cas system may only be related to the carrying rate of some drug-resistant genes and the drug-resistant phenotype. In conclusion, the distribution of the enterococcus CRISPR-Cas system varies greatly among different species and the presence of CRISPR loci reduces the horizontal transfer of some drug resistance genes.

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Section: Figurecontrasting

confidence: 73%

Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains

et al. 2023

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“…About one-third of spacers in K. variicola were homologous to plasmids or phages. The proportion of K. variicola spacers targeting foreign genetic elements was significantly higher than other bacteria, such as Staphylococcus [50] and Clostridium perfringens [51]. It might be owing to that the sequencing ofK.…”

Section: Discussionmentioning

confidence: 95%

Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola

Xi¹,

Zhao²,

Zhang³

et al. 2023

Preprint

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Klebsiella variicola (K. variicola) is an emerging human pathogen, which poses a threat to public health. The horizontal gene transfer (HGT) of plasmids is an important driver for the emergence of multiple antibiotic-resistant K. variicola. The clustered regularly interspersed short palindromic repeats coupled with the CRISPR-associated genes (CRISPR/Cas) constitute an adaptive immune system in bacteria, which provide acquired immunity against HGT. However, the information about CRISPR/Cas system in K. variicola is still limited. In this study, a total of 487 genomes from NCBI database were used to analyze the characterization of CRISPR/Cas systems. 105 of the 487 genomes harbored at least one confirmed CRISPR array. Three types of CRISPR/Cas system, including types I-E, I-E*, and Ⅳ-A systems, were identified among 105 strains. The distribution of type I system was strongly associated with MLST, whereas type IV system was randomly distributed. Approximately one-third of spacer origins were homologous with plasmids or phages, indicating the role of CRISPR/Cas systems in controlling HGT. Moreover, spacers in K. variicola tended to target mobile genetic elements (MGEs) from Klebsiella pneumoniae, which provides new evidence for their interaction during evolution. Collectively, our results provide valuable insights into the role of CRISPR/Cas systems in K. variicola.

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“…Recent research has shown that 40 % of CRISPR-Cas loci are away from any associated cas genes or are not associated with cas genes, which are known as orphan CRISPR arrays [76]. Like many other bacterial species such as Listeria monocytogenes, Aggregatibacter actinomycetemcomitans, Enterococcus faecalis, Staphylococcus spp., Pseudomonas aeruginosa and Salmonella enterica [77][78][79][80][81], orphan CRISPR arrays were found in N. seriolae genomes. These incomplete CRISPR-Cas systems may be a remnant of decaying loci that are recruited and/or selectively maintained to perform important, but as yet unknown, biological functions [73].…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam

et al. 2022

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Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N . seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.

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Analysis of the structures of confirmed and questionable CRISPR loci in 325 Staphylococcus genomes

Cited by 8 publications

References 40 publications

Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains

Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains

Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola

Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam

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