Genetic analysis of Salmonella enterica serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence

Xie, Xiaolei; Hu, Yachen; Xu, Yaohui; Yin, Kequan; Li, Yang; Chen, Yun; Xia, Jie; Xu, Lijuan; Liu, Zijian; Geng, Shizhong; Li, Qiuchun; Jiao, Xinan; Chen, Xiang; Pan, Zhiming

doi:10.1016/j.vetmic.2017.02.010

Cited by 30 publications

(22 citation statements)

References 30 publications

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“…Thus, alternative methodologies for genotyping and correct identification should be used in addition to traditional tools. CRISPR-Cas systems have been used for identifying: (i) industrial microbes, including: Streptococcus thermophilus, Lactobacillus casei , and Lactobacillus paracasei (Horvath et al, 2008 ; Broadbent et al, 2012 ; Smokvina et al, 2013 ), (ii) food pathogens: Lactobacillus buchneri (Briner and Barrangou, 2014 ) and (iii) human pathogens: Campilobacter jejuni (Kovanen et al, 2014 ), Clostridium difficile (Andersen et al, 2016 ), Mycobacterium tuberculosis (Sola et al, 2015 ; Freidlin et al, 2017 ), Salmonella enterica (Shariat et al, 2013 , 2015 ; Bachmann et al, 2014 ; Almeida et al, 2017 ; Xie et al, 2017 ), Vibrio parahaemolyticus (Sun H. et al, 2015 ), Yersinia pestis (Barros et al, 2014 ; Xu et al, 2017 ) and Yersinia pseudotuberculosis (Koskela et al, 2015 ), among others. However, genotyping through CRISPR technologies has been seldom applied to probiotics, with few exceptions in Lactobacillus rhamnosus (Douillard et al, 2013 ) and Lactobacillus gasseri (Sanozky-Dawes et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum

et al. 2017

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Diverse CRISPR-Cas systems provide adaptive immunity in many bacteria and most archaea, via a DNA-encoded, RNA-mediated, nucleic-acid targeting mechanism. Over time, CRISPR loci expand via iterative uptake of invasive DNA sequences into the CRISPR array during the adaptation process. These genetic vaccination cards thus provide insights into the exposure of strains to phages and plasmids in space and time, revealing the historical predatory exposure of a strain. These genetic loci thus constitute a unique basis for genotyping of strains, with potential of resolution at the strain-level. Here, we investigate the occurrence and diversity of CRISPR-Cas systems in the genomes of various Bifidobacterium longum strains across three sub-species. Specifically, we analyzed the genomic content of 66 genomes belonging to B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis, and identified 25 strains that carry 29 total CRISPR-Cas systems. We identify various Type I and Type II CRISPR-Cas systems that are widespread in this species, notably I-C, I-E, and II-C. Noteworthy, Type I-C systems showed extended CRISPR arrays, with extensive spacer diversity. We show how these hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates. By investigating CRISPR spacer sequences, we reveal their origin and implicate phages and prophages as drivers of CRISPR immunity expansion in this species, with redundant targeting of select prophages. Analysis of CRISPR spacer origin also revealed novel PAM sequences. Our results suggest that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in B. longum, and show that these sequences are useful for typing across three subspecies.

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Section: Discussionmentioning

confidence: 99%

Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum

et al. 2017

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“…Furthermore, CRISPR-multi-virulence-locus sequence typing (MVLST) has been frequently used to subtype Salmonella serovars [10,11]. The conserved genetic organization of the cas genes in some Salmonella serovars is consistent with its biological function in these bacteria [12][13][14]. In addition, some reports found that in S. Typhi, this system consists of five transcriptional units, including two messenger ribonucleic acids (CRISPR-cas and cas3), one sense ribonucleic acid (scse2), and two antisense RNAs (ascse2-1 and ascas2-1) [15].…”

Section: Introductionmentioning

confidence: 99%

CRISPR-cas3 of Salmonella Upregulates Bacterial Biofilm Formation and Virulence to Host Cells by Targeting Quorum-Sensing Systems

et al. 2020

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Salmonella is recognized as one of the most common microbial pathogens worldwide. The bacterium contains the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems, providing adaptive immunity against invading foreign nucleic acids. Previous studies suggested that certain bacteria employ the Cas proteins of CRISPR-Cas systems to target their own genes, which also alters the virulence during invasion of mammals. However, whether CRISPR-Cas systems in Salmonella have similar functions during bacterial invasion of host cells remains unknown. Here, we systematically analyzed the genes that are regulated by Cas3 in a type I-E CRISPR-Cas system and the virulence changes due to the deletion of cas3 in Salmonella enterica serovar Enteritidis. Compared to the cas3 gene wild-type (cas3 WT) Salmonella strain, cas3 deletion upregulated the lsrFGBE genes in lsr (luxS regulated) operon related to quorum sensing (QS) and downregulated biofilm-forming-related genes and Salmonella pathogenicity island 1 (SPI-1) genes related to the type three secretion system (T3SS). Consistently, the biofilm formation ability was downregulated in the cas3 deletion mutant (Δcas3). The bacterial invasive and intracellular capacity of Δcas3 to host cells was also reduced, thereby increasing the survival of infected host cells and live chickens. By the transcriptome-wide screen (RNA-Seq), we found that the cas3 gene impacts a series of genes related to QS, the flagellum, and SPI-1-T3SS system, thereby altering the virulence phenotypes. As QS SPI-1-T3SS and CRISPR-Cas systems are widely distributed in the bacteria kingdom, our findings extend our understanding of virulence regulation and pathogenicity in mammalian hosts for Salmonella and potentially other bacteria.

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“…The pullorum disease also called bacillary white diarrhea (BWD), is caused by Salmonella pullorum bacteria. This disease is a severe septicemia disease that causes high morbidity and mortality in young birds, especially newly hatched chicks (Xie et al 2017). In many developing countries, S. pullorum infection in poultry is common and pullorum disease remains a major disease threat in the poultry industry, causes severe economic losses (Guo et al 2016).…”

Section: Introductionmentioning

confidence: 99%

g.640T>C Polymorphism of the TGF-β2 Gene is Associated with Salmonella pullorum Resistance in Indonesian Chickens

Muhsinin

Ulupi

Gunawan

et al. 2018

anprod

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The objectives of this study were to identify polymorphism of transforming growth factor β2 (TGF-β2) gene associated with Salmonella pullorum resistance in Indonesian chickens. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assays were used to genotype Indonesian chickens. Analysis of polymorphism was conducted by using PopGen 3.2 software. The effect of genotype on S. pullorum resistance was analyzed using the SAS General Linear Model (GLM) procedure. Genotyping was performed on 278 chickens from 7 Indonesian chicken populations (Sentul, Merawang, Pelung, Kampung, Parent Cobb broiler, The F1 crossbreed of Kampung x Parent Cobb broiler (KB) and F2 KB x KB. The product of amplification was 284 bp. The TGF-β2| RsaI locus was polymorphic in all populations, producing two alleles (T and C) and three genotypes (TT, CT, and CC). The result from the analysis of the allele and genotype frequency showed that the T allele had a higher frequency than the C allele in all populations. The χ2 analysis showed that the 6 chicken populations were deviated from Hardy-Weinberg equilibrium, with the exception of the Parent Cobb broiler chicken. The association result showed that TT genotype was significantly associated with S. pullorum resistance in Sentul chicken. Although the leukocyte concentration, leukocyte differentiation and H/L ratio in Sentul chicken with three of TGF-β2 genotypes (TT, TC, and CC) were not statistically different. In conclusion, polymorphism in the TGF-β2 chicken gene can be used as a candidate marker to increase S. pullorum immune response.

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Genetic analysis of Salmonella enterica serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence

Cited by 30 publications

References 30 publications

Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum

Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum

CRISPR-cas3 of Salmonella Upregulates Bacterial Biofilm Formation and Virulence to Host Cells by Targeting Quorum-Sensing Systems

g.640T>C Polymorphism of the TGF-β2 Gene is Associated with Salmonella pullorum Resistance in Indonesian Chickens

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