Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme

Li, Yanjun; Cui, Yu‐Jun; Cui, Baizhong; Yan, Yanfeng; Wang, Haidong; Zhang, Qi; Zhang, Qingwen; Xiao, Xiao; Guo, Zhaobiao; Ma, Cong; Wang, Jing; Song, Yajun

doi:10.1371/journal.pone.0066567

Cited by 22 publications

(34 citation statements)

References 39 publications

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“…The MLtree of 78 Guertu isolates and 368 public Y. pestis strains indicated that all Guertu isolates belong to a same phylogroup, 0.ANT1 ( Supplementary Fig. 3), which is only distributed in the Guertu region according to previous studies 44,54 .…”

Section: Methodsmentioning

confidence: 81%

Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment

et al. 2020

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Yersinia pestis is transmitted from fleas to rodents when the bacterium develops an extensive biofilm in the foregut of a flea, starving it into a feeding frenzy, or, alternatively, during a brief period directly after feeding on a bacteremic host. These two transmission modes are in a trade-off regulated by the amount of biofilm produced by the bacterium. Here by investigating 446 global isolated Y. pestis genomes, including 78 newly sequenced isolates sampled over 40 years from a plague focus in China, we provide evidence for strong selection pressures on the RNA polymerase ω-subunit encoding gene rpoZ. We demonstrate that rpoZ variants have an increased rate of biofilm production in vitro, and that they evolve in the ecosystem during colder and drier periods. Our results support the notion that the bacterium is constantly adapting-through extended phenotype changes in the fleas-in response to climate-driven changes in the niche. w | www.nature.com/naturecommunications 1 1234567890():,; † Two small clusters (at CO92 position 2,577,933 and 2,606,316) were excluded as they were the result of copy-number variations in tandem repeat loci * K, the number of variations within a cluster # N, region size of the cluster NATURE COMMUNICATIONS | https://doi.

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Section: Methodsmentioning

confidence: 81%

Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment

et al. 2020

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“…The repeat numbers for 25 VNTR loci in 97 Y. pestis strains representing the genetic diversity of the whole species, four Yersinia pseudotuberculosis strains, 15 and 38 Y. pestis strains from FSU plague foci 14 were obtained from previously published articles (Supplemental Table 1). The VNTR diversity information for these strains was obtained from the MLVA bank for Microbes Genotyping database (http://microbesgenotyping.…”

Section: Methodsmentioning

confidence: 99%

“…13 Understanding the phenotypic features and genetic diversity of Y. pestis isolates is important in characterizing a plague focus and contributes to the prevention and control of plague. Molecular genotyping and evolutionary analyses were used to describe the phylogenetic positions of the Junggar strains, including a multiple-locus variable number of tandem repeats analysis (MLVA), which is based on the diversity of variable numbers of tandem repeats (VNTR), 14,15 typing with clustered regularly interspaced short palindromic repeats (CRISPR), which is based on the varying compositions of the spacer arrays in three CRISPR loci in the genome, 16 and whole-genome single-nucleotide polymorphism (SNP) analysis. 17 However, only 1-3 Junggar strains were used in those studies, so the fully representative genetic diversity of the Y. pestis population in Junggar Basin focus was not determined.…”

Section: Introductionmentioning

confidence: 99%

Phenotypic and Molecular Genetic Characteristics of Yersinia pestis at an Emerging Natural Plague Focus, Junggar Basin, China

Zhāng

Luò

Yang

et al. 2018

The American Journal of Tropical Medicine and Hygiene

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The 15th natural plague focus in China, the Junggar Basin plague focus, is located near an important communication route connecting China and Central Asia and was discovered after 2005. To characterize the phenotypic and genetic diversity of the population in this newly established focus, we collected 25 strains from six counties across Junggar Basin in 2005-2006, and determined their biochemical features and genotypes based on multiple-locus variable number of tandem repeats analysis and clustered regularly interspaced short palindromic repeats analysis. We inferred the phylogenetic positions and possible sources of the Junggar strains by comparing their genotypes with the genetic diversity for known representative strains. Our results indicate that the major genotype of Junggar strains belongs to 2.MED1, a lineage of biovar Medievalis with identical biochemical characters and high virulence in mice. Although share a similar ecology, the 2.MED1 in Junggar Basin are not descended from known strains in the neighboring Central Asian Desert plague foci. Therefore, the emergence of the Junggar Basin plague focus is not attributable to the recent clonal spread of from Central Asia. We also identified two distinct minor genotypes in Junggar Basin, one of which clusters genetically with the 0.ANT1 strains of the Tianshan Mountain natural plague focus and another belongs to a 1.IN lineage not previously reported. Our study clarifies the phenotypic and genetic characters of Junggar strains. These findings extend our knowledge of the population diversity of and will facilitate future plague surveillance and prevention in Junggar Basin and adjacent regions.

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“…To establish a genotyping system for tracing the source of this notorious pathogen, Li et al [25] studied the traits of VNTRs in the Y. pestis genome and established a simple hierarchical genotyping system based on MLVA-CE analysis. Their results demonstrate that the MLVA-CE genotyping method improves the study of Y. pestis with respect to source tracing and microevolution of this pathogen, which compares favorably with single nucleotide polymorphismbased phylogenic analysis, but costs less time and money.…”

Section: Detecting and Diagnosing Bacteriamentioning

confidence: 99%

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

Lian

Zhao

2016

Clinical Chemistry and Laboratory Medicine (CCLM)

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Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.

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Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme

Cited by 22 publications

References 39 publications

Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment

Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment

Phenotypic and Molecular Genetic Characteristics of Yersinia pestis at an Emerging Natural Plague Focus, Junggar Basin, China

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

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