Homology Analysis of Pathogenic Yersinia Species Yersinia enterocolitica, Yersinia pseudotuberculosis, and Yersinia pestis Based on Multilocus Sequence Typing

Duan, Ran; Liang, Junrong; Shi, Guey‐Yueh; Cui, Zhigang; Hai, Rong; Wang, Peng; Xiao, Yuchun; Li, Kewei; Qiu, Haiyan; Gu, Wenpeng; Du, Xin; Jing, Huaiqi; Wang, Xin

doi:10.1128/jcm.02185-13

Cited by 37 publications

(29 citation statements)

References 33 publications

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“…5, S1). Core-based and pan-based-genome analysis showed Y. pestis and Y. pseudotuberculosis closely related to each other, similar to previously published data (Duan et al 2014;Reuter et al 2012), and Y. enterocolitica was as an independent branch including the strain LC20 (Fig. 6).…”

Section: Discussionsupporting

confidence: 85%

“…Many reports focused their studies on the evolution of pathogenic Yersinia during the last half-century. Using multilocus sequence typing or comparative genome analysis suggests Y. pestis may be a clone of O: 1b serotyped Y. pseudotuberculosis that emerged within the last 1500-20,000 years (Achtman et al 2004(Achtman et al , 1999Chain et al 2004;Duan et al 2014). However, Y. pestis has many disparities compared to Y. enterocolitica and Y. pseudotuberculosis in pathogenicity and the mode of transmission (Achtman et al 1999;Spinner et al 2010).…”

Section: Introductionmentioning

confidence: 99%

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Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

Shi

Liang

et al. 2016

Arch Microbiol

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Yersinia enterocolitica is the most diverse species among the Yersinia genera and shows more polymorphism, especially for the non-pathogenic strains. Individual non-pathogenic Y. enterocolitica strains are wrongly identified because of atypical phenotypes. In this study, we isolated an unusual Y. enterocolitica strain LC20 from Rattus norvegicus. The strain did not utilize urea and could not be classified as the biotype. API 20E identified Escherichia coli; however, it grew well at 25 °C, but E. coli grew well at 37 °C. We analyzed the genome of LC20 and found the whole chromosome of LC20 was collinear with Y. enterocolitica 8081, and the urease gene did not exist on the genome which is consistent with the result of API 20E. Also, the 16 S and 23 SrRNA gene of LC20 lay on a branch of Y. enterocolitica. Furthermore, the core-based and pan-based phylogenetic trees showed that LC20 was classified into the Y. enterocolitica cluster. Two plasmids (80 and 50 k) from LC20 shared low genetic homology with pYV from the Yersinia genus, one was an ancestral Yersinia plasmid and the other was novel encoding a number of transposases. Some pathogenic and non-pathogenic Y. enterocolitica-specific genes coexisted in LC20. Thus, although it could not be classified into any Y. enterocolitica biotype due to its special biochemical metabolism, we concluded the LC20 was a Y. enterocolitica strain because its genome was similar to other Y. enterocolitica and it might be a strain with many mutations and combinations emerging in the processes of its evolution.

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Section: Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

Shi

Liang

et al. 2016

Arch Microbiol

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“…There is a well-established MLST scheme available for Y. pseudotuberculosis (14) that has been used to delineate the population structure of the species complex (15); however, this scheme has not been designed to be robust across the genus. Similarly, there have been attempts to create MLST schemes for Y. enterocolitica (16)(17)(18); however, these have not been informed by genomic data and their suitability for identification to the species and subspecies levels is questionable compared to that of our previous whole-genome phylogeny study (13). Here, we present the design and validation of a new pan-Yersinia MLST scheme that provides identification to the species level that is completely concordant with our previous whole-genome phylogeny (13).…”

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confidence: 55%

“…While the loci in this scheme are among the 84 genes conserved across the genus, in silico analysis suggests that the primers designed may not be optimal across the genus due to base mismatches at the primer sites and as such would not be suitable for the purposes of identifying Yersinia isolates to the species level. Most recently, a scheme was developed to differentiate the three human-pathogenic species of the Yersinia genus using a 7-locus MLST scheme (18). This scheme accurately subtyped Y. enterocolitica into distinct subtypes, including serotype-specific clades within the low-pathogenic strains, as observed both in our scheme and in our genomic phylogeny (13).…”

Section: Discussionmentioning

confidence: 98%

Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

et al. 2015

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hThe genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica. The Gram-negative Yersinia is one of the most important and well-studied bacterial genera, consisting of three human pathogens. Y. pestis is the causative agent of bubonic and pneumonic plague and is a recently diverged clone of Yersinia pseudotuberculosis (1), which alongside Y. enterocolitica is a zoonotic gastrointestinal pathogen (2). The remaining species are not associated with human disease and are considered to be environmental organisms, with the exception of the common fish pathogen Y. ruckeri (2) and the insecticidal species Y. entomophaga. Of the human-pathogenic species, Y. enterocolitica is the most common etiological agent of human disease, and in Germany and Scandinavia, the numbers of cases of human intestinal yersiniosis caused by Y. enterocolitica rival those caused by Salmonella (3). Y. enterocolitica is in itself a very diverse species that is classically subdivided into nonpathogenic, low-pathogenic, and high-pathogenic biotypes based on virulence in a mouse infection model (4). Biotype 1A isolates are considered nonpathogenic, which is concordant with a lack of the major Y. enterocolitica virulence factors such as pYV, invasin, YadA, and Ail (5), although there are numerous reports of biotype 1A human carriage (6, 7). Biotype 1B isolates are high pathogenic, which is concordant with carriage of the high-pathogenicity island, but isolation from human disease cases is very rare with the exception of notable outbreaks such as the recent emergence in Poland (8). Biotype 2 to 4 isolates are low pathogenic and are globally the most common causes of human gastrointestinal yersiniosis (4). Biotype 5 isolates are also considered low pathogenic but have only been isolated from wild hare populations and are very rare in nature (5).From a clinical perspective, the isolation and subsequent identification of Yersinia and in particular Y. enterocoli...

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“…Then, all the specimens were inoculated onto the CIN media for identification. The determinations of the primers and amplification profile for conventional PCR used the method of Huang et al (6), and culture isolation was performed using the method of Duan et al (8). Positive or negative results for real-time PCR were defined as follows.…”

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confidence: 99%

Real-Time TaqMan PCR for Yersinia enterocolitica Detection Based on theailandfoxAGenes

et al. 2014

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Y ersinia enterocolitica, a cause of emerging enteric infections, is a foodborne pathogen associated with various enteric and systemic syndromes, e.g., diarrhea, enteritis, and enterocolitis. Therefore, the detection of this pathogen has important significance. Previous real-time PCR for detection of Y. enterocolitica was primarily based on the ail gene; biotype 1A nonpathogenic strains were not included (1-3). However, recent studies (4,5) showed that biotype 1A ystB-positive strains are potentially pathogenic and related outbreaks were reported. We therefore designed a TaqMan real-time PCR method for detection of both pathogenic and nonpathogenic Y. enterocolitica strains.Using data from sequence analysis of the ail and foxA genes from many Y. enterocolitica strains (6), we designed TaqMan probes and primers (Table 1).An experiment using the entire reaction system was performed using a 20-l volume containing 10 l premix (TaKaRa; China), 7.2 l ultrapure distilled water, 0.2 l ROXII, and 0.2 l (100 nmol/liter) of each primer and probe. A two-step method was adopted. The cycling conditions for the use of a Rotor-Gene Q system consisted of 1 cycle of initial denaturation at 95°C for 10 s followed by 40 cycles of melting at 95°C for 5 s and elongation at 60°C for 30 s. And for the use of a ABI 7500 Fast system, cycling was performed using one initial denaturation at 95°C for 20 s followed by 40 cycles of melting at 95°C for 3 s and elongation at 60°C for 30 s.A total of 168 pathogenic Y. enterocolitica strains (3 ail sequence patterns and 8 foxA sequence patterns) and a total of 41 nonpathogenic Y. enterocolitica strains (13 foxA sequence patterns) were used to assess the sensitivity and specificity of the method. Most of these strains were isolated from animals, mainly swine and mice, in China. Furthermore, 258 non-Y. enterocolitica strains were used to test the specificity of the two detection systems. Most of the strains were Gram-negative bacteria of various genera. All the strains were isolated from patients and identified by using a Vitek Compact 2 biochemical identification instrument (bioMérieux). The results showed that both the ail and foxA gene detection systems have 100% specificity.Standard curves and sensitivity data were obtained by amplifying standard plasmid that had been serially diluted 10-fold. In parallel, we detected the sensitivity of conventional PCR. The results suggested that the slope was Ϫ3.09 and the R 2 was 0.99 for the ail system and that the slope was Ϫ3.16 and the R 2 was 0.99 for the foxA system. The detection limit was 10 2 copies/l for both detection systems. This represented sensitivity 10 times greater than that of the conventional PCR detection.To exclude false-negative results caused by potential inhibitors, we used the internal amplification control (IAC) developed by Fricker et al. (7). A total of 15 pathogenic Y. enterocolitica strains were used to test the IAC with the ail and foxA detection systems. When the ail and foxA detection systems were mixed with the IAC, both of...

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Homology Analysis of Pathogenic Yersinia Species Yersinia enterocolitica, Yersinia pseudotuberculosis, and Yersinia pestis Based on Multilocus Sequence Typing

Abstract: dWe developed a multilocus sequence typing (MLST) scheme and used it to study the population structure and evolutionary relationships of three pathogenic Yersinia species. MLST of these three Yersinia species showed a complex of two clusters, one com-

Cited by 37 publications

References 33 publications

Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

Real-Time TaqMan PCR for Yersinia enterocolitica Detection Based on theailandfoxAGenes

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