scholarly journals In silico comparative analysis of crispr-cas system structures of Yersinia pseudotuberculosis causing different clinical manifestations of pseudotuberculosis

2019 ◽  
Vol 11 (2) ◽  
pp. 80-87
Author(s):  
N. P. Peretolchina ◽  
Yu. P. Dzhioev ◽  
A. Yu. Borisenko ◽  
L. A. Stepanenko ◽  
E. A. Voskresenskaya ◽  
...  

The aim of this research was to analyze and compare CRIPSR loci and cas-proteins of Yersinia pseudotuberculosis strains isolated in different territories from patients with various clinical manifestations of pseudotuberculosis.Materials and Methods. Complete genomes of Y. pseudotuberculosis IP329353 (NC_006155) and IP31758 (NC_009708) were obtained from NCBI Nucleotide Database. Strains were isolated from patients with gastroenteritis and systemic infection respectively. Search, identification, and analysis of CRISPR systems were carried out by onlinetools CRISPROne, CRISPRDetect, and CRISPRTarget.Results. Analyzed strains have CRISPR-Cas systems that include one set of cas-genes and arrays situated at the long distances from each other. We defined three CRISPR arrays in Y. pseudotuberculosis IP32953: array YP1 located near cas-genes, arrays YP2 and YP3. CRISPR-Cas system of Y. pseudotuberculosis IP31758 includes two arrays – YP1 and YP3. CRISPR systems do not share similar spacers.Conclusion. CRISPR systems of the analyzed strains differ in CRISPR loci and cas-protein structures that can be used as specific molecular marks of analyzed strains during the study of intra-species variability and evolution of Y. pseudotuberculosis.

2018 ◽  
Vol 3 (5) ◽  
pp. 54-59
Author(s):  
N. P. Peretolchina ◽  
A. Y. Borisenko ◽  
Yu. P. Dzhioev ◽  
V. I. Zlobin

Background. Pseudotuberculosis is still relevant problem in medical science and public health of Russia and other countries. Typing of Y. рseudotuberculosis strains by their CRISPR systems is a perspective tool for monitoring of Yersinia populations as was shown in Y. pestis.Aims. Here we describe and compare CRISPR-Cas systems of Yersinia pseudotuberculosis strains IP32953 and IP31758 causing classic pseudotuberculosis and Far-East scarlet-like fever (FESLF) respectively.Materials and methods. Complete genomes of Y. pseudotuberculosis IP329353 and IP31758 (NC_006155 and NC_009708 respectively) were obtained from NCBI Nucleotide Database. Search; identification; and analysis of CRISPR systems were carried out by online-tools CRISPROne; CRISPRDetect; and CRISPRTarget.Results and discussion. Analyzed strains have CRISPR-Cas systems that include one set of cas-genes and arrays situated at the long distances from each other. We defined three CRISPR arrays in Y. pseudotuberculosis IP32953 by the combination of program methods. CRISPR-Cas system of this strain consist of array YP1 located near cas-genes; arrays YP2 and YP3. CRISPR-Cas system of Y. pseudotuberculosis IP31758 includes two arrays – YP1 and YP3. CRISPR systems do not share similar spacers. CRISPR systems of the analyzed strains differ in CRISPR loci and cas-protein structures that can be used as specific marks of analyzed strains.Conclusions. We suggest that acquisition of certain spacers may play a role in evolution and divergence of Y. pseudotuberculosis strains.


2015 ◽  
Vol 33 (2) ◽  
pp. 190-199 ◽  
Author(s):  
Thomas Marth

Background: The actinobacterium Tropheryma whipplei was detected 20 years ago by molecular techniques, and following its culture has been characterized as the cause of a systemic infection known as Whipple's disease (WD). T. whipplei occurs in the environment, is prevalent only in humans, is believed to be transmitted via oral routes and to be host dependent. Key Messages: The classical form of T. whipplei infection, i.e. classical WD (CWD), is rare. It is well defined as slowly progressing chronic infection with arthralgia, diarrhea and weight loss, mostly in middle-aged men. However, current research revealed a much broader spectrum of clinical features associated with T. whipplei infection. Thus, T. whipplei may cause acute and transient infections (observed primarily in children) and the bacterium, which is found in soil and water, occurs in asymptomatic carriers as well as in CWD patients in clinical remission. In addition, T. whipplei affects isolated and localized body compartments such as heart valves or the central nervous system. Subtle immune defects and HLA associations have been described. New findings indicate that the progression of asymptomatic T. whipplei infection to clinical WD may be associated with medical immunosuppression and with immunomodulatory conditions. This explains that there is a discrepancy between the widespread occurrence of T. whipplei and the rareness of WD, and that T. whipplei infection triggered by immunosuppression presents with protean clinical manifestations. Conclusions: This review highlights recent findings and the clinical spectrum of infection with T. whipplei and WD, focusing specifically on the role of host immunity and immunosuppression. Current concepts of the pathogenesis, diagnosis and therapy are discussed.


Lupus ◽  
2018 ◽  
Vol 27 (8) ◽  
pp. 1296-1302 ◽  
Author(s):  
J Tanwani ◽  
K Tselios ◽  
D D Gladman ◽  
J Su ◽  
M B Urowitz

Background Lupus myocarditis (LM) is reported in 3–9% of patients with systemic lupus erythematosus (SLE) but limited evidence exists regarding optimal treatment and prognosis. This study aims to describe LM in a defined lupus cohort as compared with the existing literature. Patients and methods Patients with LM were identified from the University of Toronto Lupus Clinic database. Diagnosis was based on clinical manifestations and electrocardiographic, imaging, and biochemical criteria. Demographic, clinical, diagnostic and therapeutic variables and outcomes were collected in a standardized data retrieval form. A literature review was performed to identify cohort studies reporting on LM treatment and outcome. A comparative analysis was conducted between our patients and the combined cohort of the existing studies. Results Thirty patients were diagnosed with LM (prevalence 1.6%) and compared with a cumulative cohort of 117 patients from five distinct studies. No significant differences were found regarding the age at diagnosis (32.6 ± 13.4 years) and SLE duration (2.5 years median). Concomitant lupus activity from other organ systems was observed in 97% of the patients. Chest pain was more frequently reported in our cohort whereas dyspnea was more prominent in the other studies. Diagnostic criteria were similar across studies. Therapeutic approach was comparable and consisted of glucocorticosteroids (96.6%) and immunosuppressives (70%). Mortality was approximately 20% whereas another 20% of the patients achieved partial and 60% complete recovery. Conclusions LM usually occurs early in the disease course and in the context of generalized lupus activity. Despite aggressive therapy, approximately 40% of the patients died or had residual heart damage.


2020 ◽  
Vol 92 (2) ◽  
pp. 43-47
Author(s):  
Yu. G. Sandler ◽  
K. G. Saliev ◽  
S. N. Backih ◽  
S. G. Khomeriki ◽  
T. Yu. Khaymenova ◽  
...  

Due to the absence of the pathognomonic diagnostic criteria and to the diversity of clinical, serological and morphological manifestations, the diagnostic of the autoimmune hepatitis (AIH) remains to be a difficult task, which might lead to the delay of the timely beginning of the immunosuppressive therapy (IST), which in turn affects the disease outcomes. Aim.To studying the clinical, biochemical, immunological and morphological markers in patients with seronegative (SN) and seropositive (SP) AIH and the qualities of their response to the IST. Materials and methods.This retrospective cohort study included 82 AIH patients over the course of the years 20142019. All patients were selected in accordance with the criteria of the simplified assessment system of the IAIHG. Clinical, laboratorial and morphological characteristics of the AIH were analyzed. Therapy response was evaluated by the level of the ALT and IgG in 612 months after the start of the IST. The study material underwent statistical analysis using methods of parametrical and nonparametrical analysis. Statistical analysis was performed in the Statistica 13.3 (developed by StatSoft Inc., USA). Results.67/82 (81.70%) of the patients studied were women, median age of 54 years old [38; 70]. Patients with the diagnosis of the possible AIH according to the IAIHG made 85.4% (70 people). Almost everyone 96% (79/82) had morphological features of the interface-hepatitis with the lymphocytic/plasmocytic infiltration; emperipolesis was discovered in 63% of patients (49/82), hepatocellular rosette in 23% (19/82). Patients with SN AIH comprised 36.5% (30/82), with SP 63.4% (52/82). Comparative analysis demonstrated that the clinical profile in patients with SN and SP AIH is the same, while the incidence of immuno-associated diseases is significantly higher in the group of seronegative AIH. The morphological profile in the two AIH groups is identical in both typical and atypical manifestations. The number of responders to IST was 63% (19/30) SN AIH vs 67% SP AIH (35/52), did not differ significantly (p=0.529).However, that the number of patients with liver cirrhosis in the SN AIH group was twice as big as the ones with SP: 37% vs 17% (p=0.089). Conclusions.A comparative analysis of clinical, laboratory, morphological and clinical manifestations in the SN and SP AIH groups did not detected statistically significant significant differences, which may indicate that SN and SP AIH are the faces of one disease. It is possible that AB cannot be identified within the known spectrum of antibodies, or antibodies have slow expression, or are suppressed by the immune system. In any case, suspicions of AIH, in the absence of antibodies, it is recommended that liver biopsy be performed for the timely diagnosis of AIH and IST. Сirrhosis was more often diagnosed in the group SN AIH, which may be due to a later diagnosis, and therefore to untimely IST. The found frequent association of SN AIH with other immune-associated diseases requires a carefully study of this problem. The variety of clinical manifestations of AIH requires further study, the identification of clinical phenotypes with certain feature. This can help in the future to timely identify potentially problematic patients and predict a response to IST.


2021 ◽  
Vol 7 (2) ◽  
Author(s):  
Ahmad-Kamal Ghazali ◽  
Su-Anne Eng ◽  
Jia-Shiun Khoo ◽  
Seddon Teoh ◽  
Chee-Choong Hoh ◽  
...  

Burkholderia pseudomallei , a soil-dwelling Gram-negative bacterium, is the causative agent of the endemic tropical disease melioidosis. Clinical manifestations of B. pseudomallei infection range from acute or chronic localized infection in a single organ to fulminant septicaemia in multiple organs. The diverse clinical manifestations are attributed to various factors, including the genome plasticity across B. pseudomallei strains. We previously characterized B. pseudomallei strains isolated in Malaysia and noted different levels of virulence in model hosts. We hypothesized that the difference in virulence might be a result of variance at the genome level. In this study, we sequenced and assembled four Malaysian clinical B. pseudomallei isolates, UKMR15, UKMPMC2000, UKMD286 and UKMH10. Phylogenomic analysis showed that Malaysian subclades emerged from the Asian subclade, suggesting that the Malaysian strains originated from the Asian region. Interestingly, the low-virulence strain, UKMH10, was the most distantly related compared to the other Malaysian isolates. Genomic island (GI) prediction analysis identified a new island of 23 kb, GI9c, which is present in B. pseudomallei and Burkholderia mallei , but not Burkholderia thailandensis . Genes encoding known B. pseudomallei virulence factors were present across all four genomes, but comparative analysis of the total gene content across the Malaysian strains identified 104 genes that are absent in UKMH10. We propose that these genes may encode novel virulence factors, which may explain the reduced virulence of this strain. Further investigation on the identity and role of these 104 proteins may aid in understanding B. pseudomallei pathogenicity to guide the design of new therapeutics for treating melioidosis.


2020 ◽  
pp. 1086-1088
Author(s):  
Michael Prentice

Yersiniosis is caused by the enteropathogenic Gram-negative organisms Yersinia enterocolitica and Yersinia pseudotuberculosis, which are worldwide zoonotic pathogens. Disease is acquired by consumption of contaminated food or water and is commonest in childhood, and in colder climates. Presentation is with diarrhoea, fever, and abdominal pain, which may mimic appendicitis. Late complications include reactive arthritis, erythema nodosum, and erythema multiforme. Systemic infection is more likely with Y. pseudotuberculosis and a subgroup of Y. enterocolitica, and also in patients with diabetes or iron overload. Diagnosis is by culture of the organism or convalescent serology. Most cases of enteritis are self-limiting and antimicrobials are not indicated, but septicaemia or focal infection outside the gastrointestinal tract requires antibiotics (usually cefotaxime, ceftriaxone, or ciprofloxacin). Prevention is by standard food hygiene precautions.


2020 ◽  
Vol 22 ◽  
pp. 02013
Author(s):  
Natalya Ozhgikhina ◽  
Daria Kiseleva ◽  
Evgeny Shagalov ◽  
Evgenia Bimbas ◽  
Natalya Myagkova

Enamel hypoplasia is the most common disease of hard tooth tissues of non-carious origin emerging before their eruption. It develops as a result of a delayed and perverse function of ameloblasts leading to the violation of the processes of formation and mineralization of tooth protein structures. The clinical manifestations of enamel hypoplasia are spots, defects in the form of pits, cup-shaped depressions, grooves on various surfaces of child’s teeth. The work is devoted to a comparative investigation of microstructural and compositional features of intact and hypoplastic enamel in children’s permanent teeth using analytical scanning electron microscopy with energy-dispersive X-ray spectroscopy. The hypoplastic enamel is enriched in organic substance and has an irregular structure without keyhole-shaped prismatic structure. Mineral deposition is indicated for hypoplastic enamel including hydroxyapatite with globular structure and calcite and halite, which might have been caused by the violation of extracellular local environment probably due to the enamel hypoplasia development.


Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 795
Author(s):  
Sergei N. Shchelkunov ◽  
Stanislav N. Yakubitskiy ◽  
Alexander A. Sergeev ◽  
Alexei S. Kabanov ◽  
Tatiana V. Bauer ◽  
...  

The mass smallpox vaccination campaign has played a crucial role in smallpox eradication. Various strains of the vaccinia virus (VACV) were used as a live smallpox vaccine in different countries, their origin being unknown in most cases. The VACV strains differ in terms of pathogenicity exhibited upon inoculation of laboratory animals and reactogenicity exhibited upon vaccination of humans. Therefore, each generated strain or clonal variant of VACV needs to be thoroughly studied in in vivo systems. The clonal variant 14 of LIVP strain (LIVP-14) was the study object in this work. A comparative analysis of the virulence and immunogenicity of LIVP-14 inoculated intranasally (i.n.), intradermally (i.d.), or subcutaneously (s.c.) to BALB/c mice at doses of 108, 107, and 106 pfu was carried out. Adult mice exhibited the highest sensitivity to the i.n. administered LIVP-14 strain, although the infection was not lethal. The i.n. inoculated LIVP-14 replicated efficiently in the lungs. Furthermore, this virus was accumulated in the brain at relatively high concentrations. Significantly lower levels of LIVP-14 were detected in the liver, kidneys, and spleen of experimental animals. No clinical manifestations of the disease were observed after i.d. or s.c. injection of LIVP-14 to mice. After s.c. inoculation, the virus was detected only at the injection site, while it could disseminate to the liver and lungs when delivered via i.d. administration. A comparative analysis of the production of virus-specific antibodies by ELISA and PRNT revealed that the highest level of antibodies was induced in i.n. inoculated mice; a lower level of antibodies was observed after i.d. administration of the virus and the lowest level after s.c. injection. Even at the lowest studied dose (106 pfu), i.n. or i.d. administered LIVP-14 completely protected mice against infection with the cowpox virus at the lethal dose. Our findings imply that, according to the ratio between such characteristics as pathogenicity/immunogenicity/protectivity, i.d. injection is the optimal method of inoculation with the VACV LIVP-14 strain to ensure the safe formation of immune defense after vaccination against orthopoxviral infections.


2007 ◽  
Vol 36 (Supplement_1) ◽  
pp. D504-D511 ◽  
Author(s):  
Yi Huang ◽  
Susanna K. P. Lau ◽  
Patrick C. Y. Woo ◽  
Kwok-yung Yuen

Abstract The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis.


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