Genotyping of Acanthamoeba Species Isolated from Keratitis Patients by PCR Sequencing Methods in Tehran, Iran

2019 ◽  
Author(s):  
Tooran Nayeri Chegeni ◽  
Fatemeh Ghaffarifar ◽  
Majid Pirestani ◽  
Fariba Khoshzaban ◽  
Abdolhosein Dalimi Asl ◽  
...  
Keyword(s):  
Contact Lenses ◽  
Pcr Amplification ◽  
Acanthamoeba Keratitis ◽  
Local Alignment ◽  
Sequencing Analysis ◽  
Search Tool ◽  
Skin Nodules ◽  
Acanthamoeba Species ◽  
Eye Clinic

  Background and Aims: Amoebae of the genus Acanthamoeba are unicellular amphizoic opportunistic pathogens that may cause fatal granulomatous encephalitis, eye keratitis, amebic pneumonitis and skin nodules as well as abscesses in humans and animals. Acanthamoeba keratitis is caused by trauma to the eye, contaminated cleaning solutions and the use of contact lenses. The aim of the present study was to identify the genotypes of Acanthamoeba in all patients with a clinical diagnosis of Acanthamoeba keratitis referring to eye clinic in Tehran using polymerase chain reaction (PCR).  Materials and Methods: In this study, samples were collected from 35 patients who had referred to the eye clinic and were cultured on 1.5% non-nutrient agar. DNA was extracted, and then PCR amplification was performed using genus specific primers. Sequencing analysis and basic local alignment search tool search were conducted to determine the genotypes. Phylogenetic tree was generated using maximum likely algorithm in phylogenetic program MEGA version 6.  Results: Eight cases were positive for Acanthamoeba using genus specific primer pairs. All specimens were reported as genotype T4. Conclusions: Determination of genotypes showed all isolates belonging to genotype T4; this abundance may be due to its higher prevalence in the environment or its greater virulence. However, further analysis of clinical and environmental samples is necessary to clarify this property.   

scholarly journals Morphology and Molecular Biology of Benthic Java Sea Shark Ray Rhina ancylostoma Bloch and Scheider 1801 (Elasmobranchia: Rhinidae)

2020 ◽  
pp. 19-31
Author(s):  
Agus Hartoko ◽  
Delianis Pringgenies ◽  
Amelia Cahya Anggelina ◽  
Takashi Matsuishi
Keyword(s):  
Molecular Biology ◽  
Genetic Distance ◽  
Dna Analysis ◽  
Pcr Amplification ◽  
Local Alignment ◽  
Total Length ◽  
Search Tool ◽  
Java Sea ◽  
Bootstrap Replication ◽  
Pcr Method

Aims: Morphology and molecular biology of a rare shark-rays Rhina ancylostoma caught from Java sea.Indonesia. Study Design: Morphology, morphometry and DNA analysis of the fish specimen. Place and Duration of Study: Sample wascollected from fish auction hall at north Java, specimen now stored in Lab of Ichtiology. Department of Fisheries. Faculty of Fisheries and Marine Science. Diponegoro University, between March to December 2019. Methodology: DNA extraction, amplification and molecular identification of fish sample.Yield of DNA supernatant transferred in an eppendeorf tube and stored in 4°C for further process. PCR amplification. Part of Mithocondrial DNA COI (Cytochrome Oxidase subunit-I) gen was amplified using Polymerase Chain Reaction (PCR) method. Then matched up with GenBank database at NCBI using Basic Local Alignment Search Tool (BLAST) analysis. Philogenetic tree was set using Neighbor-Joining method, Kimura-2 parameter model and 1,000 bootstrap replication. Some sequence from NCBI GenBank were inputted into philogenetic tree as comparison. Results: Rhina ancylostoma as one of demersal shark rays catch from tropical shallow Java sea. Range of Total Length 73 – 200 cm and dominant Total Length catch 125 cm. Morphologyis characterised with three lines of spine thorn on the head, morphometry characteriswide of head to TL ratio 0.77. DNA analysis had confirmed the specimen of AH2 as Rhina ancylostoma based on homological match up of sequence of Gen Bank database with reference accesion number KU721837.1 with length sequence of 665 bpand identical similarity of 99.84% for specimen Accession number LC 505461. Conclusion: Rhina ancylostoma as one of demersal shark rays catch from Java sea. Range Total Length (TL) of catch 73 – 200 cm and dominant TL catch range 101 – 125 cm. Morphologically character of wide head ratio with three lines of spine thorn on the head. Nearest genetic distance of 0.02 to Rhincobatushorkelii and 0.017 to R. australiae. Longest genetic distance of 0.243 to Potamotrygon motoro.

scholarly journals rDNA based analysis of autochtonous fungal species from Serbia

Genetika ◽  
2014 ◽  
Vol 46 (1) ◽  
pp. 33-42
Author(s):  
Eleonora Capelja ◽  
Nevena Stevic ◽  
Vladislava Galovic ◽  
Milana Novakovic ◽  
Maja Karaman
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Data ◽  
Fungal Species ◽  
Its Sequences ◽  
Local Alignment ◽  
Phylogenetic Species Concept ◽  
Morphological Approach ◽  
Search Tool ◽  
Morphological And Molecular Data

Determination of fungal species by traditional morphological approach can often be problematic. In the phylum Basidiomycota, sporocarps of different species can share very similar morphoanatomical characteristics. Using molecular markers and phylogenetic species concept this problem can be reduced. In this study identification of six autochtonous fungal species, collected from several locations in Serbia (Tara, Kopaonik, Stara planina) was done by comparison between morphological and molecular data of fungal species, as well as information obtained from phylogenetic tree. ITS sequences amplified from 11 specimens of two genera of ph. Basidiomycota: Marasmius and Ganoderma, were compared with ITS sequences from database using basic local alignment search tool (BLAST). Phylogenetic tree was constructed using Neighbor joining method based on differences between analyzed ITS sequences. Our results showed that within genera Marasmius and Ganoderma morphological and molecular determinations are usually in accordance, but for proper species delimitation both approaches should be used.

scholarly journals Acanthamoeba Keratitis and Acanthamoeba Conjunctivitis: A Case Report

2020 ◽  
Author(s):  
Oktay ALVER ◽  
Mehmet BAYKARA ◽  
Merve YÜRÜK ◽  
Nazmiye ÜLKÜ TÜZEMEN
Keyword(s):  
Visual Loss ◽  
Contact Lenses ◽  
Acanthamoeba Keratitis ◽  
Eyelid Edema ◽  
History Of ◽  
Laboratory Examinations ◽  
Acanthamoeba Species ◽  
Eye Infection ◽  
The Right ◽  
Microbial Agents

Acanthamoeba species are vision-threatening agents by causing cornea infections known as Acanthamoeba keratitis. A 5 year-old kid with the complaints of erythema, eyelid edema, inflammation, limitation of eye movements in the right eye, and having no history of wearing contact lenses or trauma, was diagnosed of Acanthamoeba conjunctivitis through laboratory examinations in the Ophthalmology clinic. The visual sharpness of the patient improved after the treatment. A 44 year-old female patient suffering from pain, stinging, irritation, and inability to see in the left eye with the history of wearing contact lenses or trauma was diagnosed of Acanthamoeba keratitis through laboratory examinations. The agent was isolated and identified as "A. castellani" in the Genotype "T2". Examination of the left eye on the 15th day of treatment indicated that all complaints disappeared except for the cataract originated visual loss. However, the first diagnosis of Acanthamoeba keratitis appeared in the literature on a case with no history of wearing contact lenses and trauma it is found to be attention grabbing. We think that Acanthamoeba should not be ignored among microbial agents that cause eye infection with or without trauma and contact lens usage history.

scholarly journals Investigating Domestic Shower Settings as a Risk Factor for Acanthamoeba Keratitis

Water ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3493
Author(s):  
Binod Rayamajhee ◽  
Dinesh Subedi ◽  
Seoyoung Won ◽  
Jamie (Jung Yun) Kim ◽  
Ajay Vijay ◽  
...  
Keyword(s):  
Risk Factors ◽  
Risk Factor ◽  
Water Contamination ◽  
18S Rrna ◽  
Pcr Amplification ◽  
Acanthamoeba Keratitis ◽  
Domestic Water ◽  
Online Questionnaire ◽  
Hygiene Practices ◽  
Acanthamoeba Species

Acanthamoeba keratitis (AK) is a sight-threatening infection of the cornea, which is caused by soil and the waterborne protist Acanthamoeba spp. AK most commonly occurs during contact lens (CL) wear. Risk factors for AK have been linked to non-optimal lens hygiene practices and Acanthamoeba contamination of domestic water. This study investigated the prevalence of Acanthamoeba species in domestic showers in the greater Sydney region, as well as the perception of water contamination of CL as being a risk factor for AK among previous AK patients and their family and friends. Samples from four locations of 13 participants’ shower areas were cultured and Acanthamoeba 18S rRNA was amplified by PCR, followed by sequencing. Twenty-six responses were received to the online questionnaire. Fifteen water samples (29%, 15/52) contained amoeba that were morphologically classified as Acanthamoeba spp. PCR amplification confirmed the presence of Acanthamoeba spp. in four samples (8%, 4/52). Three isolates belonged to the T4, and one isolate to the T3 genotype. On the questionnaire survey, 96% (25/26) of respondents believed that water contamination was likely to be a risk factor for Acanthamoeba keratitis and 58% rated showering with CL as ‘extremely likely’ to be a risk factor for AK. Acanthamoeba pathogenic genotypes (T3 and T4) in the domestic bathroom water suggest that clinicians should remain vigilant in educating CL wearers about avoiding domestic water contamination of CL.

scholarly journals Lumpy skin disease outbreaks in Egypt during 2017-2018 among sheeppox vaccinated cattle: Epidemiological, pathological, and molecular findings

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258755
Author(s):  
Sherin R. Rouby ◽  
Nesreen M. Safwat ◽  
Khaled H. Hussein ◽  
Aml M. Abdel- Ra’ouf ◽  
Bahaa S. Madkour ◽  
...  
Keyword(s):  
Skin Disease ◽  
Clinical Signs ◽  
Disease Outbreaks ◽  
Pcr Amplification ◽  
Sequencing Analysis ◽  
Protein Coding ◽  
Lumpy Skin Disease ◽  
P32 Gene ◽  
Skin Nodules ◽  
General Organization

The General Organization of the Veterinary Services in Egypt has adopted a sheeppox vaccination policy to control lumpy skin disease (LSD) in cattle. Over the course of the last two years, recurrent outbreaks were reported, with animals showing severe clinical signs and consequentially higher fatalities than that of cases reported in previous LSD outbreaks. A total of 1050 cattle showing typical clinical signs suggestive of LSD were clinically and pathologically investigated during 2017–2018. Skin nodules were collected and lumpy skin disease virus (LSDV) was screened in collected skin samples using PCR for the RPO-30 gene. Furthermore, the entire P32 protein coding gene was sequenced. Histopathology and immunohistochemistry of the skin nodules were also conducted. The obtained results showed an overall mortality rate of 6.86%. LSDV was confirmed in all the examined nodules as evidenced by immunohistochemistry and positive PCR amplification of the RPO30 gene. Sequencing analysis of the P32 gene revealed a highly conserved nature and genetic stability of the LSDV. The results of the present study show that the current vaccination protocol was not effective for a multitude of reasons. These results also serve as evidence for a strong recommendation of an amendment of homologous vaccine use aside from a complete coverage of cattle populations in order to reduce the incidence of LSD among cattle population in Egypt.

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