scholarly journals Sequence phylogenetic analysis and associative genetic diversity of Sarcocystis hirsuta based on 18S rRNA gene

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Vikrant Sudan ◽  
Rahul Kumar ◽  
Daya Shanker ◽  
Amit Singh
Keyword(s):  
Gene Locus ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Nucleotide Substitutions ◽  
Phylogenetic Characterization ◽  
Nucleotide Homology ◽  
Sarcocystis Hirsuta ◽  
Indian Isolates ◽  
Global Presence ◽  
Pcr Products

Abstract Background Sarcocystis hirsuta, a tissue cyst-forming coccidian parasite of cattle, is worldwide in distribution. In spite of its global presence, limited literature is available on its characterization studies. No literature is available from India on molecular aspects of S. hirsuta. The present study was designed to characterize the isolates of S. hirsuta on the 18S gene locus. A total of five isolates of S. hirsuta were characterized. PCR products were cloned, sequenced, and compared with other sequences across the world. A phylogenetic tree was constructed based on the maximum parsimony (MP) method with the tree–bisection–regrafting (TBR) algorithm. Results An appreciable genetic variability was noticed between various S. hirsuta isolates at the 18S gene locus. Sequences generated from the present study (MN121567–MN121571) represented two haplotypes with 99.74–100.00% nucleotide homology within themselves. Alongside, a nucleotide homology of 97.82–99.92% was observed between Indian isolates and isolates across the globe. The two haplotypes were markedly distinct from each other with 3 nucleotide substitutions within themselves. Overall, Indian isolates of S. hirsuta were close to those from China and Vietnam than to those from New Zealand, Brazil, and Germany. Conclusion The present communication describes the first report of phylogenetic characterization of S. hirsuta from India. The findings are very much important in delineating the evolutionary phylogenetics of S. hirsuta.

Identification of new 18S rRNA strains of Babesia canis isolated from dogs with subclinical babesiosis

2015 ◽  
Vol 18 (3) ◽  
pp. 573-577 ◽  
Author(s):  
P. Łyp ◽  
Ł. Adaszek ◽  
B. Furmaga ◽  
S. Winiarczyk
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Venous Blood ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Babesia Canis ◽  
Gene Fragment ◽  
Nucleotide Substitutions ◽  
New Variant ◽  
Pcr Products

Abstract In this study, we used PCR to detect and characterize B. canis from naturally infected dogs in Poland with subclinical babesiosis by amplifying and sequencing a portion of the 18S ribosomal RNA (rRNA) gene. Venous blood samples were collected from ten dogs with subclinical babesiosis. A 559-bp fragment of the B. canis 18S rRNA gene was amplified by PCR. Sequencing of the PCR products led to the identification of a new variant of Babesia canis, differing from the previously detected protozoa genotypes (18S rRNA-A and 18S rRNA-B) with nucleotide substitutions in positions 150 and 151 of the tested gene fragment. The results indicate the emergence within the Polish territory of a new, previously unencountered Babesia canis genotype responsible for the development of subclinical babesiosis.

scholarly journals Emergence of Babesia Conradae Infection in Coyote-hunting Greyhounds in Oklahoma, USA

2021 ◽  
Author(s):  
Erin M Stayton ◽  
Megan Lineberry ◽  
Jennifer Thomas ◽  
Tina Bass ◽  
Kelly Allen ◽  
...  
Keyword(s):  
18S Rrna ◽  
Clinical Signs ◽  
18S Rrna Gene ◽  
Post Treatment ◽  
Rrna Gene ◽  
Babesia Gibsoni ◽  
Wide Range ◽  
Pcr Products ◽  
Life Threatening ◽  
Tick Vectors

Abstract Background: Babesia species are intraerythrocytic Apicomplexan parasites that infect a wide range of vertebrate hosts. These pathogens are typically transmitted either by tick vectors or by direct blood-to-blood contact, and may cause life-threatening clinical disease such as thrombocytopenia, hemolytic anemia, and acute renal failure in canine hosts. While Babesia vogeli and Babesia gibsoni infections have both been reported in Oklahoma, reports of B. conradae infections have been limited to California. Methods: Whole blood samples were collected in EDTA tubes from all dogs in four separate kennels in Oklahoma. DNA was extracted from each blood sample and a nested PCR was performed using general Apicomplexan primers for the partial 18S rRNA gene. PCR products were electrophoresed in agarose matrix and appropriately sized amplicons were sequenced. Sequences were compared to reference 18S rRNA sequences available in GenBank, and samples with >98% homology to B. conradae (GenBank MK256976) were considered positive. B. conradae positive dogs were then treated with atovaquone (13.5 mg/kg TID) and azithromycin (10 mg/kg SID) for 10 days and retested at 30 and 60 days post treatment by PCR. Results: Fifteen of 40 dogs tested positive for B. conradae with 98–100% sequence homology to B. conradae from California. All positive cases were coyote-hunting Greyhounds. Treatment of clinically ill dogs with atovaquone and azithromycin resulted in complete clinical recovery in clinically ill dogs and all treated dogs had negative follow-up PCR at 30 and 60 days post treatment. Conclusions: Collectively, this study (i) documents the occurrence of B. conradae in Oklahoma, (ii) highlights this pathogen as a differential to be considered when clinical signs are present, and (iii) supports the use of atovaquone and azithromycin as effective treatment in these cases.

scholarly journals Stenamoeba dejonckheerei sp. nov., a Free-Living Amoeba Isolated from a Thermal Spring

Pathogens ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 586
Author(s):  
Manuel Alejandro Borquez-Román ◽  
Luis Fernando Lares-Jiménez ◽  
Libia Zulema Rodriguez-Anaya ◽  
Jose Reyes Gonzalez-Galaviz ◽  
Paul A. Fuerst ◽  
...  
Keyword(s):  
Thermal Spring ◽  
Small Subunit ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Likelihood Analysis ◽  
Ribosomal Ribonucleic Acid ◽  
Pcr Products ◽  
Northwestern Mexico ◽  
Rrna Gene Sequencing ◽  
A New Species

Two amoeboid organisms were obtained from water samples taken from a thermal spring, "Agua Caliente", in Northwestern Mexico. The isolates were obtained when samples were cultivated at 37 °C on non-nutrient agar coated with Escherichia coli. The initial identification of the isolates was performed morphologically using light microscopy. The samples were found to have trophozoite morphology consistent with members of the genus Stenamoeba, a genus derived in 2007 from within the abolished polyphyletic genus Platyamoeba. Further analysis was performed by sequencing PCR products obtained using universal eukaryotic primers for the small subunit ribosomal ribonucleic acid (SSU rRNA) gene. Sequencing primers were designed to allow the comparison of the 18S rRNA gene sequences of the new isolates with previous sequences reported for Stenamoeba. Phylogenetic relationships among sequences from Stenamoeba were determined using Maximum Likelihood analysis. The results showed the two "Agua Caliente" sequences to be closely related, while clearly separating them from those of other Stenamoeba taxa. The degrees of sequence differentiation from other taxa were considered sufficient to allow us to propose that the Mexican isolates represent a new species.

scholarly journals Cryptosporidium spp. in Domestic Dogs: the “Dog” Genotype

2000 ◽  
Vol 66 (5) ◽  
pp. 2220-2223 ◽  
Author(s):  
Una M. Morgan ◽  
Lihua Xiao ◽  
Paul Monis ◽  
Abbie Fall ◽  
Peter J. Irwin ◽  
...  
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Domestic Dogs ◽  
Heat Shock Gene ◽  
Valid Species ◽  
Rrna Gene ◽  
Phylogenetic Characterization ◽  
Cryptosporidium Spp ◽  
Shock Gene

ABSTRACT Genetic and phylogenetic characterization ofCryptosporidium isolates at two loci (18S rRNA gene and heat shock gene) from both Australian and United States dogs demonstrated that dog-derived Cryptosporidium isolates had a distinct genotype which is conserved across geographic areas. Phylogenetic analysis provided support for the idea that the “dog” genotype is, in fact, a valid species.

scholarly journals Phylogenetic information of freshwater copepod (Diaptomus sicilis) with special reference to 18S rRNA

2016 ◽  
Vol 4 (1) ◽  
pp. 25 ◽  
Author(s):  
Gomathi Jeyam Mookkaiah ◽  
Ramanibai Ravichandran
Keyword(s):  
Tamil Nadu ◽  
18S Rrna ◽  
Molecular Data ◽  
Small Subunit ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Calanoid Copepods ◽  
Universal Primer ◽  
Pcr Products ◽  
The Individual

<p>In the present investigation to isolate freshwater calanoid copepods (<em>Diaptomus sicilis</em>) was characterized and identify the organisms by 18S rRNA sequencing. Plankton samples containing <em>D. sicilis</em> were collected during January 2014 (Post-monsoon) from Madippakkam Lake (12°57'41"N80°11'27"E) Chennai, Tamil Nadu. Immediately after sampling, specimens for genetic analyses were fixed in 95% ethyl alcohol. The total DNA was extracted from the individual copepod <em>D. sicilis</em> using Qiagen Blood tissue kit. The nuclear small subunit 18S rRNA gene was amplified using the Universal primer LCO —1490 (5’-GGTCAACAAATCATAAAGATATTGG-3’) and HCO-2198 (5’-TAAACTTCAGGGTGACCAAAAAATCA-3’). PCR products were loaded onto a 1% TAE agarose gel. Sequences were carried out an automated sequencer. The nucleotide sequence of 1282 base pair region of 18S rRNA was determined for D. sicilis. The similarity of sequences of <em>D. sicilis</em> was retrieved by BLASTn pro­gram and maximum identity and E-value was 76% and 0.00, respectively. The PCR products of <em>D. sicilis</em> individuals showed 80% similarity with the partial nuclear small subunit 18S rRNA gene region of other calanoid copepods. Based on molecular data the freshwater Calanoid copepods showed different algorithms and similar types of topologies useful for designing molecular analyses using phylogeny tree construction.Present molecular stud­ies on the relationship of D. sicilis with other freshwater calanoid copepods indicate that this species is close to <em>D. castor</em> followed by <em>D. keniraensis</em><em>.</em></p>

Molecular approaches in species identification of Sarcocysts in Indian buffalo meat

2018 ◽  
Author(s):  
C. Ramakrishn ◽  
S. Vaithiyanathan ◽  
M. Muthukumar ◽  
L., P. Lavanya and V.V. Kulkarni. R. Chatlod ◽  
P. Lavanya ◽  
...  
Keyword(s):  
Restriction Enzymes ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Restriction Enzyme Digestion ◽  
Pcr Assay ◽  
Naked Eye ◽  
Molecular Approaches ◽  
Pcr Product ◽  
Pcr Products ◽  
Eye Examination

DNA was extracted from sarcocysts (visible on naked eye examination) collected from 168 buffaloes belonging to Mumbai (60), Hyderabad (54) and Kolkata (54) cities of India. They were subjected to PCR assay using 18S rRNA gene primer. All the PCR amplicons of about 900 bp were subjected to restriction enzyme digestion with four different restriction enzymes (BslI, DraI, FokI and RsaI). PCR amplicons showed two different patterns (Pattern A and Pattern B) on RFLP. Twenty one PCR products from Pattern A and one PCR product from Pattern B were subjected to DNA sequencing. S. fusiformis and S. taeniata were identified from Pattern A and S. buffalonis was identified from Pattern B on sequencing.

scholarly journals Design of primer pairs for species-specific diagnosis of Leishmania (Leishmania) infantum chagasi using PCR

2012 ◽  
Vol 21 (3) ◽  
pp. 304-307 ◽  
Author(s):  
Osvaldo José da Silveira Neto ◽  
Sabrina Castilho Duarte ◽  
Hérika Xavier da Costa ◽  
Guido Fontgalland Coelho Linhares
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Reference Sequence ◽  
Rrna Gene ◽  
Analytical Sensitivity ◽  
Specific Detection ◽  
Pcr Products ◽  
Specific Amplification ◽  
Pcr Assays ◽  
Species Specific

The objective of this study was to design and evaluate new primers for species-specific detection of L. infantum chagasi using PCR. Two combinations of primer pairs were established with the aim of obtaining specific amplification products from the L. infantum chagasi 18S rRNA gene. The combinations of the primer pairs and the respective sizes of the PCR products, based on the U422465 GenBank reference sequence of L. infantum chagasi, were: LCS1/LCS3 (259 bp) and LCS2/LCS3 (820 bp). It was concluded that the new PCR assays optimized using the primer pairs LCS1/LCS3 and LCS2/LCS3 were effective for specific detection of L. infantum chagasi, with analytical sensitivity to detect 1 pg/µL of DNA.

scholarly journals Phylogenetic Analysis of the Hypervariable Region of the 18S rRNA Gene of Cryptosporidium Oocysts in Feces of Canada Geese (Branta canadensis): Evidence for Five Novel Genotypes

2004 ◽  
Vol 70 (1) ◽  
pp. 452-458 ◽  
Author(s):  
Kristen L. Jellison ◽  
Daniel L. Distel ◽  
Harold F. Hemond ◽  
David B. Schauer
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Hypervariable Region ◽  
Pcr Amplification ◽  
The United States ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Canada Geese ◽  
Pcr Products

ABSTRACT To assess genetic diversity in Cryptosporidium oocysts from Canada geese, 161 fecal samples from Canada geese in the United States were analyzed. Eleven (6.8%) were positive for Cryptosporidium spp. following nested PCR amplification of the hypervariable region of the 18S rRNA gene. Nine PCR products from geese were cloned and sequenced, and all nine diverged from previously reported Cryptosporidium 18S rRNA gene sequences. Five sequences were very similar or identical to each other but genetically distinct from that of Cryptosporidium baileyi; two were most closely related to, but genetically distinct from, the first five; and two were distinct from any other sequence analyzed. One additional sequence in the hypervariable region of the 18S rRNA gene isolated from a cormorant was identical to that of C. baileyi. Phylogenetic analysis provided evidence for new genotypes of Cryptosporidium species in Canada geese. Results of this study suggest that the taxonomy of Cryptosporidium species in geese is complex and that a more complete understanding of genetic diversity among these parasites will facilitate our understanding of oocyst sources and species in the environment.

scholarly journals Molecular and Microscopic Investigation of Sarcocystis Species Isolated from Sheep Muscles in Iran

2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Nader Pestechian ◽  
Hossein Ali Yousefi ◽  
Reza Kalantari ◽  
Rasool Jafari ◽  
Faham Khamesipour ◽  
...  
Keyword(s):  
Distribution Patterns ◽  
18S Rrna Gene ◽  
Microscopic Investigation ◽  
Economic Losses ◽  
Rrna Gene ◽  
Sarcocystis Species ◽  
Digestion Method ◽  
Naked Eye ◽  
Sarcocystis Spp ◽  
Pcr Products

Sarcocystis species is a genus of cyst-forming parasites infecting both humans and animals globally. Some of these species cause clinical and subclinical diseases in the host and may lead to economic losses. This study was carried out to identify the distribution patterns of Sarcocystis spp. in slaughtered sheep based on the digestion method and PCR-RFLP in Isfahan, the center of Iran. In total, 150 fresh muscle samples (30 hearts, 60 esophagi, and 60 diaphragms) were investigated by naked eye observation and then scrutinized based on the digestion method. To this end, pepsin and HCl were used to observe the Sarcocystis parasite via a light microscope. The PCR was carried out to intensify a fragment of the 18S rRNA gene. Afterward, the PCR products were exposed to digestion by endonuclease TaqI, HindII, EcoRI, and AvaI. Consequently, the results of RFLP were confirmed by sequencing, and the phylogenetic placement of all species was analyzed. Through the examination by the naked eye, 5/150 (3.33%) macroscopic cysts were found in the samples. With the tissue digestion and microscopic examination, 116 (77.33%) samples were positive for Sarcocystis spp.; however, 125 (83.33%) samples were positive with PCR. Moreover, the results of sequence analysis on macrocysts and microcysts showed that 4% and 96% of the species belonged to S. gigantea and S. tenella, respectively. According to the results of the current study, sarcocystosis caused by S. tenella are highly prevalent among sheep in the Isfahan region. Due to the high prevalence of Sarcocystis infection in the world and Iran, the development of disease control and prevention policies in sheep would be essential, and changing attitudes in the way of keeping livestock from the traditional type to the industrial method is recommended in this regard.

scholarly journals Identification of the etiological agent of equine piroplasmosis in Western and Eastern Siberia

2018 ◽  
Vol 22 (2) ◽  
pp. 224-229
Author(s):  
V. A. Rar ◽  
V. A. Marchenko ◽  
E. A. Efremova ◽  
O. V. Suntsova ◽  
O. V. Lisak ◽  
...  
Keyword(s):  
18S Rrna Gene ◽  
Etiological Agent ◽  
Rrna Gene ◽  
Theileria Equi ◽  
Nucleotide Substitutions ◽  
Blood Samples ◽  
Equine Piroplasmosis ◽  
The Republic ◽  
Group B ◽  
Almost All

Equine piroplasmosis is a natural tick-borne infection caused by hemoprotozoan parasites of the order Piroplasmida, Babesia caballi and Theileria equi. Animals that recover from piroplasmosis remain persistently infected carriers and can transmit pathogens to vector ticks. Cases of equine piroplasmosis are periodically observed in Siberia, however, no agent of equine piroplasmosis has yet been genetically characterized in Russia. The aim of this work was studying the prevalence of the infectious agents of piroplasmosis in horses from Siberia and genotyping the detected agents. Blood samples from 155 horses were examined for the presence of Babesia and Theileria DNA by nested PCR with the subsequent sequencing of positive samples. DNA of T. equi was found in blood samples from 57.9 %, 38.5 % and 65.0 % of horses from Novosibirsk province, Irkutsk province, and the Republic of Altai, respectively. T. equi DNA was found in the samples from almost all sampling sites included in this study, indicating that most of the studied sites are endemic for equine theileriosis. Surprisingly, DNA of B. caballi was not found in any of the samples examined, even though this agent had previously been detected in many regions in Russia, including Altai. The analysis of the determined 18S rRNA gene sequences demonstrated that T. equi samples belonged to two genetic groups, which differed significantly by the sequences of the variable (V4) region of the gene. All T. equi sequences from group B were identical and corresponded to T. equi sequences found in the blood of horses from China and Korea, while T. equi sequences from group A differed by 1–5 nucleotide substitutions and were identical to the sequences from the blood of horses from India and Brazil or differed from them by single mismatches. Notably, in this study the presence of etiological agent of piroplasmosis in blood samples from horses in Russia was genetically confirmed for the first time.

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