scholarly journals Comparison of PCR, Isoenzyme Analysis, and Antigen Detection for Diagnosis of Entamoeba histolyticaInfection

1998 ◽  
Vol 36 (2) ◽  
pp. 449-452 ◽  
Author(s):  
Rashidul Haque ◽  
I. K. M. Ali ◽  
S. Akther ◽  
William A. Petri
Keyword(s):  
Specific Antigen ◽  
Small Subunit ◽  
Antigen Detection ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Isoenzyme Analysis ◽  
Pcr Product ◽  
Stool Samples ◽  
Stool Specimens ◽  
Fresh Stool

The diagnosis of amebiasis by microscopic identification of the parasite in stool is insensitive and unable to distinguish the invasive parasite Entamoeba histolytica from the commensal parasite E. dispar. In this study, we have tested a PCR technique for the detection of E. histolytica and compared it with isoenzyme analysis and the TechLab E. histolytica-specific antigen detection test. The nested-PCR test we used is based on amplification of the small subunit rRNA gene ofE. histolytica and E. dispar followed by restriction digest analysis of the PCR product. Single stool samples were obtained from 98 patients from Dhaka, Bangladesh, with diarrhea: 88 patients diagnosed by microscopy and/or culture with E. histolytica and/or E. dispar infection and 10 patients without infection. Isoenzyme analysis identified 53 of the infections as E. histolytica and 28 as E. dispar. PCR and isoenzyme identification of E. histolytica agreed in 96% (51 of 53) of amebic cultures. PCR forE. histolytica was negative in all 10 samples that were negative for E. histolytica by isoenzyme and antigen detection. PCR and antigen detection had comparable sensitivities when performed directly on fresh stool specimens, identifying 87% (46 of 53) and 85% (45 of 53), respectively, of E. histolyticainfections identified by isoenzyme analysis. The correlation of results by antigen detection and PCR for identification of E. histolytica in stool was 93% (45 of 48 cases). Mixed infections with E. histolytica and E. dispar were detected by PCR in 14% (12 of 88) of cases. In conclusion, all three techniques for specific identification of E. histolytica in fresh stool showed excellent correlation. Only the TechLab E. histolytica antigen detection test was both rapid and technically simple.

scholarly journals Identification of Blastocystis subtypes in clinical stool samples from Sao Paulo City, Brazil

2017 ◽  
Vol 3 ◽  
Author(s):  
GESSICA B. MELO ◽  
FABIANA M. PAULA ◽  
FERNANDA M. MALTA ◽  
CELINA W. MARUTA ◽  
PAULO R. CRIADO ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Small Subunit ◽  
Sao Paulo ◽  
Rrna Gene ◽  
São Paulo ◽  
Small Subunit Rrna ◽  
Direct Dna Sequencing ◽  
Positive Stool ◽  
Pcr Products ◽  
Stool Samples

SUMMARY Blastocystis sp. is a protozoan commonly found in human and animal stool samples. Several pathogenic and zoonotic aspects of this organism are still unknown. The aim of the present study was to investigate Blastocystis subtypes (STs) in samples from patients of the Hospital das Clínicas of the Faculdade de Medicina at the Universidade de São Paulo (HC-FMUSP), Brazil. Blastocystis sp.-positive stool samples diagnosed at the Section of Parasitology of the Central Laboratory (HC-FMUSP) were used for DNA isolation. Polymerase chain reaction (PCR) was performed using specific primers targeting the small-subunit rRNA gene. Direct DNA sequencing of the PCR products was performed and the DNA sequences were then aligned and compared with other sequences obtained from the GenBank database. Phylogenetic analysis was used to identify STs and determine the phylogenetic relationships between the sequences. Four STs were identified: ST1 (22·5%), ST2 (12·5%), ST3 (60%) and ST6 (5%). In conclusion, ST3 was the most prevalent ST among the human isolates followed by ST1. The present study is one of the few providing STs data from the human population in South America. Determining ST prevalence in human samples may contribute to the monitoring of Blastocystis sp. infection transmission in endemic regions.

scholarly journals Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions

2020 ◽  
Vol 9 (1) ◽  
pp. 21
Author(s):  
Abdul Ghafar ◽  
Anson V. Koehler ◽  
Ross S. Hall ◽  
Charles G. Gauci ◽  
Robin B. Gasser ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Water Buffalo ◽  
Hypervariable Region ◽  
Small Subunit ◽  
Rrna Gene ◽  
Next Generation ◽  
Small Subunit Rrna ◽  
Tropical Theileriosis ◽  
Ecological Zones ◽  
Generation Sequencing

Protists of the genera Babesia and Theileria (piroplasms) cause some of the most prevalent and debilitating diseases for bovines worldwide. In this study, we established and used a next-generation sequencing-informatic approach to explore the composition of Babesia and Theileria populations in cattle and water buffalo in a country (Pakistan) endemic for these pathogens. We collected individual blood samples from cattle (n = 212) and water buffalo (n = 154), extracted genomic DNAs, PCR-amplified the V4 hypervariable region of 18S small subunit rRNA gene from piroplasms, sequenced amplicons using Illumina technology, and then analysed data using bioinformatic platforms. The results revealed piroplasms in 68.9% (252/366) samples, with overall occurrence being markedly higher in cattle (85.8%) than in water buffaloes (45.5%). Babesia (B.) occultans and Theileria (T.) lestoquardi-like species were recorded for the first time in Pakistan, and, overall, T. annulata was most commonly detected (65.8%) followed by B. bovis (7.1%), B. bigemina (4.4%), and T. orientalis (0.5%), with the genetic variability within B. bovis being pronounced. The occurrence and composition of piroplasm species varied markedly across different agro-ecological zones. The high detection of T. annulata in asymptomatic animals suggested a relatively high level of endemic stability of tropical theileriosis in the bovine population.

scholarly journals Differences in Microbial Activity and Microbial Populations of Peat Associated with Suppression of Damping-Off Disease Caused by Pythium sylvaticum

2006 ◽  
Vol 72 (10) ◽  
pp. 6452-6460 ◽  
Author(s):  
Paul J. Hunter ◽  
Geoff M. Petch ◽  
Leo A. Calvo-Bado ◽  
Tim R. Pettitt ◽  
Nick R. Parsons ◽  
...  
Keyword(s):  
Microbial Activity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Small Subunit ◽  
Disease Suppression ◽  
Rrna Gene ◽  
Damping Off ◽  
Small Subunit Rrna ◽  
Pythium Sylvaticum ◽  
Gradient Gel Electrophoresis ◽  
Microbial Groups

ABSTRACT The microbiological characteristics associated with disease-suppressive peats are unclear. We used a bioassay for Pythium sylvaticum-induced damping-off of cress seedlings to identify conducive and suppressive peats. Microbial activity in unconditioned peats was negatively correlated with the counts of P. sylvaticum at the end of the bioassay. Denaturing gradient gel electrophoresis (DGGE) profiling and clone library analyses of small-subunit rRNA gene sequences from two suppressive and two conducive peats differed in the bacterial profiles generated and the diversity of sequence populations. There were also significant differences between bacterial sequence populations from suppressive and conducive peats. The frequencies of a number of microbial groups, including the Rhizobium-Agrobacterium group (specifically sequences similar to those for the genera Ochrobactrum and Zoogloea) and the Acidobacteria, increased specifically in the suppressive peats, although no single bacterial group was associated with disease suppression. Fungal DGGE profiles varied little over the course of the bioassay; however, two bands associated specifically with suppressive samples were detected. Sequences from these bands corresponded to Basidiomycete yeast genera. Although the DGGE profiles were similar, fungal sequence diversity also increased during the bioassay. Sequences highly similar to those of Cryptococcus increased in relative abundance during the bioassay, particularly in the suppressive samples. This study highlights the importance of using complementary approaches to molecular profiling of complex populations and provides the first report that basidiomycetous yeasts may be associated with the suppression of Pythium-induced diseases in peats.

Detection of Kobe-typeBabesia microtiassociated with Japanese human babesiosis in field rodents in central Taiwan and southeastern mainland China

Parasitology ◽  
2008 ◽  
Vol 135 (6) ◽  
pp. 691-699 ◽  
Author(s):  
A. SAITO-ITO ◽  
N. TAKADA ◽  
F. ISHIGURO ◽  
H. FUJITA ◽  
Y. YANO ◽  
...  
Keyword(s):  
Mainland China ◽  
Small Subunit ◽  
Human Infection ◽  
Babesia Microti ◽  
Rrna Gene ◽  
Microscopical Examination ◽  
Small Subunit Rrna ◽  
Central Taiwan ◽  
Field Rodents ◽  
Human Babesiosis

SUMMARYField rodent surveys forBabesiainfection were performed from 2002 to 2005 in the vicinities of human babesiosis occurrences in Taiwan and mainland China.Babesia microtiwas identified by microscopical examination and/or PCR in 1Rattus coxingaand 1Crocidura horsfieldiiin central Taiwan and in 13Niviventer confucianusand 1Apodemus agrariusin Zhejiang and Fujian Provinces of southeastern China. Of 15B. microtisamples detected by PCR, all except 1 were shown to be the Kobe-type, the aetiological small subunit rRNA gene-type of the first Japanese patient; the exception was also a Kobe-related type. The Kobe-type had been found in rodents only in a few places including the human infection occurrence place in Japan. The internal transcribed spacer 1 to 2 sequences of the Taiwanese and Chinese Kobe-types were very similar to each other but considerably different (approx. 94% pairwise identities) from that of the Japanese Kobe-type. A Taiwanese Kobe-type strain was serologically differentiated from the Kobe strain originating from the Japanese first patient. The distribution of the Kobe-type in the vicinities of human babesiosis occurrences in Taiwan and China as well as in Japan is suggestive of involvement of the Kobe-type in Asian human babesiosis.

Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences

2003 ◽  
Vol 126 (1) ◽  
pp. 119-123 ◽  
Author(s):  
Christophe Noël ◽  
Corinne Peyronnet ◽  
Delphine Gerbod ◽  
Virginia P Edgcomb ◽  
Pilar Delgado-Viscogliosi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Gene Sequences ◽  
Small Subunit Rrna Gene

scholarly journals Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

1998 ◽  
Vol 64 (12) ◽  
pp. 5064-5066 ◽  
Author(s):  
Clifford F. Brunk ◽  
Nicole Eis
Keyword(s):  
Internal Standard ◽  
Pcr Amplification ◽  
Quantitative Measure ◽  
Pcr Primers ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequence ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

Genetic interrelationships of proteolyticClostridium botulinum types A, B, and F and other members of theClostridium botulinum complex as revealed by small-subunit rRNA gene sequences

1994 ◽  
Vol 64 (3-4) ◽  
pp. 273-283 ◽  
Author(s):  
R. A. Hutson ◽  
D. E. Thompson ◽  
P. A. Lawson ◽  
R. P. Schocken-Itturino ◽  
E. C. B�ttger ◽  
...  
Keyword(s):  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Gene Sequences ◽  
Small Subunit Rrna Gene

Free-living nematodes associated with pine cones of Pinus thunbergii and P. taeda at Japanese coastal and inland forest sites

Nematology ◽  
2019 ◽  
Vol 21 (4) ◽  
pp. 389-400 ◽  
Author(s):  
Yudai Kitagami ◽  
Natsumi Kanzaki ◽  
Toko Tanikawa ◽  
Yosuke Matsuda
Keyword(s):  
Gene Sequence ◽  
Small Subunit ◽  
Pinus Thunbergii ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Free Living ◽  
Small Subunit Rrna Gene ◽  
Forest Sites ◽  
High Bootstrap ◽  
Pine Cones

Summary We surveyed the distribution of nematodes in 56 cones of Pinus thunbergii collected from both live branches and on the forest floor in three coastal and inland habitats and in 11 cones of P. taeda collected at different heights. We identified 47 nematodes to family or genera by analysis of an 18S small subunit rRNA gene sequence. The frequencies of occurrence of free-living cone nematodes were 97% in coastal P. thunbergii, 92% in inland P. thunbergii, and 82% in P. taeda. Phylogenetic analysis assigned the nematodes to four clades with high bootstrap values. Nine sequences that were found only in cones on live branches were clustered with Panagrobelus stammeri and an unknown Panagrobelus sp. Our results imply that nematodes are commonly associated with cones in pine forest ecosystems and that a capacity for anhydrobiosis may be a key to surviving above-ground.

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