scholarly journals Molecular detection of DHFR gene polymorphisms in Pneumocystis jirovecii isolates from Indian patients

2015 ◽  
Vol 9 (11) ◽  
pp. 1250-1256 ◽  
Author(s):  
Yogita Singh ◽  
Bijay Ranjan Mirdha ◽  
Randeep Guleria ◽  
Shehla Khalil ◽  
Ashutosh Panda ◽  
...  
Keyword(s):  
Gene Polymorphisms ◽  
Large Subunit ◽  
Tertiary Care ◽  
Pneumocystis Jirovecii ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Dhfr Gene ◽  
Pcr Assay ◽  
Nucleotide Substitutions ◽  
Lsu Rrna

Introduction: Pneumocystis pneumonia (PCP) is an opportunistic life-threatening infection, especially for immunocompromised individuals. A trimethoprim-sulfamethoxazole (TMP-SMX) combination is commonly used for the treatment of PCP, targeting both dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) enzymes. Several studies have already shown that polymorphisms in the DHPS gene are associated with drug resistance. The present study analyzed DHFR gene polymorphisms in Pneumocystis jirovecii recovered from clinical samples from patients admitted to a tertiary care health center in New Delhi, India. Methodology: Detection of P. jirovecii was performed using Gomori methenamine silver staining (GMS) and nested polymerase chain reaction (PCR) assay targeting the mitochondrial large subunit ribosomal RNA (mt LSU rRNA) gene. The DHFR gene was amplified using nested PCR protocol and was sequenced for detection of polymorphisms. Results: Of 180 clinical samples, only 4% (7/180) were positive by GMS staining, and 10% (18/180) were positive by mt LSU rRNA PCR assay. Of these 18 positive samples, only 77% (14/18) were amplified by the DHFR gene PCR assay. A total of 16 nucleotide substitutions were observed in 42% (6/14) samples targeted for the DHFR gene, of which 8 nucleotide substitutions were synonymous and the rest were non-synonymous. Conclusions: The DHFR gene mutations found in this study may possibly indicate an association of process likely to contribute to therapeutic failure or an evolutionary process, and warrant continuous monitoring.

scholarly journals Papiliotrema siamense f.a., sp. nov., a yeast species isolated from plant leaves

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3058-3062 ◽  
Author(s):  
Janjira Surussawadee ◽  
Pannida Khunnamwong ◽  
Nantana Srisuk ◽  
Savitree Limtong
Keyword(s):  
Type Strain ◽  
External Surface ◽  
Novel Species ◽  
Large Subunit ◽  
Its Region ◽  
Rrna Gene ◽  
Plant Leaves ◽  
Nucleotide Substitutions ◽  
Lsu Rrna Gene ◽  
Lsu Rrna

Two strains representing a novel species were isolated from the external surface of a sugar cane leaf (DMKU-SP85T) and tissue of a rice leaf (DMKU-RE97) collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, the two strains were determined to represent a novel species of the genus Papiliotrema although sexual reproduction was not observed. The sequences of the D1/D2 region of the LSU rRNA gene and ITS region of the two strains were identical, but differed from those of the type strain of Cryptococcus nemorosus by 0.6 % nucleotide substitutions (four nucleotide substitutions out of 597 nucleotides) in the D1/D2 region of the LSU rRNA gene and 1.8 % nucleotide substitutions (nine nucleotide substitutions out of 499 nucleotides) in the ITS region. The name Papiliotrema siamense f.a., sp. nov. is proposed. The type strain is DMKU-SP85T( = BCC 69499T = CBS 13330T).

scholarly journals Wickerhamiella osmotolerans sp. nov. and Wickerhamiella tropicalis sp. nov., novel ascomycetous yeast in the family Wickerhamiellaceae

2020 ◽  
Vol 70 (4) ◽  
pp. 2596-2601 ◽  
Author(s):  
Varunya Sakpuntoon ◽  
Jirameth Angchaun ◽  
Chanita Boonmak ◽  
Chin-Feng Chang ◽  
Shiu-Mei Liu ◽  
...  
Keyword(s):  
Type Strain ◽  
Large Subunit ◽  
Its Region ◽  
Surface Microlayer ◽  
Rrna Gene ◽  
Nucleotide Substitutions ◽  
D2 Domain ◽  
Sea Surface Microlayer ◽  
Lsu Rrna Gene ◽  
Lsu Rrna

Seven yeast strains, DMKU VGT1-14T, DMKU VGT1-19T, DMKU-JMGT1-28, DMKU-JMGT1-32, DMKU VGT2-06, DMKU VGT2-19 and DMKU VGT6-14, were isolated from a grease trap in Thailand and two strains, SJ-1 and SN-102 were isolated from the sea surface microlayer in Taiwan. On the basis of phenotypic characteristics and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, these strains represented two novel yeast species of the genus Wickerhamiella. In terms of pairwise sequence similarity, four strains, DMKU VGT1-14, DMKU-JMGT1-32, DMKU VGT6-14 and SN-102, were closely related to Wickerhamiella infanticola NRRL Y-17858T but differed by 13 nucleotide substitutions with one gap (2.46 %) in the D1/D2 domain of the LSU rRNA gene and 15 nucleotide substitutions with 23 gaps (4.2 %) in the ITS region. The strains DMKU VGT1-19T, DMKU-JMGT1-28, DMKU VGT2-06, DMKU VGT2-19 and SJ-1, differed from the type strain of the most closely related species, Wickerhamiella sorbophila NRRL Y-7921T, by nine nucleotide substitutions with one gap (1.66 %) in the D1/D2 domain of the LSU rRNA gene and nine nucleotide substitutions with 17 gaps (2.52%) in the ITS region. Hence, the names Wickerhamiella osmotolerans sp. nov. and Wickerhamiella tropicalis sp. nov. are proposed to accommodate these species in the genus Wickerhamiella. The holotypes are W. osmotolerans DMKU VGT1-14T (ex-type strain TBRC 11425=PYCC 8359=CGMCC 2.6179; Mycobank number 833394) and W. tropicalis DMKU VGT1-19T (ex-type strain TBRC 11426=PYCC 8360=CGMCC 2.6180; Mycobank number 833393).

scholarly journals Barnettozyma siamensis f.a., sp. nov., a lipid-accumulating ascomycete yeast species

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3053-3057 ◽  
Author(s):  
Pirapan Polburee ◽  
Wichien Yongmanitchai ◽  
Takao Ohashi ◽  
Kazuhito Fujiyama ◽  
Savitree Limtong
Keyword(s):  
Type Strain ◽  
Yeast Species ◽  
Novel Species ◽  
Large Subunit ◽  
Its Region ◽  
Rrna Gene ◽  
Nucleotide Substitutions ◽  
Isolation Technique ◽  
Lsu Rrna Gene ◽  
Lsu Rrna

Two strains, DMKU-UbN24(1)T and DMKU-CPN24(1), of a novel yeast species were obtained from soil and palm oil fruit, respectively, collected in Thailand by an enrichment isolation technique using a nitrogen-limited medium containing glycerol as the sole source of carbon. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, the two strains were found to represent a novel species of the genus Barnettozyma although the formation of ascospores was not observed. The novel species was related most closely to the type strain of Candida montana but differed by 5.4 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene and by 10.3–10.5 % nucleotide substitutions in the ITS region. The name Barnettozyma siamensis f.a., sp. nov. is proposed. The type strain is DMKU-UbN24(1)T ( = BCC 61189T = NBRC 109701T = CBS 13392T).

scholarly journals Hannaella phyllophila sp. nov., a basidiomycetous yeast species associated with plants in Thailand and Taiwan

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2135-2140 ◽  
Author(s):  
Janjira Surussawadee ◽  
Sasitorn Jindamorakot ◽  
Takashi Nakase ◽  
Ching-Fu Lee ◽  
Savitree Limtong
Keyword(s):  
Yeast Species ◽  
Novel Species ◽  
Large Subunit ◽  
Its Region ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Nucleotide Substitutions ◽  
Lsu Rrna Gene ◽  
Anamorphic Yeast ◽  
Lsu Rrna

Five strains representing one novel anamorphic yeast species were isolated from plant leaves collected in Thailand (strains DMKU-SP186T, ST-111 and ST-201) and Taiwan (strains FN20L02 and SM13L16). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, they were assigned to a single novel species of the genus Hannaella. The sequences of the D1/D2 regions of the LSU rRNA genes of four of the strains (DMKU-SP186T, ST-111, FN20L02 and SM13L16) were identical, while differing from strain ST-201 by 2 substitutions and 2 gaps. The nucleotide sequence of the ITS regions of the five strains differed from each other by between 0 and 3 nucleotide substitutions. The novel species was most closely related to Hannaella luteola, but showed 1.0–1.3 % nucleotide substitutions (between 6 substitutions out of 568–606 nt and 8 substitutions, and 2 gaps out of 597 nt) in the D1/D2 region of the LSU rRNA gene and 1.4–2.0 % nucleotide substitutions (6–9 substitutions out of 435 nt) in the ITS region. Ballistospores were produced by three of the strains on cornmeal agar at 15 and 20 °C after 4 weeks, while H. luteola did not produce ballistospores. The name Hannaella phyllophila sp. nov. is proposed. The type strain is DMKU-SP186T ( = BCC 69500T = NBRC 110428T = CBS 13921T).

scholarly journals Occultifur tropicalis f.a., sp. nov., a novel cystobasidiomycetous yeast species isolated from tropical regions

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1578-1582 ◽  
Author(s):  
Pannida Khunnamwong ◽  
Janjira Surussawadee ◽  
Sasitorn Jindamorakot ◽  
José R. A. Ribeiro ◽  
Allen N. Hagler ◽  
...  
Keyword(s):  
Sugar Cane ◽  
Yeast Species ◽  
Large Subunit ◽  
Its Region ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Nucleotide Substitutions ◽  
Tropical Regions ◽  
Lsu Rrna Gene ◽  
Lsu Rrna

Five strains representing a single novel anamorphic yeast species were isolated from sugar cane. Two strains were from tissue (DMKU-SE38, DMKU-SE59T) and two from the external surface (DMKU-SP385, DMKU-SP403) of leaves collected in Thailand and the fifth (IMUFRJ 52020) from the rhizoplane of sugar cane in an organically cultivated field in Brazil. On the basis of sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, they were classified as representing a single species of the genus Occultifur. The sequences of the D1/D2 region of the LSU rRNA genes and the ITS regions of the five strains were either identical or differed from each other by only one nucleotide substitution. The novel species was related most closely to Occultifur brasiliensis f.a. CBS 12687T but with 0.7–1.0 % nucleotide substitutions (4–6 nt) in the D1/D2 region of the LSU rRNA gene and 2.5–2.7 % nucleotide substitutions (14–15 nt) in the ITS region. The name Occultifur tropicalis f.a., sp. nov. is proposed. The type strain is DMKU-SE59T ( = BCC 61184T = NBRC 109696T = CBS 13389 T).

Wickerhamomyces siamensis sp. nov., a novel yeast species isolated from the phylloplane in Thailand

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1568-1573 ◽  
Author(s):  
Rungluk Kaewwichian ◽  
Hiroko Kawasaki ◽  
Savitree Limtong
Keyword(s):  
External Surface ◽  
Yeast Species ◽  
Novel Species ◽  
Large Subunit ◽  
Its Region ◽  
Rrna Gene ◽  
The Novel ◽  
Nucleotide Substitutions ◽  
Lsu Rrna Gene ◽  
Lsu Rrna

Strain DMKU-RK359T, representing a novel yeast species, was isolated from the external surface of a sugar-cane leaf collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 region of the large-subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, strain DMKU-RK359T was assigned to a novel Wickerhamomyces species. The novel species was closest to Wickerhamomyces ciferrii, but differed from it by 0.7 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene and 6 % nucleotide substitutions in the ITS region. The name Wickerhamomyces siamensis sp. nov. is proposed (type strain DMKU-RK359T  = BCC 50732T  = NBRC 108900T  = CBS 12570T).

scholarly journals Savitreea pentosicarens gen. nov., sp. nov., a yeast species in the family Saccharomycetaceae isolated from a grease trap

2020 ◽  
Vol 70 (11) ◽  
pp. 5665-5670
Author(s):  
Varunya Sakpuntoon ◽  
Jirameth Angchuan ◽  
Chanita Boonmak ◽  
Pannida Khunnamwong ◽  
Noémie Jacques ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Yeast Species ◽  
Sequence Divergence ◽  
Its Region ◽  
Rrna Gene ◽  
Nucleotide Substitutions ◽  
D2 Domain ◽  
The Family ◽  
Lsu Rrna Gene ◽  
Lsu Rrna

Two strains (DMKU-GTCP10-8 and CLIB 1740) representing a novel anamorphic yeast species were isolated from a grease sample collected from a grease trap in Thailand and from an unidentified fungus collected in French Guiana, respectively. On the basis of phylogenetic analysis based on the combined D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, Lachancea fermentati CBS 707T was the closely related species with 12.8 % sequence divergence (70 nucleotide substitutions and three gaps in 571 nucleotides) and 28.1 % sequence divergence (93 nucleotide substitutions and 90 gaps in 651 nucleotides) in the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. Phylogenetic analysis based on the concatenated sequences of the five genes including the small subunit rRNA gene, the D1/D2 domain of the LSU rRNA gene, the ITS region, translation elongation factor-1 alpha (TEF1) and RNA polymerase II subunit 2 (RPB2) genes confirmed that the two strains (DMKU-GTCP10-8 and CLIB 1740) were well-separated from other described yeast genera in Saccharomycetaceae. Hence, Savitreea pentosicarens gen. nov., sp. nov. is proposed to accommodate these two strains as members of the family Saccharomycetaceae. The holotype is S. pentosicarens DMKU-GTCP10-8T (ex-type strain TBRC 12159=PYCC 8490; MycoBank number 835044).

Ogataea kolombanensis sp. nov., Ogataea histrianica sp. nov. and Ogataea deakii sp. nov., three novel yeast species from plant sources

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3115-3123 ◽  
Author(s):  
Neža Čadež ◽  
Dénes Dlauchy ◽  
Peter Raspor ◽  
Gábor Péter
Keyword(s):  
Sequence Analysis ◽  
Olive Oil ◽  
Type Strain ◽  
Yeast Species ◽  
Novel Species ◽  
Large Subunit ◽  
Virgin Olive Oil ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Lsu Rrna

Nine methanol-assimilating yeast strains isolated from olive oil sediments in Slovenia, extra virgin olive oil from Italy and rotten wood collected in Hungary were found to form three genetically separated groups, distinct from the currently recognized yeast species. Sequence analysis from genes of the small subunit (SSU) rRNA, internal transcribed spacer region/5.8S rRNA, large subunit (LSU) rRNA D1/D2 domains and translational elongation factor-1α (EF-1α) revealed that the three closely related groups represent three different undescribed yeast species. Sequence analysis of the LSU rRNA gene D1/D2 domains placed the novel species in the Ogataea clade. The three novel species are designated as Ogataea kolombanensis sp. nov. (type strain: ZIM 2322T = CBS 12778T = NRRL Y-63657T), Ogataea histrianica sp. nov. (type strain: ZIM 2463T = CBS 12779T = NRRL Y-63658T) and Ogataea deakii sp. nov. (type strain: NCAIM Y.01896T = CBS 12735T = NRRL Y-63656T).

Coleopuccinia in China and its relationship to Gymnosporangium

Phytotaxa ◽  
2018 ◽  
Vol 347 (3) ◽  
pp. 235 ◽  
Author(s):  
BIN CAO ◽  
SIQI TAO ◽  
CHENGMING TIAN ◽  
YINGMEI LIANG
Keyword(s):  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Rust Fungi ◽  
Internal Transcribed Spacers ◽  
Western China ◽  
Rrna Gene ◽  
Morphological Examination ◽  
Separate Genus ◽  
Lsu Rrna Gene ◽  
Lsu Rrna

The rust species Coleopuccinia sinensis was collected during an investigation of rust fungi in Tibet, a region in south-western China. Through morphological examination, we clarified that C. kunmingensis is a synonym of C. sinensis. Phylogenetic analyses using the combined loci of the internal transcribed spacers (ITS) and the partial large subunit (LSU) rRNA gene revealed that Coleopuccinia should be treated as a separate genus from Gymnosporangium.

Sign in / Sign up

Export Citation Format

Share Document