Development of type-specific PCR for typing Pneumocystis carinii f. sp. hominis based on nucleotide sequence variations of internal transcribed spacer regions of rRNA genes

Bingdong Jiang, Jang Jih Lu, Baozheng Li, Xing Tang, Marilyn S. Bartlett, James W. Smith, Chao-Hung Lee

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

The nucleotide sequence variations in the internal transcribed spacer region 1 (ITS1) and region 2 (ITS2) of rRNA genes were found to be useful for typing Pneumocystis carinii isolates that infect humans. Two types of ITS1 (A and B) and three types of ITS2 (a, b, and c) sequences have been found, and P. carinii isolates are classified based on sequence types of ITS1 and ITS2 as Ax or Bx (where x may be a, b, or c). Type determination has been achieved by sequencing the ITS regions or by reacting the ITS regions amplified by PCR with type-specific oligonucleotide (TSO) probes. However, TSO typing alone does not work on a specimen from an individual who is infected by more than one strain of P. carinii where different ITS1 types are present in the same specimen. In this study, type-specific PCR assays were developed to supplement TSO typing. Type-specific PCR primers were made so that they differ at their 3' ends by the two nucleotides which distinguish type A from type B of ITS1 plus an additional 'A' residue at the extreme 3' ends of the primers. These two primers were paired separately with a general primer which anneals to a region downstream from ITS2 to specifically amplify Ax or Bx. The amplified products were then reacted separately with ITS2-specific probes 2-a, 2-b, and 2-c to identify their types.

Original languageEnglish
Pages (from-to)3245-3248
Number of pages4
JournalJournal of Clinical Microbiology
Volume34
Issue number12
StatePublished - Dec 1996

Fingerprint

Pneumocystis carinii
rRNA Genes
Oligonucleotides
Polymerase Chain Reaction
Oligonucleotide Probes
Nucleotides

ASJC Scopus subject areas

  • Microbiology (medical)
  • Microbiology

Cite this

Development of type-specific PCR for typing Pneumocystis carinii f. sp. hominis based on nucleotide sequence variations of internal transcribed spacer regions of rRNA genes. / Jiang, Bingdong; Lu, Jang Jih; Li, Baozheng; Tang, Xing; Bartlett, Marilyn S.; Smith, James W.; Lee, Chao-Hung.

In: Journal of Clinical Microbiology, Vol. 34, No. 12, 12.1996, p. 3245-3248.

Research output: Contribution to journalArticle

Jiang, Bingdong ; Lu, Jang Jih ; Li, Baozheng ; Tang, Xing ; Bartlett, Marilyn S. ; Smith, James W. ; Lee, Chao-Hung. / Development of type-specific PCR for typing Pneumocystis carinii f. sp. hominis based on nucleotide sequence variations of internal transcribed spacer regions of rRNA genes. In: Journal of Clinical Microbiology. 1996 ; Vol. 34, No. 12. pp. 3245-3248.
@article{caab845cad2f4e8091065cd7cbeab723,
title = "Development of type-specific PCR for typing Pneumocystis carinii f. sp. hominis based on nucleotide sequence variations of internal transcribed spacer regions of rRNA genes",
abstract = "The nucleotide sequence variations in the internal transcribed spacer region 1 (ITS1) and region 2 (ITS2) of rRNA genes were found to be useful for typing Pneumocystis carinii isolates that infect humans. Two types of ITS1 (A and B) and three types of ITS2 (a, b, and c) sequences have been found, and P. carinii isolates are classified based on sequence types of ITS1 and ITS2 as Ax or Bx (where x may be a, b, or c). Type determination has been achieved by sequencing the ITS regions or by reacting the ITS regions amplified by PCR with type-specific oligonucleotide (TSO) probes. However, TSO typing alone does not work on a specimen from an individual who is infected by more than one strain of P. carinii where different ITS1 types are present in the same specimen. In this study, type-specific PCR assays were developed to supplement TSO typing. Type-specific PCR primers were made so that they differ at their 3' ends by the two nucleotides which distinguish type A from type B of ITS1 plus an additional 'A' residue at the extreme 3' ends of the primers. These two primers were paired separately with a general primer which anneals to a region downstream from ITS2 to specifically amplify Ax or Bx. The amplified products were then reacted separately with ITS2-specific probes 2-a, 2-b, and 2-c to identify their types.",
author = "Bingdong Jiang and Lu, {Jang Jih} and Baozheng Li and Xing Tang and Bartlett, {Marilyn S.} and Smith, {James W.} and Chao-Hung Lee",
year = "1996",
month = "12",
language = "English",
volume = "34",
pages = "3245--3248",
journal = "Journal of Clinical Microbiology",
issn = "0095-1137",
publisher = "American Society for Microbiology",
number = "12",

}

TY - JOUR

T1 - Development of type-specific PCR for typing Pneumocystis carinii f. sp. hominis based on nucleotide sequence variations of internal transcribed spacer regions of rRNA genes

AU - Jiang, Bingdong

AU - Lu, Jang Jih

AU - Li, Baozheng

AU - Tang, Xing

AU - Bartlett, Marilyn S.

AU - Smith, James W.

AU - Lee, Chao-Hung

PY - 1996/12

Y1 - 1996/12

N2 - The nucleotide sequence variations in the internal transcribed spacer region 1 (ITS1) and region 2 (ITS2) of rRNA genes were found to be useful for typing Pneumocystis carinii isolates that infect humans. Two types of ITS1 (A and B) and three types of ITS2 (a, b, and c) sequences have been found, and P. carinii isolates are classified based on sequence types of ITS1 and ITS2 as Ax or Bx (where x may be a, b, or c). Type determination has been achieved by sequencing the ITS regions or by reacting the ITS regions amplified by PCR with type-specific oligonucleotide (TSO) probes. However, TSO typing alone does not work on a specimen from an individual who is infected by more than one strain of P. carinii where different ITS1 types are present in the same specimen. In this study, type-specific PCR assays were developed to supplement TSO typing. Type-specific PCR primers were made so that they differ at their 3' ends by the two nucleotides which distinguish type A from type B of ITS1 plus an additional 'A' residue at the extreme 3' ends of the primers. These two primers were paired separately with a general primer which anneals to a region downstream from ITS2 to specifically amplify Ax or Bx. The amplified products were then reacted separately with ITS2-specific probes 2-a, 2-b, and 2-c to identify their types.

AB - The nucleotide sequence variations in the internal transcribed spacer region 1 (ITS1) and region 2 (ITS2) of rRNA genes were found to be useful for typing Pneumocystis carinii isolates that infect humans. Two types of ITS1 (A and B) and three types of ITS2 (a, b, and c) sequences have been found, and P. carinii isolates are classified based on sequence types of ITS1 and ITS2 as Ax or Bx (where x may be a, b, or c). Type determination has been achieved by sequencing the ITS regions or by reacting the ITS regions amplified by PCR with type-specific oligonucleotide (TSO) probes. However, TSO typing alone does not work on a specimen from an individual who is infected by more than one strain of P. carinii where different ITS1 types are present in the same specimen. In this study, type-specific PCR assays were developed to supplement TSO typing. Type-specific PCR primers were made so that they differ at their 3' ends by the two nucleotides which distinguish type A from type B of ITS1 plus an additional 'A' residue at the extreme 3' ends of the primers. These two primers were paired separately with a general primer which anneals to a region downstream from ITS2 to specifically amplify Ax or Bx. The amplified products were then reacted separately with ITS2-specific probes 2-a, 2-b, and 2-c to identify their types.

UR - http://www.scopus.com/inward/record.url?scp=0029972328&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0029972328&partnerID=8YFLogxK

M3 - Article

C2 - 8940486

AN - SCOPUS:0029972328

VL - 34

SP - 3245

EP - 3248

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

SN - 0095-1137

IS - 12

ER -