Genotyping of Pneumocystis jirovecii by Use of a New Simplified Nomenclature System Based on the Internal Transcribed Spacer Regions and 5.8S rRNA Gene of the rRNA Operon

Abstract

Genotyping based on internal transcribed spacer 1 (ITS1) and ITS2 of the rRNA operon has played an important role in understanding the transmission and epidemiology of Pneumocystis jirovecii, one of the major opportunistic pathogens in individuals with AIDS and other immunocompromised individuals. The widespread use of this typing system has resulted in several problems, including inconsistent genotype nomenclatures, difficult data transferability, and complicated interpretation of the length variation in multiple homopolymeric tracts. The aim of this study was to establish a new, simplified genotype nomenclature system for P. jirovecii based on the ITS1 and ITS2 sequences. We first analyzed the complete ITS1, 5.8S rRNA gene, and ITS2 sequences (termed ITS1-5.8S-ITS2) in 27 recent P. jirovecii isolates from China and identified 18 unique genotypes. Subsequently, we performed a comprehensive classification of more than 400 ITS1-and ITS2-related sequences from GenBank and an in-depth evaluation of the length variation of multiple homopolymeric tracts within ITS1-5.8S-ITS2. Integration of the results from these analyses led to a new, simplified genotype nomenclature system including 62 unique ITS1-5.8S-ITS2 genotypes, simply designated types 1 through 62. This new system offers several advantages over traditional ITS1-and ITS2-based typing systems, including a simpler analysis and interpretation process, a higher discriminative power, and no limitation in assigning potential new genotypes. This new system is expected to facilitate the standardization of P. jirovecii genotyping and easy data exchanges across different laboratories.

Genetic Polymorphisms of 3 Cases Pneumocystis jirovecii in Shanxi Province PR China

“…The ITS region of P. jirovecii is the most polymorphic loci and widely used for genotyping [1]. In this study, we assessed and analyzed the P. jirovecii ITS genotype of 3 clinical samples from Shanxi province according to the new, simpli ed genotype nomenclature system [2]. We found ITS 4, ITS10 and ITS 59 genotypes, which were also identi ed in our previous study [2].…”

“…The most prevalent genotype of ITS in Japan was Genotype 10 [24], which was observed in our study. In previous studies in China, Genotype 22 was most common in Beijing, Tianjin and Liaoning [2,15], whereas, Genotype 1 in Guangzhou [14]. However, it is di cult to accurately assess and statistically analyze the correlation between geographic diversity and P. jirovecii ITS genotypes based on the small sample size in this study.…”

“…Pneumocystis jirovecii (P. jirovecii), the species that infects humans, can lead to life-threatening P. jirovecii pneumonia (PJP) or Pneumocystis pneumonia (PCP), most commonly in immunode cient people such as those infected with human immunode ciency virus (HIV), solid organ transplant recipients, and patients with malignant tumors [1]. Recent numerous studies indicated that the high prevalence of P. jirovecii colonization and infection is found in pulmonary diseases particularly in chronic obstructive pulmonary disease (COPD) [2][3][4][5]. However, it is di cult to clearly understand the biology and epidemiology of P. jirovecii infection and colonization, since there is no reliable and continuous cultivable system in vitro.…”

Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii

“…As a result, eight genetic regions were explored in this study as potential loci which could be included in a global consensus scheme, by analysing their amplification ability and demonstrating their discriminatory power. The whole ITS region is widely reported to have the most variability within P. jirovecii and is highly useful when identifying and genotyping other invasive fungi [ 74 ]. Unfortunately, it also has been reported to have a high amplification failure when applied to P. jirovecii [ 59 ], which was also evident in the current study, as ITS1 alone and ITS1/2 regions showed to have the lowest amplification capability, unable to amplify and successfully sequence more than 50% of the studied isolates for either primer set.…”

“…The ITS1 and ITS2 regions have demonstrated the highest sequence variation among all loci of the rDNA gene cluster, as evident when sequenced as separate loci or in combination of the two regions (including the 5.8S gene), using nested-PCR techniques [ 3 ]. This has resulted in over 120 unique genotypes for both ITS regions reported and submitted to GenBank [ 74 ]. The ITS1 and ITS2 regions were chosen over the other genes in the rDNA gene cluster due to their superior discriminative power.…”