Sun Lan, Huang Minjun, Wang Jiancheng, Xue Feng, Hong Cailing, Guo Zengzhu, Gu Junchao
Beijing Friendship Hospital, Capital Medical University, Beijing, China; Beijing Tropical Medicine Research Institute, Beijing, China; Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Beijing, China.
Department of Clinical Laboratory Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
Infect Genet Evol. 2015 Apr;31:209-15. doi: 10.1016/j.meegid.2015.01.021. Epub 2015 Jan 31.
Pneumocystis jirovecii is a fungus that causes Pneumocystis pneumonia in immuno-compromised patients. To analyze the genetic diversity of P. jirovecii in HIV-negative patients in China, respiratory specimens were obtained from 105 patients who tested PCR-positive for the presence of the P. jirovecii mitochondrial large subunit ribosomal RNA (mtLSU rRNA) between 2011 and 2013. P. jirovecii isolates were genotyped based on the upstream conserved sequence (UCS) of the major surface glycoprotein (MSG) gene and the internal transcribed spacer (ITS) of nuclear rRNA operon. Eighty-one of the 105 isolates showed a positive PCR for the UCS region. We identified six different patterns comprising two, three, four, or five UCS repeats, including 1, 2, 3 (69.14%), 1, 2, 3, 3 (22.22%), 1, 2 (3.7%), 1, 1, (2.47%), 2, 2, 3, 3 (1.23%), and 1, 1, 2, 3, 3 (1.23%). In regard to the ITS region, 58 of the 105 isolates were cloned and sequenced successfully. Six known ITS1 alleles (A, B, DEL1, E, N, and SYD1), two new alleles (designated as BTM3 and BTM4), six known ITS2 alleles (a, b, i, g, h and O) and one new allele (designated as btm6) were observed. A total of 19 P. jirovecii ITS haplotypes were identified. The most frequent type was Bi (25.9%), followed by Ai (13.8%), Eb (10.3%), and SYD1g (6.9%). Among the 58 specimens examined, 49 (84.5%) were found to contain a single type of P. jirovecii, while 9 (15.5%) contained multiple genotypes. A total of 34 allelic profiles were observed in 58 isolates when the two loci were combined with each other. A Fisher's exact test revealed that there was no statistically significant (P=0.330) association between the most frequent UCS and ITS genotypes. An analysis of the phylogenetic relationship between different patient groups identified two major groups based on the sequence variations of concatenated UCS and ITS sequences in 49 isolates. Our results demonstrated the high genetic variability of P. jirovecii in HIV-negative patients in China.
耶氏肺孢子菌是一种可在免疫功能低下患者中引起肺孢子菌肺炎的真菌。为分析中国HIV阴性患者中耶氏肺孢子菌的遗传多样性，于2011年至2013年期间从105例耶氏肺孢子菌线粒体大亚基核糖体RNA（mtLSU rRNA）PCR检测呈阳性的患者中获取呼吸道标本。基于主要表面糖蛋白（MSG）基因的上游保守序列（UCS）和核rRNA操纵子的内部转录间隔区（ITS）对耶氏肺孢子菌分离株进行基因分型。105株分离株中有81株UCS区域PCR检测呈阳性。我们鉴定出六种不同模式，包括两个、三个、四个或五个UCS重复序列，分别为1, 2, 3（69.14%）、1, 2, 3, 3（22.22%）、1, 2（3.7%）、1, 1（2.47%）、2, 2, 3, 3（1.23%）和1, 1, 2, 3, 3（1.23%）。关于ITS区域，105株分离株中有58株成功克隆并测序。观察到六个已知的ITS1等位基因（A、B、DEL1、E、N和SYD1）、两个新等位基因（命名为BTM3和BTM4）、六个已知的ITS2等位基因（a、b、i、g、h和O）以及一个新等位基因（命名为btm6）。共鉴定出19种耶氏肺孢子菌ITS单倍型。最常见的类型是Bi（25.9%），其次是Ai（13.8%）、Eb（10.3%）和SYD1g（6.9%）。在检测的58个标本中，49个（84.5%）被发现只含有单一类型的耶氏肺孢子菌，而9个（15.5%）含有多种基因型。当两个基因座相互组合时，在58株分离株中总共观察到34种等位基因谱。Fisher精确检验显示，最常见的UCS和ITS基因型之间无统计学显著关联（P = 0.330）。基于49株分离株中串联的UCS和ITS序列的序列变异，对不同患者组之间的系统发育关系分析确定了两个主要组。我们的结果表明中国HIV阴性患者中耶氏肺孢子菌具有高度的遗传变异性。
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