Department of Microbiology and Immunology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA.
J Clin Microbiol. 2010 Mar;48(3):741-52. doi: 10.1128/JCM.01948-09. Epub 2009 Dec 30.
The species-level identification of sterile and/or arthroconidium-forming filamentous fungi presumed to be basidiomycetes based upon morphological or physiological features alone is usually not possible due to the limited amount of hyphal differentiation. Therefore, a reliable molecular approach capable of the unambiguous identification of clinical isolates is needed. One hundred sixty-eight presumptive basidiomycetes were screened by sequence analysis of the internal transcribed spacer (ITS) and D1/D2 ribosomal DNA regions in an effort to obtain a species identification. Through the use of this approach, identification of a basidiomycetous fungus to the species level was obtained for 167/168 of the isolates. However, comparison of the BLAST results for each isolate for both regions revealed that only 28.6% (48/168) of the isolates had the same species identification by use of both the ITS and the D1/D2 regions, regardless of the percent identity. At the less stringent genus-only level, the identities for only 48.8% (82/168) of the isolates agreed for both regions. Investigation of the causes for this low level of agreement revealed that 14% of the species lacked an ITS region deposit and 16% lacked a D1/D2 region deposit. Few GenBank deposits were found to be complete for either region, with only 8% of the isolates having a complete ITS region and 10% having a complete D1/D2 region. This study demonstrates that while sequence-based identification is a powerful tool for many fungi, sequence data derived from filamentous basidiomycetes should be interpreted carefully, particularly in the context of missing or incomplete GenBank data, and, whenever possible, should be evaluated in light of compatible morphological features.
由于菌丝分化有限，单凭形态学或生理学特征对被认为是担子菌的无菌和/或分生孢子形成丝状真菌进行种水平鉴定通常是不可能的。因此，需要一种可靠的分子方法，能够明确鉴定临床分离株。通过对内部转录间隔区（ITS）和核糖体 DNA 的 D1/D2 区进行序列分析，筛选了 168 株假定的担子菌，以获得种的鉴定。通过使用这种方法，对 168 株分离株中的 167 株进行了担子菌真菌的种水平鉴定。然而，对两个区域的每个分离株的 BLAST 结果进行比较后发现，无论同一性百分比如何，只有 28.6%（48/168）的分离株使用 ITS 和 D1/D2 区域都具有相同的种鉴定。在不那么严格的属级水平上，两个区域的同一性仅为 48.8%（82/168）的分离株。对造成这种低水平一致性的原因的调查显示，14%的种缺乏 ITS 区存款，16%的种缺乏 D1/D2 区存款。很少有 GenBank 存款被发现两个区域都完整，只有 8%的分离株具有完整的 ITS 区，10%的分离株具有完整的 D1/D2 区。本研究表明，虽然基于序列的鉴定是许多真菌的强大工具，但应谨慎解释来自丝状担子菌的序列数据，特别是在 GenBank 数据缺失或不完整的情况下，并且，只要有可能，应根据相容的形态特征进行评估。
