Division of Clinical Microbiology, Department of Laboratory Medicine, West China Hospital Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, Sichuan, P.R. China.
Sichuan Clinical Research Center for Laboratory Medicine, Chengdu, China.
BMC Microbiol. 2024 Sep 20;24(1):358. doi: 10.1186/s12866-024-03483-2.
Nocardiosis, despite its rarity and underreporting, is significant due to its severe impact, characterized by high morbidity and mortality rates. The development of a precise, reliable, rapid, and straightforward technique for identifying the pathogenic agent in clinical specimens is crucial to reduce fatality rates and facilitate timely antimicrobial treatment. In this study, we aimed to identify Nocardia spp. in clinical isolates, using MALDI-TOF MS as the primary method, with molecular methods as the gold standard. Clinical Nocardia isolates were identified using 16S rRNA/hsp65/gyrB/secA1/rpoB gene sequencing. Identification performance of the Bruker MALDI Biotyper 3.1 (V09.0.0.0_8468) and MBT Compass 4.1 (V11.0.0.0_10833) for Nocardia identification was evaluated.
Seventy-six Nocardia isolates were classified into 12 species through gene sequencing. The MALDI Biotyper 3.1 (V09.0.0.0_8468) achieved 100% genus-level accuracy and 84.2% species accuracy (64/76). The MBT Compass 4.1 with the BDAL Database (V11.0.0.0_10833) improved species identification to 98.7% (75/76). The updated database enhanced species level identification with scores > 1.7, increasing from 77.6% (59/76) to 94.7% (72/76), a significant improvement (P = 0.001). The new and simplified extraction increased the proportion of strains identified to the species level with scores > 1.7 from 62.0% (18/29) to 86.2% (25/29) (P = 0.016). An in-house library construction ensured accurate species identification for all isolates.
The Bruker mass spectrometer can accurately identify Nocardia species, albeit with some variations observed between different database versions. The MALDI Biotyper 3.1 (V09.0.0.0_8468) has limitations in identifying Nocardia brasiliensis, with some strains only identifiable to the genus level. MBT Compass 4.1 (V11.0.0.0_10833) effectively addresses this shortfall, improving species identification accuracy to 98.7%, and offering quick and reliable identification of Nocardia. Both database versions incorrectly identified the clinically less common Nocardia sputorum as Nocardia araoensis. For laboratories that have not upgraded their databases and are unable to achieve satisfactory identification results for Nocardia, employing the new and simplified extraction method can provide a degree of improvement in identification outcomes.
尽管诺卡氏菌病发病率低且报告不足，但由于其严重的影响，包括高发病率和死亡率，因此仍然具有重要意义。开发一种精确、可靠、快速和直接的技术来鉴定临床标本中的病原体对于降低死亡率和促进及时使用抗菌药物治疗至关重要。在本研究中，我们旨在使用 MALDI-TOF MS 作为主要方法，以分子方法为金标准，鉴定临床分离株中的诺卡氏菌。临床诺卡氏菌分离株通过 16S rRNA/hsp65/gyrB/secA1/rpoB 基因测序进行鉴定。评估了 Bruker MALDI Biotyper 3.1（V09.0.0.0_8468）和 MBT Compass 4.1（V11.0.0.0_10833）对诺卡氏菌鉴定的性能。
通过基因测序将 76 株诺卡氏菌分为 12 个种。MALDI Biotyper 3.1（V09.0.0.0_8468）在属水平上的准确率为 100%，在种水平上的准确率为 84.2%（64/76）。使用 BDAL 数据库的 MBT Compass 4.1（V11.0.0.0_10833）将种的鉴定提高到 98.7%（75/76）。更新后的数据库提高了物种水平的鉴定，评分>1.7 的比例从 77.6%（59/76）增加到 94.7%（72/76），差异具有统计学意义（P=0.001）。新的简化提取方法增加了评分>1.7 的菌株鉴定为种的比例，从 62.0%（18/29）增加到 86.2%（25/29）（P=0.016）。内部文库构建确保了所有分离株的准确物种鉴定。
Bruker 质谱仪可以准确鉴定诺卡氏菌属，尽管不同数据库版本之间存在一些差异。MALDI Biotyper 3.1（V09.0.0.0_8468）在鉴定巴西诺卡氏菌方面存在局限性，一些菌株只能鉴定到属水平。MBT Compass 4.1（V11.0.0.0_10833）有效地解决了这一问题，将种的鉴定准确率提高到 98.7%，并能快速可靠地鉴定诺卡氏菌。两个数据库版本都错误地将临床上较少见的鼻疽诺卡氏菌鉴定为阿劳诺卡氏菌。对于尚未升级数据库且无法对诺卡氏菌获得满意鉴定结果的实验室，采用新的简化提取方法可以在一定程度上提高鉴定结果。
