Application of MALDI-TOF mass spectrometry for identification of Nocardia species

• Published in: BMC microbiology 2024-09, Vol.24 (1), p.358-11, Article 358
• Main Authors: Liu, Ya, Wu, Si-Ying, Deng, Jin, Zhuang, Kai-Wen, Tang, Ying, Wu, Nan, Zhang, Wei-Li, Liao, Quan-Feng, Xiao, Yu-Ling, Kang, Mei
• Format: Article
• Language: English
• Subjects: Acids; Analysis; Bacteria; Bacterial Proteins - genetics; Bacterial Typing Techniques - methods; Clinical isolates; Control; DNA sequencing; DNA, Bacterial - genetics; Gene sequencing; Genes; Health aspects; Heat shock proteins; Hsp65 protein; Humans; Identification; Identification and classification; Immune response; Infections; Instrument industry; MALDI-TOF MS; Mass spectrometry; Mass spectroscopy; Medical laboratories; Methods; Microbiology; Morbidity; Mortality; Nocardia; Nocardia - chemistry; Nocardia - classification; Nocardia - genetics; Nocardia - isolation & purification; Nocardia Infections - diagnosis; Nocardia Infections - microbiology; Nocardiosis; Physical characteristics; Proteins; Rapid identification; RNA polymerase; RNA, Ribosomal, 16S - genetics; RpoB protein; rRNA 16S; Scientific imaging; Sequence Analysis, DNA - methods; Software; Species; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods; Time-of-flight mass spectrometry; United States
• ISSN: 1471-2180; 1471-2180
• 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.