Table 1.
Nocardia isolates examined (n = 25) in the present study.
Table 2.
Identification results of 25 Nocardia clinical isolates by DNA sequencing and MALDI-TOF MS after interrogation against the Biotyper database (version 3.1) and the “in-house” database.
Fig 1.
Phylogenetic trees are shown and were conducted using the maximum-likelihood method.
Fig 1a. Phylogenetic tree based on the concatenated gyrB-16S-secA1-hsp65-rpoB sequences of 25 Nocardia clinical isolates and 20 Nocardia type strains, using Gordonia bronchialis strain ATCC 25592T as an outgroup (S1 Table). Fig 1b. Phylogenetic tree based on the hsp65 gene sequences of 12 N. cyriacigeorgica clinical isolates and nine Nocardia cyriacigeorgica isolates whose genotypes have previously been determined by Schlaberg et al. [29] using the sequence of a Nocardia farcinica strain as an outgroup.
Table 3.
Genetic polymorphisms contained within the 16S rRNA, gyrB, secA1, hsp65 and rpoB genes for 25 clinical Nocardia isolates studied.
Fig 2.
The main spectrum profile (MSP) dendrogram constructed using spectra of 25 Nocardia clinical strains along with 37 reference spectra of 32 Nocardia species contained in the original Biotyper database (version 3.1; Bruker).
Strain identification numbers of clinical isolates collected in the present study are shown underlined, and isolates used for establishment of the “in-house” database was labeled with asterisks.
Table 4.
Review of publications for evaluation of MALDI-TOF MS for the identification of Nocardia species.
Fig 3.
Proposed algorithm for laboratory identification of Nocardia isolates (solid lines) and establishment and expansion of ongoing “in-house” mass spectrum database (dashed lines).