Abstract
Nocardia species are difficult to identify, a consequence of the ever increasing number of species known and their homogeneous genetic characteristics. 16S rRNA analysis has been the gold standard for identifying these organisms, but proteomic techniques such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF MS) and housekeeping gene analysis, have also been explored. One hundred high (n = 25), intermediate (n = 20), and low (n = 55) prevalence (for Spain) Nocardia strains belonging to 30 species were identified via 16S rRNA and MALDI-TOF MS analysis. The manufacturer-provided database MALDI Biotyper library v4.0 (5.627 entries, Bruker Daltonik) was employed. In the high prevalence group (Nocardia farcinica, N. abscessus, N. cyriacigeorgica and N. nova), the 16S rRNA and MALDI-TOF MS methods provided the same identification for 76% of the strains examined. For the intermediate prevalence group (N. brasiliensis, N. carnea, N. otitidiscaviarum and N. transvalensis complex), this figure fell to 45%. In the low-prevalence group (22 species), these two methods were concordant only in six strains at the species level. Tetra-gene multi-locus sequencing analysis (MLSA) involving the concatemer gyrB-16S rRNA-hsp65-secA1 was used to arbitrate between discrepant identifications (n = 67). Overall, the MLSA confirmed the results provided at species level by 16S rRNA analysis in 34.3% of discrepancies, and those provided by MALDI-TOF MS in 13.4%. MALDI-TOF MS could be a strong candidate for the identification of Nocardia species, but only if its reference spectrum database improves, especially with respect to unusual, recently described species and species included in the described Nocardia complexes.
Highlights
The members of Nocardia are branched Gram-positive opportunistic pathogens that live in soils rich in organic matter
Similarity values of 99.0– 99.5% were obtained for eight strains, not enough to assign them to any Nocardia species, they can be assumed to belong to different Nocardia complexes (Schlaberg et al, 2013)
For the 67 strains, not concordant in the identification made by the 16S rRNA and MALDI-TOF mass spectra (MS) methods, multi-locus sequencing analysis (MLSA) was performed
Summary
The members of Nocardia are branched Gram-positive opportunistic pathogens that live in soils rich in organic matter. The MALDI-TOF MS identification harbors limitations when only manufacturer-provided database has been applied It was stated in a literature review displaying low values of correct Nocardia species assignment (≈15–53%) (Xiao et al, 2016). The constantly increasing number of, recognized Nocardia species means that the commercial MALDITOF MS spectrum database for the genus can become outdated. Both facts made that requiring laboratories to compile their own libraries to get a successful identification (Brown-Elliott et al, 2015; Buckwalter et al, 2016). This step could not be feasible for many of the routine clinical laboratories, in which MALDI-TOF MS has been widely introduced
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