Nocardia in German Hospital. Characterization and improved diagnostics of Nocardia strains isolated over the last two decades at a German tertiary care center

We studied 39 Nocardia strains isolated from 33 patient samples between 2000 and 2018. Twenty-four patients (72.7%) were immunocompromised. Whole genome sequencing (WGS) revealed a broad taxonomic range of those isolates spanning 13 different species, including four strains that belonged to three novel species based on average nucleotide identity (ANI < 95% with currently available genome sequences). 16S rRNA gene-analyses mirrored WGS results. Conventional MALDI-TOF analysis correctly identified 29 isolates at the species level (74.4%). Our advanced protocol with formic acid and acetonitrile treatment increased identification to 35 isolates (89.7%). Antibiotic resistance was tested based on both a microdilution method and MIC strip tests. Results were in good concordance with an overall trimethoprim-sulfamethoxazole (TMP-SMX) resistance rate of 13.5%. WGS of one TMP-SMX resistant N. farcinica isolate showed a deletion of several amino acids in a homolog of dihydropteroate synthase (FolP2).