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

ABSTRACT: Nocardia in German Hospital

PROVIDER: PRJEB43439 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5416490_1.fastq.gz	Fastqsanger.gz
	ERR5416490_2.fastq.gz	Fastqsanger.gz
	ERR5416500_1.fastq.gz	Fastqsanger.gz
	ERR5416500_2.fastq.gz	Fastqsanger.gz
	ERR5416510_1.fastq.gz	Fastqsanger.gz

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Molecular characterization and improved diagnostics of <i>Nocardia</i> strains isolated over the last two decades at a German tertiary care center.

Project description:Nocardiosis is a rare but life-threatening infection caused by aerobic Actinomycetes of the genus Nocardia particularly affecting immunocompromised hosts. The identification of Nocardia ssp. and antibiotic susceptibility testing by standard microbiological methods are incomplete and molecular techniques may improve diagnostics. We studied 39 Nocardia strains isolated from 33 patients 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 using both a microdilution method and MIC strip testing. Results were in good concordance with an overall trimethoprim-sulfamethoxazole (SXT) resistance rate of 13.5 %. WGS of a SXT resistant N. farcinica isolate showed a deletion of several amino acids in a homolog of dihydropteroate synthase (FolP2) that was not seen in sensitive members of this species. Diversity of Nocardia isolates was high and involved many different species, suggesting that this taxon has broadly distributed mechanisms for infecting individuals. Widely applicable diagnostic methods including MALDI-TOF and 16S rRNA gene analyses correctly identified most strains. WGS additionally revealed molecular insights into SXT resistance mechanisms of clinical Nocardia isolates highlighting the potential application of (meta)genomic-based diagnostics in the future.

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Project description:Our aim was to investigate the relationship between additional iodinated contrast medium (CM) application for acute stroke imaging and Post-Contrast Acute Kidney Injury (PC-AKI). We performed a retrospective analysis of consecutive patients with acute stroke who received a CT angiogram (CTA) with or without additional CT perfusion (CTP) at admission between 2017 and 2020. The primary endpoint was the incidence of PC-AKI. Potential causes of renal function impairment were recorded and logistic regression was performed to determine predictors of PC-AKI. Of 3134 cases screened, n = 989 met the predefined inclusion criteria. PC-AKI occurred in 22 (5.4%) patients who received CTA only and 18 (3.1%) patients who received CTA and additional CTP (unadjusted OR, CI; 0.59, 0.29-1.05). In 31/40 (77.5%) patients who suffered PC-AKI, a non-CM-related cause of renal function impairment was identified. Stroke etiology (hemorrhagic vs. ischemic) and indicators of prior kidney disease were independent predictors of PC-AKI. Additional administration of CM for perfusion imaging in acute stroke did not show a relevant influence on the occurrence of PC-AKI. Patients with intracranial hemorrhage and/or prior kidney disease are at particular risk of developing AKI.

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