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Whole-genome sequencing reveals misidentification of a multidrug-resistant urine clinical isolate as Corynebacterium urealyticum

Abstract: Objectives Corynebacterium urealyticum is a non-diphtherial urease-producing clinically relevant corynebacterium associated with urinary tract infections. Most clinical C. urealyticum isolates are multidrug-resistant. Whole-genome sequencing (WGS) of C. urealyticum VH4248 isolated from a clinical urine sample at Hospital Universitario Marqués de Valdecilla, Santander, Spain, was performed to predict its antimicrobial resistance profile and to compare it with results of culture-based phenotypic antimicrobial susceptibility testing. Methods Classical microbiological methods and VITEK® MS were used for isolation and initial identification of strain VH4248. Draft genome sequencing was performed on an Illumina HiSeq 2500 platform, followed by assembly and annotation using SPAdes and RAST. Resistance genes were identified through PATRIC, the Pathosystems Resource Integration Center. Average nucleotide identity (ANI) analysis was done using the EDGAR and OrthoANI databases. Antimicrobial susceptibility was determined by Etest. Results Isolate VH4248 was initially identified asC. urealyticum. Its genome size is 2 261 231 bp with 64.4% GC content. Genome-based identification tools showed an average 93.7% similarity between VH4248 and C. urealyticum genomes deposited in public databases. Therefore, this isolate must be classified as Corynebacterium sp. The blaA and ermX genes as well as a class 1 integron including the aadB and sul1 genes are present in the VH4248 genome. This isolate is highly resistant to ampicillin, erythromycin and trimethoprim/sulfamethoxazole, and moderately resistant to gentamicin and kanamycin. Conclusions WGS is a powerful tool forCorynebacterium identification to species level and for detection of unusual resistance determinants, such as that encoded by the class 1 integron in isolate VH4248.

 Fuente: Journal of Global Antimicrobial Resistance. Volume 23, December 2020, Pages 16-19

Editorial: Elsevier

 Año de publicación: 2020

Nº de páginas: 4

Tipo de publicación: Artículo de Revista

DOI: /10.1016/j.jgar.2020.07.020

ISSN: 2213-7165,2213-7173

Autores/as

ROCHA, DANILO J.P

VASCO, AZEVEDO

BRENING, BERTRAM

SILVA, ARTUR

BLOM, JOCHEM

RAMOS, ROMMEL T.

AGIAR, ERIC R.G

ITZIAR CHAPARTEGUI GONZALEZ

FERNÁNDEZ MARTÍNEZ, MARTA

MARTÍNEZ MARTÍNEZ, LUÍS

PACHECO, LUIS G.C