Danilo J P Rocha1, Vasco Azevedo2, Bertram Brenig3, Artur Silva4, Jochen Blom5, Rommel T Ramos4, Eric R G Aguiar1, Itziar Chapartegui-González6, Marta Fernández-Martínez7, Luis Martínez-Martínez8, Luis G C Pacheco1, Jesús Navas9. 1. Post-Graduate Program in Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil. 2. Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte-MG, Brazil. 3. University of Göttingen, Institute of Veterinary Medicine, Göttingen, Germany. 4. Institute of Biological Sciences, Federal University of Para, Belém-PA, Brazil. 5. Bioinformatics and Systems Biology, Justus Liebig University Gießen, Ludwigstraße 23, D-35390 Gießen, Germany. 6. Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Herrera Oria 2, 39011 Santander, Spain. 7. Valdecilla Biomedical Research Institute (IDIVAL), Santander, Spain. 8. Unidad de Gestión Clínica, Hospital Universitario Reina Sofía, Av. Menéndez Pidal, s/n, 14004 Córdoba, Spain; Departamento de Microbiología, Universidad de Córdoba, Campus Rabanales. Edif. Severo Ochoa (C6), 14071 Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Av. Menéndez Pidal, s/n, 14004 Córdoba, Spain. 9. Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Herrera Oria 2, 39011 Santander, Spain. Electronic address: navasj@unican.es.
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.
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. urealyticumVH4248 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.