RESUMO
Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C. striatum, including isolates from "normal skin microbiome" and from MDR infections, to gain insights into genetic factors contributing to pathogenicity and multidrug resistance in this species. For this, three novel genome sequences were obtained from clinical isolates of C. striatum of patients from Brazil, and other 24 complete or draft C. striatum genomes were retrieved from GenBank, including the ATCC6940 isolate from the Human Microbiome Project. Analysis of C. striatum strains demonstrated the presence of an open pan-genome (α = 0.852803) containing 3816 gene families, including 15 antimicrobial resistance (AMR) genes and 32 putative virulence factors. The core and accessory genomes included 1297 and 1307 genes, respectively. The identified AMR genes are primarily associated with resistance to aminoglycosides and tetracyclines. Of these, 66.6% are present in genomic islands, and four AMR genes, including aac(6')-ib7, are located in a class 1-integron. In conclusion, our data indicated that C. striatum possesses genomic characteristics favorable to the invasive phenotype, with high genomic plasticity, a robust genetic arsenal for iron acquisition, and important virulence determinants and AMR genes present in mobile genetic elements.
Assuntos
Antibacterianos , Corynebacterium , Humanos , Fenótipo , Fatores de Virulência/genética , Farmacorresistência Bacteriana Múltipla/genética , Testes de Sensibilidade MicrobianaRESUMO
Corynebacterium amycolatum is a nonlipophilic coryneform which is increasingly being recognized as a relevant human and animal pathogen showing multidrug resistance to commonly used antibiotics. However, little is known about the molecular mechanisms involved in transition from colonization to the MDR invasive phenotype in clinical isolates. In this study, we performed a comprehensive pan-genomic analysis of C. amycolatum, including 26 isolates from different countries. We obtained the novel genome sequences of 8 of them, which are multidrug resistant clinical isolates from Spain and Tunisia. They were analyzed together with other 18 complete or draft C. amycolatum genomes retrieved from GenBank. The species C. amycolatum presented an open pan-genome (α = 0.854905), with 3,280 gene families, being 1,690 (51.52%) in the core genome, 1,121 related to accessory genes (34.17%), and 469 related to unique genes (14.29%). Although some classic corynebacterial virulence factors are absent in the species C. amycolatum, we did identify genes associated with immune evasion, toxin, and antiphagocytosis among the predicted putative virulence factors. Additionally, we found genomic evidence for extensive acquisition of antimicrobial resistance genes through genomic islands.
RESUMO
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.
Assuntos
Antibacterianos , Corynebacterium , Antibacterianos/farmacologia , Corynebacterium/genética , Testes de Sensibilidade Microbiana , EspanhaAssuntos
COVID-19 , Humanos , Disseminação de Informação , Testes Imediatos , SARS-CoV-2 , TecnologiaRESUMO
A multiplex-PCR (mPCR) assay was designed with species-specific primers which generate amplicons of 226bp, 434bp and 106bp for differentiating the species C. striatum, C. amycolatum, and C. xerosis, respectively. mPCR results were 100% in agreement with identifications achieved by 16S rRNA and rpoB gene sequencing and by VITEK-MS.