The Pan-Genome of the Emerging Multidrug-Resistant Pathogen Corynebacterium striatum (original) (raw)
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Memorias do Instituto Oswaldo Cruz, 2018
Multidrug-resistant (MDR) Corynebacterium striatum has been cited with increased frequency as pathogen of nosocomial infections. In this study, we report the draft genome of a C. striatum isolated from a patient with bloodstream infection in a hospital of Rio de Janeiro, Brazil. The isolate presented susceptibility only to tetracycline, vancomycin and linezolid. The detection of various antibiotic resistance genes is fully consistent with previously observed multidrug-resistant pattern in Corynebacterium spp. A large part of the pTP10 plasmid of MDR C. striatum M82B is present in the genome of our isolate. A SpaDEF cluster and seven arrays of CRISPR-Cas were found.
Archives of Microbiology
Corynebacterium striatum is part of microbiota of skin and nasal mucosa of humans and has been increasingly reported as the etiologic agent of community-acquired and nosocomial diseases. Antimicrobial multidrug-resistant (MDR) C. striatum strains have been increasingly related to various nosocomial diseases and/or outbreaks worldwide, including fatal invasive infections in immunosuppressed and immunocompetent patients. Although cases of infections by C. striatum still neglected in some countries, the improvement of microbiological techniques and studies led to the increase of survival of patients with C. striatum nosocomial infections at different levels of magnitude. Biofilm formation on abiotic surfaces contributes for the persistence of virulent C. striatum and dissemination of antimicrobial resistance in hospital environment. Besides that, empirical antibiotic therapy can select multi-resistant strains and transfer intra and interspecies genes horizontally. In this study, a worldwide survey of C. striatum human infections and nosocomial outbreaks was accomplished by the analysis of clinical-epidemiological and microbiological features of reported cases from varied countries, during a 44-year period (1976-2020).
Journal of Global Antimicrobial Resistance, 2020
Objectives Corynebacterium urealyticum is a non-diphtherial urease-producing clinically relevant corynebacterial associated with urinary tract infections. Most of the C. urealyticum clinical isolates are multidrug-resistant. Whole genome sequencing of C. urealyticum VH4248, isolated from a urine sample at the Hospital Universitario Marqués de Valdecilla, Santander, Spain, was performed to predict its antimicrobial resistance profile and compare it with results of culture-based phenotypic antimicrobial susceptibility test. 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 the Pathosystems Resource Integration Center (PATRIC). Average Nucleotide Identity (ANI) analysis was done using the EDGAR and OrthoANI databases. Antimicrobial susceptibilities were determined by Epsilon-test. Results The isolate VH4248 was initially identified asC. urealyticum. Its genome size is 2,261,231 bp with 64.4% GC. 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 spp. The blaA and ermX genes, as well as a class 1 integron including the aadB and sul1 genes, are present in VH4248 genome. This isolate is highly resistant to ampicillin, erythromycin, and co-trimoxazole, and moderately resistant to gentamicin and kanamycin. Conclusions Whole genome sequencing is a powerful tool for Corynebacterium identification at the species level, and for detection of unusual resistance determinants, as that encoded by the class I integron in isolate VH4248.
Journal of Genomics, 2015
Non-diphtheriae Corynebacterium species have been increasingly recognized as the causative agents of infections in humans. Differential identification of these bacteria in the clinical microbiology laboratory by the most commonly used biochemical tests is challenging, and normally requires additional molecular methods. Herein, we present the annotated draft genome sequences of two isolates of "difficult-to-identify" human-pathogenic corynebacterial species: C. xerosis and C. minutissimum. The genome sequences of ca. 2.7 Mbp, with a mean number of 2,580 protein encoding genes, were also compared with the publicly available genome sequences of strains of C. amycolatum and C. striatum. These results will aid the exploration of novel biochemical reactions to improve existing identification tests as well as the development of more accurate molecular identification methods through detection of species-specific target genes for isolate's identification or drug susceptibility profiling.
Functional & integrative genomics, 2018
Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis. In order to identify the genomic basis contributing for the biochemical variabilities observed in phenotypic identification methods of these bacteria, we combined a comprehensive literature review with a bioinformatics approach based on reconstruction of six specific biochemical reactions/pathways in 33 r...
CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips
Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics.
Authorea (Authorea), 2023
Corynebacterium spp. have emerged as opportunistic pathogens, with increasing reports of isolation from patients with mild and severe infections. Corynebacterial isolates were found expressing multidrug-resistant (MDR) phenotypes in most cases. In the present work, we report the isolation of an MDR C. glucuronolyticum strain from the human urogenital tract. In addition, we provide comprehensive genomic data of the isolate that was first identified by mass spectrometry (MALDI-TOF) and had its antimicrobial susceptibility profile determined by the disc diffusion method. Genomic analyses were applied to confirm the species identification and predict genes involved in the virulence, antimicrobial resistance, and CRISPR-Cas systems. C. glucuronolyticum isolate exhibited resistance to benzylpenicillin, clindamycin, and tetracycline. Two virulence (mprA and tlyC) and several antimicrobial genes, including those related to tetracycline and lincosamides, were found in the genome. Additionally, the Type I-E CRISPR-Cas system was detected. Although C. glucuronolyticum has been isolated from patients with human infections, mostly male patients with genitourinary tract infections, its pathogenic potential is unclear. Presently, the clinical resolution only occurred with antimicrobial treatment considering our results, reinforcing that the antimicrobial susceptibility profile should be performed in cases of infection caused by Corynebacterium spp., especially in the face of the emergence of MDR isolates. Moreover, our data revealed putative virulence and antimicrobial resistance factors, which should be better characterized to understand the pathogenicity potential of C. glucuronolyticum for the genitourinary tract. RESEARCH PAPER Phenotypic characterization and whole genome analysis of a multidrug-resistant Corynebacterium glucuronolyticum strain isolated from genitourinary tract for the first time in Latin America
Journal of Bacteriology, 2005
Corynebacterium jeikeium is a “lipophilic” and multidrug-resistant bacterial species of the human skin flora that has been recognized with increasing frequency as a serious nosocomial pathogen. Here we report the genome sequence of the clinical isolate C. jeikeium K411, which was initially recovered from the axilla of a bone marrow transplant patient. The genome of C. jeikeium K411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp bacteriocin-producing plasmid pKW4. The chromosome of C. jeikeium K411 contains 2,104 predicted coding sequences, 52% of which were considered to be orthologous with genes in the Corynebacterium glutamicum, Corynebacterium efficiens, and Corynebacterium diphtheriae genomes. These genes apparently represent the chromosomal backbone that is conserved between the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial genomes, many are located close to transposable elements or revealed an atypical G+C content,...
New microbes and new infections, 2016
During a 12-year period we isolated five Corynebacterium argentoratense strains identified by phenotypic methods, including the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA gene sequencing. In addition, antimicrobial susceptibility was determined, and genome sequencing for the detection of antibiotic resistance genes was performed. The organisms were isolated from blood and throat cultures and could be identified by all methods used. All strains were resistant to cotrimoxazole, and resistance to β-lactams was partly present. Two strains were resistant to erythromycin and clindamycin. The draft genome sequences of theses isolates revealed the presence of the erm(X) resistance gene that is embedded in the genetic structure of the transposable element Tn5423. Although rarely reported as a human pathogen, C. argentoratense can be involved in bacteraemia and probably in other infections. Our results also show that horizontal...
2021
Corynebacterium striatum, a bacterium that is part of the normal skin microbiota, is also an opportunistic pathogen. In recent years, reports of infections and in-hospital and nosocomial outbreaks caused by antimicrobial multidrug-resistant C. striatum strains have been increasing worldwide. However, there are no studies about the genomic determinants related to antimicrobial resistance in C. striatum. This review updates global information related to antimicrobial resistance found in C. striatum and highlights the essential genomic aspects in its persistence and dissemination. The resistome of C. striatum comprises chromosomal and acquired elements. Resistance to fluoroquinolones and daptomycin are due to mutations in chromosomal genes. Conversely, resistance to macrolides, tetracyclines, phenicols, beta-lactams, and aminoglycosides are associated with mobile genomic elements such as plasmids and transposons. The presence and diversity of insertion sequences suggest an essential ro...