Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples (original) (raw)
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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.
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 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.
BMC Genomics, 2012
Background Corynebacterium resistens was initially recovered from human infections and recognized as a new coryneform species that is highly resistant to antimicrobial agents. Bacteremia associated with this organism in immunocompromised patients was rapidly fatal as standard minocycline therapies failed. C. resistens DSM 45100 was isolated from a blood culture of samples taken from a patient with acute myelocytic leukemia. The complete genome sequence of C. resistens DSM 45100 was determined by pyrosequencing to identify genes contributing to multi-drug resistance, virulence, and the lipophilic lifestyle of this newly described human pathogen. Results The genome of C. resistens DSM 45100 consists of a circular chromosome of 2,601,311 bp in size and the 28,312-bp plasmid pJA144188. Metabolic analysis showed that the genome of C. resistens DSM 45100 lacks genes for typical sugar uptake systems, anaplerotic functions, and a fatty acid synthase, explaining the strict lipophilic lifesty...
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...
In order to investigate whether 16s-23s ribosomal DNA (rDNA) spacer region length polymorphisms are suitable for identification of Corynebacterium strains at the species level, the 16s-23s rDNA intergenic spacer region lengths of 128 strains belonging to 11 Corynebacterium species were studied by a PCR-based method. The lengths of the 16s-23s rDNA spacer regions varied from 394 to 585 bp, fragment lengths which are similar to those described for other genera. A single PCR profile was obtained for each of the following species: Corynebacterium renale, Corynebacterium urealyticum, Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium pseudodiphtheriticum, and Corynebacterium kutscheri. In contrast, two and three PCR patterns were detected for Corynebacterium minutissimum, Corynebacterium striatum, Corynebacterium amycolatum, and Corynebacterium jeikeium, suggesting that genomic heterogeneity occurs in these four species. The 16s-23s rDNA spacer region length polymorphisms allowed us to discriminate among C. minutissimum, C. striatum, and C. amycolatum, three species that are frequently isolated and misidentified in clinical laboratories. Type strain Corynebacterium xerosis ATCC 373, which exhibited a PCR pattern similar to that of C. amycolatum strains classified in PCR group I, could nevertheless be discriminated from PCR group I1 (C. amycolatum) strains, as well as C. minutissimum and C. striatum strains. Type strain C. xerosis ATCC 373 and C. amycolatum strains classified in PCR group I could not be distinguished from strains belonging to C. diphtheriae, C. ulcerans, and C. pseudodiphtheriticum. The lipophilic species C. urealyticum and C. jeikeium, which are frequently encountered in clinical specimens, could be clearly distinguished from each other by this method. The use of 16s-23s spacer region length data determined by PCR-mediated amplification is suitable for identification of several Corynebacterium species. This rapid and easy method may be a useful identification tool for clinical microbiologists.
Brazilian Journal of Microbiology, 2003
Over a five-year period, 163 strains of Corynebacterium sp. were recovered from different clinical specimens of patients from a Brazilian University hospital. Genitourinary tract and intravenous sites specimens were the most frequent sources of corynebacteria (46.62%). Corynebacterium amycolatum (29.55%), Corynebacterium minutissimum (20.45%) and Corynebacterium pseudodiphtheriticum (13.63%) were the predominant species found in genitourinary tract. C. minutissimum (24.14%) and Corynebacterium propinquum (17.24%) in surgical and/or other skin wounds and abscesses; Corynebacterium xerosis (25%), C. amycolatum (21.87%) and C. pseudodiphtheriticum (18.75%) in intravenous sites; C. pseudodiphtheriticum (33.33%) and C. propinquum (33.33%) in lower respiratory tract. Microorganisms were all susceptible to vancomycin and most of the species was predominantly resistant to b-lactams. Antimicrobial susceptibility patterns of corynebacteria were not predictable. Multiple antibiotic resistance observed in C. jeikeium was also found among C. xerosis, C. minutissimum, C. afermentans, C. propinquum, C. amycolatum and C. pseudodiphtheriticum strains. Data suggest awareness of clinicians and microbiologists to nosocomial infections especially due to antimicrobial multiresistant strains of Corynebacterium sp.
Antibiotics
Antimicrobial resistance is one of the most important public health issues. Besides classical multidrug resistance species associated with medical care involved in superficial or invasive infections, there are strains less commonly associated with hospital or outpatient setting’s infections. Non-diphtheria Corynebacterium spp. could produce infections in patients with or without immune-compromised status. The aim of our study was to determine the susceptibility to antimicrobial agents to Corynebacterium spp. from clinical samples collected from Romanian hospitalized individuals and outpatients. Twenty Corynebacterium strains were isolated and identified as Corynebacterium striatum (n = 7), Corynebacterium amycolatum (n = 7), C. urealyticum (n = 3), Corynebacterium afermentans (n = 2), and Corynebacterium pseudodiphtheriticum (n = 1). All isolates have been tested for antibiotic susceptibility by standardized disc diffusion method and minimal inhibitory concentration (MIC) tests. Sev...
Insight of Genus Corynebacterium: Ascertaining the Role of Pathogenic and Non-pathogenic Species
Frontiers in microbiology, 2017
This review gathers recent information about genomic and transcriptomic studies in the Corynebacterium genus, exploring, for example, prediction of pathogenicity islands and stress response in different pathogenic and non-pathogenic species. In addition, is described several phylogeny studies to Corynebacterium, exploring since the identification of species until biological speciation in one species belonging to the genus Corynebacterium. Important concepts associated with virulence highlighting the role of Pld protein and Tox gene. The adhesion, characteristic of virulence factor, was described using the sortase mechanism that is associated to anchorage to the cell wall. In addition, survival inside the host cell and some diseases, were too addressed for pathogenic corynebacteria, while important biochemical pathways and biotechnological applications retain the focus of this review for non-pathogenic corynebacteria. Concluding, this review broadly explores characteristics in genus ...