Ribosomal DNA Sequencing for Identification of Aerobic Gram-Positive Rods in the Clinical Laboratory (an 18-Month Evaluation)

Bosshard, Philipp P.; Abels, Susanne; Zbinden, Reinhard; Böttger, Erik C.; Altwegg, Martin

doi:10.1128/jcm.41.9.4134-4140.2003

Cited by 189 publications

(158 citation statements)

References 28 publications

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“…It appears that 16S rRNA gene sequencing is a more accurate and objective method than conventional phenotypic identification (9,10). The microarray technique has been assessed for bacterial identification in blood of septic patients (12,13).…”

Section: T a B L E 1 P A T I E N T Da T Amentioning

confidence: 99%

Rapid Identification of Bacterial Species with Bacterial DNA Microarray in Cirrhotic Patients with Spontaneous Bacterial Peritonitis

et al. 2009

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Section: T a B L E 1 P A T I E N T Da T Amentioning

confidence: 99%

Rapid Identification of Bacterial Species with Bacterial DNA Microarray in Cirrhotic Patients with Spontaneous Bacterial Peritonitis

et al. 2009

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“…Routine 16S rRNA gene sequencing is implemented in our laboratory and is a fixed part of our diagnostic algorithms for identification of bacterial isolates (1,2,32). We retrospectively reanalyzed 16S rRNA gene sequences collected during 2004 to 2008 to identify potentially novel bacterial taxa of clinical relevance.…”

mentioning

confidence: 99%

Recognition of Potentially Novel Human Disease-Associated Pathogens by Implementation of Systematic 16S rRNA Gene Sequencing in the Diagnostic Laboratory

Keller

Rampini²,

Büchler

et al. 2010

J Clin Microbiol

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Clinical isolates that are difficult to identify by conventional means form a valuable source of novel human pathogens. We report on a 5-year study based on systematic 16S rRNA gene sequence analysis. We found 60 previously unknown 16S rRNA sequences corresponding to potentially novel bacterial taxa. For 30 of 60 isolates, clinical relevance was evaluated; 18 of the 30 isolates analyzed were considered to be associated with human disease.16S rRNA gene sequence analysis is broadly considered the "gold standard" in bacterial identification (6,29). In daily clinical diagnostics, accurate bacterial identification is essential in judging whether a bacterial isolate is to be considered the causative agent of an infectious disease or merely a colonizer. In our study, we aimed to characterize the bacterial diversity encountered in a diagnostic laboratory by revealing potentially novel, clinically relevant species, according to the current species definition by the Clinical and Laboratory Standards Institute (22).Routine 16S rRNA gene sequencing is implemented in our laboratory and is a fixed part of our diagnostic algorithms for identification of bacterial isolates (1, 2, 32). We retrospectively reanalyzed 16S rRNA gene sequences collected during 2004 to 2008 to identify potentially novel bacterial taxa of clinical relevance. The Institute of Medical Microbiology (IMM) serves the 850-bed University Hospital of Zurich and surrounding smaller hospitals. Bacterial isolates from blood, cerebrospinal fluid, wounds, joint aspirates, respiratory samples, genitourinary swabs, feces, and urine were recovered by culture on appropriate media according to standard procedures (19). Isolates that could not be identified by phenotypic methods underwent sequencing. 16S rRNA gene analysis was performed as previously described (1). Homology analyses were performed using the SmartGene Integrated Database Network System (IDNS) (24) and NCBI GenBank databases. For the first screening of our large data collection, we selected isolates with sequence homology of Ͻ99.0% to members of described taxa, regarding these as potentially novel species; isolates with sequence homology of Ͻ95% were regarded as representatives of a novel genus (2). The boundary for novel families was Ͻ87.5% homology and, for novel orders, Ͻ78.4% 16S rRNA sequence homology (30). After the first screening, we used more stringent cutoff values (Ͻ97.5% for species) for taxa with significant interspecies 16S rRNA divergence; i.e., members of the Paenibacillaceae family and the Clostridiales order (6, 25).During the 5-year study period, 1,663 cultured isolates were subjected to 16S rRNA gene sequence analysis (Table 1). Of those, 60 isolates (0.4‰; see Table S1 in the supplemental material) had a 16S rRNA gene homology of Ͻ99% to members of accepted taxa on the date of the first interpretation. A total of 11 of the 60 sequences with a 16S rRNA homology of Ͻ99% in the first-time analysis could be allocated to a species established during the study term as a novel species by othe...

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“…Organisms with 99% or more sequence similarity to be considered from the same species and between 93% and 98% similarity to be considered from the same genus over the organism in consideration to previously unidentified if the ITS Sequence similarity is below 93% (Bosshard et al 2003). The endophyte had 99% similarity to Cladosporium cladosporioides (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

Antiangiogenic, wound healing and antioxidant activity ofCladosporium cladosporioides(Endophytic Fungus) isolated from seaweed (Sargassum wightii)

et al. 2016

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Endophytic fungi from marine seaweeds are the less studied group of organisms with vast medical applications. The aim of the present study was to evaluate antioxidant, antiangiogenic as well as wound healing potential of the endophytic fungus isolated from the seaweed Sargassum wightii. The morphological characters and the rDNA internal transcribed spacer sequence analysis (BLAST search in Gen Bank database) was used for the identification of endophytic fungus. The antioxidant potential of the ethyl acetate extract of endophytic fungus was assessed by, 1,1-diphenyl-2-picryl-hydrazyl radical scavenging method. The fungal extract was also analysed for reducing power, total phenolic and flavonoid content. Antiangiogenic activity of the fungal extract was studied in vitro by inhibition of wound healing scratch assay and in vivo by Chick chorioallantoic membrane assay. The endophytic fungus was identified as Cladosporium cladosporioides (Gen Bank ID – KT384175). The ethyl acetate extract of C. cladosporioides showed a significant antioxidant and angiosuppressive activity. The ESI-LC-MS analysis of the extract revealed the presence of wide range of secondary metabolites. Results suggest that C. cladosporioides extract could be exploited as a potential source for angiogenic modulators.

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Ribosomal DNA Sequencing for Identification of Aerobic Gram-Positive Rods in the Clinical Laboratory (an 18-Month Evaluation)

Cited by 189 publications

References 28 publications

Rapid Identification of Bacterial Species with Bacterial DNA Microarray in Cirrhotic Patients with Spontaneous Bacterial Peritonitis

Rapid Identification of Bacterial Species with Bacterial DNA Microarray in Cirrhotic Patients with Spontaneous Bacterial Peritonitis

Recognition of Potentially Novel Human Disease-Associated Pathogens by Implementation of Systematic 16S rRNA Gene Sequencing in the Diagnostic Laboratory

Antiangiogenic, wound healing and antioxidant activity ofCladosporium cladosporioides(Endophytic Fungus) isolated from seaweed (Sargassum wightii)

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