Search results for " typing"
showing 10 items of 273 documents
Identification of Candida auris and related species by multiplex PCR based on unique GPI protein‐encoding genes
2020
Background The pathogen Candida auris is rapidly gaining clinical importance because of its resistance to antifungal treatments and its persistence in hospital environments. Early and accurate diagnosis of C. auris infections is crucial, however, the fungus has often been misidentified by commercial systems. Objectives To develop conventional and real-time PCR methods for accurate and rapid identification of C. auris and its discrimination from closely related species by exploiting the uniqueness of certain glycosylphosphatidylinositol-modified protein-encoding genes. Methods Species-specific primers for two unique putative GPI protein-encoding genes per species were designed for C. auris, …
Whole-genome sequencing of Neisseria gonorrhoeae in a forensic transmission case.
2019
Abstract Molecular epidemiology and phylogenetic analyses are frequently used in the investigation of viral transmission cases in forensic contexts. Here, we present the methods and results of the analysis of a bacterial transmission episode in an alleged child abuse case using complete genome sequences obtained by high-throughput sequencing (HTS) methods. We obtained genomes of Neisseria gonorrhoeae from the victim, the suspect, and 29 unrelated controls. The analysis of the genomes revealed that the victim and suspect isolates had identical sequences in both the bacterial chromosome and the single plasmid present in them. One of the local controls was very similar (differing in only 2 SNP…
Photobacterium toruni sp. nov., a bacterium isolated from diseased farmed fish.
2017
Three bacterial strains were isolated from liver and spleen of diseased farmed redbanded seabream (Pagrus auriga) in south-west Spain. Their partial 16S rRNA gene sequences clustered within those of the genus Photobacterium , showing high similarity (98.6–99.3 %) to the type strains of Photobacterium iliopiscarium , P. piscicola , P. kishitanii , P. aquimaris and P. phosphoreum . Multilocus sequence analysis using six housekeeping genes (gapA, topA, mreB, ftsZ, gyrB and 16S rRNA) confirmed the new strains as forming an independent branch with a bootstrap value of 100, likely to represent a novel species. To confirm this, we used whole genome sequencing and genomic analysis (ANIb, ANIm and i…
Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis.
2018
Strain CECT 5091T, an aerobic, marine, Gram-reaction- and Gram-stain-negative, chemoheterotrophic bacterium was isolated from oysters harvested off the Spanish Mediterranean coast. Analysis of the 16S rRNA gene sequence placed the strain within the genus Ruegeria , in the family Rhodobacteraceae , with 16S rRNA gene similarities of 98.7, 98.7 and 98.4 % to Ruegeria conchae , Ruegeria atlantica and Ruegeria arenilitoris , respectively. Average nucleotide identities (ANI) and in silico DNA–DNA hybridization (DDH) were determined, comparing the genome sequence of CECT 5091T with those of the type strains of 12 species of the genus Ruegeria : the values obtained were always below the thresholds…
Marinomonas spartinae sp. nov., a novel species with plant-beneficial properties.
2016
Two strains of Gram-stain-negative, chemo-organotrophic, aerobic and halophilic gammaproteobacteria, isolated from within the stem and roots of Spartina maritima in salt marshes from the south Atlantic Spanish coast, were found to represent a novel species in the genus Marinomonas through phylogenetic analysis of their 16S rRNA genes and phenotypic characterization. 16S rRNA gene sequences of the two strains shared < 96.2 % similarity with other Marinomonas species, with Marimonas alcarazii being the most similar in sequence. They required sodium ions for growth, were able to thrive at low (4 °C) temperatures and at salinities of 12–15 %, were unable to hydrolyse any tested macromolecule ex…
Marinomonas blandensis sp. nov., a novel marine gammaproteobacterium.
2016
A novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121T, was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to Marinomonas dokdonensis and other Marinomonas species (96.3 and 93.3–95.7 % sequence similarities, respectively), within the family Oceanospirillaceae . Strain MED121T was included into a whole-genome sequencing study and, subsequently, it was characterized using a polyphasic taxonomic approach. It was found to be o…
Recommendations for enterovirus diagnostics and characterisation within and beyond Europe
2018
Enteroviruses (EV) can cause severe neurological and respiratory infections, and occasionally lead to devastating outbreaks as previously demonstrated with EV-A71 and EV-D68 in Europe. However, these infections are still often underdiagnosed and EV typing data is not currently collected at European level. In order to improve EV diagnostics, collate data on severe EV infections and monitor the circulation of EV types, we have established European non-polio enterovirus network (ENPEN). First task of this cross-border network has been to ensure prompt and adequate diagnosis of these infections in Europe, and hence we present recommendations for non-polio EV detection and typing based on the co…
Whole genome sequences reveal Vibrio hemicentroti Kim et al. 2013 as a later heterotypic synonym of Vibrio splendidus (Beijerinck 1900) Baumann et al…
2017
The synonymy between Vibrio hemicentroti Kim et al. 2013 and Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981 was suggested after a recent multilocus sequence analysis of the Splendidus clade, which included the type strains of both species. To clarify their status, we have determined genomic indexes from whole genome sequences of strains V. hemicentroti CECT 8714T and V. splendidus NCCB 53037T. Average Nucleotide Identities of 96.0–96.7 % and an in silico DNA–DNA hybridization value of 70.2 %, as well as similarity levels of selected housekeeping gene sequences support the consideration of V. hemicentroti as a later heterotypic synonym of V. splendidus .
High prevalence and moderate diversity of Pseudomonas aeruginosa in the U-bends of high-risk units in hospital
2017
The presence of P. aeruginosa in water supply is clearly identified as a risk factor for P. aeruginosa infection in critical care units, even if routes of transmission are often unclear and remain a matter of debate. We determined here the frequency of U-bends contaminated with P. aeruginosa in high-risk units and described the population structure of this opportunistic pathogen in a non-outbreak situation. Eighty-seven U-bends from sinks of rooms in five wards were sampled 3 times and P. aeruginosa was detected in 121 of the 261 (46.4%) U-bend samples. We genotyped 123 P. aeruginosa isolates with pulsed-field gel electrophoresis and multilocus sequence typing and found 41 pulsotypes distri…
Exploring the biodiversity of two groups of Oenococcus oeni isolated from grape musts and wines: Are they equally diverse?
2016
One hundred and four Oenococcus oeni isolates were characterised by the carbohydrate fermentation (CH) profile and DNA fingerprinting. Forty-four isolates came from grape must, and 60 from wines sampled at the end of alcoholic fermentation or during malolactic fermentation. The grape must isolates fermented more CH than the wine isolates. In genotypical terms, no clear boundary between grape must and wine isolates was found. Diversities were deduced by considering the isolates of grape must and of wine separately and jointly. By considering only CH fermentation abilities, the group of grape must isolates gave higher diversity index (DICH) values than those isolated from wine; i.e., these is…