Ontology highlight
ABSTRACT:
PROVIDER: PRJEB15286 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mycobacterium abscessus [M. abscessus (sensu lato) or M. abscessus group] comprises three closely related taxa with taxonomic status under revision: M. abscessus sensu stricto, M. bolletii and M. massiliense. We describe here a simple, robust and cost effective PCR-based method for distinguishing among M. abscessus, M. massiliense and bolletii. Based on the M. abscessus ATCC 19977T genome, discriminatory regions were identified between M. abscessus and M. massiliense from array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense and 2 M. bolletii previously identified by multi-target sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full length erm(41) instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for a straightforward identification of M. abscessus, M. massiliense and M. bolletii and assessment of inducible clarithromycin resistance. This method can be easily implemented into a routine workflow providing subspecies level identification within 24 hours of isolation of M. abscessus group.
2013-07-17 | GSE43629 | GEO
Project description:Mycobacterium abscessus [M. abscessus (sensu lato) or M. abscessus group] comprises three closely related taxa with taxonomic status under revision: M. abscessus sensu stricto, M. bolletii and M. massiliense. We describe here a simple, robust and cost effective PCR-based method for distinguishing among M. abscessus, M. massiliense and bolletii. Based on the M. abscessus ATCC 19977T genome, discriminatory regions were identified between M. abscessus and M. massiliense from array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense and 2 M. bolletii previously identified by multi-target sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full length erm(41) instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for a straightforward identification of M. abscessus, M. massiliense and M. bolletii and assessment of inducible clarithromycin resistance. This method can be easily implemented into a routine workflow providing subspecies level identification within 24 hours of isolation of M. abscessus group. Two-color CGH with 4 independent Mycobacterium clinical isolates and the M massiliense type strain (CCUG 48898) labeled with Cy3 were cohybridized with the M abscessus type strain (ATCC 19977) labeled with Cy5 on a tiling array designed against the M abscessus type strain
2013-07-17 | E-GEOD-43629 | biostudies-arrayexpress
Project description:Fusobacterium nucleatum-treated HCT116 cells reported an increased adhesion to endothelial cells compared with PBS control. To understand the underlying mechanisms of Fusobacterium nucleatum-induced intercellular adhesion ability of CRC cells, we performed RNA-sequencing in HCT116 cells with or without Fusobacterium nucleatum treatment with three independent biological replicates.
2022-03-09 | GSE171611 | GEO
Project description:Fusobacterium nucleatum-treated LoVo cells reported an increased promoting CRC metastasis effect compared with PBS control. To understand the underlying mechanisms of Fusobacterium nucleatum-induced metastasis ability of CRC cells, we performed RNA-sequencing in LoVo cells s with or without Fusobacterium nucleatum treatment with three independent biological replicates.
2021-10-19 | GSE173549 | GEO
Project description:To investigate the role of Fusobacterium nucleatum-mediated m6A modification, we performed m6A-sequencing to map the m6A modification in control or Fusobacterium nucleatum-treated HCT116 cells.
2022-02-07 | GSE150308 | GEO
Project description:Actinotignum massiliense, a Gram-positive, facultatively anaerobic coccoid rod, is a rare human pathogen able to infect the urinary tract and belongs to the order of Actinomycetales. We identified A. massiliense as a resident of microbial biofilms growing on indwelling urethral catheter surfaces that were isolated from two patients with neurogenic bladders. These catheter biofilms (CBs) also harbored common uropathogens such as Proteus mirabilis and Aerococcus urinae, supporting the notion that A. massiliense depends on other co-colonizing microbes for survival. We isolated the bacterium from an anaerobically grown culture of a clinical sample, identified the species by 16S rRNA gene sequencing and verified this result via shotgun proteomics. Bacterial proteomes were profiled from the in vitro grown strain and four clinical ‘in vivo’ samples. The quantified proteomes allowed us to infer metabolic pathways and virulence/survival factors of importance in the CB milieu. Two putative subtilisin-like proteases, two Rib/Esp surface antigen repeat-containing proteins, a papain-like cysteine protease and a metal/heme/oligopeptide uptake system were highly expressed in vivo, but less so in vitro. We predict these proteins to be critical for adhesion and growth in CBs attacked by the host’s innate immune system or to improve bacterial fitness. Mixed acid fermentation following uptake and metabolism of xylose and glucuronate, sugars highly represented in proteoglycans and glycoglycerolipids of the urothelial mucosa and, in the case of glucuronate, shed into urine via renal xenobiotic conjugates, is inferred to be a major pathway for A. massiliense to generate energy under microaerobic conditions in CBs. The bacteria also appear to have active pathways for storage and utilization of glycogen as a carbon resource. Finally, we identified a putative polyketide synthase which may generate a secondary metabolite that interacts with either the host or co-colonizing organisms to enable A. massiliense survival in CBs.
2019-11-12 | PXD011327 | Pride