Similar Datasets
Project description:The spread of carbapenemase-producing Enterobacterales (CPE) is emerging as a significant clinical concern in tertiary hospitals and in particular, long-term care facilities with deficiencies in infection control. This study aims to evaluate an advanced matrix-assisted laser desorption/ionization mass spectrometry (A-MALDI) method for the identification of carbapenemases and further discrimination of their subtypes in clinical isolates. The A-MALDI method was employed to detect CPE target proteins. Enhancements were made to improve detectability and mass accuracy through the optimization of MALDI-TOF settings and internal mass calibration. A total of 581 clinical isolates were analyzed, including 469 CPE isolates (388 KPC, 51 NDM, 40 OXA, and 2 GES) and 112 carbapenemase-negative isolates. Clinical evaluation of the A-MALDI demonstrated 100% accuracy and precision in identifying all the collected CPE isolates. Additionally, A-MALDI successfully discriminated individual carbapenemase subtypes (KPC-2 or KPC-3/4; OXA-48 or OXA-181 or OXA-232; GES-5 or GES-24) and also differentiated co-producing carbapenemase strains (KPC & NDM; KPC & OXA; KPC & GES; NDM & OXA), attributed to its high mass accuracy and simultaneous detection capability. A-MALDI is considered a valuable diagnostic tool for accurately identifying CPE and carbapenemase’s subtypes in clinical isolates. It may also aid in selecting appropriate antibiotics for each carbapenemase subtype. Ultimately, we expect that the A-MALDI method will contribute to preventing the spread of antibiotic resistance and improving human public health.
2024-11-25 | PXD046179 | Pride
Project description:The spread of carbapenemase-producing Enterobacterales (CPE) is emerging as a significant clinical concern in tertiary hospitals and in particular, long-term care facilities with deficiencies in infection control. This study aims to evaluate an advanced matrix-assisted laser desorption/ionization mass spectrometry (A-MALDI) method for the identification of carbapenemases and further discrimination of their subtypes in clinical isolates. The A-MALDI method was employed to detect CPE target proteins. Enhancements were made to improve detectability and mass accuracy through the optimization of MALDI-TOF settings and internal mass calibration. A total of 581 clinical isolates were analyzed, including 469 CPE isolates (388 KPC, 51 NDM, 40 OXA, and 2 GES) and 112 carbapenemase-negative isolates. Clinical evaluation of the A-MALDI demonstrated 100% accuracy and precision in identifying all the collected CPE isolates. Additionally, A-MALDI successfully discriminated individual carbapenemase subtypes (KPC-2 or KPC-3/4; OXA-48 or OXA-181 or OXA-232; GES-5 or GES-24) and also differentiated co-producing carbapenemase strains (KPC & NDM; KPC & OXA; KPC & GES; NDM & OXA), attributed to its high mass accuracy and simultaneous detection capability. A-MALDI is considered a valuable diagnostic tool for accurately identifying CPE and carbapenemase’s subtypes in clinical isolates. It may also aid in selecting appropriate antibiotics for each carbapenemase subtype. Ultimately, we expect that the A-MALDI method will contribute to preventing the spread of antibiotic resistance and improving human public health.
2024-11-26 | PXD058284 | Pride
Project description:the genetic inactivation of Khk-C enhanced the survival of KPC-driven PDAC model even in absence of high fructose diet. Moreover Khk-C knock out decreased the viability of KPC organoids and cancer cells, the migratory capability of PDAC cells in vitro and the growth of KPC cells in vivo in a cell autonomous manner.
2023-07-07 | E-MTAB-12746 | biostudies-arrayexpress
Project description:New and rapid antimicrobial susceptibility/resistance testing methods are required for bacteria from positive blood cultures. In the current study we developed and evaluated a targeted LC-MS/MS assay for the detection of beta-lactam, aminoglycoside and fluoroquinolone resistance mechanisms in blood cultures positive for E. coli or K. pneumoniae. Selected targets were the beta-lactamases SHV, TEM, OXA-1-like, CTX-M-1-like, CMY-2-like, chromosomal E. coli AmpC, OXA-48-like, NDM, VIM and KPC, the aminoglycoside modifying enzymes AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6’)-Ib, ANT(2”)-I and APH(3’)-VI, the 16S-RMTases ArmA, RmtB, RmtC and RmtF, the quinolone resistance mechanisms QnrA, QnrB, AAC(6’)-Ib-cr, the wildtype QRDR of GyrA, and for E. coli, the porins OmpC and OmpF. The developed assay was evaluated using 100 prospectively collected positive blood cultures, 100 negative blood cultures inoculated with isolates that were previously collected from blood cultures, and 48 isolates inoculated with isolates carrying genes of less prevalent resistance mechanisms.
2022-07-01 | PXD025365 | Pride
Project description:Pancreatic cancer is among the deadliest cancers that affects almost 54,000 patients in United States alone, with 90% of them succumbing to the disease. Lack of early detection is considered to be the foremost reason for such dismal survival rates. Our study shows that resident gut microbiota is altered at the early stages of tumorigenesis much before development of observable tumors in a spontaneous, genetically engineered mouse model for pancreatic cancer. In the current study, we analyzed the microbiome of in a genetic mouse model for PDAC (KRASG12DTP53R172HPdxCre or KPC) and age-matched controls using WGS at very early time points of tumorigenesis. During these time points, the KPC mice do not show any detectable tumors in their pancreas. Our results show that at these early time points, the histological changes in the pancreas correspond to a significant change in certain gut microbial population. Our predictive metabolomic analysis on the identified bacterial species reveal that the primary microbial metabolites involved in progression and development of PDAC tumors are involved in polyamine metabolism.
2019-07-07 | E-MTAB-6921 | biostudies-arrayexpress
Project description:Bacterial persister cells are phenotypic variants of regular cells that are tolerant to antibiotics. Analysis of clinical isolates of M. tuberculosis showed that strains vary substantially in their tolerance to antibiotics. The level of persisters was very high is some isolates, suggesting that these are hip mutants. We investigated gene expression differences in eight clinical isolates, four of which we characterized as high-persister strains and four as low-persister, or regular, strains. Comparison of gene expression patterns may provide clues as to the genetic mechanisms underlying persister formation.
2015-01-01 | GSE62025 | GEO
Project description:To investigate the virological properties of SARS-CoV-2 variants, we amplified the clinical isolates of an early pandemic D614G-bearing isolate (B.1.1 lineage, strain TKYE610670; GISAID ID: EPI_ISL_479681), a Delta isolate (B.1.617.2 lineage, strain TKYTK1734; GISAID ID: EPI_ISL_2378732) and an Omicron isolate (BA.1 lineage, strain TY38-873; GISAID ID: EPI_ISL_7418017) and prepared the working viruses.
2022-01-07 | GSE192472 | GEO