Carbapenem-resistant Enterobacteriaceae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA513350 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR8777174_1.fastq.gz | Fastqsanger.gz | |||
| SRR8777174_2.fastq.gz | Fastqsanger.gz | |||
| SRR8777175_1.fastq.gz | Fastqsanger.gz | |||
| SRR8777175_2.fastq.gz | Fastqsanger.gz |
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Project description:Imipenem-Relebactam Susceptibility and Genotypic Characteristics of Carbapenem Resistant Enterobacterales (CRE) Identified during Population-Based Surveillance
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Project description:Carbapenem-resistant Enterobacteriaceae spp.Genome sequencing and assembly
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Project description:Background: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in its progression to becoming carbapenem resistant. Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/H30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. Results: All thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P<1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific adaptations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, insertion sequence 26 (IS26) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. Conclusions: ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2 subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.
2024-08-04 | GSE273456 | GEO
Project description:WGS of carbapenem-resistant Enterobacteriaceae from Nigeria
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Project description:Carbapenem reistant Enterobacteriaceae isolated from patients during a surveillance study
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Project description:Carbapenem-resistant Enterobacteriaceae (CRE) are an emerging global public health threat. Infections due to CRE are associated with significant morbidity and mortality. Few therapeutic options are available for treatment of these infections, and optimal antibiotic treatment regimens are unclear. Along with the rapidly increasing prevalence of CRE in the USA and worldwide, several studies have described the epidemiology of CRE in the adult population. While CRE are now also reported sporadically in children, there is a significant lack of data on the epidemiology, risk factors, treatment, and outcomes in this population. This article provides a comprehensive review of what is known to date about CRE, including clinical and molecular epidemiology, microbiologic diagnosis, antibiotic treatment options, and outcomes. In particular, this review will focus on the available data on CRE in the pediatric population.
| S-EPMC4975038 | biostudies-literature
Project description:This study aims to determine the epidemiology of Enterobacteriaceae resistant to antibiotics of last resort in pregnant women in labour at a tertiary hospital, Pretoria, South Africa. Rectal swabs shall be used to screen for colonisation with CRE and colistin-resistant Enterobacteriales in pregnant women during labour. Carbapenem and colistin-resistant Enterobacterales can cause the following infections: bacteraemia; nosocomial pneumonia; urinary tract infections, and intra-abdominal infections. Due to limited treatment options, infections caused by these multidrug-resistant organisms are associated with a mortality rate of 40-50%. Screening for colonisation of carbapenem-resistant Enterobacteriaceae (CRE) and colistin-resistant Enterobacteriaceae will help implement infection and prevention measures to limit the spread of these multidrug-resistant organisms.
2022-07-20 | GSE208573 | GEO
Project description:We evaluated the number of deaths attributable to carbapenem-resistant Enterobacteriaceae by using studies from around the world published before April 9, 2012. Attributable death was defined as the difference in all-cause deaths between patients with carbapenem-resistant infections and those with carbapenem-susceptible infections. Online databases were searched, and data were qualitatively synthesized and pooled in a metaanalysis. Nine studies met inclusion criteria: 6 retrospective case-control studies, 2 retrospective cohort studies, and 1 prospective cohort study. Klebsiella pneumoniae was the causative pathogen in 8 studies; bacteremia was the only infection in 5 studies. We calculated that 26%-44% of deaths in 7 studies were attributable to carbapenem resistance, and in 2 studies, which included bacteremia and other infections, -3% and -4% of deaths were attributable to carbapenem resistance. Pooled outcomes showed that the number of deaths was significantly higher in patients with carbapenem-resistant infections and that the number of deaths attributable to carbapenem resistance is considerable.
| S-EPMC4073868 | biostudies-literature
Project description:Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids. Improved characterization helps detail the co-occurrence of other antibiotic resistance genes in CRE isolates and helps identify pan-drug resistance mechanisms. The novel β-lactamase inhibitor, avibactam, combined with ceftazidime or aztreonam, is a promising CRE treatment compared to current colistin or tigecycline regimens. To halt increasing CRE-associated morbidity and mortality, we must continue quality, cooperative monitoring and urgently investigate novel treatments.
| S-EPMC5140036 | biostudies-literature
Project description:A survey for antibiotic-resistant (AR) Escherichia coli in wastewater was undertaken by collecting samples from primary clarifiers and secondary effluents from seven geographically dispersed US wastewater treatment plants (WWTPs). Samples were collected at each WWTP in cool and summer months and cultured using selective media. The resulting isolates were characterized for resistance to imipenem, ciprofloxacin, cefotaxime, and ceftazidime, presence of carbapenemase and extended-spectrum beta-lactamase (ESBL) genes, and phylogroups and sequence types (STs). In total, 322 AR E. coli isolates were identified, of which 65 were imipenem-resistant. Of the 65 carbapenem-resistant E. coli (CREC) isolates, 62% were positive for more than one and 31% were positive for two or more of carbapenemase and ESBL genes targeted. The most commonly detected carbapenemase gene was blaVIM (n = 36), followed by blaKPC (n = 2). A widespread dispersal of carbapenem-resistant STs and other clinically significant AR STs observed in the present study suggested the plausible release of these strains into the environment. The occurrence of CREC in wastewater is a potential concern because this matrix may serve as a reservoir for gene exchange and thereby increase the risk of AR bacteria (including CR) being disseminated into the environment and thence back to humans.
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