Ontology highlight
ABSTRACT:
PROVIDER: PRJNA374677 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5253020_1.fastq.gz | Fastqsanger.gz | |||
| SRR5253020_2.fastq.gz | Fastqsanger.gz | |||
| SRR5253030_1.fastq.gz | Fastqsanger.gz | |||
| SRR5253030_2.fastq.gz | Fastqsanger.gz | |||
| SRR5253040_1.fastq.gz | Fastqsanger.gz |
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Project description:Genomic analysis of diversification and resistance of the predominant clinical Enterobacter cloacae clones in NYC
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Project description:Enterobacter cloacae is a Gram-negative nosocomial pathogen of the ESKAPE (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, and Enterobacter spp.) priority group with increasing multi-drug resistance via the acquisition of resistance plasmids. However, E. cloacae can also display forms of antibiotic refractoriness, such as heteroresistance and tolerance. Here, we report that E. cloacae displays transient heteroresistance to aminoglycosides, which is accompanied with the formation of small colony variants (SCVs) with increased minimum inhibitor concentration (MIC) of gentamicin and other aminoglycosides used in the clinic, but not other antibiotic classes. To explore the underlying mechanisms, we performed RNA sequencing of heteroresistant bacteria, which revealed global gene-expression changes and a signature of the CpxRA cell envelope stress response. Deletion of the cpxRA two-component system abrogated aminoglycoside heteroresistance and SCV formation, pointing to its indispensable role in these processes. The introduction of a constitutively active allele of cpxA led to high aminoglycoside MICs, consistent with cell envelope stress response driving these behaviours in E. cloacae. Cell envelope stress can be caused by environmental cues, including heavy metals. Indeed, bacterial exposure to copper increased gentamicin MIC in the wild-type, but not in the ΔcpxRA mutant. Moreover, copper exposure also elevated the gentamicin MICs of clinical isolates from bloodstream infections, suggesting that CpxRA- and copper-dependent aminoglycoside resistance is broadly conserved in E. cloacae strains. Altogether, we establish that E. cloacae relies on transcriptional reprogramming via the envelope stress response pathway for transient resistance to a major class of frontline antibiotic.
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Project description:The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages. As a consequence, not only phage genes are transferred, but also genes that have no particular function in the phage's lysogenic cycle. If they provide benefits to the phage's host, such genes are referred to as ‘morons’. The present study was aimed at characterizing a set of Enterobacter cloacae, Klebsiella pneumoniae and Escherichia coli isolates with exceptional antibiotic resistance phenotypes from patients in a neonatal ward. Unexpectedly, these analyses unveiled the existence of a novel family of closely related MGIs in Enterobacteriaceae. The respective MGI from E. cloacae was named MIR17-GI. Importantly, our observations show that MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin resistance amongst Enterobacteriaceae. The discovery of a novel family of MGIs spreading ‘cephalosporinase morons’ is of high clinical relevance, because high-level cephalosporin resistance has serious implications for the treatment of patients with Enterobacteriaceal infections.
2018-08-21 | PXD007113 | Pride
Project description:Background: Enterobacter cloacae complex (ECC) is a common opportunistic pathogen and is responsible for causing various infections in humans. Owing to its inducible chromosomal AmpC β-lactamase (AmpC), ECC is inherently resistant to the 1st- and 2nd- generation cephalosporins. However, whether β-lactams antibiotics enhance ECC resistance remains unclear. Results: In this study, we found that subinhibitory concentrations (SICs) of cefazolin (CFZ) and imipenem (IMP) can advance the expression of AmpC and enhance its resistance towards β-lactams through NagZ in Enterobacter cloacae (EC). Further, AmpC manifested a substantial upregulation in EC in response to SICs of CFZ and IMP. In nagZ knockout EC (ΔnagZ), the resistance to β-lactam antibiotics was rather weakened and the effect of CFZ and IMP on AmpC induction was completely abrogated. NagZ ectopic expression can rescue the induction effects of CFZ and IMP on AmpC and increase ΔnagZ resistance. More importantly, CFZ and IMP have the potential to induce the expression of AmpR's target genes in a NagZ-dependent manner. Conclusions: Our findings suggest that NagZ is a critical determinant for CFZ and IMP to promote AmpC expression and resistance and that CFZ and IMP should be used with caution since they may aggravate ECC resistance. At the same time, this study further improves our understanding of resistance mechanisms in ECC.
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Project description:Colistin-resistance in Enterobacter cloacae
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Project description:Cefiderocol resistance in enterobacter cloacae
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Project description:Heteroresistance in bacteria describes a subpopulational phenomenon of transient antibiotic resistance variation among cells of a generally susceptible population. Here, we investigated the molecular mechanisms and phenotypic characteristics underlying heteroresistance to ceftazidime (CAZ) in a clinical Enterobacter cloacae complex strain (ECC). We identified a plasmid-borne gene duplication-amplification (GDA) event of a region harboring an ampC gene encoding a β-lactamase blaDHA-1 as the key determinant of heteroresistance. Individual colonies exhibited variations in the copy number of the genes resulting in resistance level variation which correlated with growth onset (lag times) and growth rates in the presence of CAZ, analysed in linear models. GDA copy number heterogeneity occurred within single resistant colonies, demonstrating heterogeneity of GDA on the single-cell level. The interdependence between GDA, lag time and antibiotic treatment and the strong plasticity underlying heteroresistance underlines the high risk for misdetection of antimicrobial heteroresistance and subsequent treatment failure.
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