scholarly journals Rapid in vivo development of resistance to daptomycin in vancomycin-resistant Enterococcus faecium due to genomic rearrangements

2021 ◽  
Author(s):  
Sarah Mollerup ◽  
Christine Elmeskov ◽  
Heidi Gumpert ◽  
Mette Pinholt ◽  
Tobias Steen Sejersen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Enterococcus Faecium ◽  
Chromosomal Rearrangements ◽  
Resistance Mechanisms ◽  
Resistant Isolate ◽  
Wall Structure ◽  
Whole Genome ◽  
Cyclic Lipopeptide ◽  
Vancomycin Resistant

AbstractBackgroundDaptomycin is a cyclic lipopeptide used in the treatment of vancomycin-resistant Enterococcus faecium (VREfm). However, the development of daptomycin-resistant VREfm challenges the treatment of nosocomial VREfm infections. Resistance mechanisms of daptomycin are not fully understood. Here we analysed the genomic changes leading to a daptomycin-susceptible VREfm isolate becoming resistant after 40 days of daptomycin and linezolid combination therapy.MethodsThe two isogenic VREfm isolates (daptomycin-susceptible and daptomycin-resistant) were analysed using whole genome sequencing with Illumina and Nanopore.ResultsWhole genome comparative analysis identified the loss of a 46.5 kb fragment and duplication of a 29.7 kb fragment in the daptomycin-resistant isolate, with many implicated genes involved in cell wall synthesis. Two plasmids of the daptomycin-susceptible isolate were also found integrated in the chromosome of the resistant isolate. One nonsynonymous SNP in the rpoC gene was identified in the daptomycin-resistant isolate.ConclusionsDaptomycin resistance developed through chromosomal rearrangements leading to altered cell wall structure. Such novel types of resistance mechanisms can only be identified by comparing closed genomes of isogenic isolates.

scholarly journals Resistance Mechanisms of Saccharomyces cerevisiae to Commercial Formulations of Glyphosate Involve DNA Damage Repair, the Cell Cycle, and the Cell Wall Structure

2020 ◽  
Vol 10 (6) ◽  
pp. 2043-2056
Author(s):  
Apoorva Ravishankar ◽  
Amaury Pupo ◽  
Jennifer E. G. Gallagher
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Wall ◽  
Resistance Mechanisms ◽  
Mapk Signaling ◽  
Fragile Sites ◽  
Cell Wall Structure ◽  
Wall Structure ◽  
Global Changes ◽  
Expression Of Genes ◽  
Wide Range

The use of glyphosate-based herbicides is widespread and despite their extensive use, their effects are yet to be deciphered completely. The additives in commercial formulations of glyphosate, though labeled inert when used individually, have adverse effects when used in combination with other additives along with the active ingredient. As a species, Saccharomyces cerevisiae has a wide range of resistance to glyphosate-based herbicides. To investigate the underlying genetic differences between sensitive and resistant strains, global changes in gene expression were measured, when yeast were exposed to a glyphosate-based herbicide (GBH). Expression of genes involved in numerous pathways crucial to the cell’s functioning, such as DNA replication, MAPK signaling, meiosis, and cell wall synthesis changed. Because so many diverse pathways were affected, these strains were then subjected to in-lab-evolutions (ILE) to select mutations that confer increased resistance. Common fragile sites were found to play a role in adaptation to resistance to long-term exposure of GBHs. Copy number increased in approximately 100 genes associated with cell wall proteins, mitochondria, and sterol transport. Taking ILE and transcriptomic data into account it is evident that GBHs affect multiple biological processes in the cell. One such component is the cell wall structure which acts as a protective barrier in alleviating the stress caused by exposure to inert additives in GBHs. Sed1, a GPI-cell wall protein, plays an important role in tolerance of a GBH. Hence, a detailed study of the changes occurring at the genome and transcriptome levels is essential to better understand the effects of an environmental stressor such as a GBH, on the cell as a whole.

scholarly journals Outbreak of Vancomycin-resistant Enterococcus faecium in Interventional Radiology: Detection Through Whole-genome Sequencing-based Surveillance

2019 ◽  
Vol 70 (11) ◽  
pp. 2336-2343 ◽  
Author(s):  
Alexander J Sundermann ◽  
Ahmed Babiker ◽  
Jane W Marsh ◽  
Kathleen A Shutt ◽  
Mustapha M Mustapha ◽  
...  
Keyword(s):  
Interventional Radiology ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterococcus Faecium ◽  
Whole Genome ◽  
Training Video ◽  
Prevention Interventions ◽  
Vancomycin Resistant ◽  
Record Review ◽  
Hospital Acquired

Abstract Background Vancomycin-resistant enterococci (VRE) are a major cause of hospital-acquired infections. The risk of infection from interventional radiology (IR) procedures is not well documented. Whole-genome sequencing (WGS) surveillance of clinical bacterial isolates among hospitalized patients can identify previously unrecognized outbreaks. Methods We analyzed WGS surveillance data from November 2016 to November 2017 for evidence of VRE transmission. A previously unrecognized cluster of 10 genetically related VRE (Enterococcus faecium) infections was discovered. Electronic health record review identified IR procedures as a potential source. An outbreak investigation was conducted. Results Of the 10 outbreak patients, 9 had undergone an IR procedure with intravenous (IV) contrast ≤22 days before infection. In a matched case-control study, preceding IR procedure and IR procedure with contrast were associated with VRE infection (matched odds ratio [MOR], 16.72; 95% confidence interval [CI], 2.01 to 138.73; P = .009 and MOR, 39.35; 95% CI, 7.85 to infinity; P < .001, respectively). Investigation of IR practices and review of the manufacturer’s training video revealed sterility breaches in contrast preparation. Our investigation also supported possible transmission from an IR technician. Infection prevention interventions were implemented, and no further IR-associated VRE transmissions have been observed. Conclusions A prolonged outbreak of VRE infections related to IR procedures with IV contrast resulted from nonsterile preparation of injectable contrast. The fact that our VRE outbreak was discovered through WGS surveillance and the manufacturer’s training video that demonstrated nonsterile technique raise the possibility that infections following invasive IR procedures may be more common than previously recognized.

scholarly journals Homologous Recombination within Large Chromosomal Regions Facilitates Acquisition of β-Lactam and Vancomycin Resistance in Enterococcus faecium

2016 ◽  
Vol 60 (10) ◽  
pp. 5777-5786 ◽  
Author(s):  
Mónica García-Solache ◽  
Francois Lebreton ◽  
Robert E. McLaughlin ◽  
James D. Whiteaker ◽  
Michael S. Gilmore ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Genomic Dna ◽  
Large Scale ◽  
Vancomycin Resistance ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Single Nucleotide ◽  
Content Type ◽  
Donor Chromosome ◽  
Vancomycin Resistant

ABSTRACTThe transfer of DNA betweenEnterococcus faeciumstrains has been characterized both by the movement of well-defined genetic elements and by the large-scale transfer of genomic DNA fragments. In this work, we report on the whole-genome analysis of transconjugants resulting from mating events between the vancomycin-resistantE. faeciumC68 strain and the vancomycin-susceptible D344RRF strain to discern the mechanism by which the transferred regions enter the recipient chromosome. Vancomycin-resistant transconjugants from five independent matings were analyzed by whole-genome sequencing. In all cases but one, the penicillin binding protein 5 (pbp5) gene and the Tn5382vancomycin resistance transposon were transferred together and replaced the correspondingpbp5region of D344RRF. In one instance, Tn5382inserted independently downstream of the D344RRFpbp5gene. Single nucleotide variant (SNV) analysis suggested that entry of donor DNA into the recipient chromosome occurred by recombination across regions of homology between donor and recipient chromosomes, rather than through insertion sequence-mediated transposition. The transfer of genomic DNA was also associated with the transfer of C68 plasmid pLRM23 and another putative plasmid. Our data are consistent with the initiation of transfer by cointegration of a transferable plasmid with the donor chromosome, with subsequent circularization of the plasmid-chromosome cointegrant in the donor prior to transfer. Entry into the recipient chromosome most commonly occurred across regions of homology between donor and recipient chromosomes.

Cell wall alterations in staphylococci growing in situ in experimental osteomyelitis

1987 ◽  
Vol 33 (2) ◽  
pp. 142-150 ◽  
Author(s):  
J. W. Costerton ◽  
D. W. Lambe Jr. ◽  
K.-J. Mayberry-Carson ◽  
B. Tober-Meyer
Keyword(s):  
Cell Wall ◽  
Cell Size ◽  
Wall Structure ◽  
Specific Cell ◽  
Experimental Osteomyelitis ◽  
Rich Media ◽  
Rabbit Tibia ◽  
Rabbit Bone

When cells of both Staphylococcus aureus and Staphylococcus epidermidis are grown in batch culture in nutrient-rich media, their cell walls are regular in thickness, their cell size is within the normal range for each species, and their septation patterns are orderly. When cells of each of these species are examined directly in infected tissue in the rabbit tibia model infection, their cell wall thickness is often much increased and very irregular around the circumference of the cell, their cell size is often increased, and their septation patterns are often severely deranged. All of these alterations in cell wall structure occur in the absence of antibiotics, and we suggest that they may be an expression of phenotypic plasticity in response to altered environmental conditions such as specific nutrient limitations, the presence of antibacterial factors, and growth of the cells on hard surfaces such as rabbit bone or plastic catheters. Some of these specific cell wall alterations are also seen when staphylococcal cells are exposed, in vitro or in vivo, to antibiotics such as clindamycin, but we emphasize that growth in tissue alone is sufficient for their induction.

scholarly journals Development of in Vitro Resistance to Daptomycin in Enterococcus Faecium and Estimation of Its Fitness Cost

2020 ◽  
Author(s):  
Weiliang Zeng ◽  
Tao Chen ◽  
Qing Wu ◽  
Ye Xu ◽  
Kaihang Yu ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Biofilm Formation ◽  
Galleria Mellonella ◽  
Resistance Mechanisms ◽  
Fitness Cost ◽  
Resistant Bacteria ◽  
Infection Model ◽  
Dynamic Resistance ◽  
Vancomycin Resistant

Abstract BackgroundDaptomycin has broad-spectrum antibacterial activity against Gram-positive pathogens, but recent studies have revealed cases where daptomycin has failed to treat multidrug-resistant bacteria, such as vancomycin-resistant Enterococcus faecium. However, the resistance evolution of E. faecium to daptomycin in vitro and fitness cost remain unclear. In this study, we sought to analyze the resistance development and mechanism of E. faecium to datomycin, and futher to investigate the relationship between daptomycin resistance and fitness cost.MethodsTo investigate the development of daptomycin resistance in E. faecium, 6 daptomycin-susceptible (DAP-S) clinical isolates, including 3 vancomycin-resistant E. faecium (VRE) and 3 vancomycin-susceptible E. faecium (VSE), were exposured to daptomycin in vitro by serial passage experiment. Then the different resistance mechanisms of daptomycin-resistant (DAP-R) mutants were analyzed by polymerase chain reaction (PCR), cytochrome C binding assay and transmission electron microscopy. Furthermore, we also estimated the changes of fitness cost among each highly DAP-R mutants by bacterial growth curve measurement, in vitro competition experiments, infection model of Galleria mellonella larvae and biofilm formation assays.ResultsIn vitro, a total of 21 DAP-R mutants with minimal inhibitory concentration (MIC) of 4 to 512 μg/mL were obtained, and these mutants carried more than one mutation of LiaFSR and YycFG system encoding genes. More positive charges were detected among highly DAP-R mutants than parent isolates, and the cell walls of SC1174-D and SC1762-D mutants were remarkly thicker than those of the parent isolates. In comparison with parent isolates, besides, the growth, competition ability and virulence were significantly reduced, while the biofilm formation capacity was markedly elevated among each highly DAP-R mutants.ConclusionsOur findings suggest that E. faecium isolates are able to rapidly acquire DAP resistance in vitro through different dynamic resistance mechanisms, which often accompany by significant fitness cost. Intriguingly, DAP and glycopeptide antibiotics may present collateral-sensitivity during E. faecium acquired DAP resistance in vitro.

scholarly journals Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

2017 ◽  
Author(s):  
Kimon Lemonidis ◽  
Talal S. Salih ◽  
Stephanie J. Dancer ◽  
Iain S. Hunter ◽  
Nicholas P. Tucker
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterococcus Faecium ◽  
Sequence Type ◽  
Whole Genome ◽  
Vancomycin Resistant Enterococcus ◽  
Phylogenetic Comparison ◽  
Vancomycin Resistant ◽  
The Uk ◽  
Increased Susceptibility

AbstractMulti-locus sequencing typing (MLST) is widely used to monitor the phylogeny of microbial outbreaks. However, several strains of vancomycin-resistant Enterococcus faecium (VREfm) with a missing MLST locus (pstS) have recently emerged in Australia, with a few cases also reported in England. Here, we identified similarly distinct strains circulating in two closely located hospitals in Scotland. Whole genome sequencing of five VREfm strains isolated from these hospitals identified four pstS-null strains across both hospitals, while the fifth was of a multi-locus sequence type (ST) 262, which is the first documented in the UK. All five Scottish isolates had an insertion in the tetM gene, which is associated with increased susceptibility to tetracyclines, providing no other tetracycline-resistant gene is present. Such an insertion, which encompasses a dfrG gene and two currently uncharacterised genes, was additionally identified in all tested VanA-type pstS-null VREfm strains (5 English and 18 Australian). Phylogenetic comparison with other VREfm genomes indicates that the four pstS-null Scottish isolates sequenced in this study are more closely related to pstS-null strains from Australia rather than the English pstS-null isolates. Given how rapidly such pstS-null strains have expanded in Australia, the emergence of this clone in Scotland raises concerns for a potential outbreak.

scholarly journals ddcP, pstB, and excess D-lactate impact synergism between vancomycin and chlorhexidine against Enterococcus faecium 1,231,410

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249631
Author(s):  
Pooja Bhardwaj ◽  
Moutusee Z. Islam ◽  
Christi Kim ◽  
Uyen Thy Nguyen ◽  
Kelli L. Palmer
Keyword(s):  
Enterococcus Faecium ◽  
Whole Genome ◽  
Vancomycin Resistant Enterococci ◽  
Control Hospital ◽  
Skin Antisepsis ◽  
Life Threatening ◽  
Membrane Bound ◽  
Vancomycin Resistant ◽  
Hospital Associated Infections

Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens that cause life-threatening infections. To control hospital-associated infections, skin antisepsis and bathing utilizing chlorhexidine is recommended for VRE patients in acute care hospitals. Previously, we reported that exposure to inhibitory chlorhexidine levels induced the expression of vancomycin resistance genes in VanA-type Enterococcus faecium. However, vancomycin susceptibility actually increased for VanA-type E. faecium in the presence of chlorhexidine. Hence, a synergistic effect of the two antimicrobials was observed. In this study, we used multiple approaches to investigate the mechanism of synergism between chlorhexidine and vancomycin in the VanA-type VRE strain E. faecium 1,231,410. We generated clean deletions of 7 of 11 pbp, transpeptidase, and carboxypeptidase genes in this strain (ponA, pbpF, pbpZ, pbpA, ddcP, ldtfm, and vanY). Deletion of ddcP, encoding a membrane-bound carboxypeptidase, altered the synergism phenotype. Furthermore, using in vitro evolution, we isolated a spontaneous synergy escaper mutant and utilized whole genome sequencing to determine that a mutation in pstB, encoding an ATPase of phosphate-specific transporters, also altered synergism. Finally, addition of excess D-lactate, but not D-alanine, enhanced synergism to reduce vancomycin MIC levels. Overall, our work identified factors that alter chlorhexidine and vancomycin synergism in a model VanA-type VRE strain.

scholarly journals Gradual Alterations in Cell Wall Structure and Metabolism in Vancomycin-Resistant Mutants ofStaphylococcus aureus

1999 ◽  
Vol 181 (24) ◽  
pp. 7566-7570 ◽  
Author(s):  
Krzysztof Sieradzki ◽  
Alexander Tomasz
Keyword(s):  
Cell Wall ◽  
Methicillin Resistance ◽  
Specific Inhibitor ◽  
Wall Structure ◽  
Penicillin Binding Protein ◽  
Cell Wall Metabolism ◽  
Gradual Reduction ◽  
Vancomycin Resistant ◽  
Resistant Mutants ◽  
Structure And Metabolism

ABSTRACT In five vancomycin-resistant laboratory step mutants selected from the highly and homogeneously methicillin-resistant Staphylococcus aureus strain COL (MIC of methicillin, 800 μg/ml; MIC of vancomycin, 1.5 μg/ml), the gradually increasing levels of resistance to vancomycin were accompanied by parallel decreases in the levels of methicillin resistance and abnormalities in cell wall metabolism. The latter included a gradual reduction in the proportion of highly cross-linked muropeptide species in peptidoglycan, down-regulation of the production of penicillin-binding protein 2A (PBP2A) and PBP4, and hypersensitivity to β-lactam antibiotics each with a relatively selective affinity for the various staphylococcal PBPs; the PBP2-specific inhibitor ceftizoxime was particularly effective.

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