scholarly journals Discovering a novel resistance gene for carbapenem resistance in Parabacteroides timonensis using Whole Genome Sequencing

2019 ◽  
Vol 1 (7) ◽  
Author(s):  
Kathleen Boiten ◽  
Alida Veloo
Keyword(s):  
Whole Genome Sequencing ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
Carbapenem Resistance ◽  
Whole Genome

The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae

2015 ◽  
Vol 68 (10) ◽  
pp. 835-838 ◽  
Author(s):  
Björn A Espedido ◽  
Borce Dimitrijovski ◽  
Sebastiaan J van Hal ◽  
Slade O Jensen
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
De Novo ◽  
Antibiotic Resistance Genes ◽  
Whole Genome ◽  
Antimicrobial Surveillance ◽  
Metropolitan Hospital ◽  
Genetic Context

AimsTo characterise the resistome of a multi-drug resistant Klebsiella pneumoniae (Kp0003) isolated from an Australian traveller who was repatriated to a Sydney Metropolitan Hospital from Myanmar with possible prosthetic aortic valve infective endocarditis.MethodsKp0003 was recovered from a blood culture of the patient and whole genome sequencing was performed. Read mapping and de novo assembly of reads facilitated in silico multi-locus sequence and plasmid replicon typing as well as the characterisation of antibiotic resistance genes and their genetic context. Conjugation experiments were also performed to assess the plasmid (and resistance gene) transferability and the effect on the antibiotic resistance phenotype.ResultsImportantly, and of particular concern, the carbapenem-hydrolysing β-lactamase gene blaNDM-4 was identified on a conjugative IncX3 plasmid (pJEG027). In this respect, the blaNDM-4 genetic context is similar (at least to some extent) to what has previously been identified for blaNDM-1 and blaNDM-4-like variants.ConclusionsThis study highlights the potential role that IncX3 plasmids have played in the emergence and dissemination of blaNDM-4-like variants worldwide and emphasises the importance of resistance gene surveillance.

scholarly journals Imipenem Resistance Mediated by blaOXA-913 Gene in Pseudomonas aeruginosa

Antibiotics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1188
Author(s):  
Dong-Chan Moon ◽  
Abraham Fikru Mechesso ◽  
Hee-Young Kang ◽  
Su-Jeong Kim ◽  
Ji-Hyun Choi ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Carbapenem Resistance ◽  
Rrna Genes ◽  
Whole Genome ◽  
Translation Initiation Region ◽  
Broth Microdilution Method ◽  
Imipenem Resistance

Treatment of infectious diseases caused by carbapenem-resistant Pseudomonas aeruginosa is becoming a greater challenge. This study aimed to identify the imipenem resistance mechanism in P. aeruginosa isolated from a dog. Minimum Inhibitory Concentration (MIC) was determined by the broth microdilution method according to the Clinical and Laboratory Standards Institute recommendations. We performed polymerase chain reaction and whole-genome sequencing to detect carbapenem resistance genes. Genomic DNA of P. aeruginosa K19PSE24 was sequenced via the combined analysis of 20-kb PacBio SMRTbell and PacBio RS II. Peptide-Peptide Nucleic Acid conjugates (P-PNAs) targeting the translation initiation region of blaOXA-913 were synthesized. The isolate (K19PSE24) was resistant to imipenem and piperacillin/tazobactam yet was susceptible to most of the tested antimicrobials. Whole-genome sequencing revealed that the K19PSE24 genome comprised a single contig amounting to 6,815,777 base pairs, with 65 tRNA and 12 rRNA genes. K19PSE24 belonged to sequence type 313 and carried the genes aph(3)-IIb, fosA, catB7, crpP, and blaOXA-913 (an allele deposited in GenBank but not described in the literature). K19PSE24 also carried genes encoding for virulence factors (exoenzyme T, exotoxin A, and elastase B) that are associated with adhesion, invasion, and tissue lysis. Nevertheless, we did not detect any of the previously reported carbapenem resistance genes. This is the first report of the blaOXA-913 gene in imipenem-resistant P. aeruginosa in the literature. Notably, no viable colonies were found after co-treatment with imipenem (2 µg/mL) and either of the P-PNAs (12.5 µM or 25 µM). The imipenem resistance in K19PSE24 was primarily due to blaOXA-913 gene carriage.

scholarly journals Resistance Gene-Directed Genome Mining of 50 Aspergillus Species

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Inge Kjærbølling ◽  
Tammi Vesth ◽  
Mikael R. Andersen
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Resistance Gene ◽  
Secondary Metabolite ◽  
Genome Sequencing ◽  
Bioactive Compounds ◽  
Genome Mining ◽  
Whole Genome ◽  
Metabolite Production ◽  
Genetic Potential

Species belonging to the Aspergillus genus are known to produce a large number of secondary metabolites; some of these compounds are used as pharmaceuticals, such as penicillin, cyclosporine, and statin. With whole-genome sequencing, it became apparent that the genetic potential for secondary metabolite production is much larger than expected. As an increasing number of species are whole-genome sequenced, thousands of secondary metabolite genes are predicted, and the question of how to selectively identify novel bioactive compounds from this information arises. To address this question, we have created a pipeline to predict genes involved in the production of bioactive compounds based on a resistance gene hypothesis approach.

scholarly journals Deciphering the resistome of the widespreadP. aeruginosaST175 international high-risk clone through whole genome sequencing

2016 ◽  
pp. AAC.01720-16 ◽  
Author(s):  
Gabriel Cabot ◽  
Carla López-Causapé ◽  
Alain A. Ocampo-Sosa ◽  
Lea M. Sommer ◽  
María Ángeles Domínguez ◽  
...  
Keyword(s):  
High Risk ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Carbapenem Resistance ◽  
Whole Genome ◽  
Resistance Mutations ◽  
Online Databases ◽  
Genes Encoding ◽  
Resistance Traits

Whole genome sequencing (WGS) was used for the characterization of the, frequently extensively-drug resistant (XDR),P. aeruginosahigh-risk clone ST175. A total of eighteen ST175 isolates recovered from 8 different Spanish hospitals were analyzed; four isolates from four different French hospitals were included for comparison. The typical resistance profile of ST175 included penicillins, cephalosporins, monobactams, carbapenems, aminoglycosides, and fluoroquinolones. In the phylogenetic analysis, the four French isolates clustered together with the two isolates from one of the Spanish regions. Sequence variation was analyzed for 146 chromosomal genes related to antimicrobial resistance and horizontally-acquired genes were explored using online databases. The resistome of ST175 was mainly determined by mutational events, with resistance traits common to all or nearly all of the strains, including specificampRmutations leading toampCoverexpression, specific mutations inoprDconferring carbapenem resistance or amexZmutation leading to MexXY overexpression. All isolates additionally harbored anaadBgene conferring gentamicin and tobramycin resistance. Several other resistance traits were specific to certain geographic areas such as a streptomycin resistanceaadA13gene detected in all four isolates from France and in the 2 isolates from the Cantabria region or aglpTmutation conferring fosfomycin resistance detected in all but these six isolates. Finally, several unique resistance mutations were detected in single isolates; particularly interesting among them were those in genes encoding PBPs (PBP1A, PBP3 and PBP4). Thus, these results provide valuable information for understanding the genetic basis of resistance and the dynamics of dissemination and evolution of high-risk clones.

Molecular characterization of rectal isolates of carbapenemase-negative carbapenem-resistant enterobacterales obtained from ICU patients in Kuwait by whole-genome sequencing

2021 ◽  
Vol 70 (9) ◽  
Author(s):  
Amani Al Fadhli ◽  
Wafaa Jamal ◽  
Vincent O. Rotimi
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Carbapenem Resistance ◽  
Efflux Pumps ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Genetic Characteristics ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Amoxicillin Clavulanic Acid

Introduction. Carbapenem-resistant enterobacterales (CRE) are listed among the most urgent antibiotic resistance threats. Hypothesis. Previous studies on the mechanisms of CRE in Kuwait have focused on carbapenemases. There have been no studies on non-carbapenemase-producing CRE in Kuwait. Aim/Gap Statement. The aim of this study was to investigate the genetic characteristics of non-carbapenemase-producing carbapenem-resistant enterobacterales (NCPE) isolates using whole-genome sequencing (WGS). Methodology. Fourteen confirmed NCPE isolates that were negative for genes encoding carbapenemase production by polymerase chain reaction (PCR) assays using rectal swabs from intensive care unit patients were characterized using phenotypic, PCR and WGS methods. Susceptibility testing was performed via Etest and clonality via multi-locus sequence typing (MLST). Results. All of the isolates were resistant to ertapenem; 78.6 % were resistant to imipenem, meropenem and trimethoprim–sulfamethoxazole. Resistance to the other antibiotics was variable, ranging from 28.5 (colistin) through 50 (tigecycline) and 64.3 (amikacin) up to 85.7 % against both amoxicillin–clavulanic acid and ciprofloxacin. WGS detected several resistance genes mediating the production of β-lactamases, genes encoding an outer-membrane porin permeability mutation resulting in reduced susceptibility to β-lactams, including carbapenems, and genes for multidrug-resistant (MDR) efflux pumps. The isolates also possessed global activator protein MarA, which mediated reduced permeability to β-lactams. The existence of β-lactamase genes, overexpression of MDR efflux pumps and reduced permeability mediated by the porin genes were responsible for carbapenem resistance. Conclusions. This finding reflects the superior detection capabilities offered by WGS analysis, which can be used to complement traditional methods and overcome their limited resolution in clinical settings.

scholarly journals 2461. Community-Acquired in Name Only: A Cluster of Carbapenem-Resistant Acinetobacter baumannii in a Burn Intensive Care Unit

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S852-S852
Author(s):  
Erica S Shenoy ◽  
Virginia M Pierce ◽  
Mohamad Sater ◽  
Febriana Pangestu ◽  
Ian Herriott ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Carbapenem Resistance ◽  
Environmental Sampling ◽  
Whole Genome ◽  
Single Source ◽  
Carbapenem Resistant

Abstract Background Detection of nosocomial outbreaks often relies on epidemiological definitions of community and nosocomial acquisition. We report a cluster of three carbapenem-resistant Acinetobacter baumannii (CRAB) infections linked to a single source patient with infections occurring within 2 days of admission to a burn intensive care unit (ICU). The epidemiological investigation was supplemented by whole-genome sequencing (WGS) of clinical and environmental isolates. Methods Study participants included burn ICU patients identified with infections caused by CRAB. A detailed review of patient demographic and clinical data was conducted. Clinical A. baumannii isolates were assessed by antimicrobial susceptibility testing and WGS. Review of infection control practices on the affected unit was followed by environmental sampling. A. baumannii isolates obtained through environmental sampling were assessed for carbapenem resistance and then underwent WGS for comparison to the clinical isolates. Results Three cases of CRAB infection in the affected unit spanning a period of 3 months were linked to a preceding source patient, with CRAB isolates from the four patients differing by 5–7 single nucleotide variations. All case patients had been admitted to the same room within 2 days before development of CRAB infection. Environmental sampling performed while the third case patient occupied the room identified highly contaminated areas, and environmental CRAB isolates linked the patient isolates. The contaminated areas were subsequently re-sampled after enhanced terminal cleaning of the room. No additional CRAB was isolated, but other pathogenic organisms were recovered. Conclusion We report a cluster of three infections caused by highly resistant A. baumannii that occurred in a burn intensive care unit over a period of 3 months, linked to a single source patient. Three case patients developed infections classified as community-acquired using standard epidemiological definitions, however, whole-genome sequencing revealed clonality. An extensive investigation identified the role of environmental reservoirs. Burn patients may be particularly vulnerable to early-onset nosocomial infection from environmental contamination. Disclosures All authors: No reported disclosures.

scholarly journals Characterization of an Enterobacter cloacae Strain Producing both KPC and NDM Carbapenemases by Whole-Genome Sequencing

2015 ◽  
Vol 59 (10) ◽  
pp. 6625-6628 ◽  
Author(s):  
Wenjing Wu ◽  
Yu Feng ◽  
Alessandra Carattoli ◽  
Zhiyong Zong
Keyword(s):  
Whole Genome Sequencing ◽  
Bloodstream Infection ◽  
Genome Sequencing ◽  
Carbapenem Resistance ◽  
Enterobacter Cloacae ◽  
Whole Genome ◽  
Content Type ◽  
Carbapenem Resistant

ABSTRACTA carbapenem-resistantEnterobacter cloacaestrain, WCHECl-14653, causing a fatal bloodstream infection, was characterized by genome sequencing and conjugation experiments. The strain carried two carbapenemase genes,blaNDM-1andblaKPC-2, on separate IncF plasmids. The coexistence ofblaNDM-1andblaKPC-2conferred slightly higher-level carbapenem resistance compared with that ofblaNDM-1orblaKPC-2alone, and the coexistence of two IncF plasmids may generate new platforms for spreading carbapenemase genes.

scholarly journals Various Sequence Types of Escherichia coli Isolates Coharboring blaNDM-5 and mcr-1 Genes from a Commercial Swine Farm in China

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Ling-Han Kong ◽  
Chang-Wei Lei ◽  
Su-Zhen Ma ◽  
Wei Jiang ◽  
Bi-Hui Liu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
Carbapenem Resistance ◽  
Whole Genome ◽  
Swine Farm ◽  
Colistin Resistance ◽  
Content Type ◽  
E Coli ◽  
Sequence Types

ABSTRACT Sixteen different sequence types (STs) of Escherichia coli isolates from a commercial swine farm in China were confirmed to coharbor the carbapenem resistance gene bla NDM-5 and the colistin resistance gene mcr-1. Whole-genome sequencing revealed that bla NDM-5 and mcr-1 were located on a 46-kb IncX3 plasmid and a 32-kb IncX4 plasmid, respectively. The two plasmids can transfer together with a low fitness cost, which might explain the presence of various STs of E. coli coharboring bla NDM-5 and mcr-1.

scholarly journals Genomic characterization of Citrobacter freundii strains coproducing OXA-48 and VIM-1 carbapenemase enzymes isolated in leukemic patient in Spain

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Rym Lalaoui ◽  
Ana Djukovic ◽  
Sofiane Bakour ◽  
Linda Hadjadj ◽  
Jaime Sanz ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Mechanism ◽  
Carbapenem Resistance ◽  
Bioinformatic Analysis ◽  
Whole Genome ◽  
Citrobacter Freundii ◽  
Fecal Samples ◽  
Carbapenem Resistant ◽  
High Risk Populations

Abstract Background The emergence of carbapenemase-producing (CP) Citrobacter freundii poses a significant threat to public health, especially in high-risk populations. In this study, whole genome sequencing was used to characterize the carbapenem resistance mechanism of three C. freundii clinical isolates recovered from fecal samples of patients with acute leukemia (AL) from Spain. Materials and methods Twelve fecal samples, collected between 2013 and 2015 from 9 patients with AL, were screened for the presence of CP strains by selecting them on MacConkey agar supplemented with ertapenem (0.5 mg/L). Bacteria were identified by MALDI-TOF mass spectrometry and were phenotypically characterized. Whole genome sequencing of C. freundii isolates was performed using the MinION and MiSeq Illumina sequencers. Bioinformatic analysis was performed in order to identify the molecular support of carbapenem resistance and to study the genetic environment of carbapenem resistance encoding genes. Results Three carbapenem-resistant C. freundii strains (imipenem MIC≥32 mg/L) corresponding to three different AL patients were isolated. Positive modified Carba NP test results suggested carbapenemase production. The genomes of each C. freundii tested were assembled into a single chromosomal contig and plasmids contig. In all the strains, the carbapenem resistance was due to the coproduction of OXA-48 and VIM-1 enzymes encoded by genes located on chromosome and on an IncHI2 plasmid, respectively. According to the MLST and the SNPs analysis, all strains belonged to the same clone ST169. Conclusion We report in our study, the intestinal carrying of C. freundii clone ST169 coproducing OXA-48 and VIM-1 identified in leukemic patients.

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