Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

NDM-1 carbapenemase in Acinetobacter baumannii sequence type 32 in Ecuador.

ABSTRACT:

Objectives

To describe a clinical case of Acinetobacter baumannii sequence type (ST) 32 harbouring a New Delhi metallo-β-lactamase (NDM) in Ecuador.

Methods

We used multilocus sequence typing (MLST) to confirm the bacterial species and the sequence type of an A. baumannii isolate. We used synergy with the imipenem-EDTA disc method and the carbapenem inactivation method (CIM) to determine carbapenemase production; the presence of a carbapenemase gene was confirmed by PCR amplification and amplicon sequencing.

Results

Molecular characterization revealed the presence of A. baumannii ST32 harbouring the bla _NDM-1 gene in Ecuador. The bla _NDM-1 gene was isolated through PCR and amplified from a purified plasmid.

Conclusions

To the best of our knowledge, this is the first report of A. baumannii ST32 harbouring the bla _NDM-1 gene.

SUBMITTER: Villacis JE

PROVIDER: S-EPMC6438911 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

NDM-1 carbapenemase in <i>Acinetobacter baumannii</i> sequence type 32 in Ecuador.

Villacís J E JE Bovera M M Romero-Alvarez D D Cornejo F F Albán V V Trueba G G Dorn H F HF Reyes J A JA

New microbes and new infections 20190308

<h4>Objectives</h4>To describe a clinical case of <i>Acinetobacter baumannii</i> sequence type (ST) 32 harbouring a New Delhi metallo-β-lactamase (NDM) in Ecuador.<h4>Methods</h4>We used multilocus sequence typing (MLST) to confirm the bacterial species and the sequence type of an <i>A. baumannii</i> isolate. We used synergy with the imipenem-EDTA disc method and the carbapenem inactivation method (CIM) to determine carbapenemase production; the presence of a carbapenemase gene was confirmed by ...[more]

PMID: 30976430

Similar Datasets

Transposition of Tn125 Encoding the NDM-1 Carbapenemase in Acinetobacter baumannii.

Project description:The blaNDM-1 gene encodes a carbapenemase that confers resistance to almost all β-lactams, including last-resort carbapenems. This is increasingly reported worldwide in nosocomial and community-acquired Gram-negative bacteria. Acinetobacter baumannii is an important opportunistic pathogen that is considered an intermediate reservoir for the blaNDM-1 gene. In this species, the blaNDM-1 gene is located within the Tn125 composite transposon. The mechanism driving the mobility of Tn125 has not yet been elucidated. Here we experimentally demonstrated the transposition of Tn125 in A. baumannii Systematic 3-bp duplication of the target site, being the signature of transposition, was evidenced. The target site consensus sequence for Tn125 transposition was found to be GC enriched at the duplicated 3 bp and AT rich in the vicinity. Transposition frequency was not influenced by temperature changes or by exposure to subinhibitory concentrations of various antibiotics. This work is the first direct evidence of the functionality of a composite transposon in A. baumannii It provides a mechanistic clue for the dissemination of the blaNDM-1 gene in Acinetobacter spp. and subsequently among Enterobacteriaceae.

| S-EPMC5119004 | biostudies-literature

Genome Sequence of an Acinetobacter baumannii Strain Carrying Three Acquired Carbapenemase Genes.

Project description:The emergence of multiple-carbapenemase-producing Acinetobacter strains has been a serious concern during the past decade. Here, we report the draft genome sequence of an Acinetobacter baumannii strain isolated from a Japanese patient with three acquired carbapenemase genes: blaNDM-1, blaTMB-1, and blaOXA-58.

| S-EPMC5114380 | biostudies-literature

Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Sequence Type 2 Isolate from Puerto Rico.

Project description:We report here the draft genome sequence of Acinetobacter baumannii strain M3AC14-8, sequence type 2 (ST2), carrying a chromosomally carried blaKPC-2 gene. The draft genome consists of a total length of 4.11 Mbp and a G+C content of 39.25%.

| S-EPMC4991701 | biostudies-literature

OXA-48 Carbapenemase in Klebsiella pneumoniae Sequence Type 307 in Ecuador.

Project description:Antibiotic resistance is on the rise, leading to an increase in morbidity and mortality due to infectious diseases. Klebsiella pneumoniae is a Gram-negative bacterium that causes bronchopneumonia, abscesses, urinary tract infection, osteomyelitis, and a wide variety of infections. The ubiquity of this microorganism confounds with the great increase in antibiotic resistance and have bred great concern worldwide. K. pneumoniae sequence type (ST) 307 is a widespread emerging clone associated with hospital-acquired infections, although sporadic community infections have also been reported. The aim of our study is to describe the first case of Klebsiella pneumoniae (ST) 307 harboring the blaOXA-48-like gene in Ecuador. We characterized a new plasmid that carry OXA-48 and could be the source of future outbreaks. The strain was recovered from a patient with cancer previously admitted in a Ukrainian hospital, suggesting that this mechanism of resistance could be imported. These findings highlight the importance of programs based on active molecular surveillance for the intercontinental spread of multidrug-resistant microorganisms with emergent carbapenemases.

| S-EPMC7143988 | biostudies-literature

Clonal diversity of <i>Acinetobacter</i> clinical isolates producing NDM-type carbapenemase in Cuba, 2013-19.

Project description:ObjectivesOur study aimed to elucidate the clonal diversity of carbapenem-resistant Acinetobacter clinical isolates producing NDM-type carbapenemase collected through national surveillance in Cuba during a 7-year period (2013-19).MethodsA total of 199 isolates of Acinetobacter spp. from 37 hospitals in 12 provinces were genetically analyzed for their species, carbapenemase genes and genotypes. Sequence type (ST) and OXA-51-like gene type were determined for bla NDM-positive isolates.ResultsMost isolates (95%) were identified as species of Acinetobacter calcoaceticus-baumannii complex, with A. baumannii being the majority. Acquired carbapenemase genes were assigned to bla OXA or bla NDM type; the most commonly detected gene was bla OXA-23-like (49%), followed by bla OXA-24-like (20%) and bla NDM (15%). Twenty-nine bla NDM-positive isolates (22 A. baumannii, 2 A. pittii, 2 A. johnsonii, 3 other species) were differentiated into 19 STs, including the most common, ST23. Though NDM genes were mostly typed as bla NDM-1, a novel bla NDM-42 was identified in an ST79 A. baumannii isolate. bla OXA-51-like genes of NDM-positive A. baumannii were discriminated into 10 OXA types, including 2 novel ones.ConclusionsOur study indicated the spread of bla NDM to various clones of A. baumannii and other Acinetobacter spp. in Cuba.

| S-EPMC9557864 | biostudies-literature

Crystal structure of carbapenemase OXA-58 from Acinetobacter baumannii.

Project description:Class D β-lactamases capable of hydrolyzing last-resort carbapenem antibiotics represent a major challenge for treatment of bacterial infections. Wide dissemination of these enzymes in Acinetobacter baumannii elevated this pathogen to the category of most deadly and difficult to treat. We present here the structure of the OXA-58 β-lactamase, a major class D carbapenemase of A. baumannii, determined to 1.30-Å resolution. Unlike two other Acinetobacter carbapenemases, OXA23 and OXA-24, the OXA-58 enzyme lacks the characteristic hydrophobic bridge over the active site, despite conservation of the residues which participate in its formation. The active-site residues in OXA-58 are spatially conserved in comparison to those in other class D β-lactamases. Lys86, which activates water molecules during the acylation and deacylation steps, is fully carboxylated in the OXA-58 structure. In the absence of a substrate, a water molecule is observed in the active site of the enzyme and is positioned in the pocket that is usually occupied by the 6α-hydroxyethyl moiety of carbapenems. A water molecule in this location would efficiently deacylate good substrates, such as the penicillins, but in the case of carbapenems, it would be expelled by the 6α-hydroxyethyl moiety of the antibiotics and a water from the surrounding medium would find its way to the vicinity of the carboxylated Lys86 to perform deacylation. Subtle differences in the position of this water in the acyl-enzyme complexes of class D β-lactamases could ultimately be responsible for differences in the catalytic efficiencies of these enzymes against last-resort carbapenem antibiotics.

| S-EPMC4023756 | biostudies-literature

Multidrug-resistant Acinetobacter baumannii Harboring OXA-24 carbapenemase, Spain.

Project description:In February 2006, a patient colonized with a multidrug-resistant sequence type 56 Acinetobacter baumannii strain was admitted to a hospital in Madrid, Spain. This strain spread rapidly and caused a large outbreak in the hospital. Clinicians should be alert for this strain because its spread would have serious health consequences.

| S-EPMC3358182 | biostudies-literature

High prevalence of bla(NDM-1) carbapenemase-encoding gene and 16S rRNA armA methyltransferase gene among Acinetobacter baumannii clinical Isolates in Egypt.

Project description:The main objective of this study was to decipher the molecular mechanism of resistance to carbapenems and aminoglycosides in a large series of 150 Acinetobacter baumannii clinical isolates collected from July 2012 to September 2013 in Egypt. We report for the first time the emergence of bla(NDM-1) and the cooccurrence of 16S rRNA methylase armA with bla(NDM-1) and bla(OXA-23) in Egyptian hospitals. Multilocus sequence typing identified 27 distinct sequence types, 11 of which were novel.

| S-EPMC4432156 | biostudies-literature

Genomic characterization of triple-carbapenemase-producing <i>Acinetobacter baumannii</i>.

Project description:ObjectivesTo characterize Acinetobacter baumannii OCU_Ac16a, a clinical isolate co-harbouring three acquired carbapenemase genes, bla NDM-1, bla TMB-1, and bla OXA-58, and assess the clinical significance of so-called multiple-carbapenemase producers.MethodsOCU_Ac16a and its close relative, OCU_Ac16b, which lacks the bla NDM-1, were isolated from sputum cultures of a patient at Osaka City University Hospital. We subjected these strains to whole-genome analysis, particularly focusing on the genetic context of each carbapenemase gene. The transmissibility and functionality of each carbapenemase gene were analysed by conjugation and transformation experiments and antimicrobial susceptibility tests.Resultsbla TMB-1 was located in a class 1 integron on the chromosome, whereas bla NDM-1 and bla OXA-58 were found on plasmids named pOCU_Ac16a_2 and pOCU_Ac16a_3, respectively. pOCU_Ac16a_2 (which exhibited highly efficient self-transmissibility) and pOCU_Ac16a_3 (which did not show transmissibility but could be introduced into another A. baumannii strain via electroporation) could both confer carbapenem resistance (MICs ≥512 and ≥32 mg/L, respectively) on the recipient strain. The functionality of bla TMB-1 was evident from the high resistance of OCU_Ac16b to ceftazidime and cefepime (MICs ≥256 and 48 mg/L, respectively), and the high resistance of OCU_Ac16a to cefiderocol (MIC 32 mg/L) could be explained by the additive effect of bla NDM-1 and bla TMB-1.ConclusionsOur data revealed the genomic organization of OCU_Ac16a and demonstrated that all the carbapenemase genes are functional, each contributing to the extremely high broad-spectrum resistance of OCU_Ac16a to β-lactams. As multiple-carbapenemase producers can be serious health threats as drug-resistant pathogens and disseminators of carbapenemase genes, close attention should be paid to their emergence.

| S-EPMC8684466 | biostudies-literature

Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene.

Project description:The species Acinetobacter baumannii is one of the most important multidrug-resistant human pathogens. To determine its virulence and antibiotic resistance determinants, the genome of the nosocomial blaNDM-1-positive A. baumannii strain R2090 originating from Egypt was completely sequenced. Genome analysis revealed that strain R2090 is highly related to the community-acquired Australian A. baumannii strain D1279779. The two strains belong to sequence type 267 (ST267). Isolate R2090 harbored the chromosomally integrated transposon Tn125 carrying the carbapenemase gene blaNDM-1 that is not present in the D1279779 genome. To test the transferability of the metallo-β-lactamase (MBL) gene region, the clinical isolate R2090 was mated with the susceptible A. baumannii recipient CIP 70.10, and the carbapenem-resistant derivative R2091 was obtained. Genome sequencing of the R2091 derivative revealed that it had received an approximately 66-kb region comprising the transposon Tn125 embedding the blaNDM-1 gene. This region had integrated into the chromosome of the recipient strain CIP 70.10. From the four known mechanisms for horizontal gene transfer (conjugation, outer membrane vesicle-mediated transfer, transformation, and transduction), conjugation could be ruled out, since strain R2090 lacks any plasmid, and a type IV secretion system is not encoded in its chromosome. However, strain R2090 possesses three putative prophages, two of which were predicted to be complete and therefore functional. Accordingly, it was supposed that the transfer of the resistance gene region from the clinical isolate R2090 to the recipient occurred by general transduction facilitated by one of the prophages present in the R2090 genome. Hence, phage-mediated transduction has to be taken into account for the dissemination of antibiotic resistance genes within the species A. baumannii.

| S-EPMC4862468 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data