Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Biochemical analysis of metallo-?-lactamase NDM-3 from a multidrug-resistant Escherichia coli strain isolated in Japan.

ABSTRACT: New Delhi metallo-?-lactamase-3 (NDM-3) was identified in a multidrug-resistant Escherichia coli isolate, NCGM77, obtained from the feces of a patient in Japan. The enzymatic activities of NDM-3 against ?-lactams were similar to those of NDM-1, although NDM-3 showed slightly lower kcat/Km ratios for all the ?-lactams tested except for doripenem. The genetic context for blaNDM-3 was tnpA-blaNDM-3-bleMBL-trpF-dsbC-tnpA-sulI-qacEdeltaI-aadA2-dfrA1, which was present on an approximately 250-kb plasmid.

SUBMITTER: Tada T

PROVIDER: S-EPMC4068495 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Biochemical analysis of metallo-β-lactamase NDM-3 from a multidrug-resistant Escherichia coli strain isolated in Japan.

Tada Tatsuya T Miyoshi-Akiyama Tohru T Shimada Kayo K Kirikae Teruo T

Antimicrobial agents and chemotherapy 20140331 6

New Delhi metallo-β-lactamase-3 (NDM-3) was identified in a multidrug-resistant Escherichia coli isolate, NCGM77, obtained from the feces of a patient in Japan. The enzymatic activities of NDM-3 against β-lactams were similar to those of NDM-1, although NDM-3 showed slightly lower kcat/Km ratios for all the β-lactams tested except for doripenem. The genetic context for blaNDM-3 was tnpA-blaNDM-3-bleMBL-trpF-dsbC-tnpA-sulI-qacEdeltaI-aadA2-dfrA1, which was present on an approximately 250-kb plasm ...[more]

PMID: 24687501

Similar Datasets

NDM-8 metallo-β-lactamase in a multidrug-resistant Escherichia coli strain isolated in Nepal.

Project description:A novel metallo-β-lactamase, NDM-8, was identified in a multidrug-resistant Escherichia coli isolate, IOMTU11 (NCGM37), obtained from the respiratory tract of a patient in Nepal. The amino acid sequence of NDM-8 has substitutions at positions 130 (Asp to Gly) and 154 (Met to Leu) compared with NDM-1. NDM-8 showed enzymatic activities against β-lactams similar to those of NDM-1.

| S-EPMC3632942 | biostudies-literature

Emergence of metallo-?-lactamase NDM-1-producing multidrug-resistant Escherichia coli in Australia.

Project description:A multidrug-resistant Escherichia coli isolate recovered in Australia produced a carbapenem-hydrolyzing ?-lactamase. Molecular investigations revealed the first identification of the bla(NDM-1) metallo-?-lactamase gene in that country. In addition, this E. coli isolate expressed the extended-spectrum ?-lactamase CTX-M-15, together with two 16S rRNA methylases, namely, ArmA and RmtB, conferring a high level of resistance to aminoglycosides.

| S-EPMC2976126 | biostudies-literature

NDM-4 metallo-β-lactamase with increased carbapenemase activity from Escherichia coli.

Project description:A clinical Escherichia coli isolate resistant to all β-lactams, including carbapenems, expressed a novel metallo-β-lactamase (MBL), NDM-4, differing from NDM-1 by a single amino acid substitution (Met154Leu). NDM-4 possessed increased hydrolytic activity toward carbapenems and several cephalosporins compared to that of NDM-1. This amino acid substitution was not located in the known active sites of NDM-1, indicating that remote amino acid substitutions might also play a role in the extended activity of this MBL.

| S-EPMC3318389 | biostudies-literature

Emergence of Various NDM-Type-Metallo-?-Lactamase-Producing Escherichia coli Clinical Isolates in Nepal.

Project description:Of 250 clinical isolates of Escherichia coli obtained in Nepal, 38 were carbapenem resistant, with MICs of imipenem or meropenem of ?4 ?g/ml. All 38 isolates harbored the following blaNDMs: blaNDM-1, blaNDM-3, blaNDM-4, blaNDM-5, blaNDM-7, blaNDM-12, and blaNDM-13 Most of these isolates also harbored the 16S rRNA methylase gene(s) armA, rmtB, and/or rmtC.

| S-EPMC5700343 | biostudies-literature

Draft Genome Sequence of a Multidrug-Resistant New Delhi Metallo-?-Lactamase-1 (NDM-1)-Producing Escherichia coli Isolate Obtained in Singapore.

Project description:We report the draft genome sequence of a New Delhi metallo-?-lactamase-1 (NDM-1)-positive Escherichia coli isolate obtained from a surgical patient. The assembled data indicate the presence of 3 multidrug resistance plasmids, 1 of which shares 100% identity with an NDM-1 plasmid isolated previously from a nearby hospital, suggesting possible local transmission.

| S-EPMC3868851 | biostudies-literature

Identification of a New Delhi metallo-?-lactamase-4 (NDM-4)-producing Escherichia coli in Italy.

Project description:BACKGROUND: During June-July 2012, six imipenem-resistant Escherichia coli isolates were isolated from two patients hospitalized in a ward of one large tertiary-care hospital in Genoa, Italy. Genetic features associated with blaNDM-4 gene were investigated. RESULTS: The isolates exhibited the same PFGE profile and a multidrug-resistant (MDR) phenotype to aminoglycosides, fluoroquinolones, and ?-lactams. The strains produced the NDM-4 carbapenemase and the blaNDM-4 gene was part of the variable region of a class 1 integron. MLST analysis revealed that all isolates belonged to sequence type 405 (ST405). CONCLUSIONS: This is the first report on the emergence of an MDR strain of E.coli producing the NDM-4 MBL in Italy.

| S-EPMC4060580 | biostudies-literature

Novel Variant of New Delhi Metallo-β-lactamase, NDM-20, in <i>Escherichia coli</i>.

Project description:The spread of carbapenem-resistant Enterobacteriaceae (CRE) mediated by New Delhi metallo-β-lactamase (NDM) poses a serious challenge to clinicians and has become a major public health concern. NDM has been evolving into variants that possess different hydrolysis activity toward antibiotics, so as to affect treatment strategy. In addition, very few studies on NDM variants have focused on animal-derived bacterial isolates. Our study reports a novel NDM variant, NDM-20, in an isolate of Escherichia coli CCD1 recovered from the food animal swine in China. The isolate that was assigned to ST1114, exhibited high level resistance to all β-lactams tested, including aztreonam and carbapenems. The gene of blaNDM-20 was located on an IncX3-type plasmid, surrounded by multiple insertion sequences. Sequencing analysis demonstrated that blaNDM-20 contained three point mutations at positions 262 (G→T), 460 (A→C), and 809 (G→A), compared with blaNDM-1, and just one point mutation at position 809 (G→A), relative to blaNDM-5. Functional analysis revealed that the blaNDM-20 transformant, DH5α+pHSG398/NDM-20, exhibited a higher resistance to ertapenem than that of blaNDM-1 transformant DH5α+pHSG398/NDM-1. Kinetic parameter analysis showed that NDM-20 had increased enzymatic activity against some penicillins and cephalosporins but decreased carbapenemase activity relative to NDM-5. The identification of NDM-20 further confirms the evolution and prevalence of NDM variants in bacteria of food-animal origin.

| S-EPMC5826333 | biostudies-literature

Complete Genome Assembly of a Multidrug-Resistant New Delhi Metallo-?-Lactamase 1 (NDM-1)-Producing Escherichia coli Human Isolate from a New Zealand Hospital.

Project description:We report the complete genome of a multidrug-resistant Escherichia coli strain isolated from a New Zealand patient with a history of hospitalization in India. The strain, carrying eight plasmids, harbors chromosome-encoded nfsA and nfsB mutations, which cause nitrofuran resistance, and class C ?-lactamase (bla EC) and plasmid-encoded bla NDM-1, bla CTX-M-15, and bla CMY-6, as well as other antibiotic resistance genes.

| S-EPMC7441242 | biostudies-literature

Genetic and Phenotypic Characterization of the Novel Metallo-β-Lactamase NDM-29 From <i>Escherichia coli</i>.

Project description:Objectives: The New Delhi metallo-β-lactamase (NDM) can hydrolyze almost all clinically available β-lactam antibiotics and has widely spread all over the world. NDM-29, a novel carbapenemase, was discovered in an Escherichia coli (19NC225) isolated from a patient with biliary tract infection in 2019 in China. Methods: Conjugation, transformation, cloning test, fitness cost, PacBio Sequel, and Illumina sequencing were performed to analyze the genetic and phenotypic characterization of bla NDM-29. Results: The susceptibility testing results showed 19NC225 was resistant to cephalosporins, carbapenems, combinations of β-lactam and β-lactamase inhibitors, and levofloxacin. Conjugation and transformation were performed to verify the transferability of NDM-29-encoding plasmid, and cloning test was conducted to prove the function of bla NDM-29 to increase carbapenem resistance. Furthermore, fitness cost test confirmed that the presence of NDM-29 exerts no survival pressure on bacteria. PacBio Sequel and Illumina sequencing were performed to analyze the genetic characterization of 19NC225, which contains two plasmids (pNC225-TEM1B and pNC225-NDM-29). pNC225-NDM-29, exhibiting 99.96% identity and 100% coverage with pNDM-BTR (an IncN1 plasmid from an E. coli in urine specimen from Beijing in 2013), showed responsibility for the multidrug-resistant (MDR) phenotype. Compared with bla NDM-1, bla NDM-29, located on pNC225-NDM-29, carries a G388A (D130N) mutation. The region harboring bla NDM-29 is located in an ISKpn19-based transposon, and two Tn6292 remnants are symmetrically located upstream and downstream of the transposon. The sequence results also indicated several important virulence genes. Conclusion: The findings of the novel carbapenemase NDM-29 could pose a threat to the control of antimicrobial resistance and arouse attention about the mutation of bacteria.

| S-EPMC8511706 | biostudies-literature

Complete sequencing of pNDM-HK encoding NDM-1 carbapenemase from a multidrug-resistant Escherichia coli strain isolated in Hong Kong.

Project description:BackgroundThe emergence of plasmid-mediated carbapenemases, such as NDM-1 in Enterobacteriaceae is a major public health issue. Since they mediate resistance to virtually all β-lactam antibiotics and there is often co-resistance to other antibiotic classes, the therapeutic options for infections caused by these organisms are very limited.MethodologyWe characterized the first NDM-1 producing E. coli isolate recovered in Hong Kong. The plasmid encoding the metallo-β-lactamase gene was sequenced.Principal findingsThe plasmid, pNDM-HK readily transferred to E. coli J53 at high frequencies. It belongs to the broad host range IncL/M incompatibility group and is 88803 bp in size. Sequence alignment showed that pNDM-HK has a 55 kb backbone which shared 97% homology with pEL60 originating from the plant pathogen, Erwina amylovora in Lebanon and a 28.9 kb variable region. The plasmid backbone includes the mucAB genes mediating ultraviolet light resistance. The 28.9 kb region has a composite transposon-like structure which includes intact or truncated genes associated with resistance to β-lactams (bla(TEM-1), bla(NDM-1), Δbla(DHA-1)), aminoglycosides (aacC2, armA), sulphonamides (sul1) and macrolides (mel, mph2). It also harbors the following mobile elements: IS26, ISCR1, tnpU, tnpAcp2, tnpD, ΔtnpATn1 and insL. Certain blocks within the 28.9 kb variable region had homology with the corresponding sequences in the widely disseminated plasmids, pCTX-M3, pMUR050 and pKP048 originating from bacteria in Poland in 1996, in Spain in 2002 and in China in 2006, respectively.SignificanceThe genetic support of NDM-1 gene suggests that it has evolved through complex pathways. The association with broad host range plasmid and multiple mobile genetic elements explain its observed horizontal mobility in multiple bacterial taxa.

| S-EPMC3061923 | 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