Genetic and Phenotypic Characterization of the Novel Metallo-β-Lactamase NDM-29 From Escherichia coli

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 blaNDM–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 blaNDM–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 blaNDM–1, blaNDM–29, located on pNC225-NDM-29, carries a G388A (D130N) mutation. The region harboring blaNDM–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.

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Phenotypic and genotypic characterization of multidrug-resistant Acinetobacter baumannii isolated in Algerian hospitals

The Journal of Infection in Developing Countries ◽

10.3855/jidc.12348 ◽

2020 ◽

Vol 14 (12) ◽

pp. 1395-1401

Author(s):

Nabila Benamrouche ◽

Ourida Lafer ◽

Lahcen Benmahdi ◽

Akila Benslimani ◽

Wahiba Amhis ◽

...

Keyword(s):

Drug Resistance ◽

Intensive Care ◽

Acinetobacter Baumannii ◽

Multidrug Resistant ◽

Phenotypic Characterization ◽

Resistant Strains ◽

Almost All ◽

Encoding Genes ◽

Phenotypic And Genotypic Characterization

Introduction: The aim of this study was to investigate the drug-resistance and the molecular characterization of carbapenemases, ESBL, and aminoglycoside-modifying enzymes among Acinetobacter baumannii clinical isolates in Algerian hospitals. Methodology: A total of 92 A. baumannii isolates were collected between 2012 and 2016. Antimicrobial susceptibility testings were performed for β-lactams, aminoglycosides, fluoroquinolones, trimethoprim-sulfamethoxazole, rifampicin and colistin. The phenotypic characterization of β-lactamases was investigated. For 30 randomly targeted strains, the carriage of the carbapenemases, ESBL and aminoglycoside-modifying enzymes -encoding genes was determined by PCR. Sequencing was carried out for carbapenemases and ESBL genes. Results: Most of the 92 isolates studied were recovered from hospitalized patients (93.5%) and were mainly from intensive care units (51.1%) and orthopedics (19.6%). The strains were collected primarily from low respiratory tract (33.7%), wounds (23.9%) and urine (16.3%). Multidrug-resistant A. baumannii strains were prevalent (96.7%). High rates of resistance were observed for almost all antibiotics tested (>70%) excluding rifampicin (7.6%) and colistin (5.4%). For the five colistin-resistant strains, MICs ranged between 4 and 128 µg/mL. Positive MBL (83.7%) and ESBL (23.9%) strains were identified. Regarding β-lactams, the blaNDM and both blaSHV and blaCTX-M1 genes were detected in five and two strains respectively. Sequencing of the genes revealed the presence of blaNDM-1, blaCTX-M-15, and blaSHV-33. For aminoglycosides, aac(6’)-Ib, ant(2’’)-I and aph(3’)-VI genes were detected in three, seven and six strains respectively. Conclusions: Here, we report the first co-occurrence of extended-spectrum β-lactamases SHV-33 and CTX-M-15, the carbapenemase NDM-1 and the emergence of colistin-resistant A. baumannii in Algerian hospitals.

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Corrigendum: Genetic and Phenotypic Characterization of the Novel Metallo-β-Lactamase NDM-29 From Escherichia coli

Frontiers in Microbiology ◽

10.3389/fmicb.2021.795790 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ying Zhu ◽

Xinmiao Jia ◽

Peiyao Jia ◽

Xue Li ◽

Qiwen Yang

Keyword(s):

Escherichia Coli ◽

Phenotypic Characterization ◽

The Novel

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Phenotypic Characterization of Escherichia coli Isolated from Broiler Chiken

Suez Canal Veterinary Medicine Journal. SCVMJ ◽

10.21608/scvmj.2019.57368 ◽

2019 ◽

Vol 24 (1) ◽

pp. 1-12

Keyword(s):

Escherichia Coli ◽

Phenotypic Characterization

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Genome characterization of ESBL-producing multidrug-resistant Escherichia coli in Rabat, Morocco

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2021.07.008 ◽

2021 ◽

Author(s):

Jérôme Ambroise ◽

Elmostafa Benaissa ◽

Léonid M. Irenge ◽

EL Mehdi Belouad ◽

Bertrand Bearzatto ◽

...

Keyword(s):

Escherichia Coli ◽

Multidrug Resistant ◽

Genome Characterization

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Characterization of novel ybjG and dacC variants in Escherichia coli

Journal of Medical Microbiology ◽

10.1099/jmm.0.062893-0 ◽

2013 ◽

Vol 62 (11) ◽

pp. 1728-1734 ◽

Cited By ~ 4

Author(s):

Dongguo Wang ◽

Enping Hu ◽

Jiayu Chen ◽

Xiulin Tao ◽

Katelyn Gutierrez ◽

...

Keyword(s):

Escherichia Coli ◽

Multiple Drug Resistance ◽

Multiple Drug ◽

The Novel ◽

Conventional Pcr ◽

E Coli ◽

Novel Variants ◽

Restriction Sites ◽

Genetic Structures

A total of 69 strains of Escherichia coli from patients in the Taizhou Municipal Hospital, China, were isolated, and 11 strains were identified that were resistant to bacitracin, chloramphenicol, tetracycline and erythromycin. These strains were PCR positive for at least two out of three genes, ybjG, dacC and mdfA, by gene mapping with conventional PCR detection. Conjugation experiments demonstrated that these genes existed in plasmids that conferred resistance. Novel ybjG and dacC variants were isolated from E. coli strains EC2163 and EC2347, which were obtained from the sputum of intensive care unit patients. Genetic mapping showed that the genes were located on 8200 kb plasmid regions flanked by EcoRI restriction sites. Three distinct genetic structures were identified among the 11 PCR-positive strains of E. coli, and two contained the novel ybjG and dacC variants. The putative amino acid differences in the ybjG and dacC gene variants were characterized. These results provide evidence for novel variants of ybjG and dacC, and suggest that multiple drug resistance in hospital strains of E. coli depends on the synergistic function of ybjG, dacC and mdfA within three distinct genetic structures in conjugative plasmids.

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Molecular Characterization of Plasmid-Mediated Non-O157 Verotoxigenic Escherichia coli Isolated from Infants and Children with Diarrhea

Baghdad Science Journal ◽

10.21123/bsj.2020.17.3.0710 ◽

2020 ◽

Vol 17 (3) ◽

pp. 0710

Author(s):

Md Fazlul Karim Khan ◽

Shah Samiur Rashid

Keyword(s):

Escherichia Coli ◽

Virulence Gene ◽

Multidrug Resistant ◽

Plasmid Curing ◽

Health Issues ◽

E Coli ◽

Disk Diffusion Assay ◽

Microbiological Techniques ◽

Polymerase Chain

A significant increase in the incidence of non-O157 verotoxigenic Escherichia coli (VTEC) infections have become a serious health issues, and this situation is worsening due to the dissemination of plasmid mediated multidrug-resistant microorganisms worldwide. This study aims to investigate the presence of plasmid-mediated verotoxin gene in non-O157 E. coli. Standard microbiological techniques identified a total of 137 E. coli isolates. The plasmid was detected by Perfectprep Plasmid Mini preparation kit. These isolates were subjected to disk diffusion assay, and plasmid curing with ethidium bromide treatment. The plasmid containing isolates were subjected to a polymerase chain reaction (PCR) for investigating the presence of plasmid mediated verotoxin gene (VT1 and VT2) in non-O157 E. coli. Among the 137 E. coli isolates, 49 isolates were non-O157 E. coli while 29 (59.1%) isolates were verotoxin producing non-O157 serotypes and 26 non-O157 VTEC isolates possessed plasmids. Certain isolates harboured single sized plasmid while others had multiple plasmids with different size varied from 1.8kb to 7.6kb. A plasmid containing all (100%) the isolates was multidrug-resistant. Eight isolates changed their susceptibility patterns while three isolates were found to lose plasmid after post plasmid curing treatment and the rest of the isolates (15) remained constant. Different PCR sets characterized 3 plasmid-mediated verotoxins producing non-O157 E. coli. This current study demonstrated the occurrence of plasmid mediated verotoxin gene in non-O157 E. coli. To the best of our knowledge, this is the first report in the global literature on plasmid-mediated verotoxin gene in non-O157 E. coli. Timely diagnosis and surveillance of VTEC infections should prioritize to stop or slow down the virulence gene for dissemination by plasmid-mediated gene transfer amongst the same bacteria or other species.

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Genomic Characterization of A Multidrug-resistant Citrobacter freundii Strain ZT01-0079 Co-Producing blaNDM-1 and blaSHV-12 using MiSeq and MinION

10.21203/rs.3.rs-92305/v1 ◽

2020 ◽

Author(s):

Tingyan Zhang ◽

Yanfeng Lin ◽

Zhonghong Li ◽

Xiong Liu ◽

Jinhui Li ◽

...

Keyword(s):

Resistance Genes ◽

Southern Blotting ◽

Multiple Drug Resistance ◽

Carbapenem Resistance ◽

Multidrug Resistant ◽

Multiple Drug ◽

Citrobacter Freundii ◽

Rapid Spread ◽

Genomic Characterization

Abstract Background: The emergence of multi-drug resistant Citrobacter freundii poses daunting challenges to the treatment of clinical infections. The purpose of this study was to characterize the genome of a C. freundii strain with an IncX3 plasmid encoding both the blaNDM-1 and blaSHV-12 genes.Methods: Strain ZT01-0079 was isolated from a clinical urine sample. The Vitek2 system was used for identification and antimicrobial susceptibility testing. The presence of blaNDM-1 was detected by PCR and sequencing. Conjugation experiments and Southern blotting were performed to determine the transferability of the blaNDM-1- carrying plasmid. Nanopore and Illumina sequencing were performed to better understand the genomic characteristics of the strain.Results: Strain ZT01-0079 was identified as C. freundii, and the coexistence of blaNDM-1 and multiple drug resistance genes was confirmed. Electrophoresis and Southern blotting showed that blaNDM-1 was located on a ~53kb IncX3 plasmid. The NDM-1-encoding plasmid was successfully transferred at a frequency of 1.68×10−3. Both blaNDM-1 and blaSHV-12 were located on the self-transferable IncX3 plasmid.Conclusion: The rapid spread of the IncX3 plasmid highlights the importance of continuous monitoring of the prevalence of NDM-1-encoding Enterobacteriaceae. Mutations of existing carbapenem resistance genes will bring formidable challenges to clinical treatment.

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