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Article ; Online: Portable Differential Detection of CTX-M ESBL Gene Variants,

Higgins, Owen / Chueiri, Alexandra / O'Connor, Louise / Lahiff, Sinéad / Burke, Liam / Morris, Dearbhaile / Pfeifer, Nicola Maria / Santamarina, Belén González / Berens, Christian / Menge, Christian / Caniça, Manuela / Manageiro, Vera / Kisand, Veljo / Hassan, Marwa M / Gardner, Brian / van Vliet, Arnoud H M / La Ragione, Roberto M / Gonzalez-Zorn, Bruno / Smith, Terry J

Microbiology spectrum

2022 Volume 11, Issue 1, Page(s) e0331622

Abstract: Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by ...

Abstract	Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by
MeSH term(s)	Humans ; Animals ; Swine ; Escherichia coli ; Escherichia coli Infections/diagnosis ; Escherichia coli Infections/veterinary ; Escherichia coli Infections/epidemiology ; beta-Lactamases/genetics ; Anti-Bacterial Agents ; Enterobacteriaceae/genetics ; DNA
Chemical Substances	beta-lactamase TEM-3 (EC 3.5.2.-) ; beta-lactamase CTX-2 (EC 3.5.2.-) ; beta-Lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents ; DNA (9007-49-2)
Language	English
Publishing date	2022-12-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.03316-22
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Article ; Online: Multicenter clinical comparative evaluation of Alinity m HIV-1 assay performance.

Braun, Patrick / Glass, Allison / Maree, Leana / Krügel, Maria / Pacenti, Monia / Onelia, Francesco / Gunson, Rory / Goldstein, Emily / Martínez-García, Laura / Galán, Juan-Carlos / Vilas, Alba / D'costa, Jodie / Sameer, Rizmina / Ehret, Robert / Knechten, Heribert / Naeth, Gudrun / Bouvier-Alias, Magali / Marlowe, Natalia / Palm, Michael J /

Joseph, Ajith M / Dhein, Jens / Reinhardt, Birgit / Pfeifer, Karin / Lucic, Danijela / Obermeier, Martin

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2020 Volume 129, Page(s) 104530

Abstract: ... performance of the Alinity m HIV-1 assay, which uses a dual target/dual probe design against highly conserved ... target regions of the HIV-1 genome and is run on the fully automated Alinity m platform.: Study design ... This was an international, multisite study that compared the diagnostic performance of the Alinity m HIV-1 ...

Abstract	Background: Accurate, rapid detection of HIV-1 RNA is critical for early diagnosis, treatment decision making, and long-term management of HIV-1 infection. Objective: We evaluated the diagnostic performance of the Alinity m HIV-1 assay, which uses a dual target/dual probe design against highly conserved target regions of the HIV-1 genome and is run on the fully automated Alinity m platform. Study design: This was an international, multisite study that compared the diagnostic performance of the Alinity m HIV-1 assay to four commercially available HIV-1 assays routinely used in nine independent clinical laboratories. Alinity m HIV-1 assay precision, detectability, and reproducibility was compared across four study sites. Results: The Alinity m HIV-1 assay produced comparable results to currently available HIV-1 assays (correlation coefficient >0.995), with an overall bias of -0.1 to 0.10 Log Conclusions: The Alinity m HIV-1 assay provides comparable diagnostic accuracy to current HIV-1 assays, and when run on the Alinity m system, has the capacity to shorten the time between diagnosis and treatment.
MeSH term(s)	HIV Infections ; HIV-1/genetics ; Humans ; RNA, Viral ; Reagent Kits, Diagnostic ; Reproducibility of Results ; Sensitivity and Specificity ; Viral Load
Chemical Substances	RNA, Viral ; Reagent Kits, Diagnostic
Language	English
Publishing date	2020-07-03
Publishing country	Netherlands
Document type	Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104530
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Article ; Online: Multicenter clinical evaluation of alinity m HBV assay performance.

Bonanzinga, Sara / Onelia, Francesco / Jackson, Kathy / Glass, Allison / Maree, Leana / Krügel, Mari / Pacenti, Monia / Gunson, Rory / Goldstein, Emily / García, Laura Martínez / Galán, Juan-Carlos / Vilas, Alba / Ehret, Robert / Knechten, Heribert / Naeth, Gudrun / Braun, Patrick / Obermeier, Martin / Marlowe, Natalia / Palm, Michael J /

Pfeifer, Karin / Joseph, Ajith M / Dhein, Jens / Reinhardt, Birgit / Lucic, Danijela / Chevaliez, Stéphane

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2020 Volume 129, Page(s) 104514

Abstract: ... Objectives: We examined the clinical performance of the new Alinity m HBV assay, run on the fully automated ... continuous, random-access Alinity m platform, to accurately detect and quantify HBV DNA in a large series ... of the Alinity m HBV assay and compared its performance to four HBV assays currently in clinical use.: Results ...

Abstract	Background: Accurate molecular methods to detect and quantify hepatitis B virus (HBV) DNA are essential to diagnose chronic infections, guide treatment decisions, assess response to treatment, and determine risk of HBV-related complications. New generations of real-time HBV DNA assay platforms provide results in less than 2-3 h, with continuous loading of specimens and true random-access capability. Objectives: We examined the clinical performance of the new Alinity m HBV assay, run on the fully automated, continuous, random-access Alinity m platform, to accurately detect and quantify HBV DNA in a large series of patient samples infected with different HBV genotypes frequently encountered in clinical practice. Study design: This international, multisite study assessed the precision and reproducibility of the Alinity m HBV assay and compared its performance to four HBV assays currently in clinical use. Results: The Alinity m HBV assay demonstrated linear quantitation of HBV DNA in plasma samples, with high precision (coefficient of variation 4.1 %-8.8 %) and reproducibility. The Alinity m HBV assay showed excellent correlation (correlation coefficients ≥0.947) with comparator HBV assays, with an overall observed bias ranging from -0.07 to 0.17 Log Conclusions: The newly developed real-time PCR-based Alinity m HBV assay is sensitive, reproducible, and accurately quantifies HBV DNA levels from HBsAg-positive patients across the full dynamic range of quantification.
MeSH term(s)	DNA, Viral ; Hepatitis B ; Hepatitis B virus/genetics ; Humans ; Reproducibility of Results ; Sensitivity and Specificity ; Viral Load
Chemical Substances	DNA, Viral
Language	English
Publishing date	2020-07-03
Publishing country	Netherlands
Document type	Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104514
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Article ; Online: Multicenter clinical evaluation of alinity m HCV assay performance.

Chevaliez, Stéphane / Onelia, Francesco / Pacenti, Monia / Goldstein, Emily / Galán, Juan-Carlos / Martínez-García, Laura / Vilas, Alba / Glass, Allison / Maree, Leana / Krügel, Maria / Ehret, Robert / Knechten, Heribert / Braun, Patrick / Naeth, Gudrun / Bonanzinga, Sara / Jackson, Kathy / Abravaya, Klara / Dhein, Jens / Huang, Shihai /

Joseph, Ajith M / Lucic, Danijela / Marlowe, Natalia / Palm, Michael J / Pfeifer, Karin / Toolsie, Dan / Reinhardt, Birgit / Obermeier, Martin / Gunson, Rory

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2020 Volume 129, Page(s) 104531

Abstract: ... in the diagnosis of HCV infection and treatment monitoring. The Alinity m HCV assay was recently developed ... random-access Alinity m analyzer.: Objectives: Our study assessed the performance of the new Alinity m ... of the Alinity m HCV assay and its performance in comparison to three other HCV assays currently used in clinical ...

Abstract	Background: Nucleic acid testing is essential for the detection and quantification of HCV RNA in the diagnosis of HCV infection and treatment monitoring. The Alinity m HCV assay was recently developed by Abbott Molecular for rapid detection and quantification of HCV RNA on the fully automated, continuous, random-access Alinity m analyzer. Objectives: Our study assessed the performance of the new Alinity m HCV assay for detection and quantification of HCV RNA in a large series of patient samples of various genotypes. This international, multicentric study evaluated the linearity, precision, and reproducibility of the Alinity m HCV assay and its performance in comparison to three other HCV assays currently used in clinical practice. Results: The Alinity m HCV assay demonstrated high linearity (correlation coefficient r = 1.00), precision (coefficients of variation [CV] 6.6-13.5 %) and reproducibility (CV 1.7-4.3 % across three control lots). At a concentration near the lower limit of detection, the Alinity m HCV assay exhibited >98 % detectability. The Alinity m HCV assay showed excellent correlation with comparator HCV assays in serum (n = 406) and plasma (n = 1401) samples (correlation coefficients ≥0.96, bias 0.01 to 0.14 Log Conclusions: The newly developed Alinity m HCV assay is sensitive, reproducible, and accurately quantifies HCV RNA levels in serum and plasma samples from patients with chronic HCV infection, with no impact of HCV genotype on assay performance.
MeSH term(s)	Genotype ; Hepacivirus/genetics ; Hepatitis C ; Humans ; RNA, Viral ; Reproducibility of Results ; Sensitivity and Specificity ; Viral Load
Chemical Substances	RNA, Viral
Language	English
Publishing date	2020-07-03
Publishing country	Netherlands
Document type	Journal Article ; Multicenter Study
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104531
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Article ; Online: Portable Differential Detection of CTX-M ESBL Gene Variants, bla CTX-M-1 and bla CTX-M-15 , from Escherichia coli Isolates and Animal Fecal Samples Using Loop-Primer Endonuclease Cleavage Loop-Mediated Isothermal Amplification

Higgins, Owen / Chueiri, Alexandra / O'Connor, Louise / Lahiff, Sinéad / Burke, Liam / Morris, Dearbhaile / Pfeifer, Nicola Maria / Santamarina, Belén González / Berens, Christian / Menge, Christian / Caniça, Manuela / Manageiro, Vera / Kisand, Veljo / Hassan, Marwa M. / Gardner, Brian / van Vliet, Arnoud H. M. / La Ragione, Roberto M. / Gonzalez-Zorn, Bruno / Smith, Terry J.

2022

Abstract: Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced ... by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants ... CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and ...

Abstract	Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants, CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and human infection, respectively, and are an increasing antimicrobial resistance (AMR) global health concern. The blaCTX-M-1 and blaCTX-M-15 genes encoding these variants have an approximate nucleotide sequence similarity of 98.7%, making effective differential diagnostic monitoring difficult. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) enables rapid real-time multiplex pathogen detection with single-base specificity and portable on-site testing. We have developed an internally controlled multiplex CTX-M-1/15 LEC-LAMP assay for the differential detection of blaCTX-M-1 and blaCTX-M-15. Assay analytical specificity was established using a panel of human, animal, and environmental Escherichia coli isolates positive for blaCTX-M-1 (n = 18), blaCTX-M-15 (n = 35), and other closely related blaCTX-Ms (n = 38) from Ireland, Germany, and Portugal, with analytical sensitivity determined using probit regression analysis. Animal fecal sample testing using the CTX-M-1/15 LEC-LAMP assay in combination with a rapid DNA extraction protocol was carried out on porcine fecal samples previously confirmed to be PCR-positive for E. coli blaCTX-M. Portable instrumentation was used to further analyze each fecal sample and demonstrate the on-site testing capabilities of the LEC-LAMP assay with the rapid DNA extraction protocol. The CTX-M-1/15 LEC-LAMP assay demonstrated complete analytical specificity for the differential detection of both variants with sensitive low-level detection of 8.5 and 9.8 copies per reaction for blaCTX-M-1 and blaCTX-M-15, respectively, and E. coli blaCTX-M-1 was identified in all blaCTX-M positive porcine fecal samples tested. IMPORTANCE CTX-M ESBL-producing E. coli is an ...
Keywords	Text ; ddc:570 ; AMR -- CTX-M -- ESBL -- Enterobacteriaceae -- LAMP
Subject code	630
Language	English
Publishing date	2022-12-13
Publisher	American Society for Microbiology
Publishing country	de
Document type	Article ; Online
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Article: Whole Genome Sequence Analysis of CTX-M-15 Producing

Becker, Laura / Fuchs, Stephan / Pfeifer, Yvonne / Semmler, Torsten / Eckmanns, Tim / Korr, Gerit / Sissolak, Dagmar / Friedrichs, Michael / Zill, Edith / Tung, Mei-Lin / Dohle, Christian / Kaase, Martin / Gatermann, Sören / Rüssmann, Holger / Steglich, Matthias / Haller, Sebastian / Werner, Guido

Frontiers in microbiology

2018 Volume 9, Page(s) 322

Abstract: Extended-spectrum β-lactamase (ESBL) ... ...

Abstract	Extended-spectrum β-lactamase (ESBL) producing
Language	English
Publishing date	2018-02-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2018.00322
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Article ; Online: Murine Oncostatin M Has Opposing Effects on the Proliferation of OP9 Bone Marrow Stromal Cells and NIH/3T3 Fibroblasts Signaling through the OSMR.

Jakob, Lena / Müller, Tony Andreas / Rassner, Michael / Kleinfelder, Helen / Veratti, Pia / Mitschke, Jan / Miething, Cornelius / Oostendorp, Robert A J / Pfeifer, Dietmar / Waterhouse, Miguel / Duyster, Justus

International journal of molecular sciences

2021 Volume 22, Issue 21

Abstract: The IL-6 family cytokine Oncostatin M (OSM) is involved in cell development, growth, hematopoiesis ...

Abstract	The IL-6 family cytokine Oncostatin M (OSM) is involved in cell development, growth, hematopoiesis, inflammation, and cancer. Intriguingly, OSM has proliferative and antiproliferative effects depending on the target cell. The molecular mechanisms underlying these opposing effects are not fully understood. Previously, we found OSM upregulation in different myeloproliferative syndromes. However, OSM receptor (OSMR) expression was detected on stromal cells but not the malignant cells themselves. In the present study, we, therefore, investigated the effect of murine OSM (mOSM) on proliferation in stromal and fibroblast cell lines. We found that mOSM impairs the proliferation of bone marrow (BM) stromal cells, whereas fibroblasts responded to mOSM with increased proliferation. When we set out to reveal the mechanisms underlying these opposing effects, we detected increased expression of the OSM receptors OSMR and LIFR in stromal cells. Interestingly,
MeSH term(s)	Animals ; Cell Line ; Cell Proliferation ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Mesenchymal Stem Cells/cytology ; Mesenchymal Stem Cells/metabolism ; Mice ; NIH 3T3 Cells ; Oncostatin M/metabolism ; Oncostatin M Receptor beta Subunit/metabolism ; Signal Transduction
Chemical Substances	Oncostatin M Receptor beta Subunit ; Osm protein, mouse ; Osmr protein, mouse ; Oncostatin M (106956-32-5)
Language	English
Publishing date	2021-10-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222111649
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Article ; Audio / Video ; Online: Rapid detection and discrimination of closely related Enterobacteriaceae CTX-M group 1 variants, blaCTX-M-1 and blaCTX-M-15, using an internally controlled multiplex loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) assay

Higgins, Owen* / Chueiri, Alexandra / O'Connor, Louise / Burke, Liam / Morris, Dearbhaile / Hassan, Marwa M. / van Vliet, Arnoud H. M. / La Ragione, Roberto M. / Pfeifer, Nicola Maria / Santamarina, Belén González / Berens, Christian / Menge, Christian / Smith, Terry

2021

Keywords	Text ; abstract_or_summary ; ddc:570
Language	English
Publishing date	2021-04-28
Publishing country	de
Document type	Article ; Audio / Video ; Online
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Article ; Online: Third generation cephalosporin resistance in clinical nontyphoidal Salmonella enterica in Germany and emergence of blaCTX-M-harbouring pESI plasmids

Pietsch, Michael / Simon, Sandra / Meinen, Anika / Trost, Eva / Banerji, Sangeeta / Pfeifer, Yvonne / Flieger, Antje

2021

Abstract: ... cephalosporin resistance, and most prevalent were blaCTX-M-1 (n=55), blaCTX-M-14 (n=25), and blaCTX-M-65 (n=23). There was ... combinations were detected frequently, such as blaCTX-M-1 and blaCTX-M-65 in S. Infantis or blaCTX-M-14b in S ... variants, and a novel blaCTX-M-1harbouring plasmid. We conclude that third generation ...

Abstract	Non-typhoidal Salmonella enterica is an important gastrointestinal pathogen causing a considerable burden of disease. Resistance to third generation cephalosporins poses a serious threat for treatment of severe infections. In this study occurrence, phylogenetic relationship, and mechanisms of third generation cephalosporin resistance were investigated for clinical non-typhoidal S. enterica isolates in Germany. From 2017 to 2019, we detected 168 unique clinical S. enterica isolates with phenotypic resistance to third generation cephalosporins in a nation-wide surveillance. Compared to previous years, we observed a significant (P=0.0002) and consistent increase in resistant isolates from 0.41 % in 2005 to 1.71 % in 2019. In total, 34 different serovars were identified, most often S. Infantis (n=41; 24.4 %), S. Typhimurium (n=27; 16.1 %), S. Kentucky (n=21; 12.5 %), and S. Derby (n=17; 10.1 %). Whole genome analyses revealed extended-spectrum β-lactamase (ESBL) genes as main cause for third generation cephalosporin resistance, and most prevalent were blaCTX-M-1 (n=55), blaCTX-M-14 (n=25), and blaCTX-M-65 (n=23). There was no strict correlation between serovar, phylogenetic lineage, and ESBL type but some serovar/ESBL gene combinations were detected frequently, such as blaCTX-M-1 and blaCTX-M-65 in S. Infantis or blaCTX-M-14b in S. Kentucky. The ESBL genes were mainly located on plasmids, including IncI, IncA/C variants, emerging pESI variants, and a novel blaCTX-M-1harbouring plasmid. We conclude that third generation cephalosporin resistance is on the rise among clinical S. enterica isolates in Germany, and occurrence in various S. enterica serovars is most probably due to multiple acquisition events of plasmids. Peer Reviewed
Keywords	Salmonella enterica ; antibiotic resistance ; extended-spectrum β-lactamase (ESBL) ; plasmid ; pESI ; 610 Medizin und Gesundheit ; ddc:610
Language	English
Publishing date	2021-10-25
Publisher	Robert Koch-Institut
Publishing country	de
Document type	Article ; Online
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Article ; Online: Ultra-deep long-read sequencing detects IS-mediated gene duplications as a potential trigger to generate arrays of resistance genes and a mechanism to induce novel gene variants such as blaCTX-M-243.

Schuster, Christopher F / Weber, Robert E / Weig, Michael / Werner, Guido / Pfeifer, Yvonne

The Journal of antimicrobial chemotherapy

2021 Volume 77, Issue 2, Page(s) 381–390

Abstract: ... resistant to various β-lactam antibiotics. CTX-M-type enzymes are the most prevalent ESBLs and the main ... CTX-M types is continuously rising, currently comprising over 240 variants. During routine screening ... we identified a novel blaCTX-M gene.: Objectives: To characterize a novel blaCTX-M variant harboured ...

Abstract	Background: Extended-spectrum β-lactamases (ESBLs) are enzymes that can render their hosts resistant to various β-lactam antibiotics. CTX-M-type enzymes are the most prevalent ESBLs and the main cause of resistance to third-generation cephalosporins in Enterobacteriaceae. The number of described CTX-M types is continuously rising, currently comprising over 240 variants. During routine screening we identified a novel blaCTX-M gene. Objectives: To characterize a novel blaCTX-M variant harboured by a multidrug-resistant Escherichia coli isolate of sequence type ST354. Methods: Antibiotic susceptibilities were determined using broth microdilution. Genome and plasmid sequences were reconstructed using short- and long-read sequencing. The novel blaCTX-M locus was analysed using long-read and Sanger sequencing. Plasmid polymorphisms were determined in silico on a single plasmid molecule level. Results: The novel blaCTX-M-243 allele was discovered alongside a nearly identical blaCTX-M-104-containing gene array on a 219 kbp IncHI2A plasmid. CTX-M-243 differed from CTX-M-104 by only one amino acid substitution (N109S). Ultra-deep (2300-fold coverage) long-read sequencing revealed dynamic scaling of the blaCTX-M genetic contexts from one to five copies. Further antibiotic resistance genes such as blaTEM-1 also exhibited sequence heterogeneity but were stable in copy number. Conclusions: We identified the novel ESBL gene blaCTX-M-243 and illustrate a dynamic system of varying blaCTX-M copy numbers. Our results highlight the constant emergence of new CTX-M family enzymes and demonstrate a potential evolutionary platform to generate novel ESBL variants and possibly other antibiotic resistance genes.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/genetics ; Escherichia coli/genetics ; Gene Duplication ; Plasmids/genetics ; beta-Lactamases/genetics
Chemical Substances	Anti-Bacterial Agents ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2021-12-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkab407
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