Characterization of Carbapenem-Resistant Escherichia coli Isolates Through the Whole-Genome Sequencing Analysis

2018 ◽  
Vol 24 (2) ◽  
pp. 175-180 ◽  
Author(s):  
Yanping Luo ◽  
Rong Luo ◽  
Hong Ding ◽  
Xiu Ren ◽  
Haipeng Luo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Carbapenem Resistant

scholarly journals Characterization of SXT/R391 Integrative and Conjugative Elements in Proteus mirabilis Isolates from Food-Producing Animals in China

2016 ◽  
Vol 60 (3) ◽  
pp. 1935-1938 ◽  
Author(s):  
Chang-Wei Lei ◽  
An-Yun Zhang ◽  
Hong-Ning Wang ◽  
Bi-Hui Liu ◽  
Li-Qin Yang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Proteus Mirabilis ◽  
Whole Genome ◽  
Content Type ◽  
Integrative And Conjugative Elements ◽  
Animal Farms

SXT/R391 integrative and conjugative elements (ICEs) were detected in 8 out of 125Proteus mirabilisisolates from food-producing animals in China. Whole-genome sequencing revealed that seven ICEs were identical to ICEPmiJpn1, carrying the cephalosporinase geneblaCMY-2. Another one, designated ICEPmiChn1, carried five resistance genes. All eight ICEs could be transferred toEscherichia colivia conjugation. The results highlight the idea that animal farms are important reservoir of the SXT/R391 ICE-containingP. mirabilis.

scholarly journals Whole Genome Sequencing Characterization of Shiga Toxin–Producing Escherichia coli Isolated from Flour from Swiss Retail Markets

2019 ◽  
Vol 82 (8) ◽  
pp. 1398-1404 ◽  
Author(s):  
RENATE BOSS ◽  
JOERG HUMMERJOHANN
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Shiga Toxin ◽  
Severe Disease ◽  
Virulence Gene ◽  
Whole Genome ◽  
N 93 ◽  
Human Infections

ABSTRACT Shiga toxin–producing Escherichia coli (STEC) strains are often found in food and cause human infections. Although STEC O157:H7 is most often responsible for human disease, various non-O157 subtypes have caused individual human infections or outbreaks. The importance of STEC serogroup typing is decreasing while detection of virulence gene patterns has become more relevant. Whole genome sequencing (WGS) reveals the entire spectrum of pathogen information, such as toxin variant, serotype, sequence type, and virulence factors. Flour has not been considered as a vector for STEC; however, this product has been associated with several STEC outbreaks in the last decade. Flour is a natural product, and milling does not include a germ-reducing step. Flour is rarely eaten raw, but the risks associated with the consumption of unbaked dough are probably underestimated. The aim of this study was to determine the prevalence of STEC in flour samples (n = 93) collected from Swiss markets and to fully characterize the isolates by PCR assay and WGS. The prevalence of STEC in these flour samples was 10.8% as indicated by PCR, and a total of 10 STEC strains were isolated (two flour samples were positive for two STEC subtypes). We found one stx2-positve STEC isolate belonging to the classic serogroups frequently associated with outbreaks that could potentially cause severe disease. However, we also found several other common or less common STEC subtypes with diverse virulence patterns. Our results reveal the benefits of WGS as a characterization tool and that flour is a potentially and probably underestimated source for STEC infections in humans.

scholarly journals Whole-Genome Sequencing Analysis of a stx-Negative Escherichia coli O63:H6 Isolate Associated with Hemolytic Uremic Syndrome

Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1823
Author(s):  
Tae Yeul Kim ◽  
Tae-Min La ◽  
Taesoo Kim ◽  
Sun Ae Yun ◽  
Sang-Won Lee ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Hemolytic Uremic Syndrome ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Virulence Gene ◽  
Enterohemorrhagic Escherichia Coli ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
E Coli ◽  
Uremic Syndrome

Shiga toxin-encoding genes (stx) of enterohemorrhagic Escherichia coli (EHEC) can be lost during infection or in vitro cultivation, and in clinical practice, it is difficult to distinguish EHEC that have lost stx (EHEC-LST) from enteropathogenic E. coli (EPEC), as both are stx-negative and eae-positive. In this study, we performed whole-genome sequencing (WGS) of a stx-negative, eae-positive E. coli O63:H6 isolate from a child with hemolytic uremic syndrome and compared its genome with those of nine E. coli O63:H6 strains in public databases. Virulence gene profiles were analyzed and core-genome multilocus sequence typing (cgMLST) was conducted. The virulence gene profile of our isolate was consistent with EHEC, except for the absence of stx, and the isolate clustered with seven EHEC strains but was distant from two EPEC strains in cgMLST. In genome alignment, our isolate exhibited a high nucleotide identity with EHEC strain 377323_2f but displayed a gap corresponding to the stx-harboring prophage sequence. Overall, our isolate was genetically closely related to EHEC strains, consistent with this being an EHEC-LST strain. As EHEC-LST may be misdiagnosed as EPEC in routine laboratories, comparative genomic analysis using WGS can be useful to determine whether stx-negative and eae-positive isolates are EHEC-LST or EPEC.

scholarly journals Polyclonal dissemination of NDM-1- and NDM-9-producing Escherichia coli and Klebsiella pneumoniae in French Polynesia

2021 ◽  
Author(s):  
Saoussen Oueslati ◽  
Cécile Emeraud ◽  
Victor Grosperrin ◽  
Marc Levy ◽  
Garance Cotellon ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Potential Risk ◽  
French Polynesia ◽  
Foreign Country ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
E Coli

The whole genome sequencing analysis revealed a polyclonal dissemination of NDM-1 and NDM-9 variants in E. coli (n=20) and K. pneumoniae (n=2) in Tahiti since 2015 via interspecies transfer of three different blaNDM-carrying plasmids (IncR, IncHI2 and IncF) and patient-to-patient cross-transmissions. It highlights the potential risk of importation of NDM producers in France where French Polynesia is not considered stricto senso as a foreign country from which repatriated patients have to be screened.

scholarly journals MCR-1 and OXA-48 In Vivo Acquisition in KPC-Producing Escherichia coli after Colistin Treatment

2017 ◽  
Vol 61 (8) ◽  
Author(s):  
Racha Beyrouthy ◽  
Frederic Robin ◽  
Aude Lessene ◽  
Igor Lacombat ◽  
Laurent Dortet ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Content Type ◽  
First Report ◽  
E Coli ◽  
Carbapenem Resistant

ABSTRACT The spread of mcr-1-encoding plasmids into carbapenem-resistant Enterobacteriaceae raises concerns about the emergence of untreatable bacteria. We report the acquisition of mcr-1 in a carbapenem-resistant Escherichia coli strain after a 3-week course of colistin in a patient repatriated to France from Portugal. Whole-genome sequencing revealed that the Klebsiella pneumoniae carbapenemase-producing E. coli strain acquired two plasmids, an IncL OXA-48-encoding plasmid and an IncX4 mcr-1-encoding plasmid. This is the first report of mcr-1 in carbapenemase-encoding bacteria in France.

Sign in / Sign up

Export Citation Format

Share Document