Whole Genome Sequencing Analysis of Avian Pathogenic Escherichia coli from China

2021 ◽  
pp. 109158
Author(s):  
Xuhua Chen ◽  
Wenxing Liu ◽  
Huoming Li ◽  
Shigan Yan ◽  
Fengwei Jiang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Avian Pathogenic Escherichia Coli ◽  
Pathogenic Escherichia Coli

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.

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 The complete genome of carbapenem-resistant Escherichia coli ST410 harbored blaNDM-5 isolated from reservoir water in Singapore.

2021 ◽  
Author(s):  
Yang Zhong ◽  
Siyao Guo ◽  
Glendon Ong Hong Ming ◽  
Joergen Schlundt
Keyword(s):  
Escherichia Coli ◽  
Minimum Inhibitory Concentration ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Inhibitory Concentration ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Beta Lactamase ◽  
Reservoir Water ◽  
E Coli

Objective: Escherichia coli ST410 with blaNDM-5 has been increasingly detected as multidrug resistance pathogens globally, even though there are very few reports of infections caused by blaNDM-5 producing E. coli in Singapore. And significantly limit sequencing information of blaNDM-5 carried E .coli strain from Singapore. In 2018, our group obtained a carbapenem resistance E. coli ST410 strain SrichA-1 isolated from reservoir water in Singapore, determined to harbor the NDM-5 gene. (BioSample Accession: SAMN18579051). Methods: The susceptibility test to antimicrobials was performed with microdilution minimum inhibitory concentration (MIC) test and interpreted according to the Clinical And Laboratory Standards Institute (CLSI) -M100 standards. The genomic DNA of this strain was extracted and send for Whole-genome sequencing(WGS) with the Illumina platform. The WGS analysis was processed with the Center for Genomic Epidemiology (CGE, DTU) server. Results: During the minimum inhibitory concentration (MIC) test, SrichA-1 has shown strong resistance to all the beta-lactams, including cephalosporin and carbapenem, which can not be inhibited by the clavulanic acid. Further whole genome sequencing analysis has shown that the strain harboring five beta-lactamase genes covers all class A to D, including the carbapenemase genes as blaNDM-5. Conclusion: Here, we reported the complete chromosome sequence of this isolate as well as the sequence of a cycler plasmid. The pSGNDM-5 plasmid was furtherly identified to carry four beta-lactamase genes, including blaNDM-5, blaCTX-M-15, blaTEM-1B, blaOXA-1, while a blaCMY-2 was detected to be located on the chromosome.

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