scholarly journals Publisher Correction: Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC)

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Astrid von Mentzer ◽  
Joshua Tobias ◽  
Gudrun Wiklund ◽  
Stefan Nordqvist ◽  
Martin Aslett ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterotoxigenic Escherichia Coli ◽  
Whole Genome ◽  
The Novel ◽  
Colonization Factor ◽  
Identification And Characterization

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 Ornithobacterium rhinotracheale: MALDI-TOF MS and Whole Genome Sequencing Confirm That Serotypes K, L and M Deviate from Well-Known Reference Strains and Numerous Field Isolates

2021 ◽  
Vol 9 (5) ◽  
pp. 1006
Author(s):  
Merima Alispahic ◽  
Lukas Endler ◽  
Michael Hess ◽  
Claudia Hess
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Identification And Characterization ◽  
Reference Strains ◽  
Ornithobacterium Rhinotracheale ◽  
Tof Ms

Ornithobacterium rhinotracheale is one of the most important bacterial agents of respiratory diseases in poultry. For correct identification and characterization of this fastidious bacterium, reliable diagnostic tools are essential. Still, phenotypic tests are used to identify O. rhinotracheale and serotyping is the most common method for characterization, despite known drawbacks and disadvantages such as divergent results, cross-reactivity between strains, or the non-typeability of strains. The intention of the present study was to evaluate MALDI-TOF MS and whole genome sequencing for the identification and characterization of O. rhinotracheale. For this purpose, a selection of 59 well-defined reference strains and 47 field strains derived from outbreaks on Austrian turkey farms were investigated by MALDI-TOF MS. The field strains originated from different geographical areas in Austria with some of the isolates derived from multiple outbreaks on farms within a year, or recurrent outbreaks over several years. MALDI-TOF MS proved a suitable method for identification of O. rhinotracheale to genus or species level except for 3 strains representing serotypes M, K and F. Phylogenetic analysis showed that most strains grouped within one cluster even though they were comprised of different serotypes, while serotypes F, K, and M clearly formed a different cluster. All field isolates from turkey farms clustered together, independent of the origin of the isolates, e.g., geographical area, multiple outbreaks within a year or recurrent outbreaks over several years. Whole genome sequencing of serotype M, K and F strains confirmed the extraordinary status and deviation from known fully-sequenced strains due to a lack of sequence similarity. This was further confirmed by alignments of single genes (16S-RNA and rpoB) and multilocus sequence typing although the demarcation was less obvious. Altogether, the results indicate that these three serotypes belong to a different species than O. rhinotracheale, and might even be members of multiple new species.

scholarly journals First Report of OXA-181-Producing Escherichia coli in China and Characterization of the Isolate Using Whole-Genome Sequencing

2015 ◽  
Vol 59 (8) ◽  
pp. 5022-5025 ◽  
Author(s):  
Yanbin Liu ◽  
Yu Feng ◽  
Wenjing Wu ◽  
Yi Xie ◽  
Xiaohui Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
Chinese Patient ◽  
Sequence Type ◽  
Whole Genome ◽  
Travel History ◽  
Content Type

ABSTRACTWe report the first OXA-181-producing strain in China.blaOXA-181was found in sequence type 410 (ST410)Escherichia colistrain WCHEC14828 from a Chinese patient without recent travel history. Genome sequencing and conjugation experiments were performed.blaOXA-181was carried on a 51-kb self-transmissible IncX3 plasmid and was linked withqnrS1, a quinolone resistance gene.blaOXA-181was introduced onto the IncX3 plasmid from a ColE2-type plasmid, and IncX3 plasmids have the potential to mediate the dissemination ofblaOXA-181.

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