Genomic Characterization of Escherichia coli O8 Strains Producing Shiga Toxin 2l Subtype

Yang, Xi; Liu, Qian; Sun, Hui; Xiong, Yanwen; Matussek, Andreas; Bai, Xiangning

doi:10.3390/microorganisms10061245

Cited by 10 publications

(4 citation statements)

References 23 publications

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“…Reclassified for stecodeDB AM904726 (stx2l) Reclassified from stx2e to stx2l as previously noted. (7,24) Sequences trimmed AM939642 (stx2e) Not currently in STECfinder version 1.1.0 (7) ERR4297034 (stx2m) [b] Not currently in STECfinder version 1.1.0 (9) ERR4297035 (stx2m) [b]…”

Section: Table 1: Modifications Made To the Stecfinder Database For U...mentioning

confidence: 99%

STECode: an automated virulence barcode generator to aid clinical and public health risk assessment of Shiga toxin-producingEscherichia coli

Sim,

Fong,

Suster

et al. 2024

Preprint

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Shiga Toxin (Stx) producingEscherichia coli(STEC) is a subset of pathogenicE. colithat can produce two types of Stx, Stx1 and Stx2, which can be further subtyped into four and 15 subtypes respectively. Not all subtypes, however, are equal in virulence potential, and the risk of severe disease including haemolytic uraemic syndrome has been linked to certain Stx2 subtypes e.g. Stx2a, Stx2d, highlighting the importance to surveystxsubtypes. Previously, we developed a STEC virulence barcode to capture pertinent information on virulence genes to infer pathogenic potential. However, the process required multiple manual curation steps to determine the barcode. Here we introduce STECode, a bioinformatic tool to automate the STEC virulence barcode generation from sequencing reads or genomic assemblies. The development, and validation of STECode is described using a set of publicly available completed STEC genomes, along with their corresponding short reads. STECode was applied to interrogate the virulence landscape and molecular epidemiology of human STEC isolated during the period of the international border closures related to COVID-19 in the state of New South Wales, Australia.

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Section: Table 1: Modifications Made To the Stecfinder Database For U...mentioning

confidence: 99%

STECode: an automated virulence barcode generator to aid clinical and public health risk assessment of Shiga toxin-producingEscherichia coli

Sim,

Fong,

Suster

et al. 2024

Preprint

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“…Three different subtypes of stx1 and fourteen subtypes of stx2 have been described 4,5 . Therefore, we analyzed whether the most relevant Stx subtypes are detected by the assay.…”

Section: Detection Of Stx1 and Stx2 Subtypes Across Different Stec Se...mentioning

confidence: 99%

“…So far, Stx subtypes Stx1a, Stx1c, and Stx1d and Stx2a-o are known in STEC (Tab. S1) 4,5 . Stx2 and the subtypes Stx2a, Stx2c, and Stx2d are most frequently associated with HUS and severe disease 6 .…”

Section: Introductionmentioning

confidence: 99%

Rapid enzymatic detection of Shigatoxin-producingE. coliusing fluorescence-labeled oligonucleotide substrates

Ramming,

Lang,

Hauf

et al. 2023

Preprint

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Shigatoxin-producingE. coli(STEC) are important human pathogens causing disease ranging from diarrhea to severe hemolytic uremic syndrome. As STEC are transmitted via animals, food, and water, and may produce large outbreaks, their timely and qualified detection including isolate recovery is of high importance, but challenging and labor-intense. Thus, the availability of an easy-to-perform rapid test would be a tremendous advance. Since the common feature and major virulence factor of otherwise multifaceted STEC is the Shiga toxin (Stx), we developed a detection method for Stx, specifically for its catalytic RNA-N-glycosidase activity targeting the Sarcin Ricin Loop (SRL) of 28S ribosomal RNA. To this end, synthetic ssDNA substrates mimicking the SRL were designed and linked to a fluorophore and quencher pair, which conferred a fluorescence signal after cleavage by Stx. Optimal results using bacterial culture supernatants or single colonies were achieved for substrateStxSense 4following 30 to 60 minutes incubation. Importantly, different Stx1 and Stx2 subtypes, diverse STEC serotypes, andShigellawere detected. In conclusion, the assay offers rapid and facile detection of STEC based on a real-time readout for Stx activity. Therefore, it may improve STEC risk evaluation, therapy decisions, outbreak and source detection, and simplify research for antimicrobials.

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“…The results showed that all the stx2l-STEC strains categorized to the O8 serogroup. stx2l-converting prophages from several sources shared a significant sequence similarity and structure [154].…”

Section: Metagenomicsmentioning

confidence: 99%

The “Big Six”: Hidden Emerging Foodborne Bacterial Pathogens

et al. 2022

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Non-O157 Shiga toxin-producing Escherichia coli (STEC) are emerging serogroups that often result in diseases ranging from diarrhea to severe hemorrhagic colitis in humans. The most common non-O157 STEC are O26, O45, O103, O111, O121, and O145. These serogroups are known by the name “big six” because they cause severe illness and death in humans and the United States Department of Agriculture declared these serogroups as food contaminants. The lack of fast and efficient diagnostic methods exacerbates the public impact of the disease caused by these serogroups. Numerous outbreaks have been reported globally and most of these outbreaks were caused by ingestion of contaminated food or water as well as direct contact with reservoirs. Livestock harbor a variety of non-O157 STEC serovars that can contaminate meat and dairy products, or water sources when used for irrigation. Hence, effective control and prevention approaches are required to safeguard the public from infections. This review addresses the disease characteristics, reservoirs, the source of infections, the transmission of the disease, and major outbreaks associated with the six serogroups (“big six”) of non-O157 STEC encountered all over the globe.

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Genomic Characterization of Escherichia coli O8 Strains Producing Shiga Toxin 2l Subtype

Cited by 10 publications

References 23 publications

STECode: an automated virulence barcode generator to aid clinical and public health risk assessment of Shiga toxin-producingEscherichia coli

STECode: an automated virulence barcode generator to aid clinical and public health risk assessment of Shiga toxin-producingEscherichia coli

Rapid enzymatic detection of Shigatoxin-producingE. coliusing fluorescence-labeled oligonucleotide substrates

The “Big Six”: Hidden Emerging Foodborne Bacterial Pathogens

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