Identification and Characterization of ten Escherichia coli Strains Encoding Novel Shiga Toxin 2 Subtypes, Stx2n as Well as Stx2j, Stx2m, and Stx2o, in the United States
-
Published:2023-10-14
Issue:10
Volume:11
Page:2561
-
ISSN:2076-2607
-
Container-title:Microorganisms
-
language:en
-
Short-container-title:Microorganisms
Author:
Lindsey Rebecca L.1ORCID, Prasad Arjun2ORCID, Feldgarden Michael2, Gonzalez-Escalona Narjol3ORCID, Kapsak Curtis1ORCID, Klimke William2, Melton-Celsa Angela4ORCID, Smith Peyton1, Souvorov Alexandre2, Truong Jenny5ORCID, Scheutz Flemming6ORCID
Affiliation:
1. Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA 2. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA 3. Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA 4. Department of Microbiology and Immunology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20184, USA 5. Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA 6. The International Escherichia and Klebsiella Centre, Statens Serum Institut, 2300 Copenhagen, Denmark
Abstract
The sharing of genome sequences in online data repositories allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as the development of improved detection methods. Here, we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j, one Stx2m strain, and one Stx2o, were all analyzed for variability from the originally described subtypes. Complete genome sequences were assembled from short- or long-read sequencing and analyzed for serotype, and ST types. The WGS data from Stx2n- and Stx2o-producing STEC strains were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data were used to design OMNI PCR primers for the detection of all known stx1 (283 bp amplicon), stx2 (400 bp amplicon), intimin encoded by eae (221 bp amplicon), and stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. An analysis of the complete genome sequence showed variability in serogroup, virulence genes, and ST type, and Stx2 pro-phages showed variability in size, gene composition, and phage insertion sites. The strains with Stx2j, Stx2m, Stx2n, and Stx2o showed toxicity to Vero cells. Stx2j carrying strain, 2012C-4221, was induced when grown with sub-inhibitory concentrations of ciprofloxacin, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact on public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain.
Funder
Advanced Molecular Detection (AMD) Initiative National Library of Medicine National Institute of Allergy and Infectious Disease National Institutes of Health European Union’s Horizon 2020 research and innovation programme FDA Foods Program Intramural Funds
Subject
Virology,Microbiology (medical),Microbiology
Reference40 articles.
1. Gill, A., Dussault, F., McMahon, T., Petronella, N., Wang, X., Cebelinski, E., Scheutz, F., Weedmark, K., Blais, B., and Carrillo, C. (2022). Characterization of Atypical Shiga Toxin Gene Sequences and Description of Stx2j, a New Subtype. J. Clin. Microbiol., 60. 2. Bai, X., Scheutz, F., Dahlgren, H.M., Hedenstrom, I., and Jernberg, C. (2021). Characterization of Clinical Escherichia coli Strains Producing a Novel Shiga Toxin 2 Subtype in Sweden and Denmark. Microorganisms, 9. 3. European Food Safety Authority, and European Centre for Disease Prevention and Control (2021). The European Union One Health 2020 Zoonoses Report. EFSA J., 19, e06971. 4. Multicenter evaluation of a sequence-based protocol for subtyping Shiga toxins and standardizing Stx nomenclature;Scheutz;J. Clin. Microbiol.,2012 5. Identification and pathogenomic analysis of an Escherichia coli strain producing a novel Shiga toxin 2 subtype;Bai;Sci. Rep.,2018
Cited by
2 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|