Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 20, Number 4—April 2014
Letter

Whole-Genome Sequencing for Risk Assessment of Long-term Shiga Toxin–producing Escherichia coli

On This Page
Article Metrics
5
citations of this article
EID Journal Metrics on Scopus

Cite This Article

To the Editor: Long-term carriage of Shiga toxin–producing Escherichia coli (STEC) can greatly affect the social and work lives of infected patients. We describe the use of whole-genome sequencing to assess the risk from long-term STEC carriage in a patient who had been denied surgery because of the infection.

On August 18, 2013, a 64-year-old woman reporting to be a carrier of STEC since March 2013 contacted the University Medical Center Lübeck, Lubeck, Germany, seeking decolonization therapy that had been provided to long-term STEC carriers during the 2011 STEC O104:H4 outbreak (1). STEC had initially been identified in the patient during an episode of watery diarrhea. She currently had gonarthrosis grade III, indicating the need for a total knee endoprosthesis; however, the responsible orthopedic department had denied surgery because of the potential risk for development of STEC-associated hemolytic uremic syndrome (HUS) caused by the perioperative use of antimicrobial drug prophylaxis. The patient was also rejected for surgery at another orthopedic clinic. Because of this STEC-associated restriction, the patient requested decolonization therapy.

Before responding to the request, we asked the patient to provide a fecal sample for STEC strain typing. A sample provided on August 22, 2013, was confirmed positive for STEC by culturing an STEC strain on MacConkey agar (bioMérieux, Marcy l'Etoile, France) that did not grow on selective agar (CHROMagar STEC, Mast Diagnostika, Reinfeld, Germany) optimized for the detection of classical enterohemorrhagic E. coli strains. Total DNA was extracted from the isolate, and a sequencing library was generated by using the Nextera XT Sample Preparation Kit (Illumina, San Diego, CA, USA). Sequencing was performed (MiSeq Benchtop Sequencer, Illumina) in 2 batches of paired 250-bp sequencing runs. Sequencing reads were further analyzed by using the CLC Genomics Workbench software package (CLC bio, Aarhus, Denmark). De novo assembly resulted in 120 contigs with an average length of 44,331 bp (N50 = 126,317 bp). A predefined dataset of 2,456 sequences was aligned with the generated contigs in a single step by using BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) to determine the alleles and subtypes of genes usually used for E. coli and STEC strain typing and for seropathotype detection.

Presence of a Shiga toxin subtype 1a with >99.9% and 100% identity to the stx1aA and stx1aB subunit genes, respectively (GenBank accession no M19473.1), was confirmed. The STEC strain carried genes with high homology to the O91 antigen–encoding operon (GenBank accession no. AY035396.1) and the H14-flagellin gene (GenBank accession no. AY249998.1). This observation was confirmed by a 100% sequence identity of a 643-bp fragment of the gnd gene of the sequenced strain with that of a gnd reference sequence of STEC O91:H14 (www.corefacility.ca/ecoli_typer). These 2 sequences are different from the gnd sequence of reference strain STEC O91:H21. In vitro multilocus sequence typing (2) identified sequence type (ST) 33. These data were used for risk assessment.

Only strains displaying serotype O91:H21 and a single O91:H10 isolate have been associated with HUS in humans (3,4). ST33, identified in the patient in this study, has not been associated with HUS in humans despite being the most frequently identified ST of O91 STEC strains in humans (3). In addition, the identified strain carried only Shiga toxin 1a, whereas the HUS-associated strain HUSEC034 of serotype O91:H21 carried Shiga toxins 1a, 2a, and 2d (5). This data indicated the patient strain was a seropathotype D strain (6) with a relative low risk for HUS development in the patient.

The assumption that the patient strain had low pathogenicity was further corroborated by the analysis of additional marker genes (69) indicating the lack of pathogenicity islands associated with high virulence of STEC in humans. None of the 25 marker genes suggested for the LEE locus or pathogenicity islands OI-36, OI-43, OI-44, OI-48, OI-50, OI-57, OI-71 or OI-122 were identified in the patient strain, whereas most of these markers could be detected in highly pathogenic STEC/enterohemorrhagic E. coli strains used to establish the method for identifying markers (Technical Appendix Table).

After completing the STEC risk assessment, we advised the patient’s general practitioner that antimicrobial drug prophylaxis could be administered for surgery with a low calculated risk for HUS development, as observed for other non-O157 strains (1,10). In addition, we described our experience with 4 long-term carriers of STEC O91:H14 strains; the patients had been decolonized of STEC by the use of azithromycin decolonization therapy (data not shown).

The patient was added to a waiting list for surgery, and she elected to receive azithromycin as experimental decolonization therapy while awaiting surgery. Azithromycin was administered orally for 3 days (500 mg/day); fecal specimens on post-treatment days 7, 14, and 21 were negative by Shiga toxin ELISA. In addition, an stx-specific PCR using enrichment broth confirmed the sustainable eradication of the STEC infection. Our findings show that whole-genome sequencing can be used in the diagnostic process for long-term STEC carriers and might extend or replace other methods used for risk assessment (68,10) and treatment decision guidance.

Top

Johannes K.-M. KnoblochComments to Author , Stefan Niemann, Thomas A. Kohl, Ulrich Lindner, Martin Nitschke, Friedhelm Sayk, and Werner Solbach
Author affiliations: University Hospital Schleswig-Holstein, Lübeck, Germany (J.K.-M. Knobloch, U. Lindner, M. Nitschke, F. Sayk, W. Solbach); Research Center Borstel, Borstel, Germany (S. Niemann, T.A. Kohl); German Centre for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel, Germany (J.K.-M. Knobloch, S. Niemann, U. Lindner, W. Solbach)

Top

References

  1. Nitschke  M, Sayk  F, Härtel  C, Roseland  RT, Hauswaldt  S, Steinhoff  J, Association between azithromycin therapy and duration of bacterial shedding among patients with Shiga toxin–producing enteroaggregative Escherichia coli O104:H4. JAMA. 2012;307:104652 . DOIPubMedGoogle Scholar
  2. Wirth  T, Falush  D, Lan  R, Colles  F, Mensa  P, Wieler  LH, Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol. 2006;60:113651. DOIPubMedGoogle Scholar
  3. Mellmann  A, Fruth  A, Friedrich  AW, Wieler  LH, Harmsen  D, Werber  D, Phylogeny and disease association of Shiga toxin–producing Escherichia coli O91. Emerg Infect Dis. 2009;15:14747. DOIPubMedGoogle Scholar
  4. Pradel  N, Boukhors  K, Bertin  Y, Forestier  C, Martin  C, Livrelli  V. Heterogeneity of Shiga toxin–producing Escherichia coli strains isolated from hemolytic-uremic syndrome patients, cattle, and food samples in central France. Appl Environ Microbiol. 2001;67:24608. DOIPubMedGoogle Scholar
  5. Hauser  E, Mellmann  A, Semmler  T, Stoeber  H, Wieler  LH, Karch  H, Phylogenetic and molecular analysis of food-borne Shiga toxin–producing Escherichia coli. Appl Environ Microbiol. 2013;79:273140. DOIPubMedGoogle Scholar
  6. Karmali  MA, Mascarenhas  M, Shen  S, Ziebell  K, Johnson  S, Reid-Smith  R, Association of genomic O island 122 of Escherichia coli EDL 933 with verocytotoxin-producing Escherichia coli seropathotypes that are linked to epidemic and/or serious disease. J Clin Microbiol. 2003;41:493040. DOIPubMedGoogle Scholar
  7. Delannoy  S, Beutin  L, Fach  P. Discrimination of enterohemorrhagic Escherichia coli (EHEC) from non-EHEC strains based on detection of various combinations of type III effector genes. J Clin Microbiol. 2013;51:325762. DOIPubMedGoogle Scholar
  8. Delannoy  S, Beutin  L, Fach  P. Towards a molecular definition of enterohemorrhagic Escherichia coli (EHEC): detection of genes located on O island 57 as markers to distinguish EHEC from closely related enteropathogenic E. coli strains. J Clin Microbiol. 2013;51:10838. DOIPubMedGoogle Scholar
  9. Coombes  BK, Wickham  ME, Mascarenhas  M, Gruenheid  S, Finlay  BB, Karmali  MA. Molecular analysis as an aid to assess the public health risk of non-O157 Shiga toxin–producing Escherichia coli strains. Appl Environ Microbiol. 2008;74:215360. DOIPubMedGoogle Scholar
  10. Jensen  C, Schiellerup  P, Olsen  K, Scheutz  F, Petersen  E, Gerner-Smidt  P, Antimicrobial treatment of asymptomatic carriers of verocytotoxin-producing Escherichia coli: an empiric study. Scand J Infect Dis. 2005;37:613. DOIPubMedGoogle Scholar

Top

Cite This Article

DOI: 10.3201/eid2004.131782

Related Links

Top

Table of Contents – Volume 20, Number 4—April 2014

EID Search Options
presentation_01 Advanced Article Search – Search articles by author and/or keyword.
presentation_01 Articles by Country Search – Search articles by the topic country.
presentation_01 Article Type Search – Search articles by article type and issue.

Top

Comments

Please use the form below to submit correspondence to the authors or contact them at the following address:

Johannes K.-M. Knobloch, University Hospital Schleswig-Holstein, Campus Lübeck, Department of Medical Microbiology and Hygiene, Ratzeburger Allee 160, 23538 Lübeck, GermanyJohannes K.-M. Knobloch, University Hospital Schleswig-Holstein, Campus Lübeck, Department of Medical Microbiology and Hygiene, Ratzeburger Allee 160, 23538 Lübeck, Germany

Send To

10000 character(s) remaining.

Top

Page created: March 18, 2014
Page updated: March 18, 2014
Page reviewed: March 18, 2014
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external