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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. 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. Sequencing was performed MiSeq Benchtop Sequencer, Illumina in 2 batches of paired bp sequencing runs. A predefined dataset of 2, sequences was aligned with the generated contigs in a single step by using BLAST http: In vitro multilocus sequence typing 2 identified sequence type ST These data were used for risk assessment.
Only strains displaying serotype O H21 and a single O H10 isolate have been associated with HUS in humans 3 , 4. 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 6 — 9 indicating the lack of pathogenicity islands associated with high virulence of STEC in humans. 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.
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 6 — 8 , 10 and treatment decision guidance. Marker genes identified in clinical strains and the patient strain during whole-genome sequencing assessment of the risk for development of Shiga toxin—producing Escherichia coli STEC —associated hemolytic uremic syndrome in long-term Shiga toxin—producing Escherichia coli infection.