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Whole-Genome Sequencing Analysis of a stx-Negative Escherichia coli O63:H6 Isolate Associated with Hemolytic Uremic Syndrome

1
Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
2
College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea
3
Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul 06351, Korea
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Dario de Biase
Received: 18 August 2021 / Revised: 21 September 2021 / Accepted: 29 September 2021 / Published: 2 October 2021
(This article belongs to the Section Diagnostic Microbiology and Infectious Disease)
Shiga toxin-encoding genes (stx) of enterohemorrhagic Escherichia coli (EHEC) can be lost during infection or in vitro cultivation, and in clinical practice, it is difficult to distinguish EHEC that have lost stx (EHEC-LST) from enteropathogenic E. coli (EPEC), as both are stx-negative and eae-positive. In this study, we performed whole-genome sequencing (WGS) of a stx-negative, eae-positive E. coli O63:H6 isolate from a child with hemolytic uremic syndrome and compared its genome with those of nine E. coli O63:H6 strains in public databases. Virulence gene profiles were analyzed and core-genome multilocus sequence typing (cgMLST) was conducted. The virulence gene profile of our isolate was consistent with EHEC, except for the absence of stx, and the isolate clustered with seven EHEC strains but was distant from two EPEC strains in cgMLST. In genome alignment, our isolate exhibited a high nucleotide identity with EHEC strain 377323_2f but displayed a gap corresponding to the stx-harboring prophage sequence. Overall, our isolate was genetically closely related to EHEC strains, consistent with this being an EHEC-LST strain. As EHEC-LST may be misdiagnosed as EPEC in routine laboratories, comparative genomic analysis using WGS can be useful to determine whether stx-negative and eae-positive isolates are EHEC-LST or EPEC. View Full-Text
Keywords: E. coli O63:H6; STEC; EHEC; stx loss; hemolytic uremic syndrome; whole-genome sequencing E. coli O63:H6; STEC; EHEC; stx loss; hemolytic uremic syndrome; whole-genome sequencing
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MDPI and ACS Style

Kim, T.Y.; La, T.-M.; Kim, T.; Yun, S.A.; Lee, S.-W.; Huh, H.J.; Lee, N.Y. Whole-Genome Sequencing Analysis of a stx-Negative Escherichia coli O63:H6 Isolate Associated with Hemolytic Uremic Syndrome. Diagnostics 2021, 11, 1823. https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11101823

AMA Style

Kim TY, La T-M, Kim T, Yun SA, Lee S-W, Huh HJ, Lee NY. Whole-Genome Sequencing Analysis of a stx-Negative Escherichia coli O63:H6 Isolate Associated with Hemolytic Uremic Syndrome. Diagnostics. 2021; 11(10):1823. https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11101823

Chicago/Turabian Style

Kim, Tae Y., Tae-Min La, Taesoo Kim, Sun A. Yun, Sang-Won Lee, Hee J. Huh, and Nam Y. Lee. 2021. "Whole-Genome Sequencing Analysis of a stx-Negative Escherichia coli O63:H6 Isolate Associated with Hemolytic Uremic Syndrome" Diagnostics 11, no. 10: 1823. https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11101823

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