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

Nam Yong Lee,Tae Yeul Kim,Tae-Min La,Taesoo Kim,Sang-Won Lee,Sun Ae Yun,Hee Jae Huh

doi:10.3390/diagnostics11101823

Abstract

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.

Highlights

Shiga toxin-producing Escherichia coli (STEC) can cause human illnesses ranging from uncomplicated diarrhea to life-threatening complications such as hemolytic uremic syndrome (HUS)
Shiga toxin (Stx) is the primary virulence factor of STEC involved in the pathogenesis of HUS, and the genes encoding Stx are located in bacteriophage genomes integrated into the bacterial chromosome [7]
A subset of STEC strains, termed enterohemorrhagic E. coli (EHEC), possess the locus of enterocyte effacement (LEE) pathogenicity island containing eae, which encodes intimin, a protein required for intimate bacterial attachment to the host intestinal epithelium [7]

Summary

Introduction

Shiga toxin-producing Escherichia coli (STEC) can cause human illnesses ranging from uncomplicated diarrhea to life-threatening complications such as hemolytic uremic syndrome (HUS). We obtained a stx-negative, eae-positive E. coli O63:H6 isolate from a 3-yearold child diagnosed with HUS based on the presence of non-immune hemolytic anemia, thrombocytopenia, and acute kidney injury and performed whole-genome sequencing (WGS) to determine whether this isolate was EHEC-LST or EPEC. Both the stool sample and strain EC12 isolated from the sample tested negative for stx1, stx2, and stx2f but positive for eae.

Results

Conclusion