Molecular characterization of extraintestinal and diarrheagenic Escherichia coli blood isolates

ABSTRACT

Pathogenic E. coli strains can be classified into two major groups, based on the presence of specific virulence factors: extraintestinal pathogenic E. coli (ExPEC) and diarrheagenic E. coli (DEC). Several case reports describe that DEC can cause bloodstream infections in some rare cases. This mainly concerns a few specific sequence types that express virulence factors from both ExPEC and DEC. In this study, we retrospectively analysed 234 E. coli blood isolates with whole genome sequencing (WGS). WGS was performed on an Illumina NovaSeq6000. Genotyping was performed using BioNumerics software. The presence of genes was determined with a minimum percentage sequence identity (ID) threshold of 95% and a minimum length for sequence coverage of 95%. Three of the 234 (1.28%) isolates were defined as DEC, 182 (77.78%) as ExPEC, and 49 (20.94%) did not carry pathotype-associated virulence genes. We identified 112 different virulence genes, 48 O-antigens, and 28 H-antigens 82 STs, among the 234 analyzed isolates. ST131 and ST88 were related to healthcare-associated infections. This study provides insight into the prevalence of virulence factors in a large set of E. coli blood isolates from the UZ Brussel. It illustrates high diversity in virulence profiles and highlights the potential of DEC to carry virulence factors associated with extraintestinal infections, making it possible for unusual pathotypes to invade and survive in the bloodstream causing bacteraemia. Diarrheagenic strains causing bacteremia are rare and presently underreported, but modern sequencing techniques will better underscore their importance.

KEYWORDS:

• Escherichia coli
• virulence factors
• pathotypes
• sequence type
• serotype
• nosocomial
• core genome sequencing
• bacteraemia
• MLST
• hybrid pathotype

Acknowledgements

We would like to thank the lab technicians and bioinformaticians of the Brussels Interuniversity Genomics High Throughput core and clinical microbiology laboratory.

Author contributions

RV, TD, DP and FC designed the study and wrote the study protocol. RV and FC performed the DNA-extraction and purification. TJ and BC performed the WGS. RV, IW, AMC and DD performed the data analysis. RV drafted the first version of the manuscript. All authors had full access to all data, aided in finalizing the text and had final responsibility for the submission for publication.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/21505594.2022.2147735.

Data availability

The datasets generated and/or analysed during the current study are available in the National Library of Medicine repository. BioProject: PRJNA854358

Ethics approval

The Medical Ethics Committee of UZ Brussel/VUB reviewed and approved the documents concerning the project from the ethical, legal and medical science points of view (reference: 1432021000569)

Additional information

Funding

The authors declare that no funds, grants, or other support was received during the preparation of this manuscript.