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.

Antibiotic susceptibility of Escherichia coli isolated from neonates admitted to neonatal intensive care units across China from 2015 to 2020

“…MLST is a nucleic acid sequencing-based genotyping method that has been widely used in the study of E. coli and the identification of ExPEC-related clonal complexes or lineages. Different ST types have different drug resistance and virulence characteristics ( Vanstokstraeten et al., 2022 ). Manges et al.…”

“…MLST is a nucleic acid sequencing-based genotyping method that has been widely used in the study of E. coli and the identification of ExPECrelated clonal complexes or lineages. Different ST types have different drug resistance and virulence characteristics (Vanstokstraeten et al, 2022). Manges et al (2019) using metaanalysis described the type, evolution, distribution and characteristics of ExPEC, which showed that ST131 had the highest proportion, and other major lineages included ST69, ST95, ST10, ST405, ST73, ST410, and ST1193.…”

Core Genome Sequencing Analysis of E. coli O157:H7 Unravelling Genetic Relatedness among Strains from Cattle, Beef, and Humans in Bishoftu, Ethiopia

“…All of them carried the mdf A gene encoding for the non-specific MdfA multi-drug efflux pump [41]. This gene seems to be commonly present among E. coli isolates independent of the source of isolation [42,43].…”

Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates

“…The raw data were downloaded on BioNumerics v7.6.2 as previously described [ 22, 23 ]. They were trimmed (by exclusion of reads shorter than 35 bp and longer than 251 bp) and assembled de novo with a SPAdes algorithm [ 3, 24 ].…”