Emergence of Enteroaggregative Escherichia coli within the ST131 Lineage as a Cause of Extraintestinal Infections

Abstract

Escherichia coli sequence type 131 (ST131) is a major cause of urinary and bloodstream infections. Its association with extended-spectrum β-lactamases (ESBLs) significantly complicates treatment. Its best-described component is the rapidly expanding H30Rx clade, containing allele 30 of the type 1 fimbrial adhesin gene fimH. This lineage appears to have emerged in the United States and spread around the world in part due to the acquisition of the ESBL-encoding blaCTX-M-15 gene and resistance to fluoroquinolones. However, non-H30 ST131 sublineages with other acquired CTX-M-type resistance genes are also emerging. Based on whole-genome analyses, we describe here the presence of an (fimH) H27 E. coli ST131 sublineage that has recently caused an outbreak of community-acquired bacteremia and recurrent urinary tract infections (UTIs) in Denmark. This sublineage has acquired both a virulence plasmid (pAA) that defines the enteroaggregative E. coli (EAEC) diarrheagenic pathotype and multiple genes associated with extraintestinal E. coli (ExPEC); combined, these traits have made this particular ST131 sublineage successful at colonizing its human host and causing recurrent UTI. Moreover, using a historic World Health Organization (WHO) E. coli collection and publicly available genome sequences, we identified a global H27 EAEC ST131 sublineage that dates back as far as 1998. Most H27 EAEC ST131 isolates harbor pAA or pAA-like plasmids, and our analysis strongly implies a single ancestral acquisition among these isolates. These findings illustrate both the profound plasticity of this important pathogenic E. coli ST131 H27 sublineage and genetic acquisitions of EAEC-specific virulence traits that likely confer an enhanced ability to cause intestinal colonization. IMPORTANCE E. coli ST131 is an important extraintestinal pathogenic lineage. A signature characteristic of ST131 is its ability to asymptomatically colonize the gastrointestinal tract and then opportunistically cause extraintestinal infections, such as cystitis, pyelonephritis, and urosepsis. In this study, we identified an ST131 H27 sublineage that has acquired the enteroaggregative diarrheagenic phenotype, spread across multiple continents, and caused multiple outbreaks of community-acquired ESBL-associated bloodstream infections in Denmark. The strain’s ability to both cause diarrhea and innocuously colonize the human gastrointestinal tract may facilitate its dissemination and establishment in the community.

Pre- and postmenopausal women have different core urinary microbiota

“…In line with this, younger women with a low or moderate- Lactobacillus dominated urotype have been found to be associated with mixed urinary incontinence, pointing towards a dysbiosis in women lacking Lactobacillus 32 . Conversely, it might represent personal variations in the urinary microbiota or be influenced by temporal factors that could change the microbial composition, such as menstruation or coitus 33 .…”

“…Third, use of 16S rRNA gene sequencing and enhanced bacteria culture may give different urinary microbiota results 9 and one may argue that both methods should be included to proper reflect the microbiota of the bladder. Fourth, we only collected urine at a single timepoint, and as the bacterial composition has been shown by some to fluctuate over time 33 , this possible lack of temporal stability may have impacted the results. We have, however, previously shown that the composition of the urinary microbiota remains stable over a shorter time period 42 .…”

“…We have, however, previously shown that the composition of the urinary microbiota remains stable over a shorter time period 42 . Finally, we did not account for other factors that could potentially influence the urinary microbiota, such as diet 43 , fluid intake, urinary oxygen concentrations 44 , menstruation cycle 33 , sexual activity 33 , and vulvo-vaginal symptoms 45 , 46 . This could in particular be a limitation since these would be expected to differ highly between our two groups.…”

Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69 Escherichia coli Strain in Italy

“…These data support the definition of ST69 as a high-risk clone, with increased ability for antimicrobial resistance genes acquisition. Moreover, the presence of type 1 fimbriae (fimH27), has been correlated with persisting colonization and bacteremia in patients [38].…”

Escherichia coli as a Multifaceted Pathogenic and Versatile Bacterium

“…The broadly reported multidrug resistant E. coli ST131 is example of highly virulent ExPEC associated with urinary and bloodstream infections. It has also acquired enteroaggregative diarrheagenic phenotype due to pAA plasmid presence ( Boll et al., 2018 ). Many others HyPEC are described as case report, but not fully characterized.…”