Genomes of Escherichia coli bacteraemia isolates originating from urinary tract foci contain more virulence-associated genes than those from non-urinary foci and neutropaenic hosts

Abstract

ObjectivesEscherichia coli is the leading cause of bacteraemia. In an era of emerging multi-drug-resistant strains, development of effective preventative strategies will be informed by knowledge of strain diversity associated with specific infective syndromes/patient groups. We hypothesised that the number of virulence factor (VF) genes amongst bacteraemia isolates from neutropaenic patients would be lower than isolates from immunocompetent patients.MethodsImmunocompetent and neutropaenic adults with E. coli bacteraemia were recruited prospectively and the source of bacteraemia determined. VF gene profiles were established in silico following whole genome sequencing.ResultsIsolates from individual patients were monoclonal. Strains from immunocompetent patients with urinary tract infective foci (UTIF) harboured more VF genes (median number of VF genes 16, range 8–24) than isolates from both immunocompetent patients with non-UTIF (10, 2–22, p = 0.0058) and neutropaenic patients with unknown focus of infection (NPUFI) (8, 3–13, p < 0.0001). Number of VF genes (OR 1.21, 95% CIs 1.01–1.46, p = 0.039) and urinary catheter/recurrent urinary tract infection (OR 12.82, 95% CIs 1.24–132.65, p = 0.032) were independent predictors of bacteraemia secondary to UTIF vs. non-UTIF in immunocompetent patients. papA, papC, papE/F, papG, agn43, tia, iut, fyuA, kpsM and sat were significantly more prevalent amongst UTIF- vs non-UTIF-originating isolates amongst immunocompetent patients, while papC, papE/F, papG, agn43, tia, fyuA, hlyA, usp and clb were significantly more prevalent amongst UTIF- vs NPUFI-associated isolates.ConclusionsBacteraemia-associated E. coli strains originating from UTIF have distinct VF gene profiles from strains associated with non-UTIF- and NPUFI. This diversity must be addressed in the design of future vaccines to ensure adequate coverage of strains responsible for site-specific disease.

Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections

“…Despite studies reporting various VAGs linked to pyelonephritis and sepsis [15, 114, 115], we found no single gene nor plasmid replicon strongly associated with a particular pathology (correlation heat map in Data S5), nor was there a significant difference between the number of VAGs present and uro-clinical syndrome (). The discrepancy with the literature may have arisen due to sampling based on trimethoprim resistance and/or the relatively small sample size, limiting statistical power.…”

“…Despite studies reporting various VAGs linked to pyelonephritis and sepsis [15,114,115], we found no single gene nor plasmid replicon strongly associated with a particular pathology (correlation heat map in Data S5), nor was there a significant difference between the number of VAGs present and uro-clinical syndrome (Fig. 7a).…”

<p>Diversity of Virulence Genes in Multidrug Resistant <em>Escherichia coli</em> from a Hospital in Western China</p>

“…The hlyA gene was detected in 32.99% of the E. coli isolates. In Iran, Malekzadegan and Khashei22 reported that 28.6% of the E. coli strains were positive for hlyA , whereas Dale et al33 found that 26% of E. coli strains in the UK carried hlyA , and Bozcal et al34 identified this gene in 15.4% of E. coli strains in Turkey. The percentage of E. coli harboring hlyA in our study was higher than detected in the above-mentioned studies.…”

Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

“…Abricate (https://github.com/tseemann/abricate) v0.8.13 was used for (i) mass screening of contigs for (acquired) antimicrobial resistance genes using ResFinder 3.1.0 (download 24 January 2019), and (ii) to determine presence of VG by BLAST against the VFDB database (http://www.mgc.ac.cn/VFs) (download 8 February 2019) [16,17]. We searched for 49 putative VG that were previously described as extra-intestinal pathogenic E. coli (ExPEC)-associated VG [18][19][20][21][22]. If any of the predefined VG were not included in VFDB, BLAST against the eco-li_VF_collection database was performed (date 8 February 2019) [23].…”