Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

A 21-year survey of Escherichia coli from bloodstream infections (BSIs) in a tertiary hospital reveals how community-hospital dynamics, influence local BSI rates, the trends of the B2 phylogroup and the STc131 pandemic clone

Irene Rodríguez, Ana Sofia Figueiredo, Melissa Sousa, View ORCID ProfileVal F. Lanza, Concepción Rodríguez, View ORCID ProfilePatricia Mingo, View ORCID ProfileJavier Zamora, Elena Loza, Claire J. Brooks, View ORCID ProfileRafael Cantón, View ORCID ProfileFernando Baquero, View ORCID ProfileTeresa M Coque
doi: https://doi.org/10.1101/2020.04.10.034777
Irene Rodríguez
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ana Sofia Figueiredo
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
2Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Melissa Sousa
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
2Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Val F. Lanza
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
3Bioinformatics Unit, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
4Biomedical Research Center Network of Epidemiology and Public Health (CIBERESP), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Val F. Lanza
Concepción Rodríguez
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Patricia Mingo
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Patricia Mingo
Javier Zamora
4Biomedical Research Center Network of Epidemiology and Public Health (CIBERESP), Madrid, Spain
5Biostatistics Unit, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Javier Zamora
Elena Loza
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Claire J. Brooks
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Rafael Cantón
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
6Spanish Network for Research in Infectious Diseases (REIPI), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Rafael Cantón
Fernando Baquero
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
4Biomedical Research Center Network of Epidemiology and Public Health (CIBERESP), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Fernando Baquero
Teresa M Coque
1Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
4Biomedical Research Center Network of Epidemiology and Public Health (CIBERESP), Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Teresa M Coque
  • For correspondence: teresacoque@gmail.com mariateresa.coque@salud.madrid.org
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

ABSTRACT

Escherichia coli is overrepresented in all bloodstream infections (BSIs) series, mostly associated with a few clonal lineages. Its population structure has been analyzed but the dynamics remains to be fully understood. We analyze the dynamics of E. coli-BSIs in a sample of 649 isolates, representing all 7165 E. coli BSI episodes recorded in a tertiary hospital (1996-2016) according to clonal identification (phylogenetic groups/subgroups, STc131 subclades), antibiotic susceptibility (13 antibiotics), and virulence-associated genes (VAGs, 29 genes). Patient data were obtained from the laboratory system and clinical charts. The incidence of BSI-EC doubled from 1996 to 2016 (5.5 to 10.8 BSI episodes/1000 hospitalizations). Intertwined waves of community-acquired (CA) and hospital-acquired isolates (HA) episodes of both B2 and non-B2 phylogroups, occurred until B2 overtook non-B2 BSI episodes. ST131 contributed to increasing the B2 rates, but only transiently altered the population structure. B2 isolates predominates (53%), overrepresented by subgroups B2-I (STc131), B2-II, B2-IX, and B2-VI (25%, 25%, 14%, and 9%). We observed a remarkable increase only for B2-I-STc131 (C1/C2 subclades), a decreasing trend for phylogroup D, and oscillations for other B2 subgroups throughout the years. According to VAG patterns, B2 strains exhibit a population structure compatible with the niche specialization theory. A reservoir of B2 and non-B2 strains represented in human microbiota, flows from the community to the hospital and vice-versa, where they can either be selected or coexist. The increase of BSI is determined by waves of CA that predate the amplification of HA episodes of both B2 and non-B2 phylogroups in various time periods, influenced by FQR and microbiota composition.

IMPORTANCE The gut microbiota is an important reservoir for bacteria that cause extraintestinal infections including sepsis, which is the third cause of mortality in Western countries and one of the Global Health threads recognized by the WHO since 2017. Most of the bloodstream infections (BSI) and UTIs due to Escherichia coli strains originate in the gut microbiota and belong to the phylogenetic group B2. Most B2 strains recovered from BSI infections are clonal lineages predominant in fecal isolates, often associated with outbreaks. Our study analyzes the long-term dynamics of B2 E. coli subtypes and reveals waves of different E.coli lineages including pandemic clones that emerge periodically and are established in the intestinal microbiota afterward. It also reflects that clonal amplifications in the community predates the clonal increases in hospitals which may favor the acquisition of antibiotic resistance in health centers and further dissemination of well adapted clones that become multidrug resistant.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted April 12, 2020.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
A 21-year survey of Escherichia coli from bloodstream infections (BSIs) in a tertiary hospital reveals how community-hospital dynamics, influence local BSI rates, the trends of the B2 phylogroup and the STc131 pandemic clone
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
A 21-year survey of Escherichia coli from bloodstream infections (BSIs) in a tertiary hospital reveals how community-hospital dynamics, influence local BSI rates, the trends of the B2 phylogroup and the STc131 pandemic clone
Irene Rodríguez, Ana Sofia Figueiredo, Melissa Sousa, Val F. Lanza, Concepción Rodríguez, Patricia Mingo, Javier Zamora, Elena Loza, Claire J. Brooks, Rafael Cantón, Fernando Baquero, Teresa M Coque
bioRxiv 2020.04.10.034777; doi: https://doi.org/10.1101/2020.04.10.034777
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
A 21-year survey of Escherichia coli from bloodstream infections (BSIs) in a tertiary hospital reveals how community-hospital dynamics, influence local BSI rates, the trends of the B2 phylogroup and the STc131 pandemic clone
Irene Rodríguez, Ana Sofia Figueiredo, Melissa Sousa, Val F. Lanza, Concepción Rodríguez, Patricia Mingo, Javier Zamora, Elena Loza, Claire J. Brooks, Rafael Cantón, Fernando Baquero, Teresa M Coque
bioRxiv 2020.04.10.034777; doi: https://doi.org/10.1101/2020.04.10.034777

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (2518)
  • Biochemistry (4968)
  • Bioengineering (3473)
  • Bioinformatics (15185)
  • Biophysics (6886)
  • Cancer Biology (5380)
  • Cell Biology (7717)
  • Clinical Trials (138)
  • Developmental Biology (4521)
  • Ecology (7135)
  • Epidemiology (2059)
  • Evolutionary Biology (10210)
  • Genetics (7503)
  • Genomics (9772)
  • Immunology (4825)
  • Microbiology (13185)
  • Molecular Biology (5129)
  • Neuroscience (29368)
  • Paleontology (203)
  • Pathology (836)
  • Pharmacology and Toxicology (1461)
  • Physiology (2131)
  • Plant Biology (4738)
  • Scientific Communication and Education (1008)
  • Synthetic Biology (1337)
  • Systems Biology (4003)
  • Zoology (768)