The population genetics of pathogenic Escherichia coli

E Denamur, O Clermont, S Bonacorsi… - Nature Reviews …, 2021‏ - nature.com
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various
intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes …

Genomics and pathotypes of the many faces of Escherichia coli

J Geurtsen, M de Been, E Weerdenburg… - FEMS microbiology …, 2022‏ - academic.oup.com
Escherichia coli is the most researched microbial organism in the world. Its varied impact on
human health, consisting of commensalism, gastrointestinal disease, or extraintestinal …

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

Z Zhou, NF Alikhan, K Mohamed, Y Fan… - Genome …, 2020‏ - genome.cshlp.org
EnteroBase is an integrated software environment that supports the identification of global
population structures within several bacterial genera that include pathogens. Here, we …

Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports

J Sarowska, B Futoma-Koloch, A Jama-Kmiecik… - Gut pathogens, 2019‏ - Springer
Extraintestinal pathogenic E. coli (ExPEC) are facultative pathogens that are part of the
normal human intestinal flora. The ExPEC group includes uropathogenic E. coli (UPEC) …

Global extraintestinal pathogenic Escherichia coli (ExPEC) lineages

AR Manges, HM Geum, A Guo, TJ Edens… - Clinical microbiology …, 2019‏ - journals.asm.org
SUMMARY Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a
majority of human extraintestinal infections globally, resulting in enormous direct medical …

Antimicrobial resistance and population genomics of multidrug-resistant Escherichia coli in pig farms in mainland China

Z Peng, Z Hu, Z Li, X Zhang, C Jia, T Li, M Dai… - Nature …, 2022‏ - nature.com
The expanding use of antimicrobials in livestock is an important contributor to the worldwide
rapid increase in antimicrobial resistance (AMR). However, large-scale studies on AMR in …

ClermonTy**: an easy-to-use and accurate in silico method for Escherichia genus strain phyloty**

J Beghain, A Bridier-Nahmias… - Microbial …, 2018‏ - microbiologyresearch.org
The genus Escherichia is composed of Escherichia albertii, E. fergusonii, five cryptic
Escherichia clades and E. coli sensu stricto. Furthermore, the E. coli species can be divided …

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

D Berry, S Widder - Frontiers in microbiology, 2014‏ - frontiersin.org
Co-occurrence networks produced from microbial survey sequencing data are frequently
used to identify interactions between community members. While this approach has …

Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production

Y Wang, R Zhang, J Li, Z Wu, W Yin, S Schwarz… - Nature …, 2017‏ - nature.com
By 2030, the global population will be 8.5 billion, placing pressure on international poultry
production, of which China is a key producer 1. From April 2017, China will implement the …

Urinary tract infection syndromes: occurrence, recurrence, bacteriology, risk factors, and disease burden

B Foxman - Infectious Disease Clinics, 2014‏ - id.theclinics.com
Urinary tract infection (UTI), an infection anywhere in the urinary tract (urethra, bladder,
ureters, or kidneys) is very common. In 2007 in the United States there were 10.5 million …