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Open AccessArticle

Phylogeny, Resistome, and Virulome of Escherichia coli Causing Biliary Tract Infections

1
Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain
2
Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
3
LabEx Lermit, EA7361, Université Paris-Sud, Université Paris-Saclay, 91190 Saint-Aubin, France
4
The Evolution and Ecology of Resistance to Antibiotics” Unit, Institut Pasteur-APHP-Université Paris Sud, 91400 Orsay, France
5
Bacteriology Hygiene unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, 94270 Paris, France
6
Department of Microbiology, University of Seville, 41009 Seville, Spain
7
Department of Medicine, University of Seville, 41009 Seville, Spain
*
Author to whom correspondence should be addressed.
J. Clin. Med. 2019, 8(12), 2118; https://doi.org/10.3390/jcm8122118
Received: 4 November 2019 / Revised: 27 November 2019 / Accepted: 29 November 2019 / Published: 2 December 2019
(This article belongs to the Section Infectious Diseases)
Escherichia coli is the most frequent Gram-negative bacilli involved in intra-abdominal infections. However, despite high mortality rates associated with biliary tract infections due to E. coli, there is no study focusing on this pathogen. In this study, we have characterized a group of 15 E. coli isolates obtained from 12 patients with biliary tract infections. Demographic and clinical data of the patients were recovered. Phylogeny, resistome, and virulome analysis through whole genome sequencing and biofilm formation were investigated. Among the 15 E. coli isolates, no predominant sequence type (ST) was identified, although 3 of them belonged to unknown STs (20%). Resistance to ampicillin, amoxicillin/clavulanic acid, cotrimoxazole, and quinolones was more present in these isolates; whereas, third and fourth generation cephalosporins, carbapenems, amikacin, tigecycline, and colistin were highly active. Moreover, high diversity of virulence factors has been found, with sfa, fimH, and gad the most frequently detected genes. Interestingly, 26.6% of the E. coli isolates were high biofilm-producers. Altogether, our data characterized for the first time E. coli isolates associated with biliary tract infections in terms of genomic relationship, resistome, and virulome.
Keywords: Escherichia coli; biliary tract infection; virulome; resistome; biofilm Escherichia coli; biliary tract infection; virulome; resistome; biofilm
MDPI and ACS Style

Rodríguez-Villodres, Á.; Bonnin, R.A.; Ortiz de la Rosa, J.M.; Álvarez-Marín, R.; Naas, T.; Aznar, J.; Pachón, J.; Lepe, J.A.; Smani, Y. Phylogeny, Resistome, and Virulome of Escherichia coli Causing Biliary Tract Infections. J. Clin. Med. 2019, 8, 2118.

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