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Infect Drug Resist. 2018 Dec 31;12:119-127. doi: 10.2147/IDR.S179134. eCollection 2019.

Molecular epidemiology of ESBL-producing E. coli and K. pneumoniae: establishing virulence clusters.

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Infectious Diseases Department, Saint-Antoine Hospital, APHP, Paris, France,
Sorbonne University, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI Team 13, Paris, France,
Department of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA.
INSERM, Sorbonne Université, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France.
Bacteriology Department, Saint-Antoine Hospital, APHP, Paris, France.



To genetically characterize clusters of virulence factors (VFs) among extended spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae and assess whether these clusters are associated with genetic determinants or clinical outcomes.


One hundred forty-eight E. coli and 82 K. pneumoniae clinical isolates were obtained from 213 patients in Paris, France. Isolates underwent ESBL characterization, MultiLocus Sequence Typing (MLST) typing and phylogenetic group identification. Detection of ten E. coli and seven K. pneumoniae VF-encoding genes were assessed, from which a k-medians partition algorithm with Jaccard similarity measure was used to construct clusters.


CTX-M was the predominant ESBL and susceptibility to trimethoprim-sulfamethoxazole (32%), ciprofloxacin (22%) and aminoglycosides (32%) was low. In E. coli, there were five identified clusters, with significantly different distributions of ESBL-sequence type (P<0.001), ST131 (P<0.001) and phylogenetic group (P=0.001) between clusters. "Siderophore exclusive", "siderophore exclusive with iroN " and "adhesin sfa/papGIII-rich" clusters had higher 12-month mortality rates compared to others (49% vs 22%, respectively, P=0.02). In K. pneumoniae, three different clusters, with significantly different distributions of aminoglycoside-sensitivity (P<0.004), MLST-type (P<0.001) and relaxase plasmids (P=0.001) were described.


Distinct clusters of E. coli and K. pneumoniae VFs are observed within ESBL-producing isolates and are strongly associated with several genetic determinants. Their association with overall morbidity and mortality requires further evidence.


E. coli; ESBL; K. pneumoniae; mortality; virulence

Conflict of interest statement

Disclosure LS received a grant from the “Fondation pour la Recherche Médicale” (DEA20140630021). AB received post-doctoral funding from SIDACTION. PB received a Martinson-Luepker Student Travel Award from the University of Minnesota for the work presented in this manuscript. The authors report no other conflicts of interest in this work.

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