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

Molecular epidemiology of ESBL-producing E. coli and K. pneumoniae: establishing virulence clusters Laure Surgers,1,2 Peter Boersma,3 Pierre-Marie Girard,1,4 Audrey Homor,5 Delphine Geneste,2 Guillaume Arlet,2,5 Dominique Decré,2,5 Anders Boyd4 1Infectious Diseases Department, Saint-Antoine Hospital, APHP, Paris, France; 2Sorbonne University, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI Team 13, Paris, France; 3Department of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA; 4INSERM, Sorbonne Université, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France; 5Bacteriology Department, Saint-Antoine Hospital, APHP, Paris, France Objective: 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. Methods: 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. Results: 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