Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing E. Ruppé, F. Olearo, D. Pires,

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Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing E. Ruppé, F. Olearo, D. Pires, D. Baud, G. Renzi, A. Cherkaoui, D. Goldenberger, A. Huttner, P. François, S. Harbarth, J. Schrenzel Clinical Microbiology and Infection Volume 23, Issue 7, Pages 470-475 (July 2017) DOI: 10.1016/j.cmi.2017.01.015 Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 1 Schematic representation of patients’ hospitalization and first isolation of KPC-producing Klebsiella pneumoniae (star). (a) St Gallen outbreak. (b) Geneva outbreak. Wards are represented by coloured rectangles; shaded red area depicts time shared by patients in same ward before isolation of KPC-producing K. pneumoniae. KPC, K. pneumoniae carbapenemase. Clinical Microbiology and Infection 2017 23, 470-475DOI: (10.1016/j.cmi.2017.01.015) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 2 Phylogenetic tree with bootstrap values obtained by comparison of genes included in Klebsiella pneumoniae wgMLST. KPN7 is suspected index strain for outbreak. B5 and KPN1 do not appear on tree because of their high distance. wgMLST, whole-genome multilocus sequence typing. Clinical Microbiology and Infection 2017 23, 470-475DOI: (10.1016/j.cmi.2017.01.015) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 3 Phylogenetic tree obtained by comparison of common genomes of all KPC-producing Klebsiella pneumoniae and associated ARGs. B5 and KPN1 do not appear on tree because of their high distance. ARGs SHV-11 and FosA (in grey font) are intrinsic to K. pneumoniae. ARG, antibiotic resistance gene; KPC, K. pneumoniae carbapenemase. Clinical Microbiology and Infection 2017 23, 470-475DOI: (10.1016/j.cmi.2017.01.015) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 4 Number of SNVs observed in KPC-producing Klebsiella pneumoniae from index patient HUG1 since first isolation of KPC-producing K. pneumoniae in March 2012 (KPN3) and last KPC-producing K. pneumoniae recovered in March 2015 (KPN11). Shaded grey area represents 95% confidence interval for number of SNVs at each time point. KPC, K. pneumoniae carbapenemase; SNV, single nucleotide variant. Clinical Microbiology and Infection 2017 23, 470-475DOI: (10.1016/j.cmi.2017.01.015) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Clinical Microbiology and Infection 2017 23, 470-475DOI: (10. 1016/j Clinical Microbiology and Infection 2017 23, 470-475DOI: (10.1016/j.cmi.2017.01.015) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions