Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/blaCMY-2 resistance plasmids E.S. Berg, A.L. Wester,

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Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/blaCMY-2 resistance plasmids E.S. Berg, A.L. Wester, J. Ahrenfeldt, S.S. Mo, J.S. Slettemeås, M. Steinbakk, Ø. Samuelsen, N. Grude, G.S. Simonsen, I.H. Løhr, S.B. Jørgensen, S. Tofteland, O. Lund, U.R. Dahle, M. Sunde Clinical Microbiology and Infection Volume 23, Issue 6, Pages 407.e9-407.e15 (June 2017) DOI: 10.1016/j.cmi.2016.12.035 Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 1 Pipeline for selection of isolates for whole genome-based comparison of Escherichia coli from poultry and human infections. Abbreviations: AMR, antimicrobial resistance; MDR, multidrug resistance; ST, multi-locus sequence type. Clinical Microbiology and Infection 2017 23, 407.e9-407.e15DOI: (10.1016/j.cmi.2016.12.035) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 2 Genome single nucleotide polymorphism (SNP) differences in human clinical Escherichia coli isolates compared with one AmpC-producing poultry E. coli (ST38) strain collected from Norwegian retail chicken fillets. Multiple sequence alignment resulted in 56.610 valid SNPs in the core genome of 2.51 Mbp positions shared by all strains. The data labels show the span in SNP differences within the group of isolates. Clinical Microbiology and Infection 2017 23, 407.e9-407.e15DOI: (10.1016/j.cmi.2016.12.035) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 3 Dendrogram after whole genome comparison with single nucleotide polymorphism (SNP) calling and phylogenetic analysis of Escherichia coli isolates from human clinical infections, poultry samples and a selection of GenBank E. coli reference genomes retrieved from GenBank. The colours of the boxes reflect the origin of the isolates as indicated. The multilocus sequence types (STs) of the included poultry isolates and of isolates of clinical relevance are indicated on the figure. STs of all investigated isolates can be found in supplementary material. The length of the scale bar represents the average number of substitutions per site at the variable sites. Clinical Microbiology and Infection 2017 23, 407.e9-407.e15DOI: (10.1016/j.cmi.2016.12.035) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 4 Bayesian Evolutionary Analysis Sampling Trees (BEAST) analysis of the closely related human and chicken Escherichia coli isolates. Yellow boxes; poultry isolates, pink boxes; urinary tract isolates. Clinical Microbiology and Infection 2017 23, 407.e9-407.e15DOI: (10.1016/j.cmi.2016.12.035) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions