MOESM1 of Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing
Creators: name: Casanova, Carlo
name: Priore, Elia Lo
name: Egli, Adrian
name: Seth-Smith, Helena
name: Räber, Lorenz
name: Ott, Daniel
name: Pflüger, Valentin
name: Droz, Sara
name: Marschall, Jonas
name: Sommerstein, Rami
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Table S1. Overview of environmental sampling. Sampling was performed with premoistened (0,9% NaCl) sterile swabs, direct plating of contrast agents (200 μl per sample) and direct wiping of plant material on plates. Plates were incubated at 35 °C in CO2 enriched atmosphere for 6 days. MALDI-TOF MS was used for bacterial identification. Table S2. Overview of eight isolates described in this study. The genome datasets are available in the European Nucleotide Archive repository, under Project number PRJEB34002 [ https://www.ebi.ac.uk/ena/data/view/PRJEB34002 ]. Table S3. Peak list generated from visual examination of MALDI-TOF spectra of the Isolates A-H. Presence (1) or absence (0) of peaks is indicated at the m/z positions. Potentially double-ionized peaks are indicated with an asterisk (*); numbers in bold indicate peaks with a signal-to-noise ratio &gt; 10. Table S4. Results of digital DNA:DNA hybridization for isolates F, H, G and B performed against all known Agrobacterium genomospecies. A dDDH value over 70 ( http://ggdc.dsmz.de/; Formula 2) or ANI value over 95% ( http://enve-omics.ce.gatech.edu/ani/ ) indicates the same species. Table S5. Comparison of MALDI-TOF MS spectra with a database generated on the base of putatively ascribed ribosomal protein masses extracted from genomic data. G = genomospecies. Figure S1. Timeline of clinical, microbiological, environmental, and treatment features of the two Index cases (Cluster I). Figure S2. Representative differentiating mass to charge (m/z) peaks. The m/z peak 7882 (*) is present in isolates C (pink), D (violet), E (light green), F (dark green) and H (orange) – the peak at 7924 m/z (**) is present in isolates A (light blue) and B (dark blue). Both peaks are absent in isolate G (red). Four spectra were recorded for each isolate A-H. Figure S3. (A) Disposable contrast reservoir with the rubber seal (#) in resting position. The potential contaminable zone lies behind the rubber seal (★). (B) The contrast reservoir is filled with contrast media by pushing (1) the rubber-sealed plunger (*) and pulling it (2) back to resting position. (C) The reservoir is inserted in the injector device system and ready to use. Figure S4. Model highlighting the potentially contaminable area of the reservoir behind the rubber seal (★), for visualization a fluorescent solution was used (A: resting position, B: rubber seal pushed in, C: rubber seal back in resting position). Figure S5. Principal component analysis: Four spectra were recorded for each isolate A-H. Two-dimensional plot of the first two principal components indicating the two clusters I (isolates A and B) and II (isolates C, D, E and F) and the “unrelated” isolates G and H. Figure S6. PFGE based typing of isolates A-H. The scale indicates the degree of similarity (%) as calculated by dice correlation analysis.