1. Pan-genome multilocus sequence typing and outbreak-specific reference-based single nucleotide polymorphism analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services 
S. Roisin, C. Gaudin, R. De Mendonça, J. Bellon, K. Van Vaerenbergh, K. De Bruyne, B. Byl, H. Pouseele, O. Denis, P. Supply 
Clinical Microbiology and Infection 
Volume 22, Issue 6, Pages (June 2016)
DOI: /j.cmi
Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

2. Fig. 1
Timeline of methicillin-susceptible Staphylococcus aureus (MSSA) eta+ spa-type t209 outbreaks in neonatal services from two geographically proximate Belgian hospitals. Cases (infection and colonization) are ordered according to date of S. aureus positive sample, indicated by a red box. Note that positive samples were obtained after consultation following the hospitalization period for some patients in Asse. Periods from patient admission to exit are indicated by horizontal bars. Pairs of twin neonate patients are indicated by shared musical note symbols; stars indicate two samples not subjected to whole genome sequencing analysis. HCW, health care worker. The prevalence of MSSA colonization before and during the decolonization period at Erasme hospital was of 45% and 6.2%, respectively. Densities of incidence for MSSA-positive clinical sites were of 5.0/1000 patient-days before May 2011, 9,7/1000 patient-days between May and December 2011, and 1.7/1000 patient-days during the decolonization period.
Clinical Microbiology and Infection  , DOI: ( /j.cmi )
Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

3. Fig. 2
Distinction of methicillin-susceptible Staphylococcus aureus (MSSA) eta+ spa-type t209 outbreak and surveillance isolates by pan-genome multilocus sequence typing (MLST). Branches corresponding to Erasme and Asse outbreaks and surveillance isolates are shown respectively in red, green and black in an unweighted pair group method with arithmetic means-based tree, with results clipped at 200-locus differences. Note that a mean pairwise distance of > 200 alleles was also found between the outbreak A and outbreak B isolates when the analysis was based on core genome MLST (see Supplementary material, Fig. S3). The scale at the top and numbers at nodal positions refer to numbers of pan-genome MLST allelic differences. The sample selected for de novo assembly and used as a reference for single nucleotide polymorphism analysis is indicated by an arrow.
Clinical Microbiology and Infection  , DOI: ( /j.cmi )
Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

4. Fig. 3
Dissection of individual outbreaks at Erasme and Asse hospitals based on single nucleotide polymorphism (SNP) analysis on an outbreak-specific reference. Methicillin-susceptible Staphylococcus aureus (MSSA) eta+ spa-type t209 isolates from (a, b) Erasme (outbreak A) and (c, d) Asse (outbreak B). Numbers on maximum likelihood trees (a, c) indicate substitutions per site (corrected for estimated unobserved changes based on a sequence evolution model), whereas numbers on minimum spanning trees (b, d) indicate SNP distances between genome types (circles). Genome type codes refer to case numbers chronologically ordered according to Fig. 1.
Clinical Microbiology and Infection  , DOI: ( /j.cmi )
Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions