Genotypic relatedness of 1020 MRSA isolates represented as a minimum spanning tree based on MLVA types.

<p>Clustering of MLVA profiles was obtained using a categorical coefficient to create a minimum spanning tree in which the MLVA types are displayed as circles. The size of each circle indicates the number of isolates with this particular type. MLVA complexes (MC) are indicated in characters e.g. MC398 denotes MLVA complex 398.</p

Weekly relative abundance of each species throughout the swarming season.

<p>Samples were pooled across all sampled swarming sites per week to compensate for weather effects. Species are sorted based on the timing of peak swarming activity (from earliest: <i>Pipistrellus pipistrellus</i> to latest: <i>Myotis nattereri</i>). No clear peak in swarming activity was observed for <i>Myotis myotis</i> and <i>Plecotus auritus</i>.</p

Descriptive characteristics of the underground sites we sampled.

<p>Abbreviations: latitude and longitude in decimal degrees (Coordinates); altitude at the site entrance in meters (Alt); the number of entrances (N); the total entrance size (Size); the orientation of the entrance (Orientation); degree of shelter around the entrance (Shelter); the surface area of the mine in ha (Area); degree of chamber development (Chamber); hydrological activity in the mine (Hydr.); and the number of species observed during swarming (Swarm), and hibernation surveys (Hiber). All subjective mine characteristics (Orientation, Shelter, Chamber development, Hydrology) were characterized as described in Glover and Altringham [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130850#pone.0130850.ref013" target="_blank">13</a>]. Remaining measurements were obtained from the Studiegroep Onderaardse Kalksteengroeven [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130850#pone.0130850.ref036" target="_blank">36</a>], and updated based on the dataset of AJH.</p><p>Descriptive characteristics of the underground sites we sampled.</p

Unknown risk factor (MUO) and proportion of MC398 within this group, shown per hospital.

<p>Unknown risk factor (MUO) and proportion of MC398 within this group, shown per hospital.</p

MRSA sources in patients in 17 Dutch hospitals, 2009–2010.

<p>MRSA sources in patients in 17 Dutch hospitals, 2009–2010.</p

Pig-densities in the Netherlands.

<p>Hospitals with high pig-densities in the adherence areas are presented within the circle.</p

Detail of the whole genome maps of an outbreak of CA-MRSA (USA300) showing an additional DNA segment in 3 isolates.

<p>All isolates had <i>spa</i>-type t024 and MLVA-type MT308. The gel image on the right hand side shows the PFGE profiles with an additional 80 kb band in the lower 3 isolates.</p

Detail of the WGMs of two veterinarians and their household members showing transmission events.

<p>A and B denote the clusters with highly similar WGMs of isolates obtained from VET45 and his household members (light red block). C denotes the cluster with highly similar WGMs of isolates obtained from VET66 and his household members (blue block). Sampling time-points, sampling sites, <i>spa</i>-type, MLVA-type and PFGE-type are indicated on the right hand side of the maps. The PFGE-type numbers are arbitrary numbers.</p

Examples of differences between the WGMs created in the lab and their <i>in-silico</i> counterparts.

<p>The figure shows details of the comparisons of the maps of LA-MRSA strain S0385 and MRSA strains N315 and NCTC8325. The WGMs are represented as linear maps displaying the fragments in randomly chosen colours, with matching fragments sharing the same colour.</p

Bacterial strains used in this study.

*<p>VET-study, isolates collected for a longitudinal MRSA carriage study among veterinarians and written consent was provided by all participants (E. Verkade personal communication).</p