Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study

In this study, we performed a longitudinal metagenetic approach in a newly opened ward at the Charité Hospital (Berlin) to characterize the dynamics of the bacterial colonization process in the hospital environment after first patient occupancy. The sequencing data showed a site-specific taxonomic succession, which led to stable community structures after only a few weeks. This archive contains results and data of the 16S rRNA amplicon sequencing performed on 854 environmental and 408 patient DNA samples collected over the time course of 31 weeks in a newly opened ward in the neurological station at the Charité Hospital (Berlin). The files include a study information and sample metadata sheets, BIOM-tables and information about the taxonomy results and diversity metrics. Files:<br> * Study information<br> Study_information.csv<br> * Sample metadata<br> Mapping_file_patient_samples.txt<br> Mapping_file_environmental_samples.txt<br> * BIOM-tables and taxonomy summaries<br> otu_table_n10_mFr02_Patient.biom<br> otu_table_n10_mFr02_environment.biom<br> Patients_taxonomy_SILVA99_L5.txt<br> Environment_taxonomy_SILVA99_L5.txt<br> * Beta-diversity results<br> weighted_unifrac_dm_environment.txt<br> weighted_unifrac_pc_environment.txt<br> weighted_unifrac_dm_patient_environment.txt<br> weighted_unifrac_pc_patient_environment.txt<br> <br> Analyses:<br> Analyses were perfomed in QIIME v.1.9.1 using the SILVA NR REF 99 (release 132) database for taxonomic assignment.