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:
* Study information
    Study_information.csv
* Sample metadata
    Mapping_file_patient_samples.txt
    Mapping_file_environmental_samples.txt
* BIOM-tables and taxonomy summaries
    otu_table_n10_mFr02_Patient.biom
    otu_table_n10_mFr02_environment.biom
    Patients_taxonomy_SILVA99_L5.txt
    Environment_taxonomy_SILVA99_L5.txt
* Beta-diversity results
    weighted_unifrac_dm_environment.txt
    weighted_unifrac_pc_environment.txt
    weighted_unifrac_dm_patient_environment.txt
    weighted_unifrac_pc_patient_environment.txt

Analyses:
Analyses were perfomed in QIIME v.1.9.1 using the SILVA NR REF 99 (release 132) database for taxonomic assignment.