SAMEA14085705 ERS11688836 uncultured Actinomyces sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR3546782 of study SRP074153. EBI Generic Generic.1.0 ERC000047 2023-01-03 2023-01-03 SAMEA14085705 EBI European Bioinformatics Institute 2023-01-03T00:33:40Z 2023-01-03T00:33:40Z public SRR3546782_bin.35_CONCOCT_v1.1_MAG Many fragments with little to no review of assembly other than reporting of standard assembly statistics metaspadesv3.11.1 Default CONCOCT v1.1 EMG broker account, EMBL-EBI 2012-04-01 99.29 CheckM 0.95 Host-associated Human Digestive system USA 40.4308 -79.9598 metagenome-assembled genome human gut metagenome human gut metagenome Bacteria that persist in hospitals can contribute to the establishment of the microbiome in newborns and the spread of hospital-acquired diseases. Yet we know little about microbial communities in hospitals, or about the extent to which persistent vs. recently immigrated bacterial strains establish in the gastrointestinal tracts of hospitalized individuals.</p><p>In combination with BioProject PRJNA273761 (10 infants / 55 samples) we analyzed strain-resolved genomes obtained from a total of 202 samples collected over a three-year period from 21 infants hospitalized in the same intensive care unit.</p><p>Strains were rarely shared, consistent with prior analysis of a subset of these data. Enterococcus faecalis and Staphylococcus epidermidis, common gut colonists, exhibit diversity comparable to that of NCBI reference strains, suggesting no recent common ancestor for all populations in this hospital setting. Thus, we infer multiple introduction events for these species. Despite the rarity of shared strains, strains of five species exhibiting a degree of sequence variation consistent with in situ diversification were identified in different infants hospitalized three years apart. Three were also detected in multiple infants in the same year, suggesting that these strains are unusually widely dispersed and persistent in the hospital environment. Persistent strains were not significantly different from non-persistent strains with regards to pathogenicity potential including antibiotic resistance. Notably, non-identical siblings had multiple abundant strains in common, even 30 days after birth and antibiotic administration, suggesting overlapping strain sources and/or genetic selection. Our approach can be used in order to study microbial dynamics in hospitals and provides an important step towards directing health-promoting colonization in hospitalized individuals. SAMN04161035 SRR3546782_bin.35_CONCOCT_v1.1_MAG uncultured Actinomyces sp. Illumina HiSeq 2000 multi-marker approach