Metagenomes from 11 human infant fecal samples hospitalized in the same intensive care unit

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.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.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.