Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

Abstract

BackgroundThe source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW, <1,500 g) neonates via conventional broad-spectrum antibiotic treatment. We hypothesize the built environment (BE), specifically room surfaces frequently touched by humans, is a predominant source of colonizing microbes in the gut of premature VLBW infants. Here, we present the first matched fecal-BE time series analysis of two preterm VLBW neonates housed in a neonatal intensive care unit (NICU) over the first month of life.ResultsFresh fecal samples were collected every 3 days and metagenomes sequenced on an Illumina HiSeq2000 device. For each fecal sample, approximately 33 swabs were collected from each NICU room from 6 specified areas: sink, feeding and intubation tubing, hands of healthcare providers and parents, general surfaces, and nurse station electronics (keyboard, mouse, and cell phone). Swabs were processed using a recently developed ‘expectation maximization iterative reconstruction of genes from the environment’ (EMIRGE) amplicon pipeline in which full-length 16S rRNA amplicons were sheared and sequenced using an Illumina platform, and short reads reassembled into full-length genes. Over 24,000 full-length 16S rRNA sequences were produced, generating an average of approximately 12,000 operational taxonomic units (OTUs) (clustered at 97% nucleotide identity) per room-infant pair. Dominant gut taxa, including Staphylococcus epidermidis, Klebsiella pneumoniae, Bacteroides fragilis, and Escherichia coli, were widely distributed throughout the room environment with many gut colonizers detected in more than half of samples. Reconstructed genomes from infant gut colonizers revealed a suite of genes that confer resistance to antibiotics (for example, tetracycline, fluoroquinolone, and aminoglycoside) and sterilizing agents, which likely offer a competitive advantage in the NICU environment.ConclusionsWe have developed a high-throughput culture-independent approach that integrates room surveys based on full-length 16S rRNA gene sequences with metagenomic analysis of fecal samples collected from infants in the room. The approach enabled identification of discrete ICU reservoirs of microbes that also colonized the infant gut and provided evidence for the presence of certain organisms in the room prior to their detection in the gut.

Patterned progression of bacterial populations in the premature infant gut

“…First, it is important to determine where gut bacteria originate. Possibilities include an autochthonous source, especially if the fetus is colonized in utero (23) by viable progenitors of the organisms whose sequences we identified, and/or exogenous origins including nonpasteurized maternal breast milk, family or staff handlers, or fomites (24). Indeed, we recently demonstrated the simultaneous presence of specific pathogens in the stools of premature infants in proximity to each other, so patient-to-patient transmission is certainly a component (16).…”

“…Studies of gut bacteria in preterm infants have been limited in subject and/or sample numbers (24,28,29), have used cross-sectional comparisons (30), or did not stratify extensively by gestational age at birth or age postconception (30)(31)(32)(33)(34)(35)(36). Our intensive and extensive dataset suggests that limited sampling in premature neonates is problematic because of very frequent alterations in population structure.…”

Antibiotic perturbation of the preterm infant gut microbiome and resistome

“…Of the 794 functionally identified antibiotic resistance genes, 42% were encoded by E. coli, Enterobacter cloacae, and K. pneumoniae, taxa which include many pathogenic strains implicated in nosocomial infections in preterm infants. 34,43 Interestingly, the sequences of the majority of resistance determinants uncovered by the functional metagenomics screens were already present in protein databases. However, they were not found in antibiotic resistance specific databases, indicating that they had not previously been ascribed a resistance function and highlighting a key advantage of using functional metagenomics.…”

“…4,20,27,[32][33][34] Until recently, similar efforts to characterize the preterm infant gut reservoir of antibiotic resistance genes (the resistome) have been largely culture or PCR-based. While these methods can provide a high level overview of the resistome, they underestimate diversity, are limited to previously known resistance genes, and are only semi-quantitative.…”

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

“…Initial colonists are acquired maternally and from the immediate environment, but early life clinical factors (such as birth by cesarean section and neonatal antibiotic administration) can disrupt the normal acquisition process (Ding and Schloss 2014;Bäckhed et al 2015;Mueller et al 2015). Among premature infants, who generally harbor microbial communities of limited diversity and instability Sim et al 2013;Ward et al 2016), this disruption can lead to colonization by resident microbes of the neonatal intensive care unit (NICU) (Brooks et al 2014;Shin et al 2015).…”