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Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development.

Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF - Elife (2015)

Bottom Line: Thus, spread of potential pathogens among hospitalized infants is of great concern.We compared microbial communities in infants who did and did not develop necrotizing enterocolitis.Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.

ABSTRACT
Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. Thus, spread of potential pathogens among hospitalized infants is of great concern. Here, we reconstructed hundreds of high-quality genomes of microorganisms that colonized co-hospitalized premature infants, assessed their metabolic potential, and tracked them over time to evaluate bacterial strain dispersal among infants. We compared microbial communities in infants who did and did not develop necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, our genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants who developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to the spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.

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Aspartyl-tRNA synthetase from Klebsiella pneumoniaestrains in samples from infants #4, #5, #6,#7, and #8.Note the strain switch in Klebsiella pneumoniaefollowing treatment of infant #5.DOI:http://dx.doi.org/10.7554/eLife.05477.008
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fig4s2: Aspartyl-tRNA synthetase from Klebsiella pneumoniaestrains in samples from infants #4, #5, #6,#7, and #8.Note the strain switch in Klebsiella pneumoniaefollowing treatment of infant #5.DOI:http://dx.doi.org/10.7554/eLife.05477.008

Mentions: Infant #8 developed NEC 1 day after collection of the last sample. Thecommunities in the two pairs of samples from different times on the same day (Figure 8—figure supplement 3) containgenerally similar organisms, but rapid abundance shifts occur, consistent withgeneral observations over whole day periods. Especially prominent in samples frominfant #8 were a Klebsiella pneumoniae-related strain (Figure 4—figure supplement 2) and anE. cloacae (Figure4—figure supplement 1) strain. C. perfringens has anotable inventory of predicted pathogenicity-related genes. E. coli,present in the three samples collected prior to diagnosis, may have contributed tointestinal inflammation, given that it has a large inventory of type III and type VIsecretion system genes and many toxin-encoding genes (Supplementary file 4).


Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development.

Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF - Elife (2015)

Aspartyl-tRNA synthetase from Klebsiella pneumoniaestrains in samples from infants #4, #5, #6,#7, and #8.Note the strain switch in Klebsiella pneumoniaefollowing treatment of infant #5.DOI:http://dx.doi.org/10.7554/eLife.05477.008
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384745&req=5

fig4s2: Aspartyl-tRNA synthetase from Klebsiella pneumoniaestrains in samples from infants #4, #5, #6,#7, and #8.Note the strain switch in Klebsiella pneumoniaefollowing treatment of infant #5.DOI:http://dx.doi.org/10.7554/eLife.05477.008
Mentions: Infant #8 developed NEC 1 day after collection of the last sample. Thecommunities in the two pairs of samples from different times on the same day (Figure 8—figure supplement 3) containgenerally similar organisms, but rapid abundance shifts occur, consistent withgeneral observations over whole day periods. Especially prominent in samples frominfant #8 were a Klebsiella pneumoniae-related strain (Figure 4—figure supplement 2) and anE. cloacae (Figure4—figure supplement 1) strain. C. perfringens has anotable inventory of predicted pathogenicity-related genes. E. coli,present in the three samples collected prior to diagnosis, may have contributed tointestinal inflammation, given that it has a large inventory of type III and type VIsecretion system genes and many toxin-encoding genes (Supplementary file 4).

Bottom Line: Thus, spread of potential pathogens among hospitalized infants is of great concern.We compared microbial communities in infants who did and did not develop necrotizing enterocolitis.Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.

ABSTRACT
Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. Thus, spread of potential pathogens among hospitalized infants is of great concern. Here, we reconstructed hundreds of high-quality genomes of microorganisms that colonized co-hospitalized premature infants, assessed their metabolic potential, and tracked them over time to evaluate bacterial strain dispersal among infants. We compared microbial communities in infants who did and did not develop necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, our genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants who developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to the spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.

Show MeSH
Related in: MedlinePlus