Limits...
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.

Show MeSH

Related in: MedlinePlus

Alignment view of genome-wide differences in Clostridiumparaputrificum strains.This organism is one of the very few for which a single strain (found forexample in infant #5, sample 1 shown here) was detected inmultiple infants. Consensus sequence for the alignments (shown at the topof each alignment) represents the calculated order of the most frequentnucleotide residues. Alignments were done in Geneious v7.1.7 (Kearse et al., 2012), using MAFFTv7.017 (Katoh et al., 2002) withdefault parameters. Samples are ordered by similarity. For each sample,SNPs and indel locations relative to the multiple alignment are marked byblack lines or boxes. Reads from three samples, from which differentClostridium paraputrificum strains were recovered(infant #5 samples 1 and 7, infant #6 sample 3) were mappedto three 100–200 Kbp scaffolds (infant #5 sample 1,scaffolds 3 and 8, and infant #5 sample 7, scaffold 41). Shown isa multiple alignment of the consensus sequences derived for each samplefrom these mappings. The different strains are very closely related, yetmultiple SNPs and short indels are detected throughout the sequence.Large indels shown in the bottom panels are both associated with mobileelements.DOI:http://dx.doi.org/10.7554/eLife.05477.011
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4384745&req=5

fig6s1: Alignment view of genome-wide differences in Clostridiumparaputrificum strains.This organism is one of the very few for which a single strain (found forexample in infant #5, sample 1 shown here) was detected inmultiple infants. Consensus sequence for the alignments (shown at the topof each alignment) represents the calculated order of the most frequentnucleotide residues. Alignments were done in Geneious v7.1.7 (Kearse et al., 2012), using MAFFTv7.017 (Katoh et al., 2002) withdefault parameters. Samples are ordered by similarity. For each sample,SNPs and indel locations relative to the multiple alignment are marked byblack lines or boxes. Reads from three samples, from which differentClostridium paraputrificum strains were recovered(infant #5 samples 1 and 7, infant #6 sample 3) were mappedto three 100–200 Kbp scaffolds (infant #5 sample 1,scaffolds 3 and 8, and infant #5 sample 7, scaffold 41). Shown isa multiple alignment of the consensus sequences derived for each samplefrom these mappings. The different strains are very closely related, yetmultiple SNPs and short indels are detected throughout the sequence.Large indels shown in the bottom panels are both associated with mobileelements.DOI:http://dx.doi.org/10.7554/eLife.05477.011

Mentions: Both the single copy gene and CRISPR-Cas analysis suggested that E.faecalis in infants #2 and #7 are very closely related.Similarly, the strains in infant #3 and in early samples from infant #5are almost identical (a single SNP in the surveyed gene set distinguished thesequences). To gain better understanding of the type and extent of genomicdifferences between the recovered E. faecalis genomes, andspecifically of these closely related genome pairs, we mapped reads from eightsamples, representative of the eight different genotypes reported in Figure 2, to a 1 Mbp E. faecalisscaffold recovered from infant #9, sample 1 (one third of the recoveredgenome). Multiple alignment of the consensus sequences from mapping of each sampleprovided a view of sequence variability across strains (Figure 6A; a similar alignment for C.paraputrificum strains is shown in Figure 6—figure supplement 1). The analysis revealed many SNPlocations and small indels that were spread across the entire length of the sequence,as well as a small number of longer (20–30 Kbp) indel regions. These regionsincluded among other things a sucrose metabolism operon, mobile elements, and genesrelated to Fe-S protein biogenesis.10.7554/eLife.05477.010Figure 6.Alignment view of genome-wide differences in Enterococcusfaecalis strains.


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)

Alignment view of genome-wide differences in Clostridiumparaputrificum strains.This organism is one of the very few for which a single strain (found forexample in infant #5, sample 1 shown here) was detected inmultiple infants. Consensus sequence for the alignments (shown at the topof each alignment) represents the calculated order of the most frequentnucleotide residues. Alignments were done in Geneious v7.1.7 (Kearse et al., 2012), using MAFFTv7.017 (Katoh et al., 2002) withdefault parameters. Samples are ordered by similarity. For each sample,SNPs and indel locations relative to the multiple alignment are marked byblack lines or boxes. Reads from three samples, from which differentClostridium paraputrificum strains were recovered(infant #5 samples 1 and 7, infant #6 sample 3) were mappedto three 100–200 Kbp scaffolds (infant #5 sample 1,scaffolds 3 and 8, and infant #5 sample 7, scaffold 41). Shown isa multiple alignment of the consensus sequences derived for each samplefrom these mappings. The different strains are very closely related, yetmultiple SNPs and short indels are detected throughout the sequence.Large indels shown in the bottom panels are both associated with mobileelements.DOI:http://dx.doi.org/10.7554/eLife.05477.011
© Copyright Policy
Related In: Results  -  Collection

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

fig6s1: Alignment view of genome-wide differences in Clostridiumparaputrificum strains.This organism is one of the very few for which a single strain (found forexample in infant #5, sample 1 shown here) was detected inmultiple infants. Consensus sequence for the alignments (shown at the topof each alignment) represents the calculated order of the most frequentnucleotide residues. Alignments were done in Geneious v7.1.7 (Kearse et al., 2012), using MAFFTv7.017 (Katoh et al., 2002) withdefault parameters. Samples are ordered by similarity. For each sample,SNPs and indel locations relative to the multiple alignment are marked byblack lines or boxes. Reads from three samples, from which differentClostridium paraputrificum strains were recovered(infant #5 samples 1 and 7, infant #6 sample 3) were mappedto three 100–200 Kbp scaffolds (infant #5 sample 1,scaffolds 3 and 8, and infant #5 sample 7, scaffold 41). Shown isa multiple alignment of the consensus sequences derived for each samplefrom these mappings. The different strains are very closely related, yetmultiple SNPs and short indels are detected throughout the sequence.Large indels shown in the bottom panels are both associated with mobileelements.DOI:http://dx.doi.org/10.7554/eLife.05477.011
Mentions: Both the single copy gene and CRISPR-Cas analysis suggested that E.faecalis in infants #2 and #7 are very closely related.Similarly, the strains in infant #3 and in early samples from infant #5are almost identical (a single SNP in the surveyed gene set distinguished thesequences). To gain better understanding of the type and extent of genomicdifferences between the recovered E. faecalis genomes, andspecifically of these closely related genome pairs, we mapped reads from eightsamples, representative of the eight different genotypes reported in Figure 2, to a 1 Mbp E. faecalisscaffold recovered from infant #9, sample 1 (one third of the recoveredgenome). Multiple alignment of the consensus sequences from mapping of each sampleprovided a view of sequence variability across strains (Figure 6A; a similar alignment for C.paraputrificum strains is shown in Figure 6—figure supplement 1). The analysis revealed many SNPlocations and small indels that were spread across the entire length of the sequence,as well as a small number of longer (20–30 Kbp) indel regions. These regionsincluded among other things a sucrose metabolism operon, mobile elements, and genesrelated to Fe-S protein biogenesis.10.7554/eLife.05477.010Figure 6.Alignment view of genome-wide differences in Enterococcusfaecalis strains.

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