Microbiome signatures in neonatal central line associated bloodstream infections

Abstract

Neonates are at high risk for central line associated bloodstream infections (CLABSI). Biofilm formation is universal on indwelling catheters but why some biofilms seed the bloodstream to cause CLABSI is not clearly understood. With the objective to test the hypothesis that catheter biofilm microbiome in neonates with CLABSI differs than those without infection, we prospectively enrolled neonates (n = 30) with infected and uninfected indwelling central catheters. Catheters were collected at the time of removal, along with blood samples and skin swabs at the catheter insertion sites. Microbiomes of catheter biofilms, skin swabs and blood were evaluated by profiling the V4 region of the bacterial 16S rRNA gene using Illumina MiSeq sequencing platform. The microbial DNA load was higher from catheter biofilms of CLABSI patients without differences in alpha diversity when compared to that of the non-CLABSI neonates. Proteus and unclassified Staphylococcaceae were more abundant in infected catheter biofilms while Bradyrhizobium, Cloacibacterium, and Sphingomonas were more abundant in the uninfected catheters. A blood microbiome was detected in uninfected samples. The blood microbiome in CLABSI neonates clustered separately from the uninfected blood samples in beta diversity plots. We found that the microbiome signature in catheter biofilm and blood of neonates with CLABSI is different than the microbiomes of non-CLABSI neonates.

Fig 1. The bacterial load is higher in biofilms of infected catheters.

qPCR analysis of the bacterial 16S rRNA gene abundance in various samples studied. Significantly higher levels of bacterial DNA was detected in the infected catheters (n = 14) compared to the uninfected catheters (n = 12) (Mann-Whitney test p<0.05). *p<0.05, ns = non-significant (p>0.05). Cath = catheter, U = uninfected, I = infected.

Fig 2. Alpha diversity metrics in CLABSI and non-CLABSI neonates.

(A) Observed OTUs and (B) the Shannon Diversity Indices are presented in scatter plots. The alpha diversity metrics did not differ between infected and uninfected catheters.

Fig 3. Multivariate analysis of beta diversity.

PCoA plots of the microbial communities in infected (red circles) and uninfected samples (blue circles) of (A) catheter biofilms, (B) skin swab and (C) blood respectively as measured using unweighted UniFrac distances. Uninfected blood samples are clustered separately from the infected blood samples (see Fig 3C), but there is no clustering identified in the catheter biofilm or skin swab microbial communities. Figs D-F represents scatter plots of the weighted UniFrac distance metrics for the catheter, skin swab and blood microbiomes in uninfected and infected groups. Each circle represents the complete microbial community of a biological sample. The first 2 principal components (PC1and PC2), along with the amount of variation explained are shown in the figures.

Fig 4. The microbiome profile of infected catheters is distinct from uninfected catheters.

Bar plots representing the taxonomic composition of the catheter biofilm microbiota at the (A) phylum and (B) genus level for uninfected (n = 12) and infected (n = 15) catheters. Taxa with a mean relative abundance <1% are grouped together. Comparisons between infected and uninfected groups used a Mann-Whitney test. There was a significantly (p<0.05) lower abundance of Bradyrhizobium, Cloacibacterium, and Sphingomonas in infected catheters when compared to uninfected catheters (C-E). In contrast, infected catheter samples had a higher proportion of (F) Proteus and (G) unclassified Staphylococcaceae in comparison to the uninfected catheters.

Fig 5. Skin and blood microbiome composition of CLABSI and non-CLABSI neonates.

Columns represent the average relative abundance of bacterial taxa at (A) phylum and (B) genus level for uninfected (n = 5) and infected (n = 6) skin swabs collected from the non-CLABSI and CLABSI neonates, respectively. Bar plots showing the relative abundances of bacteria in individual blood samples collected from (C) blood culture negative (non-CLABSI) and (D) blood culture positive (CLABSI) neonates (identified on the x-axis). The results of the blood microbiomes are not combined for uninfected and infected groups because each individual within the group are very different in terms of their blood microbiome composition.