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. 2019 Jul:128:29-35.
doi: 10.1016/j.fgb.2019.03.008. Epub 2019 Mar 21.

Breastmilk and NICU surfaces are potential sources of fungi for infant mycobiomes

Timothy Heisel  1 , Linet Nyaribo  1 , Michael J Sadowsky  2 , Cheryl A Gale  3
Affiliations

Breastmilk and NICU surfaces are potential sources of fungi for infant mycobiomes

Timothy Heisel et al. Fungal Genet Biol. 2019 Jul.

Abstract

Surfaces within the neonatal intensive care unit (NICU), especially those handled frequently by hospital staff, provide sources of gut-colonizing bacteria for hospitalized infants, in addition to those acquired perinatally from maternal sources such as breastmilk. In comparison to bacteria, very little is known about potential sources of colonizing fungi in the NICU setting. Thus, the objective of this study was to characterize fungal communities (mycobiomes) of potential colonization sources for neonates hospitalized in a large university NICU. We hypothesized that the unit surfaces would contain different mycobiomes than those of human-associated (breastmilk) sources. We characterized mycobiomes of NICU surfaces of multiple individual patient care areas as well as those of breastmilk samples by sequencing the internal transcribed spacer region 2 (ITS2) of the fungal rDNA locus. We found that, across all samples, Candida and Saccharomyces species were the most prevalent taxa and had the greatest relative abundances. Breastmilk samples had significantly higher fungal alpha-diversities than NICU surface samples and fungal community compositions (beta diversities) differed significantly between the two sample types. Mycobiome compositions were predominantly driven by the relative abundances of three fungal taxa: Candida albicans, Candida parapsilosis, and Saccharomyces cerevisiae. In total, 21 individual fungal taxa showed significantly greater relative abundances in breastmilk as compared to NICU surfaces, with three being of particular interest to human health: Candida glabrata, Candida tropicalis, and Cryptococcus neoformans. Since no fungal DNA was detected when whole breastmilk was used as the DNA template, as opposed to breastmilk subjected to cell lysis during the DNA isolation procedure, our results indicate that DNA is from fungal cells and is not cell-free DNA. In summary, both NICU surfaces and human breastmilk harbor distinct fungal communities that could provide a source of fungi for the developing infant gut mycobiota. In particular, Candida and Saccharomyces species are abundant and prevalent for both of these potential sources that infants are exposed to.

Keywords: Breastmilk; Fungi; Hospital surfaces; Mycobiome; Newborn intensive care.

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Figures

Figure 1.
Figure 1.
Breastmilk samples yield significantly more fungal sequencing reads than NICU surfaces. Box-whisker plot of the number of sequence reads from each sample type. Mean sequence reads for each sample type are noted in Table 1.
Figure 2.
Figure 2.
Relative abundances of fungal taxa on NICU surfaces and in breastmilk. Mean fungal sequence reads are displayed as percentages of the total number of sequence reads for each sample type. The relative abundance taxonomy plots for individual samples from each site are shown in Supplementary Figures 1–5.
Figure 3.
Figure 3.
Relative abundances of Cryptococcus neoformans, Candida glabrata, and Candida tropicalis are significantly higher for breastmilk as compared to NICU surfaces. Additional taxa that differed significantly between NICU surfaces and breastmilk are shown in Supplemental Figure 6.
Figure 4.
Figure 4.
Breastmilk has significantly higher fungal diversity than any NICU surface (p<0.001 for all comparisons). Mean Shannon diversity indices are shown and significant differences between sample types were determined using Student’s t-test. Fungal diversity of NICU surfaces did not significantly differ depending on the particular surface. N.S., not significantly different with p > 0.05 for all comparisons.
Figure 5.
Figure 5.
Beta-diversity comparisons of fungal communities. PCoA of Bray-Curtis distances for (A) breastmilk (red dots) and NICU surface (black dots) samples. (B-D) Each sample (dot) is colored based on relative abundances of Candida albicans (B), Candida parapsilosis (C), and Saccharomyces cerevisiae (D), with darkest red indicating highest relative abundance values and lightest red representing lowest relative abundance, as indicated in the common heatmap shown in panel B. The proportion of variance explained by each principal coordinate (all plots) is 30.6 for PC1 and 17.0 for PC2.
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