The cutaneous microbiome in outpatients presenting with acute skin abscesses

Abstract

Background: Previous studies have demonstrated an association between antibiotic use and the development of skin abscesses. We tested the hypothesis that alterations in the composition of the cutaneous microbiota may predispose individuals to skin abscesses.

Methods: We studied 25 patients with skin abscesses and 25 age-matched controls, who each completed a questionnaire. Skin swab samples were obtained for DNA analysis from 4 sites around the abscess site (hereafter, "peri-abscess specimens") and from similar sites on the patient's contralateral side and on healthy control subjects. DNA was extracted and analyzed by quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. The purulent abscess drainage was sent for culture.

Results: Fifteen patients with abscess were infected with Staphylococcus aureus. Use of nuc qPCR to quantitate S. aureus revealed a significantly greater frequency of positive results for peri-abscess and contralateral skin samples, compared with control skin specimens. Analysis of community structure showed greater heterogeneity in the control samples than in the peri-abscess and contralateral samples. Metagenomic analysis detected significantly more predicted genes related to metabolic activity in the peri-abscess specimens than in the control samples.

Conclusions: The peri-abscess microbiome was similar to the contralateral microbiome, but both microbiomes differed from that for control patients. Host characteristics affecting microbial populations might be important determinants of abscess risk.

Keywords: MRSA; abscess; skin infection; skin microbiome.

Figure 1.

Study design and bacteriologic characteristics of the study subjects. Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus; MSSA, methicillin-susceptible Staphylococcus aureus.

Figure 2.

Comparison of quantitative polymerase chain reaction (qPCR) positivity in cutaneous samples from 50 study subjects. A, Mean log₁₀ copies (±standard error of the mean [SEM]) for each gene obtained by qPCR assays for the 4 samples per site in 25 patients (2 sampled sites each) and 25 controls (1 sampled site each). Green denotes specimens from matched control subjects (C), blue denotes contralateral specimens from patients (AC), and red denotes peri-abscess specimens from patients (A). Significance was determined by 1-way analysis of variance with the Tukey analysis for multiple comparisons. Significant differences were found between all 3 comparisons for nuc and mecA, except for A vs AC for nuc. *P < .05, **P < .01, ***P < .001, and ****P < .0001. B, Enumeration of 4 qPCR comparisons in the samples from patients and controls, based on the S. aureus status of the abscess. Mean log₁₀ copies (±SEM) for each indicator gene obtained by qPCR assays; total bacterial and Staphylococcus populations were determined by detection of 16S ribosomal RNA, the presence of S. aureus was determined on the basis of nuc detection, and methicillin-resistant Staphylococcus aureus was determined on the basis of mecA detection. The colors of the 3 groups of samples are defined as described in panel A. Significant differences were found between C and A for S. aureus (P = .0003) and for mecA (P = .041) in the samples from the S. aureus–positive groups, using the Friedman method with the Dunn multiple comparisons adjustment. Significant differences were also obtained according to S. aureus status for nuc (P < .0001) and mecA (P = .046) in the peri-abscess samples and for nuc (P = .025) in the contralateral samples, by the Mann–Whitney U test.

Figure 3.

β-diversity for 75 cutaneous samples, based on the sample site (for patients, specimens from the peri-abscess region [A] and contralateral region [AC]; for controls, specimens from the site complementary to the abscess location on the matched patient [C]). A, Clustering of study subjects by Staphylococcus aureus status, using principal coordinates analysis based on unweighted Unifrac distances. The 75 samples from 50 subjects were divided into 3 groups on the basis of sampled sited (A, AC, and C). Red denotes S. aureus positivity (n = 15 for each group), and green denotes S. aureus negativity (n = 10 for each group). By Adonis testing, P > .05 based on the S. aureus status, in all three groups. B, Intergroup and intragroup β-diversity. Mean pairwise unweighted Unifrac distances (±standard error of the mean [SEM]) are shown. Significance was determined by 1-way ANOVA with the Tukey method for correction for multiple comparisons. **P < .01, ***P < .001, and ****P < .0001 for differences in unweighted Unifrac distances. No significant differences were observed between the groups in the weighted pairwise comparisons.

Figure 4.

Clustered displays of taxonomic and functional data from 50 subjects. A, Unweighted pair group method with arithmetic mean cluster of the 75 samples from the 50 subjects, based on the unweighted Unifrac distance matrix with Jackknife analysis. The samples from the same microenvironment type are indicated by the same color, as follows: dry sites, red (n = 36); moist sites, green (n = 30); and sebaceous sites, blue (n = 9). The boxed samples are from the same subject. The 3 clusters are shown with bold numbers. In cluster 1, 20 of 27 samples (74%) are from moist skin. In cluster 3, 13 of 18 samples (72%) are from dry skin. Cluster 2 is a mixture of the 3 skin types. Jackknife support fractions of ≥0.5 are shown. B, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States–predicted metagenome with significant differences in relative abundance. Samples are from patients with abscesses who did (n = 8; red) or did not (n = 17; green) receive antibiotics, and functional gene pathways categories with linear discriminant analysis scores of ≥2 are shown. Five of 9 functional gene pathways (56%) in both groups are constituents of the metabolism category. The red box indicates gene pathways with significant abundance in the patients with a history of relatively recent antibiotic use; the green box indicates significant abundance in the patients without recent antibiotic use history. *P < .05 for gene pathway categories that are significantly different after false-discovery rate correction. Abbreviation: SD, standard deviation.