MRSA colonization and the nasal microbiome in adults at high risk of colonization and infection.

OBJECTIVE: The objective of this study was to define the nasal microbiome of hospital inpatients who are persistently colonized with methicillin-resistant Staphylococcus aureus (MRSA) compared with matched, non-colonized controls. METHODS: Twenty-six persistently MRSA-colonized subjects and 26 matched non-colonized controls were selected from the screening records of the infection control program at the Department of the Veteran Affairs Eastern Colorado Health Care System (VA-ECHCS). The nasal microbiotas were analyzed with PCR amplification and sequencing of the 16S ribosomal RNA (rRNA) gene. Comparison of all variables across the groups was performed using stratified logistic regression to account for the one-to-one matching. Canonical discriminant analysis was performed to assess differences in bacterial community across the two groups. Competing organisms were cocultured with MRSA in vitro. RESULTS: There was a negative association between MRSA colonization and colonization with Streptococcus spp. At the species level, multivariate analysis demonstrated a statistically significant negative association between colonization with Streptococcus mitis or Lactobacillus gasseri and MRSA. Coculture experiments revealed in vitro competition between S. mitis and all of the 22 MRSA strains isolated from subjects. Competition was blocked by addition of catalase to the media. Persistently colonized subjects had lesser microbial diversity than the non-colonized controls. CONCLUSION: In a high-risk inpatient setting, bacterial competition in the nasal niche protects some patients from MRSA colonization.

Intestinal lesions are associated with altered intestinal microbiome and are more frequent in children and young adults with cystic fibrosis and cirrhosis.

BACKGROUND AND AIMS: Cirrhosis (CIR) occurs in 5-7% of cystic fibrosis (CF) patients. We hypothesized that alterations in intestinal function in CF contribute to the development of CIR. AIMS: Determine the frequency of macroscopic intestinal lesions, intestinal inflammation, intestinal permeability and characterize fecal microbiome in CF CIR subjects and CF subjects with no liver disease (CFnoLIV). METHODS: 11 subjects with CFCIR (6 M, 12.8 yrs ± 3.8) and 19 matched with CFnoLIV (10 M, 12.6 yrs ± 3.4) underwent small bowel capsule endoscopy, intestinal permeability testing by urinary lactulose: mannitol excretion ratio, fecal calprotectin determination and fecal microbiome characterization. RESULTS: CFCIR and CFnoLIV did not differ in key demographics or CF complications. CFCIR had higher GGT (59±51 U/L vs 17±4 p = 0.02) and lower platelet count (187±126 vs 283±60 p = 0.04) and weight (-0.86 ± 1.0 vs 0.30 ± 0.9 p = 0.002) z scores. CFCIR had more severe intestinal mucosal lesions on capsule endoscopy (score ≥4, 4/11 vs 0/19 p = 0.01). Fecal calprotectin was similar between CFCIR and CFnoLIV (166 µg/g ±175 vs 136 ± 193 p = 0.58, nl <120). Lactulose:mannitol ratio was elevated in 27/28 subjects and was slightly lower in CFCIR vs CFnoLIV (0.08±0.02 vs 0.11±0.05, p = 0.04, nl ≤0.03). Small bowel transit time was longer in CFCIR vs CFnoLIV (195±42 min vs 167±68 p<0.001, nl 274 ± 41). Bacteroides were decreased in relative abundance in CFCIR and were associated with lower capsule endoscopy score whereas Clostridium were more abundant in CFCIR and associated with higher capsule endoscopy score. CONCLUSIONS: CFCIR is associated with increased intestinal mucosal lesions, slower small bowel transit time and alterations in fecal microbiome. Abnormal intestinal permeability and elevated fecal calprotectin are common in all CF subjects. Disturbances in intestinal function in CF combined with changes in the microbiome may contribute to the development of hepatic fibrosis and intestinal lesions.