P2C268: Clinical Factors and Microbiome Associated with Staphylococcus aureus Colonization in Neonates

Background: Staphylococcus aureus is a major pathogen in the NICU. Identification of S. aureus colonization and decolonization strategies of colonized infants can lead to decreased rates of S. aureus infections. Decolonization efforts may be unsuccessful due to persistent colonization or re-acquiring colonization during hospitalization. Little is known about the host microbiome, clinical factors, or microbial factors that may be associated with colonization or unsuccessful decolonization. Our objectives were to identify characteristics of the skin and nares bacterial microbiome as well as clinical characteristics associated with S. aureus colonization and unsuccessful decolonization, defined as S. aureus detected after decolonization strategies.

Methods: We performed a prospective cohort pilot study of inborn infants of 25-34 weeks gestational age (GA). Per hospital policy, all infants in the NICU have twice monthly surveillance for methicillin-susceptible and methicillin-resistant S. aureus (MSSA and MRSA) using pooled swabs of the anterior nares and 3 skin sites- the axilla, umbilicus, and groin. Infants colonized with S. aureus undergo decolonization with mupirocin ointment for mupirocin-susceptible S. aureus and chlorhexidine gluconate (CHG) baths during the same week. For this study, enrolled infants had individual swabs of the anterior nares, axilla and umbilicus collected within 48 hours of surveillance cultures. DNA was extracted using the Powersoil Pro kit (Qiagen) and sequencing of the 16S rRNA (V3/V4) was performed using Illumina MiSeq. The DADA2 pipeline was utilized to analyze the data and characterize the skin and nasal microbial communities over time. Demographic and clinical characteristics data were collected from enrolled infants.

Results: We enrolled 52 infants of whom ten (19.2%) acquired colonization with MSSA and 6 (60%) were successfully decolonized. None developed an invasive S. aureus infection. Two (33.3%) of 6 re-acquired MSSA colonization during hospitalization. (Figure 1). The mean GA of colonized (30.3 weeks) and uncolonized (31.8 weeks) infants were similar. Compared with uncolonized infants, colonized infants were more likely to have an endotracheal tube (5/42, 12% vs 5/10, 50% [OR 7.4, CI 1.56-34.93) and a central line (10/42, 24% vs 5/10, 50% [OR 3.2, CI 0.77-13.35]), although the latter was not significantly associated with colonization. In colonized infants, S. aureus was most often detected in the anterior nares by 16S testing. Preliminary analysis, by differential abundance testing, revealed an increased presence of common commensal organisms, such as coagulase-negative Staphylococcal species or Rothia species in colonized infants after successful decolonization. (Figure 2). We also noted increased presence of commensal organisms in uncolonized infants compared with their colonized counterparts.

Conclusion: The presence of invasive devices may be associated with increased risk of S. aureus colonization. Colonization with common commensal organisms may play a protective role against S. aureus colonization . Further investigation into the microbiome changes associated with S. aureus colonization may help improve current decolonization strategies.