Clonal sharing of antimicrobial-resistant bacterial clones and homogenization of the microbiome in the oral, nasal, and endotracheal sites of intubated ICU patients

Colonization by drug-resistant bacteria in intubated patients admitted to the intensive care unit (ICU) often causes serious infections. Therefore, assessing drug-resistant status and flora at multiple sites in patients is important. To compare the microbial composition of the oral or nasal cavity, and endotracheal intubation site (subglottic secretory site), we isolated Staphylococcus aureus (including methicillin-resistant S. aureus [MRSA]) and third-generation cephalosporin-resistant Gram-negative rods from 61 ICU patients. Whole-genome analysis of isolates was performed, and clonal concordance across sites was assessed using core-genome SNP distances. The 16S rRNA gene analysis was used to examine the microbial composition at these sites. S. aureus , MRSA, and gram-negative drug-resistant bacteria were isolated from 57.4%, 16.4% and 18.0% patients, respectively. In some patients with the same bacterial species isolated from multiple sites, SNPs among isolates were 0–9, suggesting shared clone or closely related lineage within individuals. Microbial flora analysis, based on PCoA using UniFrac distance, showed that the bacterial communities at three different sites in ICU patients were closely related. These findings suggest similar colonization of three different sites. The finding that similar colonization of three different sites was observed is expected to contribute to developing future infection prevention strategies in ICUs.