Findings from a new study in Nature Communications focused on the nasal microbiome show that people who persistently carry Staphylococcus aureus (S. aureus) in the nose have fewer types of bacterial species. The data also indicate that certain bacterial species may help to prevent S. aureus colonization. The paper is titled “Large-scale characterization of the nasal microbiome redefines Staphylococcus aureus colonization status.”
The work was done by researchers at the Wellcome Sanger Institute, University of Cambridge, Imperial College London, and their collaborators elsewhere. They collected nasal swabs from over 1,000 blood donors with an eye toward analyzing the bacterial communities that live in the human nose. Their work links interactions between those species to the persistent S. aureus colonization in some nasal passages, and sheds light into who may be at most risk of S. aureus infections.
“Persistent S. aureus carriage is a well-recognised risk factor for infection, particularly in hospital settings,” said Dinesh Aggarwal, PhD, first author on the study and clinical lecturer in the Department of Infectious Disease at Imperial College London. “By identifying the bacterial profiles that protect against S. aureus colonization, our findings could inform new, microbiome-based strategies to reduce infection risk without relying on antibiotics.”
A common bacterium found in the nose of about 30% of people, S. aureus is usually harmless, but it can cause serious infections if it enters the body through wounds, cuts, or surgical incisions. According to one estimate, S. aureus is the second most common cause of mortality related to bacterial infections after tuberculosis. Some strains are resistant to common antibiotics, which makes them harder to treat.
Because S. aureus increases the risk of post-operative infections, hospitals often screen patients before procedures and may provide nasal treatments to reduce colonization. However, the nasal microbiome, unlike the gut microbiome, has not been studied in large populations, leaving much unknown about how S. aureus interacts with other nasal bacteria. That serves as the backdrop for the current study, which recruited volunteers from across England to study how different bacteria can influence S. aureus colonization.
Specifically, the team collected three weekly nasal swabs from 1,100 healthy adults. Each sample was tested for the presence of S. aureus using standard lab culture techniques. They performed DNA sequencing to identify the full range of bacterial species present in each nose swab, and used advanced statistics to uncover patterns in the nasal microbiome and to determine whether S. aureus carriage could be predicted by the broader bacterial community.
Two main patterns emerged. Firstly, persistent carriers have a distinct microbiome with an abundance of S. aureus and a lack of other species in the nasal samples. Secondly, bacteria such as Staphylococcus epidermidis, Dolosigranulum pigrum, and Moraxella catarrhalis were less common in persistent carriers, suggesting that these species might help resist S. aureus colonization in non-carriers. The researchers were also able to predict which individuals were persistently colonized with S. aureus, providing a possible method of predicting infection risk. This information is important clinically as identifying carriers of S. aureus could help healthcare professionals better target those who may benefit from microbial decolonisation treatments.
“Everyone’s nose microbiome is unique, and this study shows that the bacteria living there can have a big impact on our health,” said Ewan Harrison, PhD, senior author on the paper and head of the Respiratory Virus and Microbiome Initiative at the Wellcome Sanger Institute. “By studying thousands of samples, we can finally see the bigger picture of how our natural bacteria either help or hinder infection.”
Furthermore, “we found that some bacterial neighbors can help keep Staph out, offering exciting new directions for preventing infections using new methods,” noted Katie Bellis, PhD, a co-author on the paper and a staff scientist with the Respiratory Virus and Microbiome Initiative at the Wellcome Sanger Institute.
As part of their next steps, the researchers will explore whether risk factors, such as medical conditions, sex, human genetics, or other environmental exposures influence S. aureus carriage.