Persistent Nasal Staph Colonization Linked to Broader Microbiome Features

Original from: genomeweb

New research suggests that individuals who consistently carry Staphylococcus aureusin their noses have other nasal microbial community features that are distinct from those found in individuals without persistent S. aureus colonization.

The work also highlighted bacterial species and microbial community compositions that may help fend off S. aureus colonization — a risk factor for infection with the bacteria.

"Our data provides multiple new insights and identifies key microbial interactions and variation that underpin the composition of the human nasal microbiome, and in particular colonization by S. aureus," senior and co-corresponding author Ewan Harrison, a researcher affiliated with the University of Cambridge and the Wellcome Sanger Institute, and his colleagues wrote in Nature Communications on Tuesday.

As part of the CARRIAGE study, researchers from the Wellcome Sanger Institute, the University of Cambridge, Imperial College London, and elsewhere used 16S ribosomal RNA sequencing to assess nasal swab samples collected between mid-October of 2016 and mid-May 2017 from 1,180 healthy blood donors enrolled at community sites in England. Participants provided up to three self-administered swab samples apiece, collected on a weekly basis.

The study is the largest of its kind that investigated the nasal microbiome in healthy adults in combination with data from typical S. aureus nasal swab culture approaches, Harrison said in an email.

When analyzed alongside that culture data, the team's sequence data suggested that at least seven distinct "community state types" can make up the human nasal microbiome.

Some 70 percent of participants classified as persistent S. aureus carriers had nasal microbiomes marked by the same CST, the researchers reported, noting that the persistent S. aureus-associated CST turned up more frequently in men than in women. The remaining six nasal microbiome CSTs were identified in S. aureus noncarriers.

While S. aureus was abundant in nasal microbiomes from persistent carriers, dominating the microbial communities found in a subset of those carriers, the team found that diminishing S. aureusrepresentation in the nasal microbiomes also tended to coincide with increasing levels of S. epidermidis, Dolosigranulum pigrum, Moraxella catarrhalis, and three species in the Corynebacteriumgenus.

"We identified a number of species that are negatively associated with S. aureus colonization," Harrison explained, noting that "it remains to be seen if these can be used to prevent or modify S. aureus colonization."

"We now need to understand the biology of these interactions," he added, calling that goal "a major future research area for our group."

For the group of 191 individuals who appeared to have intermittent S. aureus carriage, meanwhile, investigators noted that some participants had CST features that resembled noncarriers, while others had nasal microbiomes that tracked more closely with persistent carriers.

"We show that the intermittent carriers don't have a unique microbiome — and, in fact, we can see that they either have one that looks like a persistent-carrier or a noncarrier," Harrison said, "providing clear evidence that they aren't a unique group and are actually just misclassified persistent or noncarriers."

Along with follow-up analyses focused on finding the most persistent colonization-prone S. aureuslineages, the team saw clues that machine learning may help to identify individuals at risk of persistent S. aureus carriage based on their broader nasal microbiome features.

"We show that machine learning models leveraging microbiome composition can accurately predict colonization persistence," the authors wrote, "and that certain S. aureus lineages are more adept at establishing nasal colonization."

Members of the team are continuing to tease out the nasal microbiome interactions and features that may predispose some individuals to subsequent S. aureus infections. They noted that a subset of individuals with persistent S. aureus carriage had particularly high levels of the bug in their nasal microbiomes, for example, raising questions about potential ties between S. aureus-dominant microbiomes and infection risk.

Investigators plan to explore interactions between the nasal microbiome and human genetics in CARRIAGE participants, Harrison noted, along with the potential medical and lifestyle features that might influence the microbiome. They are also turning to metagenomic sequencing to get a closer look at the bacterial strains, genes, and interactions found in the nasal microbiome.

"We are investigating what biological processes decide if someone is persistently colonized by S. aureus," Harrison said.

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