April 8, 2025 | The impact of the throat microbiome on the health of older individuals has gone unappreciated, especially among individuals being cared for in long-term care facilities. One big reason is that they are largely isolated and often forgotten by the public, even as these facilities have become home to a greater proportion of the overall population, according to Sophie Miller, a Ph.D. candidate in the College of Medicine and Public Health at Flinders University (South Australia).
The other reality is that even something as seemingly simple as routine oropharyngeal swabbing is difficult to implement in the aged care setting due to chronic understaffing and a general shortage of resources. But it may be worth the effort it would take to employ such testing, based on findings of a study Miller recently led suggesting certain bacteria detectable in the back of the throat offer valuable clues about the health challenges faced by older adults (Age and Ageing, DOI: 10.1093/ageing/afaf042).
Most surprising was an identified association between Staphylococcus aureus, one of the most important disease-causing bacteria, with hospital admission, co-morbidity, and frailty—even in the absence of infection. Aged care residents carrying the bacterium were nearly 10 times more likely to die within a year compared to non-carriers, making it a stronger predictor of mortality risk than an individual’s number of comorbidities.
“We expected it to be just the methicillin-resistant bacteria that would be associated with mortality,” says Miller. That the association was seen independent of methicillin resistance means S. aureus carriage represents a potential biomarker of general health in older individuals.
The throat microbiome, a community of microorganisms in the oropharynx, is unique to individuals at every age, Miller says. This “bacterial niche” provides a critical barrier against infection by harmful pathogens and susceptibility to lower respiratory tract conditions, including pneumonia.
But like all other microbiomes in the body, it is a highly dynamic environment. With advancing age comes not only changes in airway physiology and a decline in immune system functioning, but also greater medication use and more frequent healthcare visits affecting the balance of bacteria and other microorganisms in the throat, says Miller.
For people who are younger and generally healthy, the bacteria living in the throat aren’t as plentiful and the “bugs” that are there tend to be beneficial, producing health-promoting metabolites, positively influencing immune function, and protecting the lungs from infection, she continues. In general, they also take fewer medications and visit healthcare providers far less often than older people.
Exposure to a lot of different medications, especially antibiotics and proton pump inhibitors (PPIs), alters the composition and function of microbes in the throat, says Miller. A growing number of studies have found that PPIs, commonly prescribed to older individuals to reduce stomach acid production, change the diversity of microbial species in the mouth such that it may be putting users at heightened risk of certain diseases, such as aspiration pneumonia.
The key issue with hospitalizations and other types of interactions with healthcare services is that it exposes people to many different types of potentially harmful bacteria, she adds. Older individuals don’t fight off those bad bugs as well as their younger selves, and even more so if they’re already sick, so pathogens can more easily take up residence and cause harm.
The latest study was designed to investigate the relationship between throat microbiome characteristics and all-cause mortality in long-term aged care residents. Oropharyngeal swabs were collected from 190 residents of five facilities in South Australia, with microbiota composition being assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period.
Carriage of S. aureus and methicillin resistance was confirmed by quantitative polymerase chain reaction. S. aureus was identified in 13 residents and significantly associated with an increased risk of mortality compared with non-carriers, independent of methicillin resistance.
Participants in the study were also part of a much larger investigation known as GRACE (Generating Evidence on Antimicrobial Resistance in the Aged Care Environment) on whom the throat samples were collected back in 2019 and 2020 (BMC Geriatrics, DOI: 10.1186/s12877-023-04215-3). The aim of the GRACE study was to investigate the principal risk factors of antimicrobial resistance carriage and transmission in residential aged care facilities, says Miller.
For the newer, smaller study, Miller and her colleagues looked at the throat microbiome holistically, looking for patterns in people who had passed away, she explains. This might then reveal potential biological markers of declining health.
That S. aureus was found to be associated with mortality risk even among aged individuals who weren’t methicillin resistant was a particularly important and novel finding, says Miller. Many published studies and pathology labs in high-risk settings don’t look at methicillin-sensitive S. aureus (MSSA); the focus has been largely on methicillin-resistant S. aureus (MRSA) because it can lead to serious infections that can be harder and more costly to treat.
“I think it highlights the importance of looking beyond just that very niche specific [staph] bacteria,” she says. “We’re not inferring there is a causal link between Staphylococcus aureus and mortality. We did find an association... but we don’t have cause of death data for these people.”
The finding is compelling enough to warrant a closer look at the value of a “more holistic approach towards diagnostics,” says Miller. It has started an important discussion about how to measure health within aged care facilities and “going beyond” what has been reported as clinically significant in published literature.
The hope here is that throat swabs might one day be taken routinely in aged care facilities to alert care teams of pending problems to as much as possible get ahead of them, Miller says. Given the limited resources available, however, “we’re a long way from that.” Implementation of the practice will likely require the support of leadership within the facilities as well as private institutions and government agencies.
A high proportion of people living in long-term care facilities also have cognitive impairments that might make it difficult for them to consent to swabbing, she adds, plus there’s the momentary gagging with the procedure that no one particularly enjoys. On the other hand, throat swabbing is a common hospital laboratory test done in populations that include older individuals, so it is not an entirely “fantastical” idea.
Miller says she would eventually like to be involved in a larger longitudinal study in aged care facilities in South Australia, or across the country, to further assess if S. aureus carriage in the throat microbiome could contribute to estimations of general health in older individuals and thereby inform care strategies. That will require working with those facilities and how they record their data and rely on their funding instrument known as the Australian National Aged Care Classification (AN-ACC).
The AN-ACC tool is used to determine how much funding an aged care facility in Australia needs and “each person is considered individually,” says Miller. A similar model was used in the Age and Ageing study to help researchers understand the comorbidities and care needs of individuals.
Since the AN-ACC funding model has recently changed, one hurdle in moving forward will be ensuring continued access to the same granular data from the facilities that has heretofore been available, she adds. Seeking consent to collect that information facility by facility would be impractical.
Provided the AN-ACC instrument changes to incorporate throat swabbing, implementing the practice within aged care facilities shouldn’t be particularly difficult since the test already exists. “The view of an aged care facility, at least in Australia, is shifting more toward being a healthcare facility rather than this separate entity,” Miller notes.
Interpretation of the results might logically be done by pathology services external to the aged care facilities, she says. With the microbiome approach, the trickiest part may well be deciding what to look for since it provides a wealth of data about human health.