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Bacteria diversity in airways increases during babies’ first year

But antibiotics had only minor effects on bacterial changes in babies with CF, study finds

In babies with cystic fibrosis (CF), the types of bacteria living in the upper airway become more diverse during their first year of life, a new study shows.

Findings suggest that clinical variables, including the use of antibiotics, had relatively minor effects on these bacterial changes in CF babies.

The human body is home to trillions of bacteria, including many that normally reside in the airways. While bacteria in the airways are a normal part of a healthy body, they also can grow and cause dangerous infections.

People with CF are at particularly high risk of airway infections from certain types of airway bacteria, such as Pseudomonas aeruginosa. Studies in older children and adults with CF have suggested that more severe lung disease and infections are associated with less diversity of airway bacteria, as Pseudomonas and other problematic microbes grow so much that they crowd out other types of normal airway bacteria.

In this study, researchers set out to investigate how the diversity of airway bacteria changes over the first year of life in babies diagnosed with CF via newborn screening.

The scientists used swabs of the oropharynx (the part of the throat behind the mouth) collected during a clinical trial called the Baby Observational and Nutritional Study, or BONUS (NCT01424696), which was sponsored by Seattle Children’s Hospital with the main intent of assessing factors that affect growth in CF babies.

The study included a total of 1,052 swabs collected over the first year of life from 205 babies with CF. The median number of samples per participant was five.

Most of the babies (77%) had received at least one course of antibiotics (bacteria-killing medications used to manage infections) over the course of the first year. Of the 1,052 total samples, 131 were collected while the patient was taking antibiotics.

Shannon Alpha Diversity Index

Results showed that the diversity of bacterial communities in the babies’ airways — as calculated with a measure called the Shannon Alpha Diversity Index — tended to increase over the first year of life. Overall bacterial diversity tended to be lower in patients who had been treated with antibiotics, but by the age of 1 year, there was not a significant difference in diversity between patients who had or had not received antibiotics.

“Antibiotics appears to transiently [temporarily] impact the bacterial community with a trend towards lower diversity at some time points during the first year but not at 12 months, compared to antibiotic-naive infants,” the researchers wrote.

Analyses of individual types of bacterial groups also generally suggested an increase in diversity over the first year of life. In statistical models, age was the most significant predictor of bacterial community changes. Antibiotic use and feeding method (formula vs. breastfeeding) also had an effect, but it was not as pronounced as the effect of age.

“The strong relationship between age and community metrics suggests that developmental changes, rather than clinical [traits] or clinical interventions, over the first year of life may be the primary driver of community change,” the scientists wrote.

No clear patterns

In general, the researchers found there was a lot of variation in the types of bacteria living in patients’ airways, and the team did not identify any clear patterns between airway bacteria and clinical outcomes.

“We found that bacterial diversity of the oropharynx increased markedly over the first year, with changes in diversity correlating most strongly with age,” the researchers concluded.

The team noted that the finding of increasing bacterial diversity with increasing age is a contrast to most studies of airway bacteria in CF, but this may be because other studies have focused largely on older children or adults. Broadly, they said the pattern of bacterial dynamics in these young children shows a marked contrast from what has been seen in older patients, where disease-causing bacteria become more predominant over time.

“As diversity increased, other taxa [groups of bacteria] emerged but CF-related pathogens [disease-causing bacteria] remained relatively rare,” they said.

The scientists noted that larger and longer-term studies are needed to better understand how bacterial communities in the airways change over time in people with CF, and to assess whether changes in bacterial dynamics could be exploited to help prevent dangerous infections.



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