Abstract
A longitudinal study was undertaken in infants living in the Maela refugee camp on the Thailand-Myanmar border between 2007 and 2010. Nasopharyngeal swabs were collected monthly, from birth to 24 months of age, with additional swabs taken if the infant was diagnosed with pneumonia according to WHO clinical criteria. At the time of collection, swabs were cultured for Streptococcus pneumoniae and multiple serotype carriage was assessed. The bacterial 16S rRNA gene profiles of 544 swabs from 21 infants were analysed to see how the microbiota changes with age, respiratory infection, antibiotic consumption and pneumococcal acquisition. The nasopharyngeal microbiota is a somewhat homogenous community compared to that of other body sites. In this cohort it is dominated by five taxa: Moraxella, Streptococcus, Haemophilus, Corynebacterium and an uncharacterized Flavobacteriaceae taxon of 93% nucleotide similarity to Ornithobacterium. Infant age correlates with certain changes in the microbiota across the cohort: Staphylococcus and Corynebacterium are associated with the first few months of life while Moraxella and the uncharacterised Flavobacteriaceae increase in proportional abundance with age. Respiratory illness and antibiotic use often coincide with an unpredictable perturbation of the microbiota that differs from infant to infant and in different illness episodes. The previously described interaction between Dolosigranulum and Streptococcus was observed in these data. Monthly sampling demonstrates that the nasopharyngeal microbiota is in flux throughout the first two years of life, and that in this refugee camp population the pool of potential bacterial colonisers may be limited.
Highlights
Common bacterial colonisers of the infant nasopharynx include Staphylococcus aureus, Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae [1]
The microbiota develops with age, with early colonisers such as Corynebacterium or Staphylococcus being eventually outgrown by Moraxella and an uncultured taxon described here as unclassified Flavobacteriaceae I
The Shoklo Malaria Research Unit (SMRU) clinical framework provides an opportunity to investigate the nasopharyngeal microbiota of children living in this population: how the bacterial composition develops during infancy and early childhood from frontier species to a more mature and stable community, whether respiratory illness is preceded by a change in microbiota profile, and whether the acquisition of a new serotype of S. pneumoniae may coincide with changes in the rest of the microbiota
Summary
Common bacterial colonisers of the infant nasopharynx include Staphylococcus aureus, Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae [1]. The Shoklo Malaria Research Unit (SMRU) has been providing medical and obstetric care in this refugee population living on the Thailand-Myanmar border since 1986. The camp has a population of approximately 40,000 displaced persons from Myanmar, predominantly of Karen ethnicity, living in a 4km area. The SMRU clinical framework provides an opportunity to investigate the nasopharyngeal microbiota of children living in this population: how the bacterial composition develops during infancy and early childhood from frontier species to a more mature and stable community, whether respiratory illness is preceded by a change in microbiota profile, and whether the acquisition of a new serotype of S. pneumoniae may coincide with changes in the rest of the microbiota
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