Dataset Information

Strain Level Streptococcus Colonization Patterns during the First Year of Life.

ABSTRACT: Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the Streptococcus sp. carriage using a lytA qPCR assay, whole metagenomic sequencing, and in silico serotyping of Streptococcus pneumoniae, as well as 16S rRNA amplicon based community profiling. The lytA carriage in both populations increased with infant age and lytA+ samples ranged from 24 to 85% of the samples at each sampling time point. We next developed informatic tools for determining Streptococcus community composition and pneumococcal serotype from metagenomic sequences derived from a subset of longitudinal lytA-positive Streptococcus enrichment cultures from The Philippines (n = 26 infants, 50% vaccinated) and South African (n = 7 infants, 100% vaccinated). NP samples from infants were passaged in enrichment media, and metagenomic DNA was purified and sequenced. In silico capsular serotyping of these 51 metagenomic assemblies assigned known serotypes in 28 samples, and the co-occurrence of serotypes in 5 samples. Eighteen samples were not typeable using known serotypes but did encode for capsule biosynthetic cluster genes similar to non-encapsulated reference sequences. In addition, we performed metagenomic assembly and 16S rRNA amplicon profiling to understand co-colonization dynamics of Streptococcus sp. and other NP genera, revealing the presence of multiple Streptococcus species as well as potential respiratory pathogens in healthy infants. A range of virulence and drug resistant elements were identified as circulating in the NP microbiomes of these infants. This study revealed the frequent co-occurrence of multiple S. pneumoniae strains along with Streptococcus sp. and other potential pathogens such as S. aureus in the NP microbiome of these infants. In addition, the in silico serotype analysis proved powerful in determining the serotypes in S. pneumoniae carriage, and may lead to developing better targeted vaccines to prevent invasive pneumococcal disease (IPD) in these countries. These findings suggest that NP colonization by S. pneumoniae during the first years of life is a dynamic process involving multiple serotypes and species.

SUBMITTER: Wright MS

PROVIDER: S-EPMC5592222 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Strain Level Streptococcus Colonization Patterns during the First Year of Life.

Wright Meredith S MS McCorrison Jamison J Gomez Andres M AM Beck Erin E Harkins Derek D Shankar Jyoti J Mounaud Stephanie S Segubre-Mercado Edelwisa E Mojica Aileen May R AMR Bacay Brian B Nzenze Susan A SA Kimaro Sheila Z M SZM Adrian Peter P Klugman Keith P KP Lucero Marilla G MG Nelson Karen E KE Madhi Shabir S Sutton Granger G GG Nierman William C WC Losada Liliana L

Frontiers in microbiology 20170906

Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the Streptococcus sp. carriage using a lytA qPCR assay, whole metagenomic sequencing, and <i ...[more]

PMID: 28932211

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Project description:Introduction: Pregnancy, infancy, and early childhood are periods of rapid growth and development. The role of nutrition is very important during these critical growth and development periods. The aim of the study was to investigate infant feeding practices through the first year of life in Latvia, and to compare feeding practices with nutritional guidelines in Latvia and other European countries. Methods: We analysed cross-sectional study data from food frequency questionnaires with additional questions on breastfeeding and complementary feeding introduction. A total of 266 infants from all Latvian regions from birth to 1-year-old were included in the study. Breastfeeding rates were assessed by month of age. Complementary feeding was assessed using three age groups (0?3.9 months, 4?6.9 months, and 7?12.9 months), whereas two groups were used to assess food frequency and portion sizes (0?5.9 months and 6?12.9 months). Results: The breastfeeding rate during the first month of life was 89%. At 6 months, 68% of infants received breast milk, but by 12 months, only 45% still received breast milk. Complementary foods were introduced at a mean age of 5 months (standard deviation = 1). Before 4 months of age, 9% of infants were receiving complementary food, the majority (85%) between 4 and 6 months of age. There were 6% of infants who were introduced to complementary foods after 7 months of age. First complementary food choices were mainly porridge (64%), vegetables (21%), and fruits (10%). After 6 months of age, foods from almost all food groups were present in each infant diet at least once per day, such as vegetables (85%), potatoes (85%), fruits (81%), dairy (78%), and meat (73%), less than once per day-grains (88%), fats (73%), cow's milk (66%), eggs (45%), fish (36%), and legumes (28%). Conclusion: Breastfeeding rate during first months of life is high in Latvia. Breastfeeding was sustained at the age of 6 months, in the highest rate among Baltic countries. However, only 45% continued breastfeeding at the age of 12 months, in accordance with WHO recommendations. A guideline on complementary feeding is followed by the majority of parents. There are deviations from guidelines in inclusion of some foods in the diet and frequency of consumption.

Project description:Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.

Dataset Information

Strain Level Streptococcus Colonization Patterns during the First Year of Life.

Publications

Strain Level <i>Streptococcus</i> Colonization Patterns during the First Year of Life.

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