Within-host pneumococcal serotype 3 genetic diversity and evolution during a one-year prolonged carriage episode in a healthy adult

This dataset is longitudinal, microbiological, genomic, and epidemiological. It comprises multiple types of biological and clinical data collected from asymptomatic adults in Malawi over a 12-month study period. Below is a detailed classification of the data: Study Design & Recruitment Data Longitudinal, cohort-based clinical data. To track pneumococcal carriage persistence and clearance over time. -Participant recruitment, screening procedures, inclusion criteria (adults, aged 18-45, living with children under 5), and follow-up schedule (days 3, 7, 14, 21, 28, then monthly for 12 months). Microbiological & Culture Data Laboratory-based microbiological data. To confirm the presence of Streptococcus pneumoniae and quantify bacterial density (CFU/mL). -Nasopharyngeal sample collection, standard culture methods (WHO guidelines), pneumococcal identification via morphology, optochin sensitivity, bile solubility tests, and serotyping using latex agglutination. Antimicrobial Resistance (AMR) Data Antibiotic susceptibility testing data. To characterise multidrug resistance (MDR), defined as non-susceptibility to ≥3 antibiotic classes. -Disk diffusion and Etest MICs to determine resistance to beta-lactams, macrolides, tetracyclines, and co-trimoxazole following EUCAST guidelines. Whole Genome Sequencing (WGS) & Genomic Data High-throughput sequencing data. To analyse pneumococcal genetic diversity, detect recombination events, and establish lineage relationships with global pneumococcal genomes. -DNA extraction & quality control (Qubit quantification, threshold >2.5 μg) -Illumina NovaSeq 6000 sequencing (150 bp paired-end reads, 1.8M reads per sample). -Genome assembly & quality metrics (QUAST, contig number <500, genome size 1.9–2.35 Mb). -Phylogenetics & population structure (RAxML, Gubbins, PopPUNK, GPSC lineage assignment). -Pan-genome analysis (Prokka, Panaroo, Phandango). Capsular Locus & Serotyping Data Molecular epidemiology data. To determine serotype distribution and confirm multiple serotypes in cases of co-colonization. -Capsular polysaccharide genes (Serotype 3 reference: CR931634) -Serotyping pipelines (SeroBA, SeroCall) Mobile Genetic Elements (MGE) & Resistance Gene Analysis Mobile genetic element (MGE) annotation data. To detect transposable elements (e.g., Tn5253), which may contribute to antimicrobial resistance. -ICEfinder, Geneious Prime, Artemis for MGE annotation -Resistance genes were identified using ABRicate, CARD database, and Pathogen Watch CDC pipeline. Minority Variant & Intrahost Evolution Data Variant calling and within-host evolution data: To track minority variants, which indicate within-host pneumococcal evolution. -LoFreq for low-frequency variant calling. -GATK for base quality recalibration. -Filtering criteria: ≥20X coverage, allele frequency 0.15-0.50.