DOI: 10.5061/dryad.vt4b8gv5w
title: Data from: Co-selection of genetic antibiotic resistance in <em>Streptococcus pneumoniae</em> after repeated Azithromycin mass drug administrations in Niger

description: We performed long-read whole-genome sequencing and phenotypic resistance
 analysis on Streptococcus pneumoniae isolated from the nasopharynx of
 Nigerien children from communities treated with either 6 twice-yearly
 azithromycin distributions or placebo. This dataset contains the annotated
 genome files for the 122 samples used in the study, as well as the
 associated metadata.
description: Isolated pneumococcal colonies were subjected to long-read WGS
 using the SMRTbell Prep Kit 3.0 and sequenced on the PacBio Revio platform
 (Pacific Biosciences of California). PacBio HiFi reads were <em>de
 novo</em> assembled using Canu (version 2.2) with the ‘-pacbio-hifi’
 option and evaluated for quality using BUSCO (version 5.7.1). Assemblies
 achieving a completeness score &gt;90% underwent a ‘Comprehensive
 Genome Analysis’ using BV-BRC online tools (accessed April 2025).
 BV-BRC-annotated genomes were subsequently screened for mobile elements
 utilizing ICEscreen (version 1.3.3). Annotated genomes were saved in
 genbank format.
description: # Data from: Co-selection of genetic antibiotic resistance in
 *Streptococcus pneumoniae* after repeated Azithromycin mass drug
 administrations in Niger Dataset DOI:
 [10.5061/dryad.vt4b8gv5w](https://doi.org/10.5061/dryad.vt4b8gv5w) ##
 Description of the data and file structure This repository contains the
 annotated genomes of *Streptococcus pneumoniae*, as well as associated
 metadata. Isolated pneumococcal colonies were subjected to long-read
 whole-genome-sequencing using the SMRTbell Prep Kit 3.0 and sequenced on
 the PacBio Revio platform (Pacific Biosciences of California). PacBio HiFi
 reads were *de novo* assembled using Canu (version 2.2) with the
 ‘-pacbio-hifi’ option and evaluated for quality using BUSCO (version
 5.7.1). Assemblies achieving a completeness score &gt;90% underwent a
 ‘Comprehensive Genome Analysis’ using BV-BRC online tools (accessed April
 2025). BV-BRC-annotated genomes were subsequently screened for mobile
 elements utilizing ICEscreen (version 1.3.3). Annotated genomes were saved
 in *genbank* format. ### Files and variables #### File:
 annotated_genomes.tgz **Description:** Compressed archive of the annotated
 genomes (in genbank format) used for this study. Sample names follow the
 convention
 `Streptococcus_pneumoniae_sample__canu_BV-BRC-annotated.gb`,
 where `lab_ID` is a unique identifier for each sample. Use command `tar
 cvfz annotated_genomes.tgz` to un-compress. #### File:
 genomes_metadata_v1.3.csv A comma-delimited text file containing metadata
 associated with the genomes. **Variables:** * `Lab_ID`: a unique
 identifier for each sample * `whg_code`: a unique, de-identified code for
 the village the sample originated from. (Dosso region of Niger) * `group`:
 treatment group. `A`: azithromycin, `P`: placebo * `beta_lactam`: boolean
 indicator of genetic beta-lactam resistance status (0: not resistant, 1:
 resistant) * `erythromycin`: boolean indicator of genetic erythromycin
 resistance status (0: not resistant, 1: resistant) *
 `trimethoprim_sulfamethoxazole`: boolean indicator of genetic
 trimethoprim-sulfamethoxazole resistance status (0: not resistant, 1:
 resistant) * `tetracycline`: boolean indicator of genetic tetracylcine
 resistance status (0: not resistant, 1: resistant) * `erythromycin_arup`:
 boolean indicator of phenotypic erythromycin resistance status (0: not
 resistant, 1: resistant) * `betalactams_arup`: boolean indicator of
 phenotypic beta-lactam resistance status (0: not resistant, 1: resistant)
 * `trimethoprim_sulfamethoxazole_arup`: boolean indicator of phenotypic
 trimethoprim-sulfamethoxazole resistance status (0: not resistant, 1:
 resistant) * `tetracycline_arup`: boolean indicator of phenotypic
 tetracylcine resistance status (0: not resistant, 1: resistant) *
 `genbank_filename`: The filename of the associated *Streptococcus
 pneumoniae* genome found in the `annotated_genomes.tgz` tar archive file.