ArticlePloS one2020
Longitudinal changes in the nasopharyngeal resistome of South African infants using shotgun metagenomic sequencing.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Antibiotic and healthcare exposure impact on dynamics of third-generation cephalosporin-resistant Enterobacterales colonisation in Cambodian children: a six-month cohort study.Antimicrobial resistance and infection control · 2026Article
- Functional and Resistome Profiling of Paediatric Airway Microbiota in Asthma Using Shotgun Metagenomics.Biomedicines · 2026Article
- Operationalising Genomic Surveillance for Antimicrobial Resistance in Low- and Middle-Income Countries: A One Health Perspective from Bangladesh.Microorganisms · 2026Review
- Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.Microbiology spectrum · 2026Article
- Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.Frontiers in immunology · 2025Review
- Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants.Nature communications · 2024Article
- Article
- The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients.Nature communications · 2024Observational
- Microbial DNA extraction of high-host content and low biomass samples: Optimized protocol for nasopharynx metagenomic studies.Frontiers in microbiology · 2022Article
- Effects of nasopharyngeal microbiota in respiratory infections and allergies.Clinical and experimental pediatrics · 2021Article
- Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants.Frontiers in public health · 2020Article
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Authors and funding
9 authors.
Funding
Abstract
introductionNasopharyngeal (NP) colonization with antimicrobial-resistant bacteria is a global public health concern. Antimicrobial-resistance (AMR) genes carried by the resident NP microbiota may serve as a reservoir for transfer of resistance elements to opportunistic pathogens. Little is known about the NP antibiotic resistome. This study longitudinally investigated the composition of the NP antibiotic resistome in Streptococcus-enriched samples in a South African birth cohort.
methodsAs a proof of concept study, 196 longitudinal NP samples were retrieved from a subset of 23 infants enrolled as part of broader birth cohort study. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of streptococcal and non-streptococcal bacterial reads. Contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes.
resultsAMR genes were detected in 64% (125/196) of the samples. A total of 329 AMR genes were detected, including 36 non-redundant genes, ranging from 1 to 14 genes per sample. The predominant AMR genes detected encoded resistance mechanisms to beta-lactam (52%, 172/329), macrolide-lincosamide-streptogramin (17%, 56/329), and tetracycline antibiotics (12%, 38/329). MsrD, ermB, and mefA genes were only detected from streptococcal reads. The predominant genes detected from non- streptococcal reads included blaOXA-60, blaOXA-22, and blaBRO-1. Different patterns of carriage of AMR genes were observed, with only one infant having a stable carriage of mefA, msrD and tetM over a long period.
conclusionThis study demonstrates that WMGS can provide a broad snapshot of the NP resistome and has the potential to provide a comprehensive assessment of resistance elements present in this niche.
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