ArticleScientific reports2021
Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 24 citations in OpenAlex.
- Convergent methodologies in prosthetic joint infection research: integrating transdisciplinary approaches to understand and prevent biofilm-driven failure of orthopaedic prostheses.Journal of medical microbiology · 2026Review
- From microbiome profiling to precision medicine: diagnostic and therapeutic potential in gastrointestinal disorders: current evidence, challenges, and future directions.Annals of medicine and surgery (2012) · 2026Review
- Gut check: Exploring tools, techniques, and future directions in microbiome research.Poultry science · 2026Article
- Metagenomic characterization of infected diabetic foot ulcers in North Africa: microbial diversity, virulome, and resistome profiling.Frontiers in microbiology · 2026Article
- Next-generation detection in bovine respiratory and enteric diseases: metagenomic and amplicon sequencing insights into microbial diversity.Frontiers in veterinary science · 2026Review
- Leveraging illumina iSeq100 for whole genome sequencing of Salmonella Typhi for a resource-limited setting.Scientific reports · 2025Article
- The Gut Microbiome and Colistin Resistance: A Hidden Driver of Antimicrobial Failure.International journal of molecular sciences · 2025Review
- Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis.Annals of clinical microbiology and antimicrobials · 2025Article
- Application of next-generation sequencing to identify different pathogens.Frontiers in microbiology · 2023Review
- Molecular Approach for the Laboratory Diagnosis of Periprosthetic Joint Infections.Microorganisms · 2022Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Shotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with periprosthetic tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known periprosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209 ×. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis approach clearly influenced the results, i.e. read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data.
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