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Communication

Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

1
Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway
2
Faculty of Medicine, University of Oslo, 0316 Oslo, Norway
3
Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis 88040-900, Brazil
4
Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital and University of Oslo, 1478 Lørenskog, Norway
*
Author to whom correspondence should be addressed.
Academic Editor: Costas C. Papagiannitsis
Microorganisms 2021, 9(4), 707; https://doi.org/10.3390/microorganisms9040707
Received: 10 March 2021 / Revised: 27 March 2021 / Accepted: 28 March 2021 / Published: 30 March 2021
Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types. View Full-Text
Keywords: nanopore sequencing; shotgun metagenomics; culture-independent; Staphylococcus aureus; genotyping; virulence genes; antimicrobial resistance; orthopaedic implant-associated infections nanopore sequencing; shotgun metagenomics; culture-independent; Staphylococcus aureus; genotyping; virulence genes; antimicrobial resistance; orthopaedic implant-associated infections
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MDPI and ACS Style

Noone, J.C.; Ferreira, F.A.; Aamot, H.V. Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections. Microorganisms 2021, 9, 707. https://doi.org/10.3390/microorganisms9040707

AMA Style

Noone JC, Ferreira FA, Aamot HV. Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections. Microorganisms. 2021; 9(4):707. https://doi.org/10.3390/microorganisms9040707

Chicago/Turabian Style

Noone, J. C., Fabienne A. Ferreira, and Hege V. Aamot. 2021. "Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections" Microorganisms 9, no. 4: 707. https://doi.org/10.3390/microorganisms9040707

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