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Lee AWT, Ng ICF, Wong EYK, Wong ITF, Sze RPP, Chan KY, So TY, Zhang Z, Ka-Yee Fung S, Choi-Ying Wong S, Tam WY, Lao HY, Lee LK, Leung JSL, Chan CTM, Ng TTL, Zhang J, Chow FWN, Leung PHM, Siu GKH. Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics. Food Microbiol 2024; 121:104493. [PMID: 38637066 DOI: 10.1016/j.fm.2024.104493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 04/20/2024]
Abstract
Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Given the limitations of conventional culture-based approaches, which are limited in scope and time-consuming, metagenomic sequencing of food products emerges as a promising solution. This method provides a fast and comprehensive way to detect the presence of pathogenic microbes and antimicrobial resistance genes (ARGs). Notably, nanopore long-read sequencing provides more accurate bacterial taxonomic classification in comparison to short-read sequencing. Here, we revealed the impact of food types and attributes (origin, retail place, and food processing methods) on microbial communities and the AMR profile using nanopore metagenomic sequencing. We analyzed a total of 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Importantly, even with low pathogen abundance, higher percentages of samples containing carbapenem and cephalosporin resistance genes were identified in chicken and RTE vegetables, respectively. In parallel, our results demonstrated that fresh, peeled, and minced foods exhibited higher levels of pathogenic bacteria. In conclusion, this comprehensive study offers invaluable data that can contribute to food safety assessments and serve as a basis for quality indicators.
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Affiliation(s)
- Annie Wing-Tung Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Iain Chi-Fung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Evelyn Yin-Kwan Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Ivan Tak-Fai Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Rebecca Po-Po Sze
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kit-Yu Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Tsz-Yan So
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Zhipeng Zhang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sharon Ka-Yee Fung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sally Choi-Ying Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Wing-Yin Tam
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Jiaying Zhang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China.
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Ponraj DS, Lund M, Lange J, Poehlein A, Himmelbach A, Falstie-Jensen T, Jørgensen NP, Ravn C, Brüggemann H. Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent. Front Cell Infect Microbiol 2023; 13:1165017. [PMID: 37265503 PMCID: PMC10229904 DOI: 10.3389/fcimb.2023.1165017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria.
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Affiliation(s)
| | - Michael Lund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jeppe Lange
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Orthopaedic Surgery, Regional Hospital, Horsens, Denmark
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | - Christen Ravn
- Department of Orthopaedic Surgery, Aarhus University Hospital, Aarhus, Denmark
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Hu X, Haas JG, Lathe R. The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data. BMC Microbiol 2022; 22:317. [PMID: 36550399 PMCID: PMC9773549 DOI: 10.1186/s12866-022-02671-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microbiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life. RESULTS We report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer sequences designed from small subunit ribosomal RNA (rRNA) sequences across the Tree of Life (the 'electronic tree of life', eToL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by confirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. The method reduces the computation time versus metagenomics by a factor of >1000. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. Contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method we report the use of the eToL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved. CONCLUSIONS This generic methodology is likely to find wide application in microbiome analysis including diagnostics.
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Affiliation(s)
- Xinyue Hu
- Program in Bioinformatics, School of Biological Sciences, King's Buildings, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Jürgen G Haas
- Division of Infection Medicine, University of Edinburgh, Little France, Edinburgh, EH16 4SB, UK
| | - Richard Lathe
- Division of Infection Medicine, University of Edinburgh, Little France, Edinburgh, EH16 4SB, UK.
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Purushothaman S, Meola M, Egli A. Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. Int J Mol Sci 2022; 23:9834. [PMID: 36077231 PMCID: PMC9456280 DOI: 10.3390/ijms23179834] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/21/2022] Open
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.
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Affiliation(s)
- Srinithi Purushothaman
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Marco Meola
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
- Swiss Institute of Bioinformatics, University of Basel, 4031 Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland
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Shi Y, Wang G, Lau HCH, Yu J. Metagenomic Sequencing for Microbial DNA in Human Samples: Emerging Technological Advances. Int J Mol Sci 2022; 23:ijms23042181. [PMID: 35216302 PMCID: PMC8877284 DOI: 10.3390/ijms23042181] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Whole genome metagenomic sequencing is a powerful platform enabling the simultaneous identification of all genes from entirely different kingdoms of organisms in a complex sample. This technology has revolutionised multiple areas from microbiome research to clinical diagnoses. However, one of the major challenges of a metagenomic study is the overwhelming non-microbial DNA present in most of the host-derived specimens, which can inundate the microbial signals and reduce the sensitivity of microorganism detection. Various host DNA depletion methods to facilitate metagenomic sequencing have been developed and have received considerable attention in this context. In this review, we present an overview of current host DNA depletion approaches along with explanations of their underlying principles, advantages and disadvantages. We also discuss their applications in laboratory microbiome research and clinical diagnoses and, finally, we envisage the direction of the further perfection of metagenomic sequencing in samples with overabundant host DNA.
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Affiliation(s)
| | | | | | - Jun Yu
- Correspondence: ; Tel.: +852-37636099; Fax:+852-21445330
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Target-enriched sequencing enables accurate identification of bloodstream infections in whole blood. J Microbiol Methods 2021; 192:106391. [PMID: 34915067 DOI: 10.1016/j.mimet.2021.106391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022]
Abstract
Bloodstream infections are within the top ten causes of death globally, with a mortality rate of up to 70%. Gold standard blood culture testing is time-consuming, resulting in delayed, but accurate, treatment. Molecular methods, such as RT-qPCR, have limited targets in one run. We present a new Ampliseq detection system (ADS) combining target amplification and next-generation sequencing for accurate identification of bacteria, fungi, and antimicrobial resistance determinants directly from blood samples. In this study, we included removal of human genomic DNA during nucleic acid extraction, optimized the target sequence set and drug resistance genes, performed antimicrobial resistance profiling of clinical isolates, and evaluated mock specimens and clinical samples by ADS. ADS successfully identified pathogens at the species-level in 36 h, from nucleic acid extraction to results. Besides pathogen identification, ADS can also present drug resistance profiles. ADS enabled detection of all bacteria and accurate identification of 47 pathogens. In 20 spiked samples and 8 clinical specimens, ADS detected at least 92.81% of reads mapped to pathogens. ADS also showed consistency with the three culture-negative samples, and correctly identified pathogens in four of five culture-positive clinical blood specimens. This Ampliseq-based technology promises broad coverage and accurate pathogen identification, helping clinicians to accurately diagnose and treat bloodstream infections.
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Sanabria AM, Janice J, Hjerde E, Simonsen GS, Hanssen AM. Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles. Sci Rep 2021; 11:20848. [PMID: 34675288 PMCID: PMC8531021 DOI: 10.1038/s41598-021-00383-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/08/2021] [Indexed: 11/20/2022] Open
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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Affiliation(s)
- Adriana Maria Sanabria
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Jessin Janice
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Norwegian Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Centre for Bioinformatics, Department of Chemistry, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Gunnar Skov Simonsen
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anne-Merethe Hanssen
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.
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Gamie Z, Karthikappallil D, Gamie E, Stamiris S, Kenanidis E, Tsiridis E. Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections. Expert Rev Mol Diagn 2021; 22:603-624. [PMID: 33641572 DOI: 10.1080/14737159.2021.1894929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Prosthetic joint infections (PJIs) can be challenging to eradicate and have high morbidity and mortality. Current microbiology culture methods can be associated with a high false-negative rate of up to 50%. Early and accurate diagnosis is crucial for effective treatment, and negative results have been linked to a greater rate of reoperation. AREAS COVERED There has been increasing investigation of the use of next-generation sequencing (NGS) technology such as metagenomic shotgun sequencing to help identify causative organisms and decrease the uncertainty around culture-negative infections. The clinical importance of the organisms detected and their management, however, requires further study. The polymerase chain reaction (PCR) has shown promise, but in recent years multiple studies have reported similar or lower sensitivity for bacteria detection in PJIs when compared to traditional culture. Furthermore, issues such as high cost and complexity of sample preparation and data analysis are to be addressed before it can move further toward routine clinical practice. EXPERT OPINION Metagenomic NGS has shown results that inspire cautious optimism - both in culture-positive and culture-negative cases of joint infection. Refinement of technique could revolutionize the way PJIs are diagnosed, managed, and drastically improve outcomes from this currently devastating complication.
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Affiliation(s)
- Zakareya Gamie
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK; Genomic Medicine - St George's, University of London, Cranmer Terrace, Tooting, London, SW17 0RE; King's College London, Strand, London
| | - Dileep Karthikappallil
- Department of Trauma and Orthopedics, East Cheshire NHS Trust, Macclesfield District General Hospital, Victoria Road, Macclesfield, Cheshire, SK10 3BL, UK
| | - Emane Gamie
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; MBiol, BSc Biological Sciences, University of Leeds Alumni, UK
| | - Stavros Stamiris
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
| | - Eustathios Kenanidis
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
| | - Eleftherios Tsiridis
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
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Esteban J, Gómez-Barrena E. An update about molecular biology techniques to detect orthopaedic implant-related infections. EFORT Open Rev 2021; 6:93-100. [PMID: 33828851 PMCID: PMC8022009 DOI: 10.1302/2058-5241.6.200118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Despite different criteria to diagnose a prosthetic joint infection (PJI), aetiological diagnosis of the causing microorganism remains essential to guide treatment.Molecular-biology-based PJI diagnosis is progressing (faster, higher specificity) in different techniques, from the experimental laboratory into clinical use.Multiplex polymerase chain reaction techniques (custom-made or commercial) provide satisfactory results in clinical series of cases, with specificity close to 100% and sensitivity over 70-80%.Next-generation metagenomics may increase sensitivity while maintaining high specificity.Molecular biology techniques may represent, in the next five years, a significant transformation of the currently available microbiological diagnosis in PJI. Cite this article: EFORT Open Rev 2021;6:93-100. DOI: 10.1302/2058-5241.6.200118.
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Affiliation(s)
- Jaime Esteban
- Servicio de Microbiología Clínica, Hospital Universitario Fundación Jiménez Díaz-IIS-Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Enrique Gómez-Barrena
- Servicio de Cirugía Ortopédica y Traumatología, Hospital Universitario La Paz-IdiPaz, Universidad Autónoma de Madrid, Madrid, Spain
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