Application of a metatranscriptomics technology, CSI-Dx, for the detection of pathogens associated with prosthetic joint infections

Kim, H. S. et al. Current and Future Burden of Periprosthetic Joint Infection from national claim database. J. Korean Med. Sci. 35, e410 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Leonenko, V. N., Kaliberda, Y. E., Muravyova, Y. V. & Artyukh, V. A. A decision support Framework for Periprosthetic Joint infection treatment: A cost-effectiveness analysis using two modeling approaches. J. Personalized Med. 12, 1216 (2022).Article 

Google Scholar 
Trebse, R. & Roskar, S. Evaluation and interpretation of prosthetic joint infection diagnostic investigations. Int. Orthop. 45, 847–855 (2021).Article 
PubMed 

Google Scholar 
Kurtz, S. M. et al. Infection burden for hip and knee arthroplasty in the United States. J. Arthroplasty. 23, 984–991 (2008).Article 
PubMed 

Google Scholar 
Shahi, A., Tan, T. L., Chen, A. F., Maltenfort, M. G. & Parvizi, J. In-Hospital mortality in patients with Periprosthetic Joint infection. J. Arthroplasty. 32, 948–952e1 (2017).Article 
PubMed 

Google Scholar 
Zmistowski, B., Karam, J. A., Durinka, J. B., Casper, D. S. & Parvizi, J. Periprosthetic joint infection increases the risk of one-year mortality. J. Bone Joint Surg. Am. 95, 2177–2184 (2013).Article 
PubMed 

Google Scholar 
Tan, T. L. et al. Culture-negative Periprosthetic Joint infection: An update on what to expect. JBJS Open. Access. 3, e0060 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Thoendel, M. J. et al. Identification of prosthetic joint infection pathogens using a Shotgun Metagenomics Approach. Clin. Infect. Dis. 67, 1333–1338 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Dulanto Chiang, A. & Dekker, J. P. From the Pipeline to the Bedside: advances and challenges in Clinical Metagenomics. J. Infect. Dis. 221, S331–S340 (2020).Article 
PubMed 

Google Scholar 
Huang, Z. et al. Metagenomic next-generation sequencing of synovial fluid demonstrates high accuracy in prosthetic joint infection diagnostics. Bone Joint Res. 9, 440–449 (2020).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Goswami, K. et al. Comparative meta-omics for identifying pathogens associated with prosthetic joint infection. Sci. Rep. 11, 23749 (2021).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hong, H. L. et al. Targeted Versus Shotgun Metagenomic sequencing-based detection of microorganisms in Sonicate Fluid for Periprosthetic Joint infection diagnosis. Clin. Infect. Dis. 76, e1456–e1462 (2023).Article 
PubMed 

Google Scholar 
Santoso, A., Phatama, K. Y., Rhatomy, S. & Budhiparama, N. C. Prosthetic joint infection of the hip and knee due to Mycobacterium species: A systematic review. World J. Orthop. 13, 503–514 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Shah, N. B., Tande, A. J., Patel, R. & Berbari, E. F. Anaerobic prosthetic joint infection. Anaerobe. 36, 1–8 (2015).Article 
CAS 
PubMed 

Google Scholar 
Achermann, Y., Vogt, M., Leunig, M., Wüst, J. & Trampuz, A. Improved diagnosis of periprosthetic joint infection by multiplex PCR of sonication fluid from removed implants. J. Clin. Microbiol. 48, 1208–1214 (2010).Article 
PubMed 
PubMed Central 

Google Scholar 
Azad, M. A. et al. Comparison of the BioFire Joint Infection Panel to 16S ribosomal RNA gene-based targeted metagenomic sequencing for testing synovial fluid from patients with knee arthroplasty failure. J. Clin. Microbiol. 60, e0112622 (2022).Article 
PubMed 

Google Scholar 
Hoffman, T. et al. Real-life experience and diagnostic utility of the BioFire Joint Infection PCR Panel in bone and joint infections: analysis of a prospective validation study. Infect. Dis. Ther. 12, 1437–1443 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Suen, K., Keeka, M., Ailabouni, R. & Tran, P. Synovasure ‘quick test’ is not as accurate as the laboratory-based α-defensin immunoassay: A systematic review and meta-analysis. Bone Joint J. 100-B, 66–72 (2018).Article 
CAS 
PubMed 

Google Scholar 
Bingham, J. S. et al. Screening for Periprosthetic Joint infections with ESR and CRP: The Ideal Cutoffs. J. Arthroplast. 35, 1351–1354 (2020).Article 

Google Scholar 
Lamendella, R., Wright, J. & Shope, A. Rapid isolation and collection of microbial rna from a biological specimen. (2022).Shohat, N. et al. Hip and Knee Section, What is the Definition of a Periprosthetic Joint Infection (PJI) of the Knee and the Hip? Can the Same Criteria be Used for Both Joints? Proceedings of International Consensus on Orthopedic Infections. J. Arthroplasty. 34, S325–S327 (2019).Tetreault, M. W., Wetters, N. G., Moric, M. & Gross, C. E. Della Valle, C. J. is synovial C-reactive protein a useful marker for periprosthetic joint infection? Clin. Orthop. Relat. Res. 472, 3997–4003 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Dennis, D., Parsa, A. & Pécora, J. R. What is the definition of septic arthritis in a native knee? ICM Philly. (2019). https://icmphilly.com/questions/what-is-the-definition-of-septic-arthritis-in-a-native-knee/Zymo Research, DNA/RNA & Shield ZYMO Res. (2024). https://www.zymoresearch.com/products/dna-rna-shieldChristensen, D. G. & Visick, K. L. Vibrio fischeri: Laboratory Cultivation, Storage, and common phenotypic assays. Curr. Protoc. Microbiol. 57, e103 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Biedendieck, R., Knuuti, T., Moore, S. J. & Jahn, D. The ‘beauty in the beast’-the multiple uses of Priestia megaterium in biotechnology. Appl. Microbiol. Biotechnol. 105, 5719–5737 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Brislawn, C. J., Lamendella, R., Tokarev, V. Y., Wright, J. R. & Bioinformatics pipeline and annotation systems for microbial genetic analysis. (2022).Chen, S., Zhou, Y., Chen, Y. & Gu, J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 34, i884–i890 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733–745 (2016).Article 
PubMed 

Google Scholar 
Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Moeckel, C. et al. A survey of k-mer methods and applications in bioinformatics. Comput. Struct. Biotechnol. J. 23, 2289–2303 (2024).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Miller, S. et al. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res. 29, 831–842 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 8, e61217 (2013).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2023).Oksanen, J. et al. vegan: Community Ecology Package. (2020).Arbizu, P. M. & pairwiseAdonis (2020).Kassambara, A. rstatix: Pipe-friendly Framework for Basic Statistical Tests in R. (2020).Holm, S. A. Simple sequentially rejective multiple Test Procedure. Scand. J. Stat. 6, 65–70 (1979).MathSciNet 

Google Scholar 
Mallick, H. et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput. Biol. 17, e1009442 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Benjamini, Y. & Hochberg, Y. Controlling the false Discovery rate: A practical and powerful Approach to multiple testing. J. Royal Stat. Soc. Ser. B (Methodol.). 57, 289–300 (1995).Article 
MathSciNet 

Google Scholar 
Huerta-Cepas, J. et al. Fast genome-wide functional annotation through Orthology assignment by eggNOG-Mapper. Mol. Biol. Evol. 34, 2115–2122 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods. 18, 366–368 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hyatt, D. et al. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).Article 

Google Scholar 
Huerta-Cepas, J. et al. eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).Article 
CAS 
PubMed 

Google Scholar 
KEGG Antimicrobial Resistance. KEGG Signatures. (2018). https://www.kegg.jp/kegg/annotation/br01600.htmlKanehisa, M. K. E. G. G. Kyoto Encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kanehisa, M., Furumichi, M., Sato, Y. & Kawashima, M. Ishiguro-Watanabe, M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 51, D587–D592 (2023).Article 
CAS 
PubMed 

Google Scholar 
Kanehisa, M. Toward understanding the origin and evolution of cellular organisms. Protein Sci. 28, 1947–1951 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 32, 2847–2849 (2016).Article 
CAS 
PubMed 

Google Scholar 
Pierson-Perry, J. F. et al. Evaluation of Detection Capability for Clinical Laboratory Measurement Procedures, 2nd Edition. vol. 32CLSI, (2012).Stevenson, M. et al. epiR: Tools for the Analysis of Epidemiological Data. (2023).Collett, D. Modelling Binary Data (Chapman And Hall/CRC, 1999).Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature. 514, 59–64 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chiu, C. Y. & Miller, S. A. Clinical metagenomics. Nat. Rev. Genet. 20, 341–355 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Namdari, S., Nicholson, T. & Parvizi, J. Cutibacterium acnes is isolated from Air Swabs: Time to doubt the value of traditional cultures in shoulder surgery? Arch. Bone Jt. Surg. 8, 506–510 (2020).PubMed 
PubMed Central 

Google Scholar 
Shen, J. et al. An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics. Microbiome. 10, 206 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Park, M., Park, S. & Jung, W. H. Skin commensal fungus Malassezia and its lipases. J. Microbiol. Biotechnol. 31, 637–644 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Fowler, M. L. et al. Pathogen or contaminant? Distinguishing true infection from synovial fluid culture contamination in patients with suspected septic arthritis. Infection. 45, 825–830 (2017).Article 
PubMed 

Google Scholar 
Baquero, F., Coque, T. M., Martínez, J. L., Aracil-Gisbert, S. & Lanza, V. F. Gene transmission in the one health microbiosphere and the channels of antimicrobial resistance. Front. Microbiol. 10, (2019).Samreen, A.I., Malak, H. A. & Abulreesh, H. H. Environmental antimicrobial resistance and its drivers: A potential threat to public health. J. Glob Antimicrob. Resist. 27, 101–111 (2021).Article 
CAS 
PubMed 

Google Scholar 
Heck, D., Rosenberg, A., Schink-Ascani, M., Garbus, S. & Kiewitt, T. Use of antibiotic-impregnated cement during hip and knee arthroplasty in the United States. J. Arthroplast. 10, 470–475 (1995).Article 
CAS 

Google Scholar 
Anguita-Alonso, P. et al. High rate of aminoglycoside resistance among staphylococci causing prosthetic joint infection. Clin. Orthop. Relat. Res. 439, 43–47 (2005).Article 
PubMed 

Google Scholar 
Corona, P. S. et al. Antibiotic susceptibility in gram-positive chronic joint arthroplasty infections: increased aminoglycoside resistance rate in patients with prior aminoglycoside-impregnated cement spacer use. J. Arthroplasty. 29, 1617–1621 (2014).Article 
PubMed 

Google Scholar 
Deshpande, A. et al. Are hospital floors an underappreciated reservoir for transmission of health care-associated pathogens? Am. J. Infect. Control. 45, 336–338 (2017).Article 
PubMed 

Google Scholar 
Wright, J. R. et al. Assessment of a novel continuous cleaning device using metatranscriptomics in diverse hospital environments. Front. Med. Technol. 5, (2023).Weyrich, L. S. et al. Laboratory contamination over time during low-biomass sample analysis. Mol. Ecol. Resour. 19, 982–996 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar