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Next generation sequencing technology shows potential in management of periprosthetic joint infection
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In 1881, Robert Koch, MD, was credited for being the first person to develop the method for isolating infecting organisms using the culture medium. Since then, microbiologic culture has been the “gold standard” for the identification of infecting organisms. This development marked a revolution in microbiological methods and has been the cornerstone of isolating the infecting organism and implementing the appropriate antimicrobial treatment in many specialties in medicine. Interestingly, the method of culture described by Koch has undergone little change during the last 2 centuries.
Although other fields of medicine enjoy the benefits that traditional culture brings, any specialty that deals with biofilms, including orthopedic surgery, continues to face challenges in using traditional culture to isolate the infecting organism. Microbiological culture remains the main method for determining the causative organism in periprosthetic joint infection (PJI), but there are many clinical situations when the infective organism for PJI cannot be isolated. With a sensitivity of 44%, culture remains far from perfect for the diagnosis of PJI. The negative culture poses many problems, of which the most important is the doubt over whether a real infection exists at all.
Traditional culture, molecular techniques
The other main issue relates to antimicrobial treatment. Without knowing the exact infective organism and the antimicrobial sensitivity, clinicians have to “best guess” treatment regimens that can either result in systemic toxicity, if multiple antimicrobials are administered, covering all potential pathogens or the outcome may be compromised, as the infecting organism may not be covered by the antimicrobial regimen.
Majd Tarabichi
Javad Parvizi
The primitive nature of traditional culture has compelled investigators to seek novel methods for the isolation of infecting organisms that exist in a biofilm form. The introduction of molecular methods in recent decades have had a promising role in the identification of organisms causing PJI. The major problem with some of these molecular techniques, such as polymerase chain reaction, is its extreme sensitivity and high degree of false-positive results. The second issue has been the expense associated with identification of microbial DNA using novel technologies, such as next generation sequencing (NGS).
Next generation sequencing
In recent years and since the completion of the human genome project, the cost of sequencing DNA has declined rapidly and impressively. In 2000, the cost of sequencing one gigabase of DNA would exceed $100,000,000. To accomplish the same deed today would cost less than $10.
The rapid decline in the expense of sequencing DNA has led to the emergence of NGS as a viable tool to be used in clinical practice. The NGS or high-throughput sequencing enables the sequencing of all amplicons in a given sample — unlike previous technologies, which could only produce a meaningful result if one amplicon was predominant in the sample.
The ability of NGS to detect and “quantify” the microbial DNA in a given sample has allowed for this technology to be used in the clinical arena. There are many clinical situations in which NGS has provided critical information that has led to better treatment of patients. One example is the isolation of leptospirosis in a 14-year-old patient in coma, in whom traditional cultures had failed to reveal the nature of the infection. NGS has provided critical information for the management of PJI at our institution as well.
One interesting example relates to a patient with culture-negative PJI and systemic sepsis, in whom all cultures were negative. The use of NGS led to the identification of Streptococcus canis, an organism found in dogs and cattle. Further questioning of the patient confirmed that the patient had sustained a scratch by the patient’s pet dog a few days prior to manifestation of the PJI and systemic sepsis. An ongoing study at our institution has revealed that NGS technology provides valuable, and at times, critical information that affects the management of patients with PJI.
Based on the emerging data from our institution and other clinical fields, it appears that NGS technology holds great promise in the management of infectious diseases. It is plausible that society may have stumbled on the second revolution, and the time has come to replace the 19th century technique with a modern and sophisticated technology.
- References:
- An introduction to next generation sequencing. Available at: http://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf. Accessed: Oct. 19, 2016.
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- Parvizi J, et al. J Bone Joint Am. 2014;doi:http://dx.doi.org/10.2106/JBJS.L.01793.
- Wilson MR, et al. N Engl J Med. 2014;doi:10.1056/NEJMoa1401268.
- For more information:
- Majd Tarabichi, MD, and Javad Parvizi, MD, FRCS, can be reached at The Rothman Institute at Thomas Jefferson University Hospital, Sheridan Building, Suite 1000, 125 S. 9th St., Philadelphia, PA 19107; Tarabichi’s email: mtarabichi@gmail.com; Parvizi’s email: parvj@aol.com.
Disclosures: Parvizi reports he is a consultant to Zimmer Biomet, Ceramtec, Convatec, TissueGene and MicrogenDx; and has ownership in CD Diagnostics, Hip Innovation Technology, ForMD, Alphaeon, Joint Purification Systems and MicrogenDx. Tarabichi reports no relevant financial disclosures.