Remarkable Infection Insights From Next-Gen DNA Sequencing

A new study has found that next-generation sequencing successfully isolated infective organisms when traditional culture failed. The multicenter study, “An Enhanced Understanding of Culture-Negative Periprosthetic Joint Infection with Next-Generation Sequencing: A Multicenter Study,” appears in the June 20, 2022, edition of The Journal of Bone and Joint Surgery.

When OTW asked why we have not known which organisms could be expected to be detected with use of next-generation sequencing, co-author Javad Parvizi, M.D. noted, “Next-generation sequencing is capable of detecting over 50,000 organisms in contrast to culture that can ‘grow’ (isolate) a much smaller number of organisms. We have for decades assumed that culture is the gold standard for isolation of infective organisms. So, it should not come as a surprise that many organisms causing implant-related infections, at least, cannot be isolated by culture.”

The researchers looked at individuals who had revision hip or knee arthroplasty from June 2016 to August 2020 (14 institutions). The team used the International Consensus Meeting criteria for Periprosthetic Joint Infection (PJI) and obtained intraoperative samples, sending them for both routine culture and next-generation sequencing.

Of the 301 patients who met the International Consensus Meeting criteria for PJI, 85 (28.2%) were culture-negative. The team was able to identify a pathogen using next-generation sequencing in 56 (65.9%) of these culture-negative patients.

“Seventeen species were identified as common based on a study-wide incidence threshold of 5%,” wrote the authors. “NGS [next-generation sequencing] revealed a polymicrobial infection in 91.1% of culture-negative PJI cases, with the set of common species contributing to 82.4% of polymicrobial profiles. Escherichia coli, Cutibacterium acnes, Staphylococcus epidermidis, and Staphylococcus aureus ranked highest in terms of incidence and study-wide mean relative abundance and were most frequently the dominant organism when occurring in polymicrobial infections.

“What is interesting,” stated Dr. Parvizi to OTW, “is that next-generation sequencing was able to isolate the infective organisms in a large percentage of cases when culture failed. Also, the list of organisms that were isolated by culture includes interesting organisms that we may not have naturally labelled as pathogens. It has come to light that any and all microorganisms in our body are capable of causing infections.”

“This multicenter prospective study that spanned over five years revealed that culture has limitations and next-generation sequencing appears to have promising role in isolating infective organisms in culture-negative cases. Furthermore, a polymicrobial organism profile was identified by next-generation sequencing in the majority of PJI cases, which appears to escape detection using conventional culture.”

Co-author Karan Goswami, M.D., a resident at the Rothman Orthopaedic Institute at Thomas Jefferson University in Philadelphia, commented to OTW, “Key questions for the future remain, such as how we progress from culture to the more expansive data characterized by next-generation sequencing. A corollary question relates to antibiotic choice and whether broad-spectrum antibiotics are necessary in this setting. Formal randomized trials and multicenter work including longitudinal clinical follow-up are ongoing to further investigate these issues.”