Identification of Two Pathogens in a Culture‐Negative Prosthetic Joint Infection Using Nanopore Sequencing

Abstract

Periprosthetic joint infection (PJI) following total joint arthroplasty (TJA) is challenging to diagnose due to lower yield in pathogenic identification (~50%) using conventional microbiologic culture techniques. Here we present a case in which two pathogens were detected using nanopore sequencing from a 50 year‐old male with a suspected, yet culture‐negative, PJI. Three swabs were taken from multiple sites of drainage surrounding the suspected infected right knee joint following a routine arthroplasty (original TKA was done three years prior). DNA was extracted from the swabs using the MasterPure™ Gram Positive DNA Purification Kit (Lucigen). Sample libraries were prepared using the Rapid PCR Barcoding Kit (Oxford Nanopore Technologies) and sequenced on a v9.4.1 MinION flow cell. A total of 1,056,710 reads from all three swabs combined were aligned using a minimum Q score of 7.0 to the RefSeq database on the EPI2ME platform using the “What’s in my pot?” app. A total of 5,540 reads (0.52%) aligned to the bacteria Corynebacterium with the most abundant species being detected as Corynebacterium simulans. A total of 1,886 (0.18%) mapped to the fungi Malassezia globosa. Due to the patient having a visible arthrocutaneous fistula combined with visualized drainage from the joint using a methylene blue challenge test, the prosthetic knee was removed and an antibiotic spacer that contained 6 gm vancomycin, 7.2 gm tobramycin and 100 mg of amphotericin B was implanted. The patient also received a 6 week course of ceftriaxone infusions and has shown rapid clinical improvement. While our sequencing results were not used directly for patient care in this case, it demonstrates the promise that nanopore sequencing has for future use in infectious disease diagnostics.