These authors point out that the utility of next-generation sequencing (NGS) in differentiating between active infection and contaminant or baseline flora remains unclear. They conducted a study of primary shoulder arthroplasty patients with no history of infection or antibiotic use within 60 days of surgery was enrolled. All patients received standard perioperative antibiotics. After skin incision, a sample of the medial skin edge was excised. A synovial tissue biopsy was taken from the rotator interval after subscapularis takedown. Each sample set was halved and sent for NGS and standard cultures.
The 3 most common bacteria identified by NGS of the skin samples (all species 10% of bacterial burden) were C acnes (44%, 11 individuals), Staphylococcus epidermidis (24%, 6 individuals), and Escherichia coli (20%, 5 individuals). The following species were each detected at the 10% bacterial load threshold for 1 patient: Enterococcus faecalis, Bacillus senegalensis, Staphylococcus saccharolyticys, Corynebacterium kroppenstedtii, Porphyromonas uenonis, Ureaplasma urealyticum, Arthrobacter sp, and Corynebacterium sp.
The 3 most common bacteria identified by NGS of the deep tissue samples (all species 10% of bacterial burden) were E coli (16%, 4 individuals), C acnes (12%, 3 individuals), and S epidermidis (8%, 2 individuals). The following species were each detected at the 10% bacterial load threshold for 1 patient: Staphylococcus aureus, Neisseria shayeganii, Streptococcus equinus, Catenabacterium mitsuokai, and Megamonas funiformis.
Comment: This study did not actually examine the utility of NGS for the diagnosis of infection; instead it looked at shoulders having primary arthroplasty.
The article did not directly compare the bacterial species identified by (a) culture and (b) NGS for each patient.
Finally, as in the case of the article discussed below, it would have been helpful if the authors had run negative controls for NGS to make sure that the unexpected bacterial DNA found by NGS (e.g. E Coli, Bacilli, Porphyromonas, Ureplasma, Arthrobacter, Neisseria, Megamonas) were not the result of DNA contamination unrelated to the presence of viable organisms.
Comparative study of cultures and next-generation sequencing in the diagnosis of shoulder prosthetic joint infections
In 44 patients undergoing revision shoulder arthroplasty, these authors compared bacterial identification by (1) culturing and (2) next-generation sequencing (NGS). They included patients with and without preoperative clinical signs of infection. Tissue samples were obtained from the anterior capsule, inferior capsule, glenoid, humeral canal, and underneath the prosthetic humeral head was obtained using “fresh” instruments. Culture media included anaerobic sheep blood agar and anaerobically prereduced hemin-thioglycolate broth. Aerobic media were apparently not used.
The total genomic DNA was isolated from tissue samples. These were then amplified for pyrosequencing. Amplification products were visualized, pooled, and subjected to size selection. Size-selected pools were then quantified and hybridized to generate single-stranded DNA. Single-stranded DNA was diluted and analyzed by emulsion-based polymerase chain reaction. The resulting amplification products were subsequently enriched and sequenced. Trimmed sequences were then run through USEARCH to cluster the sequences and mapped using the USEARCH UPARSE operational taxonomic unit (OTU) selection algorithm. Mapped sequences were then grouped by OTU; quality scoring-based sequence correction was then performed. Corrected sequences were then run through the Research and Testing Laboratory Genomics taxonomic analysis pipeline to determine the taxonomic classifications and abundance for each sample. Selected OTUs were then aligned using MUSCLE and a phylogenetic tree generated using FastTree. The selected OTU sequences were then globally aligned using USEARCH against a database of classified 16S sequences. Confidence values were assigned to each OTU classification, and the lowest common ancestor was determined based on these confidence values. The top hit and lowest common ancestor was then reported for each OTU.
=====
How you can support progress in shoulder surgery
You may be interested in some of our most visited web pages arthritis, total shoulder, ream and run, reverse total shoulder, CTA arthroplasty, and rotator cuff surgery as well as the 'ream and run essentials'
The article did not directly compare the bacterial species identified by (a) culture and (b) NGS for each patient.
Finally, as in the case of the article discussed below, it would have been helpful if the authors had run negative controls for NGS to make sure that the unexpected bacterial DNA found by NGS (e.g. E Coli, Bacilli, Porphyromonas, Ureplasma, Arthrobacter, Neisseria, Megamonas) were not the result of DNA contamination unrelated to the presence of viable organisms.
Comparative study of cultures and next-generation sequencing in the diagnosis of shoulder prosthetic joint infections
In 44 patients undergoing revision shoulder arthroplasty, these authors compared bacterial identification by (1) culturing and (2) next-generation sequencing (NGS). They included patients with and without preoperative clinical signs of infection. Tissue samples were obtained from the anterior capsule, inferior capsule, glenoid, humeral canal, and underneath the prosthetic humeral head was obtained using “fresh” instruments. Culture media included anaerobic sheep blood agar and anaerobically prereduced hemin-thioglycolate broth. Aerobic media were apparently not used.
Positive cultures were present in more than 50%, and positive NGS results were present in almost 40% of revision arthroplasty cases.
Cutibacterium (formerly Propionibacterium) acnes was the most common bacterial species cultured (8 of 13 [61.5%]) and identified by NGS (12 of 17 [70.1%]) in cases of definite and probable infection. The concordance (κ) between the 2 diagnostic criteria for defining infection that included culture or NGS was 0.333 (fair). Data from the 44 cases is shown below.
=====
We have a new set of shoulder youtubes about the shoulder, check them out at this link.
Be sure to visit "Ream and Run - the state of the art" regarding this radically conservative approach to shoulder arthritis at this link and this link
Use the "Search" box to the right to find other topics of interest to you.
Be sure to visit "Ream and Run - the state of the art" regarding this radically conservative approach to shoulder arthritis at this link and this link
Use the "Search" box to the right to find other topics of interest to you.
How you can support progress in shoulder surgery
You may be interested in some of our most visited web pages arthritis, total shoulder, ream and run, reverse total shoulder, CTA arthroplasty, and rotator cuff surgery as well as the 'ream and run essentials'
