Usefulness of metagenomic analysis in differential diagnosis for pyoderma gangrenosum

Abstract

Pyoderma gangrenosum (PG) is a rare ulcerative inflammatory dermatosis easily confused with wound infection following surgery. There have been seven case reports of PG occurring after total knee arthroplasty (TKA), all of which used routine tissue culture for differential diagnosis. Notably, all previous cases involved delayed diagnosis. We report a case of PG after TKA where we used shotgun metagenomics for differential diagnosis. Metagenomic analysis is a new method that can be used for pathogen detection; it is fast and sensitive, compared with traditional culture. Early application of metagenomic analysis in cases of suspicious wound infection after surgery can detect the pathogen of the infection for target therapy; it can also exclude infection for differential diagnosis of non-infectious diseases, such as autoimmune disorders. This case is presented to support the use of metagenomic analysis by surgeons and physicians for early and rapid differential diagnosis in patients who exhibit postoperative wound infections.

Metagenomic Sequencing as a Pathogen-Agnostic Clinical Diagnostic Tool for Infectious Diseases: a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies

“…Studies have demonstrated that metagenomic pipelines can provide faster diagnoses than conventional culture-based methods which may hold crucial for critically unwell patients (2). Additionally the detection of pathogens from culture-negative samples may have clinical management implications in several other settings including prosthetic joint infections, chronic wound infections and endocarditis (3)(4)(5). Where sufficient knowledge bases exist prediction of antimicrobial resistance is potentially possible and detection of mixed infections is also possible, where a subpopulation of resistant strains can be detected (6).…”

A Rare Case of Severe Post-operative Pyoderma Gangrenosum After Surgery for Perforated Diverticulitis at the Sigmoid Colon

“…Post-operative PG (PPG) is a subtype of PG with ulcerative dermatosis, which is often confused with wound infection following surgery [ 5 ]. This difficulty in diagnosis can result in unreasonable debridement and delays in appropriate treatment [ 6 ]. Here, we present a rare case of severe PPG developing after an abdominal surgery that was efficiently treated by early diagnosis and appropriate medication.…”

Metagenomic sequencing as a clinical diagnostic tool for infectious diseases: a systematic review and meta-analysis

“…in prosthetic joint infections, chronic wound infections and endocarditis. [6][7][8] Metagenomic sequencing can also be used to identify previously described, as well as potentially novel, antimicrobial resistance determinants. Provided sufficient genetic context is present within a single sequence read, chromosomal resistance determinants can be matched to the species in which they occur.…”

“…Based on a single or mean time provided from each study, sample extraction/preparation took a median 3 hours (IQR 3-5) [range 0•5-5] and library preparation a median 3 hours (2-4) [0•1-15•5]. Reported sequencing took a median of 10 hours (4•8-16)[1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16], presumably because sequencing was terminated once a diagnostic result was reached in some cases, as some of these values are below the typical run times for many Illumina and Nanopore sequencing approaches. Where sequence analysis was undertaken in real-time using the Nanopore platform, first species prediction took 1 hour(1)(2)(3)(4) [0•5-6] and AMR prediction took 3•5 hours (4•8-16) [2][3][4][5].…”