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Table 2 Key features of molecular methods for characterizing microorganisms from a diabetic foot infection

From: Microbiology of diabetic foot infections: from Louis Pasteur to ‘crime scene investigation’

Molecular Method Potential Advantages Potential Disadvantages Time to results Current cost
Bacterial identification and quantificationa     
PCR and pyrosequencing Delineates full array bacteria present, including almost all gram-positive, gram-negative and obligate anaerobic species; allows broad-range amplification by PCR; detects even small concentrations of microorganisms; avoids false-negative results related to recent antibiotic therapy; can help differentiate colonization from infection Identifies only 16S bacteria; fails to detect some bacterial and nonbacterial microorganisms; cannot reliably distinguish between viable and nonviable organisms as it amplifies dormant or dead bacteria; unable to test for phenotypic antibiotic sensitivity 4 to 24 hours About US $13/ target region
q PCR assaya Measures the quantity of a target sequence; determines the number of DNA copies in a sample; estimates bacterial load; helps differentiate colonization from infection Quantifies DNA from both viable and nonviable bacteria; requires a well-equipped laboratory with PCR facilities 2 to 6 hours About US $10 per sample
Virulence genes factors for S. aureusb     
PCR assay Allows virulence genotyping among strains of S. aureus Only patients with monomicrobial culture for S. aureus were included in published study 2 to 5 hours About US $5/assay
DNA microarray Carries a set of 334 different probes for genotyping S. aureus isolates; analyzes a large number of samples (96/well strip) Only patients with monomicrobial culture for S. aureus were included in published study 4 to ~5 hours About US $ 60/96-well strip
  1. aIndicates that these molecular methods used 16S rRNA gene. In this table we decided to present one of methods (the newest) that have been used for identification of bacterial diversity in the diabetic foot infection: PCR and pyrosequencing instead of other methods, such as PCR and Sanger sequencing. bIndicates that these methods have been used for differentiating colonization from infection and non infected from infected ulcer in diabetic foot ulcer.