This document discusses advanced next-generation DNA sequencing techniques for identifying bacteria, fungi, and viruses. It highlights how DNA sequencing can identify over 13,000 pathogen DNA codes and is not affected by transport or culture issues. Examples are given where DNA sequencing identified chronic infections that cultures failed to detect. The document emphasizes how biofilms are difficult to culture but can be identified by DNA sequencing, and are responsible for 80% of infections. It provides examples comparing DNA sequencing to traditional cultures for identifying pathogens in chronic wounds and urine samples. The document also discusses using DNA diagnostic tests to provide treatment recommendations like customized topical therapies and antibiograms.
7. Material from an
infected elbow
prosthesis stained
with the Molecular
Probes
• Seven Surgical
Procedures
• Over 5 years
• Cultures consistently Neg
• Case represented a
landmark in the diagnosis
of chronic bacterial
infection in Orthopedic
Surgery
• PCR identified the
infection
8.
9.
10.
11. Planktonic Bacteria
Single Cell
Bio Film
“Community of Bacteria”
Cause of 80% of Infections
Cause of ChronicWounds
Will not grow in traditional culture
Biofilm cells express a radically different
phenotype than planktonic bacteria
Only Diagnostic tool is Molecular
Cause of Acute Infection
Will grow in traditional Culture
17. Diagnose –The physician needs to know
what they are up against
• The current diagnostic tool for identifying bacteria in the wound
used by many physicians is traditional culture
Culture – Means to Grow
1800Technology- Louis Pasteur based
Microbiology
15 % Accuracy - Less than 5% of known
bacteria will readily grow in the lab
Culture Result – What they could
grow , not what is in the wound
biofilm
18. DNA Analysis vs.Traditional Cultures
51 Chronic wounds- Parallel Samples
16 S DNA Sequencing Traditional Culture
• 46 /51 Staph Identified
• 32 / 51 Pseud Identified
• 28/51 Staph Identified
• 8 / 51 Pseud Identified
DNA Sequencing OutperformedTraditional Cultures
DNA Sequencing identified 145 Genera – Cultures 14 !
19.
20. “The impact of proper
specimen management on
patient care is enormous”
“Specimen selection and
collection are the
responsibility of the
medical staff and not the
laboratory”
21. American Society for Microbiology Standard:
Swab transport, RoomTemperature, 2 hours
Current Lab: Swab transport, unknown
temp, end of the day.
High probability of error from the start.
29. Urine Data from PathoGenius
• Based on 1221 Urine samples
• Escherichia coli 25% When seen – avg 73% of the sample
• Proteus mirabilis 9%
• Enterococcus faecalis 9%
• Lactobacillus gasseri 8%
• Lactobacillus crispatus 7%
• Lactobacillus iners 5%
We Identified a total of 507 species of Bacteria and Fungal in
our urine samples
30.
31.
32.
33. COST AND COVERAGE OF
MOLECULAR DIAGNOSTICSTRADITIONAL CULTURE
• MEDICARE PAYS
$250
DNA SEQUENCING
• MEDICARE PAYS
$ 285
34. CUSTOMIZED FOR EACH
PATEINT TOPICAL RX
LIPOGEL BASED
DOSED 3X WEEK
CONTAINS ANTIBIOFLIM AGENTS
ANTIBIOTICS
ANTIFUNGALS
35. DNA Diagnostic “Must be expensive “
How much will it cost?
Private Office
If your patients are a Medicare patient, 100% of the
cost of your testing will be paid by Medicare.
Medicare reimburses $190 for our Level 1 and Level 2
If your patients have private insurance, 50% of
Commercial Plans pay for the test.
No sample will ever be denied by Patho Genius
No Patient will ever go to collection
36. Benefits Pathogenius DNA MolecularTesting
• Fast Identification of Biofilms and their composition in
patients referred to you—Accuracy and Speed.
• GOLD STANDARD of Microbial Diagnostics
• Medicare Covers theTest and pay $190
• Less Expensive than a Culture
38. Multiple Strategies are required to succeed
against bio-films in chronic wounds
Debridement –Is the “Corner Stone”
Biocides
Systemic Antibiotics
Topical CustomizedAntibiotics
39.
40. Diagnostic Services – What we deliver
Two molecular microbial diagnostic tests are currently used at PathoGenius®. We take
your patient's swab, washing, or tissue sample; extract the microbial DNA; and report
the microbial analysis to you.
Level 1: PCR 24-Hour Rapid Screening
Screen 8 Common ENT Bacteria and 1 Fungal
Provide Quantitative Bacterial Load
Rapid turn around time of approximately 24 hours from the time of sample
receipt.
Pathogens Identified in Level 1
Staphylococcus (including MRSA)
Streptococcus pyogenes (GAS)
Haemophilus influenza
Moraxella Catarrhalis
Pseudomonas
Streptococcus pneumonia
Streptococcus agalactiae
Candida albicans
41. Level 2: Next Generation Sequencing
Only lab in the country that can provide your patients access
to DNA Pyro Sequencing
Pyro sequencing matches the DNA from your sample to the
entire universe of know bacteria and fungal pathogens
Level 2 Report is fax/emailed to you in 5-7 days
Level 2 Report includes a table of the pathogens identified and
the antibiotics that will cover them. ( Antibiogram)
44. The Neuropathic Diabetic Foot Ulcer Microbiome Is
AssociatedWith Clinical Factors
Sue E. Gardner,1 Stephen L. Hillis,2 Kris Heilmann,2 Julia A. Segre,3 and
ElizabethA. Grice4
From the 1University of Iowa, College of Nursing, Iowa City, Iowa; the 2University
of Iowa, Carver College of Medicine, Iowa City, Iowa; the 3National
Institutes of Health, National Human Genome Research Institute
Similar to other studies
(7,12,36), we found that cultures do not fully represent
bacterial diversity as compared with 16S rRNA gene sequencing.
Microbial load is widely viewed as the reference
standard for determining problematic bioburden in chronic
wounds that may not express robust clinical signs (37).We
demonstrated for the first time that cultures underrepresent
the microbial load of the ulcer as compared with
16S rRNA gene approaches. These findings may have important
clinical implications justifying the clinical use of
molecular approaches rather than traditional cultures.
