Presentation for hospitals.

1. Advanced Next Generation-DNA Sequencing
of Bacteria, Fungal ,Viral

2. Medicine-Diagnose &Treat
The more accurate your diagnostic information the better your
treatment decisions
Infections- and identifying the microbes
Traditional Culture
Grow the microbes
OR
Extract the DNA

3. Greatest False Prophecies in the
history of medicine
• In 1821, Sir John Forbes concluded that the
newly invented stethoscope was “ludicrous”
and would never be generally adopted by
physicians.

4. Greatest False Prophecies in
Medicine
• However, this honor might better be
bestowed on many members of the
microbiology community, who before the
advent of molecular technology deemed the
body to be largely sterile.

5. PathoGenius Laboratory
• Based in LubbockTexas
• Only Lab in the Nation that is CLIA/CAP certified to do
“NextGeneration Sequencing” of Microbes
• Physicians do not buy anything or bill
• Medicare reimburses the the test at $190
• We position the technology for Chronic infections
• Wounds, UTIs, Sinus, Lung, Joint, BV

6. Human Microbiome
• Human body 1Trillion Host cells
• Human body 10Trillion bacterial cells
• 25,ooo known bacterial sequences now in the
GenBank
• 99.6 of the species in the human microbiota have not
or can not be characterized through culturing
techniques

8. “In this case, the
results of Next
Generation
Sequencing
contributed directly
to a dramatic effect
on the patient’s
care, resulting
ultimately in a
favorable
outcome”.

9. Pathogenius DNA Molecular Diagnostics.
25,000 DNA codes on file. Indifferent to time, media and transport issues.

11. Otitis Media Biofilm
Sinus Cavity Biofilm

12. BioFilms in Lung Infections
CF Patient with Biofilms throughout the lung

13. BacterialVaginosis

14. 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

18. Dr. Caroline Fife
Dr. John Steinberg Dr. Chris Attinger
Dr. James McGuire
Wound Care ENT
Dr. David Kennedy : Chairman Penn
Dr. BJ Ferguson U of Pittsburgh
Dr. Martin Citardi Chairman U ofTexas
Dr. Donald Lanza
Dr.Takashima Director SinusCenter Baylor
Dr .WinstonVaughn Stanford SinusCenter
House Ear Institute Los Angeles CA
ENT Dept. Georgetown Medical School
Dr Patrick Antonelli – Chief Otolaryngology UF

19. 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

22. Biocides vs. Biofilm

23. In conclusion, bacterial
vaginosis in our subjects was
associated with complex
vaginal bacterial communities
that included many newly
recognized bacterial species
that have not previously been
detected with conventional
cultivation techniques.

24. “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.”

25. 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 !

27. “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”

28. 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. PATHOGENIUS REPORT

30. Provide Anti Biogram

31. “I need my Sensitivity for antibiotics"
• “Biofilm-growing microorganisms are
significantly more tolerant to antibiotics [6] and
corresponding breakpoints have not been
established [34].The S-I-R results can therefore
not be used to predict therapeutic success in the
case of biofilm infections and offer no guide to
clinicians for treating such infections.”
ESCMID Guidelines for the diagnosis and treatment of biofilm infections

32. Dead Bacteria DNA
Bacterial Biofilms and Chronic Rhinosinusitis Kilty
and Desrosiers
“Most convincing was the demonstration in a chinchilla model
that live bacteria, although nonculturable, could persist in
OME for weeks, whereas DNA strands and DNA from intact
but nonviable bacteria could not exist for more than a day
[21].”
“Given the extremely short half-life of mRNA, its presence was
evidence that viable metabolically active bacterial organisms
were likely present in OME.”

35. Sputum

38. 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

41. COST AND COVERAGE OF
MOLECULAR DIAGNOSTICSTRADITIONAL CULTURE
• MEDICARE PAYS
$250
DNA SEQUENCING
• MEDICARE PAYS
$ 285

42. CUSTOMIZED FOR EACH
PATEINT TOPICAL RX
LIPOGEL BASED
DOSED 3X WEEK
CONTAINS ANTIBIOFLIM AGENTS
ANTIBIOTICS
ANTIFUNGALS

43. Economic Impact in Diabetic Foot Wounds
Treatment in 2005 Treatment in 2013
Culture and Systemic Antibiotics Molecular andTopical Antibiotics
Total Payments for related codes
$11,444
Total Payments for related codes
$3,060
Reduction in total charges of 68%
189 patients 215 Patients

44. 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

45. 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

46. Stages of Biofilm Development

47. Multiple Strategies are required to succeed
against bio-films in chronic wounds
Debridement –Is the “Corner Stone”
Biocides
Systemic Antibiotics
Topical CustomizedAntibiotics

49. 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

50. 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)

52. Questions?

53. 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.

54. Lab Requisition