Transcript Bio Lecture

Best though and continuous study
Jerome Groopman
Peter Gilligan
Professor, Pathology-Lab Medicine
UNC School of Medicine
3/27/2017
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How I became a clinical microbiologist
• Obtained doctoral degree in microbiology at the University
of Kansas
• Did post-doctoral training (2 years) in medical and public
health microbiology at UNC Hospitals
• Director of Microbiology Labs at St Christopher’s Hospital
for Children (Philadelphia) for 4 years
• Past 25+ years, Associate Director then Director of the
Clinical Microbiology-Immunology Labs at UNC Hospitals
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What do clinical microbiologists do?
• We serve:
» our patients
» our health care-providing colleagues, physicians,
nurses, physician assistants, pharmacy colleagues
» hospital administrators
• We make money for the institution
» general public by insuring the public health
• Involved in studying outbreaks of several emerging
infectious diseases including current fungal meningitis
one
• will tell you about an emerging pathogens todayClostridium difficile
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How do we serve?
• central role in the diagnosis and management of
infectious diseases
• central role in infection prevention and antimicrobial
use
• recognize emerging disease threats and outbreaks
including bioterrorism events
• we educate & train health care providers
• we create new knowledge (research) to deal with
practical problems
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Best things about my job
• Direct impact on patient care and public health of the
community
• Intellectually challenging job requiring a broad fund of
knowledge-need to know a little about a lot of things –I am
never bored!!!!!!!
• Get to work with cutting edge technology
• Work with highly motivated and intelligent individuals
• Get to be at the cutting edge of infectious disease
diagnosis
• I am involved in global issues as they relate to infectious
diseases
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Worst things about my job
• Incredible amounts of governmental oversight
• Increasing emphasis on financial aspects of the job
• Declining talent pool of technologists-THIS A GREAT JOB
MARKET FOR YOU WITH APPROPRIATE TRAINING
• Too much travel
• Need to be responsible for an organization that run
24/7/365-we never close. Personally have worked through
ice storms, blizzards, and hurricanes.
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How you can become a clinical
microbiologist
• CLS programs available here, ECU, WSSU, Wake Forest,
UNC-CH
» Education is also available on line
• 2 more years of school to get a BS in CLS
» There is no unemployment in this group
• Take ASCP certification exam to become certified as a
MT.
» Starting salary is 41,000 and up
» Career options are amazingly diverse; many former UNC
students work in leadership positions in the pharmaceutical
and biotech industries- Also have 5 former employees
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currently in Med, Grad, Pharmacy School
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Emerging Infectious Diseases in the Past 35 Years
• Clostridium difficile*#
• Ebola virus
• novel H1N1 influenza AHIV*#
• SARS and MERS CoV*
• Cryptosporidium*
• E. coli O157:H7*#
• Nipah virus
• nv Creutzfeldt-Jakob disease
• Sin Nombre Virus
• West Nile Virus
• Vibrio vulnificus*
• Cyclospora
• Bacillus anthracis #(BT agent)
• CA-ORSA*#
• TSST-1 S. aureus*#
• XDR- and MDR-TB*
• MDR- pneumococcus*#
• MDR-Acinetobacter*
• Rapidly growing mycobacterium*#
• Campylobacter*#
•3/27/2017
ESBL-Enterobactericeae*
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Rotavirus*
Norovirus*
BK virus*
Chlamydophila pneumoniae
Penicillium marneffei
Legionella*
Burkholderia cepacia complex*#
Burkholderia gladioli*#
VRE*#/VRSA
Helicobacter pylori*
HHV-6*
HPV*
HCV*
Avian influenza (H5N1)
Ehrlichia chaffenesis*
Borrelia burgdorferi* (Lyme disease)
Enterotoxigenic E. coli#
Enteroadherent E. coli*
Bordetella avium
Microsporidium*
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Clostridium difficile
• General
characteristics
» Gram positive rod
» Spore former
» Anaerobic
» Can be part of human
microflora
» Pathogenicity due to
the production of two
protein exotoxins A and
B
Chance favors only the prepared
mind
Louis Pasteur
Key events in the discovery of C.
difficile
• Larson and colleagues describe a toxin in the
feces of a child with pseudomembranous colitis
(1977)
• Bartlett and colleagues show that C difficile can
induce colitis in hamsters given clindamycin and
then a variety of antibiotics and then proves that
the organism can cause the same disease in
humans (1978)
» Serendipity is important- showed that C. sordellii
antitoxin could neutralize toxins produced by C. difficile
in a tissue culture cytotoxicity assay.
Key events in the discovery of C.
difficile
• Among others, Gilligan
and colleagues show
that C. difficile is the
most common bacterial
agent in a general
population (1980)
• Lyerly and colleagues
purify two toxins, A and
B, from C. difficile and
also produce an
important anti-toxin
against these
organisms (1982)
US deaths due to C.
difficle has increased
2.3X since 2000 ;
mortality 4%
Peery et al, 2012
Gastroenterology (in press)
Nature Reviews Gastroenterology &
Hepatology 8, 17-26 (January 2011)
What makes C difficile an important pathogen in the
industrialized world?
• Important ideas
» Organism can survive in the environment for months as
spores; spores are refractory to disinfectants especially
alcohol and all antimicrobials
» Alternation in the gut flora is important in predisposing
patient’s to disease with this organism- antibiotics mediate
this change
• Microbiome is less diverse
» Most common diarrheal disease etiology in the industrialized
world requiring specific antimicrobial interventions
» Leading health care associated pathogen in US
Age related C. difficile incidence in
US
What factors has resulted in the reemergence of Clostridium difficile??
• Emergence of highly virulent strains
• Better case ascertainment
» Improvement in lab diagnosis
• Aging population
» Decline in Bifidobacterium with age, an organism
important in colonization resistance, in gut flora may
create more permissive environment for C. difficile
• Increased use of antimicrobials especially fluoroquinolones
with anti-anaerobic activity to which C. difficile is resistant
» This is being debated in the infectious disease
community
» 90% of C. difficile isolates are fluoroquinolone resistant
Why are antimicrobials an important risk
factor in C. difficile?
• The vast majority of
patients have received
antimicrobials that alter
the microbiome reducing
its complexity and leading
to C. difficile germination,
growth and toxin
production
• Key protective organisms
include Bacteriodes,
Ruminococcus,
Eubacterium,
Lachnospira,
Porphyromonadaceae)
•
Petrof et al 2013 Microbiome 1:3: Schubert et al.
mBio 2014 5(3): e01021-14
Taur and Pamer 2014. Nature Medicine
Clostridium difficile PMC and toxic
megacolon
C. difficile: Spectrum of disease
Asymptomatic carriage
Mild diarrhea
Profuse diarrhea with non-specific colitis
Pseudomembranous colitis
Toxic megacolon
frequency
Rules for C. difficile testing
• If the stick stands, the
test is banned (type 15)
» High carriage rate in
patients on antimicrobials
• If the stick falls, test
them all. (type 6 + 7)
Dr. Stephen Brecher
3/27/2017
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Report as positive for
C. difficile
Report as negative for
C. difficile
Based on data in literature
of PVP >95% for CDI
If NAAT for C. difficile toxin gene is positive, report as positive for C. difficile.
If NAAT for C. difficile toxin gene is negative, report as negative as C. difficile
UNC C. difficile rates for the first quarter
2014
UNC infection rate is higher than for all NC hospitals but not for ones of our
Post-analytical phase-what test best
predicts disease
• Large study of >6000 disease episodes:
» Toxin positive patients had the highest mortality
» Toxin positive and PCR positive patients had increased
length of stay compared to PCR negative patients (Lancet,
2013; 13:936-45)
• Toxin positive specimens have lower PCR Ct than NAAT
only suggesting higher organism load in toxin positive
patients (J. Hosp. Infect, 2013; 84:311-5)
How do we interpret our test results based
on these data
• GDH negative- no C. difficile (82.4%)
• GDH positive/PCR negative- no C. difficile (5.2%)
• GDH positive/PCR positive- C. difficile infection vs.
excretor (7.9%)
• GDH positive/toxin positive- C. difficile infection (4.4%)
What does “C. difficile execretor”
mean?
Likely be a clinical decision with infection
prevention ramifications
Bottom line: Need to treat the patient not the
laboratory test
Fecal Microbial Transplant (FMT)
• C. difficile recurrence rates are estimated to be 20 to 30%
• Patients may have multiple recurrences that are
increasingly refractory to antimicrobial therapy
• Random controlled trial of FMT showed a resolution in
81% of patients after one infusion and resolution in an
additional 2/3 after 2nd infusion: antimicrobial therapy was
effective in 30%
» Study stopped early by data safety monitoring board
2013; 368:407-15)
(NEJM
Fecal Microbiome Transplants
Microbiota Diversity in
after Infusion of Donor
Feces, as Compared with Diversity in Healthy Donors.
van Nood E et al. N Engl J Med 2013;368:407-415.
FMT: Donor issues
• Stool vs stool substitute
» Stool substitute-33 isolates recovered from the stool of
healthy female» 2 patients studied-both resolved diarrhea within 72 hours
(Microbiome 2013, 1:3)
• FDA would prefer the stool substitute because of safety
concerns which arise from using fecal specimens» Advocates for FMT-think of it as an “organ transplant”
» FMT-very expensive because of donor screening
• Short-term FMT data excellent-90% success rate