Emerging pathogens 2009
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Peter H. Gilligan PhD
Clinical Microbiology-Immunology Labs
UNC Hospitals
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
• Have served on medical school admission committee for
approximately 15 years and the MD/PhD advisory
(admissions) committee for the past 10 years
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-will tell you about one today-novel
H1N1 (swine flu)
How do we serve?
• central role in the diagnosis and management of
infectious diseases
• central role in infection control 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
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!!!!!!!
• Work with highly motivated and intelligent individuals
• Get to be at the cutting edge of infectious disease
diagnosis
Worst things about my job
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Incredible amounts of governmental oversight
Increasing emphasis on financial aspects of the job
Declining talent pool of technologists
Need to be responsible for an organization that run
24/7/365-we never close. Personally have worked through
ice storms, blizzards, and hurricanes.
How you can become a clinical
microbiologist
• CLS programs available here, ECU, WCU, 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 38,000 and up
» Career options are amazingly diverse; many former UNC
students work in leadership positions in the pharmaceutical
and biotech industries
Emerging Infectious Diseases in the Past 30 Years
• novel H1N1 influenza A
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Clostridium difficile*#
HIV*#
SARS*
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*#
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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*
How do new pathogens emerge
• Changing ecosystems
• Changes in food production techniques
• Evolution of medical devices and care
» Long term survival of immunosuppressed
• Pathogens that are detected because of new
technology
• Misuse of micro-organisms
» Biocrime/bioterrorism
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Organism evolution as a result of human intervention
» Antibiotic pressure
• Organisms that jump species barriers
How do microbes change?
• Bacteria, because they evolve very quickly, can readily
adapt to hostile environments
» Assume a generation time for a bacteria of 50 minutes
» 30 generations/day; or 220,000 bacterial generations for
each human generation (assume generation is 20 years)
» Bacteria have a huge evolutionary advantage over humans
How emerging pathogens develop?
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Mutation drives evolution
» constantly occurring
» usually silent or lethal
» environmental pressure such as antibiotics may select
“resistance” mutation
• Key feature of success of antibiotic resistant strains is their
genetic fitness I.e. their ability to compete in a complex microbial
environment
» Recognition that certain bacteria may be hypermutators
because of mutation in DNA repair genes
• These strains may not be as “fit” as wild-types but may
predominant in certain chronic infections such as
P.
aeruginosa causing chronic pulmonary infections in CF patients
How do emerging pathogens develop?
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Recombination
» Resistance genes from antibiotic producing
organisms
» genetic exchange of resistant genes can occur
among organisms which are genetically
diverse
• Think Cholera toxin genes to E. coli
» transfer of resistance/virulence genes can be
mediated by plasmids/phage/transposons/
integrons
Changing ecosystems
• Lyme disease
» A perfect storm
• Farmland in New England returned to forest
• Natural predators for deer were eliminated
• Deer populations and the ticks they carried increased
because of ecosystem changes
• People built homes and spent increasing amounts of time
in the woods
• This resulted in increased exposure to deer ticks that
carried Borrelia
» Ticks were pencil point in size and often difficult to see
Changes in food production techniques
• Increased use of factory farming
• Feedlots bring together large numbers of animals who
produce large amounts of waste
» Waste can lead to run-off of EHEC that can contaminant
adjacent fields as was seen in recent spinach outbreaks
• Large meat packing operations can result in 50 ton lots of
ground meat containing 100s of animals
» Meat can be distributed throughout the US
» Contaminated lots can then lead to large scale outbreaks
Changes in medical care
• Immunosuppression either as a result of HIV or medically
therapy (ex. transplants) results in emerging infections
» Pneumocystis, MAC, toxoplasma and CMV in HIV patients
» CMV, adenovirus and HHV-6 in transplant patients
• The use of indwelling artificial materials such as catheters,
shunts, artificial joints present new ecosystems and new
organisms
» Examples-coagulase negative staphylococci growing as a
biofilm on artificial joints/catheters/shunts
» Rapidly growing mycobacteria causing keratitis following
LASIK surgery
Pathogens detected with new technology
• Prime example is HCV
» Viral genome elucidated using molecular cloning techniques
• Broad range 16S RNA primers are used to detect noncultivable bacteria
• Next big thing- application of molecular tools to
understand how mixed microbial populations cause
disease
» Likely diseases caused by mixed microbial populations are
bacterial vaginosis, peridontal disease, inflammatory bowel
disease, CF lung disease
How does bacterial resistance
develop?
• Bacterial resistance develops in response to antimicrobial
pressure
» It is estimated that 3 million lbs of antimicrobials are used
each year in the US
• Much of it is used in children to treat viral respiratory
illness
• Estimated that 3/4 of children in US younger than two
receive antimicrobials
• Children then may serve as a key role for the emergence of
antimicrobial resistance
» 10x that amount are used in animals
» End result- tremendous selective pressure that results in the
emergence of bacterial resistance
Antibiotic associated adverse effects
• Antimicrobial toxicity and allergic reactions
» Anti-parasitic>anti-fungal>anti-viral>antibacterials
» 20% of ER visits for drug adverse events are due to
antimicrobials
• Alteration in the microbial flora
» Candida vaginitis and thursh
» C. difficile infection
» Salmonellosis
• Emergence of resistance
» Few organisms where resistance is not clinically important
Organisms that jump species barriers
• HIV, SARS, Novel H1N1 flu
» HIV likely jumped from primates to humans
» SARS from pigs(?)
» Novel H1N1 is a reassorted strain of H1N1 with genes from
two swine viruses and avian virus, and human virus
» Technology allows us to quickly develop diagnostics for new
pathogens
• Took years to develop HIV diagnostics
• Took weeks to develop SARS diagnostics
• Took 3 day to develop novel H1N1 diagnostic testing strategy
in our lab and a few weeks more to develop a specific novel
H1N1 assay
Structure of the Influenza Virus
Hemagglutinin (HA)
16 types in influenza A
Neuraminidase (NA)
9 types in influenza A
ssRNA–highly mutable
8 segments: allows
reassortment during
double infection
Adapted from: Hayden FG et al. Clin Virol. 1997:911-42.
Pathology of Influenza Virus
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Virus attaches to sialic acid
receptors on columnar epithelial
cells
Viral proteins take over cellular
machinery
Shuts down host cellular protein
synthesis
» Eventually results in cell
death
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Virus is released from cell and
initiates infection in adjacent cells
End result: necrosis of respiratory
tissue
Defect in ciliary function puts
patients at risk for secondary
bacterial infections
Antigenic Drift
• Minor genetic variations in HA and NA
• Accumulation of point mutations (≥2)
Antigenic Shift
• Major genetic changes in HA and NA
• Reassortment in double infected cell
• Human and non-human
Novel H1N1-an overview
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In April 09, a novel variant of the H1N1 virus was reported from CDC from two
California cases
In late April 09, news reports of young adults with severe disease and deaths
were being reported from Mexico City
» This resulted in school closures in Mexico City for approximately 3 weeks
and recommendation for “social distancing” nationwide including soccer
games played in empty stadiums
» First report of disease from Mexico City showed mortality was highest in
children and young adults (NEJM 361:680, 2009)
By May 5, 09, 642 confirmed cases of novel H1N1 had been reported in US
(NEJM 360:2605, 2009)
» Included closure of one school in NYC-epidemic began after students
returned from a trip to Cancun; similar outbreak seen in New Zealand
starting with individuals who recently visited Mexico
By late May, we were beginning to see cases of the novel H1N1 @ UNC
Health Care
» By early June we had a validated, PCR specific for novel H1N1; the initial
PCR test we had for influenza A did not detect this variant of the virus
indicating changes in the matrix protein which were subsequently reported
Novel H1N1-an overview
• By early June the World Health Organization (WHO)
declared a global pandemic
• With the arrival of students back to Chapel Hill, we have
begun to see a resurgence in “probable” cases of novel
H1N1 cases
Emergence of Quadruple-Reassortant
H1N1/09
Garten et al., Science, 2009; 325:198
Novel H1N1-what we know as of 10-4-09
• From briefing note 9 of WHO (published Aug 28 @ who.int./csr/disease/swineflu)
» H1N1 is the dominant virus globally
» Large population are susceptible to infection
• Specific populations are at risk
» Important to monitor for drug resistant
» Disease is not the same as seasonal flu
» For patients requiring hospitalization, requirement for intensive
care is greatly increased
» Little data from developing world
» Co-infection with HIV
• Does not appear to result in more severe illness in those receiving
antiretrovirals –these data are limited
• What will happen in the 16 million HIV infected patients not receiving
drug is unknown
Novel H1N1-what we know as of 10-4-09
• Novel H1N1 is sensitive to oseltamivir and zanamivir but
resistant to amantidine
» recombinant genes from a H1 Eurasian swine flu strain are
responsible for amantidine resistance
» Oseltamivir resistance has been recognized in
epidemiologically linked patients in NC (letter from NC PH
epidemiologist Aug 21)
» Seasonal influenza A H1 is oseltamivir resistant while H3 is
amantidine resistant
Novel H1N1-what we know as of 10-4-09
• What do we now about H1N1?
• Transmission appears to be highly efficient
• Virus is the result of a reassortment of four different viruses
» Distantly related to 1918 H1N1
» Matrix proteins and H1 proteins quite different from seasonal H1N1
• Gene segments on novel H1N1 show high identity indicating the
introduction of a single strain into humans
» Vaccination of seasonal H1N1 does not protect against novel
H1N1
» Severe respiratory illness is due directly to influenza induced
disease and not secondary bacterial agents as was seen in 1918
pandemic
• Most of the illnesses have been mild and the mortality has been
similar to seasonal influenza
H1N1/09 Age Distribution
Graph A: Novel H1N1 Confirmed
and Probable Case Rate in the
United States, By Age Group
Graph B: Novel H1N1 U.S.
Hospitalization Rate per 100,000
Population, By Age Group
www.cdc.gov
H1N1/09 Age Distribution
Graph C: Novel
H1N1 U.S.
Deaths, By Age
Group
(www.cdc.gov)
Chowell et al., NEJM 2009, 361;7
Novel H1N1-what we know as of 10-4-09
• Target groups with increased risk and thus the priority
population for novel H1N1 vaccination due in mid-October
» Pregnant women
» Health Care Workers and Emergency Medical Service
providers
» Persons living with or provide care for infants <6 months of
age
» Persons 6 months to 24 years of age
» Persons 25-64 with medical conditions that put them @
increased risk for influenza
• For the first time this will include morbidly obese individuals
International Epidemiology
International Co-circulation of 2009 H1N1 and Seasonal Influenza
(As of September 20, 2009; posted September 25, 2009)
Influenza Testing at UNC
May – November 2009
as of 10/19/09
Oct - March
as of 11/02/09
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UNC
H1N1 hospitalizations
62
H1N1 deaths
5
Diagnosis of novel H1N1-what we know
• Rapid antigen tests have low sensitivity for this virus
depending upon the population tested- used by 83% of
labs (survey of 146 labs; clinmicronet survey July 2009)
• DFA reagents will detect this virus-29% of labs (clinmicronet
survey July 2009)
• Widely used viral culture system (Rmix cells) will detect
this virus-51% of labs used (clinmicronet survey July 2009)
• PCR tests have evolved to be the gold standard for novel
H1N1-30% of labs use plus method of choice in public
health labs in US (clinmicronet survey July 2009)
» PCR can be used to do subtyping to distinguish seasonal H1N1, from novel H1N1 from
H3N2
Why do we care WHICH influenza you have?
Treatment
• Amantadine/Rimantadine
» Interfere with influenza A virus M2 protein (membrane ion channel protein)
and inhibit viral replication
• Zanamivir/Oseltamivir
» Neuraminidase inhibitors
» Results in viral aggregation at the host cell surface and reduces the
number of viruses released from the infected cell
» Must be administered in first 48 h
» Also work for chemoprophylaxis
2 in NC
www.cdc.gov/flu/weekly
What other things do we need to think about with the
novel H1N1?
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A recent study (J Infect Dis. 2008 198:962) suggest that bacterial superinfection was
the major cause of death in the US during the 1918 flu pandemic
» Organisms believed to be important were Strepococcus pneumoniae,
Haemophilus influenzae and Group A streptococci
• In August Group A streptococci activity was low with <10% of tests (culture and
rapid antigen) being positive
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» Remember there were no antibiotics, no intensive care units, and no
ECMO (Extracorporeal Membrane Oxygenation) machines
Studies so far suggest that this has not been the case with novel H1N1
We are in an era of CA-MRSA, MDR-Acinetobacter, and KPC producing
Enterobactericeae. Will they be a major problem?
Several of the organisms seen as important in the 1918 pandemic are vaccine
preventable. It is now, more than ever, important to have infant and children,
the at risk population, vaccinated against S. pneumoniae and H. influenzae
As Brian the scientist would say, “Any
Questions?”