Emerging pathogens 2009Emerging pathogens 2009

• Peter H. Gilligan PhD• Clinical Microbiology-Immunology Labs• UNC Hospitals

How I became a clinical microbiologistHow 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?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?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 jobBest 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 jobWorst things about my job• 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 How you can become a clinical microbiologistmicrobiologist

• 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 YearsEmerging Infectious Diseases in the Past 30 Years

• novel H1N1 influenza A• 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*#

• 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 emergeHow 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

• Organism evolution as a result of human intervention» Antibiotic pressure

• Organisms that jump species barriers

How do microbes change?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?How emerging pathogens develop?

• 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?How do emerging pathogens develop?

• 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 ecosystemsChanging 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 techniquesChanges 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 careChanges 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 technologyPathogens detected with new technology• Prime example is HCV

» Viral genome elucidated using molecular cloning techniques

• Broad range 16S RNA primers are used to detect non-cultivable 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 How does bacterial resistance develop?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 effectsAntibiotic 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 barriersOrganisms 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 VirusStructure of the Influenza VirusHemagglutinin (HA)

16 types in influenza A

Neuraminidase (NA)9 types in influenza A

ssRNA–highly mutable

Adapted from: Hayden FG et al. Clin Virol. 1997:911-42.

8 segments: allowsreassortment during

double infection

Pathology of Influenza VirusPathology of Influenza Virus• 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• 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 DriftAntigenic Drift

• Minor genetic variations in HA and NA• Accumulation of point mutations (≥2)

Antigenic ShiftAntigenic Shift

• Major genetic changes in HA and NA• Reassortment in double infected cell• Human and non-human

Novel H1N1-an overviewNovel H1N1-an overview• 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 overviewNovel 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 Emergence of Quadruple-Reassortant H1N1/09H1N1/09

Garten et al., Science, 2009; 325:198

Novel H1N1-what we know as of 10-4-09Novel 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 10-4-09Novel 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 10-4-09Novel 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 DistributionH1N1/09 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 DistributionH1N1/09 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 10-4-09Novel 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 EpidemiologyInternational EpidemiologyInternational Co-circulation of 2009 H1N1 and Seasonal Influenza

(As of September 20, 2009; posted September 25, 2009)

Influenza Testing at UNC Influenza Testing at UNC May – November 2009May – November 2009

as of 11/02/09#

UNC

H1N1 hospitalizations 62

H1N1 deaths 5

Oct - March

as of 10/19/09

Diagnosis of novel H1N1-what we knowDiagnosis 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?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

www.cdc.gov/flu/weekly2 in NC

What other things do we need to think about with the What other things do we need to think about with the novel H1N1?novel H1N1?

• 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

» 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, “As Brian the scientist would say, “Any Questions?”Any Questions?”