Upload
magnus-palmer
View
216
Download
0
Tags:
Embed Size (px)
Citation preview
Microsatellite genotyping of Microsatellite genotyping of environmental environmental Aspergillus Aspergillus
fumigatusfumigatus isolates isolates
Nicole AbelNicole Abel
The University of The University of TulsaTulsa
IntroductionIntroduction
• J&M FARMS– Miami, OK (Ottawa Co.)– Large outdoor compost
facility– Commercial mushroom
farm – Complaints about smell
and perceived health effects
Concerning Statistics
• 13.4% of Ottawa County residents have asthma
• Average asthma rate for rest of OK is 7.2%
Compost & Bioaerosols• Several microorganisms break down the organic matter
in compost to create a usable product
• During composting process, compost is churned mechanically
• Mechanical agitation can cause these biological agents to become aerosolized– “bioaerosol”
• Increasing concern about the potential impact of composting on human health
Aspergillus fumigatus
• Fungus of the genus Aspergillus
• Dominant bioaerosol from compost
• Most common species in this genus to cause disease in individuals with a compromised immune system
Aspergillus fumigatusAspergillus fumigatus
Aspergillus fumigatus
Aspergillus fumigatus
• Bioaerosol health concerns are focused on Aspergillus fumigatus for several reasons:– Grows abundantly in compost– Can survive at peak compost temperatures– Can survive temperature of the human body – Conidia are easily airborne – When inhaled, small enough to reach lung– Several well-known health effects
Health effects of AF• AF is known to cause a wide span of
invasive diseases collectively called “Aspergillosis”
• Traditionally viewed as weak pathogen, causing problems with asthma, allergies, and other diseases:– “Farmer’s lung”– Aspergilloma– Fungal sinusitis
Health effects of AF
– “Farmer’s lung”• Inflammation of the lungs due to
repeated exposure to the spores• Symptoms of acute farmer’s lung:
– Chills, Cough, Fever, Shortness of breath
• Symptoms of chronic farmers lung:– Breathlessness, Cough, Loss of
appetite, weight loss• Often reverseable by avoiding additional
exposure• Chronic form may lead to scarring of
lung tissue
Health effects of AF– Aspergilloma
• an overgrowth of the fungus on the surface of preexisting cavities in the lungs
• This often occurs in patients treated successfully for tuberculosis
• Often no symptoms, but most common symptom is coughing up blood (hemoptysis)
• Most cases do not require treatment
• With severe hemoptysis, surgery may be required to remove the aspergilloma and stop the bleeding
Health effects of AF
– Fungal sinusitis• Inflammation of sinuses • Patients often have allergies or
asthma• Thick fungal debris and sticky mucus
that must be surgically removed in order to keep the inflammatory condition under control
• At times this massive nasal polyposis and fungal debris can expand and erode towards the eyes or brain.
Health effects of AF
• The situation has become much more serious in recent years
– increase in the number of immunosuppressed patients
– degree of severity of modern immunosuppressive therapies,
• Now most common airborne pathogenic fungus
• Causes wide span of severe and usually fatal invasive infections in the immunocompromised
Aspergillosis
• Extrinsic asthma- most common, occurs in allergic individuals, causes cough, wheezing, chills, aches, and pains
• Extrinsic allergic alveolitis- can occur in those without allergies, but with repeated exposure to AF spores and many of the spores reach lung tissue, causes coughing, difficulty in breathing, and fever
• Allergic bronchiopulminary aspergillosis- more serious form of “Farmer’s lung”, may follow entrinsic asthma, but symptoms are chronic and more severe, treatment is required or this disease can be fatal
Aspergillosis• Invasive Aspergillosis
– Most dangerous and rare– Occurs in the immunocompromised – AF grows from the lung into other organs– Often fatal – Causes 30% of fungal infections in cancer patients – Occurs in 10-25% of patients being treated for leukemia.
Even treated, the mortality rate for these patients is 80-90%
– Major cause of death at transplant and leukemia centers
Peoria Tribe/University of Tulsa Air Quality Studies in
Miami, OK
Phase 1• Previous study recorded elevated airborne A.
fumigatus within 400 m of compost facility
• A. fumigatus spores were significantly higher downwind of compost facility than control sites
• Problem: Air samples not done in populated areas so not pertinant to public health
Present StudyPresent Study2009-20102009-2010
• Objectives:– Determine AF conc. in facility’s compost
– Determine airborne AF conc. in Ottawa Co. vs. Tulsa Co.
– Determine genetic relation between airborne AF in Ottawa Co., AF in the facilty’s compost, and if distinct from Tulsa AF controls
Hypothesis• AF concentrations in facility’s compost will be
high
• Airborne AF concentration will be greater in Ottawa Co. vs. Tulsa Co.
• AF from compost & Ottawa Co. air will be genetically identical
• AF from Tulsa air will be genetically different from AF from Ottawa Co. air and compost isolates
Compost
Compost Windrows
Miami, OK
CompostCompost• Purchased 6 truckloads of spent
compost from facility• 1 gallon bag from each truckload
was brought to our lab at TU • 10 random samples obtained from
each bag of compost • Samples dilution plated onto MEA
containing Streptomycin in dilutions of 10-1, 10-2, and 10-3
• Plated AF concentrations in the compost ranged from 0-100,000 CFU/g
Compost 1 Sample 2Compost 1 Sample 2
10-1 10-2 10-3
840 CFU/g
Compost 1 Sample 1Compost 1 Sample 1
10-1 10-2 10-3
100,000 CFU/g
Average AF Concentrations in Facility's Compost
13904
11904
154
1938
1632
660
0 5000 10000 15000
1
2
3
4
5
6
Co
mp
os
t B
ag
#
AF CFU/g
Air Samples• Ottawa Co.- samples collected from 5 locations within 5 miles of
facility (selected by the EPA)
• Tulsa Co.- samples collected from 5 random locations in Tulsa (144 km upwind from compost site) to serve as control
• Verified control sites do not use compost from this facility
• Sampling done once a week withAnderson Single Stage Samplers onto MEA plus streptomycin plates for a total of 39 weeks
Ottawa Co. Air Sample Locations
North MiamiNorth Miami
MiamiMiami
CommerceCommerce PicherPicher
QuapawQuapaw
Compost Compost Facility/ Facility/
Mushroom farmMushroom farm
Tulsa Air Sample LocationsTulsa Air Sample Locations
Mohawk Park
University of Tulsa campus
Lakewood Gardens
Kendall-Whittier
Woodward Park
-------Ottawa Co.------- -------Tulsa Co.-------
0
5
10
15
20
25A
vera
ge A
F C
FU/m
3
Sample Location
Average AF for Each Sample Location
Number of times AF collected from air in 39 weeks:Ottawa Co.- 17 Tulsa Co.-8
0
5
10
15
20
25
30
35
40
Avera
ge C
FU
/m3
Apr May Jun Jul Aug Sep Oct Nov Dec Jan
Month
Ottawa
Tulsa
Average Airborne AF each Month
Ottawa Co. vs. Tulsa Co.
0
1
2
3
4
5
6
7
8
Avera
ge C
FU
/m3
Ottawa Tulsa
P=0.0238
(Statistically Significant)
Overall Average Airborne AF CFU/m3 Ottawa Co. vs. Tulsa Co.
Mushroom Side Project
• Several samples of the compost had extremely high levels of AF
• Commercial mushrooms are grown in the compost
• Could their mushrooms have elevated AF on their surface when sold in grocery store?
Mushrooms
• Purchased 7 brands of mushrooms (including J&M)
• Compost from each brand was removed from surface of mushrooms
• Samples diluted to 10-1, 10-2, and 10-3 onto MEA plates with Streptomycin and incubated
• AF colonies were identified and counted
J&M Grocery Mushrooms
AF on Surface of 7 Brands of Grocery Store Mushrooms
16933
613 20
2400
0 40
8000
0
2000
4000
6000
8000
10000
12000
14000
16000
18000
AF
CFU
/g
Mushroom Side project #2
• J&M mushrooms have excessive AF on their surface
• AF is hydrophobic and becomes airborne easily
• If these mushrooms are washed in a sink, will they become airborne in the kitchen?
Mushroom Washing
• J&M mushrooms were purchased and washed in a sink to mimic home use
• Air samples collected next to the sink using an Anderson single stage sampler with MEA plates before, during, and after washing
• This process was repeated with separate packages of mushrooms for a total of three trials
Airborne AF During Mushroom Washing
0 0 0
35 35
70
0 0
35
0
10
20
30
40
50
60
70
AF
(C
FU
/m3 )
before during after
trial 1
trial 2
trial 3
SubculturesSubcultures• All plates from air samples, compost, and
mushrooms were incubated at 45° C for 48 hours
• All AF isolates were sub-cultured & grown
in malt extract broth
Microsatellite• A microsatellite is a specific sequence of
DNA bases which are repeated a certain # of times. For example:– GTGTGTGTGTGT---’GT’ X 6– CTGCTGCTGCTG---’CTG’ X 4– ACTCACTCACTCACTC---’ACTC’ X 4
• Microsastellites can differ in # of repeats & are hereditary, so # of repeats can determine relatedness
• AKA– simple sequence repeats (SSR) – short tandem repeats (STR)– variable number tandem repeats (VNTR)
Microsatellite Applications
• Forensics– Link a suspect with a sample of blood, semen
or hair taken from a crime– Link a sample found on a suspect's clothing
with a victim– Investigating paternity in order to establish
rape or incest– Linking DNA samples with relatives of a
missing person
Microsatellite Applications
– Diagnosis & identification of human diseases
• Change in length early in development of some cancers
• Early cancer detection
• Polymorphic, so useful in locating genes responsible for various genetic disorders
Microsatellite Applications
– Population studies
• Variation of microsatellites in populations can help to make inferences about pop.
–Structures
–Differences
–Genetic drift
–Genetic bottlenecks
–Date of a last common ancestor
Microsatellite Applications
• Conservation biology
• Detect sudden change in population,
• Effects of population fragmentation
• Interaction of different populations
• Identification of new and incipient populations.
DNA extractionDNA extraction• The DNA was extracted from all
isolates using EZNA kit
• DNA concentrations extracted from each isolate were documented using the Nanodrop 8000
Identification and PCR
• Isolates positively identified as AF using:
– Microscopic analysis
– DNA analysis of ITS gene• DNA extraction• PCR• Sequencing
Genotyping• 9 microsatellites were used to discriminate
between the isolates of AF using the method of de Valk et al. (2005)
– Genotyped using complete panel of 9 microsatellites (ABI 3130xl Capillary Sequencer)
– Genotypes analyzed
– Strains and relatedness determined (GeneMapper v 4.0)
AF STRAINS
ConclusionsCompost
• Aspergillus fumigatus concentration in J&M’s compost was extremely variable (0-100,000 CFU/g)
• Bags #1 & #2 contains extremely high amounts of AF
• Some J&M compost contains very high levels of AF and is mechanically agitated, it is possible this could cause elevated airborne AF in the surrounding area.
ConclusionsAir Samples
• Total airborne spore concentration significantly higher in Ottawa Co. vs. Tulsa Co.
• P=0.0238
• The sampling location with highest airborne conc. Is most often downwind from J&M
ConclusionsGenetic Analysis
• Genetic variation exists amongst the isolates; however:– 3 of 3 isolates from mushrooms match compost– 2 of 2 Isolates from air sampling during
mushroom washing match compost – 12 of 19 isolates from Ottawa Co. air match
compost – 30 of 48 isolates from compost match Ottawa
Co. air samples – Tulsa isolates distinct from all J&M isolates
Acknowledgments
• Dr. Estelle Levetin• Dr. Mark BuchheimDr. Mark Buchheim• Dr. Ron Bonett Dr. Ron Bonett • Jacob Crowley Jacob Crowley • Justin Downs and Brandon Bartley Justin Downs and Brandon Bartley • Funding for this study was provided by the Funding for this study was provided by the
Peoria Tribe of Indians through an Peoria Tribe of Indians through an • EPA grantEPA grant
Thank you!Questions?