Transcript Molecular Fingerprinting

APIC Greater NY Chapter 13
Infection Prevention & Control Champion Presentation
Beth Nivin MPH
Research Scientist, Bureau of Communicable Diseases
New York City Department of Health and Mental Hygiene
December 17, 2014
Molecular Fingerprinting In
Epidemiology Investigations
A technique for comparing the nucleotide sequences of
fragments of DNA from different sources.
The fragments are obtained by treating the DNA with
various endonucleases, enzymes that break DNA strands
at specific sites.
Why Molecular Fingerprinting
• I’d like to share with you examples of how
molecular fingerprinting uncovered cases of
nosocomial transmission.
• In each case the facility worked with the local
and State DOH to try to identify the mode of
transmission and rectify the infection control
breach.
• Sometimes it works and sometimes it doesn’t.
Types of Molecular Fingerprinting
• RFLP- restriction fragment length polymorphism- difference
between samples of homologous DNA molecules that come
from differing locations of restriction enzyme sites
• PFGE-is a technique used for the separation of large
deoxyribonucleic acid (DNA) molecules by applying to a gel
matrix an electric field that periodically changes direction.
• Pyrosequencing- method of determining the order of
nucleotides in DNA which relies on the detection of
pyrophosphate release on nucleotide incorporation.
My First Publication
• A Continuing Outbreak of Multidrug-Resistant
Tuberculosis, with Transmission in a Hospital
Nursery
• Beth Nivin, Peter Nicholas, Mitchell Gayer,
Thomas R. Frieden, and Paula I. Fujiwara
• Clinical Infectious Diseases (CID) 1997
MDRTB in Hospital A
• Outbreak of MDRTB at Hospital A in 1990-92- 16 patients.
• Matching of bed registry at TB case registry identified new cases linked to
hospital A through December 1994.
• In 1993-94, six cases of MDRTB in infants diagnosed in NYC.
– Three infants born at Hospital A Dec/92-Jan/93.
– One woman who delivered at Hospital A developed TB.
– Two HCWs from nursery during this time developed TB.
– One non-nursery HCW diagnosed (sputum positive)in January 1993
visited nursery on several occasions- unknown when he became
symptomatic.
– Strains of all identical to each other and to outbreak strain from
medical unit one floor below.
MDR TB in Hospital
• Outbreak at urban hospital A of MDRTB from
1/1/90-12/31/92. CDC investigation.
• Nosocomial transmission due to
– delayed diagnosis and treatment
– lack of negative air pressure in isolation rooms
– Inadequately masked TB patients walking in
hospital wards
– All same strain of TB- Strain W.
MDRTB in Nursery
• First documented outbreak of MDRTB in a
hospital nursery.
• Follow-up of all infants born during suspected
period
– 43% TST positive
• Demonstrates that the possibility of exposure to
unrecognized active tuberculosis in nursery and
hospital personnel is always present.
• Infection and active disease in the infants
developed after a relatively short period of
exposure.
Non-Travel Malaria
• 3/9/2012 BCD notified about case of malaria
(P. falciparum) at hospital.
– Patient previously hospitalized at same hospital
February 2012.
– No risk factors, no travel history
– Laparoscopic cholecystectomy
– No receipt of blood or blood products
Investigation-Malaria
• Blood sent to NYSDOH Wadsworth for
pyrosequencing-mutations in drug resistance
gene can identify origin of parasite.
• Chart review of potential risk factors.
• Investigation for potential of local mosquito
transmission.
• Review of hospital records of all patients
hospitalized at same time during 2/12 admission,
looking for anyone with undiagnosed malaria.
Results- Malaria Investigation
• Chart review confirmed no risk factors Patient 1.
• Pyrosequencing identified mutations that occurred in an
African (Nigerian) P. falciparum.
• Review of hospital records identified a patient hospitalized at
same time as patient 1, after returning from Nigeria, no
malaria prophylaxis.
• Patient 2 ‘s room 3 doors away from Patient 1.
• Patient 2 had not been reported to BCD for her malariacontrary to usual hospital practices.
• Pyrosequencing for Patient 2 identical to results of Patient 1not possible by chance alone, and Pt 1 originated from Pt. 2.
Conclusion-Malaria
• Nosocomial transmission from Patient 2 to
Patient 1.
• No shared nursing and phlebotomy personnel,
times of blood draws and glucose tests, times
for all parenteral medications, intravenous
fluids and flushes were administered and
when IV lines were inserted.
• Mechanism of transmission still unknown.
Listeria Cluster in Hospital
• 11/14/2012- BCD notified of Listeria case with
onset 10/29/12, at hospital A 10/8-11/5/2012.
• 11/21/2012-BCD notified of second case,
onset 11/5/2012, on same floor in hospital as
Case 1.
• 11/27/2012-PFGE results from both cases
indistinguishable.
• 11/29/2012- Chart reviews at hospital.
Epidemiological Investigation
• Chart reviews for two known cases to obtain
illness onset, comorbidities, medication, food
history and common exposure.
Environmental Investigation
• Observation of food handling practices and
refrigeration on floor of two known cases.
• Sanitary inspection of hospital kitchen-Office
of Environmental Investigations.
• Environmental swabs collected from food
contact and variety of kitchen surfaces.
• PFGE on environmental and patient swabs
Results (1): Listeria Investigation
• Both cases on soft GI diet but hard to identify
common foods.
• Both cases underwent sigmoidoscopies but no
common scopes or staff.
• Review of Listeria PFGE results in BCD database
identified five additional cases with same PFGE
pattern.
– All had been hospitalized at Hospital A from
9/20/2012 till 3/5/2013-on same (3) and different
units (4) and on same and different diets.
Results (2): Listeria Investigation
• Hot food brought to patients from kitchen on
carts and distributed to patient rooms- not
known how long food kept at room temperature.
• Refrigerator for patient snacks had no
thermometer.
• Kitchen visit- dirty and disorganized, creates
potential for cross-contamination.
• Protocols and procedures not uniformly
observed- communication problems.
Laboratory Results
• 21 samples collected- 9 (43%) grew Listeria
with same PFGE pattern and same pattern as
cases.
– Deli slicers
– Cutting boards
– Can openers
– Sink drains
PFGE Dendogram
Generated with the enzymes Asc I and Apa
Recommendations
• Improve conditions in kitchen/cafeteria.
• Ensure that hospitalized patients not served
food at risk of Listeria contamination.
• Improve communication between managerial
and food preparation staff.