APIC Greater NY Chapter 13Infection Prevention & Control Champion Presentation

Beth Nivin MPHResearch 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 malaria-

contrary to usual hospital practices.• Pyrosequencing for Patient 2 identical to results of Patient 1-

not 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 DendogramGenerated 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.