APHL 2018 Annual Meeting Poster Abstracts
Genomic Investigation of a Protracted Carbapenem-
Resistant Enterobacter aerogenes Outbreak in a Cardiac
ICU at a Tertiary Care Center in Rochester, New York
(complete abstract in Antimicrobial Resistance, p. 42)
Expanding the Timeframe for Whole Genome Sequence
Analysis of Listeria monocytogenes: New York State’s
Experience with an Outbreak Spanning Multiple Years
L. Mingle 1 , D. Baker 1 , S. Wirth 1 , W. Wolfgang 1 , M. Dickinson 1 , L.
Thompson 1 , D. Wroblewski 1 , D. Nicholas 2 , M. Anand 3 , K. Ajileye 3 ,
C. Hidalgo 1 , M. Walawander 4 , J. Jurewicz 4 , N. Dumas 1 , K. Musser 1 ,
G. Smith 3 , A. Saylors 1 , A. Robbins 1 , M. Amato 1 ; 1 Wadsworth Center,
New York State Department of Health, Albany, NY, 2 Bureau of
Community Environmental Health and Food Protection, New York
State Department of Health, Albany, NY, 3 Bureau of Communicable
Disease Control, New York State Department of Health, Albany, NY,
4
Erie County Department of Health, Erie, PA
Presenter: Kimberlee Musser, PhD, Wadsworth Center, New York
State Department of Health, Albany, NY, Phone: 518.474.4177,
Email: [email protected]
PublicHealthLabs
@APHL
APHL.org
P. Root, IDEXX Laboratories, Inc., Westbrook, ME
(complete abstract in Environmental Health, p. 55)
Suitability of Self-collected Swabs for Influenza and
Respiratory Pathogen Detection
E. Reisdorf 1 , P. Shult 1 , J. Temte 2 , M. Wedig 1 , S. Barlow 2 , A. Uzicanin 3 ,
Y. Zheteyeva 3 , M. Landsverk 2 , A. Schemmel 2 , E. Temte 2 , L. Comp 2 ,
B. Maerz 2 ; 1 Wisconsin State Laboratory of Hygiene, Madison, WI,
2
University of Wisconsin Dept. of Family Medicine, Madison, WI,
3
Centers for Disease Control and Prevention, Atlanta, GA
Background: Surveillance for respiratory viruses in Wisconsin relies
upon specimen collection performed in clinical or research settings,
which may overly burden trained personnel. We examined the
suitability of self-collected mid-turbinate nasal swabs for monitoring
influenza activity.
Methods: The Oregon Child Absenteeism due to Respiratory
Disease Study (ORCHARDS) is carried out in 6 schools within the
Oregon School District in south-central Wisconsin. Anterior nares
or oropharyngeal (OP) swab specimens were collected during the
2016-2017 school year from students (K-12) exhibiting respiratory
illness by trained research staff using foam swabs (Pur-Wraps ® )
and flocked swabs (Remel ® ), respectively. Household members of
ill students self-collected either a mid-turbinate specimen using
flocked swabs (COPAN ® ) (2016-17 school year) or a nasal specimen
using a foam swab (Quidel ® ) (2017-18 school year) to study
household transmission dynamics. Household members received
training. Staff did not observe specimen collection. All respiratory
specimens were tested for influenza using PCR (CDC Human
Influenza Virus RT-PCR Panel). Detection of the human RNAse P
(RP) gene, an indicator of the presence of epithelial cells, was used
to determine specimen acceptability. Failure to detect the RP gene
(Ct>38) indicated that the specimen collected was suboptimal
(inconclusive). Collected and self-collected swabs were compared.
Results: A total of 873 ORCHARDS study participants from the
2016-2017 school year (319 students and 554 household members
[collected on day 0 and day 7]) submitted specimens. Of the 319
student OP swabs collected by trained staff, none were determined
to be inconclusive. Forty-one of the 1,108 (3.7%) self-collected
mid-turbinate nasal swabs were determined to be inconclusive.
Of the specimens tested, the mean RP Ct value was 26.4 for the
swabs collected by trained staff from students and 31.7 for the self-
collected swabs (p<.00001). More of the self-collected specimens
were acceptable after switching swab types (foam-tipped) and
collection site (nasal) during the 2017–2018 school year.
Conclusions: A small percentage of the self-collected mid-turbinate
nasal swabs were determined to be unsuitable for PCR testing.
However, of the specimens tested, the mean RP Ct difference
indicated fewer epithelial cells were present on the self-collected
swabs, meaning the likelihood of detecting influenza in the self-
collected specimen may be lower than in the staff-collected ones.
Data indicated that switching from flocked swabs to foam-tipped
swabs and changing the specimen collected from mid-turbinate to
nasal improved the suitability of self-collected swabs for influenza
detection. Reasons may be the larger surface area of the foam-
tipped swab or better tolerance of nasal than of mid-turbinate
collection.
Summer 2018 LAB MATTERS
75
The CDC PulseNet laboratory network has used pulsed-field gel
electrophoresis (PFGE) as the primary method for cluster detection
of Listeria monocytogenes for over 20 years. In January 2018,
PulseNet transitioned from PFGE to whole-genome sequencing
(WGS) analysis which provides a higher level of discrimination over
PFGE. Using BioNumerics 7.6 whole-genome multilocus sequence
typing (wgMLST) analysis, New York State Department of Health
(NYSDOH) identified an outbreak of Listeria monocytogenes which
continued intermittently during a period of just under three years.
Between 2014–2017, seven cases, which included three deaths,
of Listeria monocytogenes were identified from the same county
with PFGE patterns that were indistinguishable. NYSDOH Listeria
monocytogenes PFGE clusters are detected by evaluating isolates
collected within a 120-day timeframe. Therefore, three separate
PFGE clusters were identified due to the length of time between
cases [2014 (three cases), 2016 (two cases), 2017 (two cases)].
One additional out-of-state PFGE match was also detected between
2014–2017. Prior discussions between NYSDOH epidemiologists
and the Wadsworth Center Bacteriology Laboratory had established
that WGS cluster analysis would include all Listeria monocytogenes
isolates present in the NYS database instead of limiting analysis
to the 120-day window as was the practice for PFGE. Analysis of
the entire NYS database using wgMLST identified that the isolates
from the seven cases which occurred between 2014–2017
were highly related, differing by 0-3 alleles. Additionally, wgMLST
analysis indicated that the recent out-of-state PFGE match was not
related to the NYS cases. A common food preparation and delivery
establishment was identified for six of the seven NYS clinical
cases. Environmental sampling was performed at the facility and
Listeria monocytogenes was recovered from four of the 40 samples
collected. The environmental isolates had PFGE patterns which were
indistinguishable from those of the clinical isolates. Furthermore,
wgMLST analysis confirmed that the environmental isolates and
clinical isolates were highly-related, differing by 1-6 alleles. Use of
the expanded timeframe for WGS analysis was crucial in confirming
the relatedness of these intermittent Listeria monocytogenes cases
and in the determination of the source of this outbreak.
Public Health Role in Reducing Legionnaires’ Disease Risk