Lab Matters Summer 2018 - Page 77

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: kimberlee.musser@health.ny.gov 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