Lab Matters Summer 2019 - Page 54

APHL 2019 POSTER ABSTRACTS Methods: US states voluntarily report cryptosporidiosis cases to CDC through NNDSS. Eleven states participate in enhanced cryptosporidiosis surveillance through CryptoNet; other states can also submit specimens for genotyping. State collaborators 1) genotype Cryptosporidium specimens or send them to CDC and 2) complete the CryptoNet case investigation form, which focuses on exposures (e.g., waterborne, foodborne, person-to-person, and zoonotic). NNDSS and CryptoNet data from 2016 were analyzed using R and SAS 9.4. Results: For 2016, 13,471 cases were identified in the NNDSS database; a subset (321, 2%) had genotyping and exposure data in the CryptoNet database. Demographic similarities were noted between NNDSS and CryptoNet datasets; females accounted for >50% of cases, and children ages 0–14 years accounted for >25% of cases. Most (>90%) of CryptoNet specimens were C. hominis or C. parvum. Treated recreational water (e.g., pool) exposure, contact with children in childcare, and contact with diapered persons were each noted more frequently among C. hominis cases. Untreated recreational water (e.g., lake), drinking water (e.g., private well, bottled water), and animal contact (e.g., calf) were each noted more frequently among C. parvum cases. Presenter: Dawn Roellig, Centers for Disease Control and Prevention, Atlanta, GA, iyd4@cdc.gov Is a Positive Shiga Toxin Test a Shiga Toxin-Producing E. coli Infection? — Foodborne Diseases Active Surveillance Network (FoodNet) — 2012−2017 D. Tack 1 , K. Barrett 1 , C. Medus 2 , K. Garmen 3 , J. Dunn 3 , S. Hurd 4 , J. Hatch 5 , K. Parada 6 , S. Wilson 7 , E. Wilson 8 , K. Wymore 9 , P. Griffin 1 , A. Geissler 1 ; 1 Centers for Disease Control and Prevention, 2 Minnesota Department of Health, 3 Tennessee Department of Health, 4 Connecticut Emerging Infections Program, 5 Oregon Health Authority, 6 Georgia Emerging Infections Program, 7 Georgia Department of Public Health, 8 Colorado Department of Public Health and Environment, 9 California Emerging Infections Program Background: FoodNet conducts active laboratory-based surveillance for Shiga toxin-producing E. coli (STEC) in 10 US sites. During 2007– 2017, FoodNet reported increased culture-independent diagnostic test (CIDT) use and decreased isolation of STEC by culture. In the absence of an STEC isolate, FoodNet has excluded cases whose Shiga toxin (Stx) CIDT results were not confirmed by a public health laboratory (PHL). In 2018, the STEC national case definition was updated to include infections diagnosed by any CIDT. Methods: We examined STEC infections reported to FoodNet during 2012−2017 with a positive Stx immunoassay (IA) or polymerase 52 LAB MATTERS Summer 2019 Results: During 2012−2017, 8,260 (76% of all STEC reported) cases tested positive by IA or PCR at a clinical laboratory followed by an IA or PCR at a PHL. Among these, 1,736 (21%) were excluded from FoodNet case counts. Twenty-nine percent of cases had positive results by CIDT alone. Some cases had two CIDT tests performed, resulting in 8,989 total test combinations. The most frequent combination was IA/PCR (57%), followed by IA/IA (26%) and PCR/PCR (25%); most (98%) were also tested by culture. Of the test combinations performed, 1,911 (29%) were discordant (range by state, 10%–44%). Among the IA/PCR test results, 18% were discordant, and 14% of those cultured had STEC isolated. A higher proportion of IA/IA (27%) and PCR/PCR (23%) results were discordant, and 5% of those cultured had STEC isolated. Persons with discordant test results were less likely to have diarrhea (91% vs. 97%) or bloody diarrhea (28% vs. 57%). Test result discordance increased markedly from 2012 to 2017 in all sites for IA/PCR (11% to 21%), IA/IA (17% to 34%), and PCR/PCR (6% to 24%). Conclusions: Accepting multiple test results with differing sensitivity and specificity complicates surveillance. Marked variation in frequency of discordant Stx results and identification of STEC isolates by state highlights how sensitivity and specificity of different test types, test targets, and specimen transport might affect STEC results and surveillance. Including all infections diagnosed by any CIDT could increase FoodNet STEC case counts and challenge interpretation of national trends. Presenter: Danielle Tack, Centers for Disease Control and Prevention, Atlanta, GA, dot7@cdc.gov Detecting Potential Outbreaks and Related Isolates Quickly and Easily Using MASH L. Fink, C. Kapsak, J. Sevinsky and E. Travanty, Colorado Department of Public Health and Environment Identifying foodborne outbreaks of bacterial disease quickly and efficiently is a major goal of public health laboratories, both at the state and federal level. While national organizations have many resources, both computationally and personnel-wise to combat outbreaks that are noticed across multiple states, many state partners lack sufficient resources to track and identify state-wide outbreaks before they become major problems. Towards this end, we have been experimenting with the open-source program MASH as a way to generate a MinHash representation of all the isolates that have come through the Colorado Department of Public Health and Environment (CDPHE) for whole genome sequencing (WGS). This quasi-database distills down the information to a small and useable search space, such that when any new isolates are sequenced, they can be sketched and compared to the entirety of the previously sequenced isolates in a fast and easy manner. In this way, isolates which may be close genetic matches to one another can be identified rapidly. Then, more robust snp, wgMLST, or core genome comparison methods can be applied in a targeted manner to determine true genetic distance, and give information on whether epidemiologists need to be informed. This system has the potential PublicHealthLabs @APHL APHL.org Discussion: Analysis of early enhanced surveillance data suggest that exposures differ by Cryptosporidium species. Strengthening surveillance by increasing the systematic collection of genotyping and exposure data will be used to develop and implement increasingly effective cryptosporidiosis prevention measures. CryptoNet is helping to modernize national cryptosporidiosis surveillance in two ways: first, CryptoNet laboratory database will be integrated into the PulseNet BioNumerics platform (i.e., this will be used in the future to streamline workflows); and second, exposure data defined by the CryptoNet case report form are included in the Foodborne and Diarrheal Diseases Message Mapping Guide as part of the NNDSS Modernization Initiative to support standardized HL7 messaging of exposure data from states to CDC. chain reaction (PCR) test at a clinical laboratory, followed by testing of the same or another specimen at a PHL. Three test type combinations were assessed (IA/IA, PCR/PCR, and IA/PCR) by state, symptoms, test discordance, and culture result. A positive Stx CIDT at a clinical laboratory followed by a negative Stx CIDT at the PHL was considered discordant.