Lab Matters Fall 2020 - Page 37

APHL 2020 POSTER ABSTRACTS specific requirements which include testing spent irrigation water for Salmonella and E . coli O157 : H7 . STEC testing is not included in this requirement . Given the fact that there have been other reports of non-O157 STEC outbreaks and the recent occurrence of this E . coli O103 outbreak associated with sprouts has major implications to the FSMA Produce Rule . STEC testing of SIW should be recommended as best practice for improving sprout safety to prevent future outbreaks of toxigenic E . coli .
Presenter : Nancy Hall , State Hygienic Laboratory at the University of Iowa , Iowa City , IA , nhall @ uhl . uiowa . edu
GLOBAL HEALTH
Community Health Screening and Education Through Laboratory Science Workshop : Participant Evaluation of the 2018 Pilot Program in Aco , Peru
J . R . Ellis 1 , J . Vreeland 2 , F . Jaimes 2 ; 1 Texas State University , San Marco , TX , 2 Seton Family of Hospitals , Austin , TX
Public health outreach initiatives underutilize laboratory medicine students and professionals . This is a missed opportunity to engage lab science students in the health screening and education of their local communities as well as in partnerships with lab science students from other countries . This poster will discuss a novel bilingual community health screening and education ( CHS & E ) through laboratory science service-learning ( SL ) study abroad ( SA ) program that could be utilized to improve community engagement and understanding of public health and laboratory science .
In collaboration with The Foundation for International Medical Relief of Children ( FIMRC ), Clinical Associate Professor and 2019 Adult , Professional , and Community Education doctoral student , Joanna Ellis traveled with five CLS senior-level students to Huancayo , Peru in June of 2018 for a CHS & E through laboratory science SL-SA program . Utilizing the self-powered Lab-in-a-Suitcase from International Aid , the group conducted four CHS & E through lab science events in four different communities . We conducted hemoglobin , urinalysis , glucose , cholesterol , and sexually transmitted infection screenings on more than 160 people . The CUY Project was the most involved activity with six interactive stations for the families to learn about anemia , parasites , and nutrition through lab tests . Parents and children learned more about their conditions through fun and interesting laboratory science activities and tests . The lab-science based activities illustrated the biological impact of their lifestyle and dietary choices in a new and impactful way . This poster will describe the preparation , implementation , and first stage of evaluation of the CHS & E through laboratory science workshops . One hundred percent of the parent participants surveyed stated that the workshop would help them make decisions in caring for their children and would help prevent future health problems . This poster session is an opportunity to discuss how laboratory professionals can interact with their community and showcase the value of the field in public health education initiatives .
Presenter : Joanna Howard Ellis , Texas State University , San Marcos , TX , joannarellis @ txstate . edu
INFECTIOUS DISEASE
Tracking Antimicrobial Resistance with the Oxford Nanopore Technologies MinION Sequencer
M . Sylvester , R . Mukhopadhyay , T . Mitsunaga , E . Epson and Z . Berrada , California Department of Public Health , Richmond , CA
Tracking the spread of antimicrobial resistance genes is critical in the context of preventing and controlling healthcare-associated infections , including those caused by carbapenemase-producing organisms . However , the short reads generated by commonly-used sequencing platforms limit interpretation because they are not able to completely resolve features such as the location of resistance genes and the organization of resistance-bearing plasmids . The Oxford Nanopore Technologies MinION sequencer provides long reads which overcome these limitations and additionally promises rapid sequencing library preparation and faster turnaround times with little capital investment . Together , this suggests that it could be useful either as a supplement or an alternative to short-read sequencing platforms . As part of a feasibility study to determine the utility of the MinION in healthcare-associated outbreak detection and characterization , carbapenemase-producing organisms were sequenced on both the Illumina and MinION platforms . Inclusion of long-read data provided additional information that may be useful for inferring relatedness and transmission dynamics , and MinION data alone was sufficient for antimicrobial resistance gene localization and preliminary characterization .
Presenter : Matthew Sylvester , California Department of Public Health , Richmond , CA , matthew . sylvester @ cdph . ca . gov
An Automated Whole Genome Sequence Analysis and Data Visualization Pipeline Used to Investigate Antimicrobial Resistance Patterns in Cases of Shigellosis in California
L . Walker , J . Crandall , S . Chou , M . Sylvester , R . Mukhopadhyay , S . Abromaitis and Zenda Berrada , California Department of Public Health , Richmond , CA
The California Department of Public Health ’ s Infectious Disease Laboratory Branch has significantly increased its phylogenetic analysis of bacterial and viral isolates for epidemiology and other public health applications . Manual sequence analysis methods that were satisfactory on small data sets did not scale well for larger work volumes due to the increased complexity of integration and visualization of phylogeny data with clinical / epidemiological information , manual data entry and report generation , and dependence on costly proprietary software . To solve this , we developed an automated pipeline that streamlines de novo assembly , phylogenic tree building , and data visualization of outbreak whole genome samples using a series of open source command line tools and custom scripts . The pipeline takes in raw whole genome sequencing ( WGS ) data and completes quality control , de novo assembly , phage masking , single nucleotide polymorphism ( SNP ) calling , plasmid assembly and characterization , and antimicrobial resistance ( AMR ) gene detection . SNP data is used to create a phylogenetic tree that is overlaid with plasmid , AMR gene , phenotypic lab testing , and other epidemiological data . In addition to the pipeline , we created a custom AMR gene database using multiple sources . The AMR database is normalized to allow for consistent annotations across sources that can be automatically
Global Health / Infections Disease
Fall 2020 LAB MATTERS 35