Lab Matters Fall 2020 - Page 45

APHL 2020 POSTER ABSTRACTS to help better diagnose and treat the unique AMR profile of each patient ’ s disease .
Presenter : Erin Tacheny , MRIGlobal , Gaithersburg , MD , etacheny @ mriglobal . org
Mosquito-borne Disease Impact of Environmental and National Disasters : Lessons Learned from Brazil and Mozambique
K . Yeh , MRIGlobal , Gaithersburg , MD
Natural and environmental disasters similarly cause significant changes in the environment including flooding , contamination of water supplies and displacement of human populations that can affect the ecosystem in unpredictable ways . The environmental impact of these disasters can potentially increase risk factors for mosquito-borne disease transmission that can result in serious public health problems long after the initial impact of the disaster . We aimed to investigate the infectious disease impact of two disasters of major significance in 2019 : a dam break in Minas Gerais , Brazil , and the cyclones in Mozambique . We conducted an assessment of surveillance data of several mosquito-borne diseases including malaria , dengue , chikungunya and Zika from each affected region before and after each disaster and compared 2019 data to previous years during the same time period and / or transmission season . In Brazil , the disaster contaminated the Rio Paraopeba , which has an extensive river basin that encompasses 48 cities . In 2019 , the river basin area reported 28.3 % of the probable dengue cases in Minas Gerais . Compared to 2018 , there was a substantial increase in confirmed dengue cases in the river basin area , 488 cases in 2018 vs . 46,961 in 2019 . Mozambique reported decreased cases of malaria immediately after the cyclone most likely as a result of disruption of health systems in the affected areas and significant displacement of human populations . Innovative surveillance approaches in the wake of a disaster may be necessary to improve data collection in the immediate and longterm aftermath of a disaster to inform where interventions should be implemented . We aim to continue this analysis during the 2020 transmission season to determine if these disasters could affect mosquito-borne disease transmission across multiple seasons .
Presenter : Falgunee Parekh , Epipointe , fparekh @ epipointe . com
Real-Time Metagenomics with PanGIA K . Yeh , MRIGlobal , Gaithersburg , MD
As the technology of sequencing evolves with lower costs , more affordable applications arise . Portable sequencing platforms such as the Oxford Nanopore Technologies MinION is enabling fieldforward genomic or metagenomic sequencing . While targeted molecular amplification-based assays such as quantitative real-time PCR ( qPCR ) confirm the presence or absence of a specific and well characterized organism , these assays do not survey the myriad of flora that are present , nor are they resilient to mutations in their genomic targets . For this reason , portable technologies relevant to various sectors including those working in public health laboratory professions . The ability of Next Generation Sequencing to broadly identify as many organisms in a given sample as possible could vastly improve our health and safety standards by elucidating more of the truth of our environment . Sample preparation for MinION is typically shorter than for less mobile sequencing platforms , saving time in the field . Further , the MinION produces read data in realtime , allowing for “ sequence until ” style analyses with the potential to drastically reduce sample to answer timeframes . Toward this goal , we are presenting “ real-time PanGIA ,” an algorithmic change to MRIGlobal ’ s PanGenomics of Infectious Agents metagenomic biosurveillance program so that it takes advantage of the data streaming feature of the MinION . PanGIA was designed as the bioinformatics portion of the Defense Threat Reduction Agency ’ s Sample to Sequence program . While PanGIA was intended for the detection of pathogens , its database can readily be customized to favor food-borne , public health concerning organisms . PanGIA bioinformatics displays a combination of taxonomic profiles and genetic markers of interest through an intuitive graphical user interface that updates as more data is produced by the MinION . This GUI reduces or removes the need for a trained bioinformatician to run sample analysis by automatically generating a dynamic and interactive report that clearly illustrates the contents of the sequencing run . We believe that technologies like real-time PanGIA can pave the way for more complete infectious disease surveillance , outbreak response , and inspection of environmental health threats .
Presenter : Shelton Bradrick , MRIGlobal , Gaithersburg , MD , sbradrick @ mriglobal . org
Analysis of Genetic Variation of Carbapenemase-producing Carbapenem-resistant Organisms Within Individual Patients : A Clinical Workflow Revisited
J . L . Chan , W . Haas , E . A . Snavely , K . J . Cummings , P . Weeber , J . Bodnar , C . J . Wagner , S . Morris , E . Nazarian and K . A . Musser , Wadsworth Center , New York State Department of Health , Albany , NY
According to the 2019 Antibiotic Resistance Threats Report issued by the Centers for Disease Control and Prevention , carbapenemresistant Acinetobacter species and carbapenem-resistant Enterobacteriaceae are designated as urgent threats in the United States . The rise of carbapenem resistance in nosocomial settings is of great concern as dissemination of carbapenemase genes can occur rapidly throughout health care facilities , geographic regions , and among bacterial species . Current clinical laboratory workflows to characterize carbapenemase-producing carbapenem-resistant organisms ( CP-CROs ) from patient specimens often entails the analysis of a single cultured bacterial isolate . This isolate is used for all phenotypic , molecular , and genomic analyses . Yet , the genetic variability of CP-CROs within individuals has not been well described . Here , we evaluate the degree of genetic variation of CP-CROs , isolated from a subset of colonized individuals , to aid in establishing thresholds for the determination of relatedness through Whole-genome sequencing ( WGS ) analysis . Patient rectal swabs routinely submitted through the Northeast Antibiotic Resistance Laboratory Network are screened by molecular methods to detect colonization of CP-CROs . Swabs are tested using the Cepheid Xpert ® Carba-R assay that detects the presence of beta-lactamase ( bla ) genes : blaKPC , blaNDM , blaVIM , blaIMP , and blaOXA-48 . Positive swabs are cultured with selective media : MacConkey agar , CHROMagar™ mSuperCARBA™ agar , and MacConkey broth . Distinct colony morphologies are sub-cultured and screened for the presence of carbapenemase genes with lab-developed real time PCR assays . The PCR-positive isolates are identified with MALDI-TOF mass spectrometry . For this study , an additional 5 to 10 colonies demonstrating the same PCR-positive morphology description are cultured and confirmed for carbapenemase gene presence . This
Infectious Disease
Fall 2020 LAB MATTERS 43