APHL 2022 POSTER ABSTRACTS
Infectious Diseases developed quantitative calibration controls for the targets to convert the qPCR data to viable genomic units ( vGU , a surrogate for CFU ). In addition , an internal positive control template was included in the qPCR master mixes , controlling for the presence of PCR inhibitors that are commonly present in water samples , often causing false-negative results . With the combined workflow including filtration of water samples , treatment with crosslinker , automated DNA purification and probe-hydrolysis qPCR we were able to rapidly enumerate viable L . pneumophila and Legionella spp . from water samples in a culture-independent manner . The results were confirmed using the standard culture-based method utilizing BCYE ( Buffered Charcoal Yeast Extract ) agar that detects Legionella species in 7-10 days .
Presenter : Nathan Feirer , Promega Corporation , nathan . feirer @ promega . com
MacConkey Agar with Meropenem for the Detection of Carbapenemase Producing Enterobacteriaceae from Rectal Swabs . A Proof-of-concept Study
M Nelson , R Jepson and G Lester , State Hygienic Laboratory at the University of Iowa
The State Hygienic Laboratory at The University of Iowa completed a proof-of-concept study utilizing MacConkey agar supplemented with Meropenem for the recovery of carbapenem-resistant Enterobacteriaceae ( CRE ) from rectal swabs . Evaluation of agar dilution media was completed by prospectively testing 16 rectal swabs from two separate ( CRE ) outbreaks in long-term care facilities in Iowa . Colonization screening was conducted at the first longterm care facility in July 2019 ( n = 7 ). Colonization screening was conducted at a different long-term care facility in December 2020 ( n = 9 ). Using the combined results from both screening events , the MacConkey w / Meropenem agar had a sensitivity of 86 %, a specificity of 88 %, positive predictive value of 78 % and negative predictive value of 88 %. This method does not require broth enrichment or PCR for the detection of CRE . PCR is only required for the identification of the CRE mutation after the culture has been allowed to grow for 24-48 hours . The use of agar dilution media for colonization screening reduces turnaround time to detection of CRE , reduces cost and is not limited by gene targets like PCR based assays .
Presenter : Geoffrey Lester , State Hygienic Laboratory at the University of Iowa , geoffrey-lester @ uiowa . edu
Prevalidation of Bioinformatics Pipeline for Healthcare- Associated Infections ( HAI ) Testing at State Hygienic Laboratory ( SHL ), University of Iowa
K Sompallae , V Reeb , A Kampoowale , W Hottel , W Aldous and M Pentella , State Hygienic Laboratory at the University of Iowa
This study represents the initial prevalidation phase of NGS bioinformatics pipelines to detect and report HAI occurring in facilities across the State of Iowa . We surveyed available NGS bioinformatics pipelines for microbial characterization such as bacterial genotyping , SNP detection , species identification and phylogenetic analyses . HAI and other bacterial reference material sequences were collected from public databases such as ATCC and NCBI . Using these reference materials , we optimized a SHL
NGS bioinformatics pipeline to meet the needs for identification , characterization and reporting of current HAI in Iowa . Furthermore , we are working on i ) validation plan to implement bioinformatics pipelines , ii ) workflows to automate the data analysis , iii ) and a preliminary results template layout to report HAI results . Based on our observations in optimizing NGS bioinformatics pipelines at public health laboratory and the complexity of NGS assays for clinical validation , the prevalidation phase is important in assessing bioinformatics pipeline performance for validation prior to wet lab sequencing . The prevalidation phase is cost effective , it reduces sequencing cost , while provides an opportunity to utilize informatics resources using known reference material sequences .
Presenter : Krishnaveni Sompallae , State Hygienic Laboratory at the University of Iowa , krishnaveni-sompallae @ uiowa . edu
Use of Molecular Diagnostic Testing and Traditional Virology Techniques to Surveil for Mosquito-Borne Arboviruses in Texas
B Bolling , M D ’ Anton , C Van Cleave and R Lee , Texas Department of State Health Services
The State of Texas is vulnerable to mosquito-borne arboviral diseases for numerous reasons including unique ecosystems that support high densities of vector mosquito populations , areas with significant poverty , and periodic climatic disturbances such as hurricanes , floods and droughts . In addition , the Texas- Mexico border is a frequently crossed border , increasing the risk of emerging mosquito-borne diseases being introduced , like chikungunya , Zika and yellow fever . The primary objective of the Texas Department of State Health Services-Laboratory Services Section ( TDSHS-LSS ) Arbovirus / Entomology Laboratory is to detect arboviruses in mosquito populations before human cases occur . This information is used by local jurisdictions to initiate diseaseprevention strategies and to inform mosquito control activities . The TDSHS-LSS Arbovirus / Entomology Laboratory currently provides mosquito species identification , population counts , arbovirus testing and insecticide resistance testing . Mosquitoes are collected throughout the state by various city and county health departments , health service regions , military installations , universities and local mosquito control programs in Texas and submitted to the Arbovirus / Entomology Laboratory . Historically , all arbovirus testing was conducted using virus isolation in cell culture . Recently , molecular diagnostic tools were incorporated into the program to increase capacity and decrease turnaround time for result reporting . Currently , these two testing workflows are used to screen the mosquitoes for endemic viruses as well as newly emerging or reemerging viruses . Molecular testing capabilities include realtime RT-PCR assays for detecting West Nile , St . Louis encephalitis , western equine encephalitis , Zika , chikungunya , dengue and eastern equine encephalitis viruses . Traditional virus isolation techniques using cell culture are conducted on approximately 20 % of mosquito trap submissions to screen for new arboviruses . The combination of these two workflows has allowed the Arbovirus / Entomology Laboratory to provide quick turnaround times for reporting the detection of endemic viruses and to provide broad surveillance testing for unexpected arboviral introductions . Data will be presented from the last 5 years , demonstrating how the Arbovirus / Entomology Laboratory has played a critical role in the