APHL 2022 POSTER ABSTRACTS
Food Safety samples positive at each level ), but false negative results were obtained among samples with 1 , 5 or 10 C . cayetanensis oocysts ( 11-67 %). These results provide a parasitologically relevant LOD for the BioFire ® FilmArray ® GI panel that should enable comparison to non-molecular C . cayetanensis detection techniques ( such as acid-fast staining ) that are still widely used for cyclosporiasis diagnostics . This information may also help to inform and improve outbreak investigations by providing insight into specimens that fail to genotype in the CDC genotyping workflow .
Presenter : Anna Peterson , Oak Ridge Institute for Science and Education , yyi6 @ cdc . gov
Partnerships and the Epidemiological Advancements of Cyclosporiasis detection facilitated by Next Generation Sequencing
SL Butler , D Dunbar , Y Sun , C Wang and R Lee , Texas Department of State Health Services Laboratory
Pathogenic coccidia , Cyclospora cayetanensis , are intestinal protozoans directly responsible for cyclosporiasis . Cyclosporiasis is a disease known to cause intermittent prolific diarrhea , low grade fevers , myalgia , anorexia , fatigue , weight loss and vomiting . Onset of illness typically begins a few days after ingestion of fecal contaminated food such as fruits and vegetables and last as much as three weeks . The occurrence of other species is recognized ; However , C . cayetanensis is thought to be the only species to cause human illness and has no known animal hosts . Morphologically , species of this genus are indistinguishable . Still the gold standard for medical parasitology , microscopy , is used as a diagnostic tool for suspected cyclosporiasis cases . With a worldwide geographical distribution , outbreaks of cyclosporiasis have occurred every year since the early 1990s with peaks between May and August . However , this nationally reportable disease is difficult to investigate . There are currently no immunodiagnostic tools available , subtyping technologies are very limited and outbreaks can contain a mixture of species . No successful in-vitro culture of Cyclospora exists and there are no known animal hosts , thus leaving stool samples collected from infected humans to be the model source . In 2014 , the CDC partnered with the Texas Department of State Health Services ( DSHS ) Laboratory and several other state public health laboratories in an effort to develop a real-time epidemiological tool for the detection of Cyclospora . During peak seasons , anonymized human stool samples were routed to the CDC as part of surveillance . These samples were speciated to help develop a more efficient subtyping tool . Using a CDC-developed next generation sequencing ( NGS ) method , our laboratory collaborated with the CDC in 2017 to initiate targeted NGS testing of eight genetic markers for Cyclospora and submit sequence data generated to CDC for analysis . A total of 720 samples were tested from 2018-2021 . This poster will depict our role in the CDC Cyclospora Surveillance Project , illustrate how different areas of the DSHS Laboratory and epidemiologists work collaboratively , and the surveillance results from Texas . The accumulation of genomic data is expected to facilitate development of a repository , provide case and cluster linkage and , consequently , aid in the investigation of future Cyclospora outbreaks .
Presenter : Susan Butler , Texas Department of State Health Services Laboratory , Susan . butler @ dshs . texas . gov
Bactopia v2 : Highly Scalable , Portable and Customizable Bacterial Genome Analyses
R Petit , Theiagen Genomics & Wyoming Public Health Laboratory
Generation of sequence data for bacterial genomes has become standardized to the point that bioinformatic analysis is the major bottleneck . There is now , more than ever , a need for bioinformatic workflows to be highly scalable and adaptable to the user ’ s needs . In order to address this we created Bactopia , a Nextflow workflow to provide efficient and flexible comparative genomic analyses for any bacterial species or genera . Bactopia can process Illumina and / or Nanopore sequences with more than 100 bioinformatic tools and many publicly available datasets . Furthermore , Bactopia includes more than 20 additional workflows to select high quality samples for downstream comparative analyses , such as pan-genome , phylogenetic and functional analyses . We have rewritten the original workflow to take advantage of Nextflow DSL2 , allowing users to customize Bactopia by including different tools for each step and simplifying integrations with other bacterial analysis workflows from the popular nf-core community . Bactopia v2 is a significant step forward , as it allows users to easily adapt Bactopia to fit their organism-specific needs . To demonstrate this , we implemented Staphopia as a custom Bactopia workflow for the analysis of Staphylococcus aureus genomes . This sub-workflow supplements the standard Bactopia workflow with additional S . aureus specific analyses such as methicillin-resistance ( MRSA ), spa typing and agr typing . In addition , we created the Merlin sub-workflow , which automatically executes species-specific analyses for many public health pathogens . Bactopia ( v1 and v2 ) is an open source system that has been shown to scale from projects as small as one bacterial genome to tens of thousands of bacterial genomes . In the latest release of Bactopia , the scalability remains and we have introduced even greater flexibility to meet the needs of our users . The documentation and code for Bactopia can be accessed at https :// bactopia . github . io /.
Presenter : Robert Petit , Theiagen Genomics , robert . petit @ theiagen . com
Vibrio cholerae Infections Following Consumption of River Water in Nebraska
T Wahlig , University of Nebraska Medical Center
Introduction : Although cholera caused by toxigenic Vibrio cholerae was historically noted to pose a significant threat to Indigenous peoples and European settlers in the US in the 1850s , recent cases of cholera in the US are sporadic and almost always associated with international travel . With the introduction of culture independent diagnostic tests ( CIDT ) to detect non-toxigenic cases of V . cholerae , diagnosing gastrointestinal ( GI ) vibriosis has become more common , especially following consumption of undercooked shellfish . This report describes two cases of GI vibriosis in individuals who consumed untreated river water in Nebraska .
Case Reports : Two cases of V . cholerae were identified in two partnered individuals in July 2021 . The patients were a male ( 33 years old ) and female ( 35 years old ), who were experiencing homelessness and had spent a month camping near the Platte River in Scottsbluff , NE . The patients reported drinking untreated river water while camping . The patients experienced diarrhea , vomiting , cramps , fever and muscle pain , starting on 20 July2021 ,