Lab Matters Summer 2018 - Page 63

APHL 2018 Annual Meeting Poster Abstracts level MOH representatives, as well as the clear goals and timelines for work achieved by each technical group. Collaborative efforts of all laboratory network stakeholders (public, private, military, Universities, implementing partners) will ensure ownership of the work featured in the document. Presenter: Pat Sadate-Ngatchou, University of Washington, I-TECH, Seattle, WA, Email: psn@uw.edu Infectious Disease Whole Genome MLST-based Typing and Strain Nomenclature for Clostridium difficile Isolates S. Kiekens 1 , K. De Bryune 1 , K. Kingsley 2 ; 1 Applied Maths NV, Sint- Martens-Latem, Belgium, 2 Applied Maths, Inc., Austin, TX Materials/methods: We created a core (n=1999 loci) and pangenomic (n=6713 loci) schema based on 259 reference sequences reflecting the known diversity of C. difficile. Also capturing the accessory loci greatly increased the discriminatory power of the schema. Adding MLST, CWP and loci associated with antibiotic resistance and virulence maximized consistency with classical typing methods. Assembly-free and BLAST-based algorithms determined locus presence and detected allelic variants. wgSNP further characterized defined clusters by mapping the reads to a reference chosen from within the cluster and filtering the variants. High-throughput data processing pipelines in BioNumerics ® implemented both methods on publicly available data. Results: We ran wgMLST on +1,500 samples to identify closely related clusters. We detected a wide diversity of samples and defined clusters at various allele difference cutoffs, allowing the creation of a stable strain nomenclature on the sample set. The defined thresholds determined 36 clusters for which additional resolution was obtained by running the wgSNP analysis, identifying linked clinical cases and linking additional metadata (e.g., date of isolation, geo information) to the results. Conclusions: WGS combined with automated analysis pipelines holds great promise for bacterial epidemiological surveillance. The pangenomic schema for C. difficile includes over 8000 loci and allows for the detection of subtype- or outbreak-specific markers. BioNumerics ® and integrated wgMLST and wgSNP functionality allows for accessible cluster analysis and typing of C. difficile isolates down to strain level. Presenter: Kyle Kingsley, Applied Maths, Inc., Austin, TX, Phone: 512.482.9700, Email: kyle.kingsley@biomerieux.com PublicHealthLabs @APHL APHL.org L.S. Berman 1 , J.R. Murray 2 , J. Liu 3 , C.M. Warnes 1 , K. Wu 1 , S. Burke 2 , S. Lindstrom 1 ; 1 Centers for Disease Control and Prevention, Atlanta, GA, 2 CDC/Battelle, Atlanta, GA, 3 CDC/ARED, Atlanta, GA Background: The CDC Human Influenza Real-Time RT-PCR Diagnostic Panel is used in real-time RT-PCR (rRT-PCR) assays on the Applied Biosystems ® (ABI) 7500 Fast Dx Real-Time PCR system. The panel is configured in four separate kits. Each kit consists of oligonucleotide primers, fluorescently labeled hydrolysis probes and controls that are used in rRT-PCR assays for the in vitro qualitative detection and characterization of influenza virus RNA in respiratory specimens from patients presenting with influenza-like illness (ILI) or from virus culture. Six RNA extraction methods have been approved for use with the CDC rRT-PCR Flu Panel: the automated Roche MagNA Pure LC Total Nucleic Acid Isolation kit, Roche MagNA Pure Com Á…ÐI9%ͽ±…Ñ¥½¸­¥Ð$°E¥…•¸ƒ ¸E%…µÀY¥É…°)I9µ…¹Õ…°•áÑɅÑ¥½¸°E¥…•¸ƒ ¸I9•…ÍäI9µ…¹Õ…°•áÑɅÑ¥½¸°)E¥…•¸ƒ ¸E%Õ‰”Á±…Ñ™½É´ÕÍ¥¹œE¥…•¸ƒ ¸E%…µÀY¥É…°I9­¥Ð…¹)Ñ¡” ¥½5•É¥•Õà9Ս±¥M9L•…Íå5¸%¸½É‘•ÈÑ¼Õ¹‘•ÉÍх¹Ñ¡”)Á•É™½Éµ…¹”½˜…‘‘¥Ñ¥½¹…°¡¥ …¹±½ÜÑ¡É½Õ¡ÁÕЁ…Õѽµ…Ñ•)•áÑɅÑ¥½¸µ•Ñ¡½‘́Õ͕¥¸‘½µ•ÍÑ¥ŒAՉ±¥Œ!•…±Ñ 1…‰½É…ѽɥ•Ì(¡A!1̤°Ý”•Ù…±Õ…Ñ•Ñݼ…‘‘¥Ñ¥½¹…°…Õѽµ…Ñ••áÑɅÑ¥½¸µ•Ñ¡½‘̸)Q¡”E¥…•¸hā‘Ù…¹•a0•áÑɅÑ¥½¸Á±…Ñ™½É´ÕÍ¥¹œÑ¡”hāM@)Y¥ÉṌ-¥Ð…¹hāI9Q¥ÍÍՔ5¥¹¤-¥Ð…¹Ñ¡”I½¡”5…9AÕɔ(ä؁ÕÍ¥¹œÑ¡”9…¹Y¥É…°9Mµ…±°Y½±Õµ”-¥Ð¸)5•Ñ¡½èÍÑՑäÝ…́Á•É™½Éµ•Ñ¼…Í͕Í́ѡ”É•Áɽ‘Ս¥‰¥±¥Ñ䁽˜Ñ¡”)I½¡”5…9AÕɔ€ä؁…¹E¥…•¸hā‘Ù…¹•a0¥¹ÍÑÉÕµ•¹Ñ̸)Q¡”I½¡”5…9AÕɔ€ä؁݅́•Ù…±Õ…Ñ•Ý¥Ñ Ñ¡”I½¡”9)…¹Y¥É…°9Mµ…±°Y½±Õµ”-¥Ð¸Q¡”E¥…•¸hā‘Ù…¹•a0Ý…Ì)•Ù…±Õ…Ñ•Ý¥Ñ Ñ¡”E¥…•¸M@Y¥ÉṌ-¥Ð…¹Ñ¡”E¥…•¸I9)Q¥ÍÍՔ5¥¹¤-¥Ð¸‰±¥¹‘•Á…¹•°½˜½¹ÑɥٕÍ…µÁ±•Ì½¹Ñ…¥¹¥¹œ)„‰…­É½Õ¹½˜‰•Ñ„µÁɽÁ¥½±…Ñ½¹”€¡ A0¤Ñɕ…Ñ•ÔÐ䁍•±±Ì¥¸)Y¥É…°QɅ¹ÍÁ½ÉЁ5•‘¥Õ´€¡YQ4¤Ý…́…Í͕µ‰±•‰ä…‘‘¥¹œ„ A0)¥¹…Ñ¥Ù…Ñ•¥¹™±Õ•¹é„¡ Í8ȤÙ¥ÉÕÌ°½!½¹œ-½¹œ¼ÐàÀļÈÀÄиQ¡”)ͅµÁ±•Ì¥¹±Õ‘•„µ½‘•É…Ñ”Á½Í¥Ñ¥Ù”Í…µÁ±”°„±½ÜÁ½Í¥Ñ¥Ù”Í…µÁ±”)¹•…ȁѡ”•Íх‰±¥Í¡•…Íͅ䁱¥µ¥Ð½˜‘•Ñ•Ñ¥½¸™½ÈÑ¡”  %¹™±Õ•¹é„)MՉÑåÁ¥¹œ-¥Ð…¹„¹•…Ñ¥Ù”Í…µÁ±”½¹Í¥ÍÑ¥¹œ½˜‰…­É½Õ¹)ÔÐ䁍•±±Ì…¹YQ4¸Q¡É•”Í•Á…É…Ñ”Ñ•ÍÑ¥¹œÍ¥Ñ•ÌÝ•É”Í•±•Ñ•™½È)•… •áÑɅÑ¥½¸¥¹ÍÑÉÕµ•¹ÐÁ±…Ñ™½É´¸Q¡”Í…µÁ±”Á…¹•°Ý…ÌÑ•Íѕ€Ô)Ñ¥µ•Ì‰äÑݼ‘¥™™•É•¹Ð…¹…±åÍÑ́…Ё•… Í¥Ñ”½Ù•È™¥Ù”‘¥™™•É•¹Ð‘…å̸)¹…±åÍÑ́Á•É™½Éµ••áÑɅÑ¥½¹ÌÝ¥Ñ Ñ¡”¥¹Ù•ÍÑ¥…Ñ¥½¹…°¥¹ÍÑÉÕµ•¹Ð)…¹µ•Ñ¡½…¹Ñ•ÍѕÑ¡”•áÑɅÑ•¹Õ±•¥Œ…¥‘́ݥѠÑ¡”%¹™° Ì)…¹I@…Íͅ䁵…É­•É́™É½´Ñ¡”  %¹™±Õ•¹é„MՉÑåÁ¥¹œ-¥ÐÕÍ¥¹œ)%¹Ù¥Ñɽ•¸MÕÁ•ÉMÉ¥Áӊˆ…¹ÕÑ¥±¥é¥¹œÑ¡” $€ÜÔÀÀ…ÍЁàÉ•…°µÑ¥µ”)A HÍåÍѕ´¸M…µÁ±•ÌÝ•É”…¹…±å镐ÕÍ¥¹œÑ¡” $MLÍ½™Ñ݅ɔ)ٕÉÍ¥½¸€Ä¸ÐÝ¥Ñ €ÈÅ HÁ…ÉЀÄā½µÁ±¥…¹Ðµ½‘Õ±”¸I•ÍÕ±Ñ́ݕɔ)½µÁ…É•Í¥‘”µ‰äµÍ¥‘”…¹Ý¥Ñ ‘…Ñ„•¹•É…Ñ•ÕÍ¥¹œ…ÁÁɽٕ)µ•Ñ¡½‘̸)I•ÍÕ±ÑÌèQ¡”E¥…•¸hā‘Ù…¹•a0…¹I½¡”5…9AÕɔ€äØ)Á±…Ñ™½ÉµÌÝ¥Ñ Ñ¡•¥ÈÉ•ÍÁ•Ñ¥Ù”É•…•¹Ð­¥Ñ́…¹Á…¥É•Áɽѽ½±Ì)‘•µ½¹ÍÑɅѕ€ÄÀÀ”É•Áɽ‘Ս¥‰¥±¥Ñ䀠ÌÀ¼ÌÀ½ÉɕÐÉ•ÍÕ±Ñ́Á•È)•áÑɅÑ¥½¸Á±…Ñ™½É´¤…É½Í́µÕ±Ñ¥Á±”Í¥Ñ•Ì°…¹…±åÍÑ́…¹‘…å̸ ½Ñ )¹•ÜÁ±…Ñ™½ÉµÌ…¹µ•Ñ¡½‘́Á•É™½Éµ•½µÁ…É…‰±äÑ¼µ•Ñ¡½‘Ì)Áɕ٥½ÕͱäÅՅ±¥™¥•Ñ¼‰”Õ͕Ý¥Ñ Ñ¡”  ÉIPµA H±ÔA…¹•°)…Íͅä¸) ½¹±ÕÍ¥½¹ÌèQ•ÍЁɕÍÕ±Ñ́¥¹‘¥…Ñ•Ñ¡…Ё‰½Ñ Ñ¡”E¥…•¸hÄ)‘Ù…¹•a0…¹I½¡”5…9AÕɔ€ä؁Á•É™½Éµ•Ý•±°Õ¹‘•È)MÕµµ•È€ÈÀÄà15QQIL(ØÄ) …­É½Õ¹è ±½ÍÑÉ¥‘¥Õ´‘¥™™¥¥±”¥Ì„‰…Ñ•É¥Õ´Ñ¡…Ё…Õ͕Ì)ÍåµÁѽµÌÉ…¹¥¹œ™É½´‘¥…ÉÉ¡•„Ñ¼±¥™”µÑ¡É•…Ñ•¹¥¹œ¥¹™±…µµ…Ñ¥½¸½˜)Ñ¡”½±½¸°µ½ÍЁ½µµ½¹±ä…™™•Ñ¥¹œ½±‘•È½È¥µµÕ¹½½µÁɽµ¥Í•)…‘Õ±Ñ́¥¸¡½ÍÁ¥Ñ…±Ì½È±½¹œµÑ•É´…É”™…¥±¥Ñ¥•Ì¸%¸É••¹Ðå•…ÉÌ°) ¸‘¥™™¥¥±”¥¹™•Ñ¥½¹Ì¡…Ù”‰•½µ”µ½É”™É•ÅՕ¹Ð°Í•Ù•É”…¹)‘¥™™¥Õ±ÐÑ¼Ñɕ…иI…Á¥ÑåÁ¥¹œ…¹¡…É…Ñ•É¥é…Ñ¥½¸µ•Ñ¡½‘́…É”)•Í͕¹Ñ¥…°•Á¥‘•µ¥½±½¥…°Ñ½½±ÌÑ¼Áɕٕ¹Ð…¹½¹Ñɽ°¥¹™•Ñ¥½¸¸)±Ñ¡½Õ ‰…Ñ•É¥…°]L¡…́‰•½µ”™•…Í¥‰±”¥¸Íµ…±±•È±¥¹¥…°)±…‰½É…ѽɥ•Ì°¹½¸µÍх¹‘…É‘¥é•‘…Ñ„…¹…±åͥ́ɕµ…¥¹Ì„‰½Ñѱ•¹•¬)™½ÈÉ½ÕÑ¥¹”ÍÕÉٕ¥±±…¹”¸%¸Ñ¡¥ÌÝ½É¬°Ý”…Í͕Í͕Ý51MP…¹)ݝM9@™½È ¸‘¥™™¥¥±”ÑåÁ¥¹œ¸) ½µÁ…ɥͽ¸½˜Õѽµ…Ñ•áÑɅÑ¥½¸5•Ñ¡½‘́UÍ¥¹œÑ¡”)  !Õµ…¸%¹™±Õ•¹é„Y¥ÉṌI•…°µÑ¥µ”IPµA H•Ñ•Ñ¥½¸)…¹ ¡…É…Ñ•É¥é…Ñ¥½¸A…¹•±Ì