Lab Matters Fall 2023 | Page 57

APHL 2023 POSTER ABSTRACTS gastrointestinal and urogenital tracts . Host genetics , age , gender , environment , medications and diet can impact the composition of the microbiome . In addition , the individual species within the microbiome contribute to the host immune responses which can impact the abundance of other species within the microbiome . We are interested in identifying the composition of the microbiome and its impact on host transcriptome within the nasal cavity in influenza infection and vaccination . Current methodologies require three human clinical nasal swab specimens ; one to study the microbial populations , one for the viral populations and one for analysis of the host transcriptome . We are optimizing the protocol and establishing the workflow for RNA extraction methods and metatranscriptomics to identify the microbial and viral species , and the host transcriptome from a single nasal swab . The revised workflow significantly reduces the number of samples collected and the samples required for analysis . This will positively impact sample collection logistics and patients ’ comfort , as well as sample processing time . We will use the new workflow to assess the impact of the route of influenza vaccine administration ([ intranasal ( Flumist ) vs . intramuscular ( Flucelvax )], as well as influenza break-through infections , on the composition of the nasal microbiome , host transcriptome and the impact on the adaptive immune responses .

Presenter : Kayla Griffith , uah5 @ CDC . gov

Establishment of Whole Genome Sequencing to Predict Resistant Strains of Mycobacterium tuberculosis

W . N . Heard , S . Hall , E . Geeter , E . Dean , A . Martin , H . Putnam , A . Walker , T . Hatchett ; Alabama Department of Public Health , Bureau of Clinical Laboratories

Diagnostic delay is defined as the time interval between the onset of symptoms and confirmed diagnosis of a disease . Current diagnostic tools for Mycobacterium tuberculosis ( Mtb ) limit the scope of detecting patterns due to this delay . The goal of this project is to develop the detection of Mtb outbreaks , including patterns of Rifampin-resistant Mtb and other local strains present in the population utilizing whole genome sequencing ( WGS ). This project has been simplified to six steps : identify , culture , extract , sequence , analyze , and educate . New Mtb patients will be identified through standard mycobacteria isolation protocols for further characterization . These specimens are cultured through BACTEC MGIT 960 ® to provide ample template for extraction and downstream applications . Positive cultures are heat-killed and tested for viability . Relevant MTb complex ( MtbC ) nucleic acid is extracted from a primary BACTEC MGIT 960 + culture for the purposes of whole genome sequencing . MTbC DNA is prepped from standardized protocols for WGS organisms using the Illumina DNA Flex library preparation kit then subsequently sequenced on an Illumina platform , thus ensuring inter-laboratory comparability of sequencing results . Isolates can then be clustered which may elucidate epidemiologically relevant data . Any epidemiologic relationships identified with this process will be interpreted and informative of cases and potential outbreaks . This interpretation will then be compiled into a format that is understood for the general public for health officials and other medical professionals to utilize to educate the general public that may be most affected by these trends .

Presenter : Whitney Heard , whitneyheard97 @ gmail . com

Evaluation of Two Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry Methods for Filamentous Fungal Identification

K . Milloy , M . Scoble , E . Craig ; Virginia Division of Consolidated Laboratory Services

Objective : Validate and compare the accuracy of the Bruker BioTyper ( MBT ) and Biomérieux VITEK-MS MALDI-TOF methods for mold identification at the Virginia Division of Consolidated Laboratory Services ( DCLS ) Mycology Reference Laboratory . Study Design : The Bruker method was assessed by utilizing the direct transfer , extended direct transfer , and extraction method procedures with analysis by the MBT Filamentous Fungi Library version 4.0 ( Research Use Only ). The VITEK-MS method was assessed by utilizing the VITEK-MS Mould Extraction and Inactivation Procedure and the VITEK-MS Mould Kit with analysis by the VITEK-MS Knowledge Base version 3.2 ( FDA approved ). Eighty-two isolates were tested by both methods , 13 additional isolates were tested by the Bruker MBT method only , and 34 additional isolated were tested by the VITEK-MS method only , based on the individual species listed in the databases . Precision testing was evaluated by testing five isolates over three days , including duplicate testing and testing by two analysts . Results : Bruker MBT was able to correctly identify 72 out of 95 isolates tested for an accuracy of 75.8 % and VITEK-MS was able to correctly identify 73 out of 116 isolates for an accuracy of 62.9 %. If isolates previously identified to the genus level only are removed , the species level identification for each method was 80.8 % ( 42 / 52 isolates ) and 75.4 % ( 52 / 69 isolates ) for the Bruker MBT and VITEK-MS methods , respectively . Both methods resulted in 100 % precision . A correct identification by the method was defined as an identification to the expected identification at the genus , species , or complex / group level . Expected identification of isolates tested during the validation were previously identified isolates using microscopic / macroscopic morphology , DNA probe , biochemicals , and / or DNA sequencing . Discrepant results from the expected identification were observed in 3 % of isolates tested for the Bruker MBT method and 6 % of isolates tested for the VITEK-MS method . Conclusion : The validation testing of the Bruker MBT and VITEK- MS methods for the identification of molds resulted in an accuracy of 75.8 % for Bruker MBT and 62.9 % for VITEK MS with rare misidentifications . Although the ability of both MALDI-TOF methods for mold identification does not perform as reliably as MALDI-TOF when applied to bacterial agents , as published in the literature , the MALDI-TOF will provide important information to supplement macroscopic morphology , microscopic morphology , biochemicals and other tests , for the identification of molds .

Presenter : Kathleen Milloy , kathleen . milloy @ dgs . virginia . gov

Hepatitis C RNA Quantitative Stability Study – Report on Expansion of Nucleic Acid Testing for Diagnosis of Hepatitis C Infection and Treatment

A Mirolo 1 , C . Loring 2 , J . Alexander 1 ; 1 New Hampshire Public Health Laboratory , 2 INTEGRA Biosciences

Background : The New Hampshire PHL performs quantitative HCV RNA testing using the Roche Cobas Ampliprep / Cobas Taqman HCV Test v2.0 ( CAP / CTM ). A challenge faced by the NH PHL is the relatively short acceptable storage time ( no more than 3 days at