Lab Matters Fall 2020 - Page 40

Infectious Disease
Evaluating and Standardizing the CDC Infectious Diseases Laboratory Test Directory to Improve Specimen Submission Timeliness and Pre-analytical Quality
L . Bridwell , V . Albrecht , S . Soroka , S . Carroll , N . Gregoricus , R . White , J . Gaillard , W . Kuhnert-Tallman and A . Muehlenbachs , Centers for Disease Control and Prevention , Atlanta , GA
Background : The Centers for Disease Control and Prevention ( CDC ) Infectious Diseases Laboratory Test Directory ( TD ) is the externally facing list of test orders that public health labs and other submitters use to submit specimens to CDC for diagnostic and non-diagnostic testing . The purpose of the TD is to provide clear and uniform preanalytical specifications that expedite specimen submission transit time and ensure high specimen quality . However , per a customer feedback survey , TD content has not always been understood and at times has challenged specimen submission timeliness and preanalytical quality .
Methods : To address customers ’ concerns , CDC ’ s Infectious Disease Specimen Submission Change Control Board ( IDSS CCB ) conducted an in-depth evaluation of the TD content over the span of 20 meetings in four months , identified areas for improvement , and developed standardization guidance for each test order field . Since the TD was developed before the standardization guidance , implementation efforts were scaled to engage associated laboratories for every test order . The guidance was rolled out using a series of educational training sessions that were aligned with two previously scheduled TD update cycles . This was followed by eight months of strategic dialogue ( e . g ., broadcast communications , direct emails , and phone calls ) with laboratory points of contact regarding necessary revisions to TD content to ensure every test order complied with the guidance .
Results : As a result of these efforts , a total of 3,622 changes were reviewed and implemented in the TD during 2019 compared to routine 806 changes in 2018 . Of the 3,622 changes , a total of 38 test orders were deleted , 8 added , and 81 test order names revised . The other 3,495 changes were specific content revisions to test order fields such as point of contact , specimen labeling , acceptable sample / specimen type , CLIA regulatory status , shipping and specimen handling instructions , among others . The culmination and implementation of these changes ensured all 316 test orders within the TD were compliant with the standardization guidance by the TD ’ s annual publication date of December 6 , 2019 . Preliminary evidence also suggests that this effort has helped to better define internal CDC workflows and improve compliance with internal policies and federal regulations .
Conclusions : The purpose of this standardization effort was to improve the content within the TD to better enable customers to submit higher pre-analytic quality specimens to CDC for testing and reduce turn-around-times for submission . The IDSS CCB plans to examine anecdotal data over the next year to track its success in achieving these goals . Moving forward , CDC also plans to share information learned about further impacts of this effort as this process could be replicated by other laboratories to improve their customers ’ specimen submission quality and processes .
Presenter : Lindsey Bridwell , Booz Allen Hamilton , Centers for Disease Control and Prevention , Atlanta , GA , mvz6 @ cdc . gov
S-Typeline : A Rapid , Flexible Strain Characterization Service for Streptococcus pneumonia
J . Gerhart , J . Varghese , B . Metcalf , Y . Li and B . Beall , Centers for Disease Control and Prevention , Atlanta , GA
CDC ’ s Active Bacterial Core surveillance ( ABC ) activities include “ the determination of the incidence and epidemiological features of invasive pneumococcal disease .” The description of serotypes and AntiMicrobial Resistance ( AMR ) phenotypes of invasive pneumococcal disease ( IPD ) isolates is a critical part of epidemiological surveillance and vaccine formulation .
Currently , surveillance and serotyping of ABC reported cases are handled internally by CDC streptococcus laboratory workers , using a highly adapted automated approach tailored to our instruments and resources .
To provide this expertise to a national audience we have derived from this a more flexible , faster , serotyping , MLST and AMR description service : StrepTypeLine available through the CDC ’ s OAMD portal .
S-typeline utilizes mostly k-mer and machine learning based tools and is thus not reliant on full assembly to generate accurate MLST , serotype and antibiotic resistance data . This allows for a uniquely high degree of flexibility in NGS inputs , allowing for a wider range of sequencing data to be processed accurately .
Presenter : Jonathan Gerhart , Centers for Disease Control and Prevention , Atlanta , GA , nwx7 @ cdc . gov
Hepatitis A Virus Survival on Drug Paraphernalia
M . Medrzycki , M . Purdy and S . Kamili , Centers for Disease Control and Prevention , Atlanta , GA
Background : The ongoing hepatitis A outbreak in the United States has concerned public health authorities since March 2017 . The outbreak has already spread throughout 30 states and includes primarily persons who use drugs , including persons who inject drugs ( PWID ) and homeless individuals . Contaminated drug injection paraphernalia and sharing of these items are suspected to be one of multiple causes of hepatitis A virus ( HAV ) transmission in those populations .
Method : We used a standard plaque assay to investigate HAV infectivity . Liquid suspensions of HAV were tested to examine the effects of time and temperature on viral infectivity . We also examined HAV survival on commonly used drug paraphernalia , such as needles , syringes , cookers , tourniquets , and cotton balls / filters frequently shared among PWIDs . We investigated the effect of low pH on HAV survival using citric acid , which is frequently used by PWIDs during dose preparation . We also compared the plaque assay results with those concurrently obtained by RT-PCR to establish whether viral HAV RNA levels could be used as surrogates for plaque assay results .
Result : We found that HAV suspended in PBS at room temperature was able to infect FRhk4 cells for more than 17 weeks . HAV remained viable in syringes / needles ( semi-dry conditions ) for up to 10 weeks depending on the size of the needles and the syringe dead-volumes . HAV survival in dry conditions on cooker , tourniquet and cotton balls / filter surfaces did not exceed 4 weeks . HAV retained its infectivity for more than 10 weeks at pH as low as 2 . PCR results suggest that RNA is amplified from both infectious and non-infectious HAV .