Lab Matters Fall 2020 - Page 39

APHL 2020 POSTER ABSTRACTS among CRPA may serve as a good indicator of CP . Public health and clinical laboratories should continue efforts to detect CP-CRPA to help reduce transmission and improve patient safety .
Presenter : Amelia Bhatnagar , Centers for Disease Control and Prevention , Atlanta , GA , wmt7 @ cdc . go
Rapid , Sensitive and Cost-effective Diagnosis of Pathogens from Fixed Tissue Specimens Using Syndrome-based Pyrosequencing Panels
J . Bhatnagar , L . Estetter , A . Paulino , D . Rabeneck , E . Lee , K . Howard , W-J . Shieh and S . Zaki , Centers for Disease Control and Prevention , Atlanta , GA
Background : Rapid identification of pathogens is crucial for patient management and appropriate public health response . For investigations of infectious diseases of unknown etiologies , outbreaks and unexplained deaths , evaluation of a wide-range of pathogens is usually necessary . Culture-based identification of pathogens is tedious and time-consuming . Also , often specimens are not processed for culture , particularly in cases of sudden fatality , and fixed tissues are the only specimens available . The main objective of this work was to develop syndrome-based pyrosequencing ( PSQ ) assays / panels for rapid and specific diagnosis of pathogens from fixed tissues .
Methods : PSQ assays were developed for pathogens associated with encephalitis ( West Nile virus , eastern equine encephalitis virus , La Crosse virus ), myocarditis ( enterovirus , parvovirus B19 , adenovirus , CMV ), Zika-Dengue like illness ( Zika virus , chikungunya virus , dengue virus , Leptospira ) and granulomatous infections ( Mycobacterium spp .). Nucleic acids extracted from formalin-fixed , paraffin-embedded ( FFPE ) cell cultures and tissues from the PCRconfirmed cases of targeted pathogens were evaluated by the PSQ assays . Suspect Zika virus , chikungunya virus and Mycobacterium tuberculosis complex ( MTBC ) cases that were negative by conventional tissue-PCR were also tested . Pathogen-specific in-situ hybridization ( ISH ) was performed on selected PSQ-positive cases .
Results : PSQ assays correctly identified tested pathogens in diverse tissue types and culture controls , and showed 100 % specificity and ≥ 90 % sensitivity for all targeted pathogens . In addition , the assays were able to detect targeted pathogens from quite fragmented nucleic acids and identified Zika virus , chikungunya virus and MTBC species in 15 %, 21 % and 24 % of previously tissue-PCR negative cases , respectively . Pathogens identified by PSQ assays were also directly localized in the same tissues by pathogen-specific ISH assay . Data will be presented .
Conclusions : Syndrome-based PSQ assays are cost-effective diagnostic tools for rapid , sensitive and specific identification of pathogens , using a limited amount of tissue samples . The assays will enhance the prompt public health response to outbreaks and unexplained deaths , and particularly valuable for the cases in which conventional specimens are unavailable for testing .
Presenter : Julu Bhatnagar , Infectious Diseases Pathology Branch , Division of High-Consequence Pathogens and Pathology , NCEZID , Centers for Disease Control and Prevention , Atlanta , GA , zrn1 @ cdc . gov
Evaluating Data Quality in Antimicrobial Resistance Surveillance Laboratories : A Model from Ethiopia
S . Bollinger 1 , A . Wadhwa 1 , D . Assefa 2 , D . Beyene 2 , S . Fentaw 2 , G . Belete 2 , M . Parsons 1 , C . Hazim 1 , M . Westercamp 1 , A . Laufer Halpin 1 , T . Kanter 3 , K . Gallagher 3 , B . Amare 3 , A . Brown 1 ; 1 Centers for Disease Control and Prevention , Atlanta , GA , 2 Ethiopian Public Health Institute , Addis Ababa , Ethiopia 3 CDC Ethiopia Country Office , Addis Ababa , Ethiopia
Background : With support from CDC , the Ethiopian Public Health Institute launched an Antimicrobial Resistance ( AMR ) Surveillance Network in July 2017 , including three sentinel laboratories ( SLs ) and the National Clinical Bacteriology and Mycology Reference Laboratory ( NRL ). To monitor data quality , NRL performs confirmatory identification ( ID ) and antibiotic susceptibility testing ( AST ) on a subset of isolates , but lacked a standardized method for quantifying discordance and summarizing the findings .
Methods : To define AST error types , we adapted the categorical agreement classification scheme ( with NRL confirmatory testing results as the gold standard ): minor error ( SL-intermediate { I } / NRL-susceptible { S } or resistant { R }, or vice versa ), major error ( SL-R / NRL-S ), and very major error ( SL-S / NRL-R ). We added an “ interpretation ” error type to capture incidents of SLs interpreting zone sizes as the wrong SIR category . As an interpretation error may generate a minor , major , or very major error , each isolate-antibiotic combination may have up to 2 AST errors . ID errors were classified as major error ( species incorrect ) and very major error ( genus and species incorrect ). We developed a tool to automatically calculate error types and frequencies and analyzed retrospective laboratory data .
Results : The SLs submitted a total of 99 isolates to NRL for confirmatory testing from January 1 to September 30 , 2019 : 36 Escherichia coli , 25 Staphylococcus aureus , 21 Klebsiella pneumoniae , 13 Acinetobacter baumannii , and 4 of other genera . This represents approximately 28 % of the AMR isolate data submitted to the network during the same time frame . Five ( 5 %) isolates had ID errors : 1 major and 4 very major . Thirty-six isolates had a total of 62 AST errors : 8 ( 13 %) interpretation errors , 35 ( 56 %) minor errors , 5 ( 8 %) major errors ( ME ), and 14 ( 23 %) very major errors ( VME ). The 5 ME and 14 VME were distributed among 4 and 11 isolates , respectively . AST errors were found across multiple genera : 18 ( 29 %) E . coli ; 15 ( 24 %) S . aureus ; 23 ( 37 %) K . pneumoniae ; and 6 ( 10 %) other genera . The three SLs each submitted 22 , 32 , and 45 isolates . The per-lab percent of isolates with ID errors was 0 %, 3 %, and 9 %; the per-lab percent of isolates with major AST errors was 0 %, 0 %, and 11 %; VME were 5 %, 3 %, and 22 %.
Conclusions : In this study 11 % of isolates undergoing AST at SLs had one or more VME , results that under-estimated antibiotic resistance , a critical problem for both clinical and surveillance purposes . Applying categorical agreement criteria to proficiency testing results provides a novel framework to systematically evaluate the quality of AMR data . This can be a valuable tool to provide quantitative feedback and guide laboratory improvements in order to improve overall data quality of the AMR surveillance system .
Presenter : Susan Bollinger , Centers for Disease Control and Prevention , Atlanta , GA , ltn1 @ cdc . gov
Infectious Disease
Fall 2020 LAB MATTERS 37