Lab Matters Summer 2018 | Page 41

APHL 2018 Annual Meeting Poster Abstracts

Presenter : Mimi Precit , Centers for Disease Control and Prevention / Washington State Public Health Laboratories , Shoreline , WA , Email : mimi . precit @ doh . wa . gov

Pseudomonas aeruginosa Alters Staphylococcus aureus Sensitivity to Antibiotics

( complete abstract in Infectious Disease , p . 67 )

A Semi-Automated Method to Analyze and Report Data from Neisseria gonorrheae Antimicrobial Susceptibility Testing

J . Weiner , M . Khubbar and S . Bhattacharyya , City of Milwaukee Health Department Laboratory , Milwaukee , WI

Introduction : The Milwaukee Health Department Laboratory ( MHDL ) uses the SoftLab / SoftMic platform from Soft Computer ( SCC ) for all LIS-based operations in the lab . The platform includes a frontend GUI interface for daily lab operations and a back-end database that can be queried via Microsoft Access . We designed a system of two MS Access queries coupled to three simple programs in the Python programming language that together accomplish the task of compiling , analyzing and validating lab test results for both NAATs , cultures and susceptibility testing for Neisseria gonorrheae monthly .

Methods : Queries were designed in MS Access to return results based on lab test type , order #, patient ID #, dates collected , received and finalized , clinic where sample was collected , result including MIC values for AST analysis if available and other internal quality measures . Results were exported to CSV format and used as input for Python programs . Python programs were designed to compute the number of each specimen type for positive and negative results , the turnaround time of culture-positive samples undergoing Etesting for AST and order numbers that do not match between the LIS GUI interface and the MS Access database . SCC SoftMic Epidemiology Reports were generated in the usual manner to cross-check test order mismatches and SoftMic Micro Reports were used to diagnose the cause of any mismatches discovered .

Results : Implementation of the present method eliminated lab side data entry errors for specimen and test counts , incorrect date entry and miscalculation of turnaround times . The method also flags about 5 test orders per month with incorrect clinic or collector codes . By pulling LIS values directly from the database using an SQL query , transcription errors are eliminated . Similarly , by coding in the formulae needed to compute metrics such as turnaround time in working days and tallies of infection by specimen site by clinic , calculation errors are eliminated once the code is validated .

Discussion : The task of compiling laboratory metrics was formerly done manually , requiring laboratorians to transcribe values from the LIS into an Excel spreadsheet , make calculations based on those values and report them on a separate form . This method introduced many sources of error , including data entry error , calculation errors and the propagation of errors through multiple calculations . The method also provided an unforeseen benefit by identifying test orders with incorrect clinic codes , which results in over- or underreporting of clinic metrics if left uncorrected . Overall , the method saves laboratorians ’ time , reduces errors and helps validate data integrity within the LIS .

Presenter : Sanjib Bhattacharyya , PhD , City of Milwaukee Health Department Laboratory , Milwaukee , WI , Phone : 414.286.5702 , Email : sbhatt @ milwaukee . gov

Identification of Carbapenem-Resistant Enterobacteriaceae from Rectal Swabs Using the ABI 7500

M . Bashore , M . Soehnlen and K . Jones , Michigan Department of Health and Human Services , Lansing , MI

The emergence of Carbapenem-resistant Enterobacteriaceae ( CRE ) has become a serious concern for both clinicians and public health officials . These organisms confer antibiotic resistance through several mechanisms that often require advanced molecular methods to identify . The most common mechanism that is used to confer immunity is through the creation of extended-spectrum ß-lactamases ( ESBLs ). Common ESBLs that confer resistance of Carbapenems in the United States are Klebsiella pneumoniae carbapenemase ( KPC ), New Delhi metallo-beta-lactamase 1 ( NDM- 1 ), oxacillinase carbapenemase ( Oxa ) and Verona integron-encoded metallo-ß-lactamase ( VIM ). State public health laboratories , in correlation with the Centers for Disease Control and Prevention ( CDC ) have develop molecular methods that can be used to identify these enzymes . The issue of broad spectrum drug resistance in CRE organisms is especially concerning from a public health standpoint because , typically , healthy people do not acquire these infections . Most commonly the infections are spread in hospitals and long term care facilities . The close proximity of patients in these facilities creates massive issues in terms of infection control . Additionally , rapid identification of these organisms is difficult in clinical laboratories due to lack of automated equipment and the use of phenotypic testing yielding low specificity of results . In order to combat this issue state public health laboratories were looked at to develop methods to transport , receive , test and report specimens from clinical sites to control the spread of these organisms . Molecular testing can be utilized to identify antimicrobial resistance genes and provide accurate and timely results for use by clinicians and infection control teams . The State of Michigan has developed methods to identify organisms containing resistance genes both from culture specimens submitted by clinical laboratories and clinical specimens in the form of rectal swabs submitted from patient care facilities . The State of Michigan , Bureau of Laboratories molecular method is based off of the use of the ABI 7500 real time PCR instrument with primers , probes and controls provided by the CDC . The validation of this method for identifying gene resistance using rectal swabs examined specimen conditions and types of swabs that could be used effectively for testing . The conditions were tested to examine acceptable specimen criteria for testing of real time clinical specimens . The Bureau of Laboratories provides collection materials to care centers and understanding which conditions affect the results of testing results is vital to ensure optimal testing . Resulting data demonstrated the effectiveness of the method at isolating DNA for multiple mechanisms of CRE under various conditions without sacrificing result quality .

Presenter : Matthew Bashore , Michigan Department of Health and Human Services , Lansing , MI , Phone : 517.335.8373 , Email : bashorem @ michigan . gov

Antimicrobial Resistance