General Session IV - Dale Schwab April 20, 2017

Transcription

1 The Culture of Clinical Commercial Labs Presented by: Dale Schwab PhD, Senior Scientific Director, Infectious Disease April 20, 2017 Objectives Challenges for the reference laboratory in MTB diagnosis/opportunities for public health collaboration Understand the complexity of commercial reference laboratory client mix Appreciate challenges of high-volume workflow Recognize regulatory limitations of work-up and billing Discover opportunities for reference laboratory and public health collaboration 2 Understand the Complexity of Reference Laboratory Client Mix Multiple client types (hospitals, other reference labs, outpatients) Multiple sample types and containers Transport time Multiple test codes Little demographic data or history with sample State PH requirements for 50 States 3 1

2 Quest Diagnostics Clinical and Esoteric Lab Footprint Seattle Marlborough Troy Pittsburgh Chicago Syosset Sacramento Teterboro San Jose Denver Kansas City Cincinnati Chantilly Horsham Las Vegas Baltimore Valencia L.A. SJC Albuquerque DLO Greensboro Atlanta Dallas Houston Tampa Miami LEGEND Regional Hub Labs (RHL) Regional Service labs (RSL) Esoteric Small RSLs 4 Standardization Between Quest Laboratories Best-practice teams Need to ensure best practice for all laboratories in Quest system Establish teams in each discipline to insure best practice Each microbiology team has a director-level chair, a QA representative and technologists from multiple labs Each team is responsible for Recommending commercial vendors Establishing validation protocols Writing corporate SOPs Establishing QA parameters 5 Quest Diagnostics AFB Sample/Isolate Flow Seattle Marlborough Troy Pittsburgh Chicago Syosset Sacramento Teterboro San Jose Denver Kansas City Cincinnati Chantilly Horsham Las Vegas Baltimore Valencia L.A. SJC Albuquerque DLO Greensboro Atlanta Dallas Houston Tampa Miami LEGEND Regional Hub Labs (RHL) Esoteric Regional Service labs (RSL) Small RSLs Samples for culture MTB DST Culture and MTB DST 6 2

3 California Quest Laboratories- Example of Sample Flow Regional business units ship to esoteric Laboratory Initial Sample Shipped Sample Isolate Received at the Sacramento or San Jose Quest laboratory Received from hospitals, physician offices or other Prepared for send out to Quest West Hills Received at Quest West Hills Laboratory Culture and smear set up Positive cultures tested by MTB complex DNA probe MTB complex positives sent to Quest Diagnostics Infectious Disease (formerly Focus) for susceptibility testing Public Health notified and isolate sent to PH as required Received at Quest Diagnostics Infectious Disease (formerly Focus) for susceptibility testing Solid media or MGIT Mixed? Subculture required? Result reported to PH Since client is West Hills, we have little demographic data 7 Overview of Our Lab Overview of the AFB BSL3 suite MmicrMicro Lab Clean Room Emergency door Work-up Processing 8 High-Complexity AFB Laboratory Extensive test menu Mycobacteria culture and smear with and without MTB complex PCR MTB complex PCR LDT or Cepheid MTB/RIF PCR MAC PCR MTB complex primary broth ( MGIT) DST MTB complex agar proportion DST, primary and/or secondary drugs MIC DST for MAC, rapid growers, and other slow growers ID by DNA probe, 16s and rpob gene sequencing, conventional We take PPE seriously! 9 3

4 Distribution of Mycobacteria Test Volumes Other MIC DST 16% 2% ID & DST MTB Primary DST 10% 2% Culture and Smear 47% 23% MTB PCR 10 Mycobacterium species Distribution Percent Positive Cultures: 10.5% Percent Positive Smears: 3.9% MTBC M. tuberculosis complex MAC M. avium complex MGOR M. gordonae MABC M. abscessus complex MFOC M. fortuitum complex OTHER M. kansasii, M. marinum, other rapid and slow growers OTHER 10% MTBC MFOC 4% 29% 9% MABC 4% MGOR 44% MAC 11 Case Study 1 Molecular detection of resistance mutations A patient from Mongolia had a history of TB treatment so MDR was a concern Broth susceptibility testing using MGIT would take two weeks or more. Request was submitted from California Department of Public Health to get a specimen shipped for pyrosequencing A portion of the reseeded MGIT broth from which the DSTs were set up was forwarded to the California Department of Public Health Laboratory Pyrosequencing detected no mutations for INH and RIF 12 4

5 Pyrosequencing as a Tool for Faster TB patient Management Positive collaboration with California Department of Public Health Reliable susceptibility testing requires a pure culture Often, the MGIT is positive prior to solid media- Rather than wait for pure subculture direct MGIT DST is performed What does a resistant result mean? Contamination with none MTB? True resistance? Next Steps? Confirm off solid media Perform agar proportion Pyrosequencing from positive MGIT 13 Case 2 TB or not TB CSF AFB smear reported as no acid-fast bacilli seen MTB complex PCR reported as not detected MGIT remained negative after 6-weeks AFB recovered on 7H11/7H11 selective agar on the 6 th week MTB complex ID was made by DNA probe Epidural Space Previously known patient with MTB complex AFB smear reported as no acid-fast bacilli seen 7H11/7H11 selective biplate remained negative after 6- weeks AFB recovered from MGIT on the 2 nd week MTB complex ID was made by DNA probe Investigation Samples processed on same run Potential plate mislabel or cross-contamination Contact physician of CSF patient for clinical history CSF patient was evaluated for meningoencephalitis, most likely due to autoimmune origin, and had been released from the hospital Next steps 14 Genotyping as an Investigational Tool Public health sector as a partner California Department of Public Health Laboratory was contacted for genotypying request Per state directive, both isolates were submitted to the State of Michigan Public Health Laboratory for expedited genotyping testing MIRU-typing performed at the State of Michigan Public Health Laboratory within 3 days DNA was submitted to Centers for Disease Control (CDC) for Spoligo-typing Both isolates had the identical pattern Ordering physician was contacted with the update and a comment was added to the report There was no negative patient impact due to extensive internal monitoring and collaboration with our public health laboratories. 15 5

6 Collaboration Opportunities Between Commercial Labs and Public Health Labs How do we duplicate the California model? Commercial labs may deal with samples from all 50 states Is there a directory of state MTB laboratory directors contact information that is accessible to commercial laboratories? Is there a state-by-state directory of MTB laboratory services that is accessible to commercial laboratories? Is there a state-by-state directory describing each state s isolate submission requirements? What is the route to request MIUR-typing or Spoligo-typing outside CA? APHL can assist commercial laboratories in providing the best patient care by publishing the above 16 Acknowledgements Kamran Azad, PhD, D(ABMM) Associate Director, Microbiology, Chair, AFB BPT Subspecialty team Marose Ang CS, Manager, AFB Section 17 THANK YOU! 18 6