Validation of the MALDI-TOF for the Identification of Neisseria gonorrhoeae

Transcription

1 Proposal Validation of the MALDI-TOF for the Identification of Neisseria gonorrhoeae Laboratory Director Sandip H. Shah, Ph.D (fax) Acting Director, Division of Infectious Disease Microbiology Section Manager Marty K. Soehnlen, Ph.D (fax)

2 INTRODUCTION The Michigan Department of Health and Human Services, Bureau of Laboratories (MDHHS BOL) has a long history of participation in numerous projects including several related to Matrix- Assisted Laser Desorption Ionization Time of Flight (MALDI TOF). Most recently, BOL served as the lead laboratory for a multi-jurisdictional select agent safety and accuracy study to identify highly pathogenic organisms. MALDI-TOF CAPACITY, STAFFING, TRAINING BOL purchased a Bruker MALDI TOF in Extensive validation and verification studies took place and the system replaced most conventional biochemical tests and Gas-Liquid Chromatography for Reference Bacteriology in This testing is performed on a variety aerobic gram negative and gram positive organisms and is also utilized routinely by the Salmonella and Neisseria testing areas. Since that time period, the lab has also validated the use of MALDI-TOF for Mycobacteria from solid and liquid media and is in process of validating Nocardia species. Over 170 different isolates were selected for the initial validation. At least 20 isolates have been selected each time a newer version of software has been released to verify performance. Currently, BOL owns the Research Use Only (RUO), Clinical Application (CA), and Security-Relevant (SR) libraries. There are a total of 9 staff members trained to perform analyses on the Bruker MALDI TOF. The lab has sent two staff members to external training and hosted two Bruker led in-house trainings. Two of the 9 staff were involved in the initial MALDI validations and have performed analyses since 2012 (5 years). The other staff have 3, 2, 1, 1, 1, <1, and <1 years of experience performing MALDI, respectively. MALDI TOF analyses are performed daily by the Reference Bacteriology and Mycobacteriology staff for their respective daily needs. Reference Bacteriology is responsible for performing analyses on their assigned isolates daily (5 days/week), but Mycobacteriology rotate weeks they are responsible to perform testing. LABORATORY INFASTRUCTURE AND N. GONORRHOEAE OR RELATED ORGANISM METHODOLOGIES The Bureau of Laboratories is a modern laboratory with two Divisions; the Division of Infectious Disease

3 and Division of Chemistry and Toxicology. Within the Division of Infectious Disease there is a Virology Section and a Microbiology Section. The Microbiology Section performs a wide range of tests for bacterial, parasitic, and fungal organisms. For Neisseria gonorrhoeae the lab utilizes both molecular and traditional methods. There are two Hologic Panther systems available for nucleic acid amplification tests (avg of 60,000 tests per year). NAAT-like testing has been in use at BOL for over 17 years. A traditional culture with a reflex to antimicrobial susceptibility testing is also available (avg of 20 tests per year). 16S rrna Sequencing utilizing the ABI 3130xl and MicroSEQ ID software was validated in This testing has also been incorporated into the workflow and is performed on a once per week basis to help resolve those identifications that cannot be confirmed by MALDI-TOF or conventional biochemical testing. Four staff rotate through this testing with 7,7,1,1 years of experience respectively. Hospitals and local public health partners are also able to send referred cultures for identification and susceptibility testing (avg of 200 tests per year). For sites that need assistance in transportation of cultures to BOL, the InTray System is recommended as an alternative to assist with successful transport through the courier system although no clinical sites have yet utilized the system. Traditional methods have been in place at BOL for over 30 years. There are 5 staff trained for traditional culture and susceptibility methods with 30, 25, 10, 3, and 1 years of experience with the methods, respectively. The lab performs testing Monday through Friday on the day of receipt (if arrival before noon). Three additional weekend staff have been trained to read susceptibilities and propagate growth to minimize delay of results. There are approximately 10 specimens or cultures received for work-up per week. BOL performs regular testing on Neisseria referred cultures that often are non-gonococcal species. Neisseria culture is performed on clinical isolates and clinical specimens at BOL. Specimens are submitted on Modified Thayer Martin agar and incubated in candle jars prior to submission. Isolates are sent to the laboratory on chocolate agar slants after there is visible growth. TSA with Sheep blood, Chocolate agar, and Modified Thayer Martin agar are used to culture isolates. Identification involves a combination of gram stain, oxidase, catalase, CTA sugars, and/or MALDI TOF. 16S rrna sequencing is utilized in cases of medico-legal importance or confirmation for patients under 12 years of age. Additional conventional testing is available for

4 Neisseria species that are not identified as either N. gonorrhoeae or N. meningitidis. All Neisseria gonorrhoeae identified at BOL is followed up with antibiotic susceptibility for surveillance and confirmation of appropriate therapy. Currently Cefixime and Ceftriaxone are utilized for routine testing. Additional antibiotics may be added upon request such as Ciprofloxacin and Tetracycline. BOL is currently involved in an enhanced surveillance project looking at susceptibility patterns for Azithromycin, Cefixime, Ceftriaxone, Ciprofloxacin, Gentamicin, and Tetracycline in counties with large men who have sex with men (MSM) populations. Susceptibility is performed by a combination of disk diffusion and E- Test MIC using GC II Agar with isovitalex. LABORATORY VALIDATIONS AND SAFETY BOL performs regular testing on Neisseria meningitidis isolates for subtyping. The identification of referred cultures has led to N. meningitidis cultures often being prepared for MALDI TOF, therefore BOL completed a study of the safety and limitations for N. meningitidis isolates in-house. BOL s data indicate that a tube extraction with 0.2 micron filter is the ideal option for isolates of high pathogenic potential, such as select agents. BOL performed studies to determine if other extraction methods resulted in a safe environment for the staff performing testing. All methods of extraction were tested. It has been shown that in the case of N. meningitidis formic acid extraction results in no viable growth and has therefore been deemed as a low risk of exposure by BOL s Health and Safety Office. Although N. meningitidis isolates are not to be ordinarily run on the MALDI-TOF, this in-house study determined the risk to the staff to be low if an unknown isolate is run on the MALDI TOF and later determined to be N. meningitidis.

5 Appendix A. Minimum Requirements for the Validation of the MALDI-TOF for the Identification of Neisseria gonorrhoeae (Appendix B of RFP)

6 Michigan Departmen of Health and Human Services, Bureau of Laboratories RFP: Validation of MALDI TOF for the Identification of Neisseria gonorrhoeae Species Number of Isolates available Storage method N. gonorrhoeae 372 N. meningitidis 135 N. subflava 4 N. elongata 1 N. sicca 2 N. mucosa 5 N. lactamica 5 N. canis 2 N. flavescens 2 M. catarrhalis 10 K. kingae 9