Who is the manufacturer of VITEK MS?

bioMerieux, Inc. filed the 510(k) submission for VITEK MS (K162950).

What is the FDA product code for VITEK MS?

PEX. It is classified under 21 CFR 866.3361 as a Class 2 device in the Microbiology panel.

What is the regulatory pathway for VITEK MS?

510(k) clearance (submission type: Traditional).

Who can help prepare an FDA 510(k) submission like VITEK MS?

Innolitics — a medical-device software consultancy — provides regulatory and engineering support for FDA 510(k) submissions. See https://innolitics.com/services/510ks/ or contact https://innolitics.com/contact.

VITEK MS

Q: What are the predicate devices for VITEK MS?

VITEK® MS (DEN130013 / K124067).

K162950 · bioMerieux, Inc. · PEX · Jul 22, 2017 · Microbiology

Device Facts

Record ID	K162950
Device Name	VITEK MS
Applicant	bioMerieux, Inc.
Product Code	PEX · Microbiology
Decision Date	Jul 22, 2017
Decision	SESE
Submission Type	Traditional
Regulation	21 CFR 866.3361
Device Class	Class 2

Indications for Use

VITEK® MS is a mass spectrometry system using matrix-assisted laser desorption/ionization – time of flight mass spectrometry (MALDI-TOF MS) for the identification of microorganisms cultured from human specimens. The VITEK® MS is a qualitative in vitro diagnostic device in conjunction with other clinical and laboratory findings to aid in the diagnosis of bacterial, yeast and mould infections.

Device Story

VITEK MS is a MALDI-TOF mass spectrometry system for microbial identification. Input: cultured microbial isolates from human specimens. Process: samples spotted on target slides, matrix added, laser-pulsed for ionization; ionized molecules accelerated in electromagnetic field; time-of-flight measured at detector to determine mass-to-charge (m/z) ratio; mass spectra generated and compared against clinical knowledge base (KB v3.0.0). Output: taxonomic identification (genus/species). Used in clinical microbiology laboratories by trained professionals. Output assists clinicians in diagnosing bacterial, yeast, and mould infections, guiding therapeutic decisions. Optimization in software v1.5.0 supports detection of higher mass peaks for Mycobacterium, Nocardia, and moulds.

Clinical Evidence

Clinical performance was evaluated across five US laboratories using routine fresh clinical isolates. For moulds (n=1508), mycobacteria (n=805), and nocardia (n=382), the system demonstrated high correct identification rates. Combined correct single choice and low discrimination correct genus rates were 92.7% for moulds, 96.5% for mycobacteria, and 97.9% for nocardia. Reproducibility studies (n=600 replicates) showed 99.5% overall reproducibility. Challenge studies (n=300) confirmed 96.7% correct identification. No carry-over or cross-contamination was observed.

Technological Characteristics

MALDI-TOF mass spectrometry system. Components: acquisition station, target slides, laser source, electromagnetic field accelerator, particle detector. Software: KB v3.0.0, acquisition software v1.5.0. Connectivity: laboratory environment. Principle: ionization, separation, and detection based on m/z ratio. Analyte preparation: direct spotting or inactivation/processing for specific organisms.

Indications for Use

Indicated for the identification of cultured bacterial, yeast, mould, mycobacteria, and nocardia microorganisms from human specimens to aid in the diagnosis of infections. For prescription use only.

Regulatory Classification

Identification

A mass spectrometer system for clinical use for the identification of microorganisms is a qualitative in vitro diagnostic device intended for the identification of microorganisms cultured from human specimens. The device is comprised of an ionization source, a mass analyzer, and a spectral database. The device is indicated for use in conjunction with other clinical and laboratory findings to aid in the diagnosis of bacterial and fungal infections.

Special Controls

*Classification.* Class II (special controls). The special controls for this device are:(1) Premarket notification submissions must include detailed documentation for device software, including, but not limited to, standalone software applications and hardware-based devices that incorporate software. (2) Premarket notification submissions must include database implementation methodology, construction parameters, and quality assurance protocols. (3) A detailed explanation of the interpretation of results and acceptance criteria must be included in the device's 21 CFR 809.10(b)(9) compliant labeling. (4) As part of the risk management activities performed under 21 CFR 820.10(c) design and development, you must document an appropriate end user device training program that will be offered as part of your efforts to mitigate the risk of failure to correctly operate the instrument. (5) Premarket notification submissions must include details on the appropriate end user device training program that will be offered while marketing the device.

Predicate Devices

VITEK® MS (DEN130013 / K124067)

Related Devices

K181412 — VITEK MS · bioMerieux, Inc. · Dec 21, 2018
DEN130013 — VITEK MS · bioMerieux, Inc. · Aug 21, 2013

Submission Summary (Full Text)

{0} 1 # 510(k) SUBSTANTIAL EQUIVALENCE DETERMINATION DECISION SUMMARY A. 510(k) Number: K162950 B. Purpose for Submission: To add the additional organism identification claims (moulds, mycobacteria and nocardia) to the already cleared device DEN130013 (K124067). C. Measurand: See Intended Use D. Type of Test: A mass spectrometer system for clinical use for the identification of microorganisms is a qualitative *in vitro* diagnostic device intended for the identification of microorganisms cultured from human specimens. The device is comprised of an ionization source, a mass analyzer and a spectral database. The device is indicated for use in conjunction with other clinical and laboratory findings to aid in the diagnosis of bacterial and fungal infections. E. Applicant: bioMérieux, Inc. F. Proprietary and Established Names: VITEK MS G. Regulatory Information: 1. Regulation section: 21 CFR 866.3361 2. Classification: Class II (special controls) 3. Product code: PEX 4. Panel: Microbiology (83) H. Intended Use: 1. Intended use(s): VITEK MS is a mass spectrometer system using matrix-assisted laser desorption/ionization - time to flight (MALDI-TOF) for the identification of microorganisms cultured from human specimens. The VITEK MS is a qualitative *in vitro* diagnostic device indicated for use in conjunction with other clinical and laboratory findings to aid in the diagnosis of bacterial, yeast and mould infections. The following organisms are claimed: {1} 2 Abiotrophia defectiva Achromobacter denitrificans¹ Achromobacter xylosoxidans¹ Acinetobacter baumannii complex Acinetobacter haemolyticus Acinetobacter junii Acinetobacter lwoffii Actinomyces meyeri Actinomyces neuii Actinomyces odontolyticus Aerococcus viridans Aeromonas hydrophila/caviae² Aeromonas sobria²,³ Aggregatibacter actinomycetemcomitans Aggregatibacter aphrophilus Aggregatibacter segnis Alcaligenes faecalis ssp faecalis Bacteroides caccae Bacteroides fragilis Bacteroides ovatus⁴ Bacteroides thetaiotaomicron Bacteroides uniformis Bacteroides vulgatus Bordetella parapertussis Bordetella pertussis Brevundimonas diminuta Burkholderia multivorans Campylobacter coli Campylobacter jejuni Candida albicans Candida dubliniensis Candida famata Candida glabrata Candida guilliermondii Candida haemulonii Candida inconspicua Candida intermedia Candida kefyr Candida krusei Candida lambica Candida lipolytica Candida lusitaniae Candida norvegensis Candida parapsilosis Candida pelliculosa Candida rugosa Candida tropicalis Candida utilis Candida zeylanoides Chryseobacterium indologenes Citrobacter amalonaticus Citrobacter braaki⁵ Citrobacter freundii⁵ Citrobacter koseri Citrobacter youngae⁵ Clostridium clostridioforme Clostridium difficile Clostridium perfringens Clostridium ramosum Corynebacterium jeikeium Cronobacter sakazakii Cryptococcus neoformans Edwardsiella hoshinae Edwardsiella tarda Eikenella corrodens Elizabethkingia meningoseptica Enterobacter aerogenes Enterobacter asburiae⁶ Enterobacter cancerogenus Enterobacter cloacae⁶ Enterococcus avium Enterococcus casseliflavus Enterococcus durans Enterococcus faecalis Enterococcus faecium Enterococcus gallinarum Escherichia coli⁷ Escherichia fergusonii Escherichia hermannii Ewingella americana Finegoldia magna Fusobacterium necrophorum Fusobacterium nucleatum Gardnerella vaginalis Gemella haemolysans Gemella morbillorum {2} 3 Geotrichum capitatum Granulicatella adiacens Haemophilus influenzae Haemophilus parahaemolyticus Haemophilus parainfluenzae Hafnia alvei Kingella denitrificans Kingella kingae Klebsiella oxytoca Klebsiella pneumoniae Kodamaea ohmeri Lactococcus garvieae Lactococcus lactis ssp lactis 8 Leclercia adecarboxylata Legionella pneumophila Leuconostoc mesenteroides Leuconostoc pseudomesenteroides Listeria monocytogenes Malassezia furfur Malassezia pachydermatis Micrococcus luteus Mobiluncus curtisii Moraxella (Neisseria) ovis Morganella morganii Neisseria cinerea Neisseria gonorrhoeae 9 Neisseria meningitidis Neisseria mucosa 10 Ochrobactrum anthropi Oligella ureolytica Oligella urethralis Pantoea agglomerans Parvimonas micra Pasteurella multocida Pediococcus acidilactici Peptoniphilus asaccharolyticus Peptostreptococcus anaerobius Pluralibacter gergoviae Prevotella bivia Prevotella buccae Prevotella denticola Prevotella intermedia Prevotella melaninogenica Propionibacterium acnes Proteus mirabilis Proteus penneri 11 Proteus vulgaris 11 Providencia rettgeri Providencia stuartii Pseudomonas aeruginosa Pseudomonas fluorescens Pseudomonas putida Pseudomonas stutzeri Ralstonia pickettii Raoultella ornithinolytica Raoultella planticola Rhizobium radiobacter Rhodotorula mucilaginosa Rothia mucilaginosa Saccharomyces cerevisiae Salmonella group 9 Saprochaete capitata Serratia fonticola Serratia liquefaciens Serratia marcescens Serratia odorifera Sphingobacterium multivorum Sphingobacterium spiritivorum Sphingomonas paucimobilis Staphylococcus aureus Staphylococcus capitis Staphylococcus cohnii ssp cohnii Staphylococcus cohnii ssp urealyticus Staphylococcus epidermidis Staphylococcus haemolyticus Staphylococcus hominis ssp hominis 12 Staphylococcus lugdunensis Staphylococcus saprophyticus Staphylococcus schleiferi Staphylococcus sciuri Staphylococcus simulans Staphylococcus warneri Stenotrophomonas maltophilia Streptococcus agalactiae Streptococcus anginosus Streptococcus constellatus Streptococcus dysgalactiae Streptococcus gallolyticus ssp gallolyticus {3} 4 Streptococcus infantarius ssp coli Streptococcus infantarius ssp infantarius Streptococcus intermedius Streptococcus mitis/Streptococcus oralis Streptococcus mutans Streptococcus pneumoniae Streptococcus pyogenes Streptococcus salivarius ssp salivarius 13 Streptococcus sanguinis Trichosporon asahii Trichosporon inkin Trichosporon mucoides Vibrio cholerae Vibrio parahaemolyticus Vibrio vulnificus Yersinia enterocolitica Yersinia frederiksenii Yersinia intermedia Yersinia kristensenii Yersinia pseudotuberculosis 14 ## MYCOBACTERIUM Mycobacterium abscessus Mycobacterium avium Mycobacterium chelonae Mycobacterium fortuitum group: 15 Mycobacterium alvei Mycobacterium farcinogenes Mycobacterium fortuitum Mycobacterium houstonense Mycobacterium peregrinum Mycobacterium porcinum Mycobacterium senegalense Mycobacterium gordonae Mycobacterium haemophilum Mycobacterium immunogenum Mycobacterium intracellulare Mycobacterium kansasii Mycobacterium lentiflavum Mycobacterium malmoense Mycobacterium marinum Mycobacterium mucogenicum Mycobacterium scrofulaceum Mycobacterium simiae Mycobacterium smegmatis Mycobacterium szulgai Mycobacterium tuberculosis complex: 16 Mycobacterium africanum Mycobacterium bovis Mycobacterium canettii Mycobacterium microti Mycobacterium pinnipedii Mycobacterium tuberculosis Mycobacterium xenopi ## NOCARDIA Nocardia abscessus Nocardia asteroides Nocardia brasiliensis Nocardia cyriacigeorgica Nocardia farcinica Nocardia nova 17 Nocardia otitidiscaviarum Nocardia paucivorans Nocardia pseudobrasiliensis Nocardia transvalensis Nocardia veterana Nocardia wallacei ## MOULDS Acremonium sclerotigenum Alternaria alternata Aspergillus brasiliensis Aspergillus flavus/oryzae Aspergillus fumigatus Aspergillus lentulus Aspergillus nidulans Aspergillus niger complex Aspergillus sydowii Aspergillus terreus complex 18 Aspergillus calidoustus Aspergillus versicolor Blastomyces dermatitidis Cladophialophora bantiana Coccidioides immitis/posadasii Curvularia hawaiiensis Curvularia spicifera Epidermophyton floccosum Exophiala dermatitidis {4} 5 Exophiala xenobiotica ¹⁹ Exserohilum rostratum ¹⁹ Fusarium oxysporum complex Fusarium proliferatum Fusarium solani complex Histoplasma capsulatum Lecythophora hoffmannii Lichtheimia corymbifera Microsporum audouinii Microsporum canis Microsporum gypseum Mucor racemosus complex ²⁰ Paecilomyces variotii complex Penicillium chrysogenum Pseudallescheria boydii Purpureocillium lilacinum Rasamsonia argillacea complex ²¹ Rhizopus arrhizus complex Rhizopus microsporus complex Sarocladium kiliense Scedosporium apiospermum Scedosporium prolificans Sporothrix schenckii complex Trichophyton interdigitale Trichophyton rubrum Trichophyton tonsurans Trichophyton verrucosum Trichophyton violaceum ²² 1. Achromobacter denitrificans and Achromobacter xylosoxidans identifications should be considered as a slashline result, Achromobacter denitrificans/ Achromobacter xylosoxidans. The final identification should be confirmed before sending the final selection to the LIS or to the VITEK 2 for AST results 2. Aeromonas hydrophila/caviae and Aeromonas sobria should be considered as an Aeromonas species group identification. 3. In KB V3.0.0, Aeromonas sobria is displayed as a low discrimination result with Aeromonas veronii but only Aeromonas sobria has been clinically validated. 4. In KB V3.0.0, Bacteroides ovatus is grouped in a slashline with Bacteroides xylanisolvens. It is not possible to distinguish between the two species. B. ovatus is more commonly associated with human infection. 5. Citrobacter freundii, Citrobacter braakii and Citrobacter youngae should be considered as Citrobacter freundii complex. 6. Enterobacter cloacae and Enterobacter asburiae identifications should be considered as a slashline result, Enterobacter cloacae/ Enterobacter asburiae. The final identification should be confirmed before sending the final selection to the LIS or to the VITEK 2 for AST results. 7. Shigella species and E. coli O157 are identified as Escherichia coli. Confirmatory tests are required to differentiate Escherichia coli from Shigella species or E. coli O157. 8. In KB V3.0.0 Lactococcus lactis ssp lactis is integrated in a new group Lactococcus lactis (with two other subspecies Lactococcus lactis ssp cremoris and Lactococcus lactis ssp hordniae). In the Lactococcus lactis group only subspecies Lactococcus lactis ssp lactis has been clinically validated. 9. Confirmatory tests recommended for Neisseria gonorrhea and Salmonella species. 10. In KB V3.0.0, Neisseria mucosa is grouped in a slashline with Neisseria sicca. It is not possible to distinguish between the two species. Both species have been associated with human infection. {5} 11. Proteus penneri and Proteus vulgaris identifications should be considered as a slashline result, Proteus penneri/Proteus vulgaris. 12. In KB V3.0.0 Staphylococcus hominis ssp hominis is integrated in a new group Staphylococcus hominis (with another subspecies S. hominis ssp novobiosepticus). In the Staphylococcus hominis group only subspecies Staphylococcus hominis ssp hominis has been clinically validated. 13. In KB V3.0.0, Streptococcus salivarius ssp salivarius is displayed as a low discrimination result with Streptococcus salivarius ssp thermophilus and Streptococcus vestibularis but only Streptococcus salivarius ssp salivarius has been clinically validated. 14. There is a possibility of cross-identification between Yersinia similis and Yersinia pseudotuberculosis. 15. The Mycobacterium fortuitum complex or group displayed in VITEK MS includes the seven most prominent and closely related species. The VITEK MS group differs from the ones reported in the literature that may include up to 13 species. 16. The Mycobacterium tuberculosis complex displayed in VITEK MS includes the four most prevalent species based on different worldwide geographic regions. It does not include two additional species Mycobacterium microti and Mycobacterium pinnipedii as reported in the literature. 17. In KB V3.0.0, Nocardia nova is displayed as a low discrimination result with Nocardia africana but only Nocardia nova has been clinically validated. 18. Both Aspergillus alabamensis and Aspergillus niveus are not identified as Aspergillus terreus complex. No identification is expected with either species. 19. All of the no identifications for this organism were from multiple replicates of the same isolate. 20. Mucor racemosus f. sphaerosporus is not identified as Mucor racemosus complex. No identification is expected. The Mucor racemosus complex is comprised of M. racemosus f. brunneus, M. racemosus f. chibinensis, M. racemosus f. racemosus, and M. racemosus f. sphaerosporus. 21. Three out of the five no identifications for this organism were from multiple replicates of the same isolate. 22. All of the discordant identifications for this organism were from multiple replicates of the same isolate. 2. Indication(s) for use: Same as intended use. 3. Special conditions for use statement(s): The VITEK MS is for prescription use only in accordance with 21 CFR 801.109. 4. Special instrument requirements: - VITEK MS: Shimadzu AXIMA® Assurance mass spectrometer - VITEK MS Prep Station - VITEK MS-DS Target Slides 6 {6} 7 Reagents: - VITEK MS-CHCA (Alpha-cyano-4-hydroxy-cinnamic acid) solution - VITEK MS-FA (Formic acid) reagent - VITEK MS MYCOBACTERIUM/NOCARDIA KIT - VITEK MS LIQUID MYCO SUPPLEMENTAL KIT - VITEK MS MOULD KIT Database: - VITEK MS V3.0 Knowledge Base (KB) Software: - VITEK MS Sample Prep Station software, - VITEK MS V3 acquisition station 1.5.0.2 - VITEK MS Analysis Server / Software - VITEK MS Computation Engine - Myla® Middleware I. Device Description: The VITEK MS v3.0 system is a system consisting of kit reagents (VITEK MS-CHCA, VITEK MS-FA, VITEK MS Mycobacterium/Nocardia Kit, VITEK MS Mould Kit), VITEK MS-DS target slides, VITEK MS Prep Station, Knowledge Base v3.0, software, and the VITEK MS (original equipment manufacturer (OEM)-labeled Shimadzu AXIMA® Assurance mass spectrometer). Reagent Description: - VITEK MS-CHCA (Alpha-cyano-4-hydroxy-cinnamic acid) is the solution that serves as a matrix which will crystalize with the microbial sample on the target slide spot. 1.0 μl of the matrix is added to the spot with the sample and allowed to dry forming crystals. - The VITEK MS-FA (Formic acid) reagent is used to pre-treat yeast in order to extract protein before the VITEK MS-CHCA matrix is added to the spot containing the sample. - VITEK MS-DS target slides are single-use disposables which contain 3 acquisition groups of 16 sample spots. Each group includes 1 calibration spot. Target slides are for single use only. - VITEK MS MYCOBACTERIUM/NOCARDIA KIT includes ethanol and vials with glass beads to inactivate mycobacteria and nocardia by disrupting the cells. The kit also includes formic acid and acetonitrile to complete the extraction of proteins. - VITEK MS LIQUID MYCO SUPPLEMENTAL KIT includes the additional consumables (i.e., 5 mL conical bottom tubes and safety backed absorbent pads) needed to process samples for mycobacterium with liquid media. - VITEK MS MOULD KIT provides ethanol, formic acid and acetonitrile to inactivate moulds and extract their proteins. {7} 8 Knowledge Base: The reference database for the VITEK MS system includes data representing 1046 taxa, including 882 bacteria and 164 fungi. Each species or species group is represented by an average of 17 isolates (range 2* - 712). In order to capture the degree of acceptable variation within spectra from the same species, each reference isolate was grown on multiple media types under several growth conditions. The raw spectra were then acquired by more than one technician using multiple instruments. This process resulted in an average of 36 reference spectra per species (or 53 spectra by species or group of species). * NOTE: For two very rare species (Prevotella baroniae and Prevotella ruminicola), it was only possible to test a single strain for these organisms in the reference database build. Additional laboratory tests as determined by Microbiology laboratory protocols for low discrimination results or non-clinically validated organisms are necessary for the completion of the organism identification. Non-clinically validated organisms are displayed as $\widehat{\mathbb{N}}$ in the report. Testing of non-clinically validated species or species not found in the database may result in an unidentified result or a misidentification. Note: Interpretation of results and use of the VITEK MS system require a competent laboratorian who should judiciously make use of experience, specimen information, and other pertinent procedures before reporting the identification of test organisms. Additional information known to the user, such as Gram stain reaction, colonial and cellular morphology, and growth aerobically or in CO2 should be considered when accepting VITEK MS results. NOTE: Candida auris is not currently in the knowledge base; testing of this species will usually give no identification but may also result in a misidentification as either Candida haemulonii or Candida lusitaniae. Software: The VITEK MS system consists of a suite of applications that perform the overall system function. The system functions as a kiosk, not allowing the end-user to access any operating system functions. The end-user cannot access the native operating system or any system configuration panels. The software application contains several processes that include handling all user interactions, all network activity, communication, and synchronization with the all the components. The VITEK MS system software is comprised of four software components and MYLA middleware. 1. VITEK MS Sample Prep Station software: The VITEK MS Prep Station is used to prepare VITEK MS-DS target slides. It consists of a computer workstation equipped with a barcode reader, Touch Screen and Virtual Keyboard. {8} 2. VITEK MS acquisition station: The Acquisition Station Software controls the VITEK MS to acquire spectral data from each sample in turn and displays the spectra for the operator to review. The Acquisition Station displays the spectra and peak lists and transfers the peak lists to the VITEK MS Analysis Server. 3. VITEK MS Analysis Server / Software: The VITEK MS Analysis Server is the software that manages the VITEK MS workflow and computes VITEK MS identification results. It is a software component that resides on the Myla Server (PC). 4. VITEK MS Computation Engine: The VITEK MS analysis server sends the acquired data to the computation engine that calculates the identification results. The algorithms and mapping files required for identification are contained within the computation engine. 5. Myla Middleware: Myla™ is a computer application ("Middleware"), based on Web technology, which allows data related to the laboratory workflow, laboratory instruments, Laboratory Information System (LIS), analysis results, etc. to be grouped together. Myla™ interfaces between the bioMérieux instruments connected to the application (e.g., VITEK MS) and the Laboratory Information System (LIS). Myla™ manages the VITEK MS workflow and computes the identification results with the use of a computation engine and organism knowledge bases. ## VITEK MS bioMérieux's VITEK MS, is the same instrument as the Shimadzu Axima Assurance MALDI-TOF spectrometer. The VITEK MS is manufactured for bioMérieux by Kratos Analytical (a Shimadzu subsidiary) in Manchester, UK. The VITEK MS contains a Class 1 laser product containing a Class 3b invisible-light laser. The laser is a 337 nm nitrogen laser, fixed focus. This speed depends on the mass of the ions with heavier molecules having a higher moment of inertia resulting in a lower velocity. The time of transit is measured precisely by the ions' arrival at a particle detector. Based on the time of flight, the m/z ratio of each particle can be determined, and a mass spectrum of the sample mixture is generated. The recorded signal is processed by the Acquisition Station software and presented as a spectrum of intensity versus mass in Daltons (Da). ## J. Substantial Equivalence Information: 1. Predicate device name(s): VITEK MS 2. Predicate 510(k) number(s): DEN130013 (K124067) {9} 3. Comparison with predicate: | Similarities | | | | --- | --- | --- | | Characteristic | New Device VITEK MS v3 / KB v3.0.0 (K162950) | Predicate Device VITEK MS (DEN130013 / K124067) | | Classification | 21 CFR 866.3361 Class II System, mass spectrometry, MALDI-ToF, microorganism identification, cultured isolates | 21 CFR 866.3361 Class II System, mass spectrometry, MALDI-ToF, microorganism identification, cultured isolates | | Product Code | PEX | PEX | | Intended Use | The VITEK MS is a mass spectrometer system using matrix assisted laser desorption/ionization time to flight (MALDI-TOF) for the identification of microorganisms cultured from human specimen. The VITEK MS is a qualitative in vitro diagnostic device indicated for use in conjunction with other clinical and laboratory findings to aid in the diagnosis of bacterial, yeast and mould infections. NOTE: Addition of mould, mycobacteria and nocardia indications for use added in VITEK MS v3 / KB v3.0.0 | The VITEK MS is a mass spectrometer system using matrix assisted laser desorption/ionization time to flight (MALDI-TOF) for the identification of microorganisms cultured from human specimen. The VITEK MS is a qualitative in vitro diagnostic device indicated for use in conjunction with other clinical and laboratory findings to aid in the diagnosis of bacterial and yeast infections. | | Type of Test | Automated Mass Spectrometry System | Automated Mass Spectrometry System | | Calibration | E. coli ATCC 8739 | E. coli ATCC 8739 | | Matrix | Alpha-cyano-4-hydroxy-cinnamic acid | Alpha-cyano-4-hydroxy-cinnamic acid | | Target Slide | VITEK MS DS Target Slides 48 positions disposable plastic targets | VITEK MS DS Target Slides 48 positions disposable plastic targets | | MALDI TOF MS Instrument | Shimadzu AXIMA® Assurance MS | Shimadzu AXIMA® Assurance MS | | Method of Testing | (For bacteria and yeast) Direct testing from isolated colonies | (For bacteria and yeast) Direct testing from isolated colonies | | Age of Culture | (For bacteria and yeast) Incubation of culture should be 18 – 72 hours | (For bacteria and yeast) Incubation of culture should be 18 – 72 hours | | Sample / Media Type | Isolated colony from a patient sample source, from a media used during development of the VITEK MS Knowledge Base, including: • Columbia blood agar with 5% sheep blood • Trypticase soy agar with 5% sheep blood • Trypticase soy agar • Chocolate polyvitex agar • Campylosel agar • MacConkey agar • Modified Sabouraud dextrose agar (glucose: 20 g/l - pH: 6.1) • chromID CPS | Isolated colony from a patient sample source, from a media used during development of the VITEK MS Knowledge Base, including: • Columbia blood agar with 5% sheep blood • Trypticase soy agar with 5% sheep blood • Trypticase soy agar • Chocolate polyvitex agar • Campylosel agar • MacConkey Agar • Modified Sabouraud dextrose Agar • ChromID CPS | | Algorithm | An algorithm process known as "mass binning" is used for the differentiation of the species included in the knowledge base. | An algorithm process known as "mass binning" is used for the differentiation of the species included the knowledge base. | {10} | Similarities | | | | --- | --- | --- | | Characteristic | New Device VITEK MS v3 / KB v3.0.0 (K162950) | Predicate Device VITEK MS (DEN130013 / K124067) | | Result reporting | To detect microbial growth, the VITEK MS System uses a knowledge base developed from spectra of a number of microbial species. The resulting spectra from the VITEK MS / Acquisition Station are evaluated against this knowledge. Identification are displayed, with a confidence value when an organism or organism group is identified. Low-discrimination identifications are displayed when more than one, but not more than four identifications, are made. When more than four identifications are made, or when no match is found, the organism is considered unidentified. Data analysis is performed using software embedded on the MYLA® Server. | To detect microbial growth, the VITEK MS System uses a knowledge base developed from spectra of a number of microbial species. The resulting spectra from the VITEK MS / Acquisition Station are evaluated against this knowledge. Identification are displayed, with a confidence value when an organism or organism group is identified. Low-discrimination identifications are displayed when more than one, but not more than four identifications, are made. When more than four identifications are made, or when no match is found, the organism is considered unidentified. Data analysis is performed using software embedded on the MYLA® Server. | | Recorded Mass Range | 2,000 - 20,000 m/z | 2,000 - 20,000 m/z | | System Components, Software, Reagents | The VITEK MS system consists of a number of components (e.g. a Prep Station, the MS Instrument, an Acquisition Station), software/middleware solutions (e.g. Acquisition Station Software, an Analysis Server, a Computation Engine, and MYLA®), and the same disposables (e.g. the VITEK MS-DS Target Slides, CHCA Matrix, and Formic Acid as applicable). | The VITEK MS system consists of a number of components (e.g. a Prep Station, the MS Instrument, an Acquisition Station), software/middleware solutions (e.g. Acquisition Station Software, an Analysis Server, a Computation Engine, and MYLA®), and the same disposables (e.g. the VITEK MS-DS Target Slides, CHCA Matrix, and Formic Acid as applicable). | | Laser | The laser used for the excitation of molecules on the VITEK MS v3 is the same as the laser used for the VITEK MS (v2) (operating power and repetition rate is unchanged). | A laser is used for the excitation of molecules (the laser operates on a set power and repetition rate). | | Differences | | | | --- | --- | --- | | Characteristic | New Device VITEK MS v3 / KB v3.0.0 (K162950) | Predicate Device VITEK MS (v2) (DEN130013 / K124067) | | Knowledge Base and Indications for Use | VITEK MS v3.0 Knowledge Base (includes the previous bacteria and yeast, as well as new mycobacterium, nocardia, and mould indications for use) | VITEK MS V2.0 Knowledge Base (included bacteria and yeast isolates) | | Culture Media | The VITEK v3 / KB v3.0.0 includes new mycobacteria indications for use from both solid & liquid culture media, and nocardia and mould indications for use from solid culture media only. | VITEK MS (v2) only included indications for use for isolates from solid culture media. | | Age of Culture | (Includes new mycobacterium, nocardia, and mould indication for use): | As mycobacterium, nocardia, and mould are new indications for use, there were no previous | {11} | Differences | | | | --- | --- | --- | | Characteristic | New Device VITEK MS v3 / KB v3.0.0 (K162950) | Predicate Device VITEK MS (v2) (DEN130013 / K124067) | | | • Incubation of rapid growing mycobacteria from solid media should be 3 – 7 days • Incubation of slow growing mycobacteria from solid media should be 7 – 28 days • Incubation of mycobacteria from liquid media should be 24 – 72 hours post positivity • Incubation of nocardia cultures should be 24 – 72 hours • Incubation of rapid growing moulds should be 2 – 8 days • Incubation of slow growing moulds should be 5 – 25 days | Age of Culture requirements for these organisms on the predicate device. | | Rastering Pattern | The VITEK MS Acquisition Station was updated so that the rastering pattern exhausts raster points. | The VITEK MS Acquisition Station rastering pattern found sweet spots. | | Media Type | With the introduction of the *Mycobacterium* indications for use, the following new media types were used during the development of the VITEK MS KB v3.0 for mycobacteria identifications. • BacT/ALERT® MP • Lowenstein-Jensen • MGIT™ • Middlebrook 7H10 agar • Middlebrook 7H11 agar • Coletsos With the introduction of the mould indications for use, the following new media types were used during the development of the VITEK MS KB v3.0 for mould identifications. • Potato dextrose agar • Sabouraud dextrose agar (glucose: 40 g/l - pH: 5.6) • Sabouraud dextrose agar with Gentamicin & Chloramphenicol • Trytcase soy agar with neutralizers With the introduction of the nocardia indications for use, the following new media types were used during the development of the VITEK MS KB v3.0 for nocardia identifications. • Sabouraud dextrose agar (glucose: 40 g/l - pH: 5.6) • Buffered Charcoal Yeast Extract | As *Mycobacterium* and mould, are a new indication for use, there were no previous media types or age of culture requirements for these organisms on the predicate device. | {12} | Differences | | | | --- | --- | --- | | Characteristic | New Device VITEK MS v3 / KB v3.0.0 (K162950) | Predicate Device VITEK MS (v2) (DEN130013 / K124067) | | Sample Prep | With the introduction of the mycobacteria, nocardia and mould indications for use, an inactivation and extraction process is required for sample prep, prior to spotting the sample to the VITEK MS DS Slide. | As the predicate device only included indications for use with bacteria and yeast, sample prep consisted of direct spotting to VITEK MS DS Slide. Inactivation of the sample occurs during the addition of the CHCA Matrix. | # K. Standard/Guidance Document Referenced (if applicable): Table 1: Clinical & Laboratory Standards Institute (CLSI) Standards | Standards No. | Standards Title | Date | | --- | --- | --- | | C5O-A | Mass Spectrometry in the Clinical Laboratory: General Principles and Guidance; Approved Guideline, 1st Edition | 10/29/2007 | | EP09-A3 | Measurement Procedure Comparison and Bias Estimate Using Patient Samples; Approved Guideline, 3rd Edition | 08/30/2013 | | EP12-A | User Protocol for Evaluation of Qualitative Test Performance; Approved Guideline, 2nd Edition | 1/25/2008 | | MM09-A | Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine; Approved Guideline, 1st Edition | 12/20/2004 | | MM18-A | Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing; Approved Guideline, 1st Edition | 4/28/2008 | | M24-A2 | Susceptibility Testing of Mycobacteria, Nocardiae, and Other Aerobic Actinomycetes; Approved Standard, 2nd Edition | 03/31/2011 | | M48-A | Laboratory Detection and Identification of Mycobacterium; Approved Guideline, 1st Edition. | 05/27/2008 | | M54-A | Principles and Procedures for Detection of Fungi in Clinical Specimens-Direct Examination; Approved Guideline, 1st Edition | 10/31/2012 | # L. Test Principle: The VITEK MS system is based on a matrix-assisted laser desorption ionization-time of flight mass spectrometer (MALDI-TOF MS). The colony is mixed with a saturated matrix solution and forms crystals. The ionization of this mixture by the laser induces the desorption and transfer of protons from photo-excited matrix to analyte to form a protonated molecule. During the analysis process, proteins are ionized without fragmentation by the coordinated {13} action of the laser and the small organic acids of the matrix and separated on the basis of their mass-to-charge ratios, a process which results in a characteristic mass spectral profile. Microbial identification is based on the comparison of the protein spectrum generated from intact whole bacterial cells to the knowledge database of species-specific reference protein profiles using a particular algorithm. # M. Performance Characteristics (if/when applicable): # 1. Analytical performance: # a. Precision/Reproducibility: A panel of 10 reproducibility strains consisting of five moulds, three mycobacteria and two Nocardia organisms were tested at each of three trial sites by two technologists in duplicate on each of five days with two runs per day for a total of 60 replicates per organisms. The reproducibility study was conducted at five external sites; three sites tested the mould reproducibility strains and three sites tested the mycobacteria and Nocardia reproducibility strains. Three different lots of the VITEK MS Mycobacterium/Nocardia kit and the VITEK MS Mould kit were used during reproducibility testing. On each day of testing, sequential positions on the target slide were assigned to the first run of the selected reproducibility samples, and randomized for the second run. Spot positions were alternated each day between the technologist on each day of testing. Three organisms were used for positive quality control, and reagents alone were used for the negative control. The quality control strains were Aspergillus brasiliensis, ATCC 16404, Mycobacterium smegmatis, ATCC 19420 and Nocardia farcinica, ATCC 3308. Results are shown in Table 2 below. Table 2: Reproducibility Testing for Moulds, Mycobacteria and Nocardia -all sites combined | Sample | Organism | Day | | | | | Total (%) | 95% CI | | --- | --- | --- | --- | --- | --- | --- | --- | --- | | | | 1 | 2 | 3 | 4 | 5 | | | | R1 | Mycobacterium abscessus | 12/12 | 12/12 | 12/12 | 12/12 | 12/12 | 60/60 (100.0%) | [94.0, 100.0]% | | R2 | Mycobacterium chelonae | 12/12 | 12/12 | 12/12 | 12/12 | 12/12 | 60/60 (100.0%) | [94.0, 100.0]% | | R3 | Mycobacterium smegmatis | 12/12 | 12/12 | 12/12 | 12/12 | 12/12 | 60/60 (100.0%) | [94.0, 100.0]% | | R4 | Nocardia wallacei | 12/12 | 12/12 | 12/12 | 12/12 | 11/12 | 59/60 (98.3%) | [91.1, 100.0]% | | R5 | Nocardia otitidiscaviarum | 12/12 | 12/12 | 12/12 | 12/12 | 12/12 | 60/60 (100.0%) | [94.0, 100.0]% | | R6 | Aspergillus fumigatus | 12/12 | 12/12 | 12/12 | 12/12 | 12/12 | 60/60 (100.0%) | [94.0, 100.0]% | | R7 | Fusarium proliferatum | 12/12 | 12/12 | 12/12 | 12/12 | 12/12 | 60/60 (100.0%) | [94.0, 100.0]% | | R8 | Purpureocillium lilacinum | 12/12 | 12/12 | 12/12 | 11/12 | 11/12 | 58/60 (96.7%) | [88.5, 99.6]% | | R9 | Lecythophora hoffmannii | 12/12 | 12/12 | 12/12 | 12/12 | 12/12 | 60/60 (100.0%) | [94.0, 100.0]% | | R10 | Penicillium chrysogenum | 12/12 | 12/12 | 12/12 | 12/12 | 12/12 | 60/60 (100.0%) | [94.0, 100.0]% | | All | | 120/120 | 120/120 | 120/120 | 119/120 | 118/120 | 597/600 (99.5%) | [98.5, 99.9]% | # b. Linearity/assay reportable range: Not applicable, qualitative assay. {14} c. Traceability, Stability, Expected values (controls, calibrators, or methods): # Traceability: Calibrator: E. coli ATCC 8739 is used to as a calibrator. This organism is deposited with VITEK MS-CHCA matrix on positions: xA1, xB1, xC1, of the VITEK MS-DS target slides depending on the number of samples tested (one calibrator per acquisition group of 16 spots). The VITEK MS goes to the calibration spot in an acquisition group and performs a calibration. If the calibration passes, the instrument goes to the first spot in the acquisition group. If the calibration fails, an error is reported and VITEK MS proceeds to the next acquisition group without collecting sample spectra. After spectra have been acquired from each sample spot in an acquisition group, the calibration spot is checked again. The calibration sample should provide E. coli identification at $99.9\%$ in Myla ${}^{\mathrm{TM}}$ software. # Stability VITEK MS MYCOBACTERIUM/NOCARDIA KIT: 12 months (365 days) shelf life for VITEK -MS Mycobacterium/Nocardia IVD Ref: 415659, when stored at $2 - 25^{\circ}\mathrm{C}$ . VITEK MS MOULD KIT: 12 months (365 days) shelf life for VITEK MS MOULD KIT IVD Re:.415680, when stored at $2 - 25^{\circ}\mathrm{C}$ . Summary: Conditions and Days Post Extraction-Prior to Spotting* | Genus | Condition | Recommended | | --- | --- | --- | | Mycobacterium | Room Temperature (15-25°C) | 3 Days | | | Refrigerated (2 8°C) | 7 Days | | | Frozen (-19 to -31°C) | 14 Days | | | Freeze-Thaw cycles | 2 Freeze-thaw | | Nocardia | Room Temperature (15-25°C) | 3 Days | | | Refrigerated (2-8°C) | 7 Days | | | Frozen (-19 to -31°C) | 21 Days | | | Freeze-Thaw cycles | 3 Freeze-thaw | | Moulds | The extracts of moulds are not stable regardless of the storage conditions and must be spotted within 8 hours on the day of extraction. | | *For details see M.1.h-1 and M.1.o-s below. # Controls During the reproducibility, proficiency and clinical isolate testing, three organisms were used for positive quality control, with reagents alone used for the negative control. Quality control organism were tested by VITEK MS each day a mold, {15} mycobacterium or nocardia isolate was tested. The quality control strains were as follows: Aspergillus brasiliensis, ATCC 16404 Mycobacterium smegmatis, ATCC 19420 Nocardia farcinica, ATCC 3308 Negative Control (reagents alone) Table 3: Number and Percent of Repeat QC Testing | QC Species | N | 1 Repeat (Percent) | 2 Repeats (Percent) | | --- | --- | --- | --- | | Aspergillus brasiliensis | 162 | 19 (11.73%) | 11 (6.79%) | | Mycobacterium smegmatis | 189 | 11 (5.82%) | 1 (0.53%) | | Nocardia farcinica | 113 | 5 (4.42%) | 1 (0.88%) | | Neg control (reagents alone) | 391 | 0 (0.00%) | 0 (0.00%) | | Total | 855 | 35 (4.09%) | 13 (1.52%) | d. Detection limit: See DEN130013 (K124067) e. Biological Performance Equivalency Study Summary Report VITEK MS v2.2 vs VITEK MS v3 Biological performance equivalency was demonstrated for the 193 FDA originally claimed species using one well characterized strain per species, i.e. type or sequenced was sub-cultured on solid media and tested triplicate (from three separate subcultures) on the same slide after 18h to 24h of growth. In total, 627 distinct samples representing the 193 FDA claimed species were tested with both VITEK MS systems (V2.2 and V3.0) during the equivalency testing included: - Gram negative Bacteria: 333 samples (111 strains x 3 replicates) - Gram positive bacteria: 204 samples (68 strains x 3 replicates) - Yeasts: 90 samples (30 strains x 3 replicates) The global biological performance calculated from 627 samples (209 strains x 3 replicate) tested during this study (for each VITEK MS systems) is presented in Table 4 below. No calibration spot failures were observed with either VITEK MS system. The rate of overall correct identification rate is $94.3\%$ (591/627) from VITEK MS V2.2 and $97.3\%$ (610/627) from VITEK MS V3.0. TABLE 4: Biological Performance Equivalency Study* {16} | All families (after re-test) | | | | | | | | | | | | | | | | | | | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | VITEK MS V3.0 vs VITEK MS V2.2 | Failure | | | | | | | | | Success | | | | | | | | Total (ALL) | | | Miskidentification | | | No Identification | | | | Total (ALL) | Combined Correct Identification | | | | | | Total (ALL) | | | | | | LD Incorrect ID | | SC Incorrect ID | LD Multiple Genera | | No Matching Class | | | | LD Correct ID | | LD Same Genus | | SC Correct ID | | | | | | | N | % | N | % | N | % | N | % | N | % | N | % | N | % | N | % | N | % | | VITEK MS V2.2 | 1 | 0.16 | 4 | 0.64 | 7 | 1.12 | 24 | 3.83 | 36 | 5.74 | 25 | 3.99 | 30 | 4.78 | 536 | 85.49 | 591 | 94.26 | | VITEK MS V3.0 | 2 | 0.32 | 5 | 0.8 | . | . | 10 | 1.59 | 17 | 2.71 | 29 | 4.63 | 15 | 2.39 | 566 | 90.27 | 610 | 97.29 | *Abbreviations: Low discrimination (LD); Single choice (SC) The McNemar's test, applied on a 2x2 contingency table (Failure vs. Success) was used to attest the equivalency of both systems. In this test, the null hypothesis $(\mathrm{H}_0)$ is that the two proportions of success (PV3.0 and PV2.2) are at the same rate (PV3.0 = PV2.2) or that the contingency 2x2 table is symmetric. | Total (All families) | | | | | | | | --- | --- | --- | --- | --- | --- | --- | | | 2x2 table for global status | | | | McNemar's Test | | | | | VITEK MS V2.2 | | | Statistic (S) | 7.367 | | | | Failure | Success | Total | DF | 1 | | VITEK MS V3.0 | Failure | 2 | 15 | 17 | Pr > S | 0.007 | | | | 0.32 | 2.39 | 2.71 | | | | | Success | 34 | 576 | 610 | | | | | | 5.42 | 91.87 | 97.29 | | | | | Total | 36 | 591 | 627 | | | | | | 5.74 | 94.26 | 100.00 | | | The McNemar test resulted in the rejection the hypothesis of equivalency between both systems (p-value $< 5\%$ ). VITEK MS V3.0 (97.3% of success) produces better global performance than VITEK MS V2.2 (93.8% of success). The McNemar's test was also applied to Gram Negative, Gram Positive and Yeast groups. It was concluded that for gram negative organisms and yeast, VITEK MS V3.0 performed as good as VITEK MS V2.2 on this set of data. For Gram positive organisms, the VITEK MS V3.0 system gave higher performance than VITEK MS V2.2 on this set of data. With the new acquisition station (new system), the instrument was fine-tuned in order to produce 20 more peaks (in average). A Bland-Altman scatter-plot was built for all the samples for which provided a correct identification from both VITEK MS systems, in order to measure the average bias observed between both systems during this study. For each couple of values (number of peaks V3.0, number of peaks V2.2), the average was calculated and reported on the X-axis, and then the difference between the number of peaks from V3.0 and the number of peaks from V.2.2 was calculated and reported on the Y-axis. (Plot not shown.) The average was 19.76 peaks, which is very close to the expected value (20 peaks). All the individual observations were well distributed over and under the mean. {17} Due to update in the database (KB V3.0 0), the following bacterial identification notes have been placed: - In KB V3.0.0, *Aeromonas sobria* is displayed as a low discrimination result with *Aeromonas veronii* but only *Aeromonas sobria* has been clinically validated. *Aeromonas sobria*, has a high level of unidentified results - In KB V3.0.0, *Bacteroides ovatus* is grouped in a slashline with *Bacteroides xylanisolvens*. It is not possible to distinguish between the two species. *B. ovatus* is more commonly associated with human infection. - In KB V3.0.0, *Lactococcus lactis* ssp lactis is integrated in a new group *Lactococcus lactis* (with two other subspecies *Lactococcus lactis* ssp cremoris and *Lactococcus lactis* ssp hordniae). In the *Lactococcus lactis* group, only subspecies *Lactococcus lactis* ssp lactis has been clinically validated. - In KB V3.0.0, *Neisseria mucosa* is grouped in a slashline with *Neisseria sicca*. It is not possible to distinguish between the two species. Both species have been associated with human infection. - In KB V3.0.0, *Staphylococcus hominis* ssp hominis is integrated in a new group *Staphylococcus hominis* (with another subspecies *S. hominis* ssp novobiosepticus). In the *Staphylococcus hominis* group, only subspecies *Staphylococcus hominis* ssp hominis has been clinically validated. - In KB V3.0.0, *Streptococcus salivarius* ssp salivarius is displayed as a low discrimination result with *Streptococcus salivarius* ssp thermophilus and *Streptococcus vestibularis* but only *Streptococcus salivarius* ssp salivarius has been clinically validated. f. Age of Culture for Mycobacteria grown on Solid Media for VITEK MS Testing A total of 734 spectra were generated through 12 testing time points from the original test panel (*M. abscessus*, *M. avium*, *M. chelonae*, *M. fortuitum*, *M. kansasii*, *M. intracellulare*, *M. scrofulaceum* and *M. tuberculosis*) and 80 additional spectra generated through 10 testing time points (Day 0 to 42 days, with Day 0 being the time sufficient growth of the culture was observed) with the additional testing of *M. smegmatis*, for a total of 814 spectra. Of those 814 spectra 42 did not pass quality control checks (number of peaks and amount of noise). Results demonstrated that the increasing age of cultures for mycobacteria species had an impact on the quality of spectra, number of peaks and correct identification results. Recommended testing for correct identification for testing mycobacteria was between 0-14 days of culture growth; with 0 days being the time sufficient growth of the culture was observed. g. Age of culture for Mycobacteria from Liquid Media for VITEK MS Testing The results of prolonged incubation (age of culture) on a positive liquid mycobacteria culture used for protein extraction and identification on the VITEK MS were evaluated. Positive liquid media mycobacteria cultures were held at $35 - 37^{\circ}\mathrm{C}$ for 0, 1, 2 and 3 days (0-24, 24-48, 48-72 and 72-96 hours) post positivity by the liquid media detection instrument. A total of 8 species (30 strains) were tested in each of the three 18 {18} automated liquid media systems (MGIT, VersaTREK, and MP). VITEK MS identification results were compared to the expected reference identification and percent identification was calculated per testing time point. Additionally, protein extracts prepared for age of culture testing were used to evaluate if the age of culture from liquid media has an impact on Time To result (TTR) for total acquisition time on the VITEK MS. A total of 358 samples were tested generating 716 spectra on the VITEK MS (119 MGIT, 119 VersaTREK and 120 MP samples). Overall, 90% correct identification was achieved through three days of testing when compared to the expected reference result. Day 0 testing in the MGIT system resulted in a high number of failed acquisition spots due to low biomass at time of positivity by the detection system. To mitigate the risk of low biomass at time of positivity especially in the MGIT system, it is recommended to incubate a positive sample for a minimum of 24 hours after positivity for all liquid media types. Although all mycobacteria species tested in this report had good performance through 96 hours of testing; to mitigate the risk of mycobacteria transitioning to a stationary growth phase and altering protein profiles, the maximum recommended incubation time post positivity is 72 hours. Assessment of spot to spot variation showed no improvement as biomass increased indicating this issue is independent of biomass. No correlation was observed between age of culture and TTR. Therefore, an increase in biomass will not improve TTR. h. Nocardia Age of Culture Study for VITEK MS Testing A set of 10 nocardia isolates were tested in duplicate at 3 time points (in hours): T24h, T48h, T72h on three different media (Columbia Blood Agar, Chocolate Agar with Polyvitex and Buffered Charcoal Yeast Agar). Results demonstrated the age of culture recommended for nocardia isolates for VITEK MS acquisition is from 24 to 72 hours. i. Mould Age of Culture Study for VITEK MS Testing Two hundred and sixty-seven organisms were inoculated onto different media according to their growth requirements and incubated in appropriate conditions. Two growth times were tested per mould isolate according to their speed of growth (i.e., 2 and 8 days for rapid-growing, 5 and 10 days for medium growers and 10 and >=15 days for slow-growing organisms). 2040 spectra from 267 distinct strains, representative of 53 moulds species from 14 genera using a variety of media were included in the study. Based on these results, the age of culture recommended for mould isolates for VITEK MS acquisition is from sufficient growth until ~5 days after sufficient growth. j. Impact of Mixed Cultures on VITEK MS ID of Mycobacteria and Nocardia From Solid Media To evaluate the impact of mixed cultures on the identification of mycobacteria and 19 {19} nocardia using VITEK MS, Four mycobacteria and two nocardia were grown on solid media and protein extracts were prepared following the instructions for VITEK MS MYCOBACTERIUM/ NOCARDIA KIT. Non-diluted protein extracts (High Positive Sample and Moderate Positive Sample) were tested from each organism as well as in mixed combinations. While the spectra profiles generated from mixed protein extracts did not produce incorrect identifications, the algorithm could not consistently distinguish when two organisms were present in the sample with low discrimination. In over half of the combinations tested the High Positive Sample type outcompeted the Moderate Positive Sample type resulting in a single choice identification of the High Positive Sample. As a result pure cultures should always be used for protein extraction to obtain a sample identification on the VITEK MS. k. Impact of Mixed cultures on ID of Mycobacteria From Liquid Media For each organism combination tested (see Table 4 below), BacT/ALERT MP culture bottles were inoculated with the mixed culture and tested. Table 4: Test Organism Combinations | Combination | Organism 1 | Organism 2 | | --- | --- | --- | | 1 | M.fortuitum | M. smegmatis | | 2 | M.tuberculosis | M. lentiflavum | | 3 | Nocardia asteroids | M. fortuitum | | 4 | Staphylococcus aureus | M. smegmatis | | 5 | C.albicans | M. intracelluare | | 6 | P.aeruginosa | N. asteroides | Out of the 24 spectra generated for mixed cultures, 22 resulted in single choice identification of one of the two species present. The other two spectra generated 'Not Enough Peaks' and 'Low Discrimination' calls. Testing of pure cultures is recommended. l. Impact of Mixed Cultures on Mould ID Five molds, representative of clinically prevalent classes, were grown at $30^{\circ}\mathrm{C}$ on Sabouraud Dextrose Agar, extracted and tested in combinations of high and moderate concentrations. Each combination was tested in quadruplicate. The eight mixes were always identified to at least one of the two species or both species present in the mix. Testing of pure cultures is recommended. m. Mycobacteria Carry Over and Cross Contamination Study The potential for carry over and cross contamination of protein extracts when testing mycobacteria on the VITEK MS was evaluated. Five mycobacteria species were grown on solid medium and protein extracts were prepared following manufactures instructions for VITEK MS MYCOBACTERIUM/NOCARDIA KIT. High Positive, Moderate Positive, and Negative samples were spotted in an alternating fashion in order to assess the carry over and cross contamination. All negative samples tested resulted in 'No Identification' on the VITEK MS. indicating no carry over or cross {20} contamination was observed during this study. All High and Moderate Positive samples provided the expected results. n. Mould and Nocardia Carry Over and Cross Contamination Study Six moulds and six nocardia were grown on solid medium and protein extracts were prepared following manufactures instructions. High Positive, Moderate Positive, and Negative samples were spotted in an alternating fashion in order to assess the carry over and cross contamination. All negative samples tested resulted in No Identification on the VITEK MS. indicating no carry over or cross contamination was observed during this study. All High and Moderate Positive samples provided the expected results. o. Protein Stability for Mycobacteria and Nocardia Solid Media Extractions The stability of protein extracts of mycobacteria and nocardia prior to spotting on VITEK MS DS target slides was evaluated. The stability of a protein extract was defined as acceptable storage temperature and time after the extraction from the respective culture. Two solid media types were used for mycobacteria and one solid medium type for Nocardia species. Three extracts per organism and per media type were prepared. Protein extracts were held at refrigerated (2 - 8°C), frozen (-19 to -31°C), and room temperatures (15 - 25°C). Protein extracts were tested at different time points ranging from 0 to 21 days post extraction. Additionally, freeze-thaw cycles were also tested to determine if freezing and thawing the extracts would degrade protein extracts. Based on the data generated from this study, the preferred holding temperature and time is frozen (-19 to -31°C) up to 14 days for both mycobacteria and Nocardia species. At other temperatures, the protein extracts tend to evaporate and become difficult to obtain the sufficient volume required for spotting on VITEK MS DS target slides leading to inconsistent identification. Freeze-thaw cycle results indicate that mycobacteria and nocardia samples are stable for up to two freeze-thaw cycles. p. Protein Stability for Mycobacteria from Liquid Media Extractions The stability of protein extracts of mycobacteria from liquid medium prior to spotting on VITEK MS DS target slides was evaluated. The stability of a protein extract was defined as acceptable storage temperature and time after the extraction from the respective culture. BacT/ALERT® MP bottles (MP) and BACTEC MGIT™ 960 tubes (MGIT) were evaluated in the study. Four extracts per organism and per media type were prepared. Protein extracts were held at room temperature (15°C to 25°C), refrigerated (2°C to 8°C), and frozen (-19°C to -31°C). Protein extracts were tested at different time points ranging from 0 to 21 days post extraction. Additionally, freeze-thaw cycles were also tested to determine if freezing and thawing the extracts would degrade protein extracts. 21 {21} Based on the data generated from this study, the extract was determined to be stable when frozen (-19 to -31°C) for up to 21 days. At refrigerated and room temperature, samples remained stable for at least 36 hours but sample degradation caused a reduced rate of correct identifications by day 3. Based on the results of this study, it was recommended to test protein extracts on the same day of the extraction; however if this is not possible, it is recommended to stay consistent with extract stability recommendation for solid media mycobacterium and solid media nocardia. As such, mycobacterium protein extracts from liquid medium can be stored at frozen temperatures (-19 to -31°C) up to 14 days. Frozen extracts can be used up to two freeze thaw cycles for consistent identification results. q. Stability of Moulds Extracts Initially, a set of 10 molds were tested at 0,1,3,7,14, and 21 days post extraction using 3 storage temperatures: Room Temperature (RT): 15 - 25°C; refrigerated: 2 - 8°C; frozen: -19 to -31°C. Four freeze-thaw cycles were also performed for each mould extract. An additional set of eight molds was tested at the frozen storage temperature after obtaining inconsistent results on the first set of 10 strains. The freeze-thaw cycles experiment was performed on 18 strains that were kept in the freezer. It was determined that the extracts were not stable after one day at RT or refrigerated. Higher mould identification rates were obtained when the extracts are frozen, but the results were inconsistent and varied depending on the species and strains tested even after multiple testing on an extensive dataset. The extracts were also not stable after one freeze-thaw cycle. Therefore, it was concluded that the extracts of molds are not stable regardless of the storage conditions and must be spotted within 8 hours on the day of extraction. The package insert indicates to spot 1 μL of the supernatant immediately on a target slide. r. Stability of Extract Deposits of Moulds, Nocardia, and Mycobacteria A study was performed to determine the stability of the mycobacteria, nocardia and mould deposits on the target slide after matrix addition and before spectra acquisition. It is recommended that data acquisition be performed at a maximum of 3 days after matrix addition. s. Stability of Extract Deposits of Mycobacterium from Liquid Media The stability of mycobacteria protein extracts from liquid media deposited on a target slide with the addition of CHCA matrix was determined. Mycobacteria species were grown in different automated liquid media systems and protein extracts were prepared manufacturer's instructions. Target slides were left at room temperature in original packaging and sample acquisition of protein extracts occurred initially and every day for up to four days. Identification results of protein deposits were compared to initial 22 {22} results to assess the effects of prolonged acquisition. Overall, 90% correct identification when compared to the expected reference results was achieved through four days of testing. An increase in failed acquisition spots was observed at T4 and average peaks counts decreased from T0 - T4. Therefore, recommended storage for prepared target slides will be up to 3 days at room temperature in the original packaging. t. VITEK MS Liquid Media Interfering Substances The potential for sputum digestion/decontamination reagents and/or liquid media components to cause an interference on the VITEK MS and/or impact identification of mycobacteria protein extracts on the VITEK MS was evaluated. Mycobacteria species were grown in automated liquid media detection systems and protein extracts were prepared per manufacturer's instructions. Interference was tested using negative and positive samples with and without growth (GS) and antimicrobial (AS) supplements testeq in combination with sputum processing reagents N-acetyl-L-cysteine (NALC)- sodium hydroxide (NaOH) (NALC-NaOH). Impact on identification was tested using VersaTRE K® Myco bottles and BBL™ MGIT™ 960 tubes inoculated with patient samples processed with NALC-NaOH sputum digestion/decontamination method. Samples inoculated into VersaTREK bottles were freshly processed (never frozen). For MGIT tubes frozen processed sputum samples exposed to one or more freeze thaw cycles were used. All positive samples tested resulted in correct species level identification and all negative samples resulted in 'No Identification' due to 'Not Enough Peaks'. Results indicate that if the protocol is followed as designed, neither sputum digestion/decontamination nor liquid media components cause an interference on the VITEK MS. Identification results for samples tested in VersaTREK bottles met acceptance criteria of 90% correct identification indicating no impact on identification when using fresh (never frozen) sputum samples. Samples tested from MGIT tubes resulted in a high number of 'No Identification' results and did not meet the acceptance criteria. Upon further investigation, results indicated using frozen processed sputum samples inoculated in liquid media and then used for identification impacts identification. It is recommended to use the fresh processed sputum sample and not to use a frozen processed sputum sample as an inoculation source for liquid media to minimize the risk of 'No identification' on the VITEK MS. u. Verification of Inactivation and Extraction of Mycobacteria from Liquid Media This study was performed to verify the modifications selected for improving the robustness of mycobacteria liquid media extraction workflow. The combination of sample processing between 24-72 hour post positivity, 3 ml sample volume, and use of the 5 ml tube improved the identification success for all liquid media types. 23 {23} This study included eight (8) clinically prevalent Mycobacterium species from different automated liquid media systems including BacT/ALERT® MP bottles (MP), BACTEC™ MGIT™ 960 tubes (MGIT), and VersaTREK® Myco bottles (VersaTREK) on the VITEK MS. Testing 24-48 hours post positivity performed above 90% correct species level identification and met the acceptance criterion; however some spectra failed original quality checks (Not Enough Peaks, Too Many Peaks) and either had to be re-spotted (same extract) or re-extracted from a new culture. Testing at 48-72 hours post positivity improved identification success resulting in no final results of No ID or sample re- extractions. None of the spectra failed initial quality checks. The recommended window for testing mycobacterium from liquid medium is 24-72 hours post instrument declaring bottle/tube positive. If spectral quality checks do not pass (Not Enough Peaks, Too Many Peaks) or No Identification is resulted on the original deposit, it is recommended to re-spot from the same extract. If spectral checks still do not pass, it is recommended that the sample be re-extracted if the bottle/tube is still within 24-72 hour window. v. Validation of Inactivation of Mycobacterium and Nocardia from solid media The sample preparation of mycobacteria and nocardia requires additional steps as compared to the standard procedure due to their infectious nature. It is important to inactivate the cultures to make the samples safe for handling outside of a Biosafety Level-3 (BSL-3/P3) environment. Several studies were conducted for establishing a protocol for inactivation of mycobacteria and nocardia for VITEK MS. Inactivation studies were performed on solid media (LJ, 7H11 and TSB agar plates) with various species of mycobacteria and nocardia including drug sensitive and resistant strains of M. tuberculosis. The optimal inactivation was obtained by five minutes mechanical disruption with bead beating in ethanol using glass beads in a pre-sterile tube. This step breaks up clumps of cells allowing the ethanol to come in contact with all cells, as well as disrupting the thick waxy mycobacterial cell walls. The sample tube is then incubated at room temperature for 10 minutes in order to allow the ethanol to inactivate all cells. After inactivation, the suspension is transferred into another tube and centrifuged to create a pellet of the cell matter and the ethanol supernatant is discarded. w. Validation of Inactivation of Moulds The inactivation step was verified with 16 mould species among 12 different genera. Following manufacturer extraction instructions, it was found that the inactivation is effective after the second centrifugation step using 70% formic acid and 100% acetonitrile addition. The first step using 70% ethanol is not sufficient to allow a complete inactivation of the sample. 24 {24} The inactivation was verified after the second step of centrifugation by mixing the supernatant and the pellet. A 10 ul sample of this suspension was subcultured on Sabouraud Dextrose Agar plate and incubated from 8 days to 8 weeks depending on the tested strains. Tests were performed at two different colony ages or at least using the older culture in order to work on conidia/spores representing the more resistant stage. No growth was demonstrated after the incubation period. x. Identification of Mycobacterium spp. from BacT ALERT MP Using Simulated Sputum Processing This study was designed to demonstrate the ability of the VITEK MS to generate spectra from simulated clinical samples inoculated into liquid media and identify mycobacteria at the species level. Simulated sputum was spiked with mycobacteria and contaminating respiratory flora organisms and underwent sputum processing prior to inoculation into BacT/ALERT® MP bottles. Out of a test panel including 20 species and 77 strains, at total of 385 spectra were collected. Overall results were 99.7% correct identification (excluding no identification results) and 1.0% no identification. Based on the results of this study, the VITEK MS system performs acceptably when analyzing simulated clinical samples from BacT/ALERT® MP bottles. y. Reproducibility for Mycobacteria from Liquid Media Summary Report This study examined the reproducibility of mycobacterium identifications on the VITEK MS system from liquid media. A panel of representative mycobacteria species were grown in three different liquid media detection systems over five days on VITEK MS instruments at two different sites with multiple operators. Mycobacteria species were grown in BacT/ALERT® MP (MP) bottles at Site 1 and both BBL MGIT™ 960 tubes (MGIT) and VersaTREK™ Myco bottles (Versa Trek) at Site 2. On each day of testing, two extracts from positive liquid samples were performed for each species tested. Each technologist prepared two (2) slides per day of testing, one from each extract. Extracts were deposited in sequential order on one slide and in randomized order on the second slide for each day of testing. Extracts were prepared following manufacturer's instructions for VITEK MS MYCOBACTERIUM/NOCARDIA KIT. The organism-specific and overall rates of correct identification results for both sites combined are ≥95%. The confidence intervals for the organism specific and overall rates of correct identification contain 95%. z. Analytical specificity: 25 {25} Also see DEN130013 / K124067 Rhodococcus, Tsukamurella, Streptomyces, Segniliparus, Williamsia Study: In this study, a panel of 14 strains (including two to three representative strains of each genus) were tested with VITEK MS V3. These strains were tested in parallel using the extraction protocol and direct deposit. When tested with the extraction protocol, none of the 14 strains were identified as a mycobacteria or nocardia, which was in agreement with the acceptance criterion. When tested by direct deposit, only one strain (Segniliparus rugosus) of the 14 strains was identified as Mycobacterium szulgai. The remaining 13 strains were not identified as a mycobacterium or nocardia. A note was added to the user manual indicated that a result of mycobacteria obtained by direct deposit should be confirmed by retesting the strain using the extraction kit. When considering both approaches together (direct deposit and extraction), the panel of 14 strains representing Rhodococcus, Tsukamurella, Streptomyces, Segniliparus and Williamsia genus were not identified as a mycobacteria or nocardia. Additional exclusivity testing was performed for Actinomadura, Amycolatopsis and Nocardia species extracts (one per strain). All were prepared following manufacturer instructions for nocardia colonies. Each extract is spotted in triplicate on the VITEK MS slide. Results are found in Tables 5 and 6 below. TABLE 5: Actinomadura and Amycolatopsis species tested;VITEK MS result 'No Identification' | Reference Result | # No ID | # tests | # isolates | | --- | --- | --- | --- | | Actinomadura chibensis | 3 | 3 | 1 | | Actinomadura cremea | 3 | 3 | 1 | | Actinomadura latina | 3 | 3 | 1 | | Actinomadura vinacea | 2 | 3 | 1 | | Amycolatopsis benzoatilytica | 3 | 3 | 1 | | Amycolatopsis orientalis ssp orientalis | 3 | 3 | 1 | | Amycolatopsis palatopharyngis | 3 | 3 | 1 | TABLE 6: Nocardia species tested; VITEK MS result 'No Identification' | Reference Result | # No ID | # tests | # isolates | | --- | --- | --- | --- | | Nocardia anaemiae | 3 | 3 | 1 | | Nocardia arthritidis | 5 | 6 | 6 | | Nocardia asiatica | 1 | 5 | 5 | | Nocardia carnae | 3 | 3 | 1 | | Nocardia concava | 3 | 3 | 1 | {26} | Reference Result | # No ID | # tests | # isolates | | --- | --- | --- | --- | | Nocardia corynebacterioides = Rhodococcus corynebacterioides | 3 | 3 | 1 | | Nocardia exalbida | 3 | 3 | 1 | | Nocardia gamkensis1 | 2 | 5 | 1 | | Nocardia higoensis | 1 | 3 | 1 | | Nocardia ignorata | 3 | 3 | 1 | | Nocardia inohanensis | 3 | 3 | 1 | | Nocardia niigatensis | 3 | 3 | 1 | | Nocardia ninae | 3 | 3 | 1 | | Nocardia jiangxiensis | 3 | 3 | 1 | | Nocardia mexicana | 1 | 1 | 1 | | Nocardia niwae | 3 | 3 | 1 | | Nocardia pneumoniae | 3 | 3 | 1 | | Nocardia puris | 3 | 3 | 1 | | Nocardia rhamnosiphila | 2 | 2 | 2 | | Nocardia sienata1 | 3 | 6 | 1 | | Nocardia takedensis | 3 | 3 | 1 | | Nocardia terpenica | 3 | 3 | 1 | | Nocardia testacea | 1 | 1 | 1 | | Nocardia thailandica | 3 | 3 | 1 | | Nocardia vermiculata | 3 | 3 | 1 | | Nocardia vinacea | 3 | 3 | 1 | | Nocardia yamanashiensis | 3 | 3 | 1 | | Nocardia flavorosea | 3 | 3 | 1 | | Nocardia gamkensis | 2 | 6 | 1 | | Nocardia brevicatena | 10 | 10 | 1 | 1 = Also see Table 9: Cross-identification of Clinically Validated Taxa and Unclaimed Taxa The following mycobacteria were tested and provided no identification with the VITEK MS V3.0 Knowledge Base. Results are summarized in Table 7 below. {27} TABLE 7: Mycobacteria species tested; VITEK MS result 'No Identification' | Reference Result | # No ID | # tests | # isolates | | --- | --- | --- | --- | | M. bouchedurhonense/colombiense | 3 | 3 | 3 | | M. bouchedurhonense/colombiense/vulneris | 1 | 1 | 1 | | M. chimaera1 | 1 | 24 | 16 | | M. colombiense/ yongonense/marseillense | 1 | 1 | 1 | | M. gordonae/paragordonae2 | 1 | 2 | 1 | | M. paraense | 1 | 1 | 1 | | M. paraffinicum1 | 7 | 9 | 9 | | M. parascrofulaceum1 | 1 | 2 | 2 | | M. phocaicum1 | 1 | 21 | 21 | | M. shigaense | 3 | 3 | 3 | | M. yongonense/marseillense1 | 2 | 21 | 13 | 1 = Also see Table 9: Cross-identification of Clinically Validated Taxa and Unclaimed Taxa TABLE 8: Moulds tested; VITEK MS result 'No Identification' | Reference Result | # No ID | # tests | # isolates | | --- | --- | --- | --- | | Alternaria infectoria | 3 | 3 | 1 | | Aspergillus aculeatus | 1 | 1 | 1 | | Aspergillus alabamensis | 1 | 1 | 1 | | Aspergillus brevipes | 3 | 3 | 1 | | Aspergillus creber | 2 | 2 | 2 | | Aspergillus fumigatiaffinis | 3 | 3 | 1 | | Aspergillus glaucus | 3 | 3 | 1 | | Aspergillus jensenii | 5 | 5 | 5 | | Aspergillus niveus | 1 | 1 | 1 | | Aspergillus nomius1 | 1 | 2 | 2 | | Aspergillus ochraceus | 19 | 19 | 4 | | Aspergillus sclerotiorum | 3 | 3 | 1 | | Aspergillus section Usti | 1 | 1 | 1 | | Aspergillus striatus / Aspergillus cleistominutus | 1 | 1 | 1 | {28} | Reference Result | # No ID | # tests | # isolates | | --- | --- | --- | --- | | Aspergillus tabacinus | 1 | 1 | 1 | | Aspergillus tamarii | 1 | 1 | 1 | | Aureobasidium pullulans | 19 | 19 | 4 | | Byssochlamys nivea | 21 | 22 | 3 | | Cladophialophora carrionii | 1 | 1 | 1 | | Cladophialophora minourae | 2 | 2 | 2 | | Cladosporium cladosporioides | 1 | 1 | 1 | | Cladosporium halotolerans | 1 | 1 | 1 | | Cladosporium herbarum | 62 | 65 | 10 | | Cladosporium macrocarpum | 3 | 3 | 1 | | Cladosporium oxysporum | 11 | 38 | 4 | | Cladosporium sphaerospermum | 20 | 20 | 4 | | Coprinellus xanthothrix | 1 | 1 | 1 | | Curvularia aeria | 1 | 1 | 1 | | Curvularia hominis | 2 | 2 | 2 | | Curvularia lunata^{1} | 1 | 2 | 2 | | Curvularia pseudolunata^{1} | 2 | 3 | 3 | | Exophiala bergeri | 1 | 1 | 1 | | Exophiala oligosperma | 1 | 1 | 1 | | Fusarium brachygibbosum | 1 | 1 | 1 | | Fusarium dimerum | 2 | 2 | 2 | | Fusarium falciforme^{1} | 1 | 3 | 3 | | Fusarium formosus | 2 | 2 | 2 | | Fusarium incarnatum-equiseti species complex | 1 | 2 | 2 | | Fusarium lactis | 1 | 1 | 1 | | Fusarium lichenicola^{1} | 1 | 2 | 2 | | Fusarium fujikuroi spp. complex | 1 | 1 | 1 | | Fusarium keratoplasticum^{1} | 1 | 3 | 1 | | Fusarium oxysporum f.sp. lypopersici^{1} | 2 | 2 | 1 | | Fusarium sublutinans | 1 | 1 | 1 | {29} | Reference Result | # No ID | # tests | # isolates | | --- | --- | --- | --- | | Fusarium verticillioides | 1 | 1 | 1 | | Lecythophora canina | 3 | 3 | 1 | | Lecythophora lignicola | 3 | 3 | 1 | | Lecythophora mutabilis | 3 | 3 | 1 | | Leptosphaerulina chartarum | 68 | 68 | 10 | | Lichtheimia ramosa | 3 | 3 | 3 | | Lichtheimia ramosa vs corymbifera | 2 | 2 | 2 | | Mucor circinelloides | 1 | 1 | 1 | | Mucor plumbeus | 1 | 1 | 1 | | Mucor racemosus f. sphaerosporus | 5 | 5 | 1 | | Neosartorya fisheri1 | 4 | 8 | 1 | | Neosartorya pseudofisheri1 | 25 | 34 | 6 | | Paecilomyces brunneolus | 1 | 1 | 1 | | Paecilomyces formosus | 2 | 2 | 2 | | Paecilomyces fulvus | 13 | 13 | 2 | | Penicillium commune | 18 | 28 | 3 | | Penicillium copticola | 1 | 1 | 1 | | Penicillium crustosum | 2 | 2 | 2 | | Penicillium decumbens | 1 | 1 | 1 | | Penicillium glabrum | 35 | 35 | 31 | | Penicillium janthinellum | 1 | 1 | 1 | | Penicillium marneffei | 4 | 4 | 1 | | Penicillium paneum | 1 | 1 | 1 | | Penicillium polonicum | 1 | 1 | 1 | | Penicillium sizovae | 1 | 1 | 1 | | Rasamsonia aegroticola | 2 | 2 | 1 | | Rhinocladiella similis | 1 | 1 | 1 | | Rhizomucor pusillus | 3 | 3 | 1 | | Rhizomucor miehei | 3 | 3 | 1 | | Rhizopus chinensis | 1 | 1 | 1 | | Rhamnus niger | 1 | 1 | 1 | | Rhamnus niger niger | 1 | 1 | 1 | | Rhamnus niger niger niger | 1 | 1 | 1 | | Rhamnus niger niger niger | 1 | 1 | 1 | | Rhamnus niger niger niger | 1 | 1 | 1 | | Rhamnus niger niger | 1 | 1 | 1 | | Rhamnus niger niger | 1 | 1 | 1 | {30} | Reference Result | # No ID | # tests | # isolates | | --- | --- | --- | --- | | Rhizopus oligosporus | 1 | 1 | 1 | | Rhizopus rhizopodiformis | 1 | 1 | 1 | | Sarocladium bifurcatum | 1 | 1 | 1 | | Scopulariopsis brevicaulis | 9 | 9 | 3 | | Sporothrix albicans | 2 | 2 | 1 | | Sporothrix mexicana | 2 | 2 | 1 | | Stachybotrys chartarum | 7 | 9 | 1 | | Trichoderma atroviride | 26 | 28 | 4 | | Trichoderma longbrachiatum | 21 | 21 | 4 | | Trichophyton concentricum | 3 | 3 | 1 | | Trichophyton ferrugineum | 3 | 3 | 1 | | Trichophyton schoenleinii | 3 | 3 | 1 | | Wallemia sebi | 45 | 45 | 7 | 1 = Also see Table 9: Cross-identification of Clinically Validated Taxa and Unclaimed Taxa TABLE 9: Cross-identification of VITEK MS claimed displayed taxa and Unclaimed Taxa | Clinical Claimed Displayed Taxon | Reference ID of Unclaimed Taxa | # cross-ID | # tests | # isolates | | --- | --- | --- | --- | --- | | Aspergillus calidoustus | Aspergillus ustus | * | * | * | | Aspergillus flavus / oryzae | Aspergillus nomius | 1 | 1 | 1 | | | Neosartorya pseudofischeri | 1 | 34 | 6 | | Aspergillus fumigatus | Neosartorya fischeri | 3 | 8 | 1 | | | Neosartorya pseudofischeri | 7 | 34 | 6 | | Aspergillus lentulus | Neosartorya fischeri | 3 | 8 | 1 | | | Neosartorya pseudofischeri | 3 | 34 | 6 | | Aspergillus nidulans | Aspergillus delacrozii | 3 | 3 | 3 | | | Aspergillus quadrilineatus | 3 | 3 | 3 | | | Emericella variecolor | 1 | 1 | 1 | | Aspergillus niger complex | Aspergillus tubingensis | 1 | 1 | 1 | | | Aspergillus awamori | 10 | 10 | 10 | | | Aspergillus foetidus | 1 | 1 | 1 | | Aspergillus terreus complex | Aspergillus hortae | 1 | 1 | 1 | | Aspergillus versicolor | Aspergillus amoenus | 2 | 2 | 2 | | | Aspergillus fructus | 1 | 1 | 1 | | Curvularia hawaiiensis | Curvularia lunata | 6 | 11 | 1 | | | Curvularia senegalensis | 1 | 1 | 1 | | Curvularia spicifera | Curvularia lunata | 7 | 12 | 2 | | | Curvularia pseudolunata | 1 | 1 | 1 | {31} | Clinical Claimed Displayed Taxon | Reference ID of Unclaimed Taxa | # cross-ID | # tests | # isolates | | --- | --- | --- | --- | --- | | Fusarium oxysporum complex | Fusarium nygamai | 1 | 1 | 1 | | | Fusarium oxysporum f.sp. radicis-lycopersici | 2 | 2 | 1 | | Fusarium proliferatum | Fusarium fujikuroi | 2 | 2 | 2 | | Fusarium solani complex | Fusarium falciforme Fusarium keratoplasticum Fusarium lichenicola | 2 | 3 | 3 | | | Fusarium petroliphilum | 2 | 3 | 1 | | | | 1 | 2 | 2 | | | | 4 | 4 | 4 | | Mycobacterium abscessus | Mycobacterium abscessus ssp. abscessus | 34 | 34 | 34 | | | Mycobacterium abscessus ssp. bollettii | 3 | 3 | 1 | | | Mycobacterium abscessus ssp. massiliense | 5 | 5 | 3 | | | | | | | | Mycobacterium avium | Mycobacterium avium ssp. avium | 3 | 3 | 1 | | | Mycobacterium avium ssp. paratuberculosis | 3 | 3 | 1 | | | Mycobacterium avium ssp. silvaticum | 3 | 3 | 1 | | | Mycobacterium chimaera | 3 | 24 | 16 | | Mycobacterium gordonae | Mycobacterium paragordonae | 1 | 1 | 1 | | Mycobacterium intracellulare | Mycobacterium chimaera | 20 | 24 | 16 | | | Mycobacterium colombiense | 3 | 3 | 2 | | | Mycobacterium yongonense/marseillense | 19 | 21 | 13 | | | Mycobacterium yongonense/marseillense/vulneris | 1 | 1 | 1 | | Mycobacterium marinum | Mycobacterium ulcerans | 3 | 3 | 1 | | Mycobacterium mucogenicum | Mycobacterium phocaicum | 20 | 21 | 21 | | Mycobacterium scrofulaceum | Mycobacterium paraffinicum | 2 | 9 | 9 | | | Mycobacterium paragordonae | 1 | 1 | 1 | | | Mycobacterium parascrofulaceum | 1 | 2 | 2 | | Mycobacterium simiae | Mycobacterium palustre | 3 | 3 | 2 | | Mycobacterium tuberculosis complex | Mycobacterium pinnipedii | 2 | 2 | 1 | | Nocardia abscessus | Nocardia asiatica | 2 | 2 | 2 | | Nocardia africana1 | Nocardia aobensis | 3 | 3 | 1 | | | Nocardia cerradoensis | 3 | 3 | 1 | | Nocardia nova | Nocardia elegans | 2 | 2 | 2 | | | Nocardia kruczakiae | 1 | 1 | 1 | | Nocardia brasiliensis | Nocardia iowensis | 3 | 3 | 1 | | Nocardia longifolia | Nocardia longifolia | 2 | 2 | 2 | | Nocardia longipalpis | Nocardia longipalpis | 1 | 1 | 1 | | Nocardia longipalpis | Nocardia longipalpis | 1 | 1 | 1 | | Nocardia longipalpis | Nocardia longipalpis | 1 | 1 | 1 | | Nocardia longipalpis | Nocardia longipalpis | 1 | 1 | 1 | | Nocardia longipalpis | Nocardia longipalpis | 1 | 1 | 1 | | Nocardia longipalpis | Nocardia longipalpis | 1 | 1 | 1 | | Nocardia longipalpis | Nocardia longipalpis | 1 | 1 | 1 | | Nocardia longipalpis | Nocardia longipalpis | 1 | 1 | | {32} | Clinical Claimed Displayed Taxon | Reference ID of Unclaimed Taxa | # cross-ID | # tests | # isolates | | --- | --- | --- | --- | --- | | | Nocardia vulneris | 1 | 1 | 1 | | Nocardia farcinica | Nocardia higoensis | 2 | 3 | 1 | | | Nocardia shimofusensis | 3 | 3 | 1 | | Nocardia paucivorans | Nocardia sienata | 1 | 6 | 1 | | Nocardia wallacei | Nocardia blacklockiae | 6 | 6 | 6 | | Penicillium chrysogenum | Penicillium rubens | 2 | 2 | 2 | | Rasamsonia argillacea complex | Rasamsonia piperina | 2 | 2 | 1 | | Sporothrix schenckii complex | Sporothrix brasiliensis | 2 | 2 | 1 | | | Sporothrix globosa | 1 | 1 | 1 | | | Sporothrix luriei | 2 | 2 | 1 | | Trichophyton interdigitale | Trichophyton mentagrophytes | 27 | 30 | 1 | $^{1}$ Nocardia nova is displayed as a low discrimination result with Nocardia africana but only Nocardia nova has been clinically validated TABLE 10: Cross-identification between VITEK MS claimed displayed taxa | Displayed Taxon | Reference ID | # cross-ID | # tests | # isolates | | --- | --- | --- | --- | --- | | Mycobacterium avium | Mycobacterium intracellulare | 1 | 70 | 43 | | Mycobacterium intracellulare | Mycobacterium avium | 2 | 115 | 67 | | Nocardia abscessus | Nocardia beijingensis | 1 | 1 | 1 | | Nocardia asteroides | Nocardia neocaledoniensis | 3 | 31 | 31 | | Trichophyton tonsurans | Trichophyton interdigitale | 2 | 34 | 34 | | Trichophyton verrucosum | Trichophyton erinacei | 3 | 36 | 36 | | Trichophyton interdigitale | Trichophyton rubrum | 3 | 36 | 36 | # aa. Assay cut-off: After the calibration is accepted for an acquisition group, the VITEK MS acquires the spectra for the samples in that group. A perfect match between the spectrum and the unique spectrum of a single organism or organism group would provide a percent probability of 99.9. Results are displayed as follows: - A single identification is displayed with confidence value of 60 to 99.9 when one significant organism or organism group is retained. - Low Discrimination identifications are displayed when more than one significant organism or organism group are retained, but not for more than 4 organisms. In this case, the sum of confidence values is equal to 100. - When more than 4 organisms or organism groups are found, the organism is considered as non-identified. In this case, a list of possible organisms is displayed and the sum of confidence values is less than 100. - When no match is found, the organism is considered as non-identified. # 2. Comparison studies: {33} a. Method comparison with predicate device: $N / A$ b. Matrix comparison: $N / A$ # 3. Clinical studies: a. Clinical Sensitivity: Challenge Study: One hundred well-characterized challenge strains including 50 moulds, 35 mycobacteria and 15 nocardia strains were evaluated. Three trial sites tested the mould challenge strains and three different trial sites tested the mycobacteria and noc…

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