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The Alinity m STI Assay is an in vitro polymerase chain reaction (PCR) assay for use with the automated Alinity m System for the direct, qualitative detection and differentiation of ribosomal RNA from Chlamydia trachomatis (CT), DNA from Neisseria gonorrhoeae (NG), ribosomal RNA from Trichomonas vaginalis (TV), and ribosomal RNA from Mycoplasma genitalium (MG), to aid in the diagnosis of disease(s) caused by infection from these organisms. The assay may be used to test the following specimens from symptomatic and asymptomatic individuals for the following analytes:

• . CT: vaginal swabs (clinician-collected and self-collected in a clinical setting). endocervical swabs, gynecological specimens in ThinPrep PreservCyt Solution, female urine, male urine, oropharyngeal swabs, and rectal swabs
• . NG: vaginal swabs (clinician-collected and self-collected in a clinical setting), endocervical swabs, gynecological specimens in ThinPrep PreservCyt Solution, female urine, male urine, oropharyngeal swabs, and rectal swabs
• . TV: vaginal swabs (clinician-collected and self-collected in a clinical setting). endocervical swabs, gynecological specimens in ThinPrep PreservCyt Solution, female urine, and male urine
• . MG: vaginal swabs (clinician-collected and self-collected in a clinical setting), endocervical swabs, and male urine

A vaginal swab (self-collected or clinician-collected) is the preferred specimen type for MG testing in females due to the higher clinical sensitivity compared to endocervical swabs. If endocervical swab specimens test negative, testing with a vaginal swab may be indicated if M. genitalium infection is suspected.

The Alinity m STI Assay utilizes real time PCR to amplify and detect Chlamydia trachomatis (CT) ribosomal RNA sequences, Neisseria gonorrhoeae (NG) genomic DNA sequences, Trichomonas vaginalis (TV) ribosomal RNA sequences, Mycoplasma genitalium (MG) ribosomal RNA sequences, and human genomic DNA sequences that have been extracted from endocervical swab specimens, vaginal swab specimens, oropharyngeal swab specimens, rectal swab specimens, male and female urine specimens, and gynecological specimens preserved in PreservCyt Solution. Endocervical swab, vaginal swab, oropharyngeal swab, rectal swab, and urine specimens are collected with the Alinity m multi-Collect Specimen Transport Kit. PreservCyt specimens are transferred to a transport tube for processing on the Alinity m System.

This device is similar to the predicate device originally cleared (K202977). It does not introduce any changes to the Alinity m STI Assay reagents, sample processing, assay procedure, and data reduction. This device is updating the previous FDA-cleared Intended Use (K202977) to include claims for the following specimens for the following analytes:

• CT: Gynecological specimens in ThinPrep PreservCyt Solution, female urine .
• NG: Female urine

Two studies were initiated to support these claims (refer to Section 1.7.2.) This supplemental data was used with data previously obtained from the Alinity m STI Assay clinical testing studies submitted in K202977.

The steps of the Alinity m STI Assay consist of sample preparation. RT-PCR assembly, amplification/detection, and result calculation and reporting. All stages of the Alinity m STI Assay procedure are executed automatically by the Alinity m System. No intermediate processing or transfer steps are performed by the user. The Alinity m System is designed to be a random-access analyzer that can perform the Alinity m STI Assay in parallel with other Alinity m assays on the same instrument.

The Alinity m STI Assay is an in vitro diagnostic device for the qualitative detection and differentiation of nucleic acids from Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), and Mycoplasma genitalium (MG) in various human specimen types. The device operates on the automated Alinity m System and utilizes real-time Polymerase Chain Reaction (PCR) technology. This submission primarily focuses on supporting expanded claims for specific analytes and specimen types: CT in gynecological specimens in ThinPrep PreservCyt Solution and female urine, and NG in female urine.

Here's a breakdown of the acceptance criteria and study details:

1. Table of Acceptance Criteria and Reported Device Performance:

The document doesn't explicitly state "acceptance criteria" for the clinical performance in terms of specific thresholds (e.g., minimum PPA/NPA). Instead, it presents the Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) values with 95% Confidence Intervals (CI) as the primary performance metrics, demonstrating the device's accuracy against a Composite Comparator Algorithm (CCA).

Note: The table is constructed based on the "specimen-specific positive and negative agreement" data. The document does not provide specific acceptance thresholds, but the presented performance metrics are high, demonstrating the device's effectiveness.

2. Sample Size Used for the Test Set and Data Provenance:

• CT and NG in Female Urine:
  • Sample Size: A total of 2,798 female subjects were enrolled. 2,785 CT results and 2,784 NG results were used in the analysis after exclusions due to missing/indeterminate CCA results.
  • Data Provenance: The study was a multicenter clinical study conducted in the United States. Subjects provided urine specimens. The data includes both symptomatic and asymptomatic individuals.
• CT in PreservCyt Specimens:
  • Sample Size: 1,939 specimens from a multicenter clinical study were included in the analysis.
  • Data Provenance: The study was a multicenter clinical study conducted in the United States. Female subjects provided gynecological specimens collected in PreservCyt Solution.

3. Number of Experts Used to Establish the Ground Truth for the Test Set and Their Qualifications:

The ground truth was established using a clinical comparator method, not individual experts.

• Ground Truth Method: A Composite Comparator Algorithm (CCA) was used.
• Details: For each subject, a CCA was determined for each analyte based on the combined results from commercially available nucleic acid amplification tests (NAATs).
  • For the female urine study (CT and NG), comparator assays included 3 commercially available NAATs. Specimens were initially tested with 2 NAATs. If they disagreed or a result was missing/indeterminate, a third tiebreaker NAAT was used.
  • For the PreservCyt study (CT), specimens were tested with up to 3 comparator NAATs. Similar to the urine study, specimens were initially tested with 2 NAATs, and a third was used as a tiebreaker if needed.
• Qualifications of Experts: The document does not mention the use of human experts or their qualifications for establishing ground truth. The ground truth is effectively an "expert panel of assays" (the comparator NAATs).

4. Adjudication Method for the Test Set:

• Method: A 2+1 adjudication method was employed for establishing the Composite Comparator Algorithm (CCA).
  • Description: Specimens were initially tested with two comparator NAATs.
  • If the two initial NAATs agreed (both positive or both negative), that result formed the CCA.
  • If the two initial NAATs disagreed, or if one result was missing or indeterminate, a third "tiebreaker" NAAT was used to resolve the discrepancy and establish the CCA.
  • A subject was categorized as "Positive" if at least 2 comparator assay results were positive and "Negative" if at least 2 comparator assay results were negative.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done:

No, an MRMC comparative effectiveness study was not done. The Alinity m STI Assay is an in vitro diagnostic device (IVD) that provides a qualitative result directly. Its performance is compared against a composite reference standard (CCA) derived from other NAATs, not against human readers. Therefore, the concept of human readers improving with AI assistance is not applicable in this context.

6. If a Standalone (Algorithm Only Without Human-in-the-Loop Performance) Was Done:

Yes, a standalone performance study was done. The reported performance metrics (PPA and NPA) reflect the accuracy of the Alinity m STI Assay (algorithm and reagents performed on the automated Alinity m System) operating independently against the established ground truth (CCA). The device provides a direct, qualitative result without human interpretation of the algorithm's output for diagnosis.

7. The Type of Ground Truth Used:

The ground truth used was a Composite Comparator Algorithm (CCA), which is an expert consensus based on multiple FDA-cleared nucleic acid amplification tests (NAATs). These NAATs are considered the gold standard for detecting these pathogens. The CCA essentially serves as the "best available truth" when a true clinical outcome or pathological confirmation for all cases is not feasible or practical in a large-scale clinical trial.

8. The Sample Size for the Training Set:

The document does not explicitly describe a separate "training set" for the Alinity m STI Assay in the context of this 510(k) submission. This is typical for IVD devices, where the assay's design, reagent formulation, and analytical parameters are developed through internal R&D, rather than a machine learning training paradigm with a distinct training dataset for an "algorithm." The clinical studies mentioned (both the original K202977 studies and the supplemental studies) serve as validation/test sets to demonstrate the performance of the already developed assay.

9. How the Ground Truth for the Training Set Was Established:

Since a distinct "training set" in the machine learning sense is not described, the question of how its ground truth was established is not directly applicable. The Alinity m STI Assay's underlying technology (real-time PCR) and design would have been established and optimized based on known genetic sequences, analytical performance studies (e.g., analytical sensitivity, specificity), and prior knowledge of the target organisms, where ground truth sources for these developmental phases would likely include:

• Well-characterized isolates/strains: Known positive and negative biological samples.
• Synthetic nucleic acid targets: Designed to validate primer and probe performance.
• Spiked matrix samples: To assess analytical performance in relevant specimen types.

These developmental activities would precede the clinical validation studies that are the focus of this 510(k) submission.

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The Alinity m STI Assay is an in vitro polymerase chain reaction (PCR) assay for use with the automated Alinity m System for the direct, qualitative detection and differentiation of ribosomal RNA from Chlamydia trachomatis (CT), DNA from Neisseria gonorrhoeae (NG), ribosomal RNA from Trichomonas vaginalis (TV), and ribosomal RNA from Mycoplasma genitalium (MG), to aid in the diagnosis of disease(s) caused by infection from these organisms. The assay may be used to test the following specimens from symptomatic and asymptomatic individuals for the following analytes:

CT: vaginal swabs (clinician-collected and self-collected in a clinical setting), endocervical swabs, male urine, oropharyngeal swabs, and rectal swabs

NG: vaginal swabs (clinician-collected and self-collected in a clinical setting). endocervical swabs, gynecological specimens in ThinPrep PreservCyt Solution, male urine, oropharyngeal swabs, and rectal swabs

TV: vaginal swabs (clinician-collected and self-collected in a clinical setting), endocervical swabs, gynecological specimens in ThinPrep PreservCyt Solution, female urine, and male urine

MG: vaginal swabs (clinician-collected and self-collected in a clinical setting), endocervical swabs, and male urine

A vaginal swab (self-collected or clinician-collected) is the preferred specimen type for MG testing in females due to higher clinical sensitivity compared to endocervical swabs. If endocervical swab specimens test negative, testing with a vaginal swab may be indicated if M. genitalium infection is suspected.

The Alinity m STI Assay is a real time polymerase chain reaction (PCR) assay for the amplification and detection of Chlamydia trachomatis (CT) ribosomal RNA sequences, Neisseria gonorrhea (NG) genomic DNA sequences, Trichomonas vaginalis (TV) ribosomal RNA sequences, Mycoplasma genitalium (MG) ribosomal RNA sequences, and human genomic DNA sequences. The assay can be used with endocervical swab specimens, vaginal swab specimens, male and female urine specimens, gynecological specimens in ThinPrep® PreservCyt® Solution, oropharyngeal swab specimens, and rectal swab specimens. Endocervical swab, vaginal swab, oropharyngeal swab, rectal swab and urine specimens are collected with the Alinity m multi-Collect Specimen Collection Kit. PreservCyt Solution specimens are transferred to an Alinity m Transport Tube for processing on the Alinity m System.

The steps of the Alinity m STI Assay consist of sample preparation, RT-PCR assembly, amplification/detection, and result calculation and reporting. All stages of the Alinity m STI Assay procedure are executed automatically by the Alinity m System. No intermediate processing or transfer steps are performed by the user. The Alinity m System is designed to be a random-access analyzer that can perform the Alinity m STI Assay in parallel with other Alinity m assays on the same instrument.

The Alinity m STI Assay requires two separate assay specific kits as follows:

• . Alinity m STI AMP Kit, List No. 09N17-095 consisting of multi-well amplification plates containing lyophilized, unit-dose PCR amplification/detection reagents and multi-well activator plates containing liquid, unit-dose activation reagents (MgCl2, TMAC, and KCl). The intended storage condition for the Alinity m STI AMP Kit is 2℃ to 8℃.
• . Alinity m STI CTRL Kit, List No. 09N17-085 consisting of negative controls and positive controls, each supplied as liquid in single-use tubes. The intended storage condition for the Alinity m STI Control Kit is -15°C to -25°C.

Nucleic acids from specimens are extracted automatically on-board the Alinity m System using the Alinity m Sample Prep Kit 1, Alinity m Lysis Solution, Alinity m Ethanol Solution, and Alinity m Diluent Solution. The Alinity m System employs magnetic microparticle technology to facilitate nucleic acid capture, wash and elution. The resulting purified nucleic acids are then combined with the liquid unit-dose activator reagent, lyophilized unit-dose Alinity m STI amplification reagents, and Alinity m Vapor Barrier Solution, and transferred by the instrument to an amplification/detection module for reverse transcription, PCR amplification, and real-time fluorescence detection.

Assay controls are tested at or above an established minimum frequency of every 24 hours to help ensure that instrument and reagent performance remain satisfactory. During each control event, a negative control and a positive control are processed through sample preparation and RT-PCR procedures that are identical to those used for specimens. Assay controls are used to demonstrate proper sample processing and assay validity. The controls do not indicate if bacterial cells have been adequately lysed.

The Alinity m STI amplification reagents include primers and a probe that amplify and detect the single copy human gene, ß-globin. Amplification and detection of the ß-globin gene demonstrates proper sample processing and adequate sample input. In addition, an exogenous internal control (containing an armored RNA sequence) is included in the lyophilized Alinity m STI amplification reagents to assess amplification efficiency and to confirm that no PCR inhibitors are present in the sample. The cellular control and internal control are both used to demonstrate assay validity.

The Alinity m STI Assay also utilizes the following accessories:

• . Alinity m STI Assay Application Specification File, List No. 09N17-03A
• . Alinity m System and System Software, List No. 08N53-002
• Alinity m Sample Prep Kit 1, List No. 09N18-001 .
• Alinity m multi-Collect Specimen Collection Kit, List No. 09N19-010 .
• . Alinity m Tubes and Caps, List No. 09N49:
  • Alinity m Transport Tubes Pierceable Capped, List No. 09N49-010 .
  • . Alinity m Transport Tube, List No. 09N49-011
  • Alinity m Pierceable Cap, List No. 09N49-012 .
• Alinity m System Solutions, List No. 09N20: .
  • Alinity m Lysis Solution, List No. 09N20-001 .
  • Alinity m Ethanol Solution, List No. 09N20-002 .
  • Alinity m Diluent Solution, List No. 09N20-003
  • Alinity m Vapor Barrier Solution, List No. 09N20-004 •

The Abbott Alinity m STI Assay is an in vitro polymerase chain reaction (PCR) assay used with the automated Alinity m System for the direct, qualitative detection and differentiation of ribosomal RNA from Chlamydia trachomatis (CT), DNA from Neisseria gonorrhoeae (NG), ribosomal RNA from Trichomonas vaginalis (TV), and ribosomal RNA from Mycoplasma genitalium (MG), to aid in the diagnosis of sexually transmitted infections.

The acceptance criteria and the study results are detailed below:

1. Table of Acceptance Criteria and Reported Device Performance

The device performance is reported as Sensitivity (Positive Percent Agreement or PPA) and Specificity (Negative Percent Agreement or NPA). The document does not explicitly state pre-defined acceptance criteria (e.g., a specific threshold like "Sensitivity must be >= X%"). However, the reported performance values are the outcome of the clinical trials conducted to demonstrate the device's effectiveness.

Urogenital Specimens

Extragenital Specimens

2. Sample Size Used for the Test Set and Data Provenance

• Urogenital Specimens: A total of 7,099 male and female subjects were enrolled for the urogenital clinical study. Specimens were collected across 33 geographically diverse sites in the United States, including STI clinics, primary care offices, and gynecology practices. This was a prospective study. Data provenance is United States, from prospective collection.
  • Number of results used in analysis for each analyte:
    • CT: 12,903
    • NG: 15,655
    • TV: 18,843
    • MG: 12,829
• Extragenital Specimens: A total of 2,373 male and female subjects were enrolled. Specimens were previously collected and archived. Data provenance is United States, from archived specimens (retrospective).
  • Number of results used in analysis for each analyte:
    • CT (oropharyngeal): 2,316
    • CT (rectal): 2,053
    • NG (oropharyngeal): 2,312
    • NG (rectal): 2,049

3. Number of Experts Used to Establish the Ground Truth for the Test Set and Their Qualifications

The document does not explicitly state the "number of experts" or their "qualifications" involved in establishing the ground truth. Instead, the ground truth was established using comparator assays, which are commercially available nucleic acid amplification tests (NAATs) and, in some cases, culture. The results from these comparator assays were combined to derive a Patient Infected Status (PIS) or Composite Comparator (CC).

4. Adjudication Method for the Test Set

• Urogenital Specimens (PIS):
  • CT or NG (Female): A minimum of 2 positive results (at least 1 from each comparator NAAT) for infection, or at least 1 comparator NAAT reported negative results for all sample types for not infected.
  • TV or MG (Female): First 2 swab comparator NAAT results both positive, or 2 of 3 swab comparator NAAT results positive (if 3rd NAAT was a tie-breaker) for infection. First 2 swab comparator NAAT results both negative, or 2 of 3 swab comparator NAAT results negative (if 3rd NAAT was a tie-breaker) for not infected.
  • CT, NG, TV, or MG (Male): A minimum of two comparator positive results for infection. If the comparator TV culture assay result was positive, the subject was categorized as infected for TV regardless of NAAT results. Two or more comparator NAAT results negative for not infected (for CT, NG, MG). For TV, negative culture AND one or more negative comparator NAATs for not infected.
• Extragenital Specimens (CC): A specimen was categorized as infected (for CT or NG) if a minimum of 2 comparator positive results were reported. It was categorized as not infected if a minimum of 2 comparator negative results was reported.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done

No, an MRMC comparative effectiveness study was not done. The study compares the Alinity m STI Assay's performance against a composite ground truth derived from multiple established comparator assays, not directly evaluating human reader performance with and without AI assistance.

6. If a Standalone (i.e., algorithm only without human-in-the-loop performance) Was Done

Yes, this was a standalone performance study. The Alinity m STI Assay is an automated PCR assay, and its results are directly compared to the established ground truth without involving human interpretation or modifications of its output in the primary performance analysis.

7. The Type of Ground Truth Used

The ground truth used was a Composite Comparator / Patient Infected Status (PIS/CC), derived from the combined results of multiple commercially available and clinically cleared comparator nucleic acid amplification tests (NAATs) and, for male TV, culture results.

8. The Sample Size for the Training Set

The document does not explicitly provide the sample size for the training set for the Alinity m STI Assay. The provided performance data (Sensitivity and Specificity tables) are from the validation (test) sets.

9. How the Ground Truth for the Training Set Was Established

Since the document does not provide information about a separate training set, it is assumed that the analytical studies and the design of the assay would have utilized reference materials and potentially early clinical samples for optimization and establishment of analytical performance characteristics (like LoD, inclusivity, cross-reactivity). However, specific details on how ground truth was established for a training set are not available in this document. The clinical studies described are for validation/testing, with ground truth established by comparator assays as detailed in point 4.

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