North American and European advisory groups1,2 published testing and treatment guidelines for Sexually Transmitted Diseases in 2015 recommending nucleic acid amplification testings for the diagnosis of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) for superior sensitivity and specificity. A substantial proportion of CT and NG infections are asymptomatic, and the assays work effectively on noninvasive specimens, such as urine or vaginal swabs. The increase in molecular laboratory testing has led to an increase of the use of automated instrumentation in laboratories. Several batch-mode and random access continuous feed automated instruments are available for these purposes.
The cobas 4800 system (cobas 4800), from Roche Molecular Diagnostics (Pleasanton, Calif) and the Abbott m2000 RealTime (m2000) System (Abbott Molecular, Des Plaines, Ill) are 2-unit semiautomated batch-mode platforms. The Viper XTR (Viper) System (Becton Dickinson, Franklin Lakes, NJ) is a single-unit batch-mode instrument. Each of these instruments uses 96-well plates to process 1 to 92 to 94 samples, depending on the number of controls required. Introduction of additional specimens requires an additional run and reagent and sample processing happens in the wells. The GeneXpert Infinity 80 (Infinity 80) from Cepheid Inc. (Sunnyvale, Calif) is a continuous-load automated, random access instrument using cartridges processed in GeneXpert analyzers. Specimen and reagent processing takes place inside each test cartridge within 80 testing modules. These 4 platforms provide similar testing accuracy3–6 with variable time to results (TTR), and hands-on time (HOT), with different degrees of maintenance and consumption of reagents and disposables.7–14 We chose a wide range of specimen numbers for testing to determine the versatility of the instruments. We recorded HOT, time for maintenance, reagents and plastics consumed, and TTR during processing of 1, 24, 48, 96, and 192 urine tests. To compare testing accuracy, we challenged each platform with a panel of 90 urines blinded to each operator.
MATERIALS AND METHODS
The cobas CT/NG 4800 test was performed on a cobas 4800 instrument at the Public Health Laboratory, St. John's, Newfoundland and Labrador, Canada. The RealTime m2000 CT/NG assay was performed on an m2000 RealTime instrument at Centre de santé et de services sociaux de Trois-Rivières, Trois-Rivières, Quebec, Canada. The ProbeTec ET CT/GC Qx assay was performed on a Viper instrument at the Queen Elizabeth II Health Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada. The Xpert CT/NG assay was performed on an Infinity 80 instrument in the Research Laboratory in Sacred Heart Hospital, Pensacola, Fla.
Two investigators spent 2.5 days at each study site. Workflow and maintenance characteristics of each platform were determined based on processing urine samples for 1, 24, 48, 96, and 192 tests according to the manufacturer's package insert. The steps for processing specimens in the batch mode instruments were broken up into 6 stages: (i) preanalytical interactions, (ii) reagent preparation and loading, (iii) sample preparation and loading, (iv) in-process interactions (number of times operator is required to return to the instrument during operation), (v) postanalytical interactions, and (vi) maintenance. For the Infinity 80, samples were processed into the cartridges, outside the instrument. Based on the data obtained for the processing stages, the following 4 study parameters were determined for each instrument: (i) HOT (total time required for manual interactions from the beginning to the end of an assay run, including daily maintenance); (ii) cumulative time for daily, weekly, and monthly maintenance, which was calculated based on 96 tests per day, 5 testing days per week, and 20 testing days per month, respectively; (iii) consumables of all reagents and plastics for 1 and 192 test runs; and (iv) TTR. A panel of 90 clinical samples of urine containing 17 CT positives, 2 CT/NG coinfections and 69 negatives were shipped to each study site for testing in a blinded fashion and tests were performed within 48 hours.
Figure 1 summarizes the HOT for each instrument. Performing a single specimen in the Infinity 80 took 39 seconds of HOT compared with 24 minutes on the cobas 4800; 40 minutes on the m2000; and 1 hour and 5 minutes on the Viper. For larger numbers of specimens, the HOT on the Infinity 80 increased to approximately 9 minutes for 24 tests; 18 minutes for 48 tests; 35 minutes for 96 tests; and 1 hour and 38 minutes for 192 tests. For batching instruments, HOT times were approximately 30 minutes for 24 or 48 tests, 40 minutes for 96 tests, and 1 hour and 38 minutes for the cobas 4800; 45 minutes for 24 tests, 47 minutes for 48 tests, 1 hour for 96 tests, and 2 hours and 8 minutes for 192 tests for the m2000; and approximately 1 hour for 24 or 48 tests, 1 hour and 41 minutes for 96 tests and 2 hours and 17 minutes for 192 tests for the Viper.
Based on 96 tests per day, for 20 testing days in a month (Fig. 2), the cobas 4800 required 2 hours and 46 minutes, and the m2000 needed 9 hours and 52 minutes of maintenance. The Viper required the greatest amount of maintenance at 14 hours and 17 minutes, and the Infinity 80 required the least amount of maintenance. Most of the maintenance for each instrument was daily. Proportionately more weekly maintenance was required for the m2000 and cobas 4800 than the Infinity 80 and Viper XTR.
Table 1 summarizes the consumption of reagents and plastics for 1 and 192 tests by the 4 instruments. The Infinity 80 used 1 waste container, 1 and 192 cartridges, and 1 and 192 pipettes.
The cobas 4800 consumed 1 assay reagent kit of 24 for 1 test and 2 kits of 96 for 192 tests. Other reagents consumed were control sets, sample preparation kits, extraction and reaction carrier plates, reagent reservoirs, wash buffer containers, caps, waste container, and pipette tips.
The m2000 instrument consumed sets of 48 test kit assay reagents and control sets. Controls were already diluted so diluent was not required, and sample preparation kits were not required. Extractions were performed in tubes. One container each of lysis buffer, microparticles, and elution buffer in the reagent reservoir were required for 1 specimen, and this doubled for 192 specimens. Wash buffer containers and a waste container were also required. Deep well reaction carrier plates, and pipette tips were also consumed.
The Viper XTR also consumed reagent kits but did not consume control diluent because extractions were performed in tubes using reaction carrier troughs, and only positive samples were capped. Pipette tips and plate sealers were also consumed.
For a single specimen, the Infinity 80 provided results after 1 hour and 30 minutes compared with 2 hours 51 minutes on the cobas 4800, 3 hours and 54 minutes for the m2000, and 2 hours and 12 minutes on the Viper (Fig. 3). When samples were processed up to 48 tests in the Infinity 80, the final TTR for each specimen was between 1 hour and 30 minutes and 1 hour and 54 minutes. For 96 and 192 tests, the TTR for the final specimen in the batch from the Infinity 80 were 3 hours and 16 minutes, and 5 hours and 6 minutes. For batches of 24 to 192 on the batch-mode instruments, the times required for final results ranged from 3 hours and 6 minutes to 6 hours and 8 minutes for the cobas 4800; 4 hours and 35 minutes to 9 hours and 57 minutes for the m2000; and 2 hours and 37 minutes to 5 hours and 8 minutes on the Viper, respectively.
Detection of CT and NG in Urine
All systems detected 19 CT (90.5%) and 2 NG (100%) positives and 69 negatives and 2 samples were discordant.
The Infinity 80 had a HOT of 39 seconds for processing one specimen which was similar to a recent study comparing the Infinity to a Panther instrument15 and less than the 1 minute reported in a recent study evaluating the benefit of GeneXpert testing for CT and NG in a family planning setting.16 These differences could be due to technician speed to pipette samples and load cartridges. HOT was 24 minutes to over an hour for processing a single specimen in the batching instruments. This was expected because batch-mode platforms are designed to process larger numbers of samples. Increasing batch sizes proportionately increased the HOT needed on the Infinity 80 but the times were always less than that required in the m2000 and Viper, and almost equal to cobas 4800 for batches of 96 and 192 (Fig. 1).
The cobas 4800 processed 24 or 48 samples with 2 controls and a maximum of 94 specimens in a run but required 1 mandatory return visit. More HOT was required for specimen preparation and loading on the cobas 4800 due to uncapping sample tubes before loading. Total HOT, including daily maintenance on the cobas 4800 was 40 minutes for 96 tests, which was similar to our recent study14 and the 36.5 minutes previously reported.13 The cobas 4800 HOT approximated the Infinity 80 HOT for 96 and 192 samples (Fig. 1).
The Abbott m2000 could process 24 or 48 samples with 3 controls, and a maximum of 93 specimens could be processed in a run but required 2 return visits per run. The total HOT, including daily maintenance for a 96-test run on the m2000, was 1 hour and 4 minutes which was the same as previously determined14 but was longer than the 43 minutes reported in another study.13 Processing 192 tests doubled the total HOT on the m2000 to 2 hours, 8 minutes, and 55 seconds and increased the mandatory return visits to 4, with results from the second run extended beyond the normal 7.5-hour shift (Fig. 3), confirming previous observations.3,9,13,14
The Viper allowed 24 or 48 samples to be processed with 4 controls, and a maximum of 92 specimens could be processed in a run. The total HOT, including daily maintenance was 1 hour and 41 minutes for 96 tests. A previous study reported a total HOT of 35 minutes per run of 96 tests but did not include daily maintenance in the calculation.11
The Infinity 80 required a total of 36 minutes of cumulative hands on time for maintenance per 20-working day month compared with the batching instruments which ranged from 2.75 hours for cobas 4800 to over 14 hours for Viper (Fig. 2). This amount of maintenance on the Viper XTR is lower than the 22.5 hours reported previously.14 After the previous study, this laboratory changed its maintenance procedures to be less time-consuming on a daily basis.
Because of the differences in design and technology, the Infinity 80 consumed fewer reagents and plastics, and consumption was proportional to the number of samples processed. This analysis revealed a striking difference in environmental impact for the 3 batch-mode instruments. We attempted to do a financial comparison of the consumables but were unable to get comparative values due to variable retail costs used, according to instrument leasing terms dictated by work volumes covering all infectious disease analytes which the instrument can detect. Another weakness of this study was our inability to assess the study parameters on different occasions and at multiple laboratory sites, as some differences may occur even though all laboratories would be following the manufacturers' testing protocols. The batch mode instruments in this study are designed for processing 96-well plates. Both the cobas 4800 and m2000 instruments required extended TTR for larger batches (Fig. 3). Processing batches of 96 and 192 tests showed the Viper XTR and Infinity 80 TTR to be similar with extended time intervals. Performance of a proficiency panel of 90 clinical specimens of first catch urine showed that the 4 instruments performed equally well. This is confirmatory of other studies3–6 comparing some of these CT/NG assays. All of the systems identified 19 positives. Two positive samples were negative in the m2000, and one of them was also negative in the cobas 4800. Those 2 urines were retested in the Infinity 80 and Viper XTR and repeated negative then positive, indicating low levels of DNA in those samples. Although urine was used in this study, the operation of the instruments would not be expected to vary significantly if other approved sample types were used.
Shorter TTR is an important factor and an appropriate waiting time to enable treatment of CT and NG infections would vary according to clinical settings. The batch-mode instruments in this study all required more TTR than would be ideal for holding patients for treatment in most settings, which confirms previous studies.3,13,14 At lower batch sizes, the TTR of 1.5 hours on the Infinity 80 may provide an opportunity to treat patients at the initial clinic visit in some settings. This concept has shown promising outcomes of reducing time to treatment from 5 days to the same day in studies performed in rural Australian settings using Xpert CT/NG cartridges in GeneXpert analyzers.17,18 The Infinity system is being used at an active sexual health clinic, called the Dean Street Express in London, England, with dramatic reductions in TTR and time to effective therapy.19 Patient results are usually communicated to cell phones within 2 hours. Studies from France have demonstrated a benefit of Xpert testing and treating women infected with CT and/or NG, who are receiving pregnancy termination.16 Further study of this concept of near-patient diagnosis of CT and NG infection to enable earlier treatment is warranted.
In summary, this comparison of 4 instruments used to diagnose CT and NG infections for a variety of testing scenarios showed several distinct differences. A non–batch-mode random-access instrument, such as the Infinity 80, required less HOT for all batch sizes compared to the m2000 and Viper. Infinity 80 HOT was less than that of the cobas 4800 except with 192 tests, where the times were similar. Regardless of the number of specimens tested in a run, the Infinity 80 required minimal daily, weekly, or monthly maintenance. Our thorough review of consumables revealed a considerable amount of disposable reagents and plastics from the batch-mode platforms. Providing earlier results from the Xpert CT/NG cartridges indicates that near patient results might be achieved with the Infinity 80 in some settings.
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