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1 Author s response to reviews Title: Treatment Completion for Latent Tuberculosis Infection: A Retrospective Cohort Study Comparing 9 months of Isoniazid, 4 months of Rifampin and 3 months of Isoniazid and Rifapentine Authors: Adelaide McClintock (ahearst@uw.edu) McKenna Eastment (mceast@uw.edu) Christy McKinney (christymk@uw.edu) Caroline Pitney (carollp@uw.edu) Masahiro Narita (masa.narita@kingcounty.gov) Shireesha Dhanireddy (sdhanir@u.washington.edu) Alexandra Molnar (amolnar@uw.edu) David Park (drp@uw.edu) Version: 2 Date: 22 Nov 2016 Author s response to reviews: Dear Editorial Staff and Reviewers, Thank you for your continued review of this paper and your thoughtful comments, which we believe have strengthened the manuscript. Below are our replies to the inquiries of reviewer #2. Regarding the Methods: 1. It is still not clear why patients treated with INH-only in 2009 were included. You state that this was prior to the INH shortage and during a time when INH was standard of care but there

2 isn't any comparison between 2009 and 2013 in the analysis. The results don't show how many patients in the study received INH-only in 2009 vs 2013 or whether they differed demographically. Also, rifampin was an acceptable alternative regimen in 2009 so please explain why those patients were not included in your review. Response: There were 205 participants using INH in 2009 and only 19 participants in 2013 using INH. Those on this regimen in 2009 were included because otherwise we would have been underpowered to detect differences between INH and the other regimens. Because we did not have a scientific rationale for comparing INH to INH over time and because of concern over multiple comparisons, we do not compare year of INH regiment across time points. Similarly, we included participants on rifampin in 2009 and Rifampin was not widely used in only 3 of the 82 participants on rifampin took it in 2009; the remaining 79 took it in We have added a statement about those on these regimens stratified by the years 2009 and Discussion, paragraph 7, line 18. Rifampin alone was used much less frequently in our medical center in 2009, as INH was the standard of care. Similarly, once our medical center made the switch to Isonaizid plus Rifapentine and Rifampin only regimens, the number of people being treated with INH alone was quite small, and a simultaneous comparison of the three regimens using only 2013 data would have been underpowered to detect a difference. To adequately compare the three regimens, we pooled data from two different time points in order to have large enough sample sizes to detect a true difference. We did not set up our analysis to compare INH in 2009 to INH in 2013 because that was not our primary outcome of interest. Rather, we wanted to compare completion rates for INH, Rifampin and INH plus Rifapentine regimens in an actual use scenario (rather than research settings, where monitoring and compliance tend to be more rigorous than a true patient might actual adhere to). 2. Type of monitoring is a key variable in your analysis yet does seem highly correlated to the regimen used for weekly monitoring and INH/rifapentine. The main difference in your analysis appears to be between the monthly vs less often and between the INH and rifampin self-

3 administered regimens. (a) Since monthly monitoring is recommended by the CDC, the less then monthly monitoring needs to be described in greater detail to understand how the monitoring was conducted in those patients. (b) It may be more appropriate to limit this analysis to the selfadministered regimens only and not include the regimen given by weekly DOT. (a) The text of the paper has been altered to more clearly delineate the less than monthly monitoring. In short, less than monthly monitoring denoted patients who were non-complaint with clinic appointments. This type of monitoring was used when patients did not present for follow up at the scheduled, CDC recommended, interval, but were still picking up medications at the pharmacy. The text now reads: Patients monitored less than monthly were monitored this way because of poor attendance in clinic. When present in clinic, regular monitoring was completed as it would have been in a monthly monitoring scenario (Methods, paragraph 3, line 12). We retained the less than monthly monitoring group in our analysis because our goal was to clarify completion rates in actual use scenarios, in which case, the monitoring type of less often may be what a provider is truly able to accomplish with a given patient. The evidence in this paper is meant to guide providers through true clinical scenarios, rather than research settings. (b) Regarding the questions about analysis, we agree that the regimen chosen and the type of monitoring are highly correlated. The analysis as conducted accounts for differences in monitoring, as this was included in our model. We chose to use an adjusted model for our analysis, rather than stratification, as both can be used to control for confounding. We have retained our comparison of all three regimens and monitoring types, as we believe that while the differences were most remarkable between INH and Rifampin self-administered regimens, one of the most interesting findings is that Rifampin and the novel combination regimen are completed at similar rates. As we attempt to guide front line clinicians through reallife clinical scenarios, we believe the similar completion rates, with monthly, or occasionally less than monthly monitoring, is an important contribution to the evidence base that providers may call on when making decisions about regimen choice.

4 We have also included our initial response to a related inquiry by reviewer #2, which has further background on how our analysis was conducted. This was our response in the last review: Response: When examining the association between completion of therapy and regimen we adjusted for type/frequency of monitoring and when examining type of monitoring, we adjusted for type of treatment. We now explain this in the manuscript (Methods paragraph 5, sentence 8). Though type of monitoring and type of therapy are correlated they are not so highly correlated with regimen to represent the same concept. Because type of monitoring as well as type of treatment are likely to be associated with completion of therapy and because they were viewed as potential confounders of each other we adjusted for one when looking at the other and vice versa. As an aside, had they been entirely determinant/collinear we would not have been able to adjust for one in the presence of the other. These estimates isolate the effect of treatment (or type of monitoring) and were therefore selected as the best estimates of our associations. We have also conducted sensitivity analyses that examined the association between treatment completion and regimen with and without adjustment for type of monitoring and the findings were similar. We examined the association between treatment completion and type of monitoring with and without adjustment for treatment regimens and the results showed that this strong association went away with adjustment for treatment regimen because of the association between monitoring type and regimen type though not completely collinear. For clarity, we have included type of monitoring in Table Table 1 demonstrates significant demographic differences in the patients who received the various regimens including factors that are known to be associated with lower adherence - example homelessness and alcohol use. The methods and results don't address how these differences were addressed in the analysis. The authors agree that there were differences in the populations that the various regimens were prescribed as indicated by the p-values in Table 1. However, in particular, the homelessness and alcohol use was a small percentage of our total patients. Also, we made the determination of our confounders a priori and not based on statistically significant differences in Table 1. We did not include these variables as we did not think that they would be associated with the exposure (regimen type). Lastly, many of these patients who were homeless and had problem alcohol use were treated at one specific clinic (the homeless health clinic). We took these variables into account by adjusting for clinic type in the analyses.

5 Nevertheless, to address the reviewer concerns, we compared our reported results for all adjusted associations in Table 2 with models that also adjusted for homelessness and alcohol use. We observed no material difference in the associations (all were in the same direction and statistical significance did not change). We now include this sensitivity analysis in our methods and report this finding in our results. The text of the results (Paragraph 5, line 6) now reads: Additionally, we compared our reported results for all adjusted associations in Table 2 with models that also adjusted for homelessness and alcohol use. We observed no material difference in the associations (all were in the same direction and statistical significance did not change). 4. Paragraph 3, sentence 4 - "Efficacy data are not available for three months of isoniazid and rifapentine." Is incorrect. There are several studies evaluating the efficacy of this regimen with the largest being the CDC-funded TBTC PREVENT TB trial cited in the background. The text has been updated to accurately reflect the available literature. It now reads: Both four months of rifampin8 and 3 months of isoniazid plus rifapentine15 are also highly effective against latent TB, with similar efficacy compared to placebo or isoniazid monotherapy, respectively. (Discussion, paragraph 3, line 4). 5. Under limitations, I would not consider the exclusion of INH/rifampin for 3 months as a limitation since this regimen was not used at your site and is not generally used in the US as you point out. Consider moving this to the background instead of the discussion. This was removed from the limitations, and placed in the background. It now appears in the background, (paragraph 3, line 7) and is reproduced below.

6 Additionally, there is a fourth LTBI regimen of 3 months of daily rifampin and isoniazid. This regimen is used in parts of Europe and also carries the benefits of short duration, lower cost, and targeting TB by multiple mechanisms. 27 However, the regimen is not currently on the list of CDC recommended regimens, and is not commonly used in the US at this time, and so was not included in this study 6. I do think a major limitation to a retrospective study that by definition is not randomized is that there are significant differences in the patient populations by treatment arm which may have impacted adherence. This limits the strength of conclusions that the 2 short course regimens can be considered entirely equivalent in clinical practice. In actuality, their roles may be very different. For example, once weekly DOT is useful for achieving high treatment completion in patients populations with historically low completion whereas daily self-administered rifampin has comparably high completion in other populations and both are better than INH. Under limitations, the text now includes the following, Discussion, paragraph 7, line 1. Further, given that our study was retrospective and not randomized, the design limits the strength of the conclusions regarding the true equivalence of the regimens. Provider discretion should still guide the choices between Rifampin only regimens versus INH-Rifapentine, which may still be of greater utility in patient populations with historically low adherence, such a homeless patients and those actively using alcohol or other substances.

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