Incidence of tuberculosis among PLHIV on antiretroviral therapy who initiated isoniazid preventive therapy: A multi-center retrospective cohort study.

INTRODUCTION: Isoniazid preventive therapy (IPT) is effective in treating tuberculosis (TB) infection and hence limiting progression to active disease. However, the durability of protection, associated factors and cost-effectiveness of IPT remain uncertain in low-and-middle income countries, Uganda inclusive. The Uganda Ministry of health recommends a single standard-dose IPT course for eligible people living with HIV (PLHIV). In this study we determined the incidence, associated factors and median time to TB diagnosis among PLHIV on Antiretroviral therapy (ART) who initiated IPT.
MATERIALS AND METHODS: We conducted a retrospective cohort study at eleven The AIDS Support Organization (TASO) centers in Uganda. We reviewed medical records of 2634 PLHIV on ART who initiated IPT from 1st January 2016 to 30th June 2018, with 30th June 2021 as end of follow up date. We analyzed study data using STATA v.16. Incidence rate was computed as the number of new TB cases divided by the total person months. A Frailty model was used to determine factors associated with TB incidence.
RESULTS: The 2634 individuals were observed for 116,360.7 person months. IPT completion rate was 92.8%. Cumulative proportion of patients who developed TB in this cohort was 0.83% (22/2634), an incidence rate of 18.9 per 100,000 person months. The median time to TB diagnosis was 18.5 months (minimum- 0.47; maximum- 47.3, IQR: 10.1-32.4). World Health Organization (WHO) HIV clinical stage III (adjusted hazard ratio (aHR) 95%CI: 3.66 (1.08, 12.42) (P = 0.037) and discontinuing IPT (aHR 95%CI: 25.96(4.12, 169.48) (p = 0.001)), were associated with higher odds of TB diagnosis compared with WHO clinical stage II and IPT completion respectively.
CONCLUSION: Incidence rates of TB were low overtime after one course of IPT, and this was mainly attributed to high completion rates.

Introduction

The World Health Organization (WHO) estimates that 1.7 billion individuals globally harbor tuberculosis (TB) infection (TBI) and approximately 5–10% may progress to TB disease in their lifetime [1, 2]. In 2020, nearly ten million individuals developed illness due to TB with 1.3 million TB-related deaths recorded globally [3]. During the same period, people living with HIV (PLHIV) accounted for 792,000 and 214,000 of TB cases and deaths respectively. Disproportionately, TB morbidity and mortality among PLHIV is higher in TB/HIV high-burden countries like Uganda [4]. PLHIV possess a 5–10% annual risk of developing active TB disease compared to their HIV negative counterparts whose lifetime risk is only about 10–20% [5-7]. Moreover, PLHIV have higher risk of poor TB treatment outcomes compared to HIV negative individuals [8]. Furthermore, one in every three AIDS-related deaths is attributable to TB and its complications [9]. Therefore, prevention of TB, through treatment of TBI confers significant morbidity and mortality benefits among PLHIV.

Isoniazid preventive therapy (IPT), when combined with ART, offers between 60–90% protection against progression of TBI to active tuberculosis disease [2, 10–13]. As such, provision of IPT, particularly among the PLHIV, is a global health priority as enshrined in the Global HIV/AIDS Strategy 2021–2026 [14], WHO End TB Strategy [15] and the President’s Emergency Plan for AIDS Relief (PEPFAR) Country Operational Plan (COP) 21 [16]. This position was unanimously emphasized at the United Nations High level meeting on tuberculosis in 2018 during which countries committed to providing TB preventive therapy to six million PLHIV by 2022 [2, 6, 17, 18]. Concerns however, remain over the persistently high incidence, morbidity and mortality due to TB among PLHIV in Uganda [19, 20]. This has been attributed to low completion of IPT and other patient factors; based on which Aashna et al. consequently argue that IPT may be less cost-effective in low and middle income compared to higher income countries [12]. In addition, uncertainty of duration of IPT protectiveness among some PLHIV is also of concern [9, 10, 21, 22].

Whereas introduction of new, shorter duration IPT regimens is expected to address non-completion, the duration of protection remains contentious [23]. For example, low CD4 count of less than 200 cells, WHO clinical stage 3 or 4, male sex, unemployment and underweight appear to have significant association with active TB disease development, after IPT completion [21, 22]. Thus, the WHO guidelines on programmatic management for TBI recommend repeat or longer duration of IPT in high-risk PLHIV such as contacts of confirmed TB patients [11]. However, the Uganda MOH still implements a largely “one-size-fits-all” IPT regimen for PLHIV, and this is probably due to the paucity of data on incident TB cases among PLHIV who initiate IPT in Uganda [24]. We present the results of a multi-center retrospective cohort study that measured the incidence, associated factors and median time to TB diagnosis among PLHIV who had received IPT.

Materials and methods

Study design

This was a retrospective cohort study, involving analysis of routinely collected clinical data. At the end of 30th June 2021, we evaluated data of PLHIV who were initiated on IPT from 1st January 2016 to 30th June 2018 and followed up for a minimum of 36 months.

Study setting

The study was conducted at The AIDS Support Organization (TASO) Uganda Centers of Excellence (COEs). Mr. and Mrs. Kaleeba led a team of sixteen volunteers in 1987 to found TASO Uganda to contribute to a process of HIV prevention, restore hope and improve the quality of life of individuals, families and communities affected by the pandemic [25, 26]. Through the 11 COEs, the organization provided comprehensive HIV/TB services to 78,897 PLHIV by the end of March 2021. It is noteworthy that TASO Uganda, through its COEs, started providing IPT to PLHIV in 2015 with particular focus on children aged under 15 years. IPT was integrated in HIV clinical care based on the 1998 WHO and Uganda Ministry of Health (MOH) guidelines for a 6–9 months’ course of Isoniazid (INH) preferred [22, 27]. Sub-optimal uptake of IPT prompted MOH with partners to implement an ambitious scale up campaign dubbed ‘100 days of IPT’ aimed at scaling up IPT enrolment of PLHIV. Through this intervention, Uganda enrolled over 300,000 PLHIV on IPT in July-September 2019 quarter [28]. PLHIV were screened clinically to rule out active TB disease using the WHO intensified case finding (ICF) form [29] before initiating IPT. PLHIV at TASO COEs received a 5-10mg/kg or a maximum of 300mg/day daily dose of isoniazid, co-administered with 25-50mg/day of pyridoxine for prevention of peripheral neuropathy. The PLHIV who received IPT also benefitted from routine adherence counselling, and regular monitoring for drug side effects and repeat screening for active TB.

Study population

All PLHIV who received IPT from 1st January 2016 to 30th June 2018 at TASO COEs were eligible for inclusion in the study. Individuals with incomplete data on IPT enrolment or completion dates, were excluded from the study.

Data extraction

We abstracted a list of 2634 eligible participants from the Uganda Electronic Medical Records and TASO Management Information System at each TASO COE. This enabled identification and retrieval of individual patient file for physical verification and extraction of the required data for entry. Data were directly entered into an online-based questionnaire powered by KoboToolbox® [30]. Where certain variables were found missing in patient files, patient registers including facility-based TB registers, presumptive TB registers, ART registers, viral load and IPT registers were used.

Study variables

We collected minimally anonymized patient specific data on demographic and baseline clinical characteristics. Key variables included Age, Gender, baseline WHO clinical stage, IPT enrolment and outcome dates, Viral load status, ART regimens, ART status, baseline CD4 count and baseline functional assessment.

Exposure and outcome variables

The primary exposure was IPT initiation. We considered PLHIV on ART, who were initiated on daily INH from 1st/January/2016 to 30th/June/2018 and retrospectively followed them up for at least three years or until censorship. Those who were already on IPT were excluded from the study. We also abstracted data on IPT outcome as defined by MOH: completed–chart documentation of patient self-report and dispensing record of completion of standard IPT course; stopped–discontinued IPT because of drug stock-outs, side effects, clinician’s decision to interrupt IPT (in case of suspected drug-drug interactions, contraindications) and diagnosis of TB. Patients were documented as LTFU if they could not be returned to care after interruption, for at least three months despite active follow up. Patients were reported as dead if patient’s next of kin reported that patient had died and this verified by the counsellor through a home visit or local leader report. Information on causes of death was not available for this study.

The primary outcome was TB disease diagnosis. We stratified this by, pulmonary bacteriologically confirmed or clinically diagnosed disease, or extra-pulmonary TB. We utilized the MOH diagnostic algorithm to determine date of TB diagnosis; the date when the attending clinician made a decision to treat the patient for TB, the date of a positive microbiological test, or the date of entry into the unit TB register, whichever occurred earlier. In addition, secondary outcome of interest included time to TB diagnosis. We measured time to TB diagnosis from the date of patient enrolment on IPT to the date of TB diagnosis.

Censorship

All patients who were diagnosed with TB during the follow-up period were censored on the date of TB diagnosis. Those who did not develop TB, but died before completing the follow up period were censored on the reported date of death, while those who were still alive were censored at the pre-set end of the study period, 30th June 2021. This date allowed for a minimum follow up period of three years (36 months). Finally, for patients who were transferred out, lost to follow up and those who missed appointment, observation was censored on the last clinical encounter date.

Statistics and data analysis

Study data were downloaded as Microsoft Excel spreadsheets, cleaned and exported to STATA v.16.0 (STATA Corp, College Station, TX) for analysis. Study variables were summarized using absolute numbers and proportions. Continuous exposure variables such as age, baseline CD4, duration on ART were converted to categorical variables. Cumulative TB incidence was computed as the number of new TB cases expressed as a percentage of the total number of individuals at risk. Incidence rate of TB was computed as the number of new TB cases divided by the total person time in months presented as per 100,000 person months. To determine factors associated with incidence of TB while accounting for facility-level clustering, a Frailty model was used. Hazard ratio (HR) with 95% CI was used to compare the risk for TB diagnosis between factor-levels. Factors with p-value less than 0.2 at bivariable analysis were all subjected to a multivariable analysis and results from the latter presented as adjusted estimates. A p-value <0.05 was considered statistically significant.

Ethical approval

We received ethical approval from TASO Research Ethics Committee (REC) (TASOREC/050/2021-UG-REC-009). Since our study only involved secondary data without direct engagement of study participants, REC exempted us from obtaining informed consent from individual patients.

Results

Patient demographics

A total of 3688 individuals were initiated on IPT during the study period but 1034 were excluded due to incomplete information (see Table 1 attached as supporting document). Therefore, we collected data on the remaining 2634 PLHIV. Of the 2634 PLHIV on ART who were initiated on IPT, majority were females (65.6%), had been on ART for more than 36 months (63.3%) and initiated IPT in 2017 (67.1%) (Table 1). Nearly a third of the participants were children aged less than 15 years (32.6%). At ART initiation, 99.8% of them had a functional status of Working/Playing, 30.6% did not have baseline CD4 done, 46.7% were initiated on a Tenofovir-backbone regimen and 95.9% were on a non-nucleoside reverse transcriptase anchor regimen. Prior to IPT initiation, 32.1% had not had a viral load done and 41.2% had a detectable viral load (Table 2).

Table 1

Number of PLHIV enrolled on IPT from 1st January 2016 to 30th June 2018, and number enrolled into the study.

TASO COE	PLHIV enrolled on IPT from 1st/January/2016 to 30th/June/2018.	PLHIV enrolled into the study (%)
Entebbe	670	37 (5.5)
Gulu	381	378 (99.2)
Jinja	647	430 (68.5)
Masaka	295	283 (95.9)
Masindi	562	484 (86.1)
Mbale	231	224 (97.0)
Mbarara	62	61 (98)
Mulago	162	100 (61.7)
Rukungiri	48	44 (102.1)
Soroti	128	118 (93.8)
Tororo	482	475 (98.5)
Total	3668	2634 (72%)

Table 2

Distribution of demographic and clinical characteristics of the study participants.

Characteristics	Total (N = 2634) (%)	Characteristics	Total (N = 2634) (%)
Sex		Baseline ART regimen backbone
Female	1728 (65.6)
Male	906 (34.4)	ABC-based regimen	343 (13.0)
Age		AZT-based regimen	992 (37.7)
<15 years	859 (32.6)	D4T-based regimen	70 (2.7)
15–24 years	222 (8.4)	TDF-based regimen	1229 (46.7)
25–34 years	465 (17.7)	Baseline ART regimen anchor
35–44 years	542 (20.6)	DTG	81 (2.6)
45–54 years	375 (14.2)	PI	43 (1.4)
55+ years	171 (6.5)	NNRTI	2998 (95.9)
Marital status		Triple NRTI	1 (0.0)
Child	779 (29.6)	Viral Load status prior to IPT initiation
Married	1035 (39.3)	Detectable	1085 (41.2)
Separated/Divorced	294 (11.2)	Undetectable	704 (26.7)
Single	355 (13.5)	Not Done	845 (32.1)
Widowed	171 (6.5)	Year of IPT initiation
Baseline WHO clinical stage		2016	256 (9.7)
I	176 (6.6)	2017	1768 (67.1)
II	2235 (84.9)	2018	610 (23.2)
III	182 (6.9)	IPT outcome
IV	41 (1.6)	Completed	2444 (92.8)
Baseline CD4 count		LTFU	162 (6.2)
<200 cells/ml	595 (22.6)	Stopped	24 (0.9)
200–350 cells/ml	470 (17.8)	Died	4 (0.2)
350–500 cells/ml	285 (10.8)
Above 500 cells/ml	478 (18.2)	Baseline functional status
Not Done	806 (30.6)	Working/Playing	2628 (99.8)
Duration on ART at IPT initiation (months)		Ambulatory	4 (0.2)
<6 months	250 (9.5)	Bed-ridden	2 (0.1)
6-<12 months	175 (6.6)
12-<18months	103 (3.9)
18-<24 months	121 (4.6)
24 - <30 months	122 (4.6)
30 - <36 months	196 (7.4)
36+ months	1667 (63.3)

In this study, 92.8% of the participants were documented to have completed the IPT course. However, among the 24 who discontinued, the reasons for discontinuation included drugs out of stock 6 (25%); side effects 5 (21%), treatment interruption 5 (21%), while 6(25%) were diagnosed with active TB while still on IPT and had to initiate the full course of anti-TB treatment while 2 (8%) transferred out of care.

A total of 22 participants were diagnosed with TB during this study, majority (8/22, 36.4%) of whom were diagnosed in 2019. For the other years, the numbers were 3 (13.6%) in 2017, 5 (22.7%) in 2018, 4 (18.2%) in 2020, and 2 (9.1%) in 2021. Of those diagnosed with TB, 8 (36.4%) had pulmonary bacteriologically confirmed (PBC) disease, 6 (27.3%) were pulmonary clinically diagnosed (PCD) disease while 8 (36.4%) had extrapulmonary tuberculosis disease.

Incidence of TB and associated factors

The cumulative incidence of TB was 0.83% (22/2634). Among those diagnosed with TB, 14 (63.6%) were females, 11 (50.0%) were children less than 15 years of age, 77.3% had baseline WHO clinical stage of II, 31.8% had a baseline CD4 greater than 500 cells/ml, 15 (68.2%) had been on ART for more than 36 months, 13 (59.1%) were on an AZT backbone regimen, 12 (54.5%) were on an Efavirenz-based anchor regimen, 18 (81.8%) had completed IPT. The median time from IPT initiation to TB diagnosis was 18.5 months (interquartile range, IQR: 10–32) months (Table 3).

Table 3

Incidence of TB and associated factors.

	TB diagnosis n (%)	Total person months	Crude incidence rate per 100,000 person months (95% CI)	Crude HR* (95% CI)	p-value	Adjusted HR* (95% CI)	p-value
Overall	22	116360.7	18.9 (12.4, 28.7)
Gender
Female	14 (63.6)	76132.1	18.4 (10.9, 31.0)	Ref.
Male	8 (36.4)	40228.6	19.9 (9.9, 39.8)	1.17 (0.49, 2.80)	0.724
Age
<15 years	11 (50.0)	39484.4	27.9 (15.4, 50.3)	Ref.		Ref.
15–24 years	1 (4.5)	9671.8	10.3 (1.5, 73.4)	0.25 (0.03, 1.97)	0.188	0.29 (0.04, 2.35)	0.246
25–34 years	1 (4.5)	20094.8	5.0 (0.7, 35.3)	0.11 (0.01, 0.88)	0.037	0.18 (0.02, 1.68)	0.132
35–44 years	3 (13.6)	23314.1	12.9 (4.2, 39.9)	0.32 (0.09, 1.20)	0.092	0.36 (0.08, 1.59)	0.178
45–54 years	4 (18.2)	16405.9	24.4 (9.2, 65.0)	0.66 (0.20, 2.17)	0.495	0.73 (0.19, 2.74)	0.636
55+ years	2 (9.1)	7389.6	27.1 (6.8, 108.2)	0.76 (0.16, 3.52)	0.723	0.89 (0.18, 4.40)	0.886
Baseline WHO clinical stage
I	0 (0.0)	7906.1	0.0	0.0	---	0.0
II	17 (77.3)	98405.0	17.3 (10.7, 27.8)	Ref.		Ref.
III	4 (18.2)	8251.4	48.5 (18.2, 129.2)	4.27 (1.28, 14.29)	0.018	3.66 (1.08, 12.42)	0.037
IV	1 (4.5)	1798.1	55.6 (7.8, 394.8)	3.69 (0.47, 28.65)	0.213	2.17 (0.24, 19.26)	0.487
Baseline ART–NRTI backbone
AZT	13 (59.1)	44894.4	29.0 (16.8, 49.9)	Ref.		Ref.
ABC	4 (18.2)	15777.7	25.4 (9.5, 67.5)	0.94 (0.30, 2.88)	0.908	0.72 (0.22, 2.42)	0.599
TDF	5 (22.7)	5219.7	9.5 (3.9, 22.8)	0.27 (0.10, 0.79)	0.016	0.34 (0.09, 1.23)	0.099
D4T	0 (0.0)	2968.8	0.0	0.0	---	0.0	---
IPT outcome
Completed	18 (81.8)	108200.9	16.6 (10.5, 26.4)	Ref.		Ref.
Stopped	2 (9.1)	999.0	200.2 (50.1, 800.5)	14.54 (3.05, 69.13)	0.001	25.96 (4.12, 163.48)	0.001
LTFU	2 (9.1	6982.8	28.6 (7.2, 114.5)	1.26 (0.26, 6.16)	0.773	1.36 (0.27, 6.91)	0.707
Died	0 (0.0)	178.0	0.0	0.0	---	0.0
Baseline CD4
<200	4 (18.2)	26525.2	15.1 (5.7, 40.2)	Ref.
200–350	3 (13.6)	20573.8	14.6 (4.7, 45.2)	1.01 (0.23, 4.52)	0.990
350–500	2 (9.1)	12326.9	16.2 (4.1, 64.9)	1.06 (0.19, 5.82)	0.943
500+	7 (31.8)	21152.6	33.1 (15.8, 69.4)	2.19 (0.63, 7.58)	0.217
Not done	6 (27.3)	35782.1	16.8 (7.5, 37.3)	1.27 (0.33, 4.85)	0.730
Duration on ART at IPT initiation
<6 months	2 (9.1)	10817.5	18.5 (4.6, 73.9)	Ref.
6-<12 months	1 (4.5)	7753.1	12.9 (1.8, 91.6)	0.73 (0.08, 8.05)	0.796
12-<18 months	2 (9.1)	4537.4	44.1 (11.0, 176.2)	2.32 (0.32, 16.51)	0.402
18-<24 months	0 (0.0)	5574.2	0.0	0.0	---
24-<30 months	1 (4.5)	5567.0	18.0 (2.5, 127.5)	1.01 (0.09, 11.16)	0.994
30 -<36 months	1 (4.5)	9002.2	11.1 (1.6, 78.9)	0.60 (0.05, 6.70)	0.680
36+ months	15 (68.2)	73109.3	20.5 (12.4, 34.0)	1.16 (0.26, 5.09)	0.848
Baseline ART–other
Efavirenz	12 (54.5)	60929.1	19.7 (11.2, 34.7)	Ref.
Nevirapine	9 (40.9)	51457.8	17.5 (9.1, 33.6)	0.92 (0.38, 2.22)	0.844
PI	1 (4.5)	3435.4	29.1 (4.1, 206.6)	1.68 (0.22, 13.01)	0.618
DTG	0 (0.0)	538.4	0.0	0.0	---

Table 3 shows the number diagnosed with TB, total person months, incidence rate and Hazard Ratio (HR) by patients’ demographic and clinical characteristics. Overall, the incidence of TB per 100,000 person months was 18.9 (95% CI: 12.4, 28.7) and it was higher among males than females (Crude hazard ratio (cHR) (95% CI): 1.17 (0.49, 2.80), p = 0.724). The incidence of TB was significantly lower among patients in the age group 25–34 years compared to those aged below 15 years (cHR (95% CI): 0.11 (0.01, 0.88), p = 0.037) but not between the other age groups. Patients in the WHO clinical stage III had higher incidence of TB compared to their counterparts in stage II (cHR (95% CI): 4.27 (1.28, 14.29), p = 0.018). The incidence was lower among patients on baseline TDF-based ART regimen compared to those on AZT (cHR (95% CI): 0.27 (0.10, 0.79), p = 0.016). Patients who stopped IPT had a much higher hazard for TB infection compared to those who completed (cHR (95% CI): 14.54 (3.05, 69.13), p = 0.001).

The variables that were included and retained in the multivariable Frailty model were age group, baseline WHO stage, baseline ART regimen and IPT outcome. After adjusting for these factors, the incidence of TB did not significantly differ between age groups and ART regimen types. However, the incidence remained higher among patients in WHO stage III compared to those in stage II (adjusted hazard ratio (aHR) (95% CI): 3.66 (1.08, 12.42), p = 0.037); and higher among those who discontinued IPT compared to those who completed (aHR (95% CI): 25.96 (4.12, 163.48), p = 0.001).

Discussion

In this study, we followed up 2634 PLHIV on ART who initiated IPT for 116360.7 person-months. A 92.8% IPT completion rate was achieved and a cumulative incidence of 0.8%, an incidence rate of 18.9 per 100,000 person months of TB among PLHIV on ART who initiated IPT was recorded. TB incidence rate after IPT initiation was higher among males than females despite a higher number of TB cases among females in the study. The median time to TB incidence from IPT initiation date was 18.5 months.

The overall TB incidence in this study (equivalent to 0.019 per 100 person years) is lower than those reported by most studies. For example, studies in Zimbabwe (1.06 per 100 person years), South Africa (2.3 per 100 person years), Botswana (0.8 cases per 100 person years) and Indonesia (1.09 per 100 person years) all had higher TB incidences [5, 27, 31, 32] among PLHIV who initiated IPT. TB incidence in this study was also lower than a similar study in Ethiopia (n = 2524, 0.21/100 person years) and another in Tanzania (n = 68,378, 2.7/100 person years); both of which reported incident TB among PLHIV on ART and IPT exposed [21, 22]. Importantly, the Ethiopian study included both pre-and post-ART PLHIV and the Tanzanian study, both IPT exposed and non-exposed PLHIV, which could have contributed to a higher TB incidence. In contrast, the TB incidence in this study was higher than the findings by Nyathi et al. in Zimbabwe [5] with 0 cases recorded following IPT initiation among 214 PLHIV on ART. As Geremew et al. argue, these differences likely result from individual variances among PLIHV on ART such as adherence levels, socioeconomic gradients and country specific TB endemicity [4]. Nonetheless, our findings suggest that TB incidence remains low three years after initiation of IPT among PLHIV on ART.

The low TB incidence in this study is likely due to good adherence to both ART and IPT. Indeed, the IPT completion rate recorded was high, at 92.8%. TASO COEs are special HIV clinics that integrate multi-modal adherence support that could have contributed to high IPT completion rates. PLHIV on ART who initiated but discontinued IPT had higher hazards of incident TB compared to those who completed (see Figs 1 & 2), further underscoring the need to ensure IPT completion. As Ishani et al., and Salazar et al. argue, it is important that individuals who are initiated on IPT are supported to complete the course for maximal benefit. It is perhaps unsurprising that with a completion rate of 94%, the Zimbabwean study recorded zero cases among PLHIV who initiated IPT [5].

Fig 1

Kaplan Meier curves showing proportion surviving from TB infection by WHO HIV clinical stage (panel a) and IPT outcomes (panel b).

Fig 2

Shows probability of surviving TB disease, comparing WHO stages (panel a) and IPT outcomes (panel b) adjusted for clustering and other factors.

The rate of IPT non-completion (7.2%) in the study is comparable to that reported by Sensalire et al. from a program setting [33], but higher than that reported by Lwevola in Eastern Uganda [34] and lower (42%) than that reported by Kalema et al. [35]. Among the patients who discontinued IPT, 20% stopped because of active TB implying failure to exclude TB disease prior to IPT initiation. This underlines one of the challenges to IPT scale up among PLHIV, the inability to exclude active disease, and further validates the need for improved TB screening tools and active patient surveillance after IPT initiation [9, 10, 23]. Other reasons for IPT non-completion such as drug stockouts are the focus of national TB quality improvement programs [24].

Another important finding from this study was that individuals in WHO HIV clinical stage III were more susceptible to active TB disease development compared to those in stage II (see Figs 1 & 2). Comparatively, both the Tanzanian and Ethiopian studies reported association between WHO HIV clinical stage III and active TB disease development [21, 22]. Similarly, Umeokonkwo et al. also reported an association between TB incidence in their study with WHO clinical stages III and IV [36]. WHO clinical stages III and IV are indicators of advanced HIV disease and likely a compromised immune status [37]. As such, individuals who present in these stages often possess cell of differentiation (CD4) count of less than 200 cells/μL, making them substantially vulnerable to developing TB disease [38] regardless of IPT status. Perhaps, findings by Golub et al. substantiate this suggestion [39]. They reported an increased risk of TB incidence among PLHIV whose CD4 counts fell below 200 cells. Similarly, Samandari et al. also reported increased risk of TB incidence when CD4 was below 200 cells/μL [31]. Indeed, Sabasaba et al. reported that CD4 counts above 200 cells/μL were associated with reduced risk of active TB disease development [21]. Adhering to both ART and IPT with fidelity likely increases the CD4 count, as Abossie et al. [7] and Semu et al. [22] reported in their studies. This in turn, restores the integrity of the immune system, hence protection against opportunistic infections such as TB. The individuals who developed active TB disease in our study, likely experienced sub-optimal adherence to both IPT and ART, as evidenced by higher number of cases among those who discontinued the therapy. However, it is important to note that we were unable to rule out additional pathway which includes exposure to fresh bacilli [4] among the TB cases, due to insufficient data.

Finally, the time to TB disease diagnosis was averagely 18.9 months from IPT initiation, a similar finding to that by Semu et al. in Ethiopia [22]. It suggests the effectiveness of IPT in the first six to twelve months of therapy regardless of completion status, among PLHIV on ART.

There were three major study strengths. Firstly, the wide geographical distribution of TASO Centers across Uganda, implying that data are nationally representative. Secondly, the use of routine program data for this study provides evidence that likely reflects actual reality in the field. Finally, we also recognize that routine screening of individuals who received IPT during the follow-up visits, enabled identification of TB cases.

We also acknowledge some key study limitations such as: we used secondary and routine program data, inherently vulnerable to missing variables, leading to exclusion of certain participants who could have added more valuable data. In addition, data on TB exposure factors such as contact with chronic cough cases, smoking and occupation were not collected as these are not routinely documented. Furthermore, the IPT and ART care outcomes of individuals who were lost to follow up, missed appointment or were transferred out could not be ascertained and this could lead to inaccurate estimation of TB incidence in this population. Also, since IPT completion is not objectively measured routinely, we did not ascertain adherence to IPT; but relied on patient chart records of IPT completion that are drawn from patient self-reports, prescription and dispensing records. Furthermore, in six of the TB cases, the diagnosis was made clinically as per MOH Guidelines. Considering the complexity of TB diagnosis in PLHIV, alternative diagnoses could not be excluded and this could have potentially led to an over-estimation of TB incidence.

Recommendations and conclusions

Despite the study limitations discussed previously, our study found a significantly lower TB incidence among PLHIV initiated on IPT compared to earlier studies after three years of follow-up. This is partly attributed to the high completion rates of IPT among our study participants. We therefore, recommend that HIV programs need to support all PLHIV initiating IPT to complete the therapy. In addition, while our study provides nationally representative findings, we only included participants from TASO COEs, that provided additional adherence support which may not necessarily be available in public health facilities. Consequently, findings may be different in those settings.

(XLSX)

Click here for additional data file.

15 Dec 2021

A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Kevin Schwartzman

Academic Editor

PLOS ONE

Journal Requirements:

1. When submitting your revision, we need you to address these additional requirements.

Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Thank you for stating the following in the Acknowledgments Section of your manuscript:

(TASO acknowledges the PEPFAR funding of the eleven TASO centers through CDC, USAID and respective prime partners. The research team also sincerely appreciates the tireless efforts of the following individuals who ensured smooth implementation of the study through resource mobilization, training of research assistants, and supervision of data collection: Gordon Karukoma, Edward Ssimbwa, Esele Brian, Eunic Ajambo, Ogwang Calvin,  Ronald Achidri, Topher Ogwang, Caren Mutalwa, Emma Buxton Maedero, Shamim Namukose, Bernard Ouma Namulanda, Shadrack Ekwaro, Among Marion Gladys, Ritah Kwagala, Ronald Musisi, Banura Rehema, Brumno Kanyonyozi, Daren Mutegeki, Asaba Amos Kugonza, Dickson Niwasasira, Polly Niwamanya, Emmanuel Twesigye, Patience Kembale, Kenneth Nyeko, Emmanuel Welikhe, Nassuuna Maria Rita, Moses Okech, Christine Navvuga, Sunday Clay, and Asuman Ssewaya..)

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

(The authors received no specific funding for this work)

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

4. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For more information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions.

In your revised cover letter, please address the following prompts:

a. If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent.

b. If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories.

We will update your Data Availability statement on your behalf to reflect the information you provide.

5. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript.

6. Please include a separate caption for each figure in your manuscript.

Additional Editor Comments :

Thank you for submitting this manuscript to PLOS ONE. It contains important and useful information for readers. However, the reviewers have made a number of suggestions for improvement; please address these carefully. The manuscript could also be shortened somewhat. Reviewer 2, in particular, has made suggestions for some unnecessary details or other elements that could be shortened or removed.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: No

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Dear all

Thank you for involving me in the review of the intutile “ Incidence of Tuberculosis among PLHIV on Antiretroviral therapy who initiated TB preventive therapy: a multi-center retrospective cohort study” article which I found very interesting and which addressed an essential point of TPT which is the occurrence of TB after TPT in people living with HIV.

Major points

1-Introduction

Clarification of the national guideline in terms of screening of PLWHIV before initiation of TPT. Was TB ruled out clinically, or with a GeneXpert or with an X-ray?

2-Methods:

The usual cut-off point for multivariate regression is 0.20 or 0.25 and not 0.05

3- Results

The age variable: the reference age under 15 years old could be reviewed because in PHIV the child under 15 years old is naturally more vulnerable than an adult subject

Minor revisions

1- There are some unannounced abbreviations

2- The writing of MOH or MoH?

3- Specify the type of multivariate analysis: logistic regression or mixed regression

Ideally the mixed method is the one recommended to take into account the herogeneity between the centers. But failing that, a logistic regression can be carried out if we consider that the sites are almost identical

References

Some suggested references that could be added

1- Economic and modeling evidence for tuberculosis preventive therapy among people living with HIV: A systematic review and meta-analysis Aashna Uppal1,2,3, Samiha RahmanID 1,2,3, Jonathon R. CampbellID 1,2,3, Olivia OxladeID3,Dick MenziesID1,2,3*

2- The latent tuberculosis cascade-of-care among people living with HIV: A systematic review and meta-analysis. Mayara Lisboa Bastos, Luca Melnychuk, Jonathon R. Campbell, Olivia Oxlade, Dick Menzies

PLoS Med. 2021 Sep; 18(9): e1003703. Published online 2021 Sep 7. doi: 0.1371/journal.pmed.1003703

Reviewer #2: Incidence of Tuberculosis among PLHIV on Antiretroviral therapy who initiated TB

preventive therapy: a multi-center retrospective cohort study

This is a cohort study on medium to long-term (36 months minimum) follow up of PLH under ART having had complete or partial TPT. Data derive from routinely collected information under programmatic conditions. This is a relevant subject, as the duration of protection from TPT is controversial, with studies in various settings having shown conflicting results. Thus, there is no consensus on the need for long-term, repeated or even lifelong use of TPT in PLH.

The analysis and conclusions are sound. The treatment completion rate under routine condition was very high (>92%) and the incidence rate was low among those who completed treatment (and overall, as most did complete) over time. CD4, viral load and duration/type of ART had no effect, although clinical stage of disease had. Limitations (mainly possible bias from exclusions and absence of information on reexposure to TB index-patients) and strengths of the study are well discussed. However, the manuscript would benefit from some rewriting. General suggestions for this follow, but I would advise careful language review.

Title (and throughout the text): consider using the term isoniazide preventive therapy (or treatment) as this is what was analyzed, other TPT were not assessed. Also consider using the TBI instead of LTBI, as now suggested by WHO.

Abstract: Ugandan setting does not need to be discussed in the background of the abstract, as this is a matter of interest around the globe. Adjusted (instead of crude) HR could be displayed here. The conclusion in the abstract is misleading. The authors could highlight here the main messages: incidence rates of TB were low overtime after one course of IPT, and this was mainly due to high completion rates.

The introduction could be substantially shortened. Firstly, the need for TPT in PLH and other high-risk group is well established, and the authors do not need to make a strong case on this, just a couple of sentences are sufficient. They could cite the literature on the specific subject of their analysis (for example, Samandari et al https://doi.org/10.1097/QAD.0000000000000535, Golub et al https://doi.org/10.1093/cid/ciu849) and emphasize the need for more long-term follow up studies to generate evidence on the ideal duration of TPT. Additionally, this is a relevant matter outside Uganda as well. Thus, I recommend that the authors move some information on the Uganda national recommendations to the Methods section, under “Setting”. The Uganda case is an example of the interest of this subject, which is relevant around the globe. Finally, the Introduction needs updating (WHO report 2020 available).

In the methods section, please clarify if patients starting or using IPT in the study period were included. Later in the text it seems that this is those starting IPT. Please define “stop therapy”. The heading “sample size” is not necessary, the information contained there should be moved to the Results section. Table 1 could be moved to supplement material. The subheading “patient enrolment” could be renamed data extraction. Participants were not exactly enrolled, this is a retrospective study on existing routine data. The exposure variables should be defined in the methods section, after definition of outcomes. It is not clear how the authors “triangulated” data with de-identified registries. Variables cited in the methods section that are not reported in the results section should be suppressed from there (ART status, type of TB, microbiological tests).

Please clarify the following:

• Are registered individuals those who were prescribe or those who initiated IPT? Meaning, are those who did not start (primary drop-out) included?

• Line 47: How can death be based on clinical encounter?

• Line 123: “All PLHIV who received TPT from 1st January 2016 to 30th June 2018”… This is a 30-month period but then you refer to 3 years or 36 months. I believe this means that the period of study is those starting IPT, and then they were followed up until 2021, for a minimum of 3 years, as very clearly explained in the abstract (please use same wording).

• Was treatment interruption considered at any number of doses taken? Early studies by Comstock suggest that 80% of doses are protective. Do the authors have information on the mean number of doses taken by those who did not complete IPT?

• Do the authors have information on cause of death? How was death information collected? I suggest a sensitivity analysis including deaths as a TB outcome (instead of censoring). TB is still the most frequent cause of death among PLH.

In the Results section, please inform overall incidence rate (per 100k person-month) as defined in the methods section and shown in the abstract, first paragraph of discussion and table 3. This information is more meaningful than the cumulative incidence. The p values are unnecessary, as the CI are displayed. Please consider a “survival curve” figure to illustrate TB cases (I would choose those completing versus those not completing IPT, the difference is impressive, as expected).

In table 3, do those lost to follow up include all censored? Please add footnote to tables, with abbreviations and this kind of clarification.

The discussion needs to be substantially shortened. The main message seems to be that completed TPT (or preferably, IPT) is associated with sustained protection (at least in the period of the study), as TB incidence rates remain low after a minimum period of 3 years. Maybe also that the mean time to TB development is 18 months. Also worthy discussing effect of clinical indicators of severity of HIV disease and absence of effect of other indicators of severity of disease, such as CD4 or type/duration of ART. None of these latter findings is surprising or novel, but the information that incident TB disease remains low after this long period is relevant and adds some light to the knowledge gap defined in the Introduction. This should be the main focus of the discussion. Do not include a detailed discussion (or even less speculation on why – this was not what you assessed) on every variable that was not associated with the outcome of interest. Above all, do not repeat detailed findings in the Discussion section. You can just summarize the main results in the first paragraph. For the sake of clarity for the reader, the authors could calculate the corresponding incidence rates in Tanzania and Ethiopia in the same unit as their findings (cases per 100,000 persons-months). A striking finding that also needs discussion, and explains the low incidence rate overall of TB, is the extremely high treatment completion rates. Mechanisms of drug action and BCG vaccination were not assessed and the discussion on these aspects is not useful. This is unusual under routine conditions. The support detailed in the methods section (lines 118-120) is probably related to these high completion rates and should be discussed. Limitations and strengths of the study should be incorporated to the discussion. An additional strength of the study is the active screening for incident TB in follow up visits.

Finally, why do the authors conclude that 3 years would be a potential timing for retreatment, if they found 18m as the median time to TB diagnosis? As the authors discuss, they do not have data on re-exposure, and it is not reasonable to speculate, based on their results, a potential timing for retreatment. I also disagree that the authors identified populations who might benefit from retreatment, this was not evaluated. Conclusions should be restricted to what was evaluated, anything else can be discussed, speculated, but not concluded.

Minor comments:

Please verify all abbreviations. TASO, cHR, WHO are used in abstract without definition. In the main text, other non-defined abbreviations appear, such as ART and aHR, please check all.

Consider changing “stopping” to discontinuation of treatment.

Also in the abstract, no space between numbers and th for dates. (1st, not 1 st)

I suggest changing patients enrolled to patients initiated on IPT.

Line 126 – should be in results (exclusion)

Many words with unjustified capital letters, such as the title and the variables in the Methods section.

Line 147 follow up

The discussion states “In the present study” at least 5 times. This is not necessary. The reader will know you are discussing your results.

L. 318 – discussed highlighted

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

28 Jan 2022

1. The funding information was removed from the manuscript

2. Ethical statement only appears once, under the methodology section

3. Manuscript has been aligned with the journal standard

Submitted filename: Response to the Reviewers.docx

Click here for additional data file.

7 Mar 2022

10 Mar 2022

We have appropriately responded to the reviewers' concerns

Submitted filename: Response to Reviewers.docx

Click here for additional data file.

18 Mar 2022

Incidence of Tuberculosis among PLHIV on Antiretroviral therapy who initiated isoniazid preventive therapy: a multi-center retrospective cohort study

PONE-D-21-33906R2

Dear Dr. Oryokot ,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Kevin Schwartzman

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Thank you for making these last revisions.

Reviewers' comments:

4 May 2022

PONE-D-21-33906R2

Incidence of Tuberculosis among PLHIV on Antiretroviral therapy who initiated isoniazid preventive therapy: a multi-center retrospective cohort study

Dear Dr. Oryokot :

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Kevin Schwartzman

Academic Editor

PLOS ONE