Endogenous relapse and exogenous reinfection in recurrent pulmonary tuberculosis: A retrospective study revealed by whole genome sequencing

Characterizing the Etiology of Recurrent Tuberculosis Using Whole Genome Sequencing: Alaska, 2008-2020

BACKGROUND

Understanding the etiology of recurrent tuberculosis (rTB) is important for effective tuberculosis control. Prior to the advent of whole genome sequencing (WGS), attributing rTB to relapse or reinfection using genetic information was complicated by the limited resolution of conventional genotyping methods.

METHODS

We applied a systematic method of evaluating whole genome single-nucleotide polymorphism (wgSNP) distances and results of phylogenetic analyses to characterize the etiology of rTB in American Indian and Alaska Native (AIAN) persons in Alaska during 2008 to 2020. We contextualized our findings through descriptive analyses of surveillance data and results of a literature search for investigations that characterized rTB etiology using WGS.

RESULTS

The percentage of tuberculosis cases in AIAN persons in Alaska classified as recurrent episodes (11.8%) was 3 times the national percentage (3.9%). Of 38 recurrent episodes included in genetic analyses, we attributed 25 (65.8%) to reinfection based on wgSNP distances and phylogenetic analyses; this proportion was the highest among 16 published point estimates identified through the literature search. By comparison, we attributed 11 (28.9%) and 6 (15.8%) recurrent episodes to reinfection based on wgSNP distances alone and on conventional genotyping methods, respectively.

CONCLUSIONS

WGS and attribution criteria involving genetic distances and patterns of relatedness can provide an effective means of elucidating rTB etiology. Our findings indicate that rTB occurs at high proportions among AIAN persons in Alaska and is frequently attributable to reinfection, reinforcing the importance of active surveillance and control measures to limit the spread of tuberculosis disease in Alaskan AIAN communities.

Endogenous reactivation cases identified by whole genome sequencing of Mycobacterium tuberculosis: Exploration of possible causes in Latvian tuberculosis patients

Background

The recurrence of tuberculosis (TB) continues to place a significant burden on patients and TB programs worldwide. Repeated TB episodes can develop either due to endogenous reactivation of previously treated TB or exogenous reinfection with a distinct strain of Mycobacterium tuberculosis (Mtb). Determining the precise cause of the recurrent TB episodes and identifying reasons for endogenous reactivation of previously successfully treated patients is crucial for introducing effective TB control measures.

Methods

Here, we aimed to provide a retrospective individual analysis of the clinical data of pulmonary TB patients with assumed endogenous infection reactivation based on WGS results to identify the reasons for reactivation. Patient medical files were reviewed to describe the provoking factors for endogenous reactivation.

Results

In total, 25 patients with assumed endogenous TB reactivation were included in the study group, and 30 patients with one TB episode during the study period were included in the control group. There were no statistically significant differences identified between studied patient groups in patients age (t(53) = -1.53, p = 0.13), body mass index (t(53) = 0.82, p = 0.42), area of residency (χ2 (1;55) = 0.015, p = 0.9), employment status (χ2 (1;55) = 0.076, p = 0.78) and presence of comorbidities (χ2 (1;55) = 3.67, p = 0.78). Study group patients had statistically significantly more frequently positive sputum smear microscopy results (χ2 (1;55) = 8.72, p = 0.0031), longer time to sputum smear (t(31) = -2.2, p = 0.036) and sputum culture conversion (W (55) = 198.5, p = 0.0029). Smoking was statistically significantly (χ2 (1;55) = 5.77, p = 0.016) more frequently represented among study group patients. The median treatment duration for drug susceptible TB was 6 months in both in the control group (IQR 6-6) and among study group patients (IQR 6-7.75). The median treatment duration for multidrug-resistant TB was 20 months (IQR 17-23) in the control group and 19 months (IQR 16-19) in the study group patients.

Conclusion

Positive SSM for acid-fast bacteria, delayed time to sputum smear and sputum culture conversion, smoking, and incomplete therapy in the study group patients with multidrug-resistant TB should be considered as potential reasons for reactivation in recurrent TB patient group in our study.

Active tuberculosis disease among people living with HIV on ART who completed tuberculosis preventive therapy at three public hospitals in Uganda

Tuberculosis (TB) preventive therapy (TPT) reduces the incidence of TB among people living with the human immunodeficiency virus (PLHIV). However, despite an increase in TPT uptake, TB/HIV coinfection remains stagnant in Uganda especially in areas of increasing HIV incidence such as the Bunyoro sub-region. This study was a retrospective review records (antiretroviral therapy [ART] files) of PLHIV who were active on ART and completed TPT in 2019/2020 at three major hospitals in the Bunyoro sub-region, Uganda: Masindi General Hospital, Hoima Regional Referral Hospital, and Kiryandongo General Hospital. The sample size (987) for each facility was determined using a proportionate sampling method to ensure the study's power and precision. Factors independently associated with acquiring TB disease post TPT were determined using modified Poisson regression analysis. An adjusted prevalence risk ratio (aPRR) with corresponding 95% confidence intervals were reported. The participants' mean age was 38.23 (±11.70) and the majority were female (64.94%). Overall, 9.63% developed active TB disease post TPT completion. In the adjusted analysis, factors associated with active TB disease were a history of an unsuppressed viral load after TPT (aPRR 4.64 (2.85-7.56), p<0.001), opportunistic infections after TPT completion (aPRR 4.31 (aPRR 2.58-7.2), p<0.001), a history of TB active TB disease (aPRR 1.60 (1.06-2.41), p = 0.026), and chronic illness during or after TPT (aPRR 1.68 (1.03-2.73), p = 0.038). To reduce the development of TB disease post TPT thereby improving the effectiveness of TPT, ART adherence should be emphasized to resolve viral suppression and active management of chronic and opportunistic infections. Further clinical management consideration and research is needed for PLHIV who receive TPT but have a previous history of TB disease.

Timing of recurrence after treatment of pulmonary TB

Pulmonary TB (PTB) may recur due to reinfection or relapse after initial successful treatment. Based on microbiologically documented cases, we searched Embase, PubMed, Web of Science, and Medline for PTB recurrence. The timeframe of overall recurrences, relapse, reinfection, and risk factors were assessed. We compared the time to recurrence, relapse, and reinfection from treatment completion and plotted this using Kaplan-Meier curves. This systematic review included 23 articles describing 2,153 PTB recurrences in 75,224 treated people across all continents. Genotyping data to distinguish relapse from reinfection was available for 402 recurrences. The cumulative recurrence percentage was 2.9% over 5 years, and the median time for recurrence was 18 months (95% CI 16.99-19.0). Most recurrences (93%) were in HIV-negative people. Relapse occurred earlier than reinfection at 12 months (95% CI 10.86-13.14) vs 24 months (95% CI 21.61-26.39) (P < 0.001, χ2 59.89). In low TB burden settings, recurrences were mainly caused by relapse (85%), whereas in high-burden settings, relapses comprised 56% of recurrences. Recurrences occurred slightly earlier in HIV-positive patients (P = 0.038, χ2 4.30). The emergence of resistance to one or more first-line anti-TB agents was documented in 40 of 421 cases (9.5%). Early recurrences are mainly relapses, while late recurrences are mainly reinfections.

Antibiotic treatment modestly reduces protection against Mycobacterium tuberculosis reinfection in macaques

Concomitant immunity is generally defined as an ongoing infection providing protection against reinfection . Its role in prevention of tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is supported by epidemiological evidence in humans as well as experimental evidence in mice and non-human primates (NHPs). Whether the presence of live Mtb, rather than simply persistent antigen, is necessary for concomitant immunity in TB is still unclear. Here, we investigated whether live Mtb plays a measurable role in control of secondary Mtb infection. Using cynomolgus macaques, molecularly barcoded Mtb libraries, positron emission tomography-computed tomography (PET CT) imaging, flow cytometry, and cytokine profiling, we evaluated the effect of antibiotic treatment after primary infection on immunological response and bacterial establishment, dissemination, and burden post-secondary infection. Our data provide evidence that, in this experimental model, treatment with antibiotics after primary infection reduced inflammation in the lung but was not associated with a significant change in bacterial establishment, dissemination, or burden in the lung or lymph nodes. Nonetheless, treatment of the prior infection with antibiotics did result in a modest reduction in protection against reinfection: none of the seven antibiotic-treated animals demonstrated sterilizing immunity against reinfection, while four of the seven non-treated macaques were completely protected against reinfection. These findings support that antibiotic-treated animals were still able to restrict bacterial establishment and dissemination after rechallenge compared to naïve macaques, but not to the full extent of non-antibiotic-treated macaques.

Antibiotic treatment modestly reduces protection against Mycobacterium tuberculosis reinfection in macaques

Concomitant immunity is generally defined as an ongoing infection providing protection against reinfection1. Its role in prevention of tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is supported by epidemiological evidence in humans as well as experimental evidence in mice and non-human primates (NHPs). Whether the presence of live Mtb, rather than simply persistent antigen, is necessary for concomitant immunity in TB is still unclear. Here, we investigated whether live Mtb plays a measurable role in control of secondary Mtb infection. Using cynomolgus macaques, molecularly barcoded Mtb libraries, PET-CT imaging, flow cytometry and cytokine profiling we evaluated the effect of antibiotic treatment after primary infection on immunological response and bacterial establishment, dissemination, and burden post-secondary infection. Our data provide evidence that, in this experimental model, treatment with antibiotics after primary infection reduced inflammation in the lung but was not associated with a significant change in bacterial establishment, dissemination or burden in the lung or lymph nodes. Nonetheless, treatment of the prior infection with antibiotics did result in a modest reduction in protection against reinfection: none of the 7 antibiotic treated animals demonstrated sterilizing immunity against reinfection while 4 of the 7 non-treated macaques were completely protected against reinfection. These findings support that antibiotic-treated animals were still able to restrict bacterial establishment and dissemination after rechallenge compared to naïve macaques, but not to the full extent of non-antibiotic treated macaques.