Tracking cross-border transmission of Rwanda’s successful dominant rifampicin-resistant Mycobacterium tuberculosis clone using genomic markers

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1. 

   PREreview

   Apr 13, 2026

   This Zenodo record is a permanently preserved version of a Structured PREreview. You can view the complete PREreview at https://prereview.org/reviews/19546527.

   Does the introduction explain the objective of the research presented in the preprint? Partly Yes, but it could be clearer. The final paragraph lays out what they did in the study. They defined a unique signature for R3clone identification through targeted molecular diagnostics and used this signature to screen isolates from neighboring countries and public genomic databases to explore the geographic extent and cross-border transmission potential of the clone.

   Are the methods well-suited for this research? …

   This Zenodo record is a permanently preserved version of a Structured PREreview. You can view the complete PREreview at https://prereview.org/reviews/19546527.

   Does the introduction explain the objective of the research presented in the preprint? Partly Yes, but it could be clearer. The final paragraph lays out what they did in the study. They defined a unique signature for R3clone identification through targeted molecular diagnostics and used this signature to screen isolates from neighboring countries and public genomic databases to explore the geographic extent and cross-border transmission potential of the clone.

   Are the methods well-suited for this research? Somewhat appropriate They used appropriate techniques for WGS and phylodynamic modeling (BEAST software w/Bayesian methods). They also used three complementary markers to ID the clone (drug resistance mutations, spoligotyping, clone-specific SNP). The qPCR validation also appears to be a strong validation approach. Overall, genomic methods are excellent. The study design has some flaws. The sampling in Burundi was convenience sampling. There design also excluded low-bacterial-load cases, and had unequal sampling across the countries they were investigating. In addition, Burundi's sample ends in 2013, while Rwanda's starts in 2021. This 8 year gap makes transmission inference very challenging as the methods cannot differentiate between historical and ongoing transmission. There is also not epidemiological linkage (travel data, contact info) to support "transmission" claims.

   Are the conclusions supported by the data? Somewhat supported The R3clone dynamics in Rwanda, the qPCR specificity, the fact that the clone exits beyond Rwanda and the characteristic mutations identified consistently across samples were well-supported. The authors acknowledge the limitations of their cross-border transmission claim, but would argue that their claim that "urgent regional coordination" is needed is not supported. Their results show that this clone has spread to neighbors around a decade ago, and given the Burundi data ends in 2013, we do not know if the strain is still circulating. In addition, the "global presence" claim may be overstated because the existence of R3clone in public databases in Bangladesh, Peru and Belgium does not mean that it is truly circulating.

   Are the data presentations, including visualizations, well-suited to represent the data? Somewhat appropriate and clear The figures are generally clear overall. The flowchart shows sample flow, the Skyride plot shows the R3clone's rise and fall over time. It could be helpful to have a geographic map showing where the clone actually circulates. A timeline when samples were collected could be helpful. In addition, a figure describing qPCR validation would make limitations more transparent, and allow readers to better interpret claims about cross-border transmission.

   How clearly do the authors discuss, explain, and interpret their findings and potential next steps for the research? Somewhat clearly Limitations are honestly acknowledged, and it does show self-awareness about the data gaps. I would argue that they are unclear about the true significance of their findings or urgency of policy action. Why is coordinated action needed now when the neighbor data is over a decade old? They also don't provide very specific next steps other than, "apply this framework to other strains".

   Is the preprint likely to advance academic knowledge? Somewhat likely The preprint provides a novel clone-specific molecular diagnostic that could have immediate clinical utility. They also provide a template for other low-resource countries to track other regional TB clones. The idea that MDR TB spreads across borders, however, is not new. The main finding from their research is not necessarily novel; the novelty lies primarily within the qPCR assay that was developed.

   Would it benefit from language editing? No Writing was clear and easy to understand overall.

   Would you recommend this preprint to others? Yes, but it needs to be improved Clarifying urgency claims, separate the proven from speculative findings and strengthen the discussion around the SRA database. Adding a geographic visualization, providing next steps and explicitly acknowledging that directionality cannot be determined would be good steps to take.

   Is it ready for attention from an editor, publisher or broader audience? Yes, after minor changes

   Competing interests

   The author declares that they have no competing interests.

   Use of Artificial Intelligence (AI)

   The author declares that they did not use generative AI to come up with new ideas for their review.

   Read the original source
2. 

   PREreview

   Apr 13, 2026

   This Zenodo record is a permanently preserved version of a Structured PREreview. You can view the complete PREreview at https://prereview.org/reviews/19546597.

   Does the introduction explain the objective of the research presented in the preprint? Yes Yes, the objective is clearly stated in the final paragraph of the introduction. Their goal was twofold: 1) to define a unique unique genetic signature for the R3clone identification through targeted molecular diagnostics and 2) using this definition, screen isolates from neighbouring countries and public genomic databases to explore the geographic extent and cross-border transmission potential of the clone.

   Are the methods well-suited for this research? …

   This Zenodo record is a permanently preserved version of a Structured PREreview. You can view the complete PREreview at https://prereview.org/reviews/19546597.

   Does the introduction explain the objective of the research presented in the preprint? Yes Yes, the objective is clearly stated in the final paragraph of the introduction. Their goal was twofold: 1) to define a unique unique genetic signature for the R3clone identification through targeted molecular diagnostics and 2) using this definition, screen isolates from neighbouring countries and public genomic databases to explore the geographic extent and cross-border transmission potential of the clone.

   Are the methods well-suited for this research? Somewhat appropriate The researchers used the genomic methods appropriately. WGS and phylodynamic modeling are gold standard for tracking TB population dynamics. They also used multi-pronged identification to identify the clone, and validated the clone against WGS, which is also a strong approach. The flaws include: Sampling bias (especially convenience bias in Burundi). They also excluded low bacterial-load cases which may have undercounted their prevalence. In addition, the Burundi samples end in 2013, but Rwanda starts sampling in 2021. This 8 year gap makes it challenging to make any inferences about transmission (historical vs ongoing). They also used a self-described "loose" threshold of 12-SNP, and had to add rules after the analysis to track mutated clones.

   Are the conclusions supported by the data? Somewhat supported The R3clone's population dynamics in Rwanada are well supported, and so is the specificity of the qPCR assay developed. It is also clear that this clone does exist beyond Rwanda. Although the authors acknowledge the limitation of their cross-border transmission claim, there is no epidemiological evidence (patient travel, timing, contacts) to support this. In addition, they claim that the existence of two R3clone subgroups in Burundi with different mutations suggests "bidirectional movement". We don't have temporal data (i.e. which country had cases first?) to establish this movement. Finally, their claim that "urgent regional coordination is needed" may not be accurate given we have no current data showing that the R3clone is actively spreading in sub-Saharan Africa.

   Are the data presentations, including visualizations, well-suited to represent the data? Somewhat appropriate and clear Main figures (flowchart, Skyride plot) are clear and well-labeled with good use of color-coding and sizing. They are lacking geographic visualizations, temporal information, and the distribution of SRA isolates globally.

   How clearly do the authors discuss, explain, and interpret their findings and potential next steps for the research? Somewhat clearly They clearly explain methods, and talk about their limitations. But, they are unclear about why coordinated regional action is needed now when the data is quite old. In addition, they don't provide concrete next steps other than "apply this framework to other strains". The discussion shows knowledge of epidemiological concepts, but there should be more clarity surrounding the transmission directionality claims and urgency of regional coordination.

   Is the preprint likely to advance academic knowledge? Somewhat likely The qPCR tool and surveillence framework have real practical value, especially for lower resourced countries. The main policy conclusions about urgent regional transmission threats, however, are not supported. No real information is provided about how or when the R3clone is spreading, just that it does exist in places outside of Rwanda.

   Would it benefit from language editing? No Strong language, no major grammatical issues noted.

   Would you recommend this preprint to others? Yes, but it needs to be improved

   Is it ready for attention from an editor, publisher or broader audience? Yes, after minor changes

   Competing interests

   The author declares that they have no competing interests.

   Use of Artificial Intelligence (AI)

   The author declares that they did not use generative AI to come up with new ideas for their review.

   Read the original source
3. 

   Version published to 10.64898/2026.03.29.26349652 on medRxiv

   Mar 31, 2026