The Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium tuberculosis Strains Isolated from Patients in the Rural Eastern Cape Province

Round 1

Reviewer 1 Report (Previous Reviewer 1)

Drug-resistant tuberculosis (DR-TB) is a significant concern in South Africa, particularly in the rural Eastern Cape Province. However, no prior studies have examined gene mutations and genotyping of DR-TB in this area. The aim of this study was to identify DR-TB mutations, evaluate genetic diversity, determine prevalent mutations, and classify lineages among patients in the region.

 

Sputum samples were collected from 1157 suspected tuberculosis patients, and rifampin resistance was assessed using Xpert® MTB/RIF. GenoType MTBDRplus VER 2.0 was utilized to detect mutations associated with resistance to anti-TB drugs. Additionally, spoligotyping was performed on 441 isolates.

 

The most common mutation causing rifampin resistance was found in the rpoB codon S531L. In INH-resistant strains, the katG gene at codon S315TB and the inhA gene at codon C-15TB exhibited the highest mutation rates (54.5% and 24.7% respectively). Moreover, 24.6% of strains had mutations in both rpoB and inhA genes, while 69.9% had mutations in both katG and rpoB genes. Heteroresistance was observed in 17.9% of cases.

 

Spoligotyping analysis revealed that the dominant lineage was the Beijing family. The diversity of mutations provided valuable insights into the evolutionary lineages of M. tuberculosis isolates. The frequency of rpoB, katG, and inhA mutations in different study areas can aid in determining treatment approaches, whether standardized or individualized, in regions where these mutations are prevalent.

 

In conclusion, this study provides important information about gene mutations and genetic diversity of DR-TB in the rural Eastern Cape Province. These findings offer crucial insights for enhancing tuberculosis treatment strategies in the affected regions.

 

After revising the manuscript, the authors have made significant improvements and added additional information that enhances the overall understanding of Mtb treatment in the rural Eastern Cape Province. The revised manuscript now provides more comprehensive data and insights.

 

Author Response

Dear Editor

 

Thank you for the comments, very much appreciated.

 

Regards

Lindiwe

Reviewer 2 Report (New Reviewer)

Thank you for a highly relevant and excellently designed and developed manuscript!  

A difficult technical area is well presented and articulated very clearly for both highly specialized and non-laboratory audiences.  The research makes a significant contribution and advances the genotyping agenda for increased use for both surveillance and programmatic/clinical decision making.

The last point could be better elaborated in the discussion and recommendations section.   What is the significance of these research results for both surveillance and clinical management of DR-TB cases? 

Thanks! 

N/A

Author Response

Dear Editor

 

Thank you for the review comments, the significance of the findings are covered on lines 397 to 402.

Regards

Lindiwe

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

This article discusses a research study carried out in South Africa that aimed to evaluate the occurrence of drug resistance and gene mutations related to tuberculosis (TB). The study's objectives included identifying mutations in genes associated with drug resistance (rpoB, katG, and inhA) and determining the strains and lineages of drug-resistant TB (DR-TB). Over a span of three years, a total of 1,157 clinical isolates were examined, revealing that 82.1% of the isolates exhibited drug resistance, including multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). The most common mutations associated with resistance were observed at positions rpoB 531 and katG 315, leading to resistance against rifampicin (RIF) and isoniazid (INH), respectively. Additionally, the study identified heteroresistance in 17.9% of the isolates, which refers to the presence of both drug-resistant and drug-susceptible bacteria within a single patient. The analysis of spoligotyping unveiled various genotyping lineages, with the Beijing family being the most prevalent. This study emphasizes the significance of monitoring drug resistance and gene mutations to effectively control and manage TB in rural regions.

 

Nevertheless, it is worth noting that this preliminary information has been previously investigated and explored by other Mtb research groups, irrespective of the assertion made regarding its potential as a drug target.

 

 

 

 

 

 

Major concerns:

 

 

1-    The manuscript exhibits deficiencies in its writing style, containing numerous grammatical errors and typographical mistakes throughout, starting from the abstract and continuing until the conclusion. Furthermore, the majority of the content seems superficial and lacks clarity, thereby hindering comprehension of the article.

 

 

 

2-    Lack of clearly defined research objectives: The introduction fails to explicitly state the research objectives or questions that the study aims to address. By clearly articulating the objectives, readers would gain a better understanding of the study's purpose and focus.

 

 

3-    Limited context and background information: While the introduction briefly touches upon the global burden of tuberculosis (TB) and its impact in South Africa, it lacks a comprehensive overview of the current state of TB, drug resistance, and existing literature on the subject. Providing more context and background information would aid readers in understanding the study's significance and its contribution to the field.

 

4-    Inadequate explanation of methods: The materials and methods section offers a general overview of the study design and procedures, but it lacks specific details. It would be beneficial to provide more information about the criteria for patient enrollment, the selection process for healthcare facilities, and the specimen collection process. Additionally, additional details regarding the Xpert MTB/RIF assay and phenotypic drug susceptibility testing (DST) methods could be included.

 

5-    Limited discussion of results: Although the results section presents numerical data on the prevalence of drug resistance mutations and heteroresistance, it lacks a comprehensive analysis or interpretation of the findings. It would be valuable to discuss the implications of the results, compare them to previous studies, and highlight any noteworthy trends or patterns.

 

6-    Insufficient conclusion: The text lacks a separate conclusion section or a clear summary of the main findings. A well-structured conclusion would assist readers in understanding the key takeaways from the study and its potential implications.

 

7-    Need for additional information: The text provides limited information on the study's limitations, the significance of the findings, and potential future directions for research. Including these aspects would enhance the overall completeness of the study.

 

 

 

 

 

 

The English language employed is either difficult to understand or completely incomprehensible.

Reviewer 2 Report

Dear authors,

The work is relevant to the community, however, some points need to be clarified before it can be considered appropriate for publication.

1. In general, all figures should have their written parts edited to improve resolution and readability.

2. In the introduction, some references should be included to support the information, such as lines 39-40, 55-57, and 58-59.   The introduction should also be supplemented to define heteroresistant strain for the reader.

3. In lines 138-142, the sentences are not structured in a way that allows easy comprehension and are not supported by what is shown in Table 1. What is described as DR-TB case n (%) would not be the total? Please clarify this.

4. In the Results section, the writing should be carefully revised and described in a more concise and direct manner.

5. Please clarify the meaning of "WT" in Figure 2, what does it represent in this figure?

6. Consider using tables to represent the results of heteroresistance and Spoligotyping.

7. Why are the data not amenable to statistical analysis?

8. The discussion is the most substantiated part of the work, the other sections should strive to achieve the same level to balance the work.

My best wishes.

Minor adjustments in English editing are necessary