High proportion of RR-TB and mutations conferring RR outside of the RRDR of the rpoB gene detected in GeneXpert MTB/RIF assay positive pulmonary tuberculosis cases, in Addis Ababa, Ethiopia

Prevalence of drug-resistant Mycobacterium tuberculosis and its associated factors among tuberculosis patients attending Dilla university referral hospital, Ethiopia

BACKGROUND

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (MTB) and is the second leading cause of death from contagious diseases worldwide. Ethiopia is among the 30 countries with the highest burden of TB and TB/HIV co-infection. The emergence and spread of drug-resistant TB present significant challenges to TB care and control efforts, particularly multi-drug-resistant TB, which poses a serious public health issue in low-income countries such as Ethiopia. This study aimed to determine the prevalence of drug-resistant TB and its associated factors among TB patients in Dilla University Referral Hospital (DURH).

METHOD

A prospective cross-sectional study was conducted from March-2024 to May-2024 among 216 pulmonary TB patients attending DURH. Gene Xpert MTB/RIF Ultra and Xpert MTB/XDR assay was used to assess the pattern of drug resistance in TB. The Xpert MTB/RIF Ultra assay was used to detect rifampicin resistance, while the Xpert MTB/XDR assay was employed to identify isoniazid resistance and resistance to second-line anti-TB drugs when rifampicin resistance was detected. Data were analyzed by using the Statistical Package for Social Sciences (SPSS) version 25.

RESULT

In this study, out of 216 confirmed MTB cases, 5 (2.3%) were identified as drug-resistant TB (DR-TB), with mono-resistance to rifampicin and isoniazid at 1.4% and 0.9%, respectively. The statistical analysis revealed a significant difference in DR-TB prevalence between those with and without a history of anti-TB treatment (p = 0.001). Notably, isoniazid mono-resistant TB was more prevalent among individuals with diabetes mellitus and those with a history of previous treatment, showing p-values of 0.018 and 0.015, respectively.

CONCLUSION

Among the 216 confirmed TB cases, 5 cases of DR-TB were identified, accounting for 2.3%. DR-TB was more prevalent in patients with a history of anti-TB treatment, highlighting the urgent need for enhanced early detection and improved treatment monitoring. Additionally, isoniazid mono-resistant TB was notably prevalent in individuals with diabetes mellitus and prior treatment history, with p-values of 0.018 and 0.015, respectively. Targeted interventions for these high-risk groups are essential to address drug resistance in TB, enabling us to effectively tackle the emergence of drug-resistant TB at both local and national levels.

Retrospective epidemiological analysis of pulmonary tuberculosis in the older adult and characterization of rifampicin resistance-associated rpoB mutations in Nantong City, China (2014-2023)

Objective

To analyze the prevalence trend of older adult pulmonary tuberculosis (ETB) and the distribution and outcome of rifampicin-resistant rpoB gene mutation in ETB patients in Nantong.

Methods

The pulmonary tuberculosis patients' data in Nantong from 2014 to 2023 were from Tuberculosis Information Management Syste and ETB and rifampicin-resistant rpoB mutation patients were retrospectively analyzed.

Results

From 2014 to 2023, the overall standardized incidence of ETB in Nantong showed a trend of rapid decline and tended to a stable trend stabilized. A total of 140 older adult patients with rifampin resistance, aged 60-69 years, 87 cases (62.1%). single-gene mutation Probe E mutations were the most frequent, observed in 39 cases (60.0%). Specifically, 52 cases (80.00%) were resistant to rifampicin, and Probe E of 31 cases (59.62%) showed the most mutations. The outcome of ETB patients with rifampicin resistance were significantly correlated with treatment classification, rifampicin resistance, Xpert MTB first test, and 0-month sequential sputum positivity.

Conclusion

The number of ETB in Nantong from 2014 to 2023 showed a rapid decline and stabilized. The rpoB mutations in the ETB rifampicin-resistant patients were mainly single-gene mutations. The authorities should formulate effective regional prevention and control measures based on the characteristics of the ETB rifampicin-resistant patients.

Prevalence of Pulmonary Tuberculosis and Rifampicin Resistance Among Patients Attending Adama Hospital Medical College

Background: Tuberculosis (TB) is among the leading causes of morbidity and mortality in resource-limited countries. The burden of TB varies from country to country, depending on the country's condition and the effort made to prevent its transmission. The magnitude of pulmonary TB and drug resistance in eastern Ethiopia is mainly unknown due to limited information. Objective: This study aimed to determine the prevalence of pulmonary TB and rifampicin-resistant Mycobacterium tuberculosis and factors associated with pulmonary TB. Methods: A hospital-based prospective cross-sectional study was conducted among 424 presumptive TB patients who attended Adama Hospital Medical College from January 10, 2023, to November 10, 2023. Sputum (gastric lavage for children) was collected and diagnosed using the Ziehl-Neelsen (ZN) staining method and GeneXpert. A structured questionnaire was used to collect sociodemographic and clinical data. SPSS Version 20 computer software was used for data analysis. A variable with a p value less than 0.05 was considered statistically significant. Results: The prevalence of the ZN staining method and GeneXpert-confirmed TB was 160 (37.7%), 95% CI: 33-42.7 and 189 (44.6%), 95% CI: 39.8-49.5, respectively. Of the study participants, nine (2.1%) were infected with rifampicin-resistant M. tuberculosis. Out of the 189 confirmed TB cases, 4.7% were infected with rifampicin-resistant gene-positive M. tuberculosis. Gender-male (AOR = 1.47 [0.95-2.26], p=0.081), history of contact with TB patient (AOR = 7.19 [2.55-20.25], p < 0.001), previously treated TB patients (AOR = 3.11 [1.49-6.50], p=0.003), and smoking cigarette (AOR = 14.8 [1.88-117], p=0.010) were significantly associated with GeneXpert-confirmed pulmonary TB. Conclusion: The prevalence of pulmonary TB was high, with a moderate proportion of rifampicin-resistant gene-carrying M. tuberculosis in the study area. Being male, having a history of contact with TB patients, having a history of infection with TB, and smoking cigarettes were significant predictors of pulmonary TB.

Transmission of multidrug-resistant tuberculosis in Jiangxi, China, and associated risk factors

In order to effectively combat the urgent threat of multidrug-resistant tuberculosis (MDR-TB), it is imperative to gain a comprehensive understanding of the drug-resistant profiles, transmission dynamics, and associated risk factors. Our study encompassed a population-based retrospective analysis with 130 MDR-TB patients from 2018 to 2021. The research methodology incorporated whole-genome sequencing, drug susceptibility testing , and logistic regression analysis to discern the risk factors of genomic clustering linked to recent transmission. The findings from phenotypic drug resistance assessments revealed notable resistance rates: ethambutol at 62.3% (81/130), streptomycin at 72.3% (94/130), levofloxacin at 51.5% (67/130), and moxifloxacin at 50.0% (65/130). Furthermore, among all patients, 38 individuals (29.23%, 38/130) were found to be part of 17 clusters, indicating instances of recent MDR-TB transmission. The genomic clustering patients were deeply investigated. Lineage 2.2.1 was established as the primary sub-lineage (86.15%, 112/130), followed by lineage 4 (9.23%, 12/130). Moreover, the logistic regression analysis underscored that unemployment, farming occupations, and prior TB treatment were identified as significant risk factors for recent transmission.

IMPORTANCE

The high prevalence of multidrug-resistant tuberculosis (MDR-TB) in Jiangxi Province highlights the importance of understanding the genetic background and drug resistance patterns of these strains. This knowledge is crucial for developing effective control methods. Furthermore, in light of the significance of preventing transmission among tuberculosis patients, whole-genome sequencing was utilized to investigate the recent transmission of MDR-TB and identify associated risk factors. The findings revealed that individuals in the farming sector, those who are unemployed, and patients with a history of tuberculosis treatment are at elevated risk. Consequently, targeted public interventions for these at-risk groups are imperative.

Detection of Rifampicin Resistance rpoB Gene Using GeneXpert MTB/RIF Assay in Pulmonary Tuberculosis Cases at Debre Tabor Comprehensive Specialized Hospital, Northwest Ethiopia

BACKGROUND

Tuberculosis (TB) is a preventable and treatable disease leading to the second death globally. The evolution of drug resistance in Mycobacterium tuberculosis (MTB), particularly rifampicin resistance (RR), has hampered TB control efforts. Thus, this study aimed to provide information regarding the magnitude of MTB and rifampicin resistance among patients tested using the GeneXpert method.

METHODS

A retrospective analysis was carried out at DTCSH. The study included TB registration logbook data from all patients who visited the hospital and were tested for MTB with the Xpert MTB/RIF assay from 2017 to 2024. The laboratory-based data were entered, cleaned, and analyzed using SPSS version 26 software. Multilogistic regression analysis was employed, and a p value ≤ 0.05 was considered statistically significant.

RESULTS

A total of 12,981 patient results were included, of which 8.9% (1160/12,981) were MTB-positive and 7.1% (82/1160) were RR. Individuals aged 15-29 years (AOR = 2.13; 95% CI = 1.55-2.93, p < 0.001), living in rural areas (AOR = 1.23; 95% CI = 1.08-1.41, p = 0.003), and HIV+ (AOR = 1.79; 95% CI = 1.48-2.33, p < 0.001) had a higher risk of developing tuberculosis. While RR was identified in 63.4% (52/82) of new, 24.4% (20/82) of re-treated, and 12.2% (10/82) of failed presumptive TB patients.

CONCLUSION

In this study, MTB and RR trends were high. Productive age groups, rural populations, and HIV patients were at risk. To lessen the burden of this contagious and fatal disease, it is recommended to increase early diagnosis of drug-resistant TB and enhance infection control.

Epidemiological characteristics, diagnosis and treatment effect of rifampicin-resistant pulmonary tuberculosis (RR-PTB) in Guizhou Province

BACKGROUND

Rifampicin-resistant pulmonary tuberculosis (RR-PTB) presents a significant threat to global public health security. China bears a substantial burden of RR-PTB cases globally, with Guizhou Province experiencing particularly alarming trends, marked by a continual increase in patient numbers. Understanding the population characteristics and treatment modalities for RR-PTB is crucial for mitigating morbidity and mortality associated with this disease.

METHODS

We gathered epidemiological, diagnostic, and treatment data of all RR-PTB cases recorded in Guizhou Province from January 1, 2017 to December 31, 2023. Utilizing composition ratios as the analytical metric, we employed Chi-square tests to examine the spatiotemporal distribution patterns of RR-PTB patients and the evolving trends among different patient classifications over the study period.

RESULTS

In our study, 3396 cases of RR-PTB were analyzed, with an average age of 45 years. The number of RR-PTB patients rose significantly from 176 in 2017 to 960 in 2023, peaking notably among individuals aged 23-28 and 44-54, with a rising proportion in the 51-80 age group (P < 0.001). Since 2021, there has been a notable increase in the proportion of female patients. While individuals of Han ethnic group comprised the largest group, their proportion decreased over time (P < 0.001). Conversely, the Miao ethnicity showed an increasing trend (P < 0.05). The majority of patients were farmers, with their proportion showing an upward trajectory (P < 0.001), while students represented 4.33% of the cases. Geographically, most patients were registered in Guiyang and Zunyi, with a declining trend (P < 0.001), yet household addresses primarily clustered in Bijie, Tongren, and Zunyi. The proportion of floating population patients gradually decreased, alongside an increase in newly treated patients and those without prior anti-tuberculosis therapy. Additionally, there was a notable rise in molecular biological diagnostic drug sensitivity (real-time PCR and melting curve analysis) (P < 0.001). However, the cure rate declined, coupled with an increasing proportion of RR-PTB patients lost to follow-up and untreated (P < 0.05).

CONCLUSIONS

Enhanced surveillance is crucial for detecting tuberculosis patients aged 23-28 and 44-54 years. The distribution of cases varies among nationalities and occupations, potentially influenced by cultural and environmental factors. Regional patterns in RR-PTB incidence suggest tailored prevention and control strategies are necessary. Despite molecular tests advances, challenges persist with low cure rates and high loss to follow-up. Strengthening long-term management, resource allocation, and social support systems for RR-PTB patients is essential.

The pattern of rpoB gene mutation of Mycobacterium tuberculosis and predictors of rifampicin resistance detected by GeneXpert MTB/RIF assay in Tanzania

INTRODUCTION

Antimicrobial resistance in Mycobacterium tuberculosis (MTB) poses a significant challenge to tuberculosis (TB) management worldwide. Rifampicin resistance (RR) has been associated with the rpoB gene mutation. No study was conducted in Tanzania to determine the commonest mutation. The inconsistent findings from various studies support the need to determine whether reported mutation patterns are applicable in our setting. We determined the frequency of rpoB gene mutation and factors associated with RR, which were detected using GeneXpert MTB/RIF assay.

METHODS

We conducted a retrospective cross-sectional study involving data from the National Tuberculosis and Leprosy Program database from 2020 to 2022 for cases investigated using GeneXpert MTB/RIF assay. Descriptive analysis was performed to determine the frequency of categorical variables. The chi-square test and logistic regression analysis assessed the relationship between the independent variables and outcome. The 95% confidence interval and a significance level of p<0.05 were used to assess the strength of association.

RESULTS

A total of 56,004 participants had a status of MTB and RR, where 38,705/56,004 (69.11%) were males. Probe E mutation (codon 529-533), 89/219 (40.64%) was predominant. Human immunodeficiency virus (HIV)-positive patients had a higher gene mutation, 134/10601 (1.26%) than HIV-negative, 306/45016 (0.68%) (p<0.001). Patients with both pulmonary and extra-pulmonary TB had about four times greater odds of developing rifampicin resistance (AOR 3.88, 95%CI: 1.80-8.32). RR was nearly nine times higher in previously treated patients than new patients (AOR 8.66, 95% CI: 6.97-10.76). HIV-positive individuals had nearly twice the odds of developing RR than HIV-negative individuals (AOR 1.91, 95%CI: 1.51-2.42).

CONCLUSION

The rate of RR was lower compared to other studies in Tanzania, with probe E mutations the most prevalent. Patients with disseminated TB, HIV co-infection and those with prior exposure to anti-TB had more risk of RR. The findings highlight the need to strengthen surveillance of multidrug-resistant TB among high risk patients.

Discordance between genotypic and phenotypic methods for the detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis and the correlation with patient treatment outcomes

Background

Accurate drug susceptibility testing (DST) of Mycobacterium tuberculosis (MTB) is essential for proper patient management. We investigated discordance between genotypic (Xpert MTB/RIF and MTBDRplus) and phenotypic (MGIT 960) methods for the detection of rifampicin (RIF) and isoniazid (INH) resistant MTB and its correlation with patient treatment outcomes in Jimma, Southwest Oromia, Ethiopia.

Methods

A retrospective study was conducted on 57 stored MTB isolates with known Xpert RIF resistance status (45 RIF resistant and 12 RIF susceptible) at Jimma University Mycobacteriology Research Center from November 2, 2021, to December 28, 2022. We did MTBDRplus and phenotypic DST (using the Mycobacterial Growth Indicator Tube (MGIT) system). The Xpert and MTBDRplus results were compared using phenotypic DST as a reference standard method. The treatment outcome was determined as per national guideline. The discordance between the genotypic and phenotypic DST was calculated using GraphPad software.

Results

Among the 57 MTB isolates, six (10.5 %) had discordant results between the two DST methods. Xpert yielded five discordant results for RIF when compared with phenotypic DST (kappa coefficient (κ) = 0.76, 95 % confidence interval 0.56-0.96). The MTBDRplus compared with phenotypic DST gave three discordant results for RIF (κ = 0.86, 95 % confidence interval 0.71-1.00) and three for INH (κ = 0.86, 95 % confidence interval 0.70-1.00). Compared with Xpert, MTBDRplus yielded lower discordance with phenotypic DST for RIF. Out of six patients with discordant results, three had unfavorable outcomes while the other three were cured. Of the three patients with unfavorable outcomes, only one patient has received an inappropriate treatment regimen. There was no correlation between unfavorable outcomes and incorrect treatment regimens due to discordant results (Χ2 = 0.404; P = 0.525).

Conclusions

Discordance between genotypic and phenotypic DST for RIF or INH occurred in 10.5 % of isolates. Only one patient with discordant results has received an inappropriate treatment regimen, resulting in an unfavorable outcome. The impact of parallel use of rapid molecular assay with phenotypic DST on patient treatment outcomes requires further study.

Direct detection of drug-resistant Mycobacterium tuberculosis using targeted next generation sequencing

Mycobacterium tuberculosis complex (MTBC) infections are treated with combinations of antibiotics; however, these regimens are not as efficacious against multidrug and extensively drug resistant MTBC. Phenotypic (growth-based) drug susceptibility testing on slow growing bacteria like MTBC requires many weeks to months to complete, whereas sequencing-based approaches can predict drug resistance (DR) with reduced turnaround time. We sought to develop a multiplexed, targeted next generation sequencing (tNGS) assay that can predict DR and can be performed directly on clinical respiratory specimens. A multiplex PCR was designed to amplify a group of thirteen full-length genes and promoter regions with mutations known to be involved in resistance to first- and second-line MTBC drugs. Long-read amplicon libraries were sequenced with Oxford Nanopore Technologies platforms and high-confidence resistance mutations were identified in real-time using an in-house developed bioinformatics pipeline. Sensitivity, specificity, reproducibility, and accuracy of the tNGS assay was assessed as part of a clinical validation study. In total, tNGS was performed on 72 primary specimens and 55 MTBC-positive cultures and results were compared to clinical whole genome sequencing (WGS) performed on paired patient cultures. Complete or partial susceptibility profiles were generated from 82% of smear positive primary specimens and the resistance mutations identified by tNGS were 100% concordant with WGS. In addition to performing tNGS on primary clinical samples, this assay can be used to sequence MTBC cultures mixed with other mycobacterial species that would not yield WGS results. The assay can be effectively implemented in a clinical/diagnostic laboratory with a two to three day turnaround time and, even if batched weekly, tNGS results are available on average 15 days earlier than culture-derived WGS results. This study demonstrates that tNGS can reliably predict MTBC drug resistance directly from clinical specimens or cultures and provide critical information in a timely manner for the appropriate treatment of patients with DR tuberculosis.