Transmission of multidrug-resistant tuberculosis in Beijing, China: An epidemiological and genomic analysis

Predictors of treatment failure among patients with pulmonary tuberculosis attending public health facilities in Nairobi county

Tuberculosis (TB) is one of the infectious diseases of public health concern globally. Kenya is ranked 15th among the 22 high TB burden countries worldwide, which collectively contribute to 80% of the world's TB cases. TB Treatment failure is one of the threats to the control of TB. The research aimed at determining affordable predictors of TB treatment failure in a resource limited setting to inform policy in designing public health interventions that are best suited to the country's needs. To determine the predictors of treatment failure among patients with sputum smear positive pulmonary TB attending selected public health facilities in Nairobi Count. Data was abstracted and summarized from both patients and their medical records, focusing on socio-demographic, behavioral, and clinical exposure data. Data was collected from 4 Sub-counties, a total of 21 public health facilities with high case load of pulmonary TB were reached. Utilizing an unmatched case-control design, the study enrolled 81 patients diagnosed with TB treatment failure (cases) and 162 patients who were declared cured after completing their anti-TB treatment (controls. Strengthen contact tracing, screening, and documentation of TB treatment failure cases. Conduct further studies to elucidate the association between HIV and TB treatment failure. The factors significantly associated with treatment failure in this study encompassed prior exposure to first-line anti-Tuberculosis drugs, positive sputum smear at 2 months of treatment, and suboptimal adherence to anti-TB treatment. These findings contribute valuable insights into the identification of simple predictors of TB treatment failure such as utilizing sputum microscopy or gene expert testing at 2 months of treatment to detect individuals at risk and strengthen the implementation of DOT and TB treatment failure contact tracing protocol.

Study of fluoroquinolones resistance in rifampicin-resistant tuberculosis patients in Beijing: Characteristics, trends, and treatment outcomes

BACKGROUND

China is a high-burden country for multidrug-resistant tuberculosis/rifampin-resistant tuberculosis (MDR/RR-TB). Fluoroquinolones (FQs) are key drugs for the treatment of patients with MDR/RR-TB. However, research on the resistance of FQs in Beijing is limited.

METHODS

We collected clinical isolates from all patients with pulmonary TB in Beijing from January 2016 to December 2021, conducted drug-sensitivity tests and sequencing for levofloxacin (LFX) and moxifloxacin (MFX), and collected the treatment plans and outcomes of the patients.

RESULTS

A total of 8512 clinical isolates were collected from patients with pulmonary TB, and 261 RR-TB strains were screened. The proportions of drug-sensitive and drug-resistant strains significantly differed by age group and treatment history. The rates of LFX and MFX resistance were 27.6% (72/261) and 36.4% (95/261), respectively. The detection rates of MDR-TB and pre-extensively drug-resistant TB (pre-XDR-TB) were 73.2% (191/261) and 36.4% (95/261), respectively, and the trends were significant (χ2 trend = 9.995, p = 0.002; χ2 trend = 12.744, p = 0.026). Among the 261 RR-TB strains, 14.9% (24/261) were sensitive to LFX but resistant to MFX. Among the four patients with LFX-resistant TB who received LFX treatment failed in three patients(Fisher's exact test, p = 0.009). The common mutation sites were 94 and 90 in gyrA. A novel mutation Ala90Ser was discovered.

CONCLUSIONS

FQs resistance trends in RR-TB patients in Beijing are striking. Strains showed incomplete cross-resistance to LFX and MFX. Testing for FQs resistance and developing a reasonable treatment plan are recommended. Attention should be given to the changing trends in MDR-TB and pre-XDR-TB.

Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review

Tuberculosis remains a leading cause of infection-related mortality, and efforts to reduce its incidence have been hindered by an incomplete understanding of local Mycobacterium tuberculosis transmission dynamics. Advances in pathogen sequencing and spatial analysis have created new opportunities to map M tuberculosis transmission patterns more precisely. In this scoping review, we searched for studies combining pathogen genetics and location data to analyse the spatial patterns of M tuberculosis transmission and identified 142 studies published between 1994 and 2024. Secular changes in genetic methods were observed, with genome sequencing approaches largely replacing lower-resolution genotyping methods since 2020. The included studies addressed four primary research questions: how are tuberculosis cases and M tuberculosis transmission clusters geographically distributed; do spatially concentrated M tuberculosis clusters exist, and where are these areas located; when spatial concentration occurs, what host, pathogen, or environmental factors contribute to these patterns; and do identifiable relationships exist between the spatial proximity of tuberculosis cases and the genetic similarity of the M tuberculosis isolates infecting these individuals? Collectively, in this Review, we examined the available study data, evaluated the analytical requirements for addressing these questions, and discussed opportunities and challenges for future research. We found that the integration of spatial and genomic data can inform a detailed understanding of local M tuberculosis transmission patterns, but improved study designs and new analytical methods to address gaps in sampling completeness and to integrate additional movement data are needed to fully realise the potential of these tools.

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.

Drug-resistance characteristics, genetic diversity, and transmission dynamics of multidrug-resistant or rifampicin-resistant Mycobacterium tuberculosis from 2019 to 2021 in Sichuan, China

BACKGROUND

Multidrug- or rifampicin-resistant tuberculosis (TB; MDR/RR-TB) is a significant public health threat. However, the mechanisms involved in its transmission in Sichuan, China are unclear. To provide a scientific basis for MDR/RR-TB control and prevention, we investigated the drug-resistance characteristics, genetic diversity, and transmission dynamics and analyzed the demographic and clinical characteristics of patients to identify risk factors for the acquisition of MDR/RR-TB in Sichuan, Western China.

METHODS

Whole-genome sequencing was performed using a sample comprised of all MDR/RR-TB strains isolated from patients with pulmonary TB (≥ 15 years) at the 22 surveillance sites in Sichuan province between January 2019 and December 2021, to analyze genotypic drug resistance and genetic diversity. Moreover, we performed statistical analyses of the epidemiological characteristics and risk factors associated with the transmission dynamics of MDR/RR-TB.

RESULTS

The final analysis included 278 MDR/RR TB strains. Lineage 2.2, the major sub-lineage, accounted for 82.01% (228/278) of isolates, followed by lineage 4.5 (9.72%, 27/278), lineage 4.4 (6.83%, 19/278), and lineage 4.2 (1.44%, 4/278). The drug resistance rates, ranging from high to low, were as follows: isoniazid (229 [82.37%]), streptomycin (177 [63.67%]), ethambutol (144 [51.80%]), pyrazinamide (PZA, 119 [42.81%]), fluoroquinolones (FQs, 93 [33.45%]). Further, the clofazimine, bedaquiline, and delamanid resistance rates were 2.88, 2.88, and 1.04%, respectively. The gene composition cluster rate was 32.37% (90/278). In addition, 83.81% (233/278) of MDR/RR-TB cases were determined to be likely caused by transmission. Finally, patients infected with lineage two strains and strains with the KatG S315T amino acid substitution presented a higher risk of MDR/RR-TB transmission.

CONCLUSION

Transmission plays a significant role in the MDR/RR-TB burden in Sichuan province, and lineage 2 strains and strains harboring KatG S315T have a high probability of transmission. Further, high levels of FQ and PZA drug resistance suggest an urgent need for drug susceptibility testing prior to designing therapeutic regimens. New anti-TB drugs need to be used standardly and TB strains should be regularly monitored for resistance to these drugs.

Genomic and Spatial Analysis on the Recent Transmission of Mycobacterium tuberculosis in Eastern China: A 10-Year Retrospective Population-Based Study

Purpose

Understanding the mode of Mycobacterium tuberculosis (M. tuberculosis) transmission is crucial for disease prevention and control. Compared to traditional genotyping methods, whole genome sequencing (WGS) provides higher resolution and comprehensive genetic information, enabling the tracing of infection sources and determining of transmission routes to resolve extensive tuberculosis (TB) outbreaks. We conducted a ten-year study on the transmission of M. tuberculosis in a population in eastern China.

Patients and Methods

We selected Lianyungang, an eastern city in China, as the study site. Patients diagnosed with active pulmonary TB from 2011 to 2020 were enrolled as the study subjects. We isolated and sequenced 2252 M. tuberculosis. Strains with pairwise genetic distances of less than 12 single nucleotide polymorphisms were defined as genomic clusters and which were considered recent transmissions. Kernel density estimation and K-function analysis were applied to explore the spatial distribution of recently transmitted strains.

Results

After excluding non-tuberculous mycobacteria and duplicated samples, 2114 strains were included in the final analysis. These strains comprised lineage 2 (1593, 75.35%) and 4 (521, 24.65%). There were 672 clustered strains, with a recent transmission rate of 31.79%. The logistic regression model showed that the risk of recent transmission was high in students [adjusted odds ratio (aOR): 2.68, 95% confidence interval (CI): 1.63-4.49, P<0.001] and people infected with L2.2.1 strains (aOR: 1.59, 95% CI: 1.20-2.12). Higher spatial aggregation of TB transmission has been concentrated in Haizhou, Donghai, and Guanyun for the past 10 years. Three outbreaks affecting 46 patients were spatially spaced, with 11 to 23 persons each. Different groups exhibited varying geographic distances between the initial and later cases.

Conclusion

There are areas with a high risk of transmission for M. tuberculosis in the research site, and the risk varies among different populations. Accurate prevention strategies targeted at specific regions and key populations can help curb the prevalence of TB.

Multidrug-resistant tuberculosis clusters and transmission in Taiwan: a population-based cohort study

Introduction

Multidrug-resistant tuberculosis (MDR-TB) remains a challenge in the TB program of Taiwan, where 0.5% of new cases and 2.1% of previously treated cases were resistant to at least rifampin (RIF) and isoniazid (INH). Since >80% of our MDR-TB are new cases, genotyping of MDR Mycobacterium tuberculosis is implemented to facilitate contact investigation, cluster identification, and outbreak delineation.

Methods

This is a population-based retrospective cohort study analyzing MDR-TB cases from 2019 to 2022. Whole genome sequencing (WGS) was performed using the Illumina MiSeq and analyzed using the TB Profiler. A single nucleotide polymorphism (SNP) threshold of ≤ 12 and phylogenetic methods were used to identify putative transmission clusters. An outbreak was confirmed using genomic data and epidemiologic links.

Results

Of the 297 MDR-TB cases, 246 (82.8%), 45 (15.2%), and 6 (2.0%) were simple MDR, extensively drug-resistant tuberculosis (pre-XDR-TB) and extensively drug-resistant tuberculosis (XDR-TB), respectively. The sublineage 2.2 modern Beijing was the predominant (48.8%) MDR-TB strain in Taiwan. Phylogenetic analysis identified 25.3% isolates in 20 clusters, with cluster sizes ranging from 2 to 13 isolates. Nevertheless, only 2 clusters, one household and one community, were confirmed as outbreaks. In this study, we found that males had a higher risk of MDR-TB transmission compared to females, and those infected with the sublineage 2.1-proto-Beijing genotype isolates were at a higher risk of transmission. Furthermore, 161 (54.2%) isolates harbored compensatory mutations in the rpoC and non-rifampicin resistant determinant region (non-RRDR) of the rpoB gene. MDR-TB strains containing rpoB S450L and other compensatory mutations concurrently were significantly associated with clusters, especially the proto-Beijing genotype strains with the compensatory mutation rpoC E750D or the modern Beijing genotype strains with rpoC D485Y/rpoC E1140D.

Discussion

Routine and continuous surveillance using WGS-based analysis is recommended to warn of risks and delineate transmission clusters of MDR-TB. We proposed the use of compensatory mutations as epidemiological markers of M. tuberculosis to interrupt putative MDR-TB transmission.

Define SNP thresholds for delineation of tuberculosis transmissions using whole-genome sequencing

For facilitating tuberculosis (TB) control, we used a whole-genome sequencing (WGS)-based approach to delineate transmission networks in a country with an intermediate burden of TB. A cluster was defined as Mycobacterium tuberculosis isolates with identical genotypes, and an outbreak was defined as clustered cases with epidemiological links (epi-links). To refine a cluster predefined using space oligonucleotide typing and mycobacterial interspersed repetitive unit variable tandem repeat typing, we analyzed one pansusceptible TB (C1) and three multidrug-resistant (MDR)-TB (C2-C4) clusters from different scenarios. Pansusceptible TB cluster (C1) consisting of 28 cases had ≤5 single nucleotide polymorphisms (SNPs) difference between their isolates. C1 was a definite outbreak, with cases attending the same junior high school in 2012. Three MDR-TB clusters (C2-C4) with distinct genotypes were identified, each consisting of 12-22 cases. Some of the cases had either ≤5 or ≤15 SNPs difference with clear or probable epi-links. Of note, even though WGS could effectively assist TB contact tracing, we still observed missing epi-links in some cases within the same cluster. Our results showed that thresholds of ≤5 and ≤15 SNPs difference between isolates were used to categorize definite and probable TB transmission, respectively. Furthermore, a higher SNP threshold might be required to define an MDR-TB outbreak. WGS still needs to be combined with classical epidemiological methods for improving outbreak investigations. Importantly, different SNP thresholds have to be applied to define outbreaks.

IMPORTANCE

TB is a chronic disease. Depending on host factors and TB burden, clusters of cases may continue to increase for several years. Conventional genotyping methods overestimate TB transmission, hampering precise detection of outbreaks and comprehensive surveillance. WGS can be used to obtain SNP information of M. tuberculosis to improve discriminative limitations of conventional methods and to strengthen delineation of transmission networks. It is important to define the country-specific SNP thresholds for investigation of transmission. This study demonstrated the use of thresholds of ≤5 and ≤15 SNPs difference between isolates to categorize definite and probable transmission, respectively. Different SNP thresholds should be applied while a higher cutoff was required to define an MDR-TB outbreak. The utilization of SNP thresholds proves to be crucial for guiding public health interventions, eliminating the need for unnecessary public health actions, and potentially uncovering undisclosed TB transmissions.

Transmission dynamics of drug-resistant tuberculosis in Ningbo, China: an epidemiological and genomic analysis

Background

Tuberculosis (TB), particularly drug-resistant TB (DR-TB), remains a significant public health concern in Ningbo, China. Understanding its molecular epidemiology and spatial distribution is paramount for effective control.

Methods

From December 24, 2020, to March 12, 2023, we collected clinical Mycobacterium tuberculosis (MTB) strains in Ningbo, with whole-genome sequencing performed on 130 MTB strains. We analyzed DR-related gene mutations, conducted phylogenetic and phylodynamic analyses, identified recent transmission clusters, and assessed spatial distribution.

Results

Among 130 DR-TB cases, 41% were MDR-TB, 36% pre-XDR-TB, 19% RR-TB, and 3% HR-TB. The phylogenetic tree showed that 90% of strains were Lineage 2 (Beijing genotype), while remaining 10% were Lineage 4 (Euro-American genotype). The spatial analysis identified hotspots of DR-TB in Ningbo's northern region, particularly in traditional urban centers. 31 (24%) of the DR-TB cases were grouped into 7 recent transmission clusters with a large outbreak cluster containing 15 pre-XDR-TB patients. Epidemiological analyses suggested a higher risk of recent DR-TB transmission among young adult patients who frequently visited Internet cafes, game rooms, and factories.

Conclusion

Our study provides comprehensive insights into the epidemiology and genetics of DR-TB in Ningbo. The presence of genomic clusters highlights recent transmission events, indicating the need for targeted interventions. These findings are vital for informing TB control strategies in Ningbo and similar settings.

Insight into Population Structure and Drug Resistance of Pediatric Tuberculosis Strains from China and Russia Gained through Whole-Genome Sequencing

This study aimed to determine phenotypic and genotypic drug resistance patterns of Mycobacterium tuberculosis strains from children with tuberculosis (TB) in China and Russia, two high-burden countries for multi/extensively-drug resistant (MDR/XDR) TB. Whole-genome sequencing data of M. tuberculosis isolates from China (n = 137) and Russia (n = 60) were analyzed for phylogenetic markers and drug-resistance mutations, followed by comparison with phenotypic susceptibility data. The Beijing genotype was detected in 126 Chinese and 50 Russian isolates. The Euro-American lineage was detected in 10 Russian and 11 Chinese isolates. In the Russian collection, the Beijing genotype and Beijing B0/W148-cluster were dominated by MDR strains (68% and 94%, respectively). Ninety percent of B0/W148 strains were phenotypically pre-XDR. In the Chinese collection, neither of the Beijing sublineages was associated with MDR/pre-XDR status. MDR was mostly caused by low fitness cost mutations (rpoB S450L, katG S315T, rpsL K43R). Chinese rifampicin-resistant strains demonstrated a higher diversity of resistance mutations than Russian isolates (p = 0.003). The rifampicin and isoniazid resistance compensatory mutations were detected in some MDR strains, but they were not widespread. The molecular mechanisms of M. tuberculosis adaptation to anti-TB treatment are not unique to the pediatric strains, but they reflect the general situation with TB in Russia and China.