Long-term molecular surveillance of multidrug-resistant tuberculosis in Spain

TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data

MOTIVATION

Whole-genome sequencing (WGS) is increasingly used to aid the understanding of Mycobacterium tuberculosis (MTB) transmission. The epidemiological analysis of tuberculosis based on the WGS technique requires a diverse collection of bioinformatics tools. Effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.

RESULTS

Here, we present TransFlow (Transmission Workflow), a user-friendly, fast, efficient and comprehensive WGS-based transmission analysis pipeline. TransFlow combines some state-of-the-art tools to take transmission analysis from raw sequencing data, through quality control, sequence alignment and variant calling, into downstream transmission clustering, transmission network reconstruction and transmission risk factor inference, together with summary statistics and data visualization in a summary report. TransFlow relies on Snakemake and Conda to resolve dependencies among consecutive processing steps and can be easily adapted to any computation environment.

AVAILABILITY AND IMPLEMENTATION

TransFlow is free available at https://github.com/cvn001/transflow.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

The value of the continuous genotyping of multi-drug resistant tuberculosis over 20 years in Spain

Molecular epidemiology of circulating clinical isolates is crucial to improve prevention strategies. The Spanish Working Group on multidrug resistant tuberculosis (MDR-TB) is a network that monitors the MDR-TB isolates in Spain since 1998. The aim of this study was to present the study of the MDR-TB and extensively drug-resistant tuberculosis (XDR-TB) patterns in Spain using the different recommended genotyping methods over time by a national coordinated system. Based on the proposed genotyping methods in the European Union until 2018, the preservation of one method, MIRU-VNTR, applied to selected clustered strains permitted to maintain our study open for 20 years. The distribution of demographic, clinical and epidemiological characteristics of clustered and non-clustered cases of MDR/XDR tuberculosis with proportion differences as assessed by Pearson’s chi-squared or Fisher’s exact test was compared. The differences in the quantitative variables using the Student's-t test and the Mann–Whitney U test were evaluated. The results obtained showed a total of 48.4% of the cases grouped in 77 clusters. Younger age groups, having a known TB case contact (10.2% vs 4.7%) and XDR-TB (16.5% vs 1.8%) were significantly associated with clustering. The largest cluster corresponded to a Mycobacterium bovis strain mainly spread during the nineties. A total of 68.4% of the clusters detected were distributed among the different Spanish regions and six clusters involving 104 cases were grouped in 17 and 18 years. Comparison of the genotypes obtained with those European genotypes included in The European Surveillance System (TESSy) showed that 87 cases had become part of 20 European clusters. The continuity of MDR strain genotyping in time has offered a widespread picture of the situation that allows better management of this public health problem. It also shows the advantage of maintaining one genotyping method over time, which allowed the comparison between ancient, present and future samples.

Transmission is a Noticeable Cause of Resistance Among Treated Tuberculosis Patients in Shanghai, China

It is generally believed that drug resistance among treated tuberculosis (TB) patients is as a result of acquired drug resistance due to inappropriate treatment. Previous studies have shown that primary drug resistance caused by transmission also plays a role among treated cases. Differentiating the two types of drug resistance will help in developing appropriate strategies for control of drug resistant tuberculosis. In this study, we tested the hypothesis that drug resistance among treated TB patients is mainly caused by primary resistance rather than acquired resistance. Defining resistance profiles by molecular drug susceptibility test, we used Unit Variable Number Tandem Repeats (VNTR) to genotype and Whole Genome Sequencing (WGS) to confirm the accordance of the first and last Mycobacterium tuberculosis isolates from treated pulmonary TB patients in Shanghai from 2009–2015. Among 81 patients with increasing drug resistance, out of 390 patients enrolled, paired isolates from 59.3% (48/81) had different VNTR patterns indicating primary drug resistance. Our results have demonstrated that primary resistance due to exogenous reinfection is the major cause of drug resistance among treated TB patients in Shanghai; thus, strategies aimed at preventing and interrupting transmission are urgently needed to effectively reduce the epidemic of drug resistant tuberculosis.

Mycobacterium tuberculosis genotypes and predominant clones among the multidrug-resistant isolates in Spain 1998-2005

Although the incidence of tuberculosis (TB) is gradually decreasing in Spain, there is an increase in the proportion of foreign-born cases. This changing scenario is slowly shifting the local TB epidemiology from endemic to imported cases with an increased risk for multidrug-resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis complex. MDR/XDR strains from Spain (n=366 MTBC isolates, 1 strain per patient) isolated between 1998 and 2005 were retained for this retrospective analysis. All strains were analyzed by spoligotyping, while 12-loci MIRU-VNTR data were available for 106 isolates from 2003 to 2005. Demographic, phylogenetic, and epidemiologic analyses using anonymized data were collected and analyzed using the SITVIT2 database. Our study provides with a first snapshot of genetic diversity of MDR/XDR-TB in several autonomous regions of Spain. It highlights significantly more of SIT1/Beijing and SIT66/BOV MDR isolates (5.7% and 7.38% respectively) and increasingly more foreign-born cases from Eastern Europe. Future studies should focus on shared genotypes between Spanish and foreign-born patients to decipher the modes of transmission and risk factors involved, and decipher the proportion of imported cases of active disease versus cases of reactivation of latent TB infection among foreign-born individuals.

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

Global tuberculosis incidence has declined marginally over the past decade, and tuberculosis remains out of control in several parts of the world including Africa and Asia. Although tuberculosis control has been effective in some regions of the world, these gains are threatened by the increasing burden of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis. XDR tuberculosis has evolved in several tuberculosis-endemic countries to drug-incurable or programmatically incurable tuberculosis (totally drug-resistant tuberculosis). This poses several challenges similar to those encountered in the pre-chemotherapy era, including the inability to cure tuberculosis, high mortality, and the need for alternative methods to prevent disease transmission. This phenomenon mirrors the worldwide increase in antimicrobial resistance and the emergence of other MDR pathogens, such as malaria, HIV, and Gram-negative bacteria. MDR and XDR tuberculosis are associated with high morbidity and substantial mortality, are a threat to health-care workers, prohibitively expensive to treat, and are therefore a serious public health problem. In this Commission, we examine several aspects of drug-resistant tuberculosis. The traditional view that acquired resistance to antituberculous drugs is driven by poor compliance and programmatic failure is now being questioned, and several lines of evidence suggest that alternative mechanisms-including pharmacokinetic variability, induction of efflux pumps that transport the drug out of cells, and suboptimal drug penetration into tuberculosis lesions-are likely crucial to the pathogenesis of drug-resistant tuberculosis. These factors have implications for the design of new interventions, drug delivery and dosing mechanisms, and public health policy. We discuss epidemiology and transmission dynamics, including new insights into the fundamental biology of transmission, and we review the utility of newer diagnostic tools, including molecular tests and next-generation whole-genome sequencing, and their potential for clinical effectiveness. Relevant research priorities are highlighted, including optimal medical and surgical management, the role of newer and repurposed drugs (including bedaquiline, delamanid, and linezolid), pharmacokinetic and pharmacodynamic considerations, preventive strategies (such as prophylaxis in MDR and XDR contacts), palliative and patient-orientated care aspects, and medicolegal and ethical issues.

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.

Drug-resistant tuberculosis viewed from bacterial and host genomes

The outcome of infection with Mycobacterium tuberculosis (MTB) is largely influenced by the host-pathogen interaction in which both the human host and the MTB genetic backgrounds play an important role. Whether this interaction also influences the selection and expansion of drug-resistant MTB strains is the primary focus of this review. We first outline the main and recent findings regarding MTB determinants implicated in the development of drug resistance. Second, we examine data regarding human genetic factors that may play a role in TB drug resistance. We highlight interesting openings for TB research and therapy.

Molecular profiling of drug resistant isolates of Mycobacterium tuberculosis in the state of Santa Catarina, southern Brazil

Drug resistance is a global threat and one of the main contributing factors to tuberculosis (TB) outbreaks. The goal of this study was to analyse the molecular profile of multidrug-resistant TB (MDR-TB) in the state of Santa Catarina in southern Brazil. Fifty-three MDR Mycobacterium tuberculosisclinical isolates were analysed by spoligotyping and a partial region of therpoB gene, which is associated with rifampicin resistance (RMP-R), was sequenced. Some isolates were also distinguished by their mycobacterial interspersed repetitive units (MIRU). S531L was the most prevalent mutation found within rpoB in RMP-R isolates (58.5%), followed by S531W (20.8%). Only two MDR isolates showed no mutations withinrpoB. Isolates of the Latin American Mediterranean (LAM) family were the most prevalent (45.3%) found by spoligotyping, followed by Haarlem (9.4%) and T (7.5%) families. SIT106 was found in 26.4% of isolates and all SIT106 isolates typed by MIRU-12 (5 out of 14) belong to MIT251. There was a high correlation between the S531W mutation and the LAM family mainly because all SIT2263 (LAM9) isolates carry this mutation. Among isolates with the S531W mutation in rpoB MIRU demonstrates a cluster formed by four isolates (SIT2263 and MIT163) and very similar profiles were observed between eight of the nine isolates. Better characterisation of TB isolates may lead to new ways in which to control and treat TB in this region of Brazil.

Evolution and transmission patterns of extensively drug-resistant tuberculosis in China

The emergence and transmission of extensively drug-resistant tuberculosis (XDR-TB) pose an increasing threat to global TB control. This study aimed to identify the patterns of evolution and transmission dynamics of XDR-TB in populations in a region of China where TB is highly endemic. We analyzed a total of 95 XDR-TB isolates collected from 2003 to 2009 in Chongqing, China. Eight drug resistance genes covering 7 drugs that define XDR-TB were amplified by PCR followed by DNA sequencing. Variable-number tandem repeat 16-locus (VNTR-16) genotyping and genotypic drug resistance profiles were used to determine the evolution or transmission patterns of XDR-TB strains. Our results indicated that the Beijing genotype was predominant (85/95 [89.5%]) in XDR-TB strains, and as many as 40.0% (38/95) of the isolates were distributed into 6 clusters based on VNTR-16 genotyping and drug resistance mutation profiles. All isolates of each cluster harbored as many as six identical resistance mutations in the drug resistance genes rpoB, katG, inhA promoter, embB, rpsL, and gidB. Among the nine cases with continuous isolates from multidrug-resistant (MDR) to XDR-TB, 4 cases represented acquired drug resistance, 4 cases were caused by transmission, and 1 case was due to exogenous superinfection. The XDR-TB epidemic in China is mainly caused by a high degree of clonal transmission, but evolution from MDR to XDR and even superinfection with a new XDR strain can also occur.

Pediatric drug-resistant tuberculosis in Madrid: family matters

BACKGROUND

The rates of isoniazid (INH) and multidrug-resistant (MDR) tuberculosis (TB) among European children vary between 10.4% and 3.5%. Spain is a low endemic country with reported rates of 4.9% of INH resistance and 1.3% of MDR in adults. However, data regarding patterns of TB resistance in children are scarce. Our aim is to determine the incidence and risk factors for pediatric-resistant TB in our setting to help developing age-targeted guidelines.

METHODS

A multicenter, retrospective study including 22 hospitals from Madrid region (EREMITA study group) was performed from January 2005 to June 2010. Medical records from children diagnosed with TB were reviewed for demographic characteristics, clinical presentation and outcomes. Risk factors for INH and MDR TB were identified.

RESULTS

Of 396 children diagnosed with TB, 72.4% were born to foreign parents. Microbiologic confirmation by culture (n = 200) or PCR (n = 8) was documented in 208 children (52.5%). Drug susceptibility results were available in 188 children: 9.6% (n = 18) were resistant to INH and 3.1% (n = 6) were MDR. INH resistance was more common in immigrants compared with native families (11.9% vs. 0%; P = 0.013), as was also MDR (4.5% vs. 0%; P = 0.34). Extrapulmonary TB and previous antituberculous treatment were significantly associated with INH and MDR, while immunosuppression was associated only with MDR.

CONCLUSIONS

The rates of INH and MDR TB were different according to the parents' origin, with higher rates among children born to foreign parents. Local surveillance of drug-resistant TB is critical to develop appropriate guidelines for treatment.

Molecular surveillance of multi- and extensively drug-resistant tuberculosis transmission in the European Union from 2003 to 2011

The European Centre for Disease Prevention and Control (ECDC) initiated a project on the molecular surveillance of multi- and extensively drug-resistant tuberculosis (MDR-/XDR-TB) transmission in the European Union (EU) in the period from 2009 to 2011. In total, 2,092 variable number of tandem repeat (VNTR) patterns of MDR-/XDR-TB Mycobacterium tuberculosis isolates were collected, originating from 24 different countries in the period 2003 to 2011. Of the collected VNTR patterns, 45% (n=941) could be assigned to one of the 79 European multiple-country molecular fingerprint clusters and 50% of those (n=470) belonged to one extremely large cluster caused by Beijing strains of one genotype. We conclude that international transmission of MDR-/XDR-TB plays an important role in the EU, especially in the eastern part, and is significantly related to the spread of one strain or clone of the Beijing genotype. Implementation of international cluster investigation in EU countries should reveal underlying factors of transmission, and show how TB control can be improved regarding case finding, contact tracing, infection control and treatment in order to prevent further spread of MDR-/XDR-TB in the EU.

Single nucleotide polymorphism (SNP) analysis used for the phylogeny of the Mycobacterium tuberculosis complex based on a pyrosequencing assay

Background

Different polymorphisms have been described as markers to classify the lineages of the Mycobacterium tuberculosis complex. The analysis of nine single nucleotide polymorphisms (SNPs) was used to describe seven SNPs cluster groups (SCGs). We attempted to classify those strains that could not been categorized into lineages by the genotyping methods used in the routine testing.

Results

The M. tuberculosis complex isolates collected in 2010 in our region were analysed. A new method based on multiplex-PCRs and pyrosequencing to analyse these SNPs was designed. For the pyrosequencing assay nine SNPs that defined the seven SCGs were selected from the literature: 1977, 74092, 105139, 232574, 311613, 913274, 2460626, 3352929 and gyrA95. In addition, SNPs in katG⁴⁶³, mgtC¹⁸², Ag85C¹⁰³ and RD^Rio deletion were detected.

Conclusions

This work has permitted to achieve a better classification of Aragonian strains into SCGs and in some cases, to assign strains to its certain lineage. Besides, the description of a new pattern shared by two isolates “SCG-6c” reinforces the interest of SNPs to follow the evolution of M. tuberculosis complex.