Application of sensitive and specific molecular methods to uncover global dissemination of the major RDRio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis spoligotype family

Prevalence, drug resistance, and genotypic diversity of the RDRio subfamily of Mycobacterium tuberculosis in Ecuador: a retrospective analysis for years 2012-2016

Introduction

A major sublineage within the Mycobacterium tuberculosis (MTB) LAM family characterized by a new in-frame fusion gene Rv3346c/55c was discovered in Rio de Janeiro (Brazil) in 2007, called RDRio, associated to drug resistance. The few studies about prevalence of MTB RDRio strains in Latin America reported values ranging from 3% in Chile to 69.8% in Venezuela, although no information is available for countries like Ecuador.

Methods

A total of 814 MTB isolates from years 2012 to 2016 were screened by multiplex PCR for RDRio identification, followed by 24-loci MIRU-VNTR and spoligotyping.

Results

A total number of 17 MTB RDRio strains were identified, representing an overall prevalence of 2.09% among MTB strains in Ecuador. While 10.9% of the MTB isolates included in the study were multidrug resistance (MDR), 29.4% (5/17) of the RDRio strains were MDR.

Discussion

This is the first report of the prevalence of MTB RDRio in Ecuador, where a strong association with MDR was found, but also a very low prevalence compared to other countries in Latin America. It is important to improve molecular epidemiology tools as a part of MTB surveillance programs in Latin America to track the transmission of potentially dangerous MTB stains associated to MDR TB like MTB RDRio.

A multifaceted interplay between virulence, drug resistance, and the phylogeographic landscape of Mycobacterium tuberculosis

Latin-American Mediterranean (LAM) family is one of the most significant and global genotypes of Mycobacterium tuberculosis. Here, we used the murine model to study the virulence and lethality of the genetically and epidemiologically distinct LAM strains. The pathobiological characteristics of the four LAM strains (three drug resistant and one drug susceptible) and the susceptible reference strain H37Rv were studied in the C57BL/6 mouse model. The whole-genome sequencing was performed using the HiSeq Illumina platform, followed by bioinformatics and phylogenetic analysis. The susceptible strain H37Rv showed the highest virulence. Drug-susceptible LAM strain (spoligotype SIT264) was more virulent than three multidrug-resistant (MDR) strains (SIT252, SIT254, and SIT266). All three MDR isolates were low lethal, while the susceptible isolate and H37Rv were moderately/highly lethal. Putting the genomic, phenotypic, and virulence features of the LAM strains/spoligotypes in the context of their dynamic phylogeography over 20 years reveals three types of relationships between virulence, resistance, and transmission. First, the most virulent and more lethal drug-susceptible SIT264 increased its circulation in parts of Russia. Second, moderately virulent and pre-XDR SIT266 was prevalent in Belarus and continues to be visible in North-West Russia. Third, the low virulent and MDR strain SIT252 previously considered as emerging has disappeared from the population. These findings suggest that strain virulence impacts the transmission, irrespective of drug resistance properties. The increasing circulation of susceptible but more virulent and lethal strains implies that personalized TB treatment should consider not only resistance but also the virulence of the infecting M. tuberculosis strains. IMPORTANCE The study is multidisciplinary and investigates the epidemically/clinically important and global lineage of Mycobacterium tuberculosis, named Latin-American-Mediterranean (LAM), yet insufficiently studied with regard to its pathobiology. We studied different LAM strains (epidemic vs endemic and resistant vs susceptible) in the murine model and using whole-genome analysis. We also collected long-term, 20-year data on their prevalence in Eurasia. The findings are both expected and unexpected. (i) We observe that a drug-susceptible but highly virulent strain increased its prevalence. (ii) By contrast, the multidrug-resistant (MDR) but low-virulent, low-lethal strain (that we considered as emerging 15 years ago) has almost disappeared. (iii) Finally, an intermediate case is the MDR strain with moderate virulence that continues to circulate. We conclude that (i) the former and latter strains are the most hazardous and require close epidemiological monitoring, and (ii) personalized TB treatment should consider not only drug resistance but also the virulence of the infecting strains and development of anti-virulence drugs is warranted.

Evolutionary history and spread of the Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage, Tunisia

BACKGROUND

To infer the origin and spread of the Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage in a Mediterranean country, Tunisia, where it predominates.

METHODS

We combined Bayesian (STRUCTURE) and maximum likelihood (MIGRAINE) estimation approaches based on a global 24-loci mycobacterial interspersed repetitive units-variable numbers of tandem repeats (MIRU-VNTR24) genotyping dataset consisting of 1573 L4.3/LAM clinical strains from four continents, including 252 isolates originating from Tunisia.

RESULTS

Phylogenetic analyses coupled with Bayesian estimations suggested that the most predominant L4.3/LAM subpopulation in Tunisia (65.07%), which is dominated by a single clonal complex, TUN4.3_CC1 (94.51%), has evolved from an ancestral pool that is restricted to Europe and Africa, contrasting with the remaining L4.3/LAM subpopulations whose ancestry was traced all over the word. Maximum likelihood analysis revealed that TUN4.3_CC1 has been undergoing a demographic expansion since 131 years ago (CI95%: 90.7-205), thus explaining its preponderance relative to the second most predominant CC, TUN4.3_CC2, whose population was found under contraction.

CONCLUSIONS

The preponderance of L4.3/LAM in Tunisia stems from a 130-year expansion process of a locally evolved clone.

Mycobacterium simiae Isolates Subtypes and Molecular Drug Susceptibility in Iran

Background: Despite the clinical and epidemiological importance of Mycobacterium simiae worldwide, including in Iran, there is no clear and effective treatment regimen for M. simiae and its different subtypes. Objectives: Concerning the superiority of molecular approaches, this study aims to identify the common M. simiae subtypes submitted to the National Reference Tuberculosis (TB) Laboratory of Iran and study the presence of drug resistance by molecular detection methods. Methods: We included sputum samples with M. simiae confirmation submitted to the National Reference TB Laboratory of Iran from May 2014 to May 2016. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was used for drug susceptibility testing (DST). Results: Among 7200 TB suspected patients, a total of 60 M. simiae cases belonging to subtype I were identified. All the included clinical isolates met the American Thoracic Society (ATS) and Infectious Diseases Society of America (IDSA) diagnostic criteria and were considered the disease’s causative pathogen. Males (58.33%), elderly (68.54%), and patients with a history of TB (51.42%) were shown to be more prone to infection with the disease. All clinical isolates of M. simiae were resistant to rifampin (RIF) and isoniazid (INH). Amikacin/kanamycin (AMK/KAN) and ciprofloxacin (CIP) susceptibility was found to be 91.66% and 88.33%, respectively. Conclusions: Subtype I was exclusively identified among M. simiae patients in Iran. Molecular detection of drug resistance suggests that amikacin/kanamycin and ciprofloxacin could be used to treat patients infected with M. simiae subtype I.

Impact of pathobiological diversity of Mycobacterium tuberculosis on clinical features and lethal outcome of tuberculosis

BACKGROUND

Mycobacterium tuberculosis population in Russia is dominated by the notorious Beijing genotype whose major variants are characterized by contrasting resistance and virulence properties. Here we studied how these strain features could impact the progression of pulmonary tuberculosis (TB) concerning clinical manifestation and lethal outcome.

RESULTS

The study sample included 548 M. tuberculosis isolates from 548 patients with newly diagnosed pulmonary TB in Omsk, West Siberia, Russia. Strains were subjected to drug susceptibility testing and genotyping to detect lineages, sublineages, and subtypes (within Beijing genotype). The Beijing genotype was detected in 370 (67.5%) of the studied strains. The strongest association with multidrug resistance (MDR) was found for epidemic cluster Beijing B0/W148 (modern sublineage) and two recently discovered MDR clusters 1071-32 and 14717-15 of the ancient Beijing sublineage. The group of patients infected with hypervirulent and highly lethal (in a mouse model) Beijing 14717-15 showed the highest rate of lethal outcome (58.3%) compared to Beijing B0/W148 (31.4%; P = 0.06), Beijing Central Asian/Russian (29.7%, P = 0.037), and non-Beijing (15.2%, P = 0.001). The 14717-15 cluster mostly included isolates from patients with infiltrative but not with fibrous-cavernous and disseminated TB. In contrast, a group infected with low virulent 1071-32-cluster had the highest rate of fibrous-cavernous TB, possibly reflecting the capacity of these strains for prolonged survival and chronicity of the TB process.

CONCLUSIONS

The group of patients infected with hypervirulent and highly lethal in murine model 14717-15 cluster had the highest proportion of the lethal outcome (58.3%) compared to the groups infected with Beijing B0/W148 (31.4%) and non-Beijing (15.2%) isolates. This study carried out in the TB high-burden area highlights that not only drug resistance but also strain virulence should be considered in the implementation of personalized TB treatment.

RDRioMycobacterium tuberculosis strains associated with isoniazid resistance in Northern Mexico

BACKGROUND

It has been established that the genomic background of Mycobacterium tuberculosis may influence disease progression, in particular for the Beijing family and the Latin American and Mediterranean (LAM)/RD^Rio strains. The purpose of this study was to evaluate the prevalence of the LAM/RD^Rio genotype in cases of tuberculosis from Mexico and their drug susceptibility profile.

METHODS

Two hundred eighteen M. tuberculosis isolates were screened by 43-spacer spoligotyping. The LAM/RD^Rio genotype was confirmed by multiplex PCR, and the drug susceptibility testing was carried out in solid Löwenstein-Jensen media.

RESULTS

Among the LAM strains identified, 24 (63.1%) were confirmed as M. tuberculosis RD^Rio. All RD^Rio strains shared the RD174 deletion, that was associated with isoniazid resistance (p=0.0264).

CONCLUSIONS

We documented for the first time the isolation of the LAM/RD^Rio genotype in pulmonary cases of tuberculosis in Mexico, and we found resistance to the first-line anti-tuberculosis drug isoniazid in these strains.

Molecular epidemiology of Mycobacterium tuberculosis in Brazil before the whole genome sequencing era: a literature review

Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRU-VNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in São Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes.

RDRioMycobacterium tuberculosis strains associated with isoniazid resistance in Northern Mexico

BACKGROUND

It has been established that the genomic background of Mycobacterium tuberculosis may influence disease progression, in particular for the Beijing family and the Latin American and Mediterranean (LAM)/RDRio strains. The purpose of this study was to evaluate the prevalence of the LAM/RDRio genotype in cases of tuberculosis from Mexico and their drug susceptibility profile.

METHODS

Two hundred eighteen M. tuberculosis isolates were screened by 43-spacer spoligotyping. The LAM/RDRio genotype was confirmed by multiplex PCR, and the drug susceptibility testing was carried out in solid Löwenstein-Jensen media.

RESULTS

Among the LAM strains identified, 24 (63.1%) were confirmed as M. tuberculosis RDRio. All RDRio strains shared the RD174 deletion, that was associated with isoniazid resistance (p=0.0264).

CONCLUSIONS

We documented for the first time the isolation of the LAM/RDRio genotype in pulmonary cases of tuberculosis in Mexico, and we found resistance to the first-line anti-tuberculosis drug isoniazid in these strains.

Spatiotemporal dynamics of drug-resistant Mycobacterium tuberculosis: Contrasting trends and implications for tuberculosis control in EU high-priority country

Different and contrasting trends related to human migration and the implementation of health control programmes influence the spread of drug-resistant tuberculosis (TB). We analysed the Mycobacterium tuberculosis population structure in Estonia, a high-priority EU country for TB control, to detect the dynamic changes and underlying factors. The study collection included 278 M. tuberculosis isolates recovered in 1999 and 2014-2015. The isolates were subjected to drug susceptibility testing, genotyping and analysis of sublineage/cluster-specific markers and drug resistance mutations. The Beijing genotype was the most prevalent, and its rate increased from 28.6% in 1999 to 38.5% in 2015 (p = .09). The non-Beijing strains represented Euro-American lineage (Latin American Mediterranean [LAM], Ural, Haarlem, T, X genotypes) and Indo-Oceanic lineage (one EAI-IND isolate). The proportion of isolates resistant to two or more drugs increased from 22.4% to 29.1% (p = .1). The pre-XDR/XDR isolates were identified only within the Beijing genotype. In contrast, the drug resistance rate decreased in the LAM genotype from 42.1% to 11.8% (p = .05). The Beijing B0/W148-cluster ('successful Russian strain') included only MDR, pre-XDR or XDR isolates. All B0/W148-cluster isolates were resistant to two or more drugs compared to 28% of the Beijing 94-32-cluster (p = .0002). The Beijing genotype was not identified in the isolates from patients born in Estonia before 1940 compared to its 35.2% rate among other patients. In summary, the circulation of the highly drug-resistant isolates of the Beijing B0/W148 subtype, the increased prevalence of the Beijing genotype among HIV-coinfected patients and the increased number of patients with alcohol abuse (47.5%) present major challenges of the current TB control in Estonia. The Beijing genotype was likely brought to Estonia after 1945 due to the massive human influx from the Soviet Union. In contrast, the main genotypes of the Euro-American lineage were likely endemic in Estonia during all 20th century.

Most LAM Mycobacterium tuberculosis strains in Venezuela, but not SIT605, belong to the RDRio subfamily

Tuberculosis is a global public health problem that is resurgent in Venezuela, with 13 thousand estimated new cases in 2018. Strains of the Mycobacterium tuberculosis RD^Rio, subfamily belong to the Latín American Mediterranean (LAM) family and are a major cause of TB in Rio de Janeiro, Brazil. LAM strains predominate in Venezuela, where spoligotype SIT605 is common, but surprisingly not found elsewhere. We sought to assess the presence of RD^Rio strains in tuberculosis patients in different regions of Venezuela and determine whether SIT605 also belongs to the RD^Rio subfamily. Using spoligotyping and MIRU-VNTR 24 loci, we identified 86 clinical LAM and SIT605 isolates from the Venezuelan capital Caracas and several Venezuelan states. Region of difference deletion loci RD174 and RD^Rio, and also IS1561 were used to identify strains of the RD^Rio subfamily, while IS6110 at position 932,204 and the Ag85C¹⁰³ polymorphism were used to validate SIT 605 as a LAM family strain. We found that 69.8% of the isolates were RD^Río, including 94.3% of strains isolated in Caracas, 17.9% isolated in the state of Carabobo, the two strains analyzed from Delta Amacuro, and one each from Sucre, Apure and Aragua states. RD^Rio was in 100% of: SIT17 (LAM 2); SIT20 (LAM 1); SITs 93, 1694, 1696, 960, 1367 (LAM 5); and SITs 216 (LAM 9); but only 75% of SIT42 (LAM 9) strains. Thus, most of the LAM strains in Venezuela belong to the RD^Río subfamily. SIT 605 strains, although LAM, are not in the RD^Río subfamily.

Increased transmissibility of Russian successful strain Beijing B0/W148 of Mycobacterium tuberculosis: Indirect clues from history and demographics

The local situation with tuberculosis (TB) is shaped by the complex interplay of multiple factors related to both human host and Mycobacterium tuberculosis. We hypothesized that TB epidemiology in the rural regions in the Soviet Union was impacted by construction of the Gulag camps and significant incoming migration. This molecular M. tuberculosis study was conducted in 2017 in the Komi Republic in northern Russia, a region with high rate (26%) of primary multidrug-resistant (MDR) TB. MDR was detected in 30.8% (40/130) isolates; eight were extensively drug resistant. The Beijing genotype was predominant (56.2%). The main Beijing subtypes B0/W148 and 94-32 differed in the MDR rate, 83.3% and 27.2%, respectively. The non-Beijing isolates represented five genotypes (LAM, Ural, Haarlem, X, T). The proportion of Beijing B0/W148 in the "camp" cities (originated from Gulag camps) was twice as large as in other districts of the Komi Republic. To conclude, сirculation of the MDR-associated Beijing B0/W148 cluster critically influences the current situation with MDR-TB in this Russian region. The increased prevalence of B0/W148 in the urban setting on the whole, and in the "camp cities", in particular, indirectly points to the increased transmission capacity of this successful Russian strain of M. tuberculosis.

Mycobacterium tuberculosis RD-Rio Strain in Kazakhstan

Mycobacterium tuberculosis RD-Rio strains are still rare in the former Soviet Union countries and Asia. We describe a strain in Kazakhstan that belongs to the RD-Rio secondary branch, which is endemic to northwest Russia and eastern Europe. Although RD-Rio strains are frequently multidrug resistant, this heterogeneous branch included only drug-susceptible isolates.

Frequency of the Mycobacterium tuberculosis RDRio genotype and its association with multidrug-resistant tuberculosis

BACKGROUND

In recent decades, Mycobacterium tuberculosis with the RD^Rio genotype, frequently isolated from tuberculosis patients in Rio de Janeiro, has become part of the Latin American - Mediterranean (LAM) family and has been associated with multidrug-resistant tuberculosis (MDR-TB). The aim of this study was to investigate the frequency of M. tuberculosis RD^Rio in the state of Minas Gerais, Brazil, and its relationship with MDR-TB.

METHODS

For convenience, 172 susceptible and 63 MDR M. tuberculosis isolates were taken from pulmonary samples from patients diagnosed between January 2007 and December 2011. The DNA extracted from these isolates was analyzed by spoligotyping, PCR-RFLP to characterize fbpC¹⁰³/Ag85C103, multiplex PCR to detect RD^Rio and RD174, and MIRU-VNTR 24 loci.

RESULTS

Among the 235 isolates, the RD^Rio pattern was identified in 122 (51.9%) isolates (IC 0.45-0.58), with 100 (42.5%) wild-type and 13 (5.5%) mixed pattern isolates, whereas RD174 was identified in 93 of the 122 RD^Rio positive samples (76.3%). The LAM family and the LAM9 lineage were the most frequently identified among the isolates in this study. Among the 63 MDR isolates, 41 (65.1%) were RD^Rio and 28 (44.4%) RD174.

CONCLUSION

The association of both deletions with MDR proved to be statistically significant, corroborating the few reports that have associated RD^Rio with MDR.

Exploring the "Latin American Mediterranean" family and the RDRio lineage in Mycobacterium tuberculosis isolates from Paraguay, Argentina and Venezuela

Background

The Latin American & Mediterranean (LAM) spoligotype family is one of the most successful genotype of Mycobacterium tuberculosis worldwide and particularly prevalent in South-America. Within this family, a sublineage named Region of Difference Rio (RD^Rio) was reported initially in Brazil and is characterized by a genomic deletion of about 26.3 kb. This lineage seems to show a specific adaptation to the Euro-Latin American population. In this context, we sought to evaluate the LAM family and the presence of the RD^Rio genotype in samples from three Latin American countries including Paraguay, Venezuela and Argentina. To detect LAM strains reliably we applied a typing scheme using spoligotyping, 12 loci MIRU-VNTR, the Ag85C¹⁰³ SNP and the regions of difference RD^Rio and RD174. IS6110-RFLP results were also used when available.

Results

Genotyping of 413 M. tuberculosis isolates from three Latin-American countries detected LAM (46%) and the ill-defined T clade (16%) as the most frequent families. The highest clustering rate was detected in the sample population from the city of Caracas in Venezuela. We observed considerable differences in the presence of the RD^Rio lineage, with high frequency in Caracas-Venezuela (55%) and low frequency in Buenos Aires-Argentina (11%) and Paraguay (10%). The molecular markers (RD174, Ag85C¹⁰³, MIRU02-MIRU40 signature) of the RD^Rio lineage were essentially confirmed. For the LAM family, the most polymorphic loci were MIRU40, MIRU31, MIRU10, MIRU26, MIRU16 and the least polymorphic MIRU24, MIRU20, MIRU04, MIRU23.

Conclusions

Our results suggest a differential adaptation of LAM-sublineages in neighboring populations and that RD^Rio strains spread regionally with different rates of distribution. The Ag85C SNP and RDs (RD174, RD^Rio) tested in this study can in fact facilitate molecular epidemiological studies of LAM strains in endemic settings and low-income countries.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1479-6) contains supplementary material, which is available to authorized users.

Insights on the Mycobacterium tuberculosis population structure associated with migrants from Portuguese-speaking countries over a three-year period in Greater Lisbon, Portugal: Implications at the public health level

Tuberculosis among foreign-born patients is a key indicator of country-level epidemiological profiles and, of an increasing concern in Europe given the more intensified migratory waves of refugees. Since Portugal presents a lower immigrant-associated TB incidence rate when compared to other European countries, we sought to characterize the epidemiology and transmission dynamics among the foreign-born population coming from Portuguese-speaking countries that are associated with higher TB incidences. In the present study we analyzed 133 Mycobacterium tuberculosis isolates obtained from foreign-born individuals over a three-year period in Lisbon, Portugal, using molecular epidemiological methods such as spoligotyping and 24-loci MIRU-VNTR. Moreover, all strains were subjected to drug susceptibility testing. The genetic profiles obtained suggest that strain importation from Portuguese speaking countries plays a less important role in TB epidemiology but instead argue in favor of a high degree of penetrance of Portuguese endemic strains to the migrant population, including multidrug resistant strains, which is particularly relevant to active screening programs.

Genotypic diversity of Mycobacterium tuberculosis isolates from North-Central Indian population

BACKGROUND

Different strains of Mycobacterium tuberculosis (MTB) are known to have different epidemiological and clinical characteristics. Some of them are widely distributed and associated with drug resistance, whereas others are locally predominated. Molecular epidemiological investigations have always been beneficial in identifying new strains and studying their transmission dynamics. Sahariya a primitive tribe of North Madhya Pradesh, India, has already been reported to have high prevalence of tuberculosis (TB) than their non-tribal neighbours. However, the information about MTB genotypes prevalent in Sahariya tribe and their non-tribal neighbours is not available.

METHODS

A total of 214 clinical isolates representing Sahariya tribe and non-tribes were analyzed by spoligotyping and MIRU-VNTR typing.

RESULTS

The EAI3_IND/SIT11 genotype was observed as major genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. A 3.04 fold higher risk of getting TB with EAI3_IND/SIT11 genotype was observed in Sahariya as compared to the non-tribal population. The EAI_IND/SIT11 genotype also found to have more number of MDR-TB cases in Sahariya as well as true and possible transmission links. In Sahariya tribe, 3 clusters (6 isolates) reflected true transmission links, whereas 8 clusters consisted of 26 isolates revealed possible transmission links within the same geographical location or nearby houses.

CONCLUSION

The present study highlighted the predominance of EAI3_IND/SIT11 genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. Combined approach of MIRU-VNTR typing and spoligotyping was observed more favourable in discrimination of MTB genotypes. Further, longitudinal studies using whole genome sequencing can provide more insights into genetic diversity, drug resistance and transmission dynamics of these prevalent genotypes.

DISSEMINATED CUTANEOUS TUBERCULOSIS

Cutaneous tuberculosis is a clinically and morphologically heterogeneous group of skin diseases directly or indirectly caused by mycobacteria of the tuberculosis complex, occupying the 5th place among all localizations of extra-pulmonary tuberculosis. Manifestations of cutaneous tuberculosis are extremely diverse and depend on the immune status and ways of penetration of mycobacteria into the skin. Skin involvement can occur as a result of exogenous inoculation, contiguous spread from an adjacent focus, or hematogenous spread from other foci. Family cases of disseminated cutaneous tuberculosis are described. A combination of several clinical forms of cutaneous tuberculosis — scrofuloderma, tuberculosis cutis lichenoides (moniliformis scrophulosorum) and lupus — are observed in a 5 year old child with a family history of tuberculosis. The issues of pathogenesis and advanced methods of diagnosis of cutaneous tuberculosis are also discussed.

Genotypic diversity of Mycobacterium tuberculosis in Buenos Aires, Argentina

Buenos Aires is an overpopulated port city historically inhabited by people of European descent. Together with its broader metropolitan area, the city exhibits medium tuberculosis rates, and receives migrants, mainly from tuberculosis highly endemic areas of Argentina and neighboring countries. This work was aimed to gain insight into the Mycobacterium tuberculosis population structure in two suburban districts of Buenos Aires which are illustrative of the overall situation of tuberculosis in Argentina. The Lineage 4 Euro-American accounted for >99% of the 816 isolates analyzed (one per patient). Frequencies of spoligotype families were T 35.9%, LAM 33.2%, Haarlem 19.5%, S 3.2%, X 1.5%, Ural 0.7%, BOV 0.2%, Beijing 0.2%, and Cameroon 0.2%. Unknown signatures accounted for 5.3% isolates. Of 55 spoligotypes not matching any extant shared international type (SIT) in SITVIT database, 22 fitted into 15 newly-issued SITs. Certain autochthonous South American genotypes were found to be actively evolving. LAM3, which is wild type for RD^rio, was the predominant LAM subfamily in both districts and the RD^rio signature was rare among autochthonous, newly created, SITs and orphan patterns. Two genotypes that are rarely observed in neighboring countries ̶ SIT2/H2 and SIT159/T1 Tuscany ̶ were conspicuously represented in Argentina. The infrequent Beijing patterns belonged to Peruvian patients. We conclude that the genotype diversity observed reflects the influence of the Hispanic colonization and more recent immigration waves from Mediterranean and neighboring countries. Unlike in Brazil, the RD^rio type does not play a major role in the tuberculosis epidemic in Buenos Aires.

RDRioMycobacterium tuberculosis lineage in the Brazil/Paraguay/Argentina triple border

The high tuberculosis (TB) incidence rates, the closeness of the cities and the high migration flux on the Brazil/Paraguay/Argentina border deserves an in-depth study, using Mycobacterial Interspersed Repetitive Unit (MIRU) and Spoligotyping genetic markers to explore the impact of the Mycobacterium tuberculosis RD^Rio lineage on disease transmission and resistance to anti-TB drugs in this setting. Although without the totality of M. tuberculosis isolates causing TB in this studied setting, a number of 97 isolates obtained from sputa samples culture of patients with confirmed TB, from 2013 to 2015, were submitted to 24 loci MIRU, Spoligotyping, detection of RD^Rio lineage and detection of mutation related to isoniazid and rifampicin resistance by MTBDRplus/DNA STRIP. In this sample, it was observed high clonal variability of circulating M. tuberculosis isolates causing TB in Brazilian cities bordering Paraguay and Argentina. The percentage of RD^Rio lineage causing TB in this setting was 15.46%, and lower than the detected in different areas of Brazil. According to 24 loci MIRU, the major MIRU International Type (MIT) related with RD^Rio lineage were MIT 26, MIT 738, MIT 601 with four, two and one isolates, respectively. Eight isolates with RD^Rio marker were classified as orphans. The mainly Spoligofamily related with RD^Rio lineage was LAM1 and LAM9 and no relationship between RD^Rio lineage and resistance in M. tuberculosis isolates circulating in this setting could be established. This work is pioneer in studying the dynamics of RD^Rio lineage transmission on the Brazil/Paraguay/Argentina border and deserves further studies to analyze the real contribution of the RD^Rio lineage in outbreaks and the risk of significant development of MDR-TB in the setting studied.

Risk factors associated with cluster size of Mycobacterium tuberculosis (Mtb) of different RFLP lineages in Brazil

Background

Tuberculosis (TB) transmission is influenced by patient-related risk, environment and bacteriological factors. We determined the risk factors associated with cluster size of IS6110 RFLP based genotypes of Mycobacterium tuberculosis (Mtb) isolates from Vitoria, Espirito Santo, Brazil.

Methods

Cross-sectional study of new TB cases identified in the metropolitan area of Vitoria, Brazil between 2000 and 2010. Mtb isolates were genotyped by the IS6110 RFLP, spoligotyping and RD^Rio. The isolates were classified according to genotype cluster sizes by three genotyping methods and associated patient epidemiologic characteristics. Regression Model was performed to identify factors associated with cluster size.

Results

Among 959 Mtb isolates, 461 (48%) cases had an isolate that belonged to an RFLP cluster, and six clusters with ten or more isolates were identified. Of the isolates spoligotyped, 448 (52%) were classified as LAM and 412 (48%) as non-LAM. Our regression model found that 6–9 isolates/RFLP cluster were more likely belong to the LAM family, having the RD^Rio genotype and to be smear-positive (adjusted OR = 1.17, 95% CI 1.08–1.26; adjusted OR = 1.25, 95% CI 1.14–1.37; crude OR = 2.68, 95% IC 1.13–6.34; respectively) and living in a Serra city neighborhood decrease the risk of being in the 6–9 isolates/RFLP cluster (adjusted OR = 0.29, 95% CI, 0.10–0.84), than in the others groups. Individuals aged 21 to 30, 31 to 40 and > 50 years were less likely of belonging the 2–5 isolates/RFLP cluster than unique patterns compared to individuals < 20 years of age (adjusted OR = 0.49, 95% CI 0.28–0.85, OR = 0.43 95% CI 0.24–0.77and OR = 0. 49, 95% CI 0.26–0.91), respectively. The extrapulmonary disease was less likely to occur in those infected with strains in the 2–5 isolates/cluster group (adjustment OR = 0.45, 95% CI 0.24–0.85) than unique patterns.

Conclusions

We found that a large proportion of new TB infections in Vitoria is caused by prevalent Mtb genotypes belonging to the LAM family and RD^Rio genotypes. Such information demonstrates that some genotypes are more likely to cause recent transmission. Targeting interventions such as screening in specific areas and social risk groups, should be a priority for reducing transmission.

Major genotype families and epidemic clones of Mycobacterium tuberculosis in Omsk region, Western Siberia, Russia, marked by a high burden of tuberculosis-HIV coinfection

This population-based study characterized Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative tuberculosis (TB) patients in the Omsk region in Western Siberia, Russia. We sought to gain insight into the major genotype families and epidemic and endemic clones of M. tuberculosis in the area with a high burden and adverse trend of TB/HIV coinfection. The study collection included M. tuberculosis isolates from 207 newly-diagnosed patients with pulmonary TB; 55 (26.5%) of patients were HIV-infected. The M. tuberculosis isolates were subjected to drug susceptibility testing and molecular typing based on spoligotyping and analysis of the robust genotype and cluster-specific markers. Patients with disseminated TB disease were more prevalent in the HIV-positive (34.5%) than in the HIV-negative group (4.6%) (P < .001). The Beijing genotype was predominant (62.3% of isolates), and its major subtypes were 94-32-cluster (Central Asian/Russian strain, n = 80) and B0/W148-cluster (successful Russian strain, n = 28). The main non-Beijing families were represented by Latin-American Mediterranean (14.5%), T family (11.1%), Ural (5.8%), and Haarlem (3.9%). Under multivariate logistic regression analysis, MDR was associated with Beijing genotype and not associated with HIV coinfection status (P < .001). Beijing genotype isolates were found more frequently in TB/HIV patients than in TB HIV-negative patients (74.5% versus 57.9%, respectively; P = .031). The non-Beijing genotypes were mainly drug susceptible except for the drug-resistant Ural SIT262 isolates. To summarize, the alarming situation in the Omsk region in Siberia regarding TB/HIV coinfection is seriously influenced by the active circulation of M. tuberculosis isolates of MDR-associated Beijing genotype. Among the non-Beijing families, emergence of the drug-resistant Ural family strains of spoligotype SIT262 warrants attention.

Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates

Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of the utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study, we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M. tuberculosis Latin American-Mediterranean isolates. Using this approach, we identified 59 peptides containing single amino acid variants, which covered ∼9% of all coding nonsynonymous single nucleotide variants detected by whole-genome sequencing. Furthermore, we identified 29 distinct peptides that mapped to a hypothetical protein not present in the M. tuberculosis H37Rv reference proteome. Here, we provide evidence for the expression of this protein in the clinical M. tuberculosis SAWC3651 isolate. The strain-specific databases enabled confirmation of genomic differences (i.e., large genomic regions of difference and nonsynonymous single nucleotide variants) in these two clinical M. tuberculosis isolates and allowed strain differentiation at the proteome level. Our results contribute to the growing field of clinical microbial proteogenomics and can improve our understanding of phenotypic variation in clinical M. tuberculosis isolates.

Evolution of Mycobacterium tuberculosis: New Insights into Pathogenicity and Drug Resistance

The tuberculosis agent Mycobacterium tuberculosis has undergone a long and selective evolution toward human infection and represents one of the most widely spread pathogens due to its efficient aerosol-mediated human-to-human transmission. With the availability of more and more genome sequences, the evolutionary trajectory of this obligate pathogen becomes visible, which provides us with new insights into the molecular events governing evolution of the bacterium and its ability to accumulate drug-resistance mutations. In this review, we summarize recent developments in mycobacterial research related to this matter that are important for a better understanding of the current situation and future trends and developments in the global epidemiology of tuberculosis, as well as for possible public health intervention possibilities.

Relation of Mycobacterium tuberculosis mutations at katG315 and inhA-15 with drug resistance profile, genetic background, and clustering in Argentina

We analyzed 362 isoniazid-resistant clinical isolates of Mycobacterium tuberculosis obtained countrywide for the presence of mutation at katG315 and inhA-15 in relation to genotype, pattern of phenotypic resistance to other drugs, and ability to spread. We found the following mutation frequencies: katG315MUT/inhA-15wt 53.0%, katG315wt/inhA-15MUT 27.4%, katG315wt/inhA-15wt 19.3%, and katG315MUT/inhA-15MUT only 0.3%. Mutation at katG315 associated with the LAM superfamily; mutation at inhA-15 associated with the S family and the T1 Tuscany genotype; the combination katG315wt/inhA-15wt associated with the T1 Ghana genotype. Isolates harboring katG315MUT/inhA-15wt tended to accumulate resistance to other drugs and were more frequently found in cluster; isolates harboring katG315wt/inhA-15wt were more frequently found as orphan isolates. Although epidemiological and host factors could also be modulating the events observed, in Argentina, the systematic genotyping of drug resistant clinical isolates could help to predict an enhanced risk of transmission and a propensity to develop resistance to increasing numbers of drugs.

Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil

We recently detected the spoligotype patterns of strains of Mycobacterium pinnipedii, a species of the Mycobacterium tuberculosis complex, in sputum samples from nine cases with pulmonary tuberculosis residing in Porto Alegre, South Brazil. Because this species is rarely encountered in humans, we further characterized these nine isolates by additional genotyping techniques, including 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing, verification of the loci TbD1, RD9, pks15/1, RD(Rio), and fbpC, the insertion of IS6110 at a site specific to the M. tuberculosis Latin American Mediterranean (LAM) lineage, and whole-genome sequencing. The combined analysis of these markers revealed that the isolates are in fact M. tuberculosis and more specifically belong to the LAM genotype. Most of these isolates (n8) were shown to be multidrug resistant (MDR), which prompted us to perform partial sequencing of the rpoA, rpoB, rpoC, katG, and inhA genes. Seven isolates (77.8%) carried the S315T mutation in katG, and one of these (11%) also presented the C((-17)T single-nucleotide polymorphism (SNP) in inhA. Interestingly, six of the MDR isolates also presented an undescribed insertion of 12 nucleotides (CCA GAA CAA CCC) in codon 516 of rpoB. No putative compensatory mutation was found in either rpoA or rpoC. This is the first report of an M. tuberculosis LAM family strain with a convergent M. pinnipedii spoligotype. These spoligotypes are observed in genotype databases at a modest frequency, highlighting that care must be taken when identifying isolates in the M. tuberculosis complex on the basis of single genetic markers.

Latin-American-Mediterranean lineage of Mycobacterium tuberculosis: Human traces across pathogen's phylogeography

Currently, Mycobacterium tuberculosis isolates of Latin-American Mediterranean (LAM) family may be detected far beyond the geographic areas that coined its name 15years ago. Here, we established the framework phylogeny of this geographically intriguing and pathobiologically important mycobacterial lineage and hypothesized how human demographics and migration influenced its phylogeography. Phylogenetic analysis of LAM isolates from all continents based on 24 variable number of tandem repeats (VNTR) loci and other markers identified three global sublineages with certain geographic affinities and defined by large deletions RD115, RD174, and by spoligotype SIT33. One minor sublineage (spoligotype SIT388) appears endemic in Japan. One-locus VNTR signatures were established for sublineages and served for their search in published literature and geographic mapping. We suggest that the LAM family originated in the Western Mediterranean region. The most widespread RD115 sublineage seems the most ancient and encompasses genetically and geographically distant branches, including extremely drug resistant KZN in South Africa and LAM-RUS recently widespread across Northern Eurasia. The RD174 sublineage likely started its active spread in Brazil; its earlier branch is relatively dominated by isolates from South America and the derived one is dominated by Portuguese and South/Southeastern African isolates. The relatively most recent SIT33-sublineage is marked with enigmatic gaps and peaks across the Americas and includes South African clade F11/RD761, which likely emerged within the SIT33 subpopulation after its arrival to Africa. In addition to SIT388-sublineage, other deeply rooted, endemic LAM sublineages may exist that remain to be discovered. As a general conclusion, human mass migration appears to be the major factor that shaped the M. tuberculosis phylogeography over large time-spans.

Trends in molecular epidemiology of drug-resistant tuberculosis in Republic of Karelia, Russian Federation

Background

Russian Republic of Karelia is located at the Russian-Finnish border. It contains most of the historical Karelia land inhabited with autochthonous Karels and more recently migrated Russians. Although tuberculosis (TB) incidence in Karelia is decreasing, it remains high (45.8/100 000 in 2014) with the rate of multi-drug resistance (MDR) among newly diagnosed TB patients reaching 46.5 %. The study aimed to genetically characterize Mycobacterium tuberculosis isolates obtained at different time points from TB patients from Karelia to gain insight into the phylogeographic specificity of the circulating genotypes and to assess trends in evolution of drug resistant subpopulations.

Methods

The sample included 150 M. tuberculosis isolates: 78 isolated in 2013–2014 (“new” collection) and 72 isolated in 2006 (“old” collection). Drug susceptibility testing was done by the method of absolute concentrations. Spoligotyping was used to test genotype-specific markers of a Latin-American-Mediterranean (LAM) family and its sublineages as well as a Beijing B0/W148-cluster.

Results

The largest spoligotypes were SIT1 (Beijing family, n = 42) and SIT40 (T family, n = 5). Beijing family was the largest (n = 43) followed by T (n = 11), Ural (n = 10) and LAM (n = 8). Successful Russian clone, Beijing В0/W148, was identified in 15 (34.9 %) of 43 Beijing isolates; all В0/W148 isolates were drug-resistant. Seven of 8 LAM isolates belonged to the RD115/LAM-RUS branch, 1 - to the LAM RD174/RD-Rio sublineage. MDR was found in Beijing (32/43), Ural (3/10), and LAM (3/8). In contrast, all T isolates were pansusceptible. Comparison of drug resistant subgroups of the new and old collections showed an increasing prevalence of the B0/W148 clonal cluster, from 18.0 % (mainly polyresistant) in 2006 to 32.6 % in 2014 (mainly MDR and pre-XDR). The West–east increasing gradient is observed for the Ural genotype that may be defined a ‘Russian’ strain. In contrast, the spoligotype SIT40 of the T family appears to be a historical Karelian strain.

Conclusions

Circulation of the MDR M. tuberculosis isolates of the Beijing genotype and its B0/W148 cluster continues to critically influence the current situation with the MDR-TB control in northwestern Russia including the Republic of Karelia. Revealed phylogeographic patterns of some genotypes reflect a complex demographic history of Karelia within the course of the 20^th century.

Determinants of the Sympatric Host-Pathogen Relationship in Tuberculosis

Major contributions from pathogen genome analysis and host genetics have equated the possibility of Mycobacterium tuberculosis co-evolution with its human host leading to more stable sympatric host–pathogen relationships. However, the attribution to either sympatric or allopatric categories depends on the resolution or grain of genotypic characterization. We explored the influence on the sympatric host-pathogen relationship of clinical (HIV infection and multidrug-resistant tuberculosis [MDRTB]) and demographic (gender and age) factors in regards to the genotypic grain by using spacer oligonucleotide typing (spoligotyping) for classification of M. tuberculosis strains within the Euro-American lineage. We analyzed a total of 547 tuberculosis (TB) cases, from six year consecutive sampling in a setting with high TB-HIV coinfection (32.0%). Of these, 62.0% were caused by major circulating pathogen genotypes. The sympatric relationship was defined according to spoligotype in comparison to the international spoligotype database SpolDB4. While no significant association with Euro-American lineage was observed with any of the factors analyzed, increasing the resolution with spoligotyping evidenced a significant association of MDRTB with sympatric strains, regardless of the HIV status. Furthermore, distribution curves of the prevalence of sympatric and allopatric TB in relation to patients’ age showed an accentuation of the relevance of the age of onset in the allopatric relationship, as reflected in the trimodal distribution. On the contrary, sympatric TB was characterized by the tendency towards a typical (standard) distribution curve. Our results suggest that within the Euro-American lineage a greater degree of genotyping fine-tuning is necessary in modeling the biological processes behind the host-pathogen interplay. Furthermore, prevalence distribution of sympatric TB to age was suggestive of host genetic determinisms driven by more common variants.

Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RD^Rio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family.

Predominance of Uganda genotype of Mycobacterium tuberculosis isolated from Ugandan patients with tuberculous lymphadenitis

Background

In Uganda, the emerging Uganda genotype of Mycobacterium tuberculosis is the most common cause of pulmonary tuberculosis (PTB), and accounts for up to 70 % of isolates. Extrapulmonary TB (EPTB) is less studied in Uganda.

Methods

Molecular characterization using deletion analysis and spoligotyping was performed on 121 M. tuberculosis isolates from lymph node fine needle biopsy aspirates of Ugandan patients with tuberculous lymphadenitis. The evolutionary relationships and worldwide distribution of the spoligotypes were analyzed.

Results

Mycobacterium tuberculosis was the only cause of EPTB in this study. The T2 sublineage was the most predominant lineage and the Uganda genotype was the dominant genotype. There were 54 spoligotype patterns among the 121 study isolates. The dominant spoligotypes were shared international types (SIT) SIT420, SIT53, SIT 135, SIT 128 and SIT590 in descending order. All but SIT420 were previously reported in pulmonary TB in this setting. The phylogenetic analysis showed a long descendant branch of spoligotypes belonging to the T2-Uganda sublineage containing specifically SITs 135, 128 and 420.

Conclusion

In most cases, the spoligotypes were similar to those causing PTB, but the Uganda genotype was found to be less common in EPTB than previously reported for PTB in Uganda. The phylogenetic analysis and the study of the worldwide distribution of clustered spoligotypes indicate an ongoing evolution of the Uganda genotype, with the country of Uganda at the center of this evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-015-1362-y) contains supplementary material, which is available to authorized users.

Tuberculous spondylitis in Russia and prominent role of multidrug-resistant clone Mycobacterium tuberculosis Beijing B0/W148

Extrapulmonary and, in particular, spinal tuberculosis (TB) constitutes a minor but significant part of the total TB incidence. In spite of this, almost no studies on the genetic diversity and drug resistance of Mycobacterium tuberculosis isolates from spinal TB patients have been published to date. Here, we report results of the first Russian and globally largest molecular study of M. tuberculosis isolates recovered from patients with tuberculous spondylitis (TBS). The majority of 107 isolates were assigned to the Beijing genotype (n = 80); the other main families were T (n = 11), Ural (n = 7), and LAM (n = 4). Multidrug resistance (MDR) was more frequently found among Beijing (90.5%) and, intriguingly, Ural (71.4%) isolates than other genotypes (5%; P < 0.001). The extremely drug-resistant (XDR) phenotype was exclusively found in the Beijing isolates (n = 7). A notable prevalence of the rpoB531 and katG315 mutations in Beijing strains that were similarly high in both TBS (this study) and published pulmonary TB (PTB) samples from Russia shows that TBS and PTB Beijing strains follow the same paradigm of acquisition of rifampin (RIF) and isoniazid (INH) resistance. The 24-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) subtyping of 80 Beijing isolates further discriminated them into 24 types (Hunter Gaston index [HGI] = 0.83); types 100-32 and 94-32 represented the largest groups. A genotype of Russian successful clone B0/W148 was identified in 30 of 80 Beijing isolates. In conclusion, this study highlighted a crucial impact of the Beijing genotype and the especially prominent role of its MDR-associated successful clone B0/W148 cluster in the development of spinal MDR-TB in Russian patients.

Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

Background

Multidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades.

Results

In the present study we have genotyped and sequenced the genomes of 56 Mycobacterium tuberculosis isolates recovered mostly from Lisbon. The genotyping data revealed three major clusters associated with MDR-TB, two of which are associated with XDR-TB. Whilst the genomic data contributed to elucidate the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of Mycobacterium tuberculosis clinical isolates, revealed two major clades responsible for M/XDR-TB in the region: Lisboa3 and Q1 (LAM).

The data presented by this study yielded insights on microevolution and identification of novel compensatory mutations associated with rifampicin resistance in rpoB and rpoC. The screening for other structural variations revealed putative clade-defining variants. One deletion in PPE41, found among Lisboa3 isolates, is proposed to contribute to immune evasion and as a selective advantage. Insertion sequence (IS) mapping has also demonstrated the role of IS6110 as a major driver in mycobacterial evolution by affecting gene integrity and regulation.

Conclusions

Globally, this study contributes with novel genome-wide phylogenetic data and has led to the identification of new genomic variants that support the notion of a growing genomic diversity facing both setting and host adaptation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-991) contains supplementary material, which is available to authorized users.

Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism

Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRU-VNTR typing and presence of fbpC¹⁰³, RD^Rio and RD174. The results confirmed earlier data that predominant genotypes in Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs. 9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as “LAM-like”, 79.3% of these presenting the LAM-specific SNP fbpC¹⁰³. The frequency of RD^Rio and RD174 in the LAM strains, as defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not always a marker for LAM/RD^Rio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high incidence of TB.

Genomic variability of Mycobacterium tuberculosis strains of the Euro-American lineage based on large sequence deletions and 15-locus MIRU-VNTR polymorphism

A sample of 260 Mycobacterium tuberculosis strains assigned to the Euro-American family was studied to identify phylogenetically informative genomic regions of difference (RD). Mutually exclusive deletions of regions RD115, RD122, RD174, RD182, RD183, RD193, RD219, RD726 and RD761 were found in 202 strains; the RD^Rio deletion was detected exclusively among the RD174-deleted strains. Although certain deletions were found more frequently in certain spoligotype families (i.e., deletion RD115 in T and LAM, RD174 in LAM, RD182 in Haarlem, RD219 in T and RD726 in the “Cameroon” family), the RD-defined sublineages did not specifically match with spoligotype-defined families, thus arguing against the use of spoligotyping for establishing exact phylogenetic relationships between strains. Notably, when tested for katG463/gyrA95 polymorphism, all the RD-defined sublineages belonged to Principal Genotypic Group (PGG) 2, except sublineage RD219 exclusively belonging to PGG3; the 58 Euro-American strains with no deletion were of either PGG2 or 3. A representative sample of 197 isolates was then analyzed by standard 15-locus MIRU-VNTR typing, a suitable approach to independently assess genetic relationships among the strains. Analysis of the MIRU-VNTR typing results by using a minimum spanning tree (MST) and a classical dendrogram showed groupings that were largely concordant with those obtained by RD-based analysis. Isolates of a given RD profile show, in addition to closely related MIRU-VNTR profiles, related spoligotype profiles that can serve as a basis for better spoligotype-based classification.

Insights into the population structure of Mycobacterium tuberculosis using spoligotyping and RDRio in a southeastern Brazilian prison unit

Tuberculosis (TB) is still a serious public health problem, continuing to be an important threat for confined populations. We used spoligotyping to estimate the genotypic clades of Mycobacterium tuberculosis isolates from inmates in two blocks in a southeastern Brazilian prison unit, with TB incidence rate of 8185/100.000. The Latin American Mediterranean (LAM) clade is well represented in the country, and the LAM specific molecular markers, RD(Rio) large sequence polymorphism and the SNP on the Rv3062 [ligB(1212)], were used to characterize spoligotype signatures from prison isolates. Typing of RD(Rio) and ligB increase LAM clade from 66.7% (n=72/108) to 69.4% (n=75). The LAM2 SIT17 (n=23) and SIT179 (n=12) signatures comprised one third of all isolates, followed by Haarlem (11.5%, n=12), T (8.7%, n=9) and X (5.7%, n=6) clades. Strains with unknown signatures represented 5.5% (n=6), and four (3.7%) did not match any lineage. We observed RD(Rio) among 64 (59.2%) isolates, and 54 (50%) were of the LAM clade. In particular, the LAM2/RD(Rio) sub-lineage was significantly associated with clustering (p=0.02) and its frequency was higher (32%) when compared to that of the previous general TB cases in RJ (4.29%). Overall cluster frequency defined by spoligotyping/IS6110-RFLP was 62%. The two evolutionary markers helped to evaluate some LAM signature misconceptions and demonstrate that LAM2/RD(Rio) was found with high frequency, hitherto being unnoticed. All these data, allied to high clustering, imply that public health measures to minimize the escalation of TB in prison is essential, and both spoligotyping as well as RD(Rio) would be useful tools to monitor the effects of the measures with respect to M. tuberculosis lineage variation.

Mycobacterium tuberculosis Latin American-Mediterranean family and its sublineages in the light of robust evolutionary markers

Mycobacterium tuberculosis has a clonal population structure, and the Latin American-Mediterranean (LAM) family is one of the largest and most widespread within this species, showing evidence for remarkable pathobiology and a confusing phylogeny. Here, we applied robust phylogenetic markers to study the evolution of the LAM family and its major sublineages circulating in Russia and neighboring countries. A total of 250 M. tuberculosis isolates were confirmed to belong to the LAM family based on the analysis of the LAM-specific single-nucleotide polymorphisms (SNPs) in the Rv3062 and Rv0129c genes. At this stage, the family status was rectified for 121 isolates misleadingly assigned by CRISPR spoligotyping to non-LAM families (T1- or T5-RUS1). Consequently, the reestimated LAM prevalence rate increased 2-fold in Russia and Kazakhstan and 4-fold in Belarus. The majority (91.8 to 98.7%) of the LAM isolates from all three countries belonged to the LAM-RUS sublineage. In contrast, the Ibero-American LAM RD-Rio sublineage was identified in only 7 Russian isolates. Taken together, our findings and further analyses suggest a monophyletic origin of LAM-RUS: at a historically distant time, in Russia, in a small founding bacterial/human population. Its dissemination pattern and high prevalence rate in Northern Eurasia may indicate a long-term coexistence of the LAM-RUS sublineage and local human populations hypothetically leading to coadaptation and reduced pathogenicity of the relatively more ancient clones, such as spoligotype international type 254 (SIT254), compared to the more recent SIT252 and SIT266 clones. In contrast, rare LAM RD-Rio isolates were likely brought to Russia through occasional human contact. The spread of RD-Rio strains is not as global as commonly claimed and is determined largely by human migration flows (rather than by pathobiological properties of these strains). Consequently, a host population factor appears to play a major role in shaping the in situ dissemination pattern of the imported strains in an autochthonous population.

Real-time PCR assay for rapid detection of epidemiologically and clinically significant Mycobacterium tuberculosis Beijing genotype isolates

Mycobacterium tuberculosis Beijing genotype strains are rapidly disseminating, frequently hypervirulent, and multidrug resistant. Here, we describe a method for their rapid detection by real-time PCR that targets the specific IS6110 insertion in the dnaA-dnaN genome region. The method was evaluated with a geographically and genetically diverse collection representing areas in East Asia and the former Soviet Union in which the Beijing genotype is endemic and epidemic (i.e., major foci of its global propagation) and with clinical specimens.

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.

Infection of great apes and a zoo keeper with the same Mycobacterium tuberculosis spoligotype

An animal keeper was diagnosed with pulmonary tuberculosis (TB) after bi-annual screening for latent TB infection in zoo employees. In the same period, several bonobos of the zoo were suffering from TB as well. The Mycobacterium tuberculosis strains from both the animal keeper and the bonobos appeared identical. We provide evidence that the animals infected their keeper.

Mycobacterium tuberculosis belonging to family LAM and sublineage RD(Rio): common strains in Southern Brazil for over 10 years

A sublineage of Mycobacterium tuberculosis called RD(Rio) was described in 2007. Although only recently described, this strain may have been present previously in the population, and its identification in clinical isolates will elucidate bacterial transmission dynamics and host-pathogen interactions. This study evaluated the clonal diversity of the RD(Rio) sublineage in clinical isolates from Rio Grande-RS obtained between 1998 and 2001. Among the 45 samples analyzed by the MIRU-VNTR method, there were six clusters with two samples each and 33 orphan strains with unique pattern. The strains were distributed across several different lineages including LAM (34.04%), × (14.89%), Haarlem (12.77%), UgandaI (10.64%), S (4.26%), NEW-1 (2.13%) and Cameroon (2.13%); 14.89% of the strains matched to multiple lineages. RD(Rio) strains were present in 28.9% of the samples and 81.25% of the identified strains belonged to the LAM family. The high clonal diversity observed in this study is a constant feature in this region. The RD(Rio) sublineage has been in Rio Grande-RS since 1998. The continued monitoring of RD(Rio) in clinical isolates will enhance the understanding of its epidemiological significance.

Mycobacterium tuberculosis of the RDRio genotype is the predominant cause of tuberculosis and associated with multidrug resistance in Porto Alegre City, South Brazil

Spoligotyping has shown Mycobacterium tuberculosis strains to be composed of different lineages, and some of them are not just geographically restricted but also affect specific ethnic populations and are associated with outbreaks and drug resistance. We recently described a particular subtype within the Latin American-Mediterranean (LAM) family, called RD(Rio), widespread in Brazil. Moreover, recent data also indicate that RD(Rio) is present in many countries on all continents and is associated with cavitary disease and multidrug resistance (MDR). To further explore the relationship between RD(Rio) and MDR, we conducted a study in a tuberculosis (TB) reference center responsible for the care of MDR patients in Rio Grande do Sul, the southernmost Brazilian state. From a collection of 237 clinical isolates, RD(Rio) alone was responsible for one-half of all MDR cases, including one large group composed of strains with identical IS6110-restriction fragment length polymorphism (RFLP) and having the LAM5 signature. We additionally had complete data records for 96 patients and could make comparisons between the presence and absence of RD(Rio). No difference in clinical, radiological or laboratory features was observed, but a significantly greater number of cases with MDR were described in patients infected with an RD(Rio) strain (P = 0.0015). Altogether, RD(Rio) was responsible for 38% of all TB cases. These data support and confirmed previous findings that RD(Rio) is the main agent responsible for TB in Brazil and is associated with drug resistance. Considering that RD(Rio) is a globally distributed genotype, such findings raise concern about the increase in MDR in certain human populations.

Mycobacterium tuberculosis DNA fingerprint clusters and its relationship with RD(Rio) genotype in Brazil

Mycobacterium tuberculosis (Mtb) strains designated as RD(Rio) are responsible for a large cluster of new cases of tuberculosis (TB) in Rio de Janeiro. They were previously shown to be associated with severe manifestations of TB. Here, we used three genotyping methods (IS6110 RFLP, spoligotyping, and multiplex PCR) to characterize RD(Rio) and non-RD(Rio) strains from the metropolitan area of Vitória, State of Espirito Santo in southeast Brazil to determine strain diversity and transmission patterns. Strains with identical IS6110 RFLP patterns were considered to belong to a cluster indicative of recent transmission. Between 2000 and 2010, we identified 5470 new TB patients and genotyped 981 Mtb strains. Of these, 376 (38%) were RD(Rio). By RFLP, 180 (48%) of 376 RD(Rio) strains and 235 (40%) of 593 non-RD(Rio) strains belonged to RFLP cluster pattern groups (p = 0.023). Simpson's diversity index based on RFLP patterns was 0.96 for RD(Rio) and 0.98 for non-RD(Rio) strains. Thus, although RD(Rio) strains appear to be comprised of a fewer number of RFLP genotypes, they represent a heterogeneous group. While TB cases caused by RD(Rio) appear more likely to be due to recent transmission than cases caused by non-RD(Rio) strains, the difference is small. These observations suggest that factors other than inherent biological characteristic of RD(Rio) lineages are more important in determining recent transmission, and that public health measures to interrupt new transmissions need to be emphasized for TB control in Vitória.