Utility of new 24-locus variable-number tandem-repeat typing for discriminating Mycobacterium tuberculosis clinical isolates collected in Bulgaria

Origin and dispersal of the Mycobacterium tuberculosis Haarlem genotype: Clues from its phylogeographic landscape and human migration

The Haarlem family belongs to the Euro-American phylogenetic lineage of Mycobacterium tuberculosis and is one of the globally spread genotypes of this important human pathogen. In spite of the sporadic observations on drug resistance and peculiar virulence profile, Haarlem remains in the shade of other M. tuberculosis genotypes. I analyzed genotyping data of the Haarlem genotype in light of its pathogenic properties and relevant human migration, to gain insight into its origin, evolutionary history, and current spread. Central Europe is marked with a very high prevalence of both major Haarlem subclades ancestral H3/SIT50 and derived H1, jointly making 33-41% in Czechia, Austria, and Hungary. There is a declining gradient of Haarlem beyond central Europe with 10-18% in Italy, France, Belgium, 10-13% in the Balkan countries and Turkey. Placing the available genetic diversity and ancient DNA data within the historical context, I hypothesize that M. tuberculosis Haarlem genotype likely originated in Central Europe and its primary long-term circulation occurred within the area of the former Austria/Austria-Hungary Empire in the 14th-19th centuries. The genotype is not highly transmissible and its spread was driven by long-term human migration. The European colonial expansion (when accompanied by a sufficient volume of migration) was a vehicle of its secondary dissemination. I conclude that human migration and its lack thereof (but not strain pathobiology) was a major driving force that shaped the population structure of this global lineage of M. tuberculosis. At the same time, Haarlem strains appear over-represented in some ethnic groups which warrants in-depth experimental research.

Determination of genetic diversity of multidrug-resistant Mycobacterium tuberculosis strains in Turkey using 15 locus MIRU-VNTR and spoligotyping methods

Tuberculosis (TB) remains the leading cause of deaths from infectious disease worldwide. Nowadays, the tendency of Mycobacterium tuberculosis complex (MTBC) to spread between continents due to uncontrolled migration movements shows that TB is a global health problem. The number of studies for the detection of MTBC strains' epidemiological features in areas with TB spread risk using molecular-based methods such as spoligotyping and Mycobacterial Interspersed Repetitive Unit (MIRU) Variable Number Tandem Repeats (VNTR) at the clonal level is insufficient. In this study, it was aimed to determine the phylogenetic relationships of MTBC strains at the species level by spoligotyping and 15 locus MIRU-VNTR (MIRU-VNTR₁₅) molecular methods of 96 multidrug-resistant (MDR) MTBC strains isolated from sputum samples of patients with a preliminary diagnosis of pulmonary TB or suspected contact history those sent to National Tuberculosis Reference Laboratory from the centers that are members of the Tuberculosis Laboratory Surveillance Network. The phylogenetic relationship between 96 MDR-TB strains was investigated with the combination of bead-based spoligotyping and MIRU-VNTR₁₅ methods on the MAGPIX® Milliplex Map device. In this study, it was determined that the T1 family is more common in our country and LAM7-TUR family is less common than the Beijing family unlike other studies. It was determined that the strains in the same cluster had different locus profiles, and there was no transmission from the same clone in the clonal typing we performed with spoligotyping and MIRU-VNTR₁₅.

Ubiquitous and multifaceted: SIT53 spoligotype does not correlate with any particular family of Mycobacterium tuberculosis

Euro-American lineage (Lineage 4) of Mycobacterium tuberculosis comprises genetically and geographically diverse families that differ in their clinical and/or epidemiological capacities. Due to the characteristic structure of the CRISPR locus (presence of almost all 43 classical spacers except for deleted signals 33-36), spoligotype SIT53 takes the basal position in the evolution of this lineage. In the SITVIT database, it is assigned to the "ill-defined" T family and T1 subfamily. Here, I analyzed the phylogenetic diversity of SIT53 isolates and discussed interconnected terminological issues concerning M. tuberculosis population structure. The 24-MIRU-VNTR profiles of 266 SIT53 isolates from Europe, Asia, Africa, and South America were submitted to the phylogenetic analysis jointly with reference profiles of different families from MIRU-VNTRplus database. Under this analysis, SIT53 isolates were clustered within different and distant families such as Ghana, NEW-1 (L4.5), TUR (L4.2.2.1), etc whereas many remained unclassified within L4. This confirms the evolutionarily basal position of this spoligotype and in its turn, this demonstrates that SIT53 does not correspond to any particular family of M. tuberculosis. Instead, different SIT53 subpopulations with evolutionarily stable and unchanged CRISPR locus gave rise to different and distant families that in many instances evolved through long-term allopatric evolution.

Molecular typing of drug-resistant Mycobacterium tuberculosis strains from Turkey

OBJECTIVES

Appropriate antibiotic therapy and prevention of cross-contamination are the most important subjects in tuberculosis (TB) control. The aim of this study was to investigate the major phylogenetic clades and transmission rate of multidrug-resistant (MDR) Mycobacterium tuberculosis isolates (n = 200) from patients with TB in Sivas and Konya Provinces of Turkey.

METHODS

The phylogenetic relationship among the isolates was investigated by spoligotyping method. In addition, the 24-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing method was used to reveal cross-contamination.

RESULTS

Spoligotyping revealed 13 different spoligotypes. A total of 188 strains (94.0%) were included in the cluster. The most prominent spoligofamily was the T family (43.0% of strains), followed by LAM (26.0%), H (8.0%), X and S (both 6.0%) and U (5.0%). Also, 12 strains (6.0%) belonged to the Beijing profile. MIRU-VNTR results showed 176 (88.0%) different genotypes among the isolates. In total, 24 strains (12.0%) were in the cluster.

CONCLUSIONS

According to spoligotyping, there is a heterogeneous M. tuberculosis population in Turkey. MIRU-VNTR results showed that cross-contamination observed between MDR M. tuberculosis isolates in Turkey is controllable.

Laboratory Methods in Molecular Epidemiology: Bacterial Infections

In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial "species" and "clones." Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series. *This article is part of a curated collection.

Tuberculosis in immigrants in Finland, 1995-2013

Increasing immigration from high tuberculosis (TB) incidence countries is a challenge for surveillance and control in Finland. Here, we describe the epidemiology of TB in immigrants by using national surveillance data. During 1995-2013, 7030 (84·7%) native and 1199 (14·4%) immigrant cases were identified. The proportion of immigrant cases increased from 5·8% in 1995 to 32·1% in 2013, consistent with increasing immigrant population (2·1-5·6%) and decreasing incidence of TB in the native population (from 12·1 to 3·5/100 000). TB cases in immigrants were significantly younger, more often female, and had extrapulmonary TB more often than native cases (P < 0·01 for all comparisons); multidrug resistance was also more common in immigrants than natives (P < 0·01). Immigrant cases were born in 82 different countries; most commonly in Somalia and the former Soviet Union/Russia. During 2008-2013, 433 Mycobacterium tuberculosis isolates from immigrants were submitted for spoligotyping; 10 different clades were identified. Clades were similar to those found in the case's country of birth. Screening immigrants from high-incidence countries and raising awareness of common characteristics and symptoms of TB is important to ensure early diagnosis and to prevent transmission.

Prevalence and occurrence rate of Mycobacterium tuberculosis Haarlem family multi-drug resistant in the worldwide population: A systematic review and meta-analysis

BACKGROUND

Transmission of Mycobacterium tuberculosis (M. tuberculosis) can occur in different ways. Furthermore, drug resistant in M. tuberculosis family is a major problem that creates obstacles in treatment and control of tuberculosis (TB) in the world. One of the most prevalent families of M. tuberculosis is Haarlem, and it is associated with drug resistant. Our objectives of this study were to determine the prevalence and occurrence rate of M. tuberculosis Haarlem family multi-drug resistant (MDR) in the worldwide using meta-analysis based on a systematic review that performed on published articles.

MATERIALS AND METHODS

Data sources of this study were 78 original articles (2002-2012) that were published in the literatures in several databases including PubMed, Science Direct, Google Scholar, Biological abstracts, ISI web of knowledge and IranMedex. The articles were systematically reviewed for prevalence and rate of MDR. Data were analyzed using meta-analysis and random effects models with the software package Meta R, Version 2.13 (P < 0.10).

RESULTS

Final analysis included 28601 persons in 78 articles. The highest and lowest occurrence rate of Haarlem family in M. tuberculosis was in Hungary in 2006 (66.20%) with negative MDR-TB and in China in 2010 (0.8%), respectively. From 2002 to 2012, the lowest rate of prevalence was in 2010, and the highest prevalence rate was in 2012. Also 1.076% were positive for MDR and 9.22% were negative (confidence interval: 95%).0020.

CONCLUSION

Many articles and studies are performed in this field globally, and we only chose some of them. Further studies are needed to be done in this field. Our study showed that M. tuberculosis Haarlem family is prevalent in European countries. According to the presence of MDR that was seen in our results, effective control programs are needed to control the spread of drug-resistant strains, especially Haarlem family.

Suitability of IS6110-RFLP and MIRU-VNTR for differentiating spoligotyped drug-resistant mycobacterium tuberculosis clinical isolates from Sichuan in China

Genotypes of Mycobacterium tuberculosis complex (MTBC) vary with the geographic origin of the patients and can affect tuberculosis (TB) transmission. This study was aimed to further differentiate spoligotype-defined clusters of drug-resistant MTBC clinical isolates split in Beijing (n = 190) versus non-Beijing isolates (n = 84) from Sichuan region, the second high-burden province in China, by IS6110-restriction fragment length polymorphism (RFLP) and 24-locus MIRU-VNTRs. Among 274 spoligotyped isolates, the clustering ratio of Beijing family was 5.3% by 24-locus MIRU-VNTRs versus 2.1% by IS6110-RFLP, while none of the non-Beijing isolates were clustered by 24-locus MIRU-VNTRs versus 9.5% by IS6110-RFLP. Hence, neither the 24-locus MIRU-VNTR was sufficient enough to fully discriminate the Beijing family, nor the IS6110-RFLP for the non-Beijing isolates. A region adjusted scheme combining 12 highly discriminatory VNTR loci with IS6110-RFLP was a better alternative for typing Beijing strains in Sichuan than 24-locus MIRU-VNTRs alone. IS6110-RFLP was for the first time introduced to systematically genotype MTBC in Sichuan and we conclude that the region-adjusted scheme of 12 highly discriminative VNTRs might be a suitable alternative to 24-locus MIRU-VNTR scheme for non-Beijing strains, while the clusters of the Beijing isolates should be further subtyped using IS6110-RFLP for optimal discrimination.

Molecular epidemiology and genotyping of Mycobacterium tuberculosis isolated in Baghdad

Tuberculosis (TB) remains a major health problem in Iraq but the strains responsible for the epidemic have been poorly characterized. Our aim was to characterize the TB strains circulating in Bagdad (Iraq). A total of 270 Mycobacterium tuberculosis complex (MTBC) strains isolated between 2010 and 2011 from TB patients attending the Center of Chest and Respiratory diseases in Baghdad were analyzed by Spoligotyping. The analysis indicated that 94.1% of the isolates belong to known genotype clades: CAS 39.6%, ill-defined T clade 29.6%, Manu 7.4%, Haarlem 7%, Ural 4.1%, LAM 3.3%, X 0.7%, LAM7-TUR 0.7%, EAI 0.7%, S 0.7%, and unknown 5.9%. Comparison with the international multimarker database SITVIT2 showed that SIT 309 (CAS1-Delhi) and SIT1144 (T1) were the most common types. In addition, 44 strains were included in SITVIT2 database under 16 new Spoligotype International Types (SITs); of these, 6 SITs (SIT3346, SIT3497, SIT3708, SIT3790, SIT3791, and SIT3800) (n = 32 strains) were created within the present study and 10 were created after a match with an orphan in the database. By using 24-loci MIRU-VNTR-typing on a subset of 110 samples we found a high recent transmission index (RTI) of 33.6%. In conclusion, we present the first unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis in Iraq.

Genotypes of Mycobacterium tuberculosis isolates in rural China: using MIRU-VNTR and spoligotyping methods

BACKGROUND

The genotypes of Mycobacterium tuberculosis (MTB) have been found to be related to the risk of transmission and the development of drug resistance of this pathogen. Thus, exploring the molecular characteristics of MTB is helpful for understanding and controlling the spread of strains in areas with a high incidence of tuberculosis.

METHODS

We recruited 512 sputum smear-positive tuberculosis patients from 30 counties from 1 April to 30 June 2010; 503 MTB strains were isolated and 497 were successfully genotyped. We genotyped the strains based on a new 15-locus mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) method in combination with spacer-oligonucleotide typing (spoligotyping) technology.

RESULTS

Based on spoligotyping, 487 strains displayed known patterns, and 10 were absent from the current global spoligotyping database (SpolDB4). The predominant spoligotypes belonged to the Beijing or Beijing-like family (81.1%). When we used the new 15-locus (MIRU-15) set for the MIRU-VNTR analysis, 388 different patterns were identified, including 46 clusters and 342 unique patterns. The combination of spoligotyping and MIRU-15 demonstrated a high discriminatory power. The proportion of clusters varied significantly between the Beijing and non-Beijing family strains, but no significant association was observed between multidrug resistance and Beijing family strains.

CONCLUSIONS

The present study demonstrated that the Beijing family strains are the most prevalent in rural China. Spoligotyping in combination with the new MIRU-15 technique is useful for the epidemiological analysis of MTB transmission and could be used as a first-line method for the large-scale genotyping of MTB.

Synergistic activity of luteolin and amoxicillin combination against amoxicillin-resistant Escherichia coli and mode of action

The purpose of this research was to investigate whether luteolin has antibacterial and synergistic activity against amoxicillin-resistant Escherichia coli (AREC) when use singly and in combination with amoxicillin. The primarily mode of action is also investigated. The susceptibility assay (minimum inhibitory concentration and checkerboard determination) was carried out by the broth macrodilution method's in Müeller-Hinton medium. MIC and checkerboard determination were carried out after 20 h of incubation at 35°C by observing turbidity. The MICs of amoxicillin and luteolin against all AREC strains were >1000 and ≥ 200 μg/ml respectively. Synergistic activity were observed on amoxicillin plus luteolin against these strains. Viable count of this combination showed synergistic effect by reducing AREC cell numbers. The results indicated that this combination altered both outer and inner membrane permeabilisation. Enzyme assay showed that luteolin had an inhibitory activity against penicillinase. Fourier Transform-Infrared (FT-IR) spectroscopy exhibited that luteolin alone and when combined with amoxicillin caused increase in fatty acid and nucleic acid, but decrease in amide I of proteins in bacterial envelops compared with control. These results indicated that luteolin has the potential to reverse bacterial resistance to amoxicillin in AREC and may operate via three mechanisms: inhibition of proteins and peptidoglycan synthesis, inhibition of the activity of certain extended-spectrum β-lactamases and alteration of outer and inner membrane permeability. These findings offer the potential to develop a new generation of phytopharmaceuticals to treat AREC.

A model-based Bayesian estimation of the rate of evolution of VNTR loci in Mycobacterium tuberculosis

Variable numbers of tandem repeats (VNTR) typing is widely used for studying the bacterial cause of tuberculosis. Knowledge of the rate of mutation of VNTR loci facilitates the study of the evolution and epidemiology of Mycobacterium tuberculosis. Previous studies have applied population genetic models to estimate the mutation rate, leading to estimates varying widely from around to per locus per year. Resolving this issue using more detailed models and statistical methods would lead to improved inference in the molecular epidemiology of tuberculosis. Here, we use a model-based approach that incorporates two alternative forms of a stepwise mutation process for VNTR evolution within an epidemiological model of disease transmission. Using this model in a Bayesian framework we estimate the mutation rate of VNTR in M. tuberculosis from four published data sets of VNTR profiles from Albania, Iran, Morocco and Venezuela. In the first variant, the mutation rate increases linearly with respect to repeat numbers (linear model); in the second, the mutation rate is constant across repeat numbers (constant model). We find that under the constant model, the mean mutation rate per locus is (95% CI: ,)and under the linear model, the mean mutation rate per locus per repeat unit is (95% CI: ,). These new estimates represent a high rate of mutation at VNTR loci compared to previous estimates. To compare the two models we use posterior predictive checks to ascertain which of the two models is better able to reproduce the observed data. From this procedure we find that the linear model performs better than the constant model. The general framework we use allows the possibility of extending the analysis to more complex models in the future.

Genetically typing the bacterium responsible for tuberculosis is useful for understanding the evolutionary and epidemiological characteristics of the disease. Typing methods based on variable number tandem repeat (VNTR) loci are increasingly being used. These loci, which are composed of repeated units, mutate by increasing or decreasing in the number of these repeats. Knowledge of the mutation rate of molecular markers facilitates the epidemiological interpretation of the observed genetic variation in a sample of bacterial isolates. Few studies have examined the rate of mutation at these markers and estimates to date have varied considerably. To address this problem we develop a stochastic model of evolution of these markers and then estimate their mutation rate using approximate Bayesian computation. We examine two alternative forms of the mutation process. The observed data are from four published data sets of tuberculosis bacterial isolates sampled in Albania, Iran, Morocco and Venezuela. We find that these markers have fairly high rates of mutation compared with estimates from previous studies.

Genetic diversity of Mycobacterium tuberculosis isolates from Tibetans in Tibet, China

Background

Tuberculosis (TB) is a serious health problem in Tibet where Tibetans are the major ethnic group. Although genotyping of Mycobacterium tuberculosis (M. tuberculosis) isolates is a valuable tool for TB control, our knowledge of population structure of M. tuberculosis circulating in Tibet is limited.

Methodology/Principal Findings

In our study, a total of 576 M. tuberculosis isolates from Tibetans in Tibet, China, were analyzed via spoligotyping and 24-locus MIRU-VNTR. The Beijing genotype was the most prevalent family (90.63%, n = 522). Shared-type (ST) 1 was the most dominant genotype (88.89%, n = 512). We found that there was no association between the Beijing genotype and sex, age and treatment status. In this sample collection, 7 of the 24 MIRU-VNTR loci were highly or moderately discriminative according to their Hunter-Gaston discriminatory index. An informative set of 12 loci had similar discriminatory power with 24 loci set.

Conclusions/Significance

The population structure of M. tuberculosis isolates in Tibetans is homogeneous and dominated by Beijing genotype. The analysis of 24-locus MIRU-VNTR data might be useful to select appropriate VNTR loci for the genotyping of M. tuberculosis.

Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India

The aim of the present study was to compare polymerase chain reaction (PCR)-based methods--spoligotyping and mycobacterial interspersed repetitive units (MIRU) typing--with the gold-standard IS6110 restriction fragment length polymorphism (RFLP) analysis in 101 isolates of Mycobacterium tuberculosis to determine the genetic diversity of M. tuberculosis clinical isolates from Delhi, North India. Spoligotyping resulted in 49 patterns (14 clusters); the largest cluster was composed of Spoligotype International Types (SITs)26 [Central-Asian (CAS)1-Delhi lineage], followed by SIT11 [East-African-Indian (EAI) 3-Indian lineage]. A large number of isolates (75%) belonged to genotypic lineages, such as CAS, EAI and Manu, with a high specificity for the Indian subcontinent, emphasising the complex diversity of the phylogenetically coherent M. tuberculosis in North India. MIRU typing, using 11 discriminatory loci, was able to distinguish between all but two strains based on individual patterns. IS6110-RFLP analysis (n = 80 strains) resulted in 67 unique isolates and four clusters containing 13 strains. MIRUs discriminated all 13 strains, whereas spoligotyping discriminated 11 strains. Our results validate the use of PCR-based molecular typing of M. tuberculosis using repetitive elements in Indian isolates and demonstrate the usefulness of MIRUs for discriminating low-IS6110-copy isolates, which accounted for more than one-fifth of the strains in the present study.

One year nationwide evaluation of 24-locus MIRU-VNTR genotyping on Slovenian Mycobacterium tuberculosis isolates

BACKGROUND

Slovenia is one of the few countries where IS6110 RFLP is applied for genotyping M. tuberculosis at a nationwide level, which has been in effect since 2000. Based on S6110 RFLP clustering, typical risk factors and routes of M. tuberculosis transmission were identified, such as alcohol abuse, homelessness, and bars. However, IS6110 RFLP typing suffers from important limitations including a long wait for results, which reduces the potential benefit of molecular-guided tuberculosis (TB) control. PCR-based 24-locus MIRU-VNTR typing combined with spoligotyping has recently emerged as a potential alternative for faster, large-scale genotyping of M. tuberculosis.

METHODS

We compared these genotyping methods for analyzing 196 Slovenian Mycobacterium tuberculosis isolates representing 97.5% of all culture-positive cases included in the Slovenian TB Registry in 2008.

RESULTS

IS6110 RFLP and 24-locus MIRU-VNTR typing combined with spoligotyping identified 157 and 155 distinct profiles, 135 and 125 unique isolates, and 61 and 71 clustered isolates grouped into 22 and 29 clusters, respectively. The discriminatory indexes were very close, at 0.9963 and 0.9965, respectively. The majority of the molecular clusters defined by either of the two methods were identical, including in the few cases for which epidemiological links were available. The differences frequently consisted of single-band changes in IS6170-RFLP profiles subdividing a MIRU-VNTR/spoligotype-based cluster.

CONCLUSIONS

Our one-year nationwide study showed that the results of 24-locus MIRU-VNTR typing combined with spoligotyping reached a high level of concordance with those obtained from IS6110 RFLP typing.

The quiet and controversial: Ural family of Mycobacterium tuberculosis

The absence of lateral gene exchange is a characteristic feature defining the genome evolution and clonal population structure of Mycobacterium tuberculosis. Certain of its lineages have justly attracted more attention due to their global dissemination and/or remarkable pathogenic properties. In this critical review, I discuss the population structure and genetic geography of the less 'popular' but in some aspects no less noteworthy M. tuberculosis lineage, Ural family. Its specific signature was initially defined by single copy in MIRU26, and large (>6) copy number in MIRU10 loci, and by 43-spoligotyping as absence of signals 29-31 and 33-36. Here, I suggest to subdivide Ural strains with present and absent spoligosignal 2 into primary Ural-1 and secondary Ural-2 sublineages, respectively, while 1 copy in MIRU26 is specific of Ural-1. Furthermore, three copies were recently described in MIRU10 in Ural-1 strains which highlights a high diversity of this locus in Ural genotype. The data on the two Ural sublineages were extracted from SpolDB4 database and original publications in order to trace their distribution at global and within-country levels. Importantly, the rigorous reanalysis suggested the true rate of the Ural genotype in the Ural area in Russia to be only 7%. In contrast, the frequencies of the Ural sublineages peak elsewhere: in South Ukraine and Georgia/Abkhazia (Ural-1, up to 14-19%), and in southwestern Iran (Ural-2, up to 26%). However, as this name is used since 2005, it seems most parsimonious to continue its use even if misleading. The forest graph was built on the available spoligoprofiles of Ural family strains from Eurasia. It helped to suggest routes of their primary dispersal that are discussed in the context of the known human migrations also influenced by natural barriers. The north/east Pontic area may have been an area of origin and primary dispersal of the Ural (Ural-1) genotype in Eurasia, whereas political and natural borders may have influenced its subsequent dissemination throughout Central Asia. Studies of phenotypic properties in different models, comparison with host genetics give evidence that the Ural family strains are not associated with increased capacity to acquire drug resistance, pathogenicity or transmissibility. Instead since Ural family is rather moderately widespread in Eurasia beyond the hypothesized areas of origin, this situation may be a result of its low contagiosity as a consequence of long-term co-adaptation with human host. Future research should be focused on whole-genome sequencing in order to identify Ural-specific SNP and/or deletion, to resolve its phylogenetic and phylogeographic uncertainty and to elucidate biological features underlying its circulation and co-evolution with the human species.

The population structure of drug-resistant Mycobacterium tuberculosis clinical isolates from Sichuan in China

China ranks second next to India among 22 high-burden countries despite decades' effort on tuberculosis (TB) control. The Sichuan province today contains the second-largest number of TB cases among Chinese provinces, where the prevalence of drug-resistant TB, especially MDR-TB, is much higher than the average level in eastern China. In this study, the population structure and the transmission characteristics of drug-resistant TB in Sichuan province were studied by spoligotyping and 24-locus Mycobacterial interspersed repetitive units-variable number tandem DNA repeats (MIRU-VNTR), applied to a total of 306 clinical isolates. Spoligotyping-based analysis showed that Beijing family represented 69.28% of all isolates and constituted the largest group (66.24%) of MDR-TB in Sichuan. The remaining isolates, accounting for 33.76% of MDR isolates, belonged to the ill-defined T family, Manu2, H3, LAM9, and other minor unassigned clades. The discriminatory power evaluated for spoligotyping was poor (HGI=0.595), but high for 24-locus MIRU-VNTRs (HGI=0.999). The number of the most discriminatory loci (h>0.6) was 12, including locus 424, 802, 960, 1644, 1955, 2163b, 2996, 3007, 3192, 3690, 4348 and 4052. It was concluded that 24-locus MIRU-VNTRs could be a more discriminatory tool for differentiating clinical isolates from Sichuan region. The small clustering size obtained from the current population structure analysis suggested that the high prevalence of drug-resistant TB in this region might be attributed partially to the acquired resistance due to inappropriate drug use rather than active transmission of drug-resistant TB (primary resistance).

Epidemiological studies of Beijing strains of Mycobacterium tuberculosis from Taipei and other Asian cities based on MIRU profiles

The aim of the present study was to investigate the distribution of the Beijing strains of Mycobacterium tuberculosis (MTB) in Taipei and other Asian cities. A total of 323 MTB isolates were analyzed by spacer oligonucleotide typing (spoligotyping) and mycobacterial interspersed repetitive unit (MIRU) typing. The largest cluster of the TB isolates from Taipei was type MT11 (MIRU type 2233-2517-3533). A comparison of the MIRU type data for the Beijing strains from Taipei and previously published MIRU type data for the Beijing strains from Asian cities with major population of Chinese was analyzed. The six major Beijing MIRU types (MT01, MT02, MT08, MT11, MT21, and MT44) were found to be common in four Asian cities including Taipei, Singapore, Hong Kong, and Wuhan. Results of this study indicate that there is geographical difference in the distribution of different Beijing strains of MTB.

A first insight on the population structure of Mycobacterium tuberculosis complex as studied by spoligotyping and MIRU-VNTRs in Bogotá, Colombia

With an incidence of 25.6/100,000 in 2008, tuberculosis (TB) remains an important public health problem in Colombia. In this study, a total of 152 Mycobacterium tuberculosis complex strains isolated in Bogotá, Colombia between years 1995 and 2007 were genotyped by spoligotyping and 12-loci MIRU-VNTRs. The various spoligotyping-based genotypic lineages in our sample were: Latin American & Mediterranean (LAM) n=75, 49.34%; Haarlem, n=38, 25.0%; ill-defined T group, n=21, 13.82%; S family, n=5, 3.29%; X clade, n=2, 1.32%; Beijing, n=1, 0.65%, while strains with unknown signatures (n=10) represented 6.58% of isolates. Using spoligotyping as a first molecular marker and MIRU-VNTRs as second marker, we obtained 102 single patterns and 14 clustered patterns (n=52 strains from 49 patients, 2-8 strains per cluster). The MIRU-VNTRs patterns corresponded to 50 MITs for 109 strains and 43 orphan patterns. The most frequent patterns were MIT190 (n=12), MIT45 (n=10), and MIT25 (n=9). The Hunter & Gaston discriminatory index (HGDI) of both methodologies used together showed a value of 0.992. In our setting, the HGDI of five loci subset (MIRU10, 16, 23, 26 and 40) contributed most to the discriminatory power of 12-loci format used (HGDI=0.977). The lineage distribution of M. tuberculosis showed that more than 3/4 of strains in Bogotá are commonly found in Latin America, Caribbean, and Europe. This observation might reflect the shared post-Columbus history of Colombia and its Latin-American neighbors as well as strains brought in by 20th century immigrants from Europe. We also demonstrate the usefulness of MIRU-VNTR to detect suspected links among patients and polyclonal infections.

Genotyping of Mycobacterium tuberculosis: application in epidemiologic studies

Genotyping is used to track specific isolates of Mycobacterium tuberculosis in a community. It has been successfully used in epidemiologic research (termed 'molecular epidemiology') to study the transmission dynamics of TB. In this article, we review the genetic markers used in molecular epidemiologic studies including the use of whole-genome sequencing technology. We also review the public health application of molecular epidemiologic tools.

Transmission pattern of drug-resistant tuberculosis and its implication for tuberculosis control in eastern rural China

OBJECTIVE

Transmission patterns of drug-resistant Mycobacterium tuberculosis (MTB) may be influenced by differences in socio-demographics, local tuberculosis (TB) endemicity and efficaciousness of TB control programs. This study aimed to investigate the impact of DOTS on the transmission of drug-resistant TB in eastern rural China.

METHODS

We conducted a cross-sectional study of all patients diagnosed with drug-resistant TB over a one-year period in two rural Chinese counties with varying lengths of DOTS implementation. Counties included Deqing, with over 11 years' DOTS implementation and Guanyun, where DOTS was introduced 1 year prior to start of this study. We combined demographic, clinical and epidemiologic information with IS6110-based restricted fragment length polymorphism (RFLP) and Spoligotyping analysis of MTB isolates. In addition, we conducted DNA sequencing of resistance determining regions to first-line anti-tuberculosis agents.

RESULTS

Of the 223 drug-resistant isolates, 73(32.7%) isolates were identified with clustered IS6110RFLP patterns. The clustering proportion among total drug-resistant TB was higher in Guanyun than Deqing (26/101.vs.47/122; p,0.04), but not significantly different among the 53 multidrug-resistant isolates (10/18.vs.24/35; p,0.35). Patients with cavitary had increased risk of clustering in both counties. In Guanyun, patients with positive smear test or previous treatment history had a higher clustering proportion. Beijing genotype and isolates resistant to isoniazid and/or rifampicin were more likely to be clustered. Of the 73 patients with clustered drug-resistant isolates, 71.2% lived in the same or neighboring villages. Epidemiological link (household and social contact) was confirmed in 12.3% of the clustered isolates.

CONCLUSION

Transmission of drug-resistant TB in eastern rural China is characterized by small clusters and limited geographic spread. Our observations highlight the need for supplementing DOTS with additional strategies, including active case finding at the village level, effective treatment for patients with cavities and drug susceptibility testing for patients at increased risk for drug-resistance.

Strains of Mycobacterium tuberculosis from western Maharashtra, India, exhibit a high degree of diversity and strain-specific associations with drug resistance, cavitary disease, and treatment failure

We performed spoligotyping of Mycobacterium tuberculosis isolates from 833 systematically sampled pulmonary tuberculosis (TB) patients in urban Mumbai, India (723 patients), and adjacent rural areas in western India (110 patients). The urban cohort consisted of two groups of patients, new cases (646 patients) and first-time treatment failures (77 patients), while only new cases were recruited in the rural areas. The isolates from urban new cases showed 71% clustering, with 168 Manu1, 62 CAS, 22 Beijing, and 30 EAI-5 isolates. The isolates from first-time treatment failures were 69% clustered, with 14 Manu1, 8 CAS, 8 Beijing, and 6 EAI-5 isolates. The proportion of Beijing strains was higher in this group than in urban new cases (odds ratio [OR], 3.29; 95% confidence limit [95% CL], 1.29 to 8.14; P = 0.003). The isolates from rural new cases showed 69% clustering, with 38 Manu1, 7 CAS, and 1 EAI-5 isolate. Beijing was absent in the rural cohort. Manu1 was found to be more common in the rural cohort (OR, 0.67; 95% CL, 0.42 to 1.05; P = 0.06). In total, 71% of isolates were clustered into 58 spoligotypes with 4 predominant strains, Manu1 (26%), CAS (9%), EAI-5 (4%), and Beijing (4%), along with 246 unique spoligotypes. In the isolates from urban new cases, we found Beijing to be associated with multidrug resistance (MDR) (OR, 3.40; 95% CL, 1.20 to 9.62; P = 0.02). CAS was found to be associated with pansensitivity (OR, 1.83; 95% CL, 1.03 to 3.24; P = 0.03) and cavities as seen on chest radiographs (OR, 2.72; 95% CL, 1.34 to 5.53; P = 0.006). We recorded 239 new spoligotypes yet unreported in the global databases, suggesting that the local TB strains exhibit a high degree of diversity.

Bulgarian specificity and controversial phylogeography of Mycobacterium tuberculosis spoligotype ST 125__BGR

The local specificity of bacterial clones may be explained by long-term presence or recent importation/fast dissemination in an area. Mycobacterium tuberculosis spoligotype ST125, noticeably prevalent among Bulgaria-specific spoligotypes, has a characteristically 'abridged' profile and an uncertain clade position [Latin-American-Mediterranean (LAM)/S]. A comparison with the SITVIT2 database (Institut Pasteur de Guadeloupe) demonstrated its high gradient in Bulgaria (14.3%) compared with the negligible presence in the rest of the world. Further typing of all available Bulgarian ST125 strains revealed that they: (i) monophyletically clustered in 21-mycobacterial interspersed repetitive units (MIRU)-loci tree of all Bulgarian strains; (ii) grouped closely with the ST34 spoligotype, a prototype of the S family; and (iii) did not harbor a LAM-specific IS6110 insertion. Comparison of the 21-MIRU-based network with geographic data revealed a complex dissemination pattern of ST125 in Bulgaria. Interestingly, this variable number of tandem repeats (VNTR) network remarkably corroborated with a recent hypothesis of single repeat loss as the primary mode of evolution of VNTR loci in M. tuberculosis. In conclusion, M. tuberculosis spoligotype ST125 is phylogeographically specific for Bulgaria. This spoligotype was not associated with drug resistance or increased transmissibility; its prevalence in Bulgaria can rather be attributed to the historical circulation in the country, having led, speculatively, to adaptation to the local human population.

Genetic diversity of Mycobacterium tuberculosis isolates from a tertiary care tuberculosis hospital in South Korea

Tuberculosis (TB) remains an immense public health problem in the Republic of Korea despite a more than fivefold decrease in the prevalence of the disease over the last 3 decades. The rise in drug-resistant TB has compounded the situation. We analyzed 208 clinical isolates of M. tuberculosis from the National Masan Tuberculosis Hospital by spoligotyping, IS6110 restriction fragment length polymorphism (RFLP), and 24-locus-based mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing to assess the diversity and transmission dynamics of the tubercle bacilli in the Republic of Korea. The majority of the isolates (97.1%) belonged to the Beijing genotype. Cluster analysis by MIRU-VNTR yielded a low clustering rate of 22.3%, with most of the clusters comprising isolates with diverse drug resistance patterns. The discriminatory capacity of the typing methods was high for RFLP and MIRU-VNTR (allelic diversity [h] = 0.99) but low for spoligotyping (h = 0.31). Although analysis of 19 MIRU-VNTR loci was needed to achieve maximum discrimination, an informative set of 8 loci (960, 1955, 2163b, 2165, 2996, 3192, 4052, and 4348) (h = 0.98) that was able to differentiate most of the closely related strains was identified. These findings suggest that 24-locus-based MIRU-VNTR typing is a likely suitable alternative to RFLP to differentiate clinical isolates in this setting, which is dominated by M. tuberculosis Beijing strains. Within the study limits, our results also suggest that the problem of drug-resistant TB in the Republic of Korea may be largely due to acquired resistance as opposed to transmission.

Mycobacterium tuberculosis ecology in Venezuela: epidemiologic correlates of common spoligotypes and a large clonal cluster defined by MIRU-VNTR-24

BACKGROUND

Tuberculosis remains an endemic public health problem, but the ecology of the TB strains prevalent, and their transmission, can vary by country and by region. We sought to investigate the prevalence of Mycobacterium tuberculosis strains in different regions of Venezuela. A previous study identified the most prevalent strains in Venezuela but did not show geographical distribution nor identify clonal genotypes. To better understand local strain ecology, we used spoligotyping to analyze 1298 M. tuberculosis strains isolated in Venezuela from 1997 to 2006, predominantly from two large urban centers and two geographically distinct indigenous areas, and then studied a subgroup with MIRU-VNTR 24 loci.

RESULTS

The distribution of spoligotype families is similar to that previously reported for Venezuela and other South American countries: LAM 53%, T 10%, Haarlem 5%, S 1.9%, X 1.2%, Beijing 0.4%, and EAI 0.2%. The six most common shared types (SIT's 17, 93, 605, 42, 53, 20) accounted for 49% of the isolates and were the most common in almost all regions, but only a minority were clustered by MIRU-VNTR 24. One exception was the third most frequent overall, SIT 605, which is the most common spoligotype in the state of Carabobo but infrequent in other regions. MIRU-VNTR homogeneity suggests it is a clonal group of strains and was named the "Carabobo" genotype. Epidemiologic comparisons showed that patients with SIT 17 were younger and more likely to have had specimens positive for Acid Fast Bacilli on microscopy, and patients with SIT 53 were older and more commonly smear negative. Female TB patients tended to be younger than male patients. Patients from the high incidence, indigenous population in Delta Amacuro state were younger and had a nearly equal male:female distribution.

CONCLUSION

Six SIT's cause nearly half of the cases of tuberculosis in Venezuela and dominate in nearly all regions. Strains with SIT 17, the most common pattern overall may be more actively transmitted and SIT 53 strains may be less virulent and associated with reactivation of past infections in older patients. In contrast to other common spoligotypes, strains with SIT 605 form a clonal group centered in the state of Carabobo.

Prospective universal application of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping to characterize Mycobacterium tuberculosis isolates for fast identification of clustered and orphan cases

The use of molecular tools for genotyping Mycobacterium tuberculosis isolates in epidemiological surveys in order to identify clustered and orphan strains requires faster response times than those offered by the reference method, IS6110 restriction fragment length polymorphism (RFLP) genotyping. A method based on PCR, the mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping technique, is an option for fast fingerprinting of M. tuberculosis, although precise evaluations of correlation between MIRU-VNTR and RFLP findings in population-based studies in different contexts are required before the methods are switched. In this study, we evaluated MIRU-VNTR genotyping (with a set of 15 loci [MIRU-15]) in parallel to RFLP genotyping in a 39-month universal population-based study in a challenging setting with a high proportion of immigrants. For 81.9% (281/343) of the M. tuberculosis isolates, both RFLP and MIRU-VNTR types were obtained. The percentages of clustered cases were 39.9% (112/281) and 43.1% (121/281) for RFLP and MIRU-15 analyses, and the numbers of clusters identified were 42 and 45, respectively. For 85.4% of the cases, the RFLP and MIRU-15 results were concordant, identifying the same cases as clustered and orphan (kappa, 0.7). However, for the remaining 14.6% of the cases, discrepancies were observed: 16 of the cases clustered by RFLP analysis were identified as orphan by MIRU-15 analysis, and 25 cases identified as orphan by RFLP analysis were clustered by MIRU-15 analysis. When discrepant cases showing subtle genotypic differences were tolerated, the discrepancies fell from 14.6% to 8.6%. Epidemiological links were found for 83.8% of the cases clustered by both RFLP and MIRU-15 analyses, whereas for the cases clustered by RFLP or MIRU-VNTR analysis alone, links were identified for only 30.8% or 38.9% of the cases, respectively. The latter group of cases mainly comprised isolates that could also have been clustered, if subtle genotypic differences had been tolerated. MIRU-15 genotyping seems to be a good alternative to RFLP genotyping for real-time interventional schemes. The correlation between MIRU-15 and IS6110 RFLP findings was reasonable, although some uncertainties as to the assignation of clusters by MIRU-15 analysis were identified.

Multiple-locus variable-number tandem-repeat analysis for clonal identification of Vibrio parahaemolyticus isolates by using capillary electrophoresis

Epidemics of Vibrio parahaemolyticus in Chile have occurred since 1998. Direct genome restriction enzyme analysis (DGREA) using conventional gel electrophoresis permitted discrimination of different V. parahaemolyticus isolates obtained from these outbreaks and showed that this species consists of a highly diverse population. A multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) approach was developed and applied to 22 clinical and 91 environmental V. parahaemolyticus isolates from Chile to understand their clonal structures. To this end, an advanced molecular technique was developed by applying multiplex PCR, fluorescent primers, and capillary electrophoresis, resulting in a high-resolution and high-throughput (HRHT) genotyping method. The genomic basis of this HRHT method was eight VNTR loci described previously by Kimura et al. (J. Microbiol. Methods 72:313-320, 2008) and two new loci which were identified by a detailed molecular study of 24 potential VNTR loci on both chromosomes. The isolates of V. parahaemolyticus belonging to the same DGREA pattern were distinguishable by the size variations in the indicative 10 VNTRs. This assay showed that these 10 VNTR loci were useful for distinguishing isolates of V. parahaemolyticus that had different DGREA patterns and also isolates that belong to the same group. Isolates that differed in their DGREA patterns showed polymorphism in their VNTR profiles. A total of 81 isolates was associated with 59 MLVA groups, providing fine-scale differentiation, even among very closely related isolates. The developed approach enables rapid and high-resolution analysis of V. parahaemolyticus with pandemic potential and provides a new surveillance tool for food-borne pathogens.

First insight into genetic diversity of the Mycobacterium tuberculosis complex in Albania obtained by multilocus variable-number tandem-repeat analysis and spoligotyping reveals the presence of beijing multidrug-resistant isolates

We characterized a set of 100 Mycobacterium tuberculosis complex clinical isolates from tuberculosis (TB) patients in Albania, typing them with a 24-locus variable-number tandem-repeat-spoligotyping scheme. Depending on the cluster definition, 43 to 49 patients were distributed into 15 to 16 clusters which were likely to be epidemiologically linked, indicative of a recent transmission rate of 28 to 34%. This result suggests that TB is under control in Albania. However, two multidrug-resistant (MDR) Beijing genotypes harboring the same S531A mutation on the rpoB gene were also found, suggesting a potential recent transmission of MDR TB. Three brand new genotypes, Albania-1 to Albania-3, are also described.