Four year longitudinal study of Mycobacterium tuberculosis complex isolates in a region of North-Eastern Italy

Effects of migration on tuberculosis epidemiological indicators in low and medium tuberculosis incidence countries: A systematic review

BACKGROUND

Tuberculosis (TB) remains one of the top ten causes of death each year globally. While the risk of migrant TB is linked to the TB incidence in their country of origin, the migration process can increase the TB risk.

OBJECTIVE

We aimed to synthesis the evidence on key differences in the epidemiological profile of TB between migrants from high TB incidence birth countries and non-migrants resident in low to medium incidence TB countries.

METHODS

We conducted a systematic review where the population was all active TB cases in countries with low to medium TB incidence (<40/100,000 population), the exposure was migration to a low or medium TB incidence country and the comparator was non-migrant TB cases in low or medium incidence countries. Overall proportions were compared between migrants and non-migrants, using Fisher's exact test. Meta-analysis of proportions was carried out for the primary outcome (active TB) while meta-analyses of odds ratios (ORs) were performed using a random effects model for secondary outcomes; sputum-smear positivity, any first line drug resistance, multi-drug resistance (MDR), clustered cases, HIV coinfections and successful treatment. Heterogeneity was evaluated and sources were investigated using subgroup and sensitivity analysis.

RESULTS

Significant differences were found in the overall proportions of high TB incidence migrants and non-migrants for MDR cases, clustered cases, HIV coinfections and successful treatment, as well as a significant difference in the OR among MDR cases (3.91).

CONCLUSION

This review has demonstrated significant differences in key epidemiological indicators between high TB incidence migrants and non-migrants, indicating policy implications.

Two tales: Worldwide distribution of Central Asian (CAS) versus ancestral East-African Indian (EAI) lineages of Mycobacterium tuberculosis underlines a remarkable cleavage for phylogeographical, epidemiological and demographical characteristics

The East African Indian (EAI) and Central Asian (CAS) lineages of Mycobacterium tuberculosis complex (MTBC) mainly infect tuberculosis (TB) patients in the eastern hemisphere which contains many of the 22 high TB burden countries including China and India. We investigated if phylogeographical, epidemiological and demographical characteristics for these 2 lineages differed in SITVIT2 database. Genotyping results and associated data (age, sex, HIV serology, drug resistance) on EAI and CAS lineages (n = 10,974 strains) were extracted. Phylogenetic and Bayesian, and other statistical analyses were used to compare isolates. The male/female sex ratio was 907/433 (2.09) for the EAI group vs. 881/544 (1.62) for CAS (p-value<0.002). The proportion of younger patients aged 0-20 yrs. with CAS lineage was significantly higher than for EAI lineage (18.07% vs. 10.85%, p-value<0.0001). The proportion of multidrug resistant and extensively drug resistant TB among CAS group (30.63% and 1.03%, respectively) was significantly higher than in the EAI group (12.14% and 0.29%, respectively; p-value<0.0001). Lastly, the proportion of HIV+ patients was 20.34% among the EAI group vs. 3.46% in the CAS group (p-value<0.0001). This remarkable split observed between various parameters for these 2 lineages was further corroborated by their geographic distribution profile (EAI being predominantly found in Eastern-Coast of Africa, South-India and Southeast Asia, while CAS was predominantly found in Afghanistan, Pakistan, North India, Nepal, Middle-east, Libya, Sudan, Ethiopia, Kenya and Tanzania). Some geo-specificities were highlighted. This study demonstrated a remarkable cleavage for aforementioned characteristics of EAI and CAS lineages, showing a North-South divide along the tropic of cancer in Eastern hemisphere-mainly in Asia, and partly prolonged along the horn of Africa. Such studies would be helpful to better comprehend prevailing TB epidemic in context of its historical spread and evolutionary features, and provide clues to better treatment and patient-care in countries and regions concerned by these lineages.

Genetic Diversity of Mycobacterium tuberculosis Isolates in the Metropolitan Area of Rome

BACKGROUND

The presence in a geographic area of Mycobacterium tuberculosis (Mtb) strains belonging to different phylogeographic lineages and showing different drug susceptibility patterns may suggest recent transmission, with implications in terms of patient clinical management and disease control. The aim of this study was to carry out a preliminary epidemiological investigation of tuberculosis (TB) cases in Rome.

METHODS

A total of 232 Mtb isolates, collected from new or previously treated patients, admitted between 2008 and 2014 at 2 hospital settings in Rome with a diagnosis of TB, were analyzed by spoligotyping and analyzing 24 variable-number tandem repeats (VNTR) mycobacterial interspersed repetitive-unit (MIRU) loci. The SITVIT2 database and the MIRU-VNTRplus web applications were used to identify the strain genotypes and to generate phylogenetic trees.

RESULTS

Based on the position on the phylogenetic tree, 97.4% of the strains were associated with 1 of the 7 main lineages. The Euro-American lineage was the most commonly represented (81.9%) within both Italian and foreign-born populations, although all main lineages were present. The highest frequency of drug-resistant strains was found among the East-Asian lineage (Beijing genotype) isolated from foreign-born patients.

CONCLUSIONS

Dynamics of TB transmission in Rome indicate recent spread of Mtb strains belonging to phylogeographic lineages and clades usually found in countries and geographic areas with a high incidence of TB, similarly to what is observed in most metropolitan areas in Western Europe. Knowledge from molecular and classical epidemiology provides an important tool for disease control.

Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Mycobacterium tuberculosis (Mtb) exhibits a structured phylogeographic distribution worldwide linked with human migrations. We sought to infer how the interactions between distinct human populations shape the global population structure of Mtb on a regional scale. We applied the recently described timescaled haplotypic density (THD) technique on 638 minisatellite-based Mtb genotypes from French tuberculosis patients. THD with a long-term (200 y) timescale indicated that Mtb population in France had been mostly influenced by interactions with Eastern and Southern Europe and, to a lesser extent, Northern and Middle Africa, consistent with historical migrations favored by geographic proximity or commercial exchanges with former French colonies. Restricting the timescale to 20 y, THD identified a sustained influence of Northern Africa, but not Europe where tuberculosis incidence decreased sharply. Evolving interactions between human populations, thus, measurably influence the local population structure of Mtb. Relevant information on such interactions can be inferred using THD from Mtb genotypes.

A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto

Background

Tuberculosis (TB) incidence is decreasing worldwide and eradication is becoming plausible. In low-incidence countries, intervention on migrant populations is considered one of the most important strategies for elimination. However, such measures are inappropriate in European areas where TB is largely endemic, such as Porto in Portugal. We aim to understand transmission chains in Porto through a genetic characterization of Mycobacterium tuberculosis strains and through a detailed epidemiological evaluation of cases.

Methods

We genotyped the M. tuberculosis strains using the MIRU-VNTR system. We performed an evolutionary reconstruction of the genotypes with median networks, used in this context for the first time. TB cases from a period of two years were evaluated combining genetic, epidemiological and georeferencing information.

Results

The data reveal a unique complex scenario in Porto where the autochthonous population acts as a genetic reservoir of M. tuberculosis diversity with discreet episodes of transmission, mostly undetected using classical epidemiology alone.

Conclusions

Although control policies have been successful in decreasing incidence in Porto, the discerned complexity suggests that, for elimination to be a realistic goal, strategies need to be adjusted and coupled with a continuous genetic characterization of strains and detailed epidemiological evaluation, in order to successfully identify and interrupt transmission chains.

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

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

Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

The transmission dynamics of tuberculosis involves complex interactions of socio-economic and, possibly, microbiological factors. We describe an analytical framework to infer factors of epidemic success based on the joint analysis of epidemiological, clinical and pathogen genetic data. We derive isolate-specific, genetic distance-based estimates of epidemic success, and we represent success-related time-dependent concepts, namely epidemicity and endemicity, by restricting analysis to specific time scales. The method is applied to analyze a surveillance-based cohort of 1,641 tuberculosis patients with minisatellite-based isolate genotypes. Known predictors of isolate endemicity (older age, native status) and epidemicity (younger age, sputum smear positivity) were identified with high confidence (P < 0.001). Long-term epidemic success also correlated with the ability of Euro-American and Beijing MTBC lineages to cause active pulmonary infection, independent of patient age and country of origin. Our results demonstrate how important insights into the transmission dynamics of tuberculosis can be gained from active surveillance data.

Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis

INTRODUCTION

The diagnosis of infectious diseases is among the most successful areas of application of new generation sequencing technologies. The field has seen the development of numerous experimental and analytical approaches for the detection and the fine description of pathogenic and non-pathogenic microorganisms.

AREAS COVERED

Without claiming to be exhaustive with respect to all applications and methods developed over the years, this review focuses on the advantages and the issues brought by the new technologies, with an eye in particular to third generation sequencing methods. Both experimental procedures and algorithmic strategies are presented, following the most relevant publications which have led to progress in our ability of detecting infectious agents. Expert commentary: The technical advance brought by third generation sequencing platforms has the potential to significantly expand the range of diagnostic tools that will be available to clinicians. Nonetheless, the implementation of these technologies in clinical practice is still far from being actionable and will temporally follow the path undertaken by second generation methods, which still require the setup of standardized pipelines in both wet and dry laboratory procedures.

Genomic Diversity of Mycobacterium tuberculosis Complex Strains in Cantabria (Spain), a Moderate TB Incidence Setting

Background

Tuberculosis (TB) control strategies are focused mainly on prevention, early diagnosis, compliance to treatment and contact tracing. The objectives of this study were to explore the frequency and risk factors of recent transmission of clinical isolates of Mycobacterium tuberculosis complex (MTBC) in Cantabria in Northern Spain from 2012 through 2013 and to analyze their clonal complexity for better understanding of the transmission dynamics in a moderate TB incidence setting.

Methods

DNA from 85 out of 87 isolates from bacteriologically confirmed cases of MTBC infection were extracted directly from frozen stocks and genotyped using the mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) method. The MIRU-VNTRplus database tool was used to identify clusters and lineages and to build a neighbor joining (NJ) phylogenetic tree. In addition, data were compared to the SITVIT2 database at the Pasteur Institute of Guadeloupe.

Results

The rate of recent transmission was calculated to 24%. Clustering was associated with being Spanish-born. A high prevalence of isolates of the Euro-American lineage was found. In addition, MIRU-VNTR profiles of the studied isolates corresponded to previously found MIRU-VNTR types in other countries, including Spain, Belgium, Great Britain, USA, Croatia, South Africa and The Netherlands. Six of the strains analyzed represented clonal variants.

Conclusion

Transmission of MTBC is well controlled in Cantabria. The majority of TB patients were born in Spain. The population structure of MTBC in Cantabria has a low diversity of major clonal lineages with the Euro-American lineage predominating.

Combined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France

BACKGROUND

The present work relates to identification and a deep molecular characterization of circulating Mycobacterium tuberculosis complex (MTBC) strains in the Rhône-Alpes region, France from 2000 to 2010. It aimed to provide with a first snapshot of MTBC genetic diversity in conjunction with bacterial drug resistance, type of disease and available demographic and epidemiologic characteristics over an eleven-year period, in the south-east of France.

METHODS

Mycobacterium tuberculosis complex (MTBC) strains isolated in the Rhône-Alpes region, France (n = 2257, 1 isolate per patient) between 2000 and 2010 were analyzed by spoligotyping. MIRU-VNTR typing was applied on n = 1698 strains (with full results available for 974 strains). The data obtained were compared with the SITVIT2 database, followed by detailed genotyping, phylogenetic, and epidemiologic analyses in correlation with anonymized data on available demographic, and epidemiologic characteristics, and location of disease (pulmonary or extrapulmonary TB).

RESULTS

The most predominant spoligotyping clusters were SIT53/T1 (n = 346, 15.3%) > SIT50/H3 (n = 166, 7.35%) > SIT42/LAM9 (n = 125, 5.5%) > SIT1/Beijing (n = 72, 3.2%) > SIT47/H1 (n = 71, 3.1%). Evolutionary-recent strains belonging to the Principal Genetic Group (PGG) 2/3, or Euro-American lineages (T, LAM, Haarlem, X, S) were predominant and represented 1768 or 78.33% of all isolates. For strains having drug resistance information (n = 1119), any drug resistance accounted for 14.83% cases vs. 1.52% for multidrug resistance (MDR); and was significantly more associated with age group 21-40 years (p-value<0.001). Extra-pulmonary TB was more common among female patients while pulmonary TB predominated among men (p-value<0.001; OR = 2.16 95%CI [1.69; 2.77]). Also, BOV and CAS lineages were significantly well represented in patients affected by extra-pulmonary TB (p-value<0.001). The origin was known for 927/2257 patients: 376 (40.6%) being French-born vs. 551 (59.4%) Foreign-born. French patients were significantly older (mean age: 58.42 yrs 95%CI [56.04; 60.80]) than Foreign-born patients (mean age: 42.38 yrs. 95%CI [40.75; 44.0]).

CONCLUSION

The study underlined the importance of imported TB cases on the genetic diversity and epidemiologic characteristics of circulating MTBC strains in Rhône-Alpes region, France over a large time-period. It helps better understand intricate relationships between certain lineages and geographic origin of the patients, and pinpoints genotypic and phylogenetic specificities of prevailing MTBC strains. Lastly, it also demonstrated a slow decline in isolation of M. africanum lineage in this region between 2000 and 2010.

Finer characterization of Mycobacterium tuberculosis using spoligotyping and 15-loci MIRU-VNTRs reveals phylogeographical specificities of isolates circulating in Guyana and Suriname

In this study we used spoligotyping and 15-loci MIRU-VNTRs for a finer characterization of Mycobacterium tuberculosis strains isolated from patients residing in Guyana (n=74) and Suriname (n=80). The mean age of the patients was 38.5years (36.5 and 40.2years for Guyana vs. Suriname), with a male-to-female sex-ratio of 2.25 for Guyana vs. 4.27 in Suriname. Spoligotyping and 15-loci MIRU-VNTRs led to a total of 41 and 65 different patterns respectively, with an overall clustering rate of 83.8% vs. 68.8%. Combined spoligotyping and VNTR analysis led to the detection of 18 clusters of 2-41 isolates, with an overall clustering of 67.5% and a recent "n-1" transmission rate of 55.8%. Importantly, Guyana was characterized by a significantly higher percentage of clustered isolates than Suriname (79.7% vs. 56.3%; p=0.0019). Three big spoligo/MIRU (SIT/MIT) clusters containing >10 isolates each were shared between the 2 countries, and concerned: T1 sublineage cluster 53/861 (n=41, 37 in Guyana vs. 4 in Suriname); EAI6-BGD1 sublineage cluster 1340/860 (n=16, 3 in Guyana vs. 13 in Suriname); and T1 sublineage cluster 131/146 (n=11, 6 in Guyana vs. 5 in Suriname); as well as 2 smaller clusters of 2 and 3 isolates respectively. However, the relative phylogeographical specificities of strains in circulation as well as a lack of drug-resistance observed among strains from Suriname suggested that trans-border transmission of drug-resistant isolates occurred less frequently than thought. Tracing and interrupting transmission channels of a specific clone (SIT53/15-MIT861) should become a priority in Guyana, not only because it is by far most abundant but also because it accounts for almost half of the drug resistant isolates (n=8/17, 47.1%) in our study, and clustered 5/12 (41.7%) MDR isolates.

Study of Mycobacterium tuberculosis complex genotypic diversity in Malaysia reveals a predominance of ancestral East-African-Indian lineage with a Malaysia-specific signature

Background

Tuberculosis (TB) still constitutes a major public health problem in Malaysia. The identification and genotyping based characterization of Mycobacterium tuberculosis complex (MTBC) isolates causing the disease is important to determine the effectiveness of the control and surveillance programs.

Objectives

This study intended a first assessment of spoligotyping-based MTBC genotypic diversity in Malaysia followed by a comparison of strains with those prevailing in neighboring countries by comparison with an international MTBC genotyping database.

Methods

Spoligotyping was performed on a total of 220 M. tuberculosis clinical isolates collected in Kelantan and Kuala Lumpur. The results were compared with the SITVIT2 international database of the Pasteur Institute of Guadeloupe.

Results

Spoligotyping revealed 77 different patterns: 22 corresponded to orphan patterns while 55 patterns containing 198 isolates were assigned a Spoligo International Type (SIT) designation in the database (the latter included 6 newly created SITs). The eight most common SITs grouped 141 isolates (5 to 56 strains per cluster) as follows: SIT1/Beijing, n = 56, 25.5%; SIT745/EAI1-SOM, n = 33, 15.0%; SIT591/EAI6-BGD1, n = 13, 5.9%; SIT256/EAI5, n = 12, 5.5%; SIT236/EAI5, n = 10, 4.6%; SIT19/EAI2-Manila, n = 9, 4.1%; SIT89/EAI2-Nonthaburi, n = 5, 2.3%; and SIT50/H3, n = 3, 1.4%. The association between city of isolation and lineages was statistically significant; Haarlem and T lineages being higher in Kuala Lumpur (p<0.01). However, no statistically significant differences were noted when comparing drug resistance vs. major lineages, nor between gender and clades.

Conclusions

The ancestral East-African-Indian (EAI) lineage was most predominant followed by the Beijing lineage. A comparison of strains with those prevailing in neighboring countries in South Asia, East Asia and South East Asia underlined the phylogeographical specificity of SIT745 for Malaysia, and its probable ongoing evolution with locally evolved strains sharing a specific signature characterized by absence of spacers 37, 38, and 40. Pending complementary genotyping confirmation, we propose that SIT745/EAI-SOM is tentatively reclassified as SIT745/EAI-MYS.

Molecular epidemiology of tuberculosis in Sicily, Italy: what has changed after a decade?

Background

We aimed to investigate the molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) isolates in the province of Palermo, Sicily, Italy, by characterizing 183 isolates identified in the years 2004-2012. A comparison with 104 MTBC strains identified in the same geographic area in the years 1994-2000 was also carried out.

Methods

One hundred eighty-three MTBC isolates identified in Palermo, Italy, in the years 2004-2012 were analyzed by spoligotyping and the 24 mycobacterial interspersed repetitive unit (MIRU)-variable-number tandem-repeat (VNTR) method typing. Susceptibility testing to streptomycin, isoniazid, rifampin and ethambutol was also performed. Furthermore, the spoligotyping dataset obtained from 104 MTBC isolates identified from 1994 to 2000 was reanalyzed. Distribution into lineages and clustering of isolates in the two periods was compared.

Results

One hundred seventy-seven out of the 183 isolates of MTBC submitted to molecular typing were fully characterized. Of these, 108 were from Italian-born and 69 from foreign-born individuals. Eleven different lineages and 35 families-subfamilies were identified with the most represented lineages being Haarlem (26.5%), T (19.2%), LAM (13.6%) and S (8.5%). Except for the Haarlem lineage, where isolates from foreign-born patients were overrepresented, the distribution of isolates in the families belonging to the Euro-American clone reflected the proportions of the two subpopulations. A total of 27 (15.2%) strains were clustered and three clusters were mixed. Approximately 25% of the 183 MTBC isolates under study proved to be resistant to at least one antiTB drug, with only three isolates categorized as multidrug resistant (MDR). When MTBC isolates identified in the years 1994-2000 were reanalyzed, lineages T (30.8%), LAM (29.8%), Haarlem (16.3%) and S (13.5%) proved to be predominant. No MTBC isolates belonging to CAM, U, CAS, Turkish and Ural lineages were identified.

Conclusions

A wide heterogeneity was detected among the MTBC strains isolated in the years 2004-2012. Six lineages were not present among the isolates of the period 1994-2000. Comparison between distribution of lineages in the two consecutive periods depicts rapid and deep changes in the TB epidemiology in Palermo, Italy. An universal and continued laboratory-based surveillance of TB in Sicily is required.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-014-0602-4) contains supplementary material, which is available to authorized users.

Mycobacterium caprae infection in humans

Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex, causes tuberculosis (TB) in man and animals. Some features distinguish M. caprae from its epidemiological twin, Mycobacterium bovis: M. caprae is evolutionarily older, accounts for a smaller burden of zoonotic TB and is not globally distributed, but primarily restricted to European countries. M. caprae occurs only in a low proportion of human TB cases and this proportion may even decrease, if progress toward eradication of animal TB in Europe continues. So why bother, if M. caprae is not an enigma for diagnostic TB tests and if resistance against first-line drugs is a rarity with M. caprae? This 'European' pathogen of zoonotic TB asks interesting questions regarding the definition of a species. The latter, seemingly only an academic question, particularly requires and challenges the collaboration between human and veterinary medicine.