Epidemiology of tuberculosis on Gran Canaria: a 4 year population study using traditional and molecular approaches

Integrative transnational analysis to dissect tuberculosis transmission events along the migratory route from Africa to Europe

BACKGROUND

Growing international migration has increased the complexity of tuberculosis transmission patterns. Italy's decision to close its borders in 2018 made of Spain the new European porte entrée for migration from the Horn of Africa (HA). In one of the first rescues of migrants from this region at the end of 2018, tuberculosis was diagnosed in eight subjects, mainly unaccompanied minors.

METHODS

Mycobacterium tuberculosis isolates from these recently arrived migrants were analysed by Mycobacterial Interspersed Repetitive-Unit/Variable-Number of Tandem Repeat (MIRU-VNTR) and subsequent whole genome sequencing (WGS) analysis. Data were compared with those from collections from other European countries receiving migrants from the HA and a strain-specific PCR was applied for a fast searching of common strains. Infections in a cellular model were performed to assess strain virulence.

RESULTS

MIRU-VNTR analysis allowed identifying an epidemiological cluster involving three of the eight cases from Somalia (0 single-nucleotide polymorphisms between isolates, HA cluster). Following detailed interviews revealed that two of these cases had shared the same migratory route in most of the trip and had spent a long time at a detention camp in Libya. To confirm potential en route transmission for the three cases, we searched the same strain in collections from other European countries receiving migrants from the HA. MIRU-VNTR, WGS and a strain-specific PCR for the HA strain were applied. The same strain was identified in 12 cases from Eritrea diagnosed soon after their arrival in 2018 to the Netherlands, Belgium and Italy. Intracellular replication rate of the strain did not reveal abnormal virulence.

CONCLUSIONS

Our study suggests a potential en route transmission of a pan-susceptible strain, which caused at least 15 tuberculosis cases in Somalian and Eritrean migrants diagnosed in four different European countries.

Molecular epidemiology of tuberculosis

The application of genotyping tools allowed us to discriminate between the Mycobacterium tuberculosis isolates obtained in the laboratory. The differentiation between single strains opened the door to molecular epidemiology studies, which had helped us to progress in our knowledge of how this pathogen is transmitted in the progressively more complex socio-epidemiological scenario. The genetic stability of this microorganism led to develop specific methodologies, which are thoroughly revised in this chapter. In addition to their application in epidemiology, we review, how they can offer a response to different diagnostic and clinical challenges. Finally, we focus on describing the novel genomic revolution we are experiencing in the analysis of tuberculosis, the methodology in which it is based and the novel possibilities it offers, including new routes of integrating both the molecular and genomic languages in innovative post-genomic proposals, better suited to our real-life context.

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.

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.

Persistent Infection by a Mycobacterium tuberculosis Strain That Was Theorized To Have Advantageous Properties, as It Was Responsible for a Massive Outbreak

The strains involved in tuberculosis outbreaks are considered highly virulent and transmissible. We analyzed the case of a patient in Madrid, Spain, who was persistently infected over an 8-year period by the same Beijing Mycobacterium tuberculosis strain. The strain was responsible for a severe outbreak on Gran Canaria Island. The case provides us with a unique opportunity to challenge our assumptions about M. tuberculosis Beijing strains. No clinical/radiological findings consistent with a virulent strain were documented, and the in vitro growth rate of the strain in macrophages was only moderate. No secondary cases stemming from this prolonged active case were detected in the host population. The strain did not acquire resistance mutations, despite constant treatment interruptions, and it remained extremely stable, as demonstrated by the lack of single-nucleotide-polymorphism (SNP)-based differences between the sequential isolates. Our data suggest that the general assumption about M. tuberculosis Beijing strains having advantageous properties (in terms of virulence, transmissibility, and the tendency to acquire mutations and resistance) is not always accurate.

Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig

The Beijing family of Mycobacterium tuberculosis strains is part of lineage 2 (also known as the East Asian lineage). In clinical studies, we have observed that isolates from the sublineage RD207 of lineage 2 were more readily transmitted among humans. To investigate the basis for this difference, we tested representative strains with the characteristic Beijing spoligotype from four of the five sublineages of lineage 2 in the guinea pig model and subjected these strains to comparative whole-genome sequencing. The results of these studies showed that all of the clinical strains were capable of growing and causing lung pathology in guinea pigs after low-dose aerosol exposure. Differences between the abilities of the four sublineages to grow in the lungs of these animals were not overt, but members of RD207 were significantly more pathogenic, resulting in severe lung damage. The RD207 strains also induced much higher levels of markers associated with regulatory T cells and showed a significant loss of activated T cells in the lungs over the course of the infections. Whole-genome sequencing of the strains revealed mutations specific for RD207 which may explain this difference. Based on these data, we hypothesize that the sublineages of M. tuberculosis are associated with distinct pathological and clinical phenotypes and that these differences influence the transmissibility of particular M. tuberculosis strains in human populations.

[Influence of immigration on tuberculosis transmission patterns in Castellón, Spain (2004-2007)]

BACKGROUND

This study aimed to identify tuberculosis transmission patterns in Castellón in a period of major demographic changes.

METHODS

A prospective study of patients with positive culture in the province of Castellon over a 4-year period (2004-2007) was carried out. Cases were described by year and nationality and were compared with those reported to the Department of Public Health. We studied the population with available molecular patterns, identified through restriction fragment length polymorphism (RFLP) and analyzed the variables from patient clusters, based on data collected in surveys of the Department of Health and the Laboratory Management Program.

RESULTS

According to data from the Department of Public Health, the overall rate of tuberculosis per 100,000 inhabitants in the province of Castellón was 15.7 in 2004, 19.9 in 2005, 18.2 in 2006 and 17.5 in 2007. In our laboratory, strains were identified from 301 patients, representing 77% (301/390) of reported cases and 94% (301/321) of reported cases with a positive culture. The percentage of tuberculosis among foreigners increased with age, exceeding 50% in 2007. Molecular studies were available in 95% of patients (286); 58% were Spanish and 42% were foreigners, of whom 54% were Romanians. The cluster percentage was 40%, with 30% of mixed clusters. According to conventional contact studies, 85% of patients in clusters had been considered isolated cases.

CONCLUSIONS

The increased rate of tuberculosis in Castellón was mainly due to the increasing number of cases among foreigners, mostly Romanians. The availability of molecular studies in all patients with a positive culture allowed us to analyze how and where tuberculosis is transmitted in our province. Forty percent of the patients were grouped into clusters; of these, mixed clusters accounted for one third, indicating the high integration of immigrants in our area.

Mycobacterial factors relevant for transmission of tuberculosis

BACKGROUND

Tuberculosis (TB) transmission is associated with patient-related risk factors. However, DNA fingerprint analysis has provided anecdotal evidence suggesting a role for bacteriological factors.

METHODS

To examine the importance of the bacteriological component in TB transmission, we investigated the number of tuberculin skin test-positive (TST induration, ≥ 10 mm) contacts and secondary cases observed in contact investigations around TB cases in relation to the size of the genotype cluster the patient belonged to at the time of diagnosis. We also compared the number of TST-positive contacts and secondary cases of patients with drug-resistant and drug-susceptible TB.

RESULTS

Larger clusters were independently associated with an increased number of positive contacts. The mean number of positive contacts ranged from 3.8 for clusters of 2 cases, to 4.7 for clusters of 3-10 cases, to 6.0 for cases in clusters of >10 cases (mean increase in number of positive contacts for every extra case in the cluster, 0.21; 95% confidence interval, 0.09-0.26). The mean number of positive contacts was significantly lower among index cases with isoniazid-monoresistant TB (1.6) than among index cases with pan-susceptible TB (4.6; relative number, 0.45; 95% confidence interval, 0.22-0.92).

CONCLUSION

These results suggest that spread of tuberculosis also depends on bacteriological factors.

[Molecular epidemiology of tuberculosis in Almeria (Spain). Factors associated with recent transmission]

BACKGROUND

Molecular epidemiology is used in tuberculosis (TB) to identify clusters in which the cases are assumed to belong to the same recent transmission chain. An endogenous reactivation of latent TB is considered when the Mycobacterium tuberculosis isolates have a unique genotype.

OBJECTIVE

To describe factors associated with recent transmission of TB in Almeria, from 2003-2007.

METHODS

We conducted an observational prospective study that included patients with Mycobacterium tuberculosis positive culture. The strains were genotyped by Restriction Fragment Length Polymorphism and spoligotyping. Adjusted odds ratio and 95% confidence intervals were calculated to study factors associated with cluster groups, using a multivariate logistic regression model.

RESULTS

We analysed 427 isolates, of which 71% were from males and 56.2% of them belonged to foreign residents. Furthermore, 44% were classified as a cluster. The resistance to isoniazid was 8.4%. The factors associated with clusters were age, principally the group under 10 years (adjusted OR=12.75; 95% CI, 2.52-64.58) and the group aged between 50-59 years (adjusted OR=13.85; 95% CI, 3.04-63.17), and born in Spain (adjusted OR=2.17; 95% CI, 1.41-3.36).

CONCLUSIONS

In Almeria, native population, children under 10 years old and patients aged between 50-59 years have more probability to belong to the same recent transmission chain. The molecular epidemiology can be used to find out which population groups need more control and this information must be used in tuberculosis prevention programs.

Clustering of Mycobacterium tuberculosis cases in Acapulco: Spoligotyping and risk factors

Recurrence and reinfection of tuberculosis have quite different implications for prevention. We identified 267 spoligotypes of Mycobacterium tuberculosis from consecutive tuberculosis patients in Acapulco, Mexico, to assess the level of clustering and risk factors for clustered strains. Point cluster analysis examined spatial clustering. Risk analysis relied on the Mantel Haenszel procedure to examine bivariate associations, then to develop risk profiles of combinations of risk factors. Supplementary analysis of the spoligotyping data used SpolTools. Spoligotyping identified 85 types, 50 of them previously unreported. The five most common spoligotypes accounted for 55% of tuberculosis cases. One cluster of 70 patients (26% of the series) produced a single spoligotype from the Manila Family (Clade EAI2). The high proportion (78%) of patients infected with cluster strains is compatible with recent transmission of TB in Acapulco. Geomatic analysis showed no spatial clustering; clustering was associated with a risk profile of uneducated cases who lived in single-room dwellings. The Manila emerging strain accounted for one in every four cases, confirming that one strain can predominate in a hyperendemic area.

Guía de práctica clínica de la Sociedad Andaluza de Enfermedades Infecciosas (SAEI) sobre el tratamiento de la tuberculosis

The therapeutic scheme for initial pulmonary tuberculosis recommended by the SAEI is as follows: Initial phase, isoniazid, rifampin and pyrazinamide given daily for 2 months. In HIV(+) patients and immigrants from areas with a rate of primary resistance to isoniazid > 4%, ethambutol should be added until susceptibility studies are available. Second phase (continuation phase): rifampin and isoniazid, given daily or intermittently for 4 months in the general population. HIV(+) patients (< or = 200 CD4) and culture-positive patients after 2 months of treatment should receive a 7-month continuation phase. A 6-month regimen is recommended for extrapulmonary tuberculosis, with the exception of tuberculous meningitis, which should be treated for a minimum of 12 months and bone/joint tuberculosis, treated for a minimum of 9 months. Treatment regimens for multidrug resistant tuberculosis are based on expert opinion. These would include a combination of still-useful first-line drugs, injectable agents, and alternative agents, such as quinolones. Patients who present a special risk of transmitting the disease or of non-adherence should be treated with directly observed therapy.

Interpretation of the tuberculin skin test in bacille Calmette-Guérin vaccinated and nonvaccinated school children

BACKGROUND

Our objective was to conduct a prevalence survey of purified protein derivative (PPD) reactions among Lebanese healthy school children to identify those with tuberculosis or latent tuberculosis and to investigate the effect of bacille Calmette-Guérin (BCG) vaccine on the interpretation of PPD reactivity.

METHODS

A self-administered questionnaire, including demographic characteristics, time of prior BCG vaccine and number of doses, known household contact with tuberculosis as well as parents' characteristics and living conditions was administered. PPD testing was performed on all children in diverse Lebanese regions aged 3 to 19 years. Reactivity that measured <5 mm were considered negative induration, doubtful if between 5 and 9 mm and positive if 10 mm or above. Chest radiographs were obtained as part of the evaluation for children with positive induration.

RESULTS

Of 4895 children, 4271 entered into the final data analysis. A total of 3259 children (76.3%) did not develop a reaction to PPD (0 mm), 170 (4%) had 1 to <5 mm reading, 509 (11.9%) had 5 to 9 mm and 333 (7.8%) had > or =10 mm. Approximately 62% of the vaccinated children had received BCG vaccine in first year of life. Two hundred ninety (61.8%) of 469 children < or =5 were vaccinated and 179 (38.2%) were not. Only 22 of the youngest vaccinated had positive PPD. Twelve children were diagnosed with tuberculosis, a prevalence of 280 per 100,000. However, the prevalence of latent tuberculosis was 7.51%.

CONCLUSION

Our prevalence of tuberculosis and latent tuberculosis is a sentinel indicator of continued transmission in the community. The data support the current recommendations that children who receive BCG can and should be tested with PPD for latent tuberculosis and tuberculosis.

Population-based prospective molecular and conventional epidemiological study of tuberculosis in Hong Kong

OBJECTIVE

To study the transmission of tuberculosis using conventional and molecular epidemiology in Hong Kong.

METHODS

All patients with positive sputum culture for Mycobacterium tuberculosis residing on the Island of Hong Kong were recruited from May 1999 to April 2002. The restriction fragment length polymorphism technique was used to determine DNA patterns of isolates of M. tuberculosis using the IS6110 probe, supplemented by pTBN12 as a secondary probe.

RESULTS

One thousand five hundred and fifty-three of 2337 (66%) of the patients with bacteriologically confirmed tuberculosis had restriction fragment length polymorphism analysis of their M. tuberculosis isolates. Four hundred and fifty-four (29.2%) patients belonging to 143 clusters were identified; the estimated rate of recent transmission was 20-24%. Significant predictors of clustering included young-age groups (<40 years) versus those >60 years of age (adjusted odds ratio (OR) 1.96, 95% confidence interval 1.47-2.62), permanent residency versus new or non-residents (adjusted OR 3.40, 95% 1.84-6.26) and previous default from treatment versus new cases (adjusted OR 6.12, 95% confidence interval 1.82-20.5). Alcohol and drug abuse, history of imprisonment and HIV infection were not significant risk factors for molecular clustering. Of patients belonging to clusters, 5.1% had definite, 5.5% had probable and 24.4% had possible epidemiological link, suggesting casual contact may be responsible for a high proportion of the clustered cases.

CONCLUSION

One-fifth to one quarter of the new cases of active tuberculosis in Hong Kong are due to recent transmission. In addition to early diagnosis and successful treatment of all active disease, treatment of latent disease should receive more attention in the control of tuberculosis in Hong Kong.

Beijing genotype of Mycobacterium tuberculosis is significantly associated with human immunodeficiency virus infection and multidrug resistance in cases of tuberculous meningitis

Multidrug-resistant tuberculous meningitis is fatal without rapid diagnosis and use of second-line therapy. It is more common in human immunodeficiency virus (HIV)-positive patients. Beijing genotype strains of Mycobacterium tuberculosis are associated with drug resistance, particularly multidrug resistance, and their prevalence is increasing worldwide. The prevalence of Beijing genotype strains among Mycobacterium tuberculosis isolates from the cerebrospinal fluid of HIV-positive (n = 35) and HIV-negative (n = 187) patients in Ho Chi Minh City was determined. The Beijing genotype was significantly associated with HIV status (odds ratio [OR] = 2.95 [95% confidence interval {CI}, 1.38 to 6.44]; P = 0.016), resistance to any drug (OR = 3.34 [95% CI, 1.87 to 5.95]; P < 0.001) and multidrug resistance (Fisher's exact test; P = 0.001). The association of the Beijing genotype with drug resistance was independent of HIV status. This is the first report of Beijing genotype association with HIV status, which may be an association unique to tuberculous meningitis.