Direct DNA Extraction from Mycobacterium tuberculosis Frozen Stocks as a Reculture-Independent Approach to Whole-Genome Sequencing.

Culturing before DNA extraction represents a major time-consuming step in whole-genome sequencing of slow-growing bacteria, such as Mycobacterium tuberculosis. We report a workflow to extract DNA from frozen isolates without reculturing. Prepared libraries and sequence data were comparable with results from recultured aliquots of the same stocks.

The effectiveness of BCG vaccination in preventing Mycobacterium tuberculosis infection and disease in Greenland.

BACKGROUND: The BCG vaccine's ability to prevent Mycobacterium tuberculosis infection (MTI) remains highly debated. In Greenland, BCG vaccination was introduced in 1955, but was temporarily discontinued (1991-1996) due to nationwide policy changes. The study aimed to use the transient stop in BCG vaccination to evaluate the effect of vaccination on MTI prevalence and TB incidence. METHODS: MTI study: A cross-sectional study (2012), comprising East Greenlanders born during 1982-2006, evaluated the effect of BCG vaccination on MTI prevalence; a positive interferon γ release assay defined an MTI case. Associations were estimated using logistic regression. TB study: a cohort study covering the same birth cohorts with follow-up until 2012 evaluated the vaccine's effect on TB incidence. A personal identifier allowed for follow-up in the TB notification system. Associations were estimated using Cox regression. RESULTS: MTI study: Included 953 participants; 81% were BCG-vaccinated; 29% had MTI, 23% among vaccinated and 57% among non-vaccinated. BCG vaccination reduced the odds of MTI, OR 0.52 (95% CI 0.32 to 0.85), p=0.01. Vaccine effectiveness against MTI was 20%. TB study: Included 1697 participants followed for 21,148 person-years. 6% were notified with TB, 4% among vaccinated and 11% among non-vaccinated. BCG vaccination reduced the risk of TB, HR 0.50 (95% CI 0.26 to 0.95), p=0.03, yielding a vaccine effectiveness of 50%. CONCLUSIONS: BCG vaccination was effective in reducing both MTI and TB disease among children and young adults in a TB high-endemic setting in Greenland.

Mycobacterium tuberculosis outbreak strain of Danish origin spreading at worrying rates among greenland-born persons in Denmark and Greenland.

Transmission of Mycobacterium tuberculosis continues at high rates among Greenland-born persons in Greenland and Denmark, with 203 and 450 notified cases per 10(5) population, respectively, in the year 2010. Here, we document that the predominant M. tuberculosis outbreak strain C2/1112-15 of Danish origin has been transmitted to Greenland-born persons in Denmark and subsequently to Greenland, where it is spreading at worrying rates and adding to the already heavy tuberculosis burden in this population group. It is now clear that the C2/1112-15 strain is able to gain new territories using a new population group as the "vehicle." Thus, it might have the ability to spread even further, considering the potential clinical consequences of strain diversity such as that seen in the widely spread Beijing genotype. The introduction of the predominant M. tuberculosis outbreak strain C2/1112-15 into the Arctic circumpolar region is a worrying tendency which deserves attention. We need to monitor whether this strain already has, or will, spread to other countries.

Clustered tuberculosis in a low-burden country: nationwide genotyping through 15 years.

Molecular genotyping of Mycobacterium tuberculosis has proved to be a powerful tool in tuberculosis surveillance, epidemiology, and control. Based on results obtained through 15 years of nationwide IS6110 restriction fragment length polymorphism (RFLP) genotyping of M. tuberculosis cases in Denmark, a country on the way toward tuberculosis elimination, we discuss M. tuberculosis transmission dynamics and point to areas for control interventions. Cases with 100% identical genotypes (RFLP patterns) were defined as clustered, and a cluster was defined as cases with an identical genotype. Of 4,601 included cases, corresponding to 76% of reported and 97% of culture-verified tuberculosis cases in the country, 56% were clustered, of which 69% were Danes. Generally, Danes were more often in large clusters (≥ 50 persons), older (mean age, 45 years), and male (male/female ratio, 2.5). Also, Danes had a higher cluster frequency within a 2-year observation window (60.8%), and higher clustering rate of new patterns over time, compared to immigrants. A dominant genotype, cluster 2, constituted 44% of all clustered and 35% of all genotyped cases. This cluster was primarily found among Danish males, 30 to 59 years of age, often socially marginalized, and with records of alcohol abuse. In Danes, cluster 2 alone was responsible for the high cluster frequency level. Immigrants had a higher incidence of clustered tuberculosis at a younger age (0 to 39 years). To achieve tuberculosis elimination in Denmark, high-risk transmission environments, like the cluster 2 environment in Danes, and specific transmission chains in immigrants in the capital area, e.g., homeless/socially marginalized Somalis/Greenlanders, often with alcohol abuse, must be targeted, including groups with a high risk of reactivation.

Trends and differences in tuberculosis incidences and clustering among natives in Denmark, Sweden and Finland: comparison of native incidences and molecular epidemiology among three low-incidence countries.

OBJECTIVES: To compare the epidemiology of tuberculosis (TB) in Denmark, Sweden and Finland, by focusing on the native population in order to identify epidemiologic differences and thus indirectly possible differences in TB control. METHODS: TB incidence trends from 1990 through 2015 were compared among the countries. In addition, for the periods 2012-2013 and 2014-2015, genotyping data were compared. Genotyping was performed using the 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) method in Denmark and Sweden. For Finland, spoligotyping in conjunction with the 15-locus MIRU-VNTR method was used for 2012-2013 and translated into the 24-locus MIRU-VNTR when feasible, and for 2014-2015 only MIRU-VNTR was used. Both incidence trends and molecular epidemiology were assessed for native cases. RESULTS: The average annual rate of change in TB incidence for native Danes was -2.4% vs. -6.1% and -6.9% for native Swedes and Finns respectively. In 2012-2013 Denmark had 52 native cases in the largest transmission chain vs. three cases in Sweden and ten in Finland, and during the same period the clustering rate for native Danes was 48.8% vs. 6.5% and 18.2% for native Swedes and Finns respectively. For 2014-2015, a similar pattern was seen. CONCLUSIONS: The decline of TB among natives in Denmark is slower than for Sweden and Finland, and it seems Denmark has more active transmission among natives. The focused assessment on basic native TB epidemiology reveals striking differences in TB transmission among otherwise similar low-TB-incidence countries.

Impact of contact investigation and tuberculosis screening among high-risk groups in Denmark.

SETTING: The objective of tuberculosis (TB) screening in low-incidence countries is to identify TB patients earlier, ideally to improve health outcomes and reduce Mycobacterium tuberculosis transmission. In this retrospective study, we compare hospitalisation (morbidity) and smear positivity rates (infectiousness) in TB patients identified through active case finding (ACF) with patients identified through passive case finding (PCF). METHODS: ACF patients were identified by screening socially marginalised persons or through contact investigation. Logistic regression was used to model the associations between case-finding group (ACF/PCF) and hospitalisation, and between case-finding group and smear positivity rates. RESULTS: A total of 108 patients were identified through ACF and 332 through PCF. Thirty (27.8%) ACF patients and 153 (46.1%) PCF patients were hospitalised. In the adjusted models, ACF patients (OR 0.24, P 0.001) and ACF subgroups identified using mobile X-ray screening, spot sputum culture screening and contact investigation were significantly less likely to be hospitalised than PCF patients. Thirty-one (34.4%) ACF patients and 127 (50.4%) PCF patients were smear-positive. ACF patients (OR 0.30, P 0.001) and ACF subgroups identified through contact investigation and spot sputum culture screening were less likely to be smear-positive than PCF patients. CONCLUSIONS: These findings suggest that ACF reduces morbidity and infectiousness among TB patients, thereby potentially improving health outcomes and reducing transmission of M. tuberculosis.

Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland.

In East Greenland, a dramatic increase of tuberculosis (TB) incidence has been observed in recent years. Classical genotyping suggests a genetically similar Mycobacterium tuberculosis (Mtb) strain population as cause, however, precise transmission patterns are unclear. We performed whole genome sequencing (WGS) of Mtb isolates from 98% of culture-positive TB cases through 21 years (n = 182) which revealed four genomic clusters of the Euro-American lineage (mainly sub-lineage 4.8 (n = 134)). The time to the most recent common ancestor of lineage 4.8 strains was found to be 100 years. This sub-lineage further diversified in the 1970s, and massively expanded in the 1990s, a period of lowered TB awareness in Greenland. Despite the low genetic strain diversity, WGS data revealed several recent short-term transmission events in line with the increasing incidence in the region. Thus, the isolated setting and the uniformity of circulating Mtb strains indicated that the majority of East Greenlandic TB cases originated from one or few strains introduced within the last century. Thereby, the study shows the consequences of even short interruptions in TB control efforts in previously TB high incidence areas and demonstrates the potential role of WGS in detecting ongoing micro epidemics, thus guiding public health efforts in the future.

Tuberculosis treatment in Denmark: treatment outcome for all Danish patients in 1992.

SETTING: Denmark. OBJECTIVE: To evaluate tuberculosis (TB) treatment outcome using treatment indicators recommended by the World Health Organization (WHO) and the International Union Against Tuberculosis and Lung Disease (IUATLD). DESIGN: Retrospective cohort analysis of all TB patients notified in 1992 (n = 350). TB related information was registered and analyzed using hospital case records and laboratory data from Statens Serum Institut, Copenhagen. RESULTS: Among the 350 TB patients, cure rate was 25.7%, treatment completion rate 36.0%, death rate 12.9%, failure rate 0.9%, defaulter rate 3.1% and transfer out rate 2.3%. The remaining 19.1% 'other cases' did not fulfil any of the WHO indicators, but could be included in the treatment completion rate. During the 4 year follow-up period, 3% of all patients relapsed and 15% died. CONCLUSION: The aim set by the WHO of a cure rate of at least 95% was not achieved. The two main reasons were 1) the fact that sputum samples were not taken late during treatment, and 2) the death rate. In the future sputum examination for M. tuberculosis late during treatment will be encouraged to obtain evidence of cure, but only if the patient can produce sputum, as examination of saliva is of no interest. Death from causes other than TB accounted for 8.3%, making it impossible to attain the desired cure rate in Denmark, and possibly also in other industrialized countries with many elderly TB patients. Additional information on risk factors and methodological issues in performing a TB cohort analysis in a low incidence country is presented.

A dominant Mycobacterium tuberculosis strain emerging in Denmark.

SETTING: Denmark, a high-income country with a low prevalence of tuberculosis. OBJECTIVE AND DESIGN: Molecular epidemiological studies of Mycobacterium tuberculosis strains are conducted worldwide, and distinct strains have been associated with large outbreaks of tuberculosis. This is the first systematic population-based search for distinct strains of M. tuberculosis in Denmark among 4102 strains DNA fingerprinted nationwide from 1992 to 2001. RESULTS: A specific strain of M. tuberculosis has emerged rapidly in Denmark: in 1992, the Danish Cluster 2 strain accounted for 5.8% of all culture-positive Danish-born cases, increasing to 29.0% in 2001. The Cluster 2 cases were on average younger (41.8 vs. 51.4 years), more likely to be male (81.4% vs. 64.1%), and more likely to have pulmonary involvement only (90.3% vs. 64.6%) than other Danish-born cases. During the first 4 observation years, they were mainly found in the capital city, Copenhagen, but were later increasingly observed in the provinces. CONCLUSION: The reasons for the increasing dominance and change in geographical distribution of Cluster 2 strains in Denmark is unknown, but may be partly explained by the fact that Cluster 2 is associated with younger males with pulmonary disease manifestation. We consider it as an outbreak and believe the situation requires increased focus on early tuberculosis diagnosis and control of transmission in Denmark.

Prevalence of Beijing genotype in Latvian multidrug-resistant Mycobacterium tuberculosis isolates.

SETTING: Predominant genotypes of Mycobacterium tuberculosis include the Beijing family, which has caused large tuberculosis outbreaks and has been associated with increased virulence and multidrug resistance (MDR). OBJECTIVE: To search for the Beijing genotype among Latvian MDR patients to characterise their DNA isolates at the molecular level. DESIGN: MDR isolates were spoligotyped and tested for gene mutations by automatic nucleotide sequencing. RESULTS: Of 109 isolates examined, 95 were located in six clusters of 2 to 63 isolates each. The 63 isolates in the largest cluster had an identical pattern corresponding to the Beijing genotype. The remaining isolates were of a non-Beijing genotype and formed another large group whose similarity ranged from 72% to 100%. Mutations in the rpoB and katG genes were compared in the Beijing and non-Beijing strains. In both groups, the rpoB gene mutations predominated in codons S531L (52.2%) and D516V (14.7%). Double mutations in the rpoB gene were observed in 8.2% of the isolates, most of them located among Beijing-type isolates. The katG gene mutation S315T (98.4%) was prevalent among all isolates. CONCLUSION: Molecular analysis of MDR isolates of M. tuberculosis demonstrates that the Beijing genotype, most likely due to recent transmission, is prevalent in Latvia among MDR patients and that this genotype can be associated with double mutations.

Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: recommendations for standardised nomenclature.

Spacer oligonucleotide typing (spoligotyping) is widely used for differentiation of bacteria of the Mycobacterium tuberculosis complex. However, the absence of any standardised method for concise description of spoligotypes makes it difficult to compare the results from different laboratories. This paper describes unambiguous, interconvertible systems for the designation of spoligotype patterns, the adoption of which will be beneficial to mycobacterial research.

Tuberculosis in Greenland--current situation and future challenges.

OBJECTIVE: To describe the tuberculosis (TB) epidemiology in Greenland in 1998-2002 and to identify possible obstacles for reducing the TB incidence. STUDY DESIGN/METHODS: TB notification data were collected from the annual reports of the Chief Medical Officer, and culture verification data were collected from the International Reference Laboratory of Mycobacteriology at Statens Serum Institut, Denmark. RESULTS: The TB incidence in Greenland reached a peak of 185/100,000 in 2001. In 1999-2001, the majority of cases were related to an outbreak in the Southern districts. In 1998-2002, 0.5% drug-resistance was found among patients living in Greenland in contrast to 13.1% drug-resistance found previously among Inuit patients in Denmark. In 1998-2001, microscopy positive cases made up 65% of all culture confirmed cases and DNA subtyping demonstrated the emergence of Mycobacterium tuberculosis strains that were previously infrequently found. CONCLUSION: It is important to eliminate factors that fuel the epidemic and to improve general living conditions in Greenland. Treatment seems effective as limited drug-resistance is detected. TB reduction will therefore depend on early detection of active disease and thorough contact tracing. Greenland will face a pool of persons latently infected some of whom will progress to active disease. Sufficient resources need to be allocated for TB control in the years to come.

[Molecular epidemiology of tuberculosis among prisoners]. / Molekulární epidemiologie tuberkulózy veznu.

The subject of the investigation is a group of 27 strains of Mycobacterium tuberculosis isolated in 2000 from prisoners with the diagnosis of tuberculosis, 19 Czechs and 8 foreigners (mean age 41 and 35 years resp.). The molecular-epidemiological examination of these strains was made using the RFLP fingerprint technique (Restriction Fragment Length Polymorphism) with evidence of the insertive sequence IS6110 and the technique of spoligotyping, based on detection of hybridization of spacer oligonucleotides. DNA fingerprinting revealed a high polymorphism in the number and molecular weight of sequence IS6110 which is common in Czech and other European strains of M. tuberculosis. All strains with the exception of two had mutually different fingerprint profiles. In the two with identical fingerprints probably a duplicit examination of the same material was involved which occurred by mistake during transport or in the laboratory. The fingerprint method thus did not prove interhuman transmission of tuberculosis between the examined prisoners. The technique of spoligotyping revealed the finding of genotype Beijing M. tuberculosis in two sick prisoners, one Algerian and one Albanese, and in one Czech prisoner. This genotype found in a high percentage of patients in southeastern Asia and in migrants from this area was detected for the first time in the Czech Republic. The findings are evidence of a satisfactory standard of the programme of tuberculosis control in the Czech prison system and at the same time draw attention to the potential possibility of the spread of tuberculosis from migrants coming from areas with a high prevalence.

[Heroin abuse among Danish prisoners on remand. I. Prevalence related to form of administration]. / Heroinmisbrug blandt danske varetaegtsarrestanter. I. Proevalens relateret til administrationsform.

Two groups of Danish prisoners on remand (in solitary confinement and not in solitary confinement) were examined by interview on reception (n = 133 & n = 95) in order to evaluate the prevalence and form of administration of opioid abuse/dependence. About 50% had abused opioids during their lifetime; one third were dependent at the time of reception. Twenty percent of opioid dependent prisoners administered opioids by smoking. More intravenous users were treated with methadone before and during imprisonment than those who were dependent on smoking opioids. Few were objectively suffering from withdrawal symptoms. The psycho-social impact of dependence on smoking heroin and intravenous heroin one month prior to imprisonment was at the same level and substantial as measured by the Global Assessment Scale.

[Heroin abuse among Danish prisoners on remand. II. Consequences related to form of administration]. / Heroinmisbrug blandt danske varetaegtsarrestanter. II. Konsekvenser of afhaengighed relateret til administrationsform.

Heroin-abusing Danish prisoners remanded in custody were based on interviews grouped as either smoking dependent (n = 18) or intravenous dependent (n = 55). Intravenous users had a longer duration and earlier debut of abuse than users who smoked opiates. Only intravenous users had serious somatic complications. Both groups of opioid dependent prisoners were marked by severe psychosocial dysfunction and considerable psychiatric co-morbidity. The intravenous users were generally more affected than the smokers concerning social and psychiatric parameters and earlier criminality, perhaps due to their longer duration of abuse.

[Resistant tuberculosis in Denmark]. / Resistent tuberkulose i Danmark.

INTRODUCTION: Increased rates of multidrug-resistant (MDR) tuberculosis (TB) has been reported from countries close to Denmark. We evaluated the incidence of drug resistance in Denmark in order to determine the magnitude of the problem. MATERIALS AND METHODS: Susceptibility testing was performed in isolates from 85.4% of all notified patients during 1991-1998. Epidemiological information was retrieved from the mandatory notification forms. RESULTS: Total drug resistance remained largely constant, although a minor increase was observed in 1997-1998. Monoresistance was observed in 7.3% of the isolates. Among 3.6% polyresistant isolates, resistance to isoniazid and streptomycin accounted for 2.8%, whereas MDR accounted for 0.5%. The MDR strains displayed different restriction fragment length polymorphism (RFLP) patterns, and no matches were identified in the international MDR database. Drug resistance in untreated Danes and foreigners were 5.9% and 14.6%, respectively. Among Danes and foreigners with previous TB, 6.2% and 22.7% had drug resistance, respectively. Increased drug resistance was found among untreated Danes aged 25-54 years mainly due to a single isoniazid- and streptomycin-resistant RFLP-cluster. Among all patients with isoniazid- and streptomycin-resistance, 77.0% had clustered strains. DISCUSSION: In conclusion, although drug resistance among untreated Danes was close to the rate estimated in good national programmes, close monitoring is needed in future years, as active transmission of isoniazid- and streptomycin-resistant Mycobacterium tuberculosis was demonstrated.

First report of lung transplantation in a patient with active pulmonary Mycobacterium simiae infection.

Mycobacterium simiae is a slow-growing mycobacteria that in rare cases can cause chronic pulmonary infection. We report the first case of lung transplantation in a patient with active M simiae infection at the time of transplantation. A 56-year-old immunocompetent nonsmoking woman underwent bilateral lung transplantation for end-stage idiopathic bronchiectasis and chronic M simiae infection. The disease proved manageable on a regimen of clarithromycin, moxifloxacin, and cotrimoxazole with a successful outcome 1-year posttransplantation. There is increasing evidence that nontuberculous mycobacterium infection should no longer be an absolute contraindication for lung transplantation.

Recurrent tuberculosis in Denmark: relapse vs. re-infection.

SETTING: Denmark, a country with a low-incidence of tuberculosis (TB). OBJECTIVE: To analyse the proportion of relapse vs. re-infection and to compare selected characteristics between the two subgroups. DESIGN: A population-based cohort study. All 4154 Mycobacterium tuberculosis isolates from patients in Denmark genotyped by insertion sequence 6110 restriction fragment length polymorphism were followed for recurrent TB over 13.5 years. Recurrent cases were classified as relapse or re-infection by genotype patterns in initial and serial disease episodes. RESULTS: Recurrent TB was found in 73 (1.8%) cases. Identical M. tuberculosis genotypes in initial and serial episodes were found in 54 (1.3%), indicating relapse, whereas different genotypes, representing re-infection, were found in 19 (0.5%) cases. Cavitary TB in the initial episode was significantly associated with relapse (OR 4.6, 95%CI 1.1-26.9) compared to re-infection. CONCLUSION: The rate of recurrent TB is low in Denmark. Comparing selected characteristics between the relapse and re-infection subgroups revealed that only the presence of cavitary disease was associated with relapse. Although recurrent TB was rarely due to re-infection, the risk of re-infection increased with time.