Molecular epidemiology of tuberculosis in London 1995-7 showing low rate of active transmission

Analysis of changes in recent tuberculosis transmission patterns after a sharp increase in immigration

We conducted a population-based molecular epidemiological study of tuberculosis (TB) in Madrid, Spain (2002 to 2004), to define transmission patterns and factors associated with clustering. We particularly focused on examining how the increase in TB cases among immigrants in recent years (2.8% in 1997 to 1999 to 36.2% during the current study) was modifying transmission patterns. Mycobacterium tuberculosis isolates obtained from patients living in nine districts of Madrid (1,459,232 inhabitants) were genotyped. The TB case rate among foreign-born people was three to four times that of Spanish-born people, and the median time from arrival to the onset of treatment was 22.4 months. During the study period, 227 (36.3%) patients were grouped in 64 clusters, and 115 (50.7%) of them were in 21 clusters with mixed Spanish-born and foreign-born patients. Three of the 21 mixed clusters accounted for 21.1% of clustered patients. Twenty-two of 38 (57.9%) immigrants in mixed clusters were infected with TB strains that had already been identified in the native population in 1997 to 1999, including the three most prevalent strains. Factors identified as independent predictors of clustering were homelessness (odds ratio [OR], 2.3; 95% confidence interval [95% CI], 1.2 to 4.5; P = 0.011) and to be born in Spain (OR, 1.8; 95% CI, 1.2 to 2.6; P = 0.002). The results indicated that (i) TB transmission was higher in Spanish-born people, associated mainly with homelessness, (ii) that foreign-born people were much less likely to be clustered, suggesting a higher percentage of infection before arriving in Spain, and (iii) that an extensive transmission between Spanish- and foreign-born populations, caused mainly by autochthonous strains, was taking place in Madrid.

Tuberculosis in London: a decade and a half of no decline [corrected]

BACKGROUND

London accounts for nearly half of the national burden of tuberculosis. The incidence of tuberculosis has more than doubled in London in the past 15 years.

METHODS

Data from the enhanced tuberculosis surveillance 1999-2003, the national tuberculosis surveys of 1993 and 1998, and tuberculosis notifications were compared and analysed.

RESULTS

In 2003, 3048 patients with tuberculosis were reported in London, 45% of the national total. This represents an incidence of 41.3/100,000, five times higher than the rest of England and Wales, and in parts of London the incidence of tuberculosis is nine times the national average. 75% of people with tuberculosis in London are born abroad; nearly half have lived in the UK for <5 years, but a third for >10 years. 86% are from an ethnic minority group, and the incidence is highest in black Africans at 283/100,000 compared with 141, 141 and 8/100,000 for Pakistanis, Indians and whites, respectively. In absolute terms, a third of patients with tuberculosis in London are from Africa and nearly a third from the Indian subcontinent. Specific groups affected also include the homeless, prisoners, and hard drug and alcohol users as well as the immunosuppressed.

CONCLUSIONS

London reflects the worldwide rise in tuberculosis, with increasing incidence in ethnic minorities. Work has been carried out to combat this rise, but more is needed. Tuberculosis control and prevention strategies should be mindful of the changing epidemiology of tuberculosis in London, and provide information, diagnosis and treatment tailored to the specific needs of the capital and its at-risk groups.

Beijing/W genotype Mycobacterium tuberculosis and drug resistance

The genotype, endemic in some areas and emerging in others, may be associated with drug-resistance.

Beijing/W genotype Mycobacterium tuberculosis is widespread, may be increasing, and may have a predilection for drug resistance. Individual-level data on >29,000 patients from 49 studies in 35 countries were combined to assess the Beijing genotype’s prevalence worldwide, trends over time and with age, and associations with drug resistance. We found 4 patterns for Beijing/W genotype tuberculosis (TB): 1) endemic, not associated with drug resistance (high level in most of East Asia, lower level in parts of the United States); 2) epidemic, associated with drug resistance (high level in Cuba, the former Soviet Union, Vietnam, and South Africa, lower level in parts of Western Europe); 3) epidemic but drug sensitive (Malawi, Argentina); and 4) very low level or absent (parts of Europe, Africa). This study confirms that Beijing/W genotype TB is an emerging pathogen in several areas and a predominant endemic strain in others; it is frequently associated with drug resistance.

IS6110 restriction fragment length polymorphism typing of Mycobacterium tuberculosis isolates from East Azerbaijan Province of Iran

To investigate the genetic variation among Mycobacterium tuberculosis isolates in the East Azerbaijan Province of Iran and to evaluate the level of and risk factors for recent transmission of tuberculosis (TB), we performed IS6110-based restriction fragment length polymorphism analysis of strains, isolated from 105 patients during the period of September 2002 to March 2003 in TB centers and university hospitals of the province. Among 105 isolates, 81 different IS6110 patterns were found, of which 70 were observed only once and 11 were shared by two to eight isolates. Ninety-six isolates (91.4%) were found to have more than five copies of IS6110 and together with high patterns polymorphism, shows that IS6110-RFLP typing could be useful for studying the epidemiology of TB in Azerbaijan. The minimum estimated rate of recent transmission was 23%, suggesting that the degree of recent transmission in East Azerbaijan Province is relatively low. Clustering was not associated with age, sex or site of infection of TB but drug-resistant isolates were less likely to be clustered than sensitive isolates (p < 0.05).

Long-term population-based genotyping study of Mycobacterium tuberculosis complex isolates in the French departments of the Americas

The three French overseas departments of the Americas are characterized both by insular (Guadeloupe and Martinique) and continental (French Guiana) settings with a tuberculosis case detection rate that varies from less than 10 per 100,000 per year in insular areas to an estimated incidence of more than 55 per 100,000 in French Guiana. Under a long-term genotyping program, more than three-fourths of all the Mycobacterium tuberculosis isolates (n = 744) received from the three settings were fingerprinted over a 10-year period (1994 to 2003) by spoligotyping and variable number of tandem DNA repeats (VNTRs) in order to understand the current trends in their detection rates, drug resistance, and groups and subpopulations at risk of contracting the disease and to pinpoint the circulating phylogeographical clades of the bacilli. The major difference in the study populations was the nationality of the patients, with a high percentage of immigrants from high-incidence neighboring countries in French Guiana and a low but increasing percentage in the French Caribbean. The rate of recent transmission was calculated to be 49.3% in French Guiana, compared to 27.2% and 16.9% in Guadeloupe and Martinique, respectively. At the phylogeographic level, 77.9% of the isolates studied belonged to four major clades (Haarlem, Latin-American and Mediterranean, T, and X) which are already reported from neighboring Caribbean islands in an international database and may underline potential interregional transmission events.

Natural transposon mutagenesis of clinical isolates of Mycobacterium tuberculosis: how many genes does a pathogen need?

Transposable elements can affect an organism's fitness through the insertional inactivation of genes and can therefore be used to identify genes that are nonessential for growth in vitro or in animal models. However, these models may not adequately represent the genetic requirements during chains of human infection. We have therefore conducted a genome-wide survey of transposon mutations in Mycobacterium tuberculosis isolates from cases of human infection, identifying the precise, base-specific insertion sites of the naturally occurring transposable element IS6110. Of 294 distinct insertions mapped to the strain H37Rv genome, 180 were intragenic, affecting 100 open reading frames. The number of genes carrying IS6110 in clinical isolates, and hence apparently not essential for infection and transmission, is very much lower than the estimates of nonessential genes derived from in vitro studies. This suggests that most genes in M. tuberculosis play a significant role in human infection chains. IS6110 insertions were underrepresented in genes associated with virulence, information pathways, lipid metabolism, and membrane proteins but overrepresented in multicopy genes of the PPE family, genes of unknown function, and intergenic sequences. Population genomic analysis of isolates recovered from an organism's natural habitat is an important tool for determining the significance of genes or classes of genes in the natural biology of an organism.

Molecular typing of Mycobacterium tuberculosis by mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis, a more accurate method for identifying epidemiological links between patients with tuberculosis

IS6110 fingerprinting of Mycobacterium tuberculosis is the standard identification method in studies on transmission of tuberculosis. However, intensive epidemiological investigation may fail to confirm transmission links between patients clustered by IS6110-restriction fragment length polymorphism (RFLP) typing. We applied typing based on variable numbers of tandem repeats (VNTRs) of mycobacterial interspersed repetitive units (MIRUs) to isolates from 125 patients in 42 IS6110 clusters, for which thorough epidemiological data were available, to investigate the potential of this method in distinguishing epidemiologically linked from nonlinked patients. Of seven IS6110 clusters without epidemiological links, five were split by MIRU-VNTR typing, while nearly all IS6110 clusters with proven or likely links displayed conserved MIRU-VNTR types. These results provide molecular evidence that not all clusters determined on the basis of multibanded IS6110 RFLP patterns necessarily reflect transmission of tuberculosis. They support the use of MIRU-VNTR typing as a more reliable and faster method for transmission analysis.

Tuberculosis and pregnancy--Results of a study in a high prevalence area in London

OBJECTIVE

The aim of the study was to characterise the incidence, type and presentation of tuberculosis in pregnancy over a 5-year period in women booked for antenatal care in a District General Hospital located in a high prevalence area in London. We also aimed to identify any problems and difficulties in the diagnosis and management of tuberculosis associated with pregnancy.

DESIGN

Retrospective review of computer records and hospital notes over a period of 5 years from January 1997 to December 2001. Demographic and clinical data were collected for all the cases identified.

POPULATION

All women with tuberculosis who conceived on antituberculous treatment, or had onset of symptoms or diagnosis made in pregnancy or the immediate postpartum period (6 weeks), and booked for antenatal care at a District General Hospital located in an area of high prevalence for tuberculosis (52.2 per 100,000 population in Ealing, Hammersmith and Hounslow Health authority according to the National Tuberculosis Survey of England and Wales in 1998).

RESULTS

Thirty-two women were identified over the 5-year period, giving an incidence of 252/100,000 deliveries. The number of cases increased from 3 in 1997 to 10 in each of 2000 and 2001. All of these women were from ethnic minorities and 88% of them were immigrants with the median interval from arrival in UK being 2 years. Fifty-three percent were diagnosed with extrapulmonary tuberculosis, 38% with pulmonary tuberculosis and 9% had both. The median duration of symptoms prior to presentation was 31 days (being longer in women with extrapulmonary tuberculosis); the longest was 10 years. The median interval from presentation of symptoms to diagnosis was 32 days and the majority of women started treatment immediately. The commonest reason for a delay in diagnosis was late presentation (52%), followed by non-specific symptoms (in 38%). There was a trend towards late presentation among recent immigrants (odds ratio 2.14, 95% confidence interval 0.44-10.53) and those having extrapulmonary tuberculosis (odds ratio 1.64, 95% CI 0.32-8.45). Most of the women (28/32) showed good compliance and a good response to treatment (31/32). Maternal outcomes were good with no serious morbidity or mortality. The majority of women delivered at term (28/32), while two delivered preterm and two women miscarried. There was no perinatal mortality.

CONCLUSION

This is the largest recent series of pregnant women with tuberculosis in the UK. A high incidence of extrapulmonary tuberculosis was seen. The common causes for a delay in diagnosis were late presentation and non-specific symptoms. If recent immigrants from high prevalence areas who have been in the UK for less than 5 years were asked for symptoms suggestive of tuberculosis at the booking visit and through pregnancy, this might facilitate early diagnosis and treatment. The use of a symptom questionnaire at the booking visit for these women could be a method to alert both the women and health professionals involved in their care, to the symptoms of tuberculosis. With good compliance, there is a good response to treatment and favourable maternal and perinatal outcomes.

Mycobacterium tuberculosis lineage: a naming of the parts

There have been many reports of groups of related Mycobacterium tuberculosis strains described variously as lineages, families or clades. There is no objective definition of these groupings, making it impossible to define relationships between those groups with biological advantages. Here we describe two groups of related strains obtained from an epidemiological study in Tanzania, which we define as the Kilimanjaro and Meru lineages on the basis of IS6110 restriction fragment length polymorphism (RFLP), polymorphic GC rich sequence (PGRS) RFLP and mycobacterial interspersed repeat unit (MIRU) typing. We investigated the concordance between each of the typing techniques and the dispersal of the typing profiles from a core pattern. The Meru lineage is more dispersed than the Kilimanjaro lineage and we speculate that the Meru lineage is older. We suggest that this approach provides an objective definition that proves robust in this epidemiological study. Such a framework will permit associations between a lineage and clinical or bacterial phenomenon to be tested objectively. This definition will also enable new putative lineages to be objectively tested.

Prevalence and associations of vitamin D deficiency in foreign-born persons with tuberculosis in London

OBJECTIVES

The incidence of tuberculosis (TB) is high amongst foreign-born persons resident in developed countries. Vitamin D is important in the host defence against TB in vitro and deficiency may be an acquired risk factor for this disease. We aimed to determine the incidence and associations of vitamin D deficiency in TB patients diagnosed at an infectious diseases unit in London, UK.

METHODS

Case-note analysis of 210 unselected patients diagnosed with TB who had plasma vitamin D (25(OH)D3) levels routinely measured. Prevalence of 25(OH)D3 deficiency and its relationship to ethnic origin, religion, site of TB, sex, age, duration in the UK, month of 25(OH)D3 estimation and TB diagnosis were determined.

RESULTS

Of 210 patients 76% were 25(OH)D3 deficient and 56% had undetectable levels. 70/82 Indian, 24/28 East African Asian, 29/34 Somali, 14/19 Pakistani and Afghani, 16/22 Sri Lankan and 2/6 other African patients were deficient (with 58, 17, 23, 9, 6 and 1 having undetectable levels, respectively). Only 0/6 white Europeans and 1/8 Chinese/South East Asians had low plasma 25(OH)D3 levels. Muslims, Hindus and Sikhs all had equivalent rates of deficiency though Hindus were more likely to have undetectable levels (odds ratio 1.87, 95% CI 1.27-2.76). There was no significant association between 25(OH)D3 level and site of TB or duration of residence in the UK. There was no apparent seasonal variation in either TB diagnosis or 25(OH)D3 level.

CONCLUSIONS

25(OH)D3 deficiency commonly associates with TB among all ethnic groups apart from white Europeans, and Chinese/South East Asians. Our data support a lack of sunlight exposure and potentially a vegetarian diet as contributors to this deficiency.

IS6110 DNA fingerprinting analysis of individually separated colonies of Mycobacterium tuberculosis

There are no data so far that show IS6110 restriction fragment length polymorphism (RFLP) patterns of individually separated tuberculosis bacilli from clinical isolates, and their alterations during follow-up surveys. We picked 20-60 tuberculosis clones from clinical isolates under anti-tuberculosis medication, and individually analysed their DNA fingerprinting patterns using IS6110 RFLP as well as spoligotyping as a second typing. The study using cloned bacilli of Mycobacterium tuberculosis showed that clinical isolates contained several clones with different DNA fingerprints and that their band patterns altered weakly but distinctly during follow-up surveys. However, there was no significant difference in the fingerprinting patterns when clinical isolates were to RFLP without separating to subjected/individual colonies. In view of the IS6110 RFLP of individually separated tuberculosis bacilli, we have now speculated several possibilities: (1) that clones with different DNA fingerprints exist in clinical isolates; (2) that IS6110 RFLP patterns of the materials depend on the population of the original clone and the variants having DNA fingerprints different from the original pattern; and (3) that their band patterns are influenced not only by the stability of the original germ having its own fingerprint, but also by the fragility of the new clones.

Identification and characterization of a regulatory sequence recognized by Mycobacterium tuberculosis persistence regulator MprA

Establishment and maintenance of persistent, latent infection by Mycobacterium tuberculosis are dependent on expression of the mprA-mprB regulatory system. Previously, MprA and MprB were shown to participate in phosphotransfer reactions characteristic of two-component signaling systems. To begin identifying downstream effector genes regulated by mprA-mprB during persistent stages of infection, a search for the regulatory sequence(s) recognized by response regulator MprA was carried out. Here, evidence is presented demonstrating that MprA recognizes a 19-bp sequence comprising two loosely conserved 8-bp direct repeat subunits separated by 3 nucleotides. This motif, termed the MprA box, is found upstream of the mprA coding sequence and that of downstream gene pepD (Rv0983). Protein phosphorylation was not required for binding to this DNA sequence by MprA in vitro; however, phosphorylation enhanced DNA binding by MprA and was required for the regulation of mprA and pepD by MprA in vivo. Binding of MprA to the MprA box was dependent on conserved nucleotides contained within repeat subunits and on the spacer length separating these repeats. In addition, recognition of this sequence proceeded via tandem binding of two monomers of MprA. Identification of the genetic determinants regulated by MprA will ultimately enhance our understanding of the mechanisms utilized by M. tuberculosis to undergo latency.

Automated high-throughput mycobacterial interspersed repetitive unit typing of Mycobacterium tuberculosis strains by a combination of PCR and nondenaturing high-performance liquid chromatography

Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing of Mycobacterium tuberculosis complex isolates is portable, 100% reproducible, and highly discriminatory. Nondenaturing high-performance liquid chromatography (non-dHPLC) with use of a WAVE microbial analysis system is a promising method of PCR amplicon analysis as it is low cost and requires no preanalysis processing. The aims of this study were to validate the application of WAVE microbial analysis system technology to MIRU-VNTR typing. A collection of 70 strains were cultivated in liquid culture and extracted using the QIAamp DNA minikit. Novel primers were designed to target the 12 MIRU-VNTR loci (P. Supply et al., J. Clin. Microbiol. 39:3563-3571, 2001). After amplification, each PCR product was analyzed on a WAVE microbial analysis system. The fragment size was calculated from the chromatogram, and the number of tandem repeats at each locus was determined. For the collection of 70 strains 100% concordance was achieved when comparing MIRU-VNTR profiles obtained from agarose gel electrophoresis and PCRs analyzed on a WAVE microbial analysis system. The calculated fragment sizes, obtained from the WAVE microbial analysis system, were sufficiently accurate to ensure 100% confidence when assigning the number of tandem repeats to a MIRU-VNTR locus. This study is the first to report the successful use of non-dHPLC for screening for variations in the number of MIRU-VNTRs in mycobacterial DNA. Non-dHPLC analysis was demonstrated to be a rapid, low-labor input method for the detection and analysis of MIRU-VNTR amplicons. The combination with non-dHPLC further enhances the utility of MIRU-VNTR typing.

Molecular epidemiology of Mycobacterium tuberculosis in western Sweden

The genetic diversity of Mycobacterium tuberculosis isolates among patients from Sweden was determined by a combination of two PCR-based techniques (spoligotyping and variable number of tandem repeats analysis). It resulted in a clustering of 23.6% of the isolates and a rate of recent transmission of 14.1%. The clustered isolates mainly belonged to the Haarlem family (23.2%), followed by the Beijing (9.8%), Latin American and Mediterranean (LAM; 8%), and East African-Indian (EAI; 6.2%) families. A comparison of the spoligotypes with those in the international spoligotyping database showed that 62.5% of the clustered isolates and 36.6% of all isolates typed were grouped into six major shared types. A comparison of the spoligotypes with those in databases for Scandinavian countries showed that 33% of the isolates belonged to an ill-defined T family, followed by the EAI (22%), Haarlem (20%), LAM (11%), Central Asian (5%), X (5%), and Beijing (4%) families. Both the highest number of cases and the proportion of clustered cases were observed in patients ages 15 to 39 years. Nearly 10% of the isolates were resistant to one or more drugs (essentially limited to isoniazid monoresistance). However, none of the strains were multidrug resistant. Data on the geographic origins of the patients showed that more than two-thirds of the clustered patients with tuberculosis were foreign-born individuals or refugees. These results are explained on the basis of both the historical links within specific countries and recently imported cases of tuberculosis into Sweden.

Outbreak of isoniazid resistant tuberculosis in north London

BACKGROUND

A description is given of a major outbreak of isoniazid monoresistant tuberculosis (TB) chiefly in north London, including prisons. The earliest case was diagnosed in 1995 with most cases appearing after 1999.

METHODS

Confirmation of a local cluster of cases was confirmed by restriction fragment length polymorphism (RFLP IS6110) typing or "rapid epidemiological typing" (RAPET). Further cases were found by retrospective analysis of existing databases, prospective screening of new isolates, and targeted epidemiological case detection including questionnaire analysis.

RESULTS

By the end of 2001, 70 confirmed cases in London had been linked with a further 13 clinical cases in contacts and nine epidemiologically linked cases outside London. The epidemic curve suggests that the peak of the outbreak has not yet been reached. Cases in the outbreak largely belong to a social group of young adults of mixed ethnic backgrounds including several individuals from professional/business backgrounds. Compared with other cases of TB reported to the enhanced surveillance scheme in London during 1999-2001, the cases are more likely to be of white (26/70 (37%) v 1308/7666 (17%)) or black Caribbean ethnicity (17/70 (24%) v 312/7666 (4%)), born in the UK (41/70 (59%) v 1335/7666 (17%)), and male (52/70 (74%) v 4195/7666 (55%)). Drug misuse and/or prison detention are factors common to many cases.

CONCLUSIONS

The investigation of the outbreak revealed significant problems on an individual patient and population based level including difficulties with contact tracing, compliance, and the risk of developing multidrug resistance. This incident has demonstrated the value of molecular strain typing in investigating an extensive outbreak of TB. This is the first documented outbreak involving a UK prison.

Alcohol exacerbates murine pulmonary tuberculosis

Alcohol consumption has been described as a risk factor for infection with Mycobacterium tuberculosis, but its contribution to tuberculosis has been difficult to isolate from other adverse socioeconomic factors. Our objective was to evaluate the impact of alcohol consumption on pulmonary infection with M. tuberculosis in a murine model. BALB/c mice were maintained on the Lieber-DeCarli liquid ethanol diet or a liquid control diet and infected intratracheally with low-dose M. tuberculosis H37Rv. Lung organism burdens, lung and lung-associated lymph node CD4(+)- and CD8(+)- lymphocyte numbers and rates of proliferation, and CD4(+)-lymphocyte cytokine production levels were compared between the groups. The alcohol-consuming mice had significantly higher lung organism burdens than the control mice, and the CD4(+)- and CD8(+)-lymphocyte responses to pulmonary infection with M. tuberculosis were blunted in the alcohol group. Lymphocyte proliferation and production of gamma interferon were decreased in the CD4(+) lymphocytes from the alcohol-consuming mice. Additionally, lung granulomas were significantly smaller in the alcohol-consuming mice. In conclusion, murine alcohol consumption is associated with decreased control of pulmonary infection with M. tuberculosis, which is accompanied by alterations in the region-specific CD4(+)- and CD8(+)-lymphocyte responses and defective lung granuloma formation.

Tuberculosis: a problem with persistence

Mycobacterium tuberculosis is one of most successful pathogens of mankind, infecting one-third of the global population and claiming two million lives every year. The ability of the bacteria to persist in the form of a long-term asymptomatic infection, referred to as latent tuberculosis, is central to the biology of the disease. The persistence of bacteria in superficially normal tissue was recognized soon after the discovery of the tubercle bacillus, and much of our knowledge about persistent populations of M. tuberculosis dates back to the first half of the last century. Recent advances in microbial genetics and host immunity provide an opportunity for renewed investigation of this persistent threat to human health.

Clustered Tuberculosis Cases

Clustered tuberculosis cases with Mycobacterium tuberculosis isolates showing identical restriction fragment length polymorphism patterns are assumed to be the result of disease transmission. In a prospective, population-based study in the province of North Holland, The Netherlands, we combined molecular methods with highly detailed epidemiologic information to determine why many clustered cases are not detected at an early stage. Of 481 patients, 138 (29%) fell into 43 clusters, suggesting recent transmission in 20%. Of 155 patients in clusters occurring within 2 years before or after the diagnosis of the disease, 21 (14%) had no epidemiologic links with other patients. Independent predictors of the absence of such links were female sex and Turkish, Moroccan, or other African ethnicity. Of 47 patients with a clear epidemiologic link, 37 (24% of 155) were identified early, e.g., by contact tracing, and 10 (6%) were missed. In 85 (55%) patients, an epidemiologic link was likely but undetected when using conventional contact tracing. Compared with clearly linked patients, only male sex was independently associated with presence in this last group. Our results indicate that 86% of clustered study patients had epidemiologic links and that opportunities for earlier identification using conventional tuberculosis control strategies are limited.

Use of genetic distance as a measure of ongoing transmission of Mycobacterium tuberculosis

The stability of the genotypic marker IS6110, used to define the epidemiology of Mycobacterium tuberculosis, is one of the most important factors influencing the interpretation of DNA fingerprint data. We propose that evolved strains should be considered together with clustered strains to represent chains of ongoing transmission. For the present study we used a large set of fingerprint data for strains collected between 1992 and 1998 from residents of a community with a high incidence of tuberculosis in Cape Town, South Africa. Interstrain genetic distances were calculated by counting the banding pattern mismatches in the IS6110 DNA fingerprints of different isolates. These data demonstrate that the propensity to change by one or two bands is independent of the IS6110 copy number. Hence, the genetic distance between pairs of isolates can be simply expressed as the number of differences in the banding patterns. From this foundation, a data set which identifies newly evolved strains has been generated. Inclusion of these evolved strains into various molecular epidemiological calculations significantly increased the estimate of ongoing transmission in this study setting. The indication is that nearly all cases of tuberculosis in this community are due to ongoing transmission. This has important implications for tuberculosis control, as it indicates that the control measures used at present are unable to reduce the level of transmission. This technique may also be applicable to the study of low-incidence tuberculosis outbreaks as well as the analysis of epidemiological data from other disease epidemics.

The transmission of tuberculosis in the light of new molecular biological approaches

This review briefly summarises the recent achievements in tuberculosis epidemiology associated with the introduction of molecular methods, and considers the implications of these methods for the understanding of occupational tuberculosis transmission. Special attention is paid to the relative contribution of recently transmitted tuberculosis; risk factors for recent transmission; and the occurrence and frequency of exogenous reinfection. There is a need for occupational epidemiological studies, which should combine the methods of "classical" epidemiology with those of molecular epidemiology.

Global epidemiology of paediatric tuberculosis

Tuberculosis is one of the major infections affecting children worldwide. It causes significant morbidity and mortality, especially in infants and young children. Factors such as overcrowding, poverty and the HIV epidemic have all contributed to the resurgence of tuberculosis globally. The highest rates of tuberculosis occur in resource-poor countries and over the last decade case notifications in children have been increasing steadily, particularly in Sub-Saharan Africa. Mycobacterium tuberculosis infects millions of children worldwide every year, yet accurate information on the extent and distribution of disease in children is not available for most of the world. We describe some of the unique aspects of tuberculosis infection in children and review the epidemiology of disease in children worldwide.

Tuberculosis: amplification-based clinical diagnostic techniques

Tuberculosis (TB) is one of the major infectious causes of morbidity and mortality worldwide. TB is difficult to control due to the time taken for the microbiological diagnosis; typically culture on solid media takes 6-8 weeks. There are number of rapid molecular methods that have been developed to diagnose new cases of tuberculosis, detect drug resistance and identify the type of mycobacteria. These assays are based on recognition of mycobacterial DNA sequences and the subsequent amplification of nucleic acid sequences to facilitate detection. This review will describe some of the molecular assays that are in use for TB diagnosis and the considerations in designing and performing such assays. Early diagnosis of tuberculosis is critical for the successful management of patients allowing informed use of chemotherapy ensuring that the right patients are treated with the right antimicrobials.

Mycobacterial interspersed repetitive unit typing of Mycobacterium tuberculosis compared to IS6110-based restriction fragment length polymorphism analysis for investigation of apparently clustered cases of tuberculosis

An evaluation of the utility of IS6110-based restriction fragment length polymorphism (RFLP) typing compared to a combination of variable number tandem repeat (VNTR) typing and mycobacterial interspersed repetitive unit (MIRU) typing was undertaken. A total of 53 patient isolates of Mycobacterium tuberculosis from four presumed episodes of cross-infection were examined. Genomic DNA was extracted from the isolates by a cetyl trimethylammonium bromide method. The number of copies of tandem repeats of the five loci ETR(A) to ETR(E) and 12 MIRU loci was determined by PCR amplification and agarose gel electrophoresis of the amplicons. VNTR typing identified the major clusters of strains in the three investigations in which they occurred (each representing a different evolutionary clade: 32333, 42235, and 32433). The majority of unrelated isolates (by epidemiology and RFLP typing) were also identified by VNTR typing. The concordance between the RFLP and MIRU typing was complete, with the exception of two isolates with RFLP patterns that differed by one band each from the rest of the major epidemiologically linked groups of isolates in investigation A. All of these isolates had identical MIRU and VNTR types. A further pair of isolates differed in the number of tandem repeat copies at two MIRU alleles but had identical RFLP patterns. The speed of the combined VNTR and MIRU typing approach enabled results for some of the investigations to be supplied in "real time," influencing choices in contact tracing. The ease of comparison of results of MIRU and VNTR typing, which are recorded as single multidigit numbers, was also found to greatly facilitate investigation management and the communication of results to health care professionals.

Molecular methods for Mycobacterium tuberculosis strain typing: a users guide

There are now a wide range of techniques available to type Mycobacterium tuberculosis, the problem is to choose the correct technique. For large scale epidemiological studies the portability and standardization of IS6110 restriction fragment length polymorphism (RFLP) means that this remains the gold standard technique. In the next few years the internationally standard mycobacterial interspersed repetitive unit (MIRU) may come to challenge this primacy. Low copy number stains remain a problem and these can be typed by either polymorphic Guanine cytosine-rich repetitive sequence (PGRS) or MIRU-variable numbers of tandem repeat (VNTR). To confirm whether strains are part of a true cluster PGRS remains the method of choice. For local outbreaks and investigations of laboratory cross contamination where speed is of greatest importance suspect strains should be initially investigated using a PCR-based method. The superior reproducibility and discrimination of MIRU-VNTR means that these methods should be favoured. If matches are found, then further confirmation of identity can be achieved using IS6110 RFLP or PGRS if the strains prove to have a low IS6110 copy number.

Continued low rates of transmission of Mycobacterium tuberculosis in Norway

In this study, we determined the genetic diversity of Mycobacterium tuberculosis isolated in Norway from 1999 to 2001. The results were compared to those for strains isolated from 1994 to 1998. A total of 818 patients were diagnosed with tuberculosis (TB) during the last 3-year period. Of these cases, 576 (70%) were verified by culturing, and strains from 551 patients (96%) were analyzed by the IS6110 restriction fragment length polymorphism (RFLP) method. We excluded 13 strains (2.4%) from the analyses, since they were found to represent false-positive samples. A total of 67 strains (12%) that carried fewer than five copies of IS6110 were analyzed by spoligotyping. The strains were from 157 patients (29%) of Norwegian origin and 381 patients (71%) of foreign origin. The rate of diversity among all of the strains was 90%, while in 1994 to 1998 it was 87%. Clusters were assumed to have arisen from recent transmission; the degree of such transmission was 10% in 1999 to 2001, while for the whole 8-year period (1994 to 2001), it was 11%. Of the 109 patients diagnosed as being part of a cluster in 1999 to 2001, 89 were infected with a strain that carried more than four copies of IS6110. Among these 89 patients, 52 (58%) were infected with a strain that had already been identified in 1994 to 1998. The results indicated that most cases of TB in Norway were due to the import of new strains rather than to transmission within the country. This finding demonstrates that screening of immigrants for TB upon arrival in Norway needs to be improved. Outbreaks, however, were caused mainly by strains that have been circulating in Norway for many years.

Evaluation and utilization as a public health tool of a national molecular epidemiological tuberculosis outbreak database within the United Kingdom from 1997 to 2001

The aim of this study was to develop a national model and analyze the value of a molecular epidemiological Mycobacterium tuberculosis DNA fingerprint-outbreak database. Incidents were investigated by the United Kingdom PHLS Mycobacterium Reference Unit (MRU) from June 1997 to December 2001, inclusive. A total of 124 incidents involving 972 tuberculosis cases, including 520 patient cultures from referred incidents and 452 patient cultures related to two population studies, were examined by using restriction fragment length polymorphism IS6110 fingerprinting and rapid epidemiological typing. Investigations were divided into the following three categories, reflecting different operational strategies: retrospective passive analysis, retrospective active analysis, and retrospective prospective analysis. The majority of incidents were in the retrospective passive analysis category, i.e., the individual submitting isolates has a suspicion they may be linked. Outbreaks were examined in schools, hospitals, farms, prisons, and public houses, and laboratory cross-contamination events and unusual clinical presentations were investigated. Retrospective active analysis involved a major outbreak centered on a high school. Contact tracing of a teenager with smear-positive pulmonary tuberculosis matched 14 individuals, including members of his class, and another 60 cases were identified in schools clinically and radiologically and by skin testing. Retrospective prospective analysis involved an outbreak of 94 isoniazid-resistant tuberculosis cases in London, United Kingdom, that began after cases were identified at one hospital in January 2000. Contact tracing and comparison with MRU databases indicated that the earliest matched case had occurred in 1995. Subsequently, the MRU changed to an active prospective analysis targeting linked isoniazid-monoresistant isolates for follow up. The patients were multiethnic, born mainly in the United Kingdom, and included professionals, individuals from the music industry, intravenous drug abusers, and prisoners.

Evolutionary relationships among strains of Mycobacterium tuberculosis with few copies of IS6110

Molecular typing of Mycobacterium tuberculosis by using IS6110 shows low discrimination when there are fewer than five copies of the insertion sequence. Using a collection of such isolates from a study of the epidemiology of tuberculosis in London, we have shown a substantial degree of congruence between IS6110 patterns and both spoligotype and PGRS type. This indicates that the IS6110 types mainly represent distinct families of strains rather than arising through the convergent insertion of IS6110 into favored positions. This is supported by identification of the genomic sites of the insertion of IS6110 in these strains. The combined data enable identification of the putative evolutionary relationships of these strains, comprising three lineages broadly associated with patients born in South Asia (India and Pakistan), Africa, and Europe, respectively. These lineages appear to be quite distinct from M. tuberculosis isolates with multiple copies of IS6110.

Deciphering an outbreak of drug-resistant Mycobacterium tuberculosis

There have been ample warnings that multidrug-resistant (MDR) tuberculosis (TB) will continue to emerge if countries do not strengthen their control of TB. In low-incidence European countries, however, these warnings have been substantiated mainly by outbreaks in association with human immunodeficiency virus (HIV)-positive patients. The aim of this study was to investigate an outbreak of infection with MDR and drug-resistant Mycobacterium tuberculosis that was diagnosed among 20 HIV-negative patients living in Norway. Of these, 19 were immigrants from East Africa and one was an ethnic Norwegian. We wanted to find out if transmission had taken place in Norway or abroad and to identify the genetic basis of drug resistance. The strains were analyzed by IS6110 restriction fragment length polymorphism, antibiotic susceptibility tests, spoligotyping, reverse hybridization to regions of the rpoB gene, and sequencing of the katG gene. Epidemiological links between the patients were mapped, and the strains were compared to those isolated in 36 other countries and regions. All strains were resistant to isoniazid and carried Ala234Gly, Ser315Thr, and Arg463Leu substitutions in the katG gene. Eleven strains were MDR and carried a Ser531Leu substitution in the rpoB gene. MDR was acquired in the index patient after arrival in Norway. Links were found among 14 patients. The strain was imported from Somalia but acquired MDR and was transmitted in Norway. This demonstrated that MDR strains are not necessarily imported from high-incidence countries and can be highly communicable. The outbreak underscores a deficiency in the TB control measures employed in many countries and challenges the adequacy of the policy of screening immigrants for TB only on arrival.

Estimation of the rate of unrecognized cross-contamination with mycobacterium tuberculosis in London microbiology laboratories

Isolates from patients with confirmed tuberculosis from London were collected over 2.5 years between 1995 and 1997. Restriction fragment length polymorphism (RFLP) analysis was performed by the international standard technique as part of a multicenter epidemiological study. A total of 2,779 samples representing 2,500 individual patients from 56 laboratories were examined. Analysis of these samples revealed a laboratory cross-contamination rate of between 0.54%, when only presumed cases of cross-contamination were considered, and 0.93%, when presumed and possible cases were counted. Previous studies suggest an extremely wide range of laboratory cross-contamination rates of between 0.1 and 65%. These data indicate that laboratory cross-contamination has not been a common problem in routine practice in the London area, but in several incidents patients did receive full courses of therapy that were probably unnecessary.