Molecular epidemiology of Mycobacterium tuberculosis strains isolated during a 3-year period (1993 to 1995) in Seville, Spain

Rapidly Correcting Frameshift Mutations in the Mycobacterium tuberculosis orn Gene Produce Reversible Ethambutol Resistance and Small-Colony-Variant Morphology

We have identified a previously unknown mechanism of reversible high-level ethambutol (EMB) resistance in Mycobacterium tuberculosis that is caused by a reversible frameshift mutation in the M. tuberculosisorn gene. A frameshift mutation in orn produces the small-colony-variant (SCV) phenotype, but this mutation does not change the MICs of any drug for wild-type M. tuberculosis However, the same orn mutation in a low-level EMB-resistant double embB-aftA mutant (MIC = 8 μg/ml) produces an SCV with an EMB MIC of 32 μg/ml. Reversible resistance is indistinguishable from a drug-persistent phenotype, because further culture of these orn-embB-aftA SCV mutants results in rapid reversion of the orn frameshifts, reestablishing the correct orn open reading frame, returning the culture to normal colony size, and reversing the EMB MIC back to that (8 μg/ml) of the parental strain. Transcriptomic analysis of orn-embB-aftA mutants compared to wild-type M. tuberculosis identified a 27-fold relative increase in the expression of embC, which is a cellular target for EMB. Expression of embC in orn-embB-aftA mutants was also increased 5-fold compared to that in the parental embB-aftA mutant, whereas large-colony orn frameshift revertants of the orn-embB-aftA mutant had levels of embC expression similar to that of the parental embB-aftA strain. Reversible frameshift mutants may contribute to a reversible form of microbiological drug resistance in human tuberculosis.

Phase variation in Mycobacterium tuberculosis glpK produces transiently heritable drug tolerance

The length and complexity of tuberculosis (TB) therapy, as well as the propensity of Mycobacterium tuberculosis to develop drug resistance, are major barriers to global TB control efforts. M. tuberculosis is known to have the ability to enter into a drug-tolerant state, which may explain many of these impediments to TB treatment. We have identified a mechanism of genetically encoded but rapidly reversible drug tolerance in M. tuberculosis caused by transient frameshift mutations in a homopolymeric tract (HT) of 7 cytosines (7C) in the glpK gene. Inactivating frameshift mutations associated with the 7C HT in glpK produce small colonies that exhibit heritable multidrug increases in minimal inhibitory concentrations and decreases in drug-dependent killing; however, reversion back to a fully drug-susceptible large-colony phenotype occurs rapidly through the introduction of additional insertions or deletions in the same glpK HT region. These reversible frameshift mutations in the 7C HT of M. tuberculosis glpK occur in clinical isolates, accumulate in M. tuberculosis-infected mice with further accumulation during drug treatment, and exhibit a reversible transcriptional profile including induction of dosR and sigH and repression of kstR regulons, similar to that observed in other in vitro models of M. tuberculosis tolerance. These results suggest that GlpK phase variation may contribute to drug tolerance, treatment failure, and relapse in human TB. Drugs effective against phase-variant M. tuberculosis may hasten TB treatment and improve cure rates.

High rates of clustering of strains causing tuberculosis in Harare, Zimbabwe: a molecular epidemiological study

We examined the pattern of tuberculosis (TB) transmission (i.e., reactivation versus recent transmission) and the impact of human immunodeficiency virus (HIV) infection in Harare, Zimbabwe. Consecutive adult smear-positive pulmonary TB patients presenting to an urban hospital in Harare were enrolled. A detailed epidemiological questionnaire was completed, and tests for HIV type 1 and CD4 cell counts were performed for each patient. Molecular fingerprinting of the genomic DNA recovered from cultures of sputum was performed by two molecular typing methods: spacer oligonucleotide typing (spoligotyping) and analysis of variable number of tandem DNA repeats (VNTRs). A cluster was defined as isolates from two or more patients that shared the same spoligotype pattern or the same VNTR pattern, or both. DNA suitable for typing was recovered from 224 patients. The prevalence of HIV infection was 79%. Of 187 patient isolates (78.6%) typed by both spoligotyping and analysis of VNTRs, 147 were identified as part of a cluster by both methods. By spoligotyping alone, 84.1% of patient isolates were grouped into 20 clusters. The cluster size was generally <8 patient isolates, although three large clusters comprised 68, 25, and 23 patient isolates. A total of 89.4% of the patient isolates grouped into 12 clusters defined by analysis of VNTRs, with 2 large clusters consisting of 127 and 13 patient isolates, respectively. Thirty-six percent of patient isolates with a shared spoligotype and 17% with a shared VNTR pattern were geographically linked within Harare, but they were not linked on the basis of the patient's home district. In a multivariate analysis, there were no independent predictors of clustering, including HIV infection status. Comparison with the International Spoligotype database (Pasteur Institute, Pointe a Pitre, Guadeloupe) demonstrated that our three largest spoligotype clusters are well recognized and ubiquitous in Africa. In this epidemiologically well characterized urban population with a high prevalence of HIV infection, we identified a very high level of strain clustering, indicating substantial ongoing recent TB transmission. Geographic linkage could be detected in a proportion of these clusters. A small group of actively circulating strains accounted for most of the cases of TB transmission.

IS6110 functions as a mobile, monocyte-activated promoter in Mycobacterium tuberculosis

The mobile insertion sequence, IS6110, is an important marker in tracking of Mycobacterium tuberculosis strains. Here, we demonstrate that IS6110 can upregulate downstream genes through an outward-directed promoter in its 3' end, thus adding to the significance of this element. Promoter activity was orientation dependent and was localized within a 110 bp fragment adjacent to the right terminal inverted repeat. Transcripts from this promoter, named OP6110, begin approximately 85 bp upstream of the 3' end of IS6110. Use of green fluorescent protein (GFP) expression constructs showed that OP6110 was upregulated in M. tuberculosis during growth in human monocytes and in late growth phases in broth. Analysis of natural insertion sites in M. tuberculosis showed that IS6110 upregulated expression of several downstream genes during growth in human monocytes, including Rv2280 in H37Rv and the PE-PGRS gene, Rv1468c, in the clinical strain 210, which is a member of the Beijing family. Transcription between IS6110 and downstream genes was confirmed by reverse transcription polymerase chain reaction. The ability to activate genes during infection suggests that IS6110 has the potential to influence growth characteristics of different strains, and indicates another mechanism by which IS6110 can impact M. tuberculosis evolution.

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.

Primary Drug Resistance and Molecular Epidemiology ofMycobacterium tuberculosisIsolates from Patients in a Population with High Tuberculosis Incidence in Turkey

To determine the rate of primary drug resistance and compare the fingerprint pattern diversity of the resistant and sensitive Mycobacterium tuberculosis isolates, antituberculosis susceptibility testing and restriction fragment length polymorphism (RFLP) analysis were performed on 88 M. tuberculosis isolates of the patients who were diagnosed as new tuberculosis cases in 2000. Primary resistance to isoniazid, rifampicin, ethambutol, and streptomycin were determined by the BACTEC method. IS6110 and pTBN12 were used as molecular markers. The frequency of resistance to at least one drug was 32.95%, whereas 10.23% of the isolates were resistant to more than one drug. Single-drug resistance to isoniazid, streptomycin, ethambutol, and rifampicin was found in 9 (10.22%), 7 (7.95%), 4 (4.54%), and 0 (0.0%) strains, respectively. Two M. tuberculosis strains (2.26%) showed multiple drug resistance. The combination of two fingerprinting procedures on a total of 88 isolates identified 58 (65.9%) strains as unique and clustered 30 strains in 11 clusters (clustering = 34.1%). The clustering rate for resistant and sensitive isolates was 13.8% and 40.1%, respectively. In conclusion; drug susceptibility testing showed that the majority of the drug-resistant infections involved either isoniazid or streptomycin alone. In addition to the high tuberculosis incidence, elevated primary drug resistance and high clustering rate indicate problems in the present control programs. New control strategies supported by molecular typing might be more effective to reduce tuberculosis.

Molecular epidemiology of pulmonary tuberculosis in belgrade, central serbia

In order to gain precise data on the actual epidemiology of tuberculosis (TB) in Belgrade, central Serbia, we conducted the molecular epidemiological investigation described herein. IS6110 restriction fragment length polymorphism (RFLP) typing of 176 Mycobacterium tuberculosis isolates was performed. These strains were obtained from 48.4% of all patients diagnosed with culture-proven pulmonary TB from April through September 1998 and from May through October 1999. Clusters containing strains with identical RFLP IS6110 patterns were assumed to have arisen from recent transmission. Of the 176 cases, 55 (31.2%) were grouped into 23 clusters ranging in size from two to six patients. Nearly 80% of clustered patients were directly interviewed, and transmission between family-unrelated contacts was found to be predominant in the study population. Classical contact investigation identified only 2 (3.6%) of the 55 clustered patients. The clustering of TB patients was not associated with any demographic or clinical characteristic other than infection with multidrug-resistant (MDR) M. tuberculosis strains. Nearly 70% of MDR strains were clustered, which indicates active transmission of MDR TB in Belgrade. However, this was not observed by conventional epidemiologic surveillance. In conclusion, the first molecular epidemiologic analysis of TB in the region revealed frequent recent transmission of TB and pointed out significant shortcomings of the current concept for conventional contact tracing. The results presented also demonstrate that transmission of MDR TB in Belgrade is not optimally controlled, and they provide support for the development of improved control strategies, including application of molecular methods.

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.

Improved real-time PCR for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis clinical isolates

In this study we designed two pairs of probes for the detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis with real-time PCR procedures. One pair of probes spans the region between codon 510 and 528 of the rpoB gene, and the other one screens for mutation at the regulatory region of the inhA gene. We have evaluated these probes in combination with two other pairs of probes previously described to detect mutations in 20 susceptible and 53 unique resistant M. tuberculosis clinical isolates. We were able to detect nine different mutations affecting five codons of the rpoB gene, two different mutations at codon 315 of the katG gene and a nucleotide substitution (C209T) in the regulatory region of the inhA gene within two hours turnaround.

[Recent transmission of tuberculosis in an area with low incidence: epidemiological and molecular study]

BACKGROUND

Few reports have analysed the transmission of tuberculosis in rural areas with a low incidence of disease.

PATIENTS AND METHOD

A population-based molecular epidemiological study of patients with tuberculosis, diagnosed by culture, was conducted in Segovia (Spain) between 1995 and 1999. Clinical, demographic and epidemiological data were reviewed. Patients whose clinical isolates of Mycobacterium tuberculosis had identical restriction-fragment-length-polymorphism (RFLP) patterns with IS6110 and spoligotyping were included in clusters.

RESULTS

Of 96 patients with positive-culture for M. tuberculosis complex, 6 were considered as false-positive results. The mean incidence rate was 12.3 cases/100,000 inhabitants. Median age was 50.3 (SD: 23.1), 14% was HIV-infected, and 92% of them were living in urban areas (p < 0.01). There were no cases of primary resistance to isoniazid. DNA fingerprint was performed in 87 samples. We identified 8 clusters including 24 patients (27.7%). Clusters had between 2 and 6 cases. Patients aged < 35 years (OR = 3.1; CI 95%, 1.0-9.6) and with lung involvement (OR = 6.8; CI 95%, 1.3-46.4) were more represented in the clusters. Classical epidemiological investigation confirmed a recent transmission in 33% of clustered cases.

CONCLUSIONS

The use of both classical and molecular epidemiology reveals the existence of recent transmission cases of tuberculosis in an area with a low incidence of the disease.

Detection of unsuspected cases of nosocomial transmission of tuberculosis by use of a molecular typing method

The aim of this study was to use restriction fragment length polymorphism to detect unsuspected cases of nosocomial transmission of tuberculosis (TB) among patients who had been admitted to a university hospital. One hundred fifty-one samples of Mycobacterium tuberculosis isolated from patients with pulmonary TB were studied. The isolates from 37 patients (24.5%) defined 11 clusters. None of the patients infected with these cluster isolates had hospital stays that coincided with one another, and for 5.4% of the patients, the epidemiological link was clearly outside the hospital. Previous incarceration was associated with infection with cluster isolates. In addition, 109 patients without TB (41 of whom were infected with human immunodeficiency virus) who shared a room with patients who had TB were followed for 18-60 months. Among the patients who survived, secondary cases of TB due to nosocomial transmission were not detected.

Molecular and conventional epidemiology of Mycobacterium tuberculosis in Botswana: a population-based prospective study of 301 pulmonary tuberculosis patients

Little is known about patterns of tuberculosis (TB) transmission among populations in developing countries with high rates of TB and human immunodeficiency virus (HIV) infection. To examine patterns of TB transmission in such a setting, we performed a population-based DNA fingerprinting study among TB patients in Botswana. Between January 1997 and July 1998, TB patients from four communities in Botswana were interviewed and offered HIV testing. Their Mycobacterium tuberculosis isolates underwent DNA fingerprinting using IS6110 restriction fragment length polymorphism, and those with matching fingerprints were reinterviewed. DNA fingerprints with >5 bands were considered clustered if they were either identical or differed by at most one band, while DNA fingerprints with < or =5 bands were considered clustered only if they were identical. TB isolates of 125 (42%) of the 301 patients with completed interviews and DNA fingerprints fell into 20 different clusters of 2 to 16 patients. HIV status was not associated with clustering. Prior imprisonment was the only statistically significant risk factor for clustering (risk ratio, 1.5; 95% confidence interval, 1.1 to 2.0). In three communities where the majority of eligible patients were enrolled, 26 (11%) of 243 patients overall and 26 (25%) of 104 clustered patients shared both a DNA fingerprint and strong antecedent epidemiologic link. Most of the increasing TB burden in Botswana may be attributable to reactivation of latent infection, but steps should be taken to control ongoing transmission in congregate settings. DNA fingerprinting helps determine loci of TB transmission in the community.

Use of real-time PCR and fluorimetry for rapid detection of rifampin and isoniazid resistance-associated mutations in Mycobacterium tuberculosis

Very fast amplification of DNA in small volumes can be continuously monitored with a rapid cycler that incorporates fluorimetric detection. Primers were designed to amplify a 157-bp fragment of the rpoB gene spanning codons 526 and 531 and a 209-bp fragment of the katG gene spanning codon 315 of Mycobacterium tuberculosis. Most mutations associated with resistance to rifampin (RMP) and isoniazid (INH) in clinical isolates occur in these codons. Two pairs of hybridization probes were synthesized; one in each pair was 3' labeled with fluorescein and hybridized upstream of the codon with the mutation; the other two probes were 5' labeled with LightCycler-Red 640. Each pair of probes recognized adjacent sequences in the amplicon. After DNA amplification was finished by using a LightCycler, the temperature at which the Red 640 probe melted from the product was determined in a 3-min melt program. Twenty M. tuberculosis clinical isolates susceptible to streptomycin, INH, RMP, and ethambutol and 36 antibiotic-resistant clinical M. tuberculosis isolates (16 resistant to RMP, 16 to INH, and 4 to both antimicrobial agents) were amplified, and the presence of mutations was determined using single-strand conformation polymorphism analysis, the LiQor automated sequencer, and the LightCycler system. Concordant results were obtained in all cases. Within 30 min, the LightCycler method correctly genotyped all the strains without the need of any post-PCR sample manipulation. Overall, this pilot study demonstrated that real-time PCR coupled to fluorescence detection is the fastest available method for the detection of RMP and INH resistance-associated mutations in M. tuberculosis clinical isolates.

Usefulness of IS6110-restriction fragment length polymorphism typing of Brazilian strains of Mycobacterium tuberculosis and comparison with an international fingerprint database

Strains of Mycobacterium tuberculosis isolated from 219 different tuberculosis patients, 115 from patients residing in Rio de Janeiro, 79 from Rio Grande do Sul and the remaining from other regions of the country, were analyzed by IS6110-restriction fragment length polymorphism fingerprinting. The IS6110-DNA patterns from these strains were highly polymorphic: 174 different patterns were observed and 25 patterns were shared by 70 isolates (32%). Most strains (93.4%) had multicopy patterns and only 17% of clustered strains had less than six IS6110 copies. Strain clustering was significantly higher for isolates from Rio Grande do Sul (36.7%) in comparison with strains from Rio de Janeiro (22.6%), but only when using high stringency during cluster analysis. Upon screening of an international database containing 3,970 fingerprints of M. tuberculosis strains, 15% of the patterns of Brazilian strains (21% of the strains) were identical to a fingerprint of an isolate from another country and one particular eight-band pattern forming the largest Brazilian cluster was detected in seven additional countries, suggesting that international transmission of tuberculosis from and to Brazil could be occurring frequently. Alternatively,preferential use of certain IS6110 integration sites could also be important in high-copy number strains, having important consequences for the use of databases for epidemiological studies on a large scale.

Molecular epidemiology of tuberculosis in the Nord Department of France during 1995

In order to determine the current situation and to evaluate the human to human transmission of Mycobacterium tuberculosis in Northern France, the genetic polymorphism of strains was studied by using IS6110 fingerprint. One hundred and fifty-eight cases of bacteriologically confirmed tuberculosis were analyzed. One hundred and twenty-six patients (82%) were infected with genetically different isolates and 28 isolates (18%) were grouped into 14 clusters. No risk factors for recent Mycobacterium tuberculosis infections such as age, HIV status, immigrants, living in big cities were identified. This study shows that there was no major epidemic situation of tuberculosis in Northern France in 1995. Tuberculosis was characterized by a low proportion of HIV positive patients and a high proportion of elderly patients.

Molecular analysis of rifampin and isoniazid resistance of Mycobacterium tuberculosis clinical isolates in Seville, Spain

In this study we examined the mechanisms of resistance to rifampin (RMP) and isoniazid (INH) in 352 clinical isolates of Mycobacterium tuberculosis from Sevilla, Spain, using three different molecular methods: 1) PCR-single strand polymorphism analysis; 2) the commercial system Inno-LiPA RTB for RMP resistance; and 3) sequence analysis. Resistance to RMP was found in 21 strains, where the following mutations in the rpoB gene were detected: Ser531-->Leu (n = 14 strains); His526-->Asp (n = 3), Asn518-->Ser (n = 1), Gln513-->Leu (n = 1) and a nine nucleotide deletion (n = 1). Resistance to INH occurred in 29 strains, with mutations observed in: a) katG gene: Ser315-->Thr (n = 12), Ile304-->Val (n = 1), and a partial deletion (n = 4); b) regulatory region of the inhA gene: nucleotide substitution C209T (n = 3). No mutation was found in the ahpC promoter.

Bacteriological and molecular analysis of rifampin-resistant Mycobacterium tuberculosis strains isolated in Australia

To develop a better understanding of the epidemiology and molecular biology of rifampin-resistant Mycobacterium tuberculosis strains in Australia, 50 clinical isolates (33 rifampin-resistant and 17 rifampin-sensitive strains) cultured between 1990 and 1997 were analyzed by a number of bacteriological and molecular techniques. Examination of the drug resistance profiles of the 33 rifampin-resistant isolates revealed that 91% were resistant to rifampin in combination with resistance to isoniazid, 88% were resistant to rifampin on first isolation, and 81% showed cross-resistance with rifabutin. On the basis of the demographic data provided for the patients infected with the rifampin-resistant strains, 90% of the patients were born overseas. Of these patients, 64% developed clinical symptoms within 5 years of residence in Australia. On a molecular level, analysis of the rpoB gene revealed that 97% of the rifampin-resistant isolates had missense mutations within a conserved region of the gene, and eight types of missense mutations were detected. Of the 31 rifampin-resistant isolates that were typed by restriction fragment length polymorphism (RFLP) analysis, 28 distinct patterns were obtained by RFLP analysis with IS6110, and three clusters of genetically related isolates were identified. All isolates within the clusters were from patients who were born overseas and who had the same country of origin. The results from this study provide an overview of the current situation of rifampin resistance in Australia and can serve as a basis for continued monitoring of drug-resistant M. tuberculosis strains isolated within the country.

DNA profiling of Mycobacterium tuberculosis from the Eastern Cape Province of South Africa and the detection of a high level of genetic diversity

The genetic diversity in 502 isolates of Mycobacterium tuberculosis from the Eastern Cape Province of South Africa was DNA-profiled using random amplified polymorphic DNA sequences generated by four primers, and analyzed using the Dice similarity coefficient and the Ward cluster algorithm. Three major cluster groups and ten clusters were detected and shown to be significant at the five percent level using analysis of molecular variance (AMOVA). It is proposed that the three major cluster groups may represent three different entries of M. tuberculosis into South Africa during colonial times. No significant genetic differences could be detected between the urban and rural populations, suggesting that migration may play an important role in the wide transmission of all strains of the organism found in this province. However, a genetic distinction (p = 0.10) could be detected between rural individuals from the southern, more prosperous, region and the northern, less prosperous, regions of the province, which may represent either a limited migration between distant rural communities or a difference in health treatment historically in the two areas. AMOVA indicates the existence of a higher degree of population structure between drug sensitive and drug-resistant individuals than between urban and rural individuals (p = 0.05). Two clusters, C1 and C3, contained a large proportion of the isolates resistant to between one and three first-line drugs. Isolates resistant to more than three antibiotics were genetically diverse, suggesting that they are as yet not being transmitted at a high rate between individuals.