Molecular strain typing of Mycobacterium tuberculosis to confirm cross-contamination in the mycobacteriology laboratory and modification of procedures to minimize occurrence of false-positive cultures

Polymerase Chain Reaction for Mycobacterium tuberculosis

STUDY OBJECTIVES

Screening for pulmonary tuberculosis (TB) in war refugees entering low-prevalence countries for TB is a common policy, but workup strategies are difficult and expensive.

DESIGN

Prospective screening of war refugees for TB by chest radiograph and evaluation of the impact of additional polymerase chain reaction (PCR) testing for Mycobacterium tuberculosis complex (MTB) on clinical management in case of pulmonary infiltrates suspicious for TB.

SETTING

Academic university medical center.

PATIENTS

A total of 3,119 adult war refugees from the Kosovo war were screened by chest radiograph on arrival. Refugees with pulmonary infiltrates suspicious for TB were hospitalized, and a standardized diagnostic workup was performed.

MEASUREMENTS AND RESULTS

Of 3,119 adult war refugees screened for TB, 29 patients (0.9%) were identified with pulmonary infiltrates suspicious for TB; 103 specimens (76 sputa; 27 BAL fluids) were collected for acid-fast smear (AFS), PCR, and culture. The prevalence of culture-proven TB infection in this population was 27.6%. Sensitivity for PCR was higher compared with AFS for all specimens (64% vs 20%; p < 0.01) and also for each refugee with at least one positive specimen finding (100% vs 37.5%; p = 0.025). More important, the negative predictive value for three consecutive PCRs (in two sputa and one BAL) was 100%.

CONCLUSIONS

Repeated PCR testing for MTB in a population of asymptomatic war refugees with pulmonary infiltrates highly suggestive of TB is significantly more sensitive than AFS. Three negative PCR results allow discharge from isolation, thus reducing the economic burden of isolation strategies.

Investigation of Laboratory cross-contamination of Mycobacterium tuberculosis cultures

Many clinicians and laboratory personnel are unaware that a culture positive for Mycobacterium tuberculosis may represent contamination. Laboratory cross-contamination with the M. tuberculosis laboratory control strain (H37Ra) occurs infrequently and therefore demands heightened awareness and recognition. We report 3 occurrences of laboratory cross-contamination from the same laboratory. These occurrences illustrate the importance of interpreting laboratory results in conjunction with the patient's clinical presentation. Failure to recognize laboratory cross-contamination with M. tuberculosis leads to both erroneous administration of unnecessary medications and expenditure of resources required to conduct contact investigations.

Conventional and molecular epidemiology of tuberculosis in Manitoba

BACKGROUND

To describe the demographic and geographic distribution of tuberculosis (TB) in Manitoba, thus determining risk factors associated with clustering and higher incidence rates in distinct subpopulations.

METHODS

Data from the Manitoba TB Registry was compiled to generate a database on 855 patients with tuberculosis and their contacts from 1992-1999. Recovered isolates of M. tuberculosis were typed by IS6110 restriction fragment length polymorphisms. Bivariate and multivariate logistic regression models were used to identify risk factors involved in clustering.

RESULTS

A trend to clustering was observed among the Canadian-born treaty Aboriginal subgroup in contrast to the foreign-born. The dominant type, designated fingerprint type 1, accounts for 25.8% of total cases and 75.3% of treaty Aboriginal cases. Among type 1 patients residing in urban areas, 98.9% lived in Winnipeg. In rural areas, 92.8% lived on Aboriginal reserves. Statistical models revealed that significant risk factors for acquiring clustered tuberculosis are gender, age, ethnic origin and residence. Those at increased risk are: males (p < 0.05); those under age 65 (p < 0.01 for each age subgroup); treaty Aboriginals (p < 0.001), and those living on reserve land (p < 0.001).

CONCLUSION

Molecular typing of isolates in conjunction with contact tracing data supports the notion of the largest ongoing transmission of a single strain of TB within the treaty-status population of Canada recorded to date. This data demonstrates the necessity of continued surveillance of countries with low prevalence of the disease in order to determine and target high-risk populations for concentrated prevention and control measures.

Tuberculosis trends in the United States, 1992-2001

At the time of the last world congress on tuberculosis (TB) in 1992, the United States (US) was experiencing an unprecedented resurgence of TB. Since the mid-1950s, TB incidence had been steadily decreasing, until 1984 when this longstanding trend was reversed. The annual national total of TB cases continued to increase and peaked in 1992 with 26,673 TB cases reported (10.5 TB cases per 100,000 population). A prompt and formidable response from local, state, and federal governments helped curb the resurgence. From 1992 to 2001, total TB incidence decreased by 40% to an all-time low of 15,989 TB cases reported in 2001. The decrease in TB cases from 2000 to 2001, however, was the smallest (2.4%) since the resurgence a decade ago. This report will briefly review the trends and factors associated with the TB resurgence in the late 1980s and early 1990s, and provide a detailed description of specific TB trends in the US between 1992 and 2001.

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.

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

BACKGROUND

In recent years several population based studies using restriction fragment length polymorphism (RFLP) analysis have shown a higher rate of recent transmission of tuberculosis than previously thought. This study was undertaken to determine the transmission patterns of tuberculosis and the potential causes of recent transmission on the island of Gran Canaria (Spain).

METHODS

The strains of all patients diagnosed with tuberculosis confirmed by culture between 1 January 1993 and 31 December 1996 were typed by RFLP using the insertion sequence IS6110. A cluster was defined as two or more isolates with an identical RFLP pattern. Epidemiological linkage through contact tracing was investigated.

RESULTS

Of the total of 719 patients, 153 (21.3%) were excluded because there was inadequate bacterial DNA for genotyping (n=129) or the isolates of Mycobacterium tuberculosis had less than five copies of IS6110 (n=24). The isolates from 409 patients (72.3%) were grouped into 78 different clusters with an estimated 58.5% of the cases being due to recent transmission. Young age was the only significant predictor of clustering. Only in 147 (35.9%) of the 409 patients belonging to a cluster could an epidemiological link be found. 111 patients (19.6%) were identified as having had previous contact with a tuberculosis patient and 81 of them (72.9%) belonged to a cluster. The three largest clusters included 75, 49 and 20 patients, respectively.

CONCLUSION

Recent transmission is frequent among patients with tuberculosis on Gran Canaria and could be associated with certain aspects of control measures. Some of the clusters described in the study could be due to the prevalence of particular strains of M tuberculosis on the island.

False-positive mycobacterium tuberculosis cultures in 44 laboratories in The Netherlands (1993 to 2000): incidence, risk factors, and consequences

False-positive Mycobacterium tuberculosis cultures are a benchmark for the quality of laboratory processes and patient care. We studied the incidence of false-positive cultures, risk factors, and consequences for patients during the period from 1993 to 2000 in 44 peripheral laboratories in The Netherlands. The national reference laboratory tested 8,889 M. tuberculosis isolates submitted by these laboratories. By definition, a culture was false positive (i) if the DNA fingerprint of the isolate was identical to that of an isolate from another patient processed within 7 days in the same laboratory, (ii) if the isolate was taken from a patient without clinical signs of tuberculosis, and/or (iii) if the false-positive test result was confirmed by the peripheral laboratory and/or the public health tuberculosis officer. We identified 213 false-positive cultures (2.4%). The overall incidence of false-positive cultures decreased over the years, from 3.9% in 1993 to 1.1% in 2000. Laboratories with false-positive cultures more often processed less than 3,000 samples per year (P < 0.05). Among 110 patients for whom a false-positive culture was identified from 1995 to 1999, we found that for 36% of the patients an official tuberculosis notification had been provided to the appropriate public health services, 31% of the patients were treated, 14% of the patients were hospitalized, and a contact investigation had been initiated for 16% of the patients. The application of DNA fingerprinting to identify false-positive M. tuberculosis cultures and the provision of feedback to peripheral laboratories are useful instruments to improve the quality of laboratory processes and the quality of medical care.

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.

Estimated costs of false laboratory diagnoses of tuberculosis in three patients

We estimated direct medical and nonmedical costs associated with a false diagnosis of tuberculosis (TB) caused by laboratory cross-contamination of Mycobacterium tuberculosis cultures in Massachusetts in 1998 and 1999. For three patients who received misdiagnoses of active TB disease on the basis of laboratory cross-contamination, the costs totaled U.S. dollars 32618. Of the total, 97% was attributed to the public sector (local and state health departments, public health hospital and laboratory, and county and state correctional facilities); 3% to the private sector (physicians, hospitals, and laboratories); and <1% to the patient. Hospitalizations and inpatient tests, procedures, and TB medications accounted for 69% of costs, and outpatient TB medications accounted for 18%. The average cost per patient was dollars 10873 (range, dollars 1033-dollars 21306). Reducing laboratory cross-contamination and quickly identifying patients with cross-contaminated cultures can prevent unnecessary and potentially dangerous treatment regimens and anguish for the patient and financial burden to the health-care system.

Estimated costs of false laboratory diagnoses of tuberculosis in three patients

We estimated direct medical and nonmedical costs associated with a false diagnosis of tuberculosis (TB) caused by laboratory cross-contamination of Mycobacterium tuberculosis cultures in Massachusetts in 1998 and 1999. For three patients who received misdiagnoses of active TB disease on the basis of laboratory cross-contamination, the costs totaled U.S. dollars 32618. Of the total, 97% was attributed to the public sector (local and state health departments, public health hospital and laboratory, and county and state correctional facilities); 3% to the private sector (physicians, hospitals, and laboratories); and <1% to the patient. Hospitalizations and inpatient tests, procedures, and TB medications accounted for 69% of costs, and outpatient TB medications accounted for 18%. The average cost per patient was dollars 10873 (range, dollars 1033-dollars 21306). Reducing laboratory cross-contamination and quickly identifying patients with cross-contaminated cultures can prevent unnecessary and potentially dangerous treatment regimens and anguish for the patient and financial burden to the health-care system.

A prospective, multicenter study of laboratory cross-contamination of Mycobacterium tuberculosis cultures

A prospective study of false-positive cultures of Mycobacterium tuberculosis that resulted from laboratory cross-contamination was conducted at three laboratories in California. Laboratory cross-contamination accounted for 2% of the positive cultures. Cross-contamination should be a concern when an isolate matches the genotype of another sample processed during the same period.

Pseudo-outbreak of multidrug-resistant Mycobacterium tuberculosis associated with presumed laboratory processing contamination

An investigation prompted by six positive cultures for multidrug-resistant Mycobacterium tuberculosis during a 7-week period found that an unusual resistance pattern, temporal proximity of laboratory processing, and identical DNA fingerprints supported the theory of cross-contamination. Laboratory processing procedures included specimen batching and multi-use vials of buffer solution. Processing procedures were changed and no additional cases of suspected cross-contamination have been observed.

Characterization of a putative alpha-mannosyltransferase involved in phosphatidylinositol trimannoside biosynthesis in Mycobacterium tuberculosis

Phosphatidyl-myo-inositol mannosides (PIMs), lipomannan (LM) and lipoarabinomannan (LAM) are an important class of bacterial factors termed modulins that are found in tuberculosis and leprosy. Although their structures are well established, little is known with respect to the molecular aspects of the biosynthetic machinery involved in the synthesis of these glycolipids. On the basis of sequence similarity to other glycosyltransferases and our previous studies defining an alpha-mannosyltransferase from Mycobacterium tuberculosis, named PimB [Schaeffer, Khoo, Besra, Chatterjee, Brennan, Belisle and Inamine (1999) J. Biol. Chem. 274, 31625-31631], which catalysed the formation of triacyl (Ac(3))-PIM(2) (i.e. the dimannoside), we have identified a related gene from M. tuberculosis CDC1551, now designated pimC. The use of a cell-free assay containing GDP-[(14)C]mannose, amphomycin and membranes from Myobacterium smegmatis overexpressing PimC led to the synthesis of a new alkali-labile PIM product. Fast-atom-bombardment MS established the identity of the new enzymically synthesized product as Ac(3)PIM(3) (i.e. the trimannoside). The results indicate that pimC encodes an alpha-mannosyltransferase involved in Ac(3)PIM(3) biosynthesis. However, inactivation of pimC in Myobacterium bovis Bacille Calmette-Guérin (BCG) did not affect the production of higher PIMs, LM and LAM when compared with wild-type M. bovis BCG, suggesting the existence of redundant gene(s) or an alternate pathway that may compensate for this PimC deficiency. Further analyses, which compared the distribution of pimC in a panel of M. tuberculosis strains, revealed that pimC was present in only 22% of the clinical isolates examined.

An outbreak of bronchoscopy-related Mycobacterium tuberculosis infections due to lack of bronchoscope leak testing

BACKGROUND

Bronchoscopy-related transmission of Mycobacterium tuberculosis is rarely reported. In August 1999, five M tuberculosis-positive bronchial washing culture findings were noted in patients who underwent bronchoscopy in July in a hospital that reported only eight M tuberculosis-positive culture findings from 1995 to 1998, prompting further investigation.

METHODS

A case was defined as a M tuberculosis-positive culture finding from specimens obtained from patients who underwent bronchoscopy during January to August of 1999. Bronchoscopy and laboratory records, procedures, and practices were reviewed. M tuberculosis isolates were compared using restriction fragment length polymorphism (RFLP) analysis.

RESULTS

During July 1999, 19 bronchoscopic procedures were performed in 19 patients. Bronchial washing specimens for mycobacterial culture were obtained from 18 patients. Ten cases were identified. Two case patients, including the index patient, had signs and symptoms of active tuberculosis prior to bronchoscopy. M tuberculosis infections developed in two more case patients despite starting a standard four-drug antituberculous regimen within 3 weeks after bronchoscopy. Six case patients had positive culture findings but no evidence of infection. All M tuberculosis isolates were antituberculosis-drug susceptible, and all but one were indistinguishable by RFLP analysis. Three bronchoscopes were used during the outbreak period; one bronchoscope was used in 9 of the 10 case patients (relative risk, 8.1; 95% confidence interval, 1.3 to 52). A hole was discovered in the sheath of this bronchoscope. Leak testing, a critical step in bronchoscope reprocessing, was not routinely performed at this institution.

CONCLUSIONS

M tuberculosis contamination of the bronchoscope occurred during the index patient's procedure. The hole in the sheath provided access to a space that was difficult to mechanically clean and chemically disinfect. The reprocessing recommendations of bronchoscope manufacturers, including leak testing after each use, should be closely followed.

Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains

A large, genetically related group of Mycobacterium tuberculosis strains, variously called W or Beijing, is distinguished by specific molecular markers and referred to as the W-Beijing family strains. Molecular epidemiological studies suggest that these strains are highly prevalent throughout Asia and the countries of the former Soviet Union and they have also been reported in several other geographical regions, including North America. Although the spread of W-Beijing family strains in diverse populations is well documented, the underlying host-pathogen factors accounting for their continued dissemination and burden of disease have yet to be determined.

The effect of changes in laboratory practices on the rate of false-positive cultures for Mycobacterium tuberculosis

CONTEXT

False-positive cultures for Mycobacterium tuberculosis have been found in nearly all DNA fingerprinting studies, but the effectiveness of interventions to reduce cross-contamination has not been evaluated.

OBJECTIVE

To evaluate whether changes in laboratory policies and procedures reduced the rate of false-positive cultures.

DESIGN

Retrospective study of isolates with matching DNA fingerprints.

SETTING

A mycobacteriology laboratory serving an urban tuberculosis control program and public hospital system.

PATIENTS

All M tuberculosis isolates processed from July 1994 to December 1999.

METHODS

Isolates were fingerprinted using IS6110; pTBN12 was used to fingerprint isolates having fewer than 6 copies of IS6110. We further evaluated all patients having only one positive culture whose DNA fingerprint matched that of another isolate processed in the laboratory within 42 days.

INTERVENTIONS

We changed laboratory policy to reduce the number of smear-positive specimens processed and changed laboratory procedures to minimize the risk of cross-contamination during batch processing.

MAIN OUTCOME MEASURE

The rate of false-positive cultures.

RESULTS

Of 13 940 specimens processed during the study period, 630 (4.5%) from 184 patients and 48 laboratory proficiency specimens grew M tuberculosis. There were no cases (0/184) of probable or definite cross-contamination, compared with the 4% rate (8/199) identified in our previous study (P =.008). We also fingerprinted a convenience sample of isolates from other laboratories in Denver; 13.6% (3/22) of these were false-positive, a rate similar to the 11.9% rate (5/42) identified for other laboratories in our previous study (P =.84).

CONCLUSIONS

Laboratory cross-contamination decreased significantly after relatively simple, inexpensive changes in laboratory policies and practices. Cross-contamination continued to occur in other laboratories in Denver.

Secondary typing of Mycobacterium tuberculosis isolates with matching IS6110 fingerprints from different geographic regions of the United States

Fifty-nine isolates of Mycobacterium tuberculosis obtained from different states in the United States and representing 25 interstate clusters were investigated. These clusters were identified by computer-assisted analysis of DNA fingerprints submitted during 1996 and 1997 by different laboratories participating in the CDC National Genotyping and Surveillance Network. Isolates were fingerprinted with the IS6110 right-hand probe (IS6110-3'), the IS6110 left-hand probe (IS6110-5'), and the probe pTBN12, containing the polymorphic GC-rich sequence (PGRS). Spoligotyping based on the polymorphism in the 36-bp direct-repeat locus was also performed. As a control, 43 M. tuberculosis isolates in 17 clusters obtained from patients in Arkansas during the study period were analyzed. Of the 25 interstate clusters, 19 were confirmed as correctly clustered when all the isolates were analyzed on the same gel using the IS6110-3' probe. Of the 19 true IS6110-3' clusters, 10 (53%) were subdivided by one or more secondary typing methods. Clustering of the control group was virtually identical by all methods. Of the three different secondary typing methods, spoligotyping was the least discriminating. IS6110-5' fingerprinting was as discriminating as PGRS fingerprinting. The data indicate that the IS6110-5' probe not only is a useful secondary typing method but also probably would prove to be a more useful primary typing method for a genotyping network which involves isolates from different geographic regions.

Molecular epidemiology of Mycobacterium tuberculosis in Norway

The incidence of tuberculosis in Norway is one of the lowest in the world, and approximately half of the cases occur in first- and second-generation immigrants. In the present study, the genetic diversity of 92% of all strains of Mycobacterium tuberculosis isolated in Norway in 1994 to 1998 was assessed using restriction fragment length polymorphism (RFLP) analysis, with the insertion sequence IS6110 and the repetitive element DR as probes, to determine the degree of active transmission between patients. The DR probe was used as a secondary molecular marker to support or rule out clustering of strains with fewer than five copies of IS6110. After exclusion of 20 cultures representing laboratory contamination, 573 different IS6110 patterns were found among the 698 strains analyzed. Of these 573 patterns, 542 were observed only once and 31 were shared by 2 to 14 isolates. Among 81 strains (11.5%) carrying fewer than five copies of IS6110, 56 RFLP patterns were found when the results of both the IS6110 and DR methods were combined. Among the 698 strains, 570 were considered to be independent cases. A total of 14.5% of the native Norwegians and 19.7% of the foreign patients were part of a cluster. Thus, the degree of recent transmission of tuberculosis in Norway is low and the great majority of the cases are due to reactivation of previous disease. Transmission between immigrants and native Norwegians is uncommon. Two outbreaks, one among native Norwegians and one mainly among immigrants, have been ongoing for several years, indicating that, even in a low-incidence country such as Norway, with a good national program for tuberculosis surveillance, certain transmission chains are difficult to break.

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.

Molecular identification of streptomycin monoresistant Mycobacterium tuberculosis related to multidrug-resistant W strain

A distinct branch of the Mycobacterium tuberculosis W phylogenetic lineage (W14 group) has been identified and characterized by various genotyping techniques. The W14 group comprises three strain variants: W14, W23, and W26, which accounted for 26 clinical isolates from the New York City metropolitan area. The W14 group shares a unique IS6110 hybridizing banding motif as well as distinct polymorphic GC-rich repetitive sequence and variable number tandem repeat patterns. All W14 group members have high levels of streptomycin resistance. When the streptomycin resistance rpsL target gene was sequenced, all members of this strain family had an identical mutation in codon 43. Patients infected with the W14 group were primarily of non- Hispanic black origin (77%); all were US-born. Including HIV positivity, 84% of the patients had at least one known risk factor for tuberculosis.

Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements

In the last decade, DNA fingerprint techniques have become available to study the interperson transmission of tuberculosis and other mycobacterial infections. These methods have facilitated epidemiological studies at a population level. In addition, the species identification of rarely encountered mycobacteria has improved significantly. This article describes the state of the art of the main molecular typing methods for Mycobacterium tuberculosis complex and non-M. tuberculosis complex (atypical) mycobacteria. Important new insights that have been gained through molecular techniques into epidemiological aspects and diagnosis of mycobacterial diseases are highlighted.

Rapid identification of laboratory contamination with Mycobacterium tuberculosis using variable number tandem repeat analysis

Compared with solid media, broth-based mycobacterial culture systems have increased sensitivity but also have higher false-positive rates due to cross-contamination. Systematic strain typing is rarely undertaken because the techniques are technically demanding and the data are difficult to organize. Variable number tandem repeat (VNTR) analysis by PCR is rapid and reproducible. The digital profile is easily manipulated in a database. We undertook a retrospective study of Mycobacterium tuberculosis isolates collected over an 18-month period following the introduction of the BACTEC MGIT 960 system. VNTR allele profiles were determined with early positive broth cultures and entered into a database with the specimen processing date and other specimen data. We found 36 distinct VNTR profiles in cultures from 144 patients. Three common VNTR profiles accounted for 45% of true-positive cases. By combining VNTR results with specimen data, we identified nine cross-contamination incidents, six of which were previously unsuspected. These nine incidents resulted in 34 false-positive cultures for 29 patients. False-positive cultures were identified for three patients who had previously been culture positive for tuberculosis and were receiving treatment. Identification of cross-contamination incidents requires careful documentation of specimen data and good communication between clinical and laboratory staff. Automated broth culture systems should be supplemented with molecular analysis to identify cross-contamination events. VNTR analysis is reproducible and provides timely results when applied to early positive broth cultures. This method should ensure that patients are not placed on unnecessary tuberculosis therapy or that cases are not falsely identified as treatment failures. In addition, areas where existing procedures may be improved can be identified.

Review of false-positive cultures for Mycobacterium tuberculosis and recommendations for avoiding unnecessary treatment

We reviewed reports of false-positive cultures for Mycobacterium tuberculosis and here propose guidelines for detecting and managing patients with possible false-positive cultures. Mechanisms of false-positive cultures included contamination of clinical devices, clerical errors, and laboratory cross-contamination. False-positive cultures were identified in 13 (93%) of the 14 studies that evaluated > or = 100 patients; the median false-positive rate was 3.1% (interquartile range, 2.2%-10.5%). Of the 236 patients with false-positive cultures reported in sufficient detail, 158 (67%) were treated, some of whom had toxicity from therapy, as well as unnecessary hospitalizations, tests, and contact investigations. Having a single positive culture was a sensitive but nonspecific criterion for detecting false-positive cultures. False-positive cultures for M. tuberculosis are not rare but are infrequently recognized by laboratory and clinical personnel. Laboratories and tuberculosis control programs should develop procedures to identify patients having only 1 positive culture. Such patients should be further evaluated for the possibility of a false-positive culture.

Spoligotyping and polymorphic GC-rich repetitive sequence fingerprinting of mycobacterium tuberculosis strains having few copies of IS6110

Several genetic loci have been utilized to genotype isolates of Mycobacterium tuberculosis. A shortcoming of the most commonly used method, IS6110 fingerprinting, is that it does not adequately discriminate between isolates having few copies of IS6110. This study was undertaken to compare pTBN12 fingerprinting of polymorphic GC-rich repetitive sequence genes and spoligotyping of the direct repeat locus as secondary typing procedures for M. tuberculosis isolates having fewer than six copies of IS6110. A total of 88 isolates (100% of the isolates with fewer than six copies of IS6110 isolated in Arkansas during 1996 and 1997) were included in this study. Among the 88 isolates, 34 different IS6110 patterns were observed, 10 of which were shared by more than 1 isolate, involving a total of 64 isolates. The 64 isolates were subdivided into 13 clusters (containing 37 isolates) and 27 unique isolates based on a combination of IS6110 and pTBN12 fingerprinting and into 11 clusters (containing 51 isolates) and 13 unique isolates based on a combination of IS6110 fingerprinting and spoligotyping. Identical spoligotypes were found among isolates having different IS6110 patterns, as well as among isolates showing different pTBN12 patterns. In contrast, all isolates that had different IS6110 patterns were found to be unique by pTBN12 typing. The clustering rate was 73, 58, and 42%, respectively, for IS6110 fingerprinting alone, IS6110 fingerprinting and spoligotyping combined, and IS6110 and pTBN12 combined fingerprinting. The data indicate that the pTBN12 method has greater discriminating power among low-copy-number isolates than does spoligotyping.

Tuberculosis control and molecular epidemiology in a South African gold-mining community

BACKGROUND

Gold miners have very high rates of tuberculosis. The contribution of infections imported into mining communities versus transmission within them is not known and has implications for control strategies.

METHODS

We did a prospective, population-based molecular and conventional epidemiological study of pulmonary tuberculosis in a group of goldminers. Clusters were defined as groups of patients with Mycobacterium tuberculosis isolates with identical IS6110 DNA fingerprints. We compared the frequency of possible risk factors in the clustered and non-clustered patients whose isolates had fingerprints with more than four bands, and re-interviewed members of 45 clusters.

FINDINGS

Of 448 patients, ten were excluded because they had false-positive cultures. Fingerprints were made in 419 of 438, of which 371 had more than four bands. 248 of 371 were categorised into 62 clusters. At least 50% of tuberculosis cases were due to transmission within the community. Patients who had failed treatment at entry to the study were more likely to be in clusters (adjusted odds ratio 3.41 [95% CI 1.25-9.27]). Patients with multidrug-resistant isolates were more likely to have failed treatment but were less likely to be clustered than those with a sensitive strain (0.27 [0.09-0.83]). HIV infection was common (177 of 370 tested) but not associated with clustering.

INTERPRETATION

Despite a control programme that cures 86% of new cases, most tuberculosis in this mining community is due to ongoing transmission. Persistently infectious individuals who have previously failed treatment may be responsible for one third of tuberculosis cases. WHO targets for cure rates are not sufficient to interrupt transmission of tuberculosis in this setting. Indicators that are more closely linked to the rate of ongoing transmission are needed.

Molecular characterization of Mycobacterium tuberculosis H37Rv/Ra variants: distinguishing the mycobacterial laboratory strain

The Mycobacterium tuberculosis strains H37Rv and H37Ra are the most commonly used controls for M. tuberculosis identification in the clinical and research laboratory setting. To reduce the likelihood of misidentification and possible cross-contamination with this laboratory neotype, it is important to be able to distinguish H37 from clinical isolates. To provide a reference for identifying H37, we used multiple molecular techniques to characterize H37 strains, including 18 of the most frequently used variants available through the American Type Culture Collection. Isolates were genotyped using gene probes to IS6110 and IS1085. In addition, we performed polymorphic GC-rich sequence typing (PGRS), spoligotyping, determination of variable number of tandem repeats (VNTR), and PCR amplification of the mtp40, msx4, and mpp8 polymorphic regions. Southern hybridization with IS6110 provided the most discrimination, differentiating the 18 H37 isolates into 10 discrete patterns made up of 9 H37Rv variants and 1 H37Ra variant. PGRS, IS1085, mpp8, and spoligotyping were not able to distinguish any H37 variants, while VNTR and msx4 discriminated two. Only IS6110 and spoligotyping could distinguish the H37 strain from clinical isolates. In summary, spoligotyping and IS6110 provide a rapid and accurate way to identify H37 contamination, though IS6110 can, in addition, classify many of the H37 variants that would otherwise require phenotypic segregation.

Persistent tuberculosis or specimen contamination?

Cross-contamination during sequential processing of sputum specimens from different patients causes false-positive growth of Mycobacterium tuberculosis in culture. We describe an unusual case of cross-contamination in a 36-year-old man with acquired immunodeficiency syndrome and possible persistent tuberculosis. Culture with 1 of 3 sputum specimens was positive for rifampin-susceptible M tuberculosis. Review of processing revealed that his single culture-positive sputum specimen had followed a sputum specimen from another patient with active pulmonary tuberculosis that was positive in culture for M tuberculosis resistant to rifampin. Molecular strain typing by restriction fragment length polymorphism demonstrated the 2 isolates to be an identical strain of M tuberculosis. Agar proportion susceptibility testing of the rifampin-resistant isolate revealed low numbers of resistant organisms in a range of 1.5% to 3.3%. It was concluded that rifampin-susceptible organisms that constituted approximately 98% of the resistant isolate contaminated sputum from the patient with possible persistent tuberculosis. His culture result was, therefore, considered false positive, not an indication of tuberculosis.

Comparison of the MB/BacT and BACTEC MGIT 960 system for recovery of mycobacteria from clinical specimens

A total of 543 specimens were cultured in parallel with the MB/BacT and BACTEC MGIT 960 systems and on the conventional solid media. Mycobacteria were identified from 95 (17.5%) specimens, including 63 (66.3%) Mycobacterium tuberculosis and 32 (33.7%) nontuberculous mycobacteria. The recovery rates for the MB/BacT, MGIT 960, and solid media were 91.6, 87.4, and 54.7%, respectively, for all mycobacteria; the recovery rates were 93.6, 88.9, and 63.4%, respectively, for M. tuberculosis complex alone, and 87.5, 84.4, and 37.5%, respectively, for all nontuberculous mycobacteria. The mean times to detection of all mycobacteria by individual systems were 13. 9, 8.7, 31.7 days for the MB/BacT, MGIT 960 and solid media, respectively, 13.9, 9.3, 32.9 days for M. tuberculosis alone, and 14. 1, 8.1, 27.2 days for all nontuberculous mycobacteria. The contamination rates of the MB/BacT and MGIT 960 were 10.2 and 5.4%, respectively. With regard to detection times and recovery rates, both automated systems are superior to the conventional media (all p < 0.005). As compared to the MB/BacT, the MGIT 960 detected mycobacterial growth more rapidly (p < 0.001), and had a lower contamination rate (p = 0.003); however, there was no statistically significant difference in recovery rates between these two systems. These results indicate that both MGIT 960 and MB/BacT systems are rapid, sensitive, and efficient methods for the recovery of mycobacteria from clinical specimens.

Application of four molecular techniques for typing outbreak-associated Mycobacterium tuberculosis strains

We applied four molecular techniques for the typing of strains of Mycobacterium tuberculosis associated with outbreaks: RFLP of the IS6110 insertion sequence, spoligotyping, RAPD, and PCR-IS6110. All 4 techniques were applied to 18 strains which were shown by epidemiological data to be involved in 6 outbreaks. All the methods classified the strains into the same groups as the classical epidemiological data did, but RFLP of the IS6110 insertion sequence and spoligotyping are laborious techniques requiring more than a full day's work, whilst RAPD and PCR IS6110 are simple methods easily incorporated into the daily routine. Nevertheless, a large-scale process of standardization and evaluation is necessary in order to be able to establish the true value of the latter two methods as intraspecific characterization markers for M. tuberculosis isolates.

Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains

Mycobacterium tuberculosis (M. tb.) strains differ in the number and locations of a transposon-like insertion sequence known as IS6110. Accurate detection of this sequence can be used as a fingerprint for individual strains, but can be difficult because of noisy data. In this paper, we propose a non-parametric discriminant analysis method for predicting the locations of the IS6110 sequence from microarray data. Polymerase chain reaction extension products generated from primers specific for the insertion sequence are hybridized to a microarray containing targets corresponding to each open reading frame in M. tb. To test for insertion sites, we use microarray intensity values extracted from small windows of contiguous open reading frames. Rank-transformation of spot intensities and first-order differences in local windows provide enough information to reliably determine the presence of an insertion sequence. The nonparametric approach outperforms all other methods tested in this study.

Usefulness of spoligotyping To discriminate IS6110 low-copy-number Mycobacterium tuberculosis complex strains cultured in Denmark

Mycobacterium tuberculosis complex strains cultured in Denmark have been analyzed by IS6110 restriction fragment length polymorphism (RFLP) on a routine basis from 1992 and onwards. Due to the influx of immigrants with tuberculosis, the number of strains harboring only one to five copies of IS6110 has increased steadily. Since the discriminatory power of IS6110 fingerprinting for such strains is poor, we have performed additional genotyping of all low-copy-number strains by the recently described PCR-based method known as spoligotyping. A total of 311 clinical strains were typed: 14 Mycobacterium bovis BCG, 48 M. bovis, and 249 M. tuberculosis strains. Spoligotyping correctly differentiated M. bovis and M. bovis BCG from M. tuberculosis strains, but it did not differentiate M. bovis from M. bovis BCG. All M. bovis BCG strains exhibited identical spoligotype patterns. The discriminatory power of spoligotyping of low-copy-number M. tuberculosis strains was higher than that of IS6110 fingerprinting. Based on RFLP typing solely, 83% of the low-copy-number M. tuberculosis strains were found to form part of a cluster, and 75% were found to form a cluster on the basis of spoligotyping. When the two techniques were combined, the amount of clustering decreased to 55%. The combination of these two techniques might be valuable in studying the epidemiology of M. tuberculosis strains harboring few copies of the IS6110 element.

Inactivation of Mycobacterium tuberculosis for DNA typing analysis

DNA fingerprinting analysis of Mycobacterium tuberculosis is used for epidemiological studies and the control of laboratory cross-contamination. Because standardized procedures are not entirely safe for mycobacteriology laboratory staff, the paper proposes a new technique for the processing of specimens. The technique ensures the inactivation of M. tuberculosis before DNA extraction without the loss of DNA integrity. The control of inactivated cultures should be rigorous and should involve the use of two different culture media incubated for at least 4 months.

Extensive cross-contamination of specimens with Mycobacterium tuberculosis in a reference laboratory

A striking increase in the numbers of cultures positive for Mycobacterium tuberculosis was noticed in a mycobacterial reference laboratory in Campinas, Sao Paulo State, Brazil, in May 1995. A contaminated bronchoscope was the suspected cause of the increase. All 91 M. tuberculosis isolates grown from samples from patients between 8 May and 18 July 1995 were characterized by spoligotyping and IS6110 fingerprinting. Sixty-one of the 91 isolates had identical spoligotype patterns, and the pattern was arbitrarily designated S36. The 61 specimens containing these isolates had been processed and cultured in a 21-day period ending on 1 June 1995, but only 1 sample was smear positive for acid-fast bacilli. The patient from whom this sample was obtained was considered to be the index case patient and had a 4+ smear-positive lymph node aspirate that had been sent to the laboratory on 10 May. Virtually all organisms with spoligotype S36 had the same IS6110 fingerprint pattern. Extensive review of the patients' charts and investigation of laboratory procedures revealed that cross-contamination of specimens had occurred. Because the same strain was grown from all types of specimens, the bronchoscope was ruled out as the outbreak source. The most likely source of contamination was a multiple-use reagent used for specimen processing. The organism was cultured from two of the solutions 3 weeks after mock contamination. This investigation strongly supports the idea that M. tuberculosis grown from smear-negative specimens should be analyzed by rapid and reliable strain differentiation techniques, such as spoligotyping, to help rule out laboratory contamination.

Differences in contributing factors to tuberculosis incidence in U.S. -born and foreign-born persons

To determine the factors contributing to tuberculosis incidence in the U.S.-born and foreign-born populations in San Francisco, California, and to assess the effectiveness of tuberculosis control efforts in these populations, we performed a population-based molecular epidemiologic study using 367 patients with strains of Mycobacterium tuberculosis recently introduced into the city. IS6110-based and PGRS-based restriction fragment length polymorphism (RFLP) analyses were performed on M. tuberculosis isolates. Patients whose isolates had identical RFLP patterns were considered a cluster. Review of public health and medical records, plus patient interviews, were used to determine the likelihood of transmission between clustered patients. None of the 252 foreign-born cases was recently infected (within 2 yr) in the city. Nineteen (17%) of 115 U. S.-born cases occurred after recent infection in the city; only two were infected by a foreign-born patient. Disease from recent infection in the city involved either a source or a secondary case with human immunodeficiency virus (HIV) infection, homelessness, or drug abuse. Failure to identify contacts accounted for the majority of secondary cases. In San Francisco, disease from recent transmission of M. tuberculosis has been virtually eliminated from the foreign-born but not from the U.S.-born population. An intensification of contact tracing and screening activities among HIV-infected, homeless, and drug-abusing persons is needed to further control tuberculosis in the U.S.-born population. Elimination of tuberculosis in both the foreign-born and the U.S. -born populations will require widespread use of preventive therapy.

Mycobacteria as pathogens of respiratory infection

As the result of a formidable effort, the recent TB epidemic in the United States has abated; however, major questions remain as the risk of TB diminishes. Will we maintain an adequate public health effort not only to prevent another resurgence of TB but also to renew our pursuit of TB elimination? Do we have the will to extend the fight against TB worldwide as the TB threat in the United States declines? What is the best way to incorporate new diagnostic technology into routine practice? What are the best strategies for preventing and treating TB in AIDS patients? From the standpoint of NTM lung diseases, the major challenges are to educate clinicians about the variety and clinical presentation of NTM lung pathogens in order to recognize NTM lung disease as early as possible and to maximize treatment options. Hopefully, we can also improve upon the recent unprecedented progress in treatment regimens for NTM diseases of all types.

DNA fingerprinting as an indicator of active transmission of multidrug-resistant tuberculosis in Poland

OBJECTIVES

To use genetic fingerprinting to investigate the epidemiology of tuberculosis (TB) caused by Mycobacterium tuberculosis in Poland, a country with a relatively high incidence of tuberculosis, to improve TB control.

DESIGN

One hundred M. tuberculosis isolates from 98 patients in the Institute of Tuberculosis and Lung Diseases in Warsaw from 1993 to 1995 and 85 isolates obtained from 50 patients in the Hospital of Lung Diseases in Lodz in 1996 were subjected to DNA restriction fragment length polymorphism (RFLP) analysis, using the insertion sequence IS6110 as a probe.

RESULTS

IS6110-associated banding patterns of the M. tuberculosis isolates originating from different localities varied considerably, but isolates from Lodz had a higher degree of similarity. Strains with identical RFLP types were identified in patients of the same family or patients living in the same area, indicating active transmission. Of strains isolated in Warsaw, 45% were resistant to at least one drug, and 35% were resistant to two or more drugs and were classified as multidrug-resistant (MDR). Some drug-resistant isolates were found to have identical banding patterns and originated from epidemiologically linked cases.

CONCLUSIONS

Active transmission of TB, including MDR TB, is occurring in Poland. Active measures must be taken to prevent the spread of drug-resistant TB in Poland and potentially, the rest of Europe.

Nonrandom association of IS6110 and Mycobacterium tuberculosis: implications for molecular epidemiological studies

IS6110 restriction fragment length polymorphism typing is now established as the primary typing method for Mycobacterium tuberculosis. It has been assumed that the position of bands is random. Thus, the discrimination of the technique increases in proportion to the copy number. Two collections of M. tuberculosis were investigated to test this hypothesis. We identified 33 positions in isolates from a Tanzanian collection and 25 positions in isolates from a London, United Kingdom, collection where bands were significantly more likely to be present than would be expected by chance. These data suggest that band position is not random, and this possibility may have an impact on the interpretation of molecular epidemiological studies of M. tuberculosis.

Radiographic spectrum of adult pulmonary tuberculosis in a developed country

SETTING

Bispebjerg Hospital, Department of Pulmonary Medicine P. The referral centre of adult tuberculosis in the municipality of Copenhagen, Denmark.

OBJECTIVE

To evaluate the radiographic spectrum of pulmonary tuberculosis (TB) in adults in a low-prevalence country and to correlate radiographic appearances with bacteriological results, clinical and demographic data.

DESIGN

Retrospective review of medical files on 548 cases with pulmonary TB according to the criteria of WHO.

RESULTS

Usual radiographic pattern of reactivating TB, with upper lobe involvement, was found in 92% (n = 504), eight percent (n = 44) showed unusual X-ray patterns for adults, such as isolated lower lobe infiltrations (n = 19), hilar adenopathy (n = 10), miliary TB (n = 7), tuberculoma (n = 2), pleural effusion (n = 1) and normal chest X-ray (n = 3). Eight-nine percent of cases with cavitary lesions were positive by microscopy.

CONCLUSION

The risk of missing a diagnosis of pulmonary TB may be high if patients present with an X-ray unusual for TB, but this is fortunately seen only in 8% of cases of pulmonary tuberculosis. Unusual X-ray is more commonly found in patients with concomitant disease, such as diabetes and cancer. If chest X-ray shows cavities, but the smear is negative for Mycobacterium, TB is unlikely and further diagnostic procedures should be performed without waiting for culture results.

Molecular fingerprinting of Mycobacterium tuberculosis and risk factors for tuberculosis transmission in Paris, France, and surrounding area

Forty-three percent of the tuberculosis cases reported in France are from the Ile de France region. The incidence of tuberculosis in this region is 33 cases per 100,000 inhabitants, twice the national average. A restriction fragment length polymorphism (RFLP) analysis was performed with clinical isolates of Mycobacterium tuberculosis isolated during 1995 in 10 hospitals in Paris and surrounding areas to detect tuberculosis transmission and define the factors associated with clustering in this population. The molecular markers used were the insertion sequence IS6110 and the direct repeat (DR) sequence. Social, demographic, and clinical data were collected from the patients' medical files. Ten patients with isolates with a single copy of IS6110 were excluded from further analysis. Twenty-four patients with false-positive cultures due to laboratory contamination (based on RFLP analysis with IS6110 and examination of patient data) were also excluded. The study was then conducted with 272 strains isolated from 272 patients. Further fingerprinting was performed by using the DR element with strains with patterns by RFLP analysis with IS6110 that differed by one band only and strains with identical patterns by RFLP analysis with IS6110 and with low numbers of copies of IS6110. The combined use of both markers identified unique patterns for 177 strains and clustered 95 (35.7%) strains in 26 groups, each containing isolates from 2 to 12 patients. The clustering was strongly associated with homelessness and the male sex. It was not associated with age, birth in a foreign country, human immunodeficiency virus positivity, or residence in hostels or prison. Isolates from homeless people were often included in large clusters, and homeless people could be the source of tuberculosis transmission for more than 50% of the clustered patients. These results suggest that homeless people play a key role in the spread of M. tuberculosis in the community and that poor socioeconomic conditions are the main risk factors associated with active tuberculosis transmission.

Results from 5 years of nationwide DNA fingerprinting of Mycobacterium tuberculosis complex isolates in a country with a low incidence of M. tuberculosis infection

Results from DNA fingerprint analyses of Mycobacterium tuberculosis complex isolates from tuberculosis (TB) patients diagnosed during 5 years in Denmark are presented. The lack of success in eradicating TB in this low-incidence country may be explained by an unrecognized high frequency of active TB transmission (57%) among native Danes. Only two strains of M. tuberculosis are responsible for 40% of all clustered cases of TB among Danes.