False-positive results for Mycobacterium celatum with the AccuProbe Mycobacterium tuberculosis complex assay

Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases

Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.

A Case of False-Positive Mycobacterium tuberculosis Caused by Mycobacterium celatum

Mycobacterium celatum is a nontuberculous mycobacterium shown to cause symptoms similar to pulmonary M. tuberculosis. Certain strains have been shown to cross-react with the probes used to detect M. tuberculosis, making this a diagnostic challenge. We present a 56-year-old gentleman who developed signs and symptoms of lung infection with computed tomography scan of the chest showing right lung apex cavitation. Serial sputum samples were positive for acid-fast bacilli and nucleic acid amplification testing identified M. tuberculosis ribosomal RNA, resulting in treatment initiation. Further testing with high performance liquid chromatography showed a pattern consistent with M. celatum. This case illustrates the potential for M. celatum to mimic M. tuberculosis in both its clinical history and laboratory testing due to the identical oligonucleotide sequence contained in both. An increasing number of case reports suggest that early reliable differentiation could reduce unnecessary treatment and public health intervention associated with misdiagnosed tuberculosis.

Biosensor-based detection of tuberculosis

Tuberculosis (TB), caused byMycobacterium tuberculosis(M.tb.), is one of the most prevalent and serious infectious diseases worldwide with an estimated annual global mortality of 1.4 million in 2010.

Tenosynovitis caused by a novel nontuberculous Mycobacterium species initially misidentified as a member of the Mycobacterium tuberculosis complex

We present a case of tenosynovitis caused by a novel, slowly growing, nonchromogenic, nontuberculous mycobacterium (NTM). Originally misidentified as Mycobacterium tuberculosis complex, the NTM cross-reacts with the M. tuberculosis complex nucleic acid hybridization probe, a M. tuberculosis gamma interferon release assay, and is closely related to M. tuberculosis by 16S rRNA gene sequencing.

Mycobacterium shinjukuense lung disease that was successfully treated with antituberculous drugs

An 80-year-old woman was referred to our hospital due to a persistent productive cough. Acid-fast staining and a commercial Mycobacterium tuberculosis identification kit with TRC (TRC kit) were positive. However, a false-positive result on the TRC kit was suspected because Mycobacterium tuberculosis was not detected in the sputum culture. Finally, Mycobacterium shinjukuense was detected in an analysis of the rpoB and hsp65 gene sequences. As the diagnostic criteria proposed by the American Thoracic Society were met, a diagnosis of Mycobacterium shinjukuense lung disease was made. Following treatment with isoniazid, rifampicin and ethambutol with drug susceptibility, the patient's acid-fast culture became negative, and the areas of opacity improved.

The First Report of Mycobacterium celatum Isolation from Domestic Pig (Sus scrofa domestica) and Roe Deer (Capreolus capreolus) and an Overview of Human Infections in Slovenia

Mycobacterium celatum, a slowly growing potentially pathogenic mycobacterium first described in humans, is regarded as an uncommon cause of human infection, though capable of inducing invasive disease in immunocompromised hosts. According to some reports, a serious disease due to M. celatum may also occur in individuals with no apparent immunodeficiency. In animals, an M. celatum-related disease has been described in three cases only: twice in a domestic ferret (Mustela putorius furo) and once in a white-tailed trogon (Trogon viridis). In this paper, we report the first detection of M. celatum in a domestic pig (Sus scrofa domestica) and roe deer (Capreolus capreolus). A nation-wide overview of human M. celatum infections recorded in Slovenia between 2000 and 2010 is also given. Pulmonary disease due to M. celatum was recognized in one patient with a history of a preexisting lung disease.

Mycobacterium shinjukuense sp. nov., a slowly growing, non-chromogenic species isolated from human clinical specimens

Seven isolates of a slowly growing, non-chromogenic Mycobacterium species were obtained from sputum and bronchial lavage fluid samples from elderly patients in different regions of Japan. These isolates were distinguished from related non-tuberculous species by colony morphology, positive results for Tween hydrolysis, catalase at 68 °C, nitrate reductase and pyrazinamidase and negative results for semi-quantitative catalase, urease and arylsulfatase. The mycolic acid pattern obtained by HPLC revealed a single cluster of late-eluting mycolic acids similar to but different from those of Mycobacterium malmoense ATCC 29571(T). The 16S rRNA gene, 16S-23S internal transcribed spacer (ITS), rpoB and hsp65 sequences were unique in comparison with those of other mycobacteria. Comparison of 16S rRNA gene sequences showed that the isolates were most closely related to Mycobacterium tuberculosis H37Rv(T) (21 base differences in 1508 bp; 98.6 % 16S rRNA gene sequence similarity). A representative strain, GTC 2738(T), showed 91.9 % rpoB sequence similarity with Mycobacterium marinum strain M, 95 % hsp65 sequence similarity with Mycobacterium kansasii CIP 104589(T) and 81.1 % 16S-23S ITS sequence similarity with Mycobacterium gordonae ATCC 14470(T). Phylogenetic analysis of concatenated sequences of the 16S rRNA, rpoB and hsp65 genes showed that strain GTC 2738(T) was located on a distinct clade adjacent to M. tuberculosis, M. ulcerans and M. marinum, with bootstrap values of 81 %. DNA-DNA hybridization demonstrated less than 70 % reassociation with type strains of genetically related species and supported the novel species status of the isolates. On the basis of this evidence, a novel species with the name Mycobacterium shinjukuense sp. nov. is proposed. The type strain, isolated from a sputum sample, is strain GTC 2738(T)( = JCM 14233(T) = CCUG 53584(T)).

Rapid diagnostic testing for mycobacterial infections

Tests based on nucleic acid amplification can rapidly detect mycobacteria in clinical samples. These appear to be promising and may change how mycobacterial diseases are diagnosed in the future. Utilization of nucleic acid hybridization and DNA sequencing has enabled the identification of mycobacteria to the species level and detection of mutations associated with antimicrobial resistance. Combining nucleic acid amplification with genotypic identification methods allows detection and identification of mycobacteria directly in clinical samples and, to a limited extent, detection of antimicrobial resistance. IFN-gamma-based assays provide results faster than the tuberculin skin test and address many of its shortcomings, and are thus poised to replace the latter in the coming years.

Specimen dilution improves sensitivity of the amplified Mycobacterium tuberculosis direct test for smear microscopy-positive respiratory specimens

Specimen dilution has been proposed as a strategy to minimize amplified Mycobacterium tuberculosis direct (MTD) test inhibition (N. Pollock, J. Westerling, and A. Sloutsky, Am. J. Clin. Pathol. 126:142-147, 2006; A. Sloutsky, L. L. Han, and B. G. Werner, J. Clin. Microbiol. 42:1547-1551, 2004). We evaluated the impact of respiratory specimen dilution on MTD test accuracy in a public health laboratory. The difference in MTD test sensitivity between the dilution and conventional methods was 15.9% (P = 0.001) for smear microscopy-positive specimens and -3.6% (P = 0.38) for smear microscopy-negative specimens.

The hsp65 gene patterns of less common Mycobacterium and Nocardia spp. by polymerase chain reaction-restriction fragment length polymorphism analysis with capillary electrophoresis

To rapidly identify Mycobacterium and Nocardia spp. without costly probes, we had implemented capillary electrophoresis (CE) in polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis to analyze their 65-kDa heat shock protein (hsp65) gene. The PCR-RFLP analysis with CE (PRACE) involved only one restriction enzyme, HaeIII, and a single electrophoretic separation less than 10 min. Full-range (10-200 bp) RFLP patterns of 12 less common Mycobacterium and 7 Nocardia spp. were investigated. A good agreement was observed between the sizes of restriction fragments resolved by CE and the real sizes deduced from sequence analysis. Including hsp65 gene patterns of 12 Mycobacterium spp. published earlier, differentiation was distinct among 24 Mycobacterium and 7 Nocardia spp. Some closely related species exhibiting similar biochemical characteristics could be well discriminated by an extra HaeIII digestion site. Thus, PRACE offers a nonprobe alternative for rapid identification of various cultured Mycobacterium and Nocardia to the species level.

Molecular clues of a microepidemy among homeless tuberculosis patients in Budapest due to a new and local Mycobacterium tuberculosis clade

In Budapest, the capital of Hungary, one of the most important tuberculosis related risk factors is homelessness. The aim of this retrospective study was the genetic characterization of Mycobacterium tuberculosis strains isolated from 66 homeless tuberculosis patients by spoligotyping and mycobacterial interspersed repetitive unit (MIRU) typing. The study identified a local microepidemy in the district with the highest tuberculosis incidence of Budapest. Further genetic characterization has shown that the microepidemy was due to a locally emerged Budapest-specific lineage of M. tuberculosis. These data may serve as a reference to better monitor and understand the patterns and transmission dynamics of tuberculosis in this at-risk population and is the first report on genetic diversity of M. tuberculosis in today's Hungarians. The findings also indicate that tuberculosis control and prevention steps among the homeless need to be strengthened.

Use of the amplified mycobacterium tuberculosis direct test in a public health laboratory: test performance and impact on clinical care

BACKGROUND

The Amplified Mycobacterium tuberculosis Direct Test (MTD; Gen-Probe; San Diego, CA) is a nucleic-acid amplification test for rapid pulmonary tuberculosis (PTB) diagnosis. In a routine public health setting, test accuracy and impact on clinical decisions are unknown.

METHODS

Retrospectively, we evaluated MTD accuracy and impact on clinical decisions in a public health setting. To estimate MTD accuracy, mycobacterial culture was used as the "gold standard." To evaluate MTD impact on clinical decisions, concordance of clinician presumptive diagnosis (at time of MTD and smear availability) and definitive diagnosis, and duration of nonindicated tuberculosis therapy were determined for smear-positive PTB suspects in a period of MTD availability (MTD group) and a prior period of MTD nonavailability (non-MTD group).

RESULTS

A total of 1,151 respiratory specimens from 638 PTB suspects were analyzed. MTD sensitivity, specificity, positive predictive value, and negative predictive value were 91.7%, 98.7%, 96.7%, and 96.5% overall, respectively; and 98.7%, 97.8%, 98.7%, and 97.8% for smear-positive patients; and 62.2%, 98.9%, 85.2%, and 96.1% for smear-negative patients. In the MTD group, concordance between definitive and clinician presumptive diagnoses was 78% (95% confidence interval [CI], 64 to 88%), similar to that for the non-MTD group (79%; 95% CI, 68.4 to 89.6%). However, concordance between definitive diagnosis and the MTD test was 98% (95% CI, 94.1 to 100%). Median duration of nonindicated tuberculosis treatment was 6 days for the MTD group vs 31 days for the non-MTD group (p = 0.002).

CONCLUSION

In this public health setting, MTD was accurate and rapidly detected more than half of the smear-negative PTB cases. For smear-positive PTB suspects, MTD had excellent concordance with definitive diagnosis, but clinicians often inappropriately initiated TB therapy despite a negative MTD result.

Microepidemy due to a newly identified and specific local Mycobacterium tuberculosis clade among Hungarian homeless patients with tuberculosis in Budapest

Retrospektív tanulmányunkban, amely 2002-ben regisztrált 66 budapesti hajléktalantól származó M. tuberculosis törzset ölel fel, egy helyi mikrojárványt igazoltunk Budapest legmagasabb tuberculosis-incidenciájú kerületében. A molekuláris genetikai vizsgálatok (IS 6110 -RFLP DNS-ujjlenyomat, spoligotyping, mycobacterial interspred repetitive unit < MIRU > és katG - gyrA tipizálás) egy helyi eredetű, Budapest-specifikus M. tuberculosis törzs jelenlétét igazolták. Ugyancsak figyelemre méltó a világszerte elterjedt, virulens Beijing-törzs hiánya. Eredményeink arra utalnak, hogy a hajléktalanok között a tuberculosis kontrolljára nagyobb figyelmet kell fordítani, és a megelőzés területén komolyabb lépésekre van szükség.

Use of smear-positive samples to assess the PCR-based genotype MTBDR assay for rapid, direct detection of the Mycobacterium tuberculosis complex as well as its resistance to isoniazid and rifampin

Isoniazid (INH) and rifampin (RIF) are two of the most important antituberculosis drugs, and resistance to both of these drugs can often result in treatment failure and fatal clinical outcome. Resistance to these two first-line drugs is most often attributed to mutations in the katG, inhA, and rpoB genes. Historically, the identification and testing of the susceptibility of Mycobacterium tuberculosis complex (MTBC) strains takes weeks to complete. Rapid detection of resistance using the PCR-based Genotype MTBDR assay (Hain Lifescience GmbH, Nehren, Germany) has the potential to significantly shorten the turnaround time from specimen receipt to reporting of results of susceptibility testing. Therefore, the aim of the present study was to determine (i) the sensitivity and accuracy of the Genotype MTBDR assay for the detection of MTBC strains and (ii) the ability of the assay to detect the presence of INH and RIF resistance-associated mutations in katG and rpoB from samples taken directly from smear-positive clinical specimens. The results were compared with those obtained with the reference BACTEC 460TB system combined with standard DNA sequencing analysis methods for katG, inhA, and rpoB. A total of 92 drug-resistant and 51 pansusceptible smear-positive specimens were included in the study. The Genotype MTBDR assay accurately and rapidly detected MTBC strains in 94.4% of the 143 specimens and showed a sensitivity of 94.4% for katG and 90.9% for rpoB when used directly on smear-positive specimens. The assay correctly identified INH resistance in 48 (84.2%) of the 57 specimens containing strains with resistance to high levels of INH (0.4 microg/ml) and RIF resistance in 25 (96.2%) of the 26 specimens containing RIF-resistant strains.

Identification of mycobacteria by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry

Classical methods for identification of Mycobacterium species rely on morphology and biochemical profiles. Speciation of a Mycobacterium isolate using these standard methods is a lengthy process based on subjective data interpretation. In this study, Mycobacterium species were characterized by utilizing matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). This technology is designed to provide a characteristic mass spectral fingerprint based on desorbed ions from the cell surface. Thirty-seven strains were analyzed; these represented thirteen species and five subspecies that included the Mycobacterium tuberculosis complex and the M. avium-M. intracellulare complex, as well as rapid- and slow-growing mycobacteria. All 37 strains were analyzed in triplicate, and a database was generated. This method produced species-specific patterns for all but 1 of the 37 isolates and provided reliable differentiation at the strain level. The data suggest that whole-cell MALDI-TOF MS has potential as a rapid and reproducible method for the identification and characterization of Mycobacterium species.

Pyrosequencing as a tool for the identification of common isolates of Mycobacterium sp

Pyrosequencing technology, sequencing by addition, was evaluated for categorization of mycobacterial isolates. One hundred and eighty-nine isolates, including 18 ATCC and Trudeau Mycobacterial Culture Collection (TMC) strains, were studied. There were 38 Mycobacterium tuberculosis complex, 27 M. kansasii, 27 MAI complex, 21 M. marinum, 14 M. gordonae, 20 M. chelonae-abscessus group, 10 M. fortuitum, 5 M. xenopi, 3 M. celatum, 2 M. terrae complex, 20 M. mucogenicum, and 2 M. scrofulaceum. Nucleic acid extracts were prepared from solid media or MGIT broth. Traditional PCR was performed with one of the primers biotinylated; the assay targeted a portion of the 16S rRNA gene that contains a hypervariable region, which has been previously shown to be useful for the identification of mycobacteria. The PSQ Sample Preparation Kit was used, and the biotinylated PCR product was processed to a single-stranded DNA template. The sequencing primer was hybridized to the DNA template in a PSQ96 plate. Incorporation of the complementary nucleotides resulted in light generation peaks, forming a pyrogram, which was evaluated by the instrument software. Thirty basepairs were used for isolate categorization. Manual interpretation of the sequences was performed if the quality of the 30-bp sequence was in doubt or if more than 4 bp homopolymers were recognized. Sequences with more than 5 bp of bad quality were deemed unacceptable. When blasted against GenBank, 179 of 189 sequences (94.7%) assigned isolates to the correct molecular genus or group. Ten M. gordonae isolates had more than 5 bp of bad quality sequence and were not accepted. Pyrosequencing of this hypervariable region afforded rapid and acceptable characterization of common, routinely isolated clinical Mycobacterium sp. Algorithms are recommended for further differentiation with an additional sequencing primer or additional biochemicals.

Conventional and molecular epidemiology of tuberculosis in homeless patients in Budapest, Hungary

In Hungary the incidence of tuberculosis among the homeless population was 676 per 100,000 in 2002. Sixty-nine percent (140 patients) of all homeless tuberculosis patients were notified in Budapest (the capital). Therefore, a retrospective study that included 66 homeless tuberculosis patients notified in Budapest in 2002 was conducted to determine the rate of recent transmission of the disease and medical risk factors and to identify transmission pathways by means of conventional and molecular epidemiologic methods. IS6110 DNA fingerprinting revealed that 71.2% of the isolates could be clustered. Thirty-four (51.5%) patients belonged to five major clusters (size, from 4 to 11 individuals), and 13 (19.7%) belonged to six smaller clusters. Additional analysis of patient records found that 2 (18%) of the 11 patients in cluster A, 3 (37.5%) of the 8 patients in cluster B, and 2 (33%) of the 6 patients in cluster C were residents of the same three homeless shelters during the diagnosis of tuberculosis. Review of the database of the National Tuberculosis Surveillance Center (NTSC) revealed that 21.2% of the cases have not been reported to the NTSC. These findings indicate that the screening and treatment of tuberculosis among the homeless need to be strengthened and also warrant the review of environmental control steps in public shelters. Improvement of adherence of clinicians to surveillance reporting regulations is also necessary.

Mycobacterium celatum, an emerging pathogen and cause of false positive amplified mycobacterium tuberculosis direct test

Mycobacterium celatum is a recently described organism. Herein we describe a case of M. celatum lymphadenitis in an immunocompetent child and the first reported case of a M. celatum infection (lung abscess) in a transplant recipient. A literature review identified 19 other cases of M. celatum infection. Fifteen occurred in patients with the acquired immunodeficiency syndrome. Of these, nine were disseminated and six were localized (primarily to the lungs). The remaining 4 patients were immunocompetent and had localized infection (pneumonitis or lymphadenitis). Diagnosis of M. celatum infection can be challenging as M. celatum can cause false-positive results with the current version of the Amplified Mycobacterium tuberculosis Direct Test (Gen-Probe, San Diego, CA.). Definitive identification is available by DNA sequencing or high-performance liquid chromatography. M. celatum can cause infection in immunocompromised and immunocompetent hosts.

Mycobacterium celatum pulmonary infection

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Use of molecular methods to identify the Mycobacterium tuberculosis complex (MTBC) and other mycobacterial species and to detect rifampin resistance in MTBC isolates following growth detection with the BACTEC MGIT 960 system

A prospective study was organized by using a total of 1,585 consecutive clinical specimens to determine whether biomass obtained from positive growth in the MGIT 960 system could be used directly in AccuProbe DNA hybridization tests, the PCR-based Inno-LiPA Rif.TB (LiPA) assay, and a PCR-based DNA sequencing of the rpoB gene for the rapid identification of the Mycobacterium tuberculosis complex (MTBC) and other mycobacterial species and for the determination of rifampin (RIF) resistance in MTBC strains. The results were compared to routine culture, identification, and susceptibility testing techniques performed on the same samples. The study results revealed that the DNA AccuProbe assay (on the day of growth positivity) readily identified 95.7%, the LiPA assay readily identified 98.6%, and rpoB sequencing readily identified 97.1% of the 70 MTBC isolates from mycobacterial growth indicator tubes (MGIT). In addition, application of the LiPA for the identification and RIF susceptibility testing of the MTBC in growth-positive MGIT resulted in a turnaround time of less than 2 weeks after specimen receipt. Although DNA sequencing of rpoB required a slightly longer (16 days) turnaround time, this method was capable of identifying several species of nontuberculous mycobacteria in addition to identifying MTBC and determining RIF susceptibility or resistance. The molecular methods were also found to rapidly identify RIF-susceptible and -resistant MTBC in two of the three mixed mycobacterial cultures weeks earlier than conventional methods. In conclusion, the biomass obtained in MGIT at the time of growth positivity in the 960 system is sufficient for use in all three molecular tests, and this approach can reduce the turnaround time for reporting results.

Mycobacterium celatum pulmonary infection in the immunocompetent: case report and review

Mycobacterium celatum has been shown to cause disease in immunocompromised patients. We report a case of serious pulmonary infection caused by M. celatum in an apparently immunocompetent patient and review the characteristics of two other reported cases. Clinical and radiologic symptoms and signs included cough, malaise, and weight loss associated with cavitary lesions and pulmonary infiltrates. Although M. celatum is easy to detect in clinical specimens by liquid and solid media, it may be misidentified as a member of the M. tuberculosis complex or as M. xenopi. M. celatum pulmonary infection appears to respond to antimycobacterial chemotherapy, particularly with clarithromycin.

Diagnosis of nontuberculous mycobacterial infections

This section discusses the methods of laboratory diagnosis of nontuberculous mycobacteria (NTM) using conventional biochemical and nutritional requirements, acid-fast smear microscopy, high performance liquid chromatography (HPLC), antibiotic susceptibility testing, and newer genetic methods such as molecular probes, polymerase chain reaction restriction fragment length polymorphism analysis (PRA), and 16S rDNA sequence analysis. This article discusses how laboratory results are applied by clinicians, and some of the difficulties and controversies regarding the diagnosis of NTM disease after the laboratory work is complete.

Laboratory diagnosis of nontuberculous mycobacteria

In conclusion, it is important to realize that there is no "stand alone" assay for the identification of NTM. Many new species may not be recognized in all assays. Newer molecular tests are more accurate for identification than phenotypic tests and have significantly improved turnaround time. Clinical significance of an isolate should be determined, however, before committing resources for the identification of a mycobacterial isolate to the species level. In addition, there are significant differences in the range and quality of services provided by different laboratories. Today, techniques and equipment are increasingly complex and costly, making it more difficult to upgrade every local laboratory to perform these assays. But because specimen delivery and communication of results can be rapidly and easily achieved, utilization of reference laboratories for rarely performed sophisticated tests is a more practical approach.

Newly described or emerging human species of nontuberculous mycobacteria

The advent of molecular testing in the laboratory has brought about the recognition of multiple newly characterized mycobacterial species not previously recognizable with most standard techniques. Some of the species are nonpathogenic, but the majority may cause clinical disease. Each is likely to have its own biology, drug susceptibility pattern, and response to drug/surgical therapy. Thus, it is important to try to recognize these new species in the laboratory. A study of the phenotypic and genotypic characteristics of these new species also may help to elucidate the epidemiology and pathogenesis of these organisms. In addition, there are multiple emerging species of nontuberculous mycobacteria including M. ulcerans, M. haemophilum, M. xenopi, and M. malmoense. [table: see text] These species are being recognized increasingly as a cause of human disease and recovered within the laboratory. The clinician must learn about these new pathogens to recognize them clinically and assist the laboratory in their recovery.

Rapid detection of Mycobacterium tuberculosis in contaminated BACTEC 12B broth cultures by testing with Amplified Mycobacterium Tuberculosis Direct Test

Contamination of broth cultures of acid-fast bacilli (AFB) by bacterial species other than Mycobacterium species frequently occurs. Many of these contaminated cultures require redecontamination and reincubation before the appropriate tests can be performed for identification, significantly affecting the turnaround time for reporting culture results. In this study, the Amplified Mycobacterium Tuberculosis Direct Test (MTD; Gen-Probe) was performed to detect the Mycobacterium tuberculosis complex (MTBC) in 125 BACTEC 12B broth cultures with positive growth indices. Among these, 41 grew non-AFB bacteria only, and all 41 were negative by the MTD. The remaining 84 bottles contained contaminated cultures that grew both AFB and other bacteria or yeasts. Repeat decontamination and reincubation of these specimens required a mean time of 13 days (range, 3 to 40 days). The MTD results were positive for 10 samples, 9 of which were MTBC culture positive and 1 of which grew Myobacterium celatum, a species known to cross-react in the MTD. All cultures growing other mycobacterial species were negative by the MTD. The results of this study demonstrate that the MTD is both sensitive and specific in detecting MTBC in contaminated broth cultures and that, when used selectively, the MTD can potentially rule in or out a diagnosis of MTBC as much as 12 days earlier than using nonamplified DNA probe testing alone can.

Laboratory diagnosis of mycobacterial infections: new tools and lessons learned

Even in the 21st century, tuberculosis continues to be a problem. Although the number of cases continues gradually to decrease in the United States, cases get more difficult to treat, specifically those that are multiple-drug resistant. Infection of one-third of the world's population ensures that tuberculosis will not disappear in the near future. In light of this, it will be useful to know the goals for the health care system and how these goals may be accomplished. Laboratory testing in the mycobacteriology field is experiencing more changes today than ever before. Determining what assays will be most useful to the clinician is a challenge, and acceptance of the new technology by the medical community an even greater one. Clinicians must use the best available resources to determine the most appropriate care for their patients and work together with the laboratory to ensure that the communication channels are open. This review focuses on current state-of-the-art resources useful for accurate and rapid laboratory diagnosis of mycobacterial infections.

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.

Misidentification and diagnostic delay Caused by a false-positive amplified Mycobacterium tuberculosis direct test in an immunocompetent patient with a Mycobacterium celatum infection

The Gen-Probe amplified Mycobacterium tuberculosis direct test can give discrepant results directly in respiratory or cultured samples from patients infected with Mycobacterium celatum, leading to inappropriate therapy for, in our case, an immunocompetent patient.

Progress towards a rapid polymerase chain reaction diagnostic test for the identification of Mycobacterium avium subsp. paratuberculosis in faeces

Hybridization-capture polymerase chain reaction (HC-PCR), a nucleic acid sequence capture technique, was evaluated on faecal samples pooled from 50 sheep and individual faecal samples as a rapid diagnostic test for Mycobacterium avium subsp. paratuberculosis, the causative agent of Johne's disease. The status of each of the faecal samples was determined by radiometric culture. A simpler direct-PCR technique was evaluated on the same samples and was found to be more sensitive than HC-PCR. The lack of sensitivity of HC-PCR was neither due to location nor length of capture probe on IS 900 nor deterioration of the probe but was associated with inefficiencies in liquid phase hybridization and solid phase magnetic bead capture. Direct-PCR using primers from the 5' region of IS 900 was evaluated in a blind trial on 502 pooled faecal samples which were concurrently examined by culture. Twenty-one (64%) of the 33 culture positive pools were detected by direct PCR, representing 11 (79%) of the 14 farms with infected sheep. Direct-PCR was also more sensitive than immunomagnetic bead capture-PCR. Using individual faecal samples, 74% of culture positive samples were detected with direct-PCR compared to 44% with immunomagnetic bead capture-PCR. Direct-PCR from faeces can be used as a rapid means of screening pooled faecal samples for flock diagnosis of Johne's disease in sheep.

Application of the Sherlock Mycobacteria Identification System using high-performance liquid chromatography in a clinical laboratory

There is a growing need for a more accurate, rapid, and cost-effective alternative to conventional tests for identification of clinical isolates of Mycobacterium species. Therefore, the ability of the Sherlock Mycobacteria Identification System (SMIS; MIDI, Inc.) using computerized software and a Hewlett-Packard series 1100 high-performance liquid chromatograph to identify mycobacteria was compared to identification using phenotypic characteristics, biochemical tests, probes (Gen-Probe, Inc.), gas-liquid chromatography, and, when necessary, PCR-restriction enzyme analysis of the 65-kDa heat shock protein gene and 16S rRNA gene sequencing. Culture, harvesting, saponification, extraction, derivatization, and chromatography were performed following MIDI's instructions. Of 370 isolates and stock cultures tested, 327 (88%) were given species names by the SMIS. SMIS software correctly identified 279 of the isolates (75% of the total number of isolates and 85% of the named isolates). The overall predictive value of accuracy (correct calls divided by total calls of a species) for SMIS species identification was 85%, ranging from only 27% (3 of 11) for M. asiaticum to 100% for species or groups including M. malmoense (8 of 8), M. nonchromogenicum (11 of 11), and the M. chelonae-abscessus complex (21 of 21). By determining relative peak height ratios (RPHRs) and relative retention times (RRTs) of selected mycolic acid peaks, as well as phenotypic properties, all 48 SMIS-misidentified isolates and 39 (91%) of the 43 unidentified isolates could be correctly identified. Material and labor costs per isolate were $10.94 for SMIS, $26.58 for probes, and $42.31 for biochemical identification. The SMIS, combined with knowledge of RPHRs, RRTs, and phenotypic characteristics, offers a rapid, reasonably accurate, cost-effective alternative to more traditional methods of mycobacterial species identification.