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

Value of Acid-Fast Bacilli and Fungal Cultures in Foot and Ankle Surgery in a US Hospital System

BACKGROUND

Acid-fast bacilli(AFB) and fungi are generally slow-growing, difficult to culture, and rarely the cause of infection. The goal of this study was to evaluate the value of routinely obtaining AFB and fungal cultures in foot and ankle surgery at a US hospital.

METHODS

A retrospective review was conducted to determine the number of positive AFB and fungal cultures out of the total number of foot and ankle samples tested. Between 2014 and 2019, patients who underwent surgery for a foot and ankle infection for soft tissue infection, septic arthritis, infectious postoperative complications were identified. Charts were reviewed to identify the results of the microbiological tests performed. To determine the value of running AFB and fungal cultures, the costs of each were provided by the microbiology lab at our institution.

RESULTS

Of the 322 patient charts reviewed, there were 434 AFB and 525 fungal cultures performed. None of these cultures were indicated to be positive for AFB (0%), and 22 (4.19%) were positive for fungi. The total labor and material costs were calculated to be $38 767. The AFB cultures cost $23 967, the positive fungal cultures cost $2371, and the negative fungal cultures cost $36 395.36.

CONCLUSION

This 322-case series of surgically managed foot and ankle infections showed 0% and 4.1% positivity rates of AFB and fungal cultures, respectively. Additionally, only 20% of cases with positive cultures were identified as pathologic requiring antifungal treatment. Further analysis is needed to determine best practices for obtaining vs declining to culture for AFB or fungal species, including assessing patient outcomes in the series of culture-positive(fungal-only) cases. Our results suggest that in our clinical setting of a US hospital system, routine fungal and AFB cultures may not be necessary but should be considered for chronic/recalcitrant infections, immunocompromised patients, and those with high surgeon suspicion.

LEVEL OF EVIDENCE

Level IV, case series.

Single-Tube qPCR Detection and Quantitation of Hotspot Mutations Down to 0.01% Variant Allele Fraction

Clinically and biologically, rare DNA sequence variants are significant and informative. However, existing common detection technologies are either complex and time-consuming in workflow, or restricted in the limit of detection (LoD), or do not allow for multiplexing. Blocker displacement amplification (BDA) method can stably and effectively detect and enrich multiple rare variants with LoD around 0.1% variant allele fraction (VAF). Nonetheless, the detailed mutation information has to be identified by additional sequencing technologies. Here, we present allele-specific BDA (As-BDA), a method combining BDA with allele-specific TaqMan (As-TaqMan) probes for effective variant enrichment and simultaneous single nucleotide variant or small insertions and deletions (INDELs) profiling. We demonstrated that As-BDA could detect mutations down to 0.01% VAF. Further, As-BDA could detect up to four mutations with low to 0.1% VAF per reaction using only 15 ng DNA input. The median error of As-BDA in VAF determination is approximately 9.1%. Comparison experiments using As-BDA and droplet digital PCR on peripheral blood mononuclear cell clinical samples showed 100% concordance for samples with mutations at ≥ 0.1% VAF. Hence, we have shown that As-BDA can achieve simultaneous enrichment and identification of multiple targeted mutations within the same reaction with high clinical sensitivity and specificity, thus helpful for clinical diagnosis.

Prevention of Mycobacterium tuberculosis Transmission in Health Care Settings

Patients with tuberculosis (TB) pose a risk to other patients and health care workers, and outbreaks in health care settings occur when appropriate infection control measures are not used. This article discusses strategies to prevent transmission of Mycobacterium tuberculosis within health care settings. All health care facilities should have an operational TB infection control plan that emphasizes the use of a hierarchy of controls (administrative, environmental, and personal respiratory protection). Resources available to clinicians who work in the prevention and investigation of nosocomial transmission of M tuberculosis also are discussed.

Positive Mycobacterium tuberculosis Gastric Lavage Cultures from Asymptomatic Children With Normal Chest Radiography

Mycobacterium tuberculosis culture from gastric lavage from apparently healthy children following tuberculin skin test conversion, despite normal chest radiography (CR), is well known but is a contentious subject. A consensus statement regarding classification of childhood tuberculosis excluded this condition, stating that more data were needed. To assist in this discussion, we reviewed early publications that reported the occurrence of this phenomenon and early anatomical pathology studies that described changes that occur in children following tuberculosis infection. Pathology studies describe frequent cavitation in primary foci in children from whom positive M. tuberculosis cultures might easily arise. These foci were very small in some children who might have normal CR. Positive cultures might also arise from ulcerated mediastinal lymph nodes that are invisible on CR. Young children with recent infection very likely have active primary pulmonary tuberculosis.

False-Positive Mycobacterium tuberculosis Detection: Ways to Prevent Cross-Contamination

The gold standard method for diagnosis of tuberculosis is the isolation of Mycobacterium tuberculosis through culture, but there is a probability of cross-contamination in simultaneous cultures of samples causing false-positives. This can result in delayed treatment of the underlying disease and drug side effects. In this paper, we reviewed studies on falsepositive cultures of M. tuberculosis. Rate of occurrence, effective factors, and extent of false-positives were analyzed. Ways to identify and reduce the false-positives and management of them are critical for all laboratories. In most cases, falsepositive is occurring in cases with only one positive culture but negative direct smear. The three most crucial factors in this regard are inappropriate technician function, contamination of reagents, and aerosol production. Thus, to reduce false-positives, good laboratory practice, as well as use of whole-genome sequencing or genotyping of all positive culture samples with a robust, extra pure method and rapid response, are essential for minimizing the rate of false-positives. Indeed, molecular approaches and epidemiological surveillance can provide a valuable tool besides culture to identify possible false positives.

Laboratory Cross-Contamination of Mycobacterium tuberculosis: A Systematic Review and Meta-analysis

BACKGROUND

Microbiological cultures are the mainstay of the diagnosis of tuberculosis (TB). False-positive TB results lead to significant unnecessary therapeutic and economic burden and are frequently caused by laboratory cross-contamination. The aim of this meta-analysis was to quantify the prevalence of laboratory cross-contamination.

METHODS

Through a systematic review of five electronic databases, we identified studies reporting rates of laboratory cross-contamination, confirmed by molecular techniques in TB cultures. We evaluated the quality of the identified studies using the National Institute of Health (NIH) Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies, and conducted a meta-analysis using standard methodology recommended by the Cochrane Collaboration.

RESULTS

Based on 31 eligible studies evaluating 29,839 TB cultures, we found that 2% (95% confidence intervals [CI] 1-2%) of all positive TB cultures represent false-positive results secondary to laboratory cross-contamination. More importantly, we evaluated the rate of laboratory cross-contamination in cases where a single-positive TB culture was available in addition to at least one negative TB culture, and we found a rate of 15% (95% CI 6-33%). Moreover, 9.2% (91/990) of all patients with a preliminary diagnosis of TB had false-positive results and received unnecessary and potentially harmful treatments.

CONCLUSIONS

Our results highlight a remarkably high prevalence of false-positive TB results as a result of laboratory cross-contamination, especially in single-positive TB cultures, leading to the administration of unnecessary, harmful treatments. The need for the adoption of strict technical standards for mycobacterial cultures cannot be overstated.

A case of Mycobacterium tuberculosis laboratory cross-contamination

SETTING

A laboratory cross-contamination event was suspected because Mycobacterium tuberculosis was unexpectedly detected at a high incidence in the cultures of several clinical specimens at the National Hospital Organization, Tokyo National Hospital, Japan.

OBJECTIVE

To describe a case of Mycobacterium tuberculosis laboratory cross-contamination.

DESIGN

We reviewed the medical records of 20 patients whose clinical specimens were suspected to have been contaminated by Mycobacterium tuberculosis. Variable number of tandem repeat analysis with 15 loci, the Japan Anti-Tuberculosis Association-12, and three additional hyper-variable loci, was performed to identify the cross-contamination event.

RESULTS

The clinical, laboratory, and variable number of tandem repeat data revealed that the cross-contamination had possibly originated from one strongly positive specimen, resulting in false-positive results in 11 other specimens, including a case treated with anti-tuberculosis drugs.

CONCLUSION

Clinical and laboratory data must be re-evaluated when cross-contamination is suspected and variable number of tandem repeat analysis should be used to confirm cross-contamination. Furthermore, original isolates should be stored appropriately, without sub-culturing and genotyping should be performed at the earliest possible for better utilization of variable number of tandem repeat for the identification of cross-contamination.

Sensitivity and specificity of routine diagnostic work-up for tuberculosis in lung clinics in Yogyakarta, Indonesia: a cohort study

Background

Establishing a correct diagnosis is challenging. We aimed to investigate the sensitivity and specificity of routine tuberculosis (TB) diagnostic work-up in lung clinics in Indonesia, a country with the third highest TB burden and the second highest gap between notifications of TB cases and the best estimate of incident cases in the world.

Methods

In the lung clinics of the Province of Yogyakarta, Indonesia, we recruited all consecutive patients with symptoms suggesting TB, aged ≥18 years. Routine TB examination consisted of clinical evaluation, sputum smear microscopy, and chest radiography. For research purposes, we added sputum culture, Human Immunodeficiency Virus (HIV) testing, and follow-up for 1.5 years or 2.5 years if culture results disagreed with the initial clinical diagnosis. The initial diagnosis was considered incorrect if patients did not respond to treatment. We calculated sensitivity and specificity of the TB routine examination using culture and a composite reference standard (CRS – a combination of routine examination, culture, and follow-up) as the reference standards. All analyses were conducted with IBM SPSS Statistics 25 (IBM Corp., Armonk, NY, USA).

Results

Between 2013 and 2015, we included 360 participants, and 21 were excluded due to incomplete data. Among those analyzed, 115 were initially diagnosed with smear-positive TB, 12 with smear-negative TB, and 212 non-TB. In 15 study participants, the diagnosis was changed after median 45 (range: 14–870) days; 14 participants initially not diagnosed with TB were later diagnosed with TB, while one subject initially diagnosed with TB actually did not have TB. Compared with culture and CRS, TB routine examination had sensitivity of 85% (95%CI: 77–91) and 90% (95%CI: 84–94), and specificity of 86.3% (95%CI: 81–91) and 99.5% (95%CI: 97–100), respectively.

Conclusions

A combination of clinical evaluation with sputum microscopy and chest radiography provided high sensitivity and specificity in diagnosing TB in lung clinics; in only 4.4% the diagnosis was incorrect. There is a need to improve routine TB diagnostic work by using clinical evaluation, sputum smear microscopy, and chest radiography all together in other settings, such as in primary health centers.

Trial registration

NCT02219945, clinicaltrials.gov. Registered 19 August 2014 (retrospectively registered).

Reproducibility of positive results for rare pathogens on the FilmArray GI Panel

Though the FilmArray GI Panel has a reported aggregate specificity and reproducibility of >97% and > 99%, respectively, the reproducibility is less understood in clinical practice. We measured the reproducibility of positive results for low-prevalence pathogens. Samples with positive results for selected targets were repeated using a different FilmArray module. Overall, 331 of 373 (89%) results were reproducible. Giardia lamblia (57/57, 100%), Cryptosporidium spp. (61/63, 97%), Cyclospora cayetanensis (34/35, 97%), Plesiomonas shigelloides (17/18, 94%), and Rotavirus A (76/77, 99%) were highly reproducible, while Adenovirus F40/41 (38/54, 70%), Vibrio spp. (8/10, 80%), V. cholerae (3/8, 37.5%), and Yersinia enterocolitica (36/50, 72%) were poorly reproducible. Review of 38 patients with nonreproducible results showed that 19 (50%) had evidence of gastroenteritis and only 6 (16%) had possible infection with the organism that showed a nonreproducible result. Higher false-positive rates with certain targets on FAGP emphasize the need for diagnostic stewardship.

Practice Guidelines for Clinical Microbiology Laboratories: Mycobacteria

Mycobacteria are the causative organisms for diseases such as tuberculosis (TB), leprosy, Buruli ulcer, and pulmonary nontuberculous mycobacterial disease, to name the most important ones. In 2015, globally, almost 10 million people developed TB, and almost half a million patients suffered from its multidrug-resistant form. In 2016, a total of 9,287 new TB cases were reported in the United States. In 2015, there were 174,608 new case of leprosy worldwide. India, Brazil, and Indonesia reported the most leprosy cases. In 2015, the World Health Organization reported 2,037 new cases of Buruli ulcer, with most cases being reported in Africa. Pulmonary nontuberculous mycobacterial disease is an emerging public health challenge. The U.S. National Institutes of Health reported an increase from 20 to 47 cases/100,000 persons (or 8.2% per year) of pulmonary nontuberculous mycobacterial disease among adults aged 65 years or older throughout the United States, with 181,037 national annual cases estimated in 2014. This review describes contemporary methods for the laboratory diagnosis of mycobacterial diseases. Furthermore, the review considers the ever-changing health care delivery system and stresses the laboratory's need to adjust and embrace molecular technologies to provide shorter turnaround times and a higher quality of care for the patients who we serve.

Smelling Pseudomonas aeruginosa infections using a whole-cell biosensor - An alternative for the gold-standard culturing assay

Improved easy-to-use diagnostic tools for infections are in strong demand worldwide. Yet, despite dramatic advances in diagnostic technologies, the gold-standard remains culturing. Here we offer an alternative tool demonstrating that a bacterial biosensor can efficiently detect Pseudomonas aeruginosa infections in patients suffering from otitis externa. Detection was based on specific binding between the biosensor and 2-aminoacetophenone (2-AA), a volatile produced by P. aeruginosa in high amounts. We collected pus samples from ears of 26 subjects exhibiting symptoms of otitis externa. Detection of P. aeruginosa using the biosensor was compared to detection using gold-standard culturing assay and to gas-chromatograph-mass-spectrometry (GC-MS) analyses of 2-AA. The biosensor strain test matched the culture assay in 24 samples (92%) and the GC-MS analyses in 25 samples (96%). With this result in hand, we designed a device containing a whole-cell luminescent biosensor combined with a photo-multiplier tube. This device allowed detection of 2-AA at levels as low as 2 nmol, on par with detection level of GC-MS. The results of the described study demonstrate that the volatile 2-AA serves as an effective biomarker for P. aeruginosa in ear infections, and that activation of the biosensor strain by 2-AA provides a unique opportunity to design an easy-to-use device that can specifically detect P. aeruginosa infections.

Evaluation of a Urine-Based Rapid Molecular Diagnostic Test with Potential to Be Used at Point-of-Care for Pulmonary Tuberculosis: Cape Town Cohort

Tuberculosis (TB) diagnosis among sputum-scarce patients is time consuming. Thus, a nonsputum diagnostic alternative is urgently needed. The Mycobacterium tuberculosis-specific transrenal (Tr) DNA from urine is a potential target for TB diagnostics. In this study, a new urine-based Tr-DNA molecular assay was evaluated for diagnosis of pulmonary tuberculosis among 428 adults suspected of having pulmonary TB (164 HIV positive, 263 HIV negative) from Cape Town, South Africa. Tr-DNA was isolated from 4 mL of EDTA urine, and a rapid, double-stranded, primer-based PCR method was performed targeting the Mycobacterium tuberculosis-specific direct repeat region. Each Tr-DNA eluate was tested in triplicate using an automated molecular analyzer with controls included in each test. With liquid culture used as the gold standard, the Tr-DNA assay showed sensitivity of 42.9% (n = 75/175; 95% CI, 35.4%-50.5%) and specificity of 88.6% (n = 210/237; 95% CI, 83.9%-92.4%). Among HIV-infected patients with TB, sensitivity and specificity were 45.2% and 89.0%, respectively. The combination of smear microscopy and Tr-DNA increased the sensitivity to 83.8% (smear microscopy alone, 75.1%), with 96.6% specificity. This study indicates that Tr-DNA has a moderate specificity with low sensitivity for diagnosis of pulmonary TB. Despite low sensitivity, this diagnostic test may have potential in combination with smear microscopy to support TB diagnosis in HIV-endemic regions, where sputum-scarce patients are common.

Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial

BACKGROUND

RIFAQUIN was a tuberculosis chemotherapy trial in southern Africa including regimens with high-dose rifapentine with moxifloxacin. Here, the application of whole-genome sequencing (WGS) is evaluated within RIFAQUIN for identifying new infections in treated patients as either relapses or reinfections. WGS is further compared with mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) typing. This is the first report of WGS being used to evaluate new infections in a completed clinical trial for which all treatment and epidemiological data are available for analysis.

METHODS

DNA from 36 paired samples of Mycobacterium tuberculosis cultured from patients before and after treatment was typed using 24-loci MIRU-VNTR, in silico spoligotyping and WGS. Following WGS, the sequences were mapped against the reference strain H37Rv, the single-nucleotide polymorphism (SNP) differences between pairs were identified, and a phylogenetic reconstruction was performed.

RESULTS

WGS indicated that 32 of the paired samples had a very low number of SNP differences (0-5; likely relapses). One pair had an intermediate number of SNP differences, and was likely the result of a mixed infection with a pre-treatment minor genotype that was highly related to the post-treatment genotype; this was reclassified as a relapse, in contrast to the MIRU-VNTR result. The remaining three pairs had very high SNP differences (>750; likely reinfections).

CONCLUSIONS

WGS and MIRU-VNTR both similarly differentiated relapses and reinfections, but WGS provided significant extra information. The low proportion of reinfections seen suggests that in standard chemotherapy trials with up to 24 months of follow-up, typing the strains brings little benefit to an analysis of the trial outcome in terms of differentiating relapse and reinfection. However, there is a benefit to using WGS as compared to MIRU-VNTR in terms of the additional genotype information obtained, in particular for defining the presence of mixed infections and the potential to identify known and novel drug-resistance markers.

Trends in Testing for Mycobacterium tuberculosis Complex From US Public Health Laboratories, 2009-2013

OBJECTIVE

We investigated data from US public health laboratories funded through the Centers for Disease Control and Prevention's Tuberculosis Elimination and Laboratory Cooperative Agreement to document trends and challenges in meeting national objectives in tuberculosis (TB) laboratory diagnoses.

METHODS

We examined data on workload and turnaround time from public health laboratories' progress reports during 2009-2013. We reviewed methodologies, laboratory roles, and progress toward rapid detection of Mycobacterium tuberculosis complex through nucleic acid amplification (NAA) testing. We compared selected data with TB surveillance reports to estimate public health laboratories' contribution to national diagnostic services.

RESULTS

During the study period, culture and drug susceptibility tests decreased, but NAA testing increased. Public health laboratories achieved turnaround time benchmarks for drug susceptibility tests at lower levels than for acid-fast bacilli smear and identification from culture. NAA positivity in laboratories among surveillance-reported culture-positive TB cases increased from 26.6% (2355 of 8876) in 2009 to 40.0% (2948 of 7358) in 2013. Public health laboratories provided an estimated 50.9% (4285 of 8413 in 2010) to 57.2% (4210 of 7358 in 2013) of culture testing and 88.3% (6822 of 7727 in 2011) to 94.4% (6845 of 7250 in 2012) of drug susceptibility tests for all US TB cases.

CONCLUSIONS

Public health laboratories contribute substantially to TB diagnoses in the United States. Although testing volumes mostly decreased, the increase in NAA testing indicates continued progress in rapid M tuberculosis complex detection.

Official American Thoracic Society/Infectious Diseases Society of America/Centers for Disease Control and Prevention Clinical Practice Guidelines: Diagnosis of Tuberculosis in Adults and Children

BACKGROUND

Individuals infected with Mycobacterium tuberculosis (Mtb) may develop symptoms and signs of disease (tuberculosis disease) or may have no clinical evidence of disease (latent tuberculosis infection [LTBI]). Tuberculosis disease is a leading cause of infectious disease morbidity and mortality worldwide, yet many questions related to its diagnosis remain.

METHODS

A task force supported by the American Thoracic Society, Centers for Disease Control and Prevention, and Infectious Diseases Society of America searched, selected, and synthesized relevant evidence. The evidence was then used as the basis for recommendations about the diagnosis of tuberculosis disease and LTBI in adults and children. The recommendations were formulated, written, and graded using the Grading, Recommendations, Assessment, Development and Evaluation (GRADE) approach.

RESULTS

Twenty-three evidence-based recommendations about diagnostic testing for latent tuberculosis infection, pulmonary tuberculosis, and extrapulmonary tuberculosis are provided. Six of the recommendations are strong, whereas the remaining 17 are conditional.

CONCLUSIONS

These guidelines are not intended to impose a standard of care. They provide the basis for rational decisions in the diagnosis of tuberculosis in the context of the existing evidence. No guidelines can take into account all of the often compelling unique individual clinical circumstances.

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.

Mycobacteria

The immunocompromised host is at increased risk of Mycobacterium tuberculosis complex and nontuberculous mycobacteria infection. Although Mycobacterium tuberculosis complex is a significant mycobacterial pathogen, nontuberculous mycobacteria causes substantial disease in those with suppressed immune responses. Mycobacterial infections can cause significant morbidity and mortality in this patient population, and rapid identification and susceptibility testing of the mycobacterial species is paramount to patient management and outcomes. Mycobacterial diagnostics has undergone some significant advances in the last two decades with immunodiagnostics (interferon gamma release assay), microscopy (light-emitting diode), culture (automated broth-based systems), identification (direct PCR, sequencing and matrix-assisted laser-desorption ionization–time of flight mass spectrometry) and susceptibility testing (molecular detection of drug resistance from direct specimens or positive cultures). Employing the most rapid and sensitive methods in the mycobacterial laboratory will have a tremendous impact on patient care and, in the case of Mycobacterium tuberculosis complex, in the control of tuberculosis.

Case report of Salmonella cross-contamination in a food laboratory

Background

This paper describes a case of Salmonella cross-contamination in a food laboratory. In 2012, chocolate bars shipped from Belgium to the USA were prevented from entering the USA because a Salmonella Rissen strain had been isolated from one of the chocolate bars in a Belgian food laboratory. However, a retrospective study of the Salmonella isolates sent from the laboratory to the Belgian National Reference Laboratory for Salmonella revealed that 7 weeks prior, a Salmonella Rissen strain has been isolated from fish meal in the same food laboratory. The chocolate bars were not expected to be contaminated with Salmonella because the ingredients all tested negative during the production process. Furthermore, because Salmonella Rissen is only rarely isolated from food, it was hypothesized that the two Salmonella Rissen isolates belonged to the same strain and that the second isolation event in this laboratory was caused by cross-contamination. To confirm this hypothesis, both Salmonella Rissen isolates were fingerprinted using different molecular techniques. To evaluate the discriminatory power of the techniques used, 11 other Salmonella Rissen isolates from different origins were included in the comparison. Pulsed-field gel electrophoresis, repetitive element palindromic PCR and three random amplified polymorphic DNA PCR assays were used.

Results

Repetitive element palindromic PCR and random amplified polymorphic DNA PCR assays were insufficiently discriminatory, whereas pulsed-field gel electrophoresis using the combination of two restriction enzymes showed sufficient discrimination to confirm the hypothesis.

Conclusions

Although cross-contamination in food laboratories are rarely reported, cross-contamination can always occur. Laboratories should therefore always be aware of the possibility of cross-contamination, especially when enrichment is used in the microbiological analysis. Furthermore, it is advised that results showing isolates of the same serotype isolated in a short time frame from unrelated food products should be interpreted carefully and should be confirmed with additional strain typing.

Representativeness of Tuberculosis Genotyping Surveillance in the United States, 2009-2010

Genotyping of Mycobacterium tuberculosis isolates contributes to tuberculosis (TB) control through detection of possible outbreaks. However, 20% of U.S. cases do not have an isolate for testing, and 10% of cases with isolates do not have a genotype reported. TB outbreaks in populations with incomplete genotyping data might be missed by genotyping-based outbreak detection. Therefore, we assessed the representativeness of TB genotyping data by comparing characteristics of cases reported during January 1, 2009-December 31, 2010, that had a genotype result with those cases that did not. Of 22,476 cases, 14,922 (66%) had a genotype result. Cases without genotype results were more likely to be patients <19 years of age, with unknown HIV status, of female sex, U.S.-born, and with no recent history of homelessness or substance abuse. Although cases with a genotype result are largely representative of all reported U.S. TB cases, outbreak detection methods that rely solely on genotyping data may underestimate TB transmission among certain groups.

Acceptability of sputum specimens for diagnosing pulmonary tuberculosis

The evaluation of the quality of a sputum specimen prior to bacterial culture has been an accepted practice. However, optimal sputum criteria for pulmonary tuberculosis (TB) are not well established. We investigated indicators for sputum acceptability in tuberculosis cultures and acid-fast bacilli (AFB) smear. A post-hoc analysis of a randomized trial with 228 sputum specimens from 77 patients was conducted. In the trial, pulmonary TB suspects were requested for collecting three sputum specimens. We performed both TB study (AFB smear and M. tuberculosis culture) and Gram staining in each specimen. By using generalized estimating equations, the association between sputum characteristics and positive TB testings were analyzed. Although acceptable specimens for bacterial pneumonia showed higher TB-culture positive rates than unacceptable specimens (adjusted odds ratio [aOR]=1.66; 95% confidence interval [CI]=1.11-2.49), a specimen with ≥25 white blood cells/low-power field was the better predictor for positive M. tuberculosis cultures (aOR=2.30; 95% CI=1.48-3.58) and acid-fast bacilli smears (aOR=1.85; 95% CI=1.05-3.25). Sputum leukocytosis could be an indicator of sputum acceptability for diagnosing pulmonary tuberculosis.

False-positive tuberculous meningitis due to laboratory contamination: importance of a holistic clinical evaluation

Incidence of tuberculosis in Nebraska is 1.9/100,000 people. Tuberculous meningitis is rare and comprises 1% of extrapulmonary tuberculosis. An elderly Caucasian man presented with fever, headache, altered mentation and a history of tick bite. Cerebrospinal fluid (CSF) analysis showed negative cultures and the patient was treated empirically for tickborne illness. Forty-five days later, CSF nucleic acid amplification test (NAAT) was positive for tuberculosis. On readmission, repeat neurological examination and CSF analysis were benign and the patient was not offered antituberculous treatment. Genotype investigation of the culture and NAAT specimen by the Center for Disease Control confirmed laboratory contamination. The literature reports an incidence of 2-4% for false-positive tuberculosis cultures. Contaminated devices, clerical errors and laboratory errors have been implicated. Laboratory contamination results in smear-negative culture-positive cases. Epidemiological investigation with genotype testing is confirmatory. Detailed clinical assessment with good clinical and laboratory communication and frequent laboratory surveillance is advocated to mitigate these cases.

The combination of real-time PCR and HPLC for the identification of non-tuberculous mycobacteria

We used HPLC and AdvanSure real-time PCR (LG Life Sciences, Korea) to retrospectively analyze non-tuberculous mycobacteria (NTM) in 133 clinical specimens. The specimens were culture-positive for NTM and the HPLC method identified 130 strains of mycobacteria from the cultures (97.7%) at the species level. Among the isolates, 48 Mycobacterium. kansasii (36.1%), 39 M. intracellulare (29.3%), 17 M. avium (12.8%), 16 M. abscessus (12.0%), 6 M. fortuitum (4.5%), 2 M. szulgai (1.5%), 2 M. gordonae (1.5%), and 3 unclassified NTM strains (2.3%) were identified. The real-time PCR assay identified 60 NTM-positive specimens (45.1%), 65 negative specimens (48.9%), and 8 M. tuberculosis (TB)-positive specimens (6.0%). The real-time PCR assay is advantageous because of its rapid identification of NTM. However, in our study, the real-time PCR assay showed relatively low sensitivity (45.1%) when using direct specimens including sputum and bronchoalveolar lavage (BAL) fluid. HPLC is useful as it discriminates NTM at the species level, although it is time-consuming and requires specific equipment and technical expertise. A combination of both methods will be helpful for the rapid and accurate identification of mycobacteria in clinical laboratories.

Performance characteristics of the Cepheid Xpert MTB/RIF test in a tuberculosis prevalence survey

BACKGROUND

Xpert MTB/RIF ("Xpert") is a molecular test for detection of Mycobacterium tuberculosis (MTB) in sputum. Performance characteristics have been established for its use during passive tuberculosis (TB) case detection in symptomatic TB suspects, but Xpert performance has not been assessed in other settings. Objectives were to determine Xpert performance and costs in the context of a TB prevalence survey.

METHODOLOGY/PRINCIPAL FINDINGS

This was a diagnostic sub-study of a TB prevalence survey conducted in gold mining companies in South Africa. Sputa (one per participant) were tested using smear microscopy, liquid culture (reference comparator), and Xpert. Costs were collected using an ingredients approach and analyzed using a public health program perspective. 6893 participants provided a sputum specimen. 187/6893 (2.7%) were positive for MTB in culture, 144/6893 (2.1%) were positive for MTB by Xpert, and 91/6893 (1.3%) were positive for acid fast bacilli by microsocopy. Sensitivity, specificity, positive predictive value, and negative predictive value for detection of MTB by Xpert were 62.6% (95% confidence interval [CI] 55.2, 69.5), 99.6% (99.4, 99.7), 81.3% (73.9, 87.3), and 98.9 (98.6, 98.8); agreement between Xpert and culture was 98.5% (98.2, 98.8). Sensitivity of microscopy was 17.6% (12.5, 23.9). When individuals with a history of TB treatment were excluded from the analysis, Xpert specificity was 99.8 (99.7, 99.9) and PPV was 90.6 (83.3, 95.4) for detection of MTB. For the testing scenario of 7000 specimens with 2.7% of specimens culture positive for MTB, costs were $165,690 for Xpert and $115,360 for the package of microscopy plus culture.

CONCLUSION

In the context of a TB prevalence survey, the Xpert diagnostic yield was substantially higher than that of microscopy yet lower than that of liquid culture. Xpert may be useful as a sole test for TB case detection in prevalence surveys, particularly in settings lacking capacity for liquid culture.

Lung infection caused by Mycobacterium riyadhense confused with Mycobacterium tuberculosis: the first case in Korea

A slowly growing, non-chromogenic mycobacterial strain was isolated from sputum and bronchial lavage fluid samples of a patient presenting with productive cough, blood-tinged sputum, low-grade fever, and weakness. A positive acid-fast bacilli sputum smear result prompted the initiation of an anti-tuberculosis regimen. Multiplex real-time PCR showed a negative result for Mycobacterium tuberculosis complex and a positive result for nontuberculous mycobacteria. The DNA chip test confirmed this organism as a member of the genus Mycobacterium, but could not specify the species. Interestingly, the mycolic acid patterns obtained by HPLC nearly overlapped with those of M. simulans. The sequences of the Mycobacterium 16S rRNA gene and 16S-23S internal transcribed spacer region were unique and were found to have 100% similarity with those of M. riyadhense. After a review of the literature, we report this case as the first Korean case of M. riyadhense lung infection.

Epidemiologic surveillance to detect false-positive Mycobacterium tuberculosis cultures

This study was aimed to investigate the ability of potential indices from epidemiologic surveillance to detect false-positive cultures of Mycobacterium tuberculosis (MTB). All clinical specimens for mycobacterial culture from April 1 to August 31, 2010, were reviewed. Single-positive cultures without relevant clinical and pathologic information were categorized as suspected false-positive cultures. Genotyping methods were used to confirm false-positive cultures. The performance of epidemiologic surveillance indices to detect potential false-positive cultures was evaluated. A total of 14,462 specimens were sent to the laboratory and 214 batches were processed in 107 work days (average 67.6 specimens per batch, ranging from 21 to 130 specimens per batch). Seventy-one single-positive cultures were identified, among which 5 cultures of multidrug-resistant MTB in 1 batch were false-positive, confirmed by genotyping methods. Epidemiologic surveillance with statistical process control charts for single-positive cultures per day showed good performance in epidemiologic surveillance. The false-positive rate was 38.5% in the 13 potential false-positive cultures according to the statistical process control chart for single-positive cultures per day. Although the incidence of tuberculous disease is high in Taiwan, clustering of multidrug-resistant MTB in 1 batch or clustering of single-positive cultures still suggested the occurrence of false-positive MTB cultures. Therefore, epidemiologic surveillance for the clustering of single-positive cultures with the statistical process control chart could be used to monitor the occurrence of false-positive results.

A pivotal registration phase III, multicenter, randomized tuberculosis controlled trial: design issues and lessons learnt from the Gatifloxacin for TB (OFLOTUB) project

Background

There have been no major advances in tuberculosis (TB) drug development since the first East African/British Medical Research Council short course chemotherapy trial 35 years ago. Since then, the landscape for conducting TB clinical trials has profoundly changed with the emergence of HIV infection, the spread of resistant TB bacilli strains, recent advances in mycobacteriological capacity, and drug discovery. As a consequence questions have arisen on the most appropriate approach to design and conduct current TB trials. To highlight key issues discussed: Is a superiority, equivalence, or non-inferiority design most appropriate? What should be the primary efficacy outcome? How to consider re-infections in the definition of the outcome? What is the optimal length of patient follow-up? Is blinding appropriate when treatment duration in test arm is shorter? What are the appropriate assumptions for sample size calculation?

Methods

Various drugs are currently in the development pipeline. We are presenting in this paper the design of the most recently completed phase III TB trial, the OFLOTUB project, which is the pivotal trial of a registration portfolio for a gatifloxacin-containing TB regimen. It is a randomized, open-label, multicenter, controlled trial aiming to evaluate the efficacy and safety of a gatifloxacin-containing 4-month regimen (trial registration: ClinicalTrial.gov database: NCT00216385).

Results

In the light of the recent scientific and regulatory discussions, we discuss some of the design issues in TB clinical trials and more specifically the reasons that guided our choices, in order to best answer the trial objectives, while at the same time satisfying regulatory authority requirements.

Conclusion

When shortening TB treatment, we are advocating for a non-inferiority, non-blinded design, with a composite unfavorable endpoint assessed 12 months post treatment completion, and added trial procedures specifically aiming to: (1) minimize endpoint unavailability; and (2) distinguish between relapse and re-infection.

The Use of High Performance Liquid Chromatography to Speciate and Characterize the Epidemiology of Mycobacteria

OBJECTIVE

We evaluated high-performance liquid chromatography (HPLC) for species identification of mycobacteria from various clinical specimens in an urban hospital in South Korea between January 2005 and December 2009.

METHODS

In the study period 24,774 cultures were completed, yielding the 3215 clinical isolates cultivated for mycobacteria and positive cultures that had mycolic acid investigated by HPLC. For species identification, we compared HPLC patterns of clinical isolates with 33 standard Mycobacterium species.

RESULTS

There were 3 different HPLC groups with single, double, and triple-cluster patterns representing 9, 20, and 4 mycobacterial species, respectively. Species identification rates of HPLC for Mycobacterium tuberculosis and nontuberculous mycobacteria (NTM) were found to be 100% and 95.6%, respectively. Among mycobacterial isolates, 12.1% were NTM-positive. There were 20 different NTM species with frequencies of 0.3%~15.5%.

CONCLUSION

The HPLC method was highly sensitive identifying NTM isolated from clinical specimens.

The frequency and potential clinical impact of non-analytical errors in the RCPA Microbiology QAP 1987-2008

BACKGROUND

Reliable reporting of laboratory results is an important component in the diagnosis and management of infectious diseases. We investigated the frequency of pre- and post-analytical errors by participants in the Royal College of Pathologists of Australasia (RCPA) Microbiology Quality Assurance Program (MQAP).

METHODS

We retrospectively reviewed MQAP data 1987-1991 and 2004-2008. Pre-analytical error rates were based on participants' detection rate of clerical error for patient name and identification number for the given test item. Fictitious errors were defined as the reporting of a labelling error when in fact there was no discrepancy. Post-analytical error rates were based on clear transcription errors resulting in the test result being incorrectly assigned to another test item.

FINDINGS

When there was one clerical error 10.6% of participants failed to report it. When there were two errors 5.3% failed to report either error and 8.8% only reported one error. Fictitious errors were reported by 1.1% of participants. Pre-analytical errors have not decreased over time. Of the 106 items where direct transposition errors were possible, 73 (69%) had at least one participant who transposed the results. During 2004-2008 transposition of mycobacterial smear and culture results occurred in 18% and 16% of participants, respectively.

INTERPRETATIONS

Pre- and post-analytical errors are not rare amongst participants in the RCPA MQAP. These non-analytical components of the testing pathway require improvement because of their potential to adversely affect patient care.

Molecular bacterial load assay, a culture-free biomarker for rapid and accurate quantification of sputum Mycobacterium tuberculosis bacillary load during treatment

A molecular assay to quantify Mycobacterium tuberculosis is described. In vitro, 98% (n = 96) of sputum samples with a known number of bacilli (10(7) to 10(2) bacilli) could be enumerated within 0.5 log(10). In comparison to culture, the molecular bacterial load (MBL) assay is unaffected by other microorganisms present in the sample, results are obtained more quickly (within 24 h) and are seldom inhibited (0.7% samples), and the MBL assay critically shows the same biphasic decline as observed longitudinally during treatment. As a biomarker of treatment response, the MBL assay responds rapidly, with a mean decline in bacterial load for 111 subjects of 0.99 log(10) (95% confidence interval [95% CI], 0.81 to 1.17) after 3 days of chemotherapy. There was a significant association between the rate of bacterial decline during the same 3 days and bacilli ml(-1) sputum at day 0 (linear regression, P = 0.0003) and a 3.62 increased odds ratio of relapse for every 1 log(10) increase in pretreatment bacterial load (95% CI, 1.53 to 8.59).

The Ontario universal typing of tuberculosis (OUT-TB) surveillance program--what it means to you

BACKGROUND

Tuberculosis (TB) is a serious disease that is transmitted primarily by the airborne route. Effective disease control and outbreak management requires the timely diagnosis, isolation and treatment of infected individuals with active disease; contact tracing to identify secondary cases likely to benefit from treatment of latent infection; and laboratory identification or confirmation of epidemiologically linked cases. TB genotyping enables the comparison of Mycobacterium tuberculosis complex (MTBC) strains and the identification of cases that may or may not be linked. The increased availability of molecular methods for genotyping has allowed for greater discrimination of MTBC strains and greatly enhanced understanding of TB transmission patterns.

OBJECTIVE

To improve TB surveillance and control in Ontario, the Public Health Laboratories of the Ontario Agency for Health Protection and Promotion has introduced the Ontario Universal Typing of Tuberculosis (OUT-TB) Surveillance Program.

METHODS

The first isolate from every new TB case will be genotyped with two rapid molecular methods: spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat typing. MTBC isolates with nonunique genotypes and, thus, potentially linked to other TB cases, will also be genotyped by IS6110 restriction fragment length polymorphism analysis.

CONCLUSION

By providing TB control programs using these new genotyping tools, and using traditional and new case investigation methods (eg, social network analysis), this new program will provide a clearer picture of TB in Ontario, and permit more effective use of public health resources and improve disease control.

The realistic performance achievable with mycobacterial automated culture systems in high and low prevalence settings

Background

Diagnostic tests are generally used in situations with similar pre-test probability of disease to where they were developed. When these tests are applied in situations with very different pre-test probabilities of disease, it is informative to model the likely implications of known characteristics of test performance in the new situation. This is the case for automated Mycobacterium tuberculosis (MTB) liquid culture systems for tuberculosis case detection which were developed and are widely used in low burden settings but are only beginning to be applied on a large scale in high burden settings.

Methods

Here we model the performance of MTB liquid culture systems in high and low tuberculosis (TB) prevalence settings using detailed published data concentrating on the likely frequency of cross-contamination events.

Results

Our model predicts that as the TB prevalence in the suspect population increases there is an exponential increase in the risk of MTB cross-contamination events expected in otherwise negative samples, even with equivalent technical performance of the laboratories. Quality control and strict cross-contamination measures become increasingly critical as the burden of MTB infection among TB suspects increases. Even under optimal conditions the realistically achievable specificity of these systems in high burden settings will likely be significantly below that obtained in low TB burden laboratories.

Conclusions

Liquid culture systems can play a valuable role in TB case detection in laboratories in high burden settings, but laboratory workers, policy makers and clinicians should be aware of the increased risks, independent of laboratory proficiency, of cross-contamination events in high burden settings.

Approaches to tuberculosis screening and diagnosis in people with HIV in resource-limited settings

Tuberculosis is the main cause of morbidity and mortality in people living with HIV/AIDS worldwide. Early diagnosis and treatment is essential to addressing the dual epidemic of tuberculosis and HIV. Increasing recognition of the importance of integrating tuberculosis services--including screening--into HIV care has led to global policies and the beginnings of implementation of joint activities at the national level. However, debate remains about the best methods of screening for pulmonary tuberculosis among people living with HIV/AIDS in resource-limited settings. Mycobacterial culture, the gold standard for tuberculosis diagnosis, is too slow and complex to be a useful screening test in such settings. More widely available methods, such as symptom screening, sputum smear microscopy, chest radiography, and tuberculin skin testing have important shortcomings, especially in people living with HIV/AIDS. However, until simpler, cheaper, and more sensitive diagnostics for tuberculosis are available in peripheral healthcare settings, a strategy must be developed that uses current evidence to combine available screening tools.

Evaluation of low-colony-number counts of Mycobacterium tuberculosis on solid media as a microbiological marker of cross-contamination

Low-colony-number counts on solid media are considered characteristic of cross-contamination, although they are normally observed in true-positive cultures from some groups of patients. The aim of this study was to evaluate low-yield growth cultures as a microbiological marker for cross-contamination. We evaluated 106 cultures with <15 colonies from 94 patients, and the proportions of false-positive cultures were 0.9% per sample and 1.1% per patient, which indicates that low-yield growth is not a reliable marker of cross-contamination.

[Identification of mycobacteria species by HPLC and species distribution during five years at Ulsan university hospital]

BACKGROUND

Infections caused by mycobacteria have been significantly increasing. Due to the difficulty of making a decision about the pathogenicity of mycobacteria, species-level identification is very important for patients' diagnosis and treatment. The purpose of this study was to identify mycobacteria species using a high performance liquid chromatography (HPLC) method and to provide an initial database for the distribution of mycobacteria in Korea.

METHODS

Acid fast bacteria isolated from 3,107 clinical specimens were identified by mycolic acid analysis using HPLC. The HPLC patterns were compared with those of standard mycobacteria species.

RESULTS

The HPLC patterns were divided into single, double, and triple cluster groups, each group comprising 9, 20, and 4 species, respectively. Mycobacteria and non-tuberculous mycobacteria (NTM) were identifies by HPLC at the rates of 99.5% and 95.6%, respectively. NTM was isolated in 12.4% of the mycobacteria positive specimens. This study also found that there were 20 different NTM species with the distribution of each species ranging from 0.3% to 15.9% of the total NTM. While the rate of NTM has been increasing in Korea, M. avium-intracellulare, M. fortuitum, and M. chelonae are relatively decreasing, and M. kansasii and M. gordonae are relatively increasing.

CONCLUSIONS

HPLC method was highly discriminative for the identification of NTM in clinical specimens.

Paradoxical worsening of tuberculosis in a heart?lung transplant recipient

We report on a heart-lung transplant recipient who presented with pulmonary tuberculosis (TB) 2.5 months after transplantation and then developed a paradoxical reaction after 4 months of adequate anti-TB treatment. She eventually recovered with anti-TB and high-dose steroid treatments.

METHODS

Using sequential bronchoalveolar lavages, we assessed the inflammatory response in the lung and investigated the alveolar immune response against a Mycobacterium tuberculosis antigen.

RESULTS

The paradoxical reaction was characterized by a massive infiltration of the alveolar space by M. tuberculosis antigen-specific CD4(+) T cells and by the presence of a CD4(-)CD8(-) T lymphocyte subpopulation bearing phenotypic markers (CD16(+)/56(+)) classically associated with NK cells.

CONCLUSION

This case report illustrates that even solid organ transplant recipients receiving intense triple-drug immune suppression may be able to develop a paradoxical reaction during TB treatment. Transplant physicians should be aware of this phenomenon in order to differentiate it from treatment failure.