Unreliable detection of Mycobacterium xenopi by the nonradiometric Bactec MGIT 960 culture system

Mycobacterium avium ssp. paratuberculosis and Crohn's Disease-Diagnostic Microbiological Investigations Can Inform New Therapeutic Approaches

Mycobacterium avium ssp. paratuberculosis (MAP) is the cause of Johne's disease (JD), which is a chronic infectious gastrointestinal disease of ruminants and is often fatal. In humans, MAP has been associated with Crohn's disease (CD) for over a century, without conclusive evidence of pathogenicity. Numerous researchers have contributed to the subject, but there is still a need for evidence of the causation of CD by MAP. An infectious aetiology in CD that is attributable to MAP can only be proven by bacteriological investigations. There is an urgency in resolving this question due to the rising global incidence rates of CD. Recent papers have indicated the "therapeutic ceiling" may be close in the development of new biologics. Clinical trial outcomes have demonstrated mild or inconsistent improvements in therapeutic interventions over the last decades when compared with placebo. The necessity to revisit therapeutic options for CD is becoming more urgent and a renewed focus on causation is essential for progress in identifying new treatment options. This manuscript discusses newer interventions, such as vaccination, FMT, dietary remediation and gut microbiome regulation, that will become more relevant as existing therapeutic options expire. Revisiting the MAP theory as a potential infectious cause of CD, rather than the prevailing concept of an "aberrant immune response" will require expanding the current therapeutic programme to include potential new alternatives, and combinations of existing treatments. To advance research on MAP in humans, it is essential for microbiologists and medical scientists to microscopically detect CWDM and to biologically amplify the growth by directed culture.

A New Culture Method for the Detection of Non-Tuberculous Mycobacteria in Water Samples from Heater-Cooler Units and Extracorporeal Membrane Oxygenation Machines

The isolation of non-tuberculous mycobacteria (NTM) from cultures is particularly laborious due to the potential overgrowth of coexisting non-acid fast bacilli. To reduce the overgrowth of these non-mycobacterial organisms, a decontamination step with NaOH or cetylpyridinium chloride is highly recommended before plating the samples on the culture medium. However, due to their toxicity, decontamination solutions tend to decrease NTM recovery from clinical and environmental samples. Here, we tested an alternative method for NTM recovery based on the use of NTM Elite agar, a selective medium that does not require a decontamination step. Using NTM Elite agar, we were able to detect non-tuberculous mycobacteria in 27.7% (30/108) of water samples analyzed. The average time to NTM detection was 18 days, but some strains required longer to grow, perhaps due to the stressful environmental conditions (periodical disinfection of devices). NTM Elite agar's effectiveness in inhibiting background flora was proven by the isolation of NTM from samples with and without background flora, showing no statistically significant differences in detection rates for different total viable counts of background flora (p = 0.4989). In conclusion, our findings indicate that effective NTM recovery from HCU- and ECMO-derived water samples can be achieved via filtration and direct culture of the filters on NTM Elite agar. This simple procedure can speed up laboratory work and provide an improved method, successfully resulting in low contamination and high detection rate, in addition to being less time-consuming. Its sensitivity and lack of a decontamination step make this protocol particularly useful for monitoring the effectiveness of device disinfection in hospital settings, even in the presence of low NTM loads. Reading timeframes should probably be extended to 7 weeks (i.e., well beyond the standard 4 weeks advised by the manufacturer), in order to isolate even the slow-growing mycobacteria. However, an extended incubation period is not necessary for exclusion of M. chimaera contamination of the devices, as M. chimaera isolation times do not generally exceed 3 weeks.

Prediction of Mycobacterium tuberculosis drug resistance by nucleotide MALDI-TOF-MS

OBJECTIVES

To evaluate the performance of nucleotide matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in predicting the drug resistance of Mycobacterium tuberculosis.

METHODS

A total of 115 rifampin-resistant and 53 rifampin-susceptible tuberculosis (TB) clinical isolates were randomly selected from TB strains stored at -80℃ in the clinical laboratory of Shanghai Pulmonary Hospital. Nucleotide MALDI-TOF-MS was performed to predict the drug resistance using phenotypic susceptibility as the gold standard.

RESULTS

The overall assay sensitivities and specificities of nucleotide MALDI-TOF-MS were 92.2% and 100.0% for rifampin, 90.9% and 98.6% for isoniazid, 71.4% and 81.2% for ethambutol, 85.1% and 93.1% for streptomycin, 94.0% and 100.0% for amikacin, 77.8% and 99.3% for kanamycin, 75.0% and 93.3% for ofloxacin, and 75.0% and 93.3% for moxifloxacin. The concordances between nucleotide MALDI-TOF-MS antimicrobial susceptibility testing (AST) and phenotypic AST were 94.6% (rifampin), 90.1% (isoniazid), 79.2% (ethambutol), 89.9% (streptomycin), 99.4% (amikacin), 97.0% (kanamycin), 88.1% (ofloxacin), and 88.0% (moxifloxacin).

CONCLUSION

Nucleotide MALDI-TOF-MS could be a promising tool for rapid detection of Mycobacterium tuberculosis drug sensitivity to rifampin, isoniazid, ethambutol, streptomycin, amikacin, kanamycin, ofloxacin, and moxifloxacin.

Recovery of Mycobacteria from Heavily Contaminated Environmental Matrices

For epidemiology studies, a decontamination method using a solution containing 4.0% NaOH and 0.5% tetradecyltrimethylammonium bromide (TDAB) represents a relatively simple and universal procedure for processing heavily microbially contaminated matrices together with increase of mycobacteria yield and elimination of gross contamination. A contamination rate only averaging 7.3% (2.4% in Cluster S; 6.9% in Cluster R and 12.6% in Cluster E) was found in 787 examined environmental samples. Mycobacteria were cultured from 28.5% of 274 soil and water sediments samples (Cluster S), 60.2% of 251 samples of raw and processed peat and other horticultural substrates (Cluster R), and 29.4% of 262 faecal samples along with other samples of animal origin (Cluster E). A total of 38 species of slow and rapidly growing mycobacteria were isolated. M. avium ssp. hominissuis, M. fortuitum and M. malmoense were the species most often isolated. The parameters for the quantitative detection of mycobacteria by PCR can be significantly refined by treating the sample suspension before DNA isolation with PMA (propidium monoazide) solution. This effectively eliminates DNA residue from both dead mycobacterial cells and potentially interfering DNA segments present from other microbial flora. In terms of human exposure risk assessment, the potential exposure to live non-tuberculous mycobacteria can be more accurately determined.

Prolongation of incubation time improves clinical diagnosis of Mycobacterium xenopi infection and allows susceptibility testing of mycobacterial strains against multiple antibiotics

OBJECTIVES

Mycobacterium xenopi is a nontuberculous mycobacterium (NTM) whose clinical diagnosis and drug susceptibility studies are frequently hampered by poor in vitro growth. Extending the culture incubation time from 42 days (common-standard) to 56 days could improve the likelihood of diagnosis and provide strains for phenotypic drug susceptibility profiling of this poorly studied but clinically relevant mycobacterium.

METHODS

Time-to-positivity of mycobacterial cultures incubated for 56 days were analysed and compared. Clinical mycobacteriosis was defined by ATS/IDSA criteria. In vitro susceptibility of M. xenopi isolates was tested by broth microdilution.

RESULTS

Of 3852 mycobacteria-positive cultures (26 different mycobacterial species),M. xenopi required by far the longest growth time in culture, exceeding the 42 days commonly used in routine diagnostics in 41.2% of cases versus 4.7% for other NTM and 2.0% for Mycobacterium tuberculosis complex (P<0.001). Prolonging the incubation time to 56 days had a great impact on M. xenopi diagnosis, as 56.3% (27/48) of patients would have not fulfilled the ATS/IDSA criteria at an incubation limited to 42 days. All 40 M. xenopi isolates from patients with clinical mycobacteriosis were fully susceptibility to macrolides and rifamycins in vitro and to moxifloxacin, amikacin and linezolid.

CONCLUSION

These results indicate that a significant percentage (56.3%) of positive culture forM. xenopi would have incorrectly been reported as negative to clinicians without prolonging the incubation time to 56 days. Moreover, 56.3% of patients with M. xenopi disease would have missed the diagnosis along with an appropriate germ-based antimycobacterial treatment, otherwise fully effective.

A Practical Guide to the Role of Ancillary Techniques in the Diagnosis of Infectious Agents in Fine Needle Aspiration Samples

Fine needle aspiration samples and small biopsies provide a minimally invasive diagnostic modality for mass lesions. When an infectious process is suspected based on initial evaluation, ancillary techniques can assist in making a specific diagnosis. Here we review the cytopathology that should prompt additional testing and review the availability and interpretation of special stains, immunohistochemistry, and in situ hybridization. In addition, this review addresses when special cultures may be necessary and the use of newer molecular techniques for pathogen identification.

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.

Failure of BACTEC™ MGIT 960™ to detect <i>Mycobacterium tuberculosis </i> complex within a 42-day incubation period

For the optimal recovery of Mycobacterium tuberculosis from the BACTEC™ Mycobacterium Growth Indicator Tube 960™ system, an incubation period of 42–56 days is recommended by the manufacturer. Due to logistical reasons, it is common practice to follow an incubation period of 42 days. We undertook a retrospective study to document positive Mycobacterium Growth Indicator Tube cultures beyond the 42-day incubation period. In total, 98/110 (89%) were positive for M. tuberculosis complex. This alerted us to M. tuberculosis growth detection failure at 42 days.

Pulmonary Disease Caused by Non-Tuberculous Mycobacteria

Non-tuberculous mycobacteria (NTM) include more than 160 ubiquitous, environmental, acid-fast-staining bacterial species, some of which may cause disease in humans. Chronic pulmonary infection is the most common clinical manifestation. Although patients suffering from chronic lung diseases are particularly susceptible to NTM pulmonary disease, many affected patients have no apparent risk factors. Host and pathogen factors leading to NTM pulmonary disease are not well understood and preventive therapies are lacking. NTM isolation and pulmonary disease are reported to rise in frequency in Europe as well as in other parts of the world. Differentiation between contamination, infection, and disease remains challenging. Treatment of NTM pulmonary disease is arduous, lengthy, and costly. Correlations between results of in vitro antibiotic susceptibility testing and clinical treatment outcomes are only evident for the Mycobacterium avium complex, M. kansasii, and some rapidly growing mycobacteria. We describe the epidemiology of NTM pulmonary disease as well as emerging NTM pathogens and their geographical distribution in non-cystic fibrosis patients in Europe. We also review recent innovations for the diagnosis of NTM pulmonary disease, summarize treatment recommendations, and identify future research priorities to improve the management of patients affected by NTM pulmonary disease.

Macrocolonies (Granules) Formation as a Cause of False-Negative Results in the MGIT 960 System: Cause Analysis and Correlation with Mycobacterial Species

Background. The viable mycobacterial bacilli can sometimes form granules in the Mycobacterium Growth Indicator Tube (MGIT) to produce instrument-negative outcomes when BACTEC MGIT 960 culture is performed. The cause of this phenomenon has never been analyzed. Methods. Thirty-one instrument-negative, granule presenting MGIT vials were collected for conducting acid-fast staining and also liquid and solid subculture. Species identification and drug susceptibility test were performed with the recovered strains. Cultivation test was done by inoculating small amount of bacilli into the MGIT vials. Results. Twenty-four and twenty-nine of the tested MGIT vials were smear and culture positive, respectively. In total, 18, 4, and 7 of the cultivated strains were identified as Mycobacterium tuberculosis complex, M. intracellulare, and M. xenopi, respectively. When a limited amount of bacilli was inoculated, the granule formation was observed for M. xenopi strains in the MGIT system. Conclusions. The granules observed in the instrument-negative MGIT vials consisted of viable bacilli, which emphasized the need of visual inspection to increase recovery rate. Limited bacterial load and specific species might be the cause of granule forming.

Rapid Diagnosis of Tuberculosis by Real-Time High-Resolution Imaging of Mycobacterium tuberculosis Colonies

Culture remains the cornerstone of diagnosis for pulmonary tuberculosis, but the fastidiousness of Mycobacterium tuberculosis may delay culture-based diagnosis for weeks. We evaluated the performance of real-time high-resolution imaging for the rapid detection of M. tuberculosis colonies growing on a solid medium. A total of 50 clinical specimens, including 42 sputum specimens, 4 stool specimens, 2 bronchoalveolar lavage fluid specimens, and 2 bronchial aspirate fluid specimens were prospectively inoculated into (i) a commercially available Middlebrook broth and evaluated for mycobacterial growth indirectly detected by measuring oxygen consumption (standard protocol) and (ii) a home-made solid medium incubated in an incubator featuring real-time high-resolution imaging of colonies (real-time protocol). Isolates were identified by Ziehl-Neelsen staining and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Use of the standard protocol yielded 14/50 (28%) M. tuberculosis isolates, which is not significantly different from the 13/50 (26%) M. tuberculosis isolates found using the real-time protocol (P = 1.00 by Fisher's exact test), and the contamination rate of 1/50 (2%) was not significantly different from the contamination rate of 2/50 (4%) using the real-time protocol (P = 1.00). The real-time imaging protocol showed a 4.4-fold reduction in time to detection, 82 ± 54 h versus 360 ± 142 h (P < 0.05). These preliminary data give the proof of concept that real-time high-resolution imaging of M. tuberculosis colonies is a new technology that shortens the time to growth detection and the laboratory diagnosis of pulmonary tuberculosis.

Microbiological diagnosis of nontuberculous mycobacterial pulmonary disease

Pulmonary disease is by far the most frequent disease caused by nontuberculous mycobacteria (NTM). To diagnose NTM pulmonary disease (NTM-PD), patients should have symptoms and radiologic signs suggestive of NTM-PD, and cultures of multiple respiratory tract samples must grow the same NTM species. Thus, the microbiological laboratory has a central role in the diagnosis of NTM-PD. This review summarizes currently available data on techniques involved in the microbiological diagnosis of NTM-PD, and aims to provide a framework for optimal microbiological diagnosis.

Growth detection failures by the nonradiometric Bactec MGIT 960 mycobacterial culture system

Mycobacterial growth in liquid culture can go undetected by automated, nonradiometric growth detection systems. In our laboratory, instrument-negative tubes from the Bactec MGIT 960 system are inspected visually for clumps suggestive of mycobacterial growth, which (if present) are examined by acid-fast smear analysis. A 3-year review demonstrated that ∼1% of instrument-negative MGIT cultures contained mycobacterial growth and that 10% of all cultures yielding mycobacteria were instrument negative. Isolates from instrument-negative MGIT cultures included both tuberculous and nontuberculous mycobacteria.

Evaluation of BioFM liquid medium for culture of cerebrospinal fluid in tuberculous meningitis to identify Mycobacterium tuberculosis

The present study was designed to evaluate the sensitivity and specificity of liquid culture medium (BioFM broth) for the diagnosis of tuberculous meningitis (TBM) in cerebrospinal fluid (CSF). CSF samples from 200 patients (TBM group = 150 and non-TBM group = 50) were tested for culture of Mycobacterium tuberculosis in BioFM liquid culture medium. Out of 150 TBM cases, 120 were found to be culture positive, indicating a sensitivity of 80% in BioFM broth within 2-3 weeks of inoculation. Positive cultures were also observed for CSF from 32 (64%) out of 50 non-TBM patients in BioFM liquid culture medium within 4 days of sample inoculation. Therefore, according to our study, BioFM broth system yielded 80% sensitivity [95% confidence interval (CI): 67-93%] and 36% specificity (95% CI: 57-98%) for TBM diagnosis. Our results indicate that although BioFM broth allows the detection of positive cultures within a shorter time, it has a high potential for contamination or for the coexistence of M. tuberculosis and non-tuberculous meningitis (NTM). This coexistence may go undetected or potentially lead to erroneous reporting of results.