Laboratory diagnosis of nontuberculous mycobacteria

Fast, simple and cheap: method modified from conventional cultivation for tuberculosis diagnosis allows seeding on Löwenstein-Jensen of any swab-embedded pulmonary samples decontaminated with sodium hydroxide

Background

Few tuberculosis (TB) control programmes in low-income countries have access to culture facilities in their primary care diagnostic centres and this scenario may have worsened with the coronavirus disease 2019 pandemic. Thus the aim was to develop and evaluate a simpler TB test that allows seeding on Löwenstein–Jensen (LJ) medium of several swab-embedded samples decontaminated with sodium hydroxide (NaOH).

Methods

A cotton swab containing each sample was decontaminated in NaOH before being dipped into a slightly acidic solution to neutralize the pH in order to allow the culture to develop on LJ medium. Samples (n=543) from suspected or confirmed pulmonary TB were analysed in two phases: standardization (n=167) and evaluation of the study method (n=376).

Results

The study method showed sensitivity >95% and specificity >93% using Ogawa–Kudoh (OK) and modified Petroff (MP) as standards and was comparable to MP-LJ (p>0.05) and slightly superior to OK (p=0.03) for sputum culture and more comprehensive than the latter for other pulmonary specimens.

Conclusions

This article reports a more comprehensive, simpler and less costly method for diagnosing TB in the laboratory with fewer economic resources and biosafety equipment. Thus a patent application was filed (BR1020190103841).

Case Series and Review of the Literature of Mycobacterium chelonae Infections of the Lower Extremities

Mycobacterium chelonae infections involving the lower extremities are rare clinical entities that present a diagnostic challenge given its diverse clinical presentations ranging from superficial (e.g., cellulitis, painful vesicular lesions) to deep (e.g., tenosynovitis) infections. We present 1 cases of M chelonae infections of the feet diagnosed 6 to 12 months after initial symptoms representing the difficulty of diagnosing this condition. Both cases were successfully managed with aggressive surgical debridement and long durations of antibiotic therapy with long-term care. A comprehensive review of the literature of M chelonae infections of the lower extremities was performed to provide summary data on the presenting symptoms, examination findings, predisposing conditions, and management approaches of this rare, but emerging clinical entity. Our cases and comprehensive review serve to raise awareness of atypical mycobacterial infections, including M chelonae, and advocate for the early consideration of mycobacterial cultures in the diagnostic workup of chronic lower extremity infections especially in the setting of poor initial response to standard antibacterial therapies.

Nontuberculous mycobacteria in China: incidence and antimicrobial resistance spectrum from a nationwide survey

BACKGROUND

Information on the prevalence and resistance spectrum of nontuberculous mycobacteria (NTM) in China is mainly based on regional or local data. To estimate the proportion of NTM cases in China, a national survey of NTM pulmonary disease was carried out based on acid-fast positive sputum samples collected in 2013.

METHODS

Sputum samples collected from enrolled presumptive cases in 72 nationwide tuberculosis surveillance sites from the 31 provinces in the mainland of China were cultured using L-J medium at the National tuberculosis reference laboratory (NTRL). MALDI-TOF MS identified the species of re-cultured strains, and minimal inhibitory concentrations (MICs) were determined to evaluate the drug susceptibility of NTM isolates. Data analysis used statistical software SPSS version 22.0 for Windows statistical package.

RESULTS

Of 4917 mycobacterial isolates cultured, 6.4% [317/4917, 95% confidence interval (CI) 5.8%-7.2%] were confirmed as NTM, among which 7.7% (287/3709, 95% CI 6.9%-8.6%) were from the southern region. In inland and coastal China, 87.7% (95% CI 78.7%-93.2%) and 50.0% (95% CI 43.7%-56.3%) of isolates, respectively, were slow-growing mycobacteria (SGM), with the remaining rapid growing mycobacteria (RGM). A total of 29 species were detected, Mycobacterium abscessus had higher clarithromycin-inducible resistance rates than M. massiliense (65.67% vs 2.22%). M. kansasii presented lower resistance rates in linezolid and moxifloxacin than M. avium-intracellulare complex (3.23% vs 66.67%, 0 vs 47.22%) and other SGM (3.23% vs 38%, 0 vs 26%).

CONCLUSIONS

More NTM pulmonary disease was observed in the south and coastal China (P < 0.01). SGM was widely distributed, and more RGM are present in southern and coastal China (P < 0.01). The antimicrobial resistance spectrum of different NTM species was significantly different and accurate species identification would be facilitated to NTM pulmonary disease treatment.

Mycobacterial Infections in the Hand and Wrist

Mycobacterial hand infections are uncommon. These infections have an indolent course and are marked by variable and nonspecific presentations, often leading to diagnostic and treatment delays. The pathogens involved in mycobacterial hand infections include Mycobacterium tuberculosis complex, atypical mycobacteria, and M leprae. Initial treatment involves a combination of long-term antibiotics and surgical débridement to cure the infection. Reconstructive procedures aid in restoring hand function lost secondary to the disease.

Of tuberculosis and non-tuberculous mycobacterial infections - a comparative analysis of epidemiology, diagnosis and treatment

Pulmonary diseases due to mycobacteria cause significant morbidity and mortality to human health. In addition to tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), recent epidemiological studies have shown the emergence of non-tuberculous mycobacteria (NTM) species in causing lung diseases in humans. Although more than 170 NTM species are present in various environmental niches, only a handful, primarily Mycobacterium avium complex and M. abscessus, have been implicated in pulmonary disease. While TB is transmitted through inhalation of aerosol droplets containing Mtb, generated by patients with symptomatic disease, NTM disease is mostly disseminated through aerosols originated from the environment. However, following inhalation, both Mtb and NTM are phagocytosed by alveolar macrophages in the lungs. Subsequently, various immune cells are recruited from the circulation to the site of infection, which leads to granuloma formation. Although the pathophysiology of TB and NTM diseases share several fundamental cellular and molecular events, the host-susceptibility to Mtb and NTM infections are different. Striking differences also exist in the disease presentation between TB and NTM cases. While NTM disease is primarily associated with bronchiectasis, this condition is rarely a predisposing factor for TB. Similarly, in Human Immunodeficiency Virus (HIV)-infected individuals, NTM disease presents as disseminated, extrapulmonary form rather than as a miliary, pulmonary disease, which is seen in Mtb infection. The diagnostic modalities for TB, including molecular diagnosis and drug-susceptibility testing (DST), are more advanced and possess a higher rate of sensitivity and specificity, compared to the tools available for NTM infections. In general, drug-sensitive TB is effectively treated with a standard multi-drug regimen containing well-defined first- and second-line antibiotics. However, the treatment of drug-resistant TB requires the additional, newer class of antibiotics in combination with or without the first and second-line drugs. In contrast, the NTM species display significant heterogeneity in their susceptibility to standard anti-TB drugs. Thus, the treatment for NTM diseases usually involves the use of macrolides and injectable aminoglycosides. Although well-established international guidelines are available, treatment of NTM disease is mostly empirical and not entirely successful. In general, the treatment duration is much longer for NTM diseases, compared to TB, and resection surgery of affected organ(s) is part of treatment for patients with NTM diseases that do not respond to the antibiotics treatment. Here, we discuss the epidemiology, diagnosis, and treatment modalities available for TB and NTM diseases of humans.

Identification of Nontuberculous Mycobacteria from Clinical Isolates and Specimens using AdvanSure Mycobacteria GenoBlot Assay

The aim of this study was to evaluate the clinical performance of AdvanSure GenoBlot assay using nontuberculous mycobacteria (NTM) isolates and clinical specimens. A total of 136 NTM isolates and 176 clinical specimens were used in this study. AdvanSure Mycobacteria GenoBlot assay was performed according to the manufacturer's instructions. We compared the results with those of 16S rRNA and rpoB genes sequencing. Out of the 136 NTM isolates, 111 (81.6%) were correctly identified to the species level using the GenoBlot assay. The final concordance rate was 89.7% (122/136), including 11 Mycobacterium genus positive control (GPC) results for uncommon NTM. The most common NTM, M. avium, M. fortuitum, M. gordonae, M. intracellulare, M. chelonae, M. abscessus, and M. kansasii, were correctly identified using the GenoBlot assay. For 176 organisms in clinical specimens, 117 were identified to the species level, including single species for 111 specimens and two species for 6 specimens. The final detection and identification rates for clinical specimens were 94.9% and 66.5%, respectively. The AdvanSure GenoBlot assay performs well in identifying the most common NTM, and would be useful in a clinical laboratory.

Nontuberculous mycobacterial pulmonary disease diagnosed by two methods: a prospective cohort study

Background

Microbiological criteria for diagnosing nontuberculous mycobacterial pulmonary disease (NTM-PD) include positive culture results from at least two separately expectorated sputum specimens or one bronchial washing or lavage. However, the clinical similarities and differences between patients diagnosed by these two methods remain unclear. We compared clinical features and prognoses of patients with NTM-PD diagnosed from both specimen types.

Methods

We analysed data from patients who participated in the Seoul National University Hospital NTM-PD cohort (ClinicalTrials.gov identifier: NCT01616745). Baseline demographics, symptoms, radiographic findings, disease progression, and treatment responses were summarized and compared between patients diagnosed from sputum specimens and patients diagnosed from bronchoscopic specimens.

Results

Three hundred forty-seven patients were included in the analyses. Of these, 279 (80.4%) were diagnosed from two separately expectorated sputum specimens, and 68 (19.6%) were diagnosed from bronchoscopic specimens. Patients diagnosed from sputum specimens had more frequent and severe cough, sputum, postnasal drip, and high St. George’s Respiratory Questionnaire scores. However, the extent and severity of the radiographic lesions, disease progression, and treatment responses were similar for both groups. Further analysis based on the following three groups (sputum culture positive, sputum culture negative/bronchoscopy, and scanty sputum/bronchoscopy groups) suggested that the scanty sputum/bronchoscopy group appeared to have the worst prognosis in terms of both time to progression and time to culture conversion.

Conclusions

Although some symptoms and quality of life were worse in patients with NTM-PD diagnosed from sputum specimens, their prognoses were similar to those of patients diagnosed by bronchoscopic specimen. We recommend bronchoscopic sampling for patients in whom NTM-PD is suspected clinically or radiographically, especially those who have no or scanty sputum.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4078-0) contains supplementary material, which is available to authorized users.

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.

Cutaneous Nontuberculous Mycobacterial Infections in Alberta, Canada: An Epidemiologic Study and Review

Background:

Cutaneous infections caused by nontuberculous mycobacteria (NTM) occur infrequently. Nonetheless, the incidence of NTM infections is reported to be increasing. In Canada, cutaneous NTM infections have not been well described.

Objectives:

A database review from 2006 to 2016 was done to assess species frequency, incidence, and trends of the most common cutaneous NTMs in the province of Alberta, Canada. We also reviewed major diagnostic and epidemiologic aspects of NTM cutaneous infections with a focus on Mycobacterium marinum.

Results:

A database search identified 244 cases of NTM infections. Mycobacterium avium-intracellulare complex had the highest incidence, causing 64% of cases. Rapid growers ( Mycobacterium abscessus, Mycobacterium chelonae, Mycobacterium fortuitum) caused 23% and M marinum 13%. Information on infection site was available for 117 cases. There was no difference noted in sex distribution; however, differences in age groups between species were noted.

Conclusions:

The incidence of NTM cutaneous infections in Alberta, Canada, was reported for the first time and the incidence of M marinum was found to be similar to that reported in the worldwide literature. Patients’ age groups were different between species. Knowledge of the unique microbiological features of NTMs and the role of the diagnostic laboratory are important.

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.

Mycobacterial Infections in Solid Organ and Hematopoietic Stem Cell Transplantation

Mycobacterial infections are uncommon in solid organ and hematopoietic stem cell transplant recipients but carry significant morbidity and mortality. Donor screening strategies for tuberculosis should be emphasized in high-risk populations. Both tuberculosis and nontuberculous mycobacterial infections can have pulmonary and extrapulmonary manifestations of infections. Recommended treatment regimens typically involve multiple drugs with significant adverse effects and drug interactions.

Identification of nontuberculous mycobacteria using multilocous sequence analysis of 16S rRNA, hsp65, and rpoB

BACKGROUND

The isolation of nontuberculous mycobacteria (NTM) from clinical specimens has increased, and they now are considered significant opportunistic pathogens. The aims of this study were to develop a database and interpretive criteria for identifying individual species. In addition, using clinical isolates, we evaluated the clinical usefulness of 16S rRNA, hsp65, and rpoB as target genes for this method.

METHODS

The sequences of NTM for 16S rRNA, hsp65, and rpoB were collected from GenBank and checked by manual inspection. Clinical isolates collected between 2005 and 2010 were used for DNA extraction, polymerase chain reaction, and sequencing of these three genes. We constructed a database for the genes and evaluated the clinical utility of multilocus sequence analysis (MLSA) using 109 clinical isolates.

RESULTS

A total 131, 130, and 122 sequences were collected from GenBank for 16S rRNA, hsp65, and rpoB, respectively. The percent similarities of the three genes ranged from 96.57% to 100% for the 16S rRNA gene, 89.27% to 100% for hsp65, and 92.71% to 100% for rpoB. When we compared the sequences of 109 clinical strains with those of the database, the rates of species-level identification were 71.3%, 86.79%, and 81.55% with 16S rRNA, hsp65, and rpoB, respectively. We could identify 97.25% of the isolates to the species level when we used MLSA.

CONCLUSION

There were significant differences among the utilities of the three genes for species identification. The MLSA technique would be helpful for identification of NTM.

The epidemiology and geographic distribution of nontuberculous mycobacteria clinical isolates from sputum samples in the eastern region of China

Background

Nontuberculous mycobacteria (NTM) have been reported to be increasing worldwide and its geographic distribution differs by region. The aim of this study was to describe the epidemiology and distribution of NTM in the eastern part of China.

Methods

Sputum samples were collected from 30 surveillance sites for tuberculosis drug resistance test from May 1, 2008 to December 31, 2008. Identification was performed using a biochemical test, multiplex PCR and GenoType Mycobacterium CM/AS assay.

Results

A total of 1779 smear positive clinical isolates were obtained, of which 60 (3.37%) were NTM. Five species/complex of NTM were identified; M. intracellulare was the predominated species (68.33%), followed by M. abscessus-M. immunogenum (13.33%), Mycobacterium spec. (10.00%), M. Kansasii (6.67%) and M. peregrinum-M. alvei-M. septicum (1.67%).

Conclusion

M. intracellulare was the main species of NTM in the eastern part of China and clinical physicians should pay more attention to NTM induced pulmonary disease.

Nontuberculous mycobacteria (NTM) exist ubiquitously in the environment and cause many kinds of diseases including pulmonary infection. Despite this, NTM does not match compulsory report policy in many countries, such as China. Thus, the epidemiology of NTM is generally unknown. Furthermore, misdiagnosis of nontuberculous mycobacterium disease as multi-drug resistant tuberculosis (MDR-TB) frequently occurs in clinical settings because of similar clinical manifestations. Therefore, elucidating the epidemiology and distribution of NTM species is important and may have a profound and lasting impact on the prevalence of pulmonary NTM disease. In our study, we enrolled smear-positive sputum samples during 2008 from Jiangsu province in the eastern region of China. Traditional biochemical tests and molecular biological methods were performed to distinguish NTM isolates to species/complex level. For the first time, we provide a snapshot of the epidemiology and geographic distribution of NTM in Jiangsu province. The proportion of NTM was 3.37% of all the Mycobacterium isolates and the species of NTM differed by area.

Non-tuberculous mycobacterial infections of the hand

Non-tuberculous mycobacterial infections of the hand are difficult to treat and require a long time before remission. But how long should we wait to see an improvement? To answer this question, the published scientific literature was reviewed in English, French and German. Tuberculosis, arthritis and osteomyelitis cases were excluded. A total of 241 non-tuberculous mycobacterial hand infections in 38 scientific publications were retrieved. Most were case reports or series. The median age of the patients was 58years and one third was female. Patients were immunocompromised in 17 episodes. The most common species were Mycobacterium marinum in 198 episodes (82%), followed by M. chelonae in 13 cases (5%). There were no cases of mixed infection. Most infections were aquatic in origin and community-acquired, and were treated with a combination of surgical debridement and long-duration systemic combination antibiotic therapy (14 different regimens; no local antibiotics) for a median duration of 6months. The median number of surgical procedures was 2.5 (range 1-5). Clinical success was not immediate: a median period of 3months (range 2-6) was necessary before the first signs of improvement were observed. The majority (173 cases; 76%) remained entirely cured after a median follow-up time of 1.7years (range, 1-6). Only two microbiological recurrences occurred (1%). However, 49 patients (21%) had long-term sequelae such as pain, stiffness and swelling. The approach of long-duration antibiotic treatment in combination with repeated surgery for mycobacterial soft tissue infections of the hand leads to few recurrences. However, clinical success is not immediate and may take up to 3months.

TYPE OF STUDY

Therapeutic study: systematic review of level III studies.

LEVEL OF EVIDENCE

III.

Highlight on advances in nontuberculous mycobacterial disease in North America

Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and exist as an important cause of pulmonary infections in humans. Pulmonary involvement is the most common disease manifestation of NTM and the incidence of NTM is growing in North America. Susceptibility to NTM infection is incompletely understood; therefore preventative tools are not well defined. Treatment of pulmonary nontuberculous mycobacterial (NTM) infection is difficult and entails multiple antibiotics and an extended treatment course. Also, there is a considerable variation in treatment management that should be considered before initiating treatment. We highlight the new findings in the epidemiology diagnosis and treatment of mycobacterial infections. We debate new advances regarding NTM infection in cystic fibrosis patients and solid organ transplant recipients. Finally, we introduce a new epidemiologic model for NTM disease based on virulence-exposure-host factors.

Role of GenoType(®) Mycobacterium Common Mycobacteria/Additional Species Assay for Rapid Differentiation Between Mycobacterium tuberculosis Complex and Different Species of Non-Tuberculous Mycobacteria

Background:

Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM) may or may not have same clinical presentations, but the treatment regimens are always different. Laboratory differentiation between MTBC and NTM by routine methods are time consuming and cumbersome to perform. We have evaluated the role of GenoType^® Mycobacterium common mycobacteria/additional species (CM/AS) assay for differentiation between MTBC and different species of NTM in clinical isolates from tuberculosis (TB) cases.

Materials and Methods:

A total of 1080 clinical specimens were collected from January 2010 to June 2012. Diagnosis was performed by Ziehl-Neelsen staining followed by culture in BacT/ALERT 3D system (bioMerieux, France). A total of 219 culture positive clinical isolates (BacT/ALERT^® MP cultures) were selected for differentiation by p-nitrobenzoic acid (PNB) sensitivity test as and BIO-LINE SD Ag MPT64 TB test considering as the gold standard test. Final identification and differentiation between MTBC and different species of NTM were further confirmed by GenoType^® Mycobacterium CM/AS assay (Hain Lifescience, Nehren, Germany).

Results:

Out of 219 BacT/ALERT^® MP culture positive isolates tested by PNB as 153 MTBC (69.9%) and by GenoType^® Mycobacterium CM/AS assay as 159 (72.6%) MTBC and remaining 60 (27.4%) were considered as NTM species. The GenoType^® Mycobacterium CM/AS assay was proved 99.3% sensitive and 98.3% specific for rapid differentiation of MTBC and NTM. The most common NTM species were; Mycobacterium fortuitum 20 (33.3%) among rapid growing mycobacteria and Mycobacterium intracellulare 11 (18.3%) among slow growing mycobacteria.

Conclusion:

The GenoType^® Mycobacterium assay makes rapid and accurate identification of NTM species as compared with different phenotypic and molecular diagnostic tool and helps in management of infections caused by different mycobacteria.

Management of nontuberculous mycobacterial infection in the elderly

The incidence of nontuberculous mycobacteria (NTM) has increased over the last decades. Elderly people are more susceptible to NTM and experience increased morbidities. NTM incidence is expected to rise due to an increasing elderly population at least up to 2050. Given the importance of NTM infection in the elderly, an increasing interest exists in studying NTM characteristics in the aged population. In this review, we summarize the characteristics of NTM infection among elderly patients. We focus on epidemiology, clinical presentation, and treatment options of NTM in this age group. We highlight the differences in the diagnosis and treatment between rapid and slow growing mycobacterial infections. The current recommendation for treatment of NTM is discussed. We debate if in vitro susceptibility testing has a role in the treatment of NTM. Drug-drug interaction between antibiotics used to treat NTM and other medications, particularly warfarin, is another important issue that we discuss. Finally, we review the prognosis of NTM disease in elderly patients.

Clinical and laboratory aspects of the diagnosis and management of cutaneous and subcutaneous infections caused by rapidly growing mycobacteria

Rapidly growing mycobacteria (RGM) are known to cause pulmonary, extra-pulmonary, systemic/disseminated, and cutaneous and subcutaneous infections. The erroneous detection of RGM that is based solely on microscopy, solid and liquid cultures, Bactec systems, and species-specific polymerase chain reaction (PCR) may produce misleading results. Thus, inappropriate therapeutic measures may be used in dermatologic settings, leading to increased numbers of skin deformity cases or recurrent infections. Molecular tools such as the sequence analyses of 16S rRNA, rpoB and hsp65 or PCR restriction enzyme analyses, and the alternate gene sequencing of the superoxide dismutase (SOD) gene, dnaJ, the 16S-23S rRNA internal transcribed spacers (ITS), secA, recA1, dnaK, and the 32-kDa protein gene have shown promising results in the detection of RGM species. PCR restriction enzyme analyses (PRA) work better than conventional methods at identifying species that are closely related. Recently introduced molecular tools such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), pyrosequencing, DNA chip technology, and Beacon probes-combined PCR probes have shown comparable results in the detection of various species of RGM. Closely related RGM species (e.g., Mycobacterium fortuitum, M. chelonae, and M. abscessus) must be clearly differentiated using accurate molecular techniques because their therapeutic responses are species-specific. Hence, this paper reviews the following aspects of RGM: (i) its sources, predisposing factors, clinical manifestations, and concomitant fungal infections; (ii) the risks of misdiagnoses in the management of RGM infections in dermatological settings; (iii) the diagnoses and outcomes of treatment responses in common and uncommon infections in immunocompromised and immunocompetent patients; (iv) conventional versus current molecular methods for the detection of RGM; (v) the basic principles of a promising MALDI-TOF MS, sampling protocol for cutaneous or subcutaneous lesions and its potential for the precise differentiation of M. fortuitum, M. chelonae, and M. abscessus; and (vi) improvements in RGM infection management as described in the recent 2011 Clinical and Laboratory Standards Institute (CLSI) guidelines, including interpretation criteria of molecular methods and antimicrobial drug panels and their break points [minimum inhibitory concentrations (MICs)], which have been highlighted for the initiation of antimicrobial therapy.

Laboratory aspects of clinically significant rapidly growing mycobacteria

The pathogenic potential of the rapidly growing mycobacteria (RGM) has started being recognized. This is due to more sensitive and specific techniques in the laboratory. The RGM are generally defined as nontuberculous species of mycobacteria that show visible growth on agar media within 7 days. RGM are widely distributed in nature and have been isolated from natural water, tap water, and soil. Several biochemical tests, high performance liquid chromatography, and molecular techniques have been developed for rapid identification of these species. The American Thoracic Society and the Infectious Disease Society of America recommend that RGM should be identified to the species level using a recognized acceptable methodology such as polymerase chain reaction restriction enzyme analysis or biochemical testing and routine susceptibility testing of RGM should include amikacin, imipenem, doxycycline, the fluorinated quinolones, a sulphonamide or trimethoprim-sulphamethoxazole, cefoxitin, clarithromycin, linezolid, and tobramycin. The diseases caused by these organisms have varied manifestations. They have been responsible for a number of healthcare-associated outbreaks and pseudo-outbreaks. For recognition of outbreaks, it is important to be familiar with the causative organisms like RGM which are most frequently involved in healthcare-associated outbreaks and pseudo outbreaks. It is essential to intervene as soon as possible to interrupt this transmission. Large gaps still exist in our knowledge of RGM. Unquestionably more studies are required. Through this review, we wish to emphasize that reporting of RGM from clinical settings along with their sensitivity patterns is an absolute need of the hour.

Evaluation of BacT/Alert 3D automated unit for detection of nontuberculous mycobacteria requiring incubation at 30 degrees C for optimal growth

The reliability of the BacT/Alert 3D unit for automated detection of nontuberculous mycobacteria (NTM) that grow optimally at 30 °C was assessed. This system reliably maintained a temperature of 30 °C and detected 50% of the clinical NTM strains (5 Mycobacterium marinum and 3 Mycobacterium gordonae strains) faster than 37 °C culture.

Clinical significance of nontuberculous mycobacteria isolates in elderly Taiwanese patients

The aim of this study was to investigate the clinical significance of nontuberculous mycobacteria (NTM) isolates in elderly Taiwanese patients. From 2004 through 2008, patients >65 years old with NTM isolation were identified. The definitions of NTM disease followed the American Thoracic Society and Infectious Disease Society of America (ATS/IDSA) criteria. Among the 3,175 NTM isolates, Mycobacterium avium complex (MAC; n = 1,118, 35.2%) was the most prevalent species, followed by M. abscessus (n = 545, 17.2%). Among the 1,633 elderly patients with NTM isolates, the most prevalent NTM species were MAC (n = 592, 36.3%) and M. fortuitum complex (n = 311, 19.0%). NTM colonization was found in 1,339 (80.4%) patients and only 326 (19.6%) patients had NTM diseases. During the study period, the annual incidence rates (per 100,000 inpatients and outpatients) of NTM colonization and disease both increased significantly (p < 0.0001) from 10.5 to 15.8 and from 2.1 to 4.3, respectively. Isolated pulmonary NTM infections compromised 294 (90.2%) of the 326 elderly cases of NTM disease. In conclusion, this study found an increasing trend in the incidence of both NTM isolates and NTM diseases among elderly Taiwanese patients. MAC and M. abscessus were the most frequent species causing various types of NTM disease.

Biochip system for rapid and accurate identification of mycobacterial species from isolates and sputum

The accurate detection of mycobacterial species from isolates and clinical samples is important for pathogenic diagnosis and treatment and for disease control. There is an urgent need for the development of a rapid, simple, and accurate detection method. We established a biochip assay system, including a biochip, sample preparation apparatus, hybridization instrument, chip washing machine, and laser confocal scanner equipped with interpretation software for automatic diagnosis. The biochip simultaneously identified 17 common mycobacterial species by targeting the differences in the 16S rRNA. The system was assessed with 64 reference strains and 296 Mycobacterium tuberculosis and 243 nontuberculous mycobacterial isolates, as well as 138 other bacteria and 195 sputum samples, and then compared to DNA sequencing. The entire biochip assay took 6 h. The concordance rate between the biochip assay and the DNA sequencing results was 100%. In conclusion, the biochip system provides a simple, rapid, reliable, and highly accurate clinical assay for determination of mycobacterial species in a 6-h procedure, from either culture isolates or sputum samples, allowing earlier pathogen-adapted antimicrobial therapy in patients.

Spread of nontuberculous mycobacteria from 1993 to 2006 in Koreans

In Korea, the prevalence of nontuberculous mycobacterial (NTM) pulmonary disease has risen, observed primarily in immunocompetent patients with or without preexisting lung disease. The purpose of this study was to determine the frequency of various species of NTM isolates from respiratory specimens in a single institution over a 14-year period in Korea. All samples referred to our reference laboratory over a 14-year period in Korea were analyzed. From 1993 to 2000 our laboratory used conventional NTM identification methods, and from 2001 we adapted PCR-restriction fragment length polymorphism analysis(PRA). A total of 17,915 isolates were collected from 1993 to 2006. The most frequently isolated organisms were M. avium complex (n=11,705, 65%), M. abscessus (n=2,076, 11.59%), M. fortuitum complex (n=1,279, 7.14%). M. chelonae complex (n=1,134, 6.33%), M. kansasii (n=762, 4.25%), M. szulgai (n=139, 0.78%), M. celatum (n=87, 0.49%), M. scrofulaceum (n=18, 0.10%) and M. marium (n=11, 0.06%).

Rapid identification of mycobacteria from smear-positive sputum samples by nested PCR-restriction fragment length polymorphism analysis

The rapid identification of mycobacteria from smear-positive sputum samples is an important clinical issue. Furthermore, the availability of a cheap, technically simple, and accurate method also would benefit mycobacterial laboratories in developing countries. In the present study, we aimed to develop an assay allowing the identification of the Mycobacterium tuberculosis complex (MTBC) and other frequently isolated nontuberculous mycobacteria (NTM) directly from smear-positive sputum samples. A nested PCR-restriction fragment length polymorphism analysis (nested-PRA) assay that focuses on the analysis of the hsp65 gene was developed and evaluated for its efficiency compared to that of traditional culture methods and 16S rRNA gene sequencing identification. A total of 204 smear-positive and culture-positive sputum specimens were prospectively collected for analysis between November 2005 and May 2006. The samples were classified according to an acid-fast bacillus (AFB) staining scale as rare/1+, 2+, or 3+. The results of the nested-PRA showed that the identification rate for AFB 3+, AFB 2+, and AFB rare/1+ samples was 100, 95, and 53%, respectively, and that the overall identification rate was 89%. All positive results by the nested-PRA method agreed with the results by culture and 16S rRNA gene sequence analysis. The nested-PRA appears to have clinical applicability when used for the direct identification of mycobacterial organisms (both MTBC and NTM) that are present in smear-positive sputum samples, especially for countries in which MTBC is endemic.

Evaluation of the GenoType Mycobacterium Assay for identification of mycobacterial species from cultures

A new commercially available DNA strip assay (GenoType Mycobacterium CM/AS; Hain Lifescience, Nehren, Germany) was evaluated for the ability to differentiate mycobacterial species. The test is based on a PCR technique targeting a 23S rRNA gene region, followed by reverse hybridization and line probe technology. The GenoType CM is capable of identifying 23, the GenoType AS a further 14, species either alone or in combination with one or more species. Both tests were evaluated with 156 mycobacterial strains composed of 61 validly published species including different subspecies, 6 not validly published species, and 3 strains other than mycobacterial species. All strains were precharacterized by sequencing of the 5' region of the 16S rRNA gene and biochemical tests. In total, results for 151 strains were interpretable. Concordant results were obtained for 137 (92.6%) of 148 mycobacterial strains with the CM assay and 133 (89.9%) of 148 mycobacterial strains with the AS assay, and all three non-Mycobacterium species were identified.

Mycobacteria in drinking water distribution systems: ecology and significance for human health

In contrast to the notorious pathogens Mycobacterium tuberculosis and M. leprae, the majority of the mycobacterial species described to date are generally not considered as obligate human pathogens. The natural reservoirs of these non-primary pathogenic mycobacteria include aquatic and terrestrial environments. Under certain circumstances, e.g., skin lesions, pulmonary or immune dysfunctions and chronic diseases, these environmental mycobacteria (EM) may cause disease. EM such as M. avium, M. kansasii, and M. xenopi have frequently been isolated from drinking water and hospital water distribution systems. Biofilm formation, amoeba-associated lifestyle, and resistance to chlorine have been recognized as important factors that contribute to the survival, colonization and persistence of EM in water distribution systems. Although the presence of EM in tap water has been linked to nosocomial infections and pseudo-infections, it remains unclear if these EM provide a health risk for immunocompromised people, in particular AIDS patients. In this regard, control strategies based on maintenance of an effective disinfectant residual and low concentration of nutrients have been proposed to keep EM numbers to a minimum in water distribution systems.

The genetics of nontuberculous mycobacterial infection

The molecular aetiology of familial susceptibility to disseminated mycobacterial disease, usually involving weakly pathogenic strains of mycobacteria, has now been elucidated in more than 30 families. Mutations have been identified in five genes in the interleukin-12-dependent interferon-gamma pathway, highlighting the importance of this pathway in human mycobacterial immunity. Knowledge derived from the study of these rare patients contributes to our understanding of the immune response to common mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium leprae, which remain major public health problems globally. This knowledge can be applied to the rational development of novel therapies and vaccines for these important mycobacterial diseases.