Combined approach to the identification of clinically infrequent non-tuberculous mycobacteria in Argentina.

SETTING: Over 150 potentially pathogenic non-tuberculous mycobacteria (NTM) species have been described, posing an onerous challenge for clinical laboratory diagnosis. OBJECTIVE: To evaluate different approaches for the identification of 40 clinically relevant NTM isolates whose species were not reliably identified using our routine diagnostic workflow comprising phenotypic tests and hsp65 polymerase chain reaction restriction analysis. DESIGN: We used 1) sequencing analysis of four conserved gene targets: 16S rRNA, rpoB, hsp65 and sodA; 2) two commercial reverse hybridisation assays; and 3) protein analysis using matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS). RESULTS: Combined, but not individual, sequence analysis allowed reliable species identification for 30/40 (75%) isolates, including species previously unknown to be circulating in Argentina. Commercial kits outperformed our routine identification in only 5/35 isolates, and misclassified many more. MALDI-TOF MS accurately identified species in 22/36 (61%) isolates and did not misidentify any. CONCLUSIONS: Commercial kits did not resolve the problem of species of NTM isolates that elude identification. Combined DNA sequence analysis was the approach of choice. MALDI-TOF MS shows promise as a powerful, rapid and accessible tool for the rapid identification of clinically relevant NTM in the diagnostic laboratory, and its accuracy can be maximised by building up a customised NTM spectrum database.

Recommendations for the diagnosis of pediatric tuberculosis.

Tuberculosis (TB) is still the world's second most frequent cause of death due to infectious diseases after HIV infection, and this has aroused greater interest in identifying and managing exposed subjects, whether they are simply infected or have developed one of the clinical variants of the disease. Unfortunately, not even the latest laboratory techniques are always successful in identifying affected children because they are more likely to have negative cultures and tuberculin skin test results, equivocal chest X-ray findings, and atypical clinical manifestations than adults. Furthermore, they are at greater risk of progressing from infection to active disease, particularly if they are very young. Consequently, pediatricians have to use different diagnostic strategies that specifically address the needs of children. This document describes the recommendations of a group of scientific societies concerning the signs and symptoms suggesting pediatric TB, and the diagnostic approach towards children with suspected disease.

Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a TBNET/RESIST-TB consensus statement.

The emergence of drug-resistant strains of Mycobacterium tuberculosis is a challenge to global tuberculosis (TB) control. Although culture-based methods have been regarded as the gold standard for drug susceptibility testing (DST), molecular methods provide rapid information on mutations in the M. tuberculosis genome associated with resistance to anti-tuberculosis drugs. We ascertained consensus on the use of the results of molecular DST for clinical treatment decisions in TB patients. This document has been developed by TBNET and RESIST-TB groups to reach a consensus about reporting standards in the clinical use of molecular DST results. Review of the available literature and the search for evidence included hand-searching journals and searching electronic databases. The panel identified single nucleotide mutations in genomic regions of M. tuberculosis coding for katG, inhA, rpoB, embB, rrs, rpsL and gyrA that are likely related to drug resistance in vivo. Identification of any of these mutations in clinical isolates of M. tuberculosis has implications for the management of TB patients, pending the results of in vitro DST. However, false-positive and false-negative results in detecting resistance-associated mutations in drugs for which there is poor or unproven correlation between phenotypic and clinical drug resistance complicate the interpretation. Reports of molecular DST results should therefore include specific information on the mutations identified and provide guidance for clinicians on interpretation and on the choice of the appropriate initial drug regimen.

Revisiting susceptibility testing in MDR-TB by a standardized quantitative phenotypic assessment in a European multicentre study.

OBJECTIVES: Treatment outcome of MDR-TB is critically dependent on the proper use of second-line drugs as per the result of in vitro drug susceptibility testing (DST). We aimed to establish a standardized DST procedure based on quantitative determination of drug resistance and compared the results with those of genotypes associated with drug resistance. METHODS: The protocol, based on MGIT 960 and the TB eXiST software, was evaluated in nine European reference laboratories. Resistance detection at a screening drug concentration was followed by determination of resistance levels and estimation of the resistance proportion. Mutations in 14 gene regions were investigated using established techniques. RESULTS: A total of 139 Mycobacterium tuberculosis isolates from patients with MDR-TB and resistance beyond MDR-TB were tested for 13 antituberculous drugs: isoniazid, rifampicin, rifabutin, ethambutol, pyrazinamide, streptomycin, para-aminosalicylic acid, ethionamide, amikacin, capreomycin, ofloxacin, moxifloxacin and linezolid. Concordance between phenotypic and genotypic resistance was >80%, except for ethambutol. Time to results was short (median 10 days). High-level resistance, which precludes the therapeutic use of an antituberculous drug, was observed in 49% of the isolates. The finding of a low or intermediate resistance level in 16% and 35% of the isolates, respectively, may help in designing an efficient personalized regimen for the treatment of MDR-TB patients. CONCLUSIONS: The automated DST procedure permits accurate and rapid quantitative resistance profiling of first- and second-line antituberculous drugs. Prospective validation is warranted to determine the impact on patient care.

Non Tuberculous Cutaneous Mycobacteriosis in a primary school in Rome: epidemiological and microbiological investigation.

During the school years 2009-2010 and 2010-2011 a total of 25 cases of Non Tuberculous Cutaneous Mycobacteriosis (NTCM) were notified in children attending the same school with a swimming pool in Rome. Environmental microbiological and epidemiological investigations (only for suspected outbreaks in 2009-2010) were conducted. We screened students with skin lesions, and environmental samples were collected from the school area and the swimming pool. During the school year 2009-10 18 cases were clinically identified among 514 primary school children (3.50%) and all cases attended the swimming pool. Only 2 out of 18 cultures were positive for Mycobacterium chelonae complex (Group III, M. abscessus). Attack Rate for swimming pool use was 13,10% (17/130), with a Relative Risk 54,70 (95% CI: 9,4 - ∞). In February 2011 additional 7 cases of cutaneous NTM among children - who attended the same primary school and swimming pool were notified to the local public health authority followed by environmental microbiological investigation. Environmental samples were positive for NTM but not for M. abscessus. Mycobacteria are not included in water-quality criteria in Italy for this reason it is important to collect evidences of NTM cases caused by these infrequent pathogens, to be able to perform rapid risk assessment and to identify the best practices in prevention and management of such a risk.

Characterization of a novel variant of Mycobacterium chimaera.

In this study, nonchromogenic mycobacteria were isolated from pulmonary samples of three patients in the Netherlands. All isolates had identical, unique 16S rRNA gene and 16S-23S ITS sequences, which were closely related to those of Mycobacterium chimaera and Mycobacterium marseillense. The biochemical features of the isolates differed slightly from those of M. chimaera, suggesting that the isolates may represent a possible separate species within the Mycobacterium avium complex (MAC). However, the cell-wall mycolic acid pattern, analysed by HPLC, and the partial sequences of the hsp65 and rpoB genes were identical to those of M. chimaera. We concluded that the isolates represent a novel variant of M. chimaera. The results of this analysis have led us to question the currently used methods of species definition for members of the genus Mycobacterium, which are based largely on 16S rRNA or rpoB gene sequencing. Definitions based on a single genetic target are likely to be insufficient. Genetic divergence, especially in the MAC, yields strains that cannot be confidently assigned to a specific species based on the analysis of a single genetic target.

Detection and molecular characterization of Mycobacterium celatum as a cause of splenitis in a domestic ferret (Mustela putorius furo).

Mycobacterium celatum is a slow growing non-tuberculous mycobacterium described mainly as occurring in human patients. Only two cases of infection with this pathogen have been reported previously in animals. A 5-year-old, neutered male ferret was presented with progressive weight loss and muscle atrophy. Pale mucous membranes, slight alopecia of the tail and splenomegaly, confirmed by abdominal ultrasound, were observed. Fine-needle aspirations of the spleen revealed extramedullary haematopoiesis and marked macrophage-dominated inflammation associated with mycobacterial infection. Ziehl-Neelsen staining demonstrated sporadic acid-fast bacilli within macrophages. These organisms were identified as M. celatum by microbiological and molecular methods. Phylogenetic analysis based on the 16S rDNA gene compared this isolate with previously reported strains and demonstrated close relatedness to the human strains of M. celatum types 1 and 3. The ferret was treated with enrofloxacin, rifampicin and azithromycin, resulting in clinical improvement. After 40 days of treatment, the spleen was re-evaluated. Cytological evaluation revealed only extramedullary haematopoiesis without evidence of infection. Discontinuation of therapy was followed by rapid deterioration and death.

Impact of immigration on tuberculosis in a low-incidence area of Italy: a molecular epidemiological approach.

The effects that immigration might have on the epidemiology of tuberculosis (TB) in a low-incidence area of Italy was investigated by determining, in autochthonous and immigrant TB patients, the molecular characteristics of the Mycobacterium tuberculosis complex (MTBC) isolates, which may provide information on their phylogeographical origin. A total of 1080 MTBC strains, collected during a 4- year period in Tuscany from 614 Italian-born and 466 foreign-born patients, were genotyped by spoligotyping and assigned to the different phylogeographical lineages that constitute the MTBC. The autochthonous Euro-American phylogeographical lineage, which includes the spoligotype families T, Haarlem, Latin American­Mediterranean (LAM), S and X, was highly prevalent among Italian-born patients, with a total of 477 cases (77.7%), and foreign-born TB patients, with a total of 270 cases (57.9%); 24 Italian-born (3.9%) and 141 foreign- born (30.3%) TB cases were due to MTBC genotypic families associated with distant geographical areas, i.e. East African­Indian (EAI), Beijing, Central Asian (CAS), and Mycobacterium africanum. Strains of Mycobacterium bovis and strains of undefined genotype, which are all considered together, as it is not possible to assign a specific geographical origin, accounted for 113 (18.4%) Italian cases and 55 (11.8%) foreign-born cases. A total of 79 Italian TB cases (12.9%) have been attributed to transmission from immigrants to the local population. No significant contribution to drug resistance appeared to be associated with imported MTBC strains. It is concluded that, at present, the overall impact of imported TB on public health in the low-incidence study area is relatively modest and of the same order as in other western countries.

Infection due to a novel mycobacterium, mimicking multidrug-resistant Mycobacterium tuberculosis.

The treatment of multidrug-resistant tuberculosis (TB) requires the use, for long periods, of drugs liable to cause significant side effects. In the case of misdiagnosis of multidrug-resistant TB, the patient is exposed to toxic substances without any benefit. In low-income countries, where the microbiological diagnosis of TB relies on microscopy only, the misdiagnosis of multidrug-resistant TB is very frequent in patients persistently smear-positive despite anti-TB treatment, with the possibility of an infection due to non-tuberculous mycobacteria (NTM) being neglected. The isolation of a mycobacterium from the sputum of a Somali patient apparently confirmed the previous diagnosis of cavitary pulmonary disease. Preliminary investigations led, at first, to the strain being identified as multidrug-resistant Mycobacterium tuberculosis, with findings fully in agreement with the patient's history, which was characterized by repeated interruptions of anti-TB treatment. Thorough phenotypic and genotypic analyses led subsequently to the recognition that the strain was a previously unreported non-tuberculous mycobacterium. The patient, who was unresponsive to the anti-TB treatment, dramatically improved once a drug combination active against NTM was used. A major objective of this article is to alert the medical community to the risk, present also in settings in which sophisticated diagnostic techniques are used, that a cavitary infection due to NTM, and consequently not responding to the anti-TB standard regimen, will be mistaken for multidrug-resistant TB.

Clinical manifestations of nontuberculous mycobacteria infections.

The isolation of nontuberculous mycobacteria (NTM) from clinical specimens has become very frequent in the last years. Such organisms are typically environmental and poorly pathogenic for humans; they can, however, be responsible for opportunistic diseases in subjects presenting with various predisposing conditions. Pulmonary infections are responsible for the most frequent disease caused by NTM, although the relevance of mycobacterioses involving other parts of the body is increasing. The risk of disseminated infections characterizing immunocompromised patients is well known, and those numbers are steadily rising. The lymph nodes, cutis and soft tissues, as well as bone and joints, are also important targets of NTM infection. The problems concerning the assessment of the clinical significance of NTM, along with a consideration of the more frequent NTM pathologies, are the major objectives of this review.

Proposal to elevate Mycobacterium avium complex ITS sequevar MAC-Q to Mycobacterium vulneris sp. nov.

The Mycobacterium avium complex (MAC) consists of four recognized species, Mycobacterium avium, Mycobacterium colombiense, Mycobacterium intracellulare and Mycobacterium chimaera, and a variety of other strains that may be members of undescribed taxa. We report on two isolates of a scotochromogenic, slowly growing, non-tuberculous Mycobacterium species within the M. avium complex from a lymph node and an infected wound after a dogbite of separate patients in The Netherlands. The extrapulmonary infections in immunocompetent patients suggested a high level of virulence. These isolates were characterized by a unique nucleotide sequence in the 16S rRNA gene, 99% similar to Mycobacterium colombiense, and the MAC-Q 16S-23S internal transcribed spacer (ITS) sequence. Sequence analyses of the hsp65 gene revealed 97% similarity to M. avium. The rpoB gene sequence was 98% similar to M. colombiense. Phenotypically, the scotochromogenicity, positive semi-quantitative catalase and heat-stable catalase tests, negative tellurite reductase and urease tests and susceptibility to hydroxylamine and oleic acid set these isolates apart from related species. High-performance liquid chromatography analysis of cell-wall mycolic acid content revealed a unique pattern, related to that of M. avium and M. colombiense. Together, these findings supported a separate species status within the Mycobacterium avium complex. We propose elevation of scotochromogenic M. avium complex strains sharing this 16S gene and MAC-Q ITS sequence to separate species status, for which the name Mycobacterium vulneris sp. nov. is proposed. The type strain is NLA000700772T (=DSM 45247T=CIP 109859T).

Association of Mycobacterium tuberculosis complex isolates of BOVIS and Central Asian (CAS) genotypic lineages with extrapulmonary disease.

The association between isolate genotype, defined as in the international spoligotype database SpolDB4, and extrapulmonary tuberculosis was determined among 1009 patients in a population-based, 4-year survey performed in Tuscany, Italy. Extrapulmonary disease occurred in 24.2% of patients. A statistically significant association with extrapulmonary disease was found for the BOVIS (adjusted OR 3.2; 95% CI 1.2-8.1) and for the Central Asian (CAS) lineages (adjusted OR 2.3; 95% CI 1.0-5.1). These findings support the view that Mycobacterium tuberculosis strains within individual genotypic lineages might have evolved unique pathogenic characteristics that are capable of influencing the clinical outcome of the infection.

QuantiFERON-TB Gold and the TST are both useful for latent tuberculosis infection screening in autoimmune diseases.

Screening for active tuberculosis (TB) and latent TB infection (LTBI) is mandatory prior to the initiation of tumour necrosis factor-alpha inhibitor therapy. However, no agreement exists on the best strategy for detecting LTBI in this population. The aim of the present study was to analyse the performance of the tuberculin skin test (TST) and QuantiFERON-TB Gold in-tube (QFT-GIT) on LTBI detection in subjects with immunomediated inflammatory diseases (IMID). The TST and QFT-GIT were prospectively performed in 398 consecutive IMID subjects, 310 (78%) on immunosuppressive therapy and only 16 (4%) had been bacillus Calmette-Guérin (BCG) vaccinated. Indeterminate results to QFT-GIT were found in five (1.2%) subjects. Overall, 74 (19%) out of 393 subjects were TST-positive and 52 (13%) were QFT-GIT-positive. Concordance between TST and QFT-GIT results was good (87.7%): 13 were QFT-GIT-positive/TST-negative and 35 QFT-GIT-negative/TST-positive. By multivariate analysis both tests were significantly associated with older age. Only the TST was associated with BCG vaccination and radiological lesions of past TB. Use of immunosuppressive drugs differently modulated QFT-GIT or TST scoring. Use of the QuantiFERON-TB Gold in-tube, as a screening tool for latent tuberculosis among immunomediated inflammatory disease subjects, is feasible. Until further data will elucidate discordant tuberculin skin test/QuantiFERON-TB Gold in-tube results, a strategy of simultaneous tuberculin skin and QuantiFERON-TB Gold in-tube testing in a low prevalence bacillus Calmette-Guérin vaccinated population, should maximise potentials of latent tuberculosis diagnosis.

Use of the INNO LiPA Rif.TB for detection of Mycobacterium tuberculosis DNA directly in clinical specimens and for simultaneous determination of rifampin susceptibility.

The INNO LiPA Rif.TB (Innogenetics, Ghent, Belgium) is a reverse hybridization test developed to detect genetic markers of resistance to rifampin in Mycobacterium tuberculosis complex. In the present study, this test was used directly on 3,763 clinical specimens by adopting a nested amplification of the target. The specificity of the system (98.4%) was optimal, but sensitivity (69.5%) was unsatisfactory. However, when use of the system was limited to smear-positive specimens, the sensitivity rose to 91.7%. As expected, the ability of the system to predict rifampin resistance was not influenced by its direct use on clinical specimens and confirmed the favorable results repeatedly reported in the literature.

A case-control study for multidrug-resistant tuberculosis: risk factors in four European countries.

The aim of this study was to detect risk factors for multidrug resistance in patients with pulmonary tuberculosis in four European Union countries: France, Germany, Italy, and Spain. A prospective epidemiological case control study was conducted, made up of patients with clinically diagnosed and microbiologically confirmed pulmonary tuberculosis in the four countries between 1997 and 2000. A total of 138 cases and 276 controls were studied. Considering the four countries as a whole, the most statistically significant risk factors were as follows: intravenous drug use (OR 4.68); asylum-seeker support (OR 2.55) as income factor; living in a nursing home (OR 2.05); previous tuberculosis (OR 2.03) with pulmonary location; prison (OR 2.02); known tuberculosis contacts (OR 2.01); immunosuppression other than human immunodeficiency virus (HIV) (OR 1.96); acquired immunodeficiency syndrome (AIDS) (OR 1.96); current tuberculosis with pulmonary location (OR 1.77); and health-care worker (OR 1.69). These risk factors will have to be taken into account in the European Union as a whole, as well as in each individual country, to establish a health policy of monitoring and control for these cases of multidrug resistance. Although rare, their seriousness makes them particularly important.

Mutations responsible for Mycobacterium tuberculosis isoniazid resistance in Italy.

SETTING: The incidence of tuberculosis (TB) and drug resistance in Italy is low compared to other countries. Mutations in several genomic regions of Mycobacterium tuberculosis are involved in the occurrence of isoniazid (INH) resistance. OBJECTIVE: To investigate the mutations responsible for INH resistance among Italian isolates of M. tuberculosis, to assess the feasibility of predicting drug resistance using a genetic approach. DESIGN: The mutations responsible for INH resistance were looked for in selected regions of genes katG, kasA and ndh and in the promoter regions of inhA and ahpC by nucleotide sequencing, and the results were compared with data reported in other studies. RESULTS: Prevalent INH resistance mutations were found at codon 315 of the katG gene and at position -15 of the inhA regulatory region (respectively 37.8% and 20.0% of isolates). The prevalence of mutations at position -24 of inhA, in ahpC, and in kasA ranged from 2.2% to 4.4%. No mutations were found in 35.6% of the isolates. CONCLUSION: The identification of INH resistance by genetic analysis of the selected regions may be inappropriate in areas with a low prevalence of TB, such as Italy, as the genetic mechanisms of resistance remain unidentified for approximately one third of the isolates.

Non-tuberculous mycobacteria: patterns of isolation. A multi-country retrospective survey.

OBJECTIVE: To collect data on non-tuberculous mycobacteria (NTM) isolated from clinical laboratories in different countries to establish: 1) whether the isolation of NTM was increasing, 2) which species were increasing, and 3) whether there was any pattern of geographical distribution. DESIGN: In 1996, the Working Group of the Bacteriology and Immunology Section of the International Union Against Tuberculosis and Lung Disease contacted 50 laboratories in different countries for the necessary information. RESULTS: The number of patients reported with NTM was 36099 from 14 countries. Mycobacterium avium complex, M. gordonae, M. xenopi, M. kansasii and M. fortuitum were the five species most frequently isolated. There was a significant upward trend for M. avium complex and M. xenopi. Pigmented mycobacteria predominated in Belgium, the Czech Republic and the Mediterranean coast of Spain. Non-chromogenic mycobacteria were found to be predominant in the area of the Atlantic coast of Brazil and in Turkey, the United Kingdom, Finland and Denmark. CONCLUSIONS: There was an increase in the number of NTM isolated from clinical samples of patients. Isolation of the most frequent species is constantly changing in most of the geographical areas, and newer species are emerging due to better diagnostic techniques to detect and identify NTM.

Mycobacterial testing in hospital laboratories: results from a questionnaire survey in Italy.

Between 1999 and 2001, 355 hospital laboratories in Italy were asked to complete a questionnaire addressing mycobacterial test methods, 1-year workloads and laboratory safety features. Analysis of the data showed that rapid methods for mycobacterial testing were being used by most larger laboratories; however, sub-optimal methods were still in use in small and medium-size laboratories. In a country such as Italy, which has a low prevalence of tuberculosis cases, implementation of rapid technologies, combined with regionalisation of mycobacterial diagnostic services, seems to be the most reasonable and cost-effective strategy.

Isolation of a novel sequevar of Mycobacterium flavescens from the synovial fluid of an AIDS patient.

This report describes the characterisation of a mycobacterium involved in a case of septic arthritis in an AIDS patient that was treated successfully with specific anti-mycobacterial drugs. The biochemical and cultural features, and the mycolic acid pattern as assessed by high-performance liquid chromatography, were fully compatible with the isolate being Mycobacterium flavescens. However, the isolate's 16S rDNA sequence differed by five nucleotides from the two known sequevars of M. flavescens, thus indicating that this isolate belonged to a new 16S rDNA sequevar.

Evaluation of moxifloxacin activity in vitro against Mycobacterium tuberculosis, including resistant and multidrug-resistant strains.

The new quinolone moxifloxacin was tested against 86 strains of Mycobacterium tuberculosis including 13 resistant and 4 multiresistant strains. The antimicrobial susceptibility was tested, in parallel, using two different liquid media, the radiometric Bactec 12B and the Mycobacteria Growth Indicator Tube (Becton Dickinson, USA). All strains but two were susceptible at 0.5 microg/ml of moxifloxacin; for the remaining two strains, both multidrugresistant, the minimal inhibitory concentrations (MIC) were =2 and >4 microg/ml respectively. Our data confirm the high antitubercular in vitro activity of moxifloxacin.