[A pharmacologic approach to treatment of Mycobacterium abscessus pulmonary disease]. / Analyse pharmacologique du traitement des pneumopathies à Mycobacterium abscessus.

Mycobacterium abscessus is a fast-growing non-tuberculous mycobacteria complex causing pulmonary infections, comprising the subspecies abscessus, massiliense and bolletii. Differences are based predominantly on natural inducible macrolide resistance, active in most Mycobacterium abscessus spp abscessus species and in Mycobacterium abscessus spp bolletii but inactive in Mycobacterium abscessus spp massiliense. Therapy consists in long-term treatment, combining multiple antibiotics. Prognosis is poor, as only 40% of patients experience cure. Pharmacodynamic and pharmacokinetic data on M. abscessus have recently been published, showing that therapy ineffectiveness might be explained by intrinsic bacterial resistance (macrolides…) and by the unfavorable pharmacokinetics of the recommended antibiotics. Other molecules and inhaled antibiotics are promising.

Machine learning to improve the interpretation of intercalating dye-based quantitative PCR results.

This study aimed to evaluate the contribution of Machine Learning (ML) approach in the interpretation of intercalating dye-based quantitative PCR (IDqPCR) signals applied to the diagnosis of mucormycosis. The ML-based classification approach was applied to 734 results of IDqPCR categorized as positive (n = 74) or negative (n = 660) for mucormycosis after combining "visual reading" of the amplification and denaturation curves with clinical, radiological and microbiological criteria. Fourteen features were calculated to characterize the curves and injected in several pipelines including four ML-algorithms. An initial subset (n = 345) was used for the conception of classifiers. The classifier predictions were combined with majority voting to estimate performances of 48 meta-classifiers on an external dataset (n = 389). The visual reading returned 57 (7.7%), 568 (77.4%) and 109 (14.8%) positive, negative and doubtful results respectively. The Kappa coefficients of all the meta-classifiers were greater than 0.83 for the classification of IDqPCR results on the external dataset. Among these meta-classifiers, 6 exhibited Kappa coefficients at 1. The proposed ML-based approach allows a rigorous interpretation of IDqPCR curves, making the diagnosis of mucormycosis available for non-specialists in molecular diagnosis. A free online application was developed to classify IDqPCR from the raw data of the thermal cycler output ( http://gepamy-sat.asso.st/ ).

Treatment With a Three-Drug Regimen for Pulmonary Tuberculosis Based on Rapid Molecular Detection of Isoniazid Resistance: A Noninferiority Randomized Trial (FAST-TB).

Background: The rationale behind the use of ethambutol in the standard tuberculosis treatment is to prevent the emergence of resistance to rifampicin in case of primary resistance to isoniazid. We evaluated whether early detection of isoniazid resistance using molecular testing allows the use an ethambutol-free regimen. Methods: FAST-TB, a phase 4, French, multicenter, open-label, non-inferiority trial, compared 2 strategies: (1) polymerase chain reaction (PCR)-based detection of isoniazid and rifampicin resistance at baseline using Genotype MTBDRplus version 2.0 followed by ethambutol discontinuation if no resistance was detected (PCR arm) and (2) a standard 4-drug combination, pending phenotypic drug-susceptibility results (C arm). Adult patients with smear-positive pulmonary tuberculosis were enrolled. The primary endpoint was the proportion of patients with treatment success defined as bacteriological or clinical cure at the end of treatment. A non-inferiority margin of 10% was used. Results: Two hundred three patients were randomized, 104 in the PCR arm and 99 in the C arm: 26.6% were female, median age was 37 (interquartile range, 28-51) years, 72.4% were born in Africa, and 5.4% were infected with human immunodeficiency virus. Chest x-ray showed cavities in 64.5% of the cases. Overall, 169 patients met criteria of treatment success: 87 of 104 (83.7%) in the PCR arm and 82 of 99 (82.8%) in the C arm with a difference of +0.8% (90% confidence interval, -7.9 to 9.6), meeting the noninferiority criteria in the intention-to-treat population (P = .02). Conclusions: In a setting with low prevalence of primary isoniazid resistance, a 3-drug combination with isoniazid, rifampicin, and pyrazinamide, based on rapid detection of isoniazid resistance using molecular testing, was noninferior to starting the recommended 4-drug regimen.

Sampling strategy for bacteriological diagnosis of intrathoracic tuberculosis.

BACKGROUND: Pulmonary tuberculosis (TB) is the most frequent site of TB and the one leading its spread worldwide. Multiple specimens are commonly collected for TB diagnosis including those requiring invasive procedures. This study aimed to review the sampling strategy for the microbiological diagnosis of pulmonary TB. METHODS: A retrospective analysis of collected samples from September 1st 2014 to May 1st 2016 in the Bacteriology laboratory of Pitié-Salpêtrière Hospital (Paris, France) was performed. All the samples collected in patients aged over 18 years for the bacteriological diagnosis of pulmonary TB were included. RESULTS: A total of 6267 samples were collected in 2187 patients. One hundred and twenty-six patients (6%) had a culture confirmed pulmonary TB. Among them, multiple sputum collections were sufficient for TB diagnosis in 63.5%, gastric lavages permitted to avoid bronchoscopy in only 7.1%, and bronchoscopy was necessary in 29.4%. The culture positivity of sputa (8.6%) was higher than that of bronchial aspirations (3.1%), bronchiolo-alveolar lavages (BAL) (2.3%) or gastric lavages (4.8%) (P<0.001). From its 70.0% theoretical PPV value, the 46.1% selection in bronchial aspirations allocated to molecular test increased PPV up to 88.9%. CONCLUSIONS: Based on our data, we suggest to collect sputum consistently. If smear negative a bronchoscopy should be performed and molecular diagnosis be performed on a subset of bronchial aspirations based on expertise of the bronchoscopist.

[Molecular diagnosis of tuberculosis]. / Place de la biologie moléculaire dans le diagnostic de la tuberculose.

Tuberculosis is caused by the M. tuberculosis complex. Its slow growth delays the bacteriological diagnosis based on phenotypic tests. Molecular biology has significantly reduced this delay, notably thanks to the deployment of the Xpert® MTB/RIF test (Cepheid), which detects the M. tuberculosis complex and rifampicin resistance in 2hours. Other tests detecting isoniazid and second-line antituberculous drugs resistance have been developed. However, the performances of molecular tests are significantly reduced if the acid-fast bacilli microscopy screening is negative. It is therefore crucial to limit their indication to strong clinical suspicions. Resistance detection tests only explore certain characterized positions; however, not all drug-resistance mutations are known. Moreover, the performances vary for different antituberculous drugs. The advent of genomic sequencing is promising. Its integration into routine workflow still needs to be evaluated and the data analysis remains to be standardized. The rise of molecular biology techniques has revolutionized the diagnosis of tuberculosis and drug resistance. However, they remain screening tests; results still have to be confirmed by phenotypic reference methods.

Multidisciplinary advisory teams to manage multidrug-resistant tuberculosis: the example of the French Consilium.

SETTING: The World Health Organization (WHO) recommends that multidrug-resistant tuberculosis (MDR-TB) treatment should be managed in collaboration with multidisciplinary advisory committees (consilia). A formal national Consilium has been established in France since 2005 to provide a centralised advisory service for clinicians managing MDR-TB and extensively drug-resistant (XDR-TB) cases.OBJECTIVE: Review the activity of the French TB Consilium since its establishment.DESIGN: Retrospective description and analysis of the activity of the French TB Consilium.RESULTS: Between 2005 and 2016, 786 TB cases or contacts of TB cases were presented at the French TB Consilium, including respectively 42% and 79% of all the MDR-TB and XDR-TB cases notified in France during this period. Treatment regimens including bedaquiline and/or delamanid were recommended for 42% of the cases presented at the French TB Consilium since 2009. Patients were more likely to be presented at the French TB Consilium if they were born in the WHO Europe Region, had XDR-TB, were diagnosed in the Paris region, or had resistance to additional drugs than those defining XDR-TB.CONCLUSION: The French TB Consilium helped supervise appropriate management of MDR/XDR-TB cases and facilitated implementation of new drugs for MDR/XDR-TB treatment.

Long-term plasma pharmacokinetics of bedaquiline for multidrug- and extensively drug-resistant tuberculosis.

SETTING: Bedaquiline (BDQ) has been approved for the treatment of multidrug- and extensively drug-resistant tuberculosis (MDR/XDR-TB). For many patients treatment is prolonged beyond the recommended 6 months. The long-term pharmacokinetics of BDQ have yet to be elucidated. OBJECTIVE: To evaluate plasma concentrations of BDQ during treatment and its elimination after treatment discontinuation. DESIGN: This was a retrospective study conducted in two units in France that provide treatment for MDR/XDR-TB. Sociodemographic, clinical, biological and therapeutic parameters were collected from patients currently or formerly treated with BDQ. Plasma concentrations of BDQ and its active M2 (N-desmethyl) metabolite were determined using ultra-performance liquid chromatography with tandem mass spectrometry. RESULTS: Thirteen patients were recruited (35 samples): 10 (31 samples) during BDQ treatment and 3 (4 samples) after BDQ discontinuation. The median duration of treatment with BDQ was 11 months (interquartile range [IQR] 8-14). During treatment, the median plasma BDQ concentrations and M2 were respectively 1264 ng/ml (IQR 910-2244) and 252 ng/ml (IQR 134-290). In one patient, BDQ was detected in the plasma 200 days after treatment discontinuation (528 ng/ml). CONCLUSION: BDQ and M2 plasma concentrations were consistent with good drug efficacy/safety profiles, suggesting good treatment adherence with no relevant drug interactions. The long-term plasma detectability of BDQ after treatment discontinuation may raise the spectre of the emergence of resistance.

Bacillus Calmette-Guerin infection following intravesical instillation: Does the strain matter?

PURPOSE: Intravesical BCG is the standard treatment of non-muscle invasive bladder cancer. No difference has yet been reported in the safety profiles of the various BCG strains. METHODS: A nationwide multidisciplinary retrospective survey was conducted between January 2013 and December 2016 to identify cases of BCG infection and differentiate them based on the type of BCG strain used. RESULTS: Forty patients were identified (BCG RIVM 28; other strains 8; unknown 4). Patients treated with BCG RIVM were less severely ill, with fewer occurrences of septic shock (3.6% vs. 50%, P=0.003) and ICU admission (7.1% vs. 62.5%, P=0.003). A higher frequency of pulmonary miliaries (71.4% vs. 12.5%, P=0.005) but lower transaminase levels (mean AST 65 vs. 264 U/L, P=0.001) were observed in these patients. No difference in terms of recovery was reported. CONCLUSION: The type of BCG strain could correlate with the frequency and severity of subsequent BCG infections.

Risk factors for extensive drug resistance in multidrug-resistant tuberculosis cases: a case-case study.

SETTINGS: Identification of extensively drug-resistant tuberculosis (XDR-TB) may be delayed because of the lack of availability of molecular testing for second-line drugs (SLDs). Early suspicion of XDR-TB is therefore necessary to avoid developing further drug resistance. OBJECTIVE: To identify the characteristics associated with XDR-TB among multidrug-resistant TB (MDR-TB) cases before the availability of second-line drug susceptibility testing (DST) results. METHODS: All MDR-TB cases with available second-line DST results recorded in France from 1998 to 2013 were classified as simple MDR-TB (no resistance to fluoroquinolones [FQs] or second-line injectable drugs [SLIDs]), pre-XDR-TB (resistance to FQs or SLIDs) and XDR-TB cases (resistance to both). RESULTS: A total of 833 MDR-TB cases were analysed, including 168 (20%) pre-XDR and 62 (7%) XDR-TB cases. A previous history of treatment was acknowledged among 41% of the cases; 12% were human immunodeficiency virus-positive. Characteristics independently associated with XDR-TB were foreign birth (OR 9.5), previous anti-tuberculosis treatment (OR 2.6), smear positivity (OR 4.5) and ethambutol (EMB) resistance (OR 9.1). Characteristics independently associated with pre-XDR-TB compared to simple MDR-TB cases were male sex (OR 1.6), birth in Europe (OR 2.6) and EMB resistance (OR 1.9). CONCLUSION: The presence of clinical or bacteriological characteristics associated with XDR-TB should lead to rapid molecular testing for resistance to SLDs before starting tailored treatment.

Comparison of methods available for identification of Mycobacterium chimaera.

OBJECTIVES: Mycobacterium chimaera is a recently described nontuberculous mycobacterium belonging to the Mycobacterium avium complex (MAC). Because this species is implicated in a worldwide outbreak due to contaminated heater-cooler unit water tanks during open-heart surgery, it has become mandatory for clinical microbiology laboratories to be able to differentiate M. chimaera from the other MAC species, especially M. intracellulare. Such identification has so far been restricted to specialized laboratories because it required the analysis of several gene sequences. The aim of this study was to evaluate commercial methods for identifying M. chimaera with regard to the reference gene sequencing ITS, the internal transcribed spacer 16-23S. METHODS: Forty-seven clinical and environmental isolates including 41 MAC were identified by (a) PCR sequencing of the ITS and hsp65 genes, (b) three molecular biology kits (INNO-LiPA Mycobacteria, GenoType Mycobacterium CM and GenoType NTM-DR) and (c) matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) using Microflex LT. RESULTS: There was a high concordance for species determination between the reference ITS sequencing and the GenoType NTM-DR test (39/41, 95%), the INNO-LiPA Mycobacteria test (38/41, 93%) and the hsp65 sequencing (38/41, 93%). The GenoType Mycobacterium CM test did not distinguish M. chimaera from M. intracellulare. MALDI-TOF MS distinguished two M. chimaera-M. intracellulare groups separated from M. avium and from the other mycobacterial species on a score-oriented dendrogram, but it also failed to differentiate the two species. CONCLUSIONS: INNO-LiPA Mycobacteria and GenoType NTM-DR are efficient assays for M. chimaera identification in clinical microbiology laboratories.

Team approach to manage difficult-to-treat TB cases: Experiences in Europe and beyond.

As recommended by the World Health Organization (WHO), optimal management of MDR-TB cases can be ensured by a multi-speciality consultation body known as 'TB Consilium'. This body usually includes different medical specialities, competences and perspectives (e.g., clinical expertise both for adults and children; surgical, radiological and public health expertise; psychological background and nursing experience, among others), thus lowering the risk of making mistakes - or managing the patients inappropriately, in order to improve their clinical outcomes. At present, several high MDR-TB burden countries in the different WHO regions (and beyond) have introduced TB Consilium-like bodies at the national or subnational level to reach consensus on the best treatment approach for their patients affected by TB. In addition, in countries/settings where a formal system of consultation does not exist, specialized staff from MDR-TB reference centres or international organizations usually spend a considerable amount of their working time responding to phone or e-mail clinical queries on how to manage M/XDR-TB cases. The aim of this manuscript is to describe the different experiences with the TB Consilia both at the international level (European Respiratory Society - ERS/WHO TB Consilium) and in some of the countries where this experience operates successfully in Europe and beyond. The Consilium experiences are described around the following topics: (1) history, aims and focus; (2) management and funding; (3) technical functioning and structure; (4) results achieved. In addition a comparative analysis of the TB Consilia in the different countries has been performed.

Examples of bedaquiline introduction for the management of multidrug-resistant tuberculosis in five countries.

BACKGROUND: For the first time in almost 50 years, there are new drugs available for the treatment of tuberculosis (TB), including bedaquiline (BDQ) and delamanid (DLM). The rate of introduction, however, has not kept pace with patient needs. It is estimated that as many as 23% of multidrug-resistant TB (MDR-TB) patients have an indication for receiving BDQ. As this is the first time the MDR-TB community is introducing new medications, it is important to understand how implementation can be developed in a variety of settings. METHODS: A qualitative assessment of country TB programs in which more than 5% of MDR-TB patients were started on BDQ under program conditions. RESULTS: National TB programs in Belarus, France, Georgia, South Africa, and Swaziland all started sizeable cohorts of patients on BDQ in 2015. Common factors observed in these programs included experience with compassionate use/expanded access, support from implementing partners, and adequate national or donor-supported budgets. Barriers to introduction included restriction of BDQ to the in-patient setting, lack of access to companion drugs, and the development of systems for pharmacovigilance. CONCLUSION: The five countries in this paper are examples of the introduction of new therapeutic options for the treatment of TB.

Multidrug and extensively drug-resistant tuberculosis.

The emergence of drug-resistant tuberculosis (TB) compromises global tuberculosis control. The incidence of multidrug-resistant strains (MDR) defined as resistant to the two main antituberculosis drugs, rifampicin and isoniazid, was raised in the 1990s. Ten percent of these strains have developed additional resistance to the main second-line antituberculosis drugs: fluoroquinolones and aminoglycosides. These strains are defined as extensively drug-resistant (XDR). The prognosis of MDR-TB and XDR-TB is poor due to limited therapeutic resources. However, many new innovations may lead to a radical change in this field. Genotypic testing is now able to detect drug resistance within a few hours. Genotypic diagnosis of rifampicin resistance is now recommended in France for each new case of TB. The currently recommended treatment for MDR-TB is long (18-24 months) and toxic. It is, however, on the verge of being replaced by a 9-month treatment. New antituberculosis drugs such as bedaquiline and delamanid should also improve the prognosis of MDR-TB and XDR-TB.

Induction therapy with linezolid/clarithromycin combination for Mycobacterium chelonae skin infections in immunocompromised hosts.

BACKGROUND: The optimal management of Mycobacterium chelonae disease in immunocompromised patients remains unclear. A combination of antimicrobial agents is recommended as monotherapy with clarithromycin has been associated with clinical failures due to acquired resistance. OBJECTIVES: We aim to report the efficacy and tolerability of linezolid in association with clarithromycin for the treatment of M. chelonae infections in immunocompromised patients. METHODS: We describe four immunocompromised patients treated by linezolid and clarithromycin for cutaneous M. chelonae disease. RESULTS: This combination was associated with rapid clinical efficacy in all patients with no relapse observed after a median follow-up of 2.25 years (1.4 years). However, this treatment was responsible for frequent adverse events including thrombocytopaenia, myalgia and mitochondrial toxicity. All adverse effects were reversible after linezolid discontinuation. CONCLUSIONS: We therefore suggest linezolid/clarithromycin combination as the initial therapeutic strategy for M. chelonae skin infections in immunocompromised patients.

[Tuberculosis in 2015: From diagnosis to the detection of multiresistant cases]. / La tuberculose en 2015 : du diagnostic à la détection des formes résistantes.

Incidence of pulmonary tuberculosis, a contagious infectious disease, decreases in France with 4934 reported cases in 2013. Tuberculosis remains a global health problem as smear is positive in only 50% cases and culture methods require time. In such a context, genotypic diagnostic tools such as Xpert® MTB/RIF gained interest. This rapid and simple-to-use nucleic acid amplification test allows a diagnosis in two hours and prevents further invasive investigations in pulmonary and mediastinal tuberculosis. Because of its low sensitivity, it cannot be used in pleural fluid. Indirect immunologic tests are of no use to diagnose active tuberculosis disease. Another current area of interest is the emergence of resistant tuberculosis. In France, approximately 100 cases of multidrug resistant tuberculosis and a few extensively drug resistant tuberculosis have been reported in 2014. Even though these forms of tuberculosis are imported, it is crucial to identify hazardous situations and to optimize care of these patients. Xpert® MTB/RIF is again of marked interest here as it detects rifampin resistance with a 95% sensitivity and a 98% specificity. Interpretation of genotypic tests such as Genotype® MTBDR or Xpert® MTB/RIF depends on known detected mutations, although they do not always have a clinical or phenotypic expression. In multidrug resistant tuberculosis, the new drug bedaquiline obtained approval for temporarily use in combination with other molecules when there is no other treatment option. Results of bedaquiline are encouraging but adverse events like QT prolongation or the development of new specific drug resistance should convince clinicians to use it with caution.