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.

Comparison of a semiautomated commercial repetitive-sequence-based PCR method with spoligotyping, 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing, and restriction fragment length polymorphism-based analysis of IS6110 for Mycobacterium tuberculosis typing.

Fifty-two multidrug-resistant isolates of Mycobacterium tuberculosis representative of the currently predominant lineages in France were analyzed using repetitive-sequence-based PCR (rep-PCR) DiversiLab (DL), spoligotyping, 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing (MIRU-VNTR), and restriction fragment length polymorphism of IS6110 (IS6110-RFLP). DL, as opposed to MIRU-VNTR and IS6110-RFLP analysis, did not allow discrimination among half of the isolates, an indication of comparatively lower resolving power.

[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.

A surge of MDR and XDR tuberculosis in France among patients born in the Former Soviet Union.

A marked increase in the number of multidrug-resistant (MDR) tuberculosis (TB) cases entirely related to patients born in the Former Soviet Union was observed in France in the last two years. Very few cases were clustered, suggesting it is a consequence of recent immigration of patients already infected in their country of origin. This major increase challenges the existing structures for management of MDR and extensively drug-resistant TB (XDR-TB).

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.

Molecular investigation of resistance to the antituberculous drug ethionamide in multidrug-resistant clinical isolates of Mycobacterium tuberculosis.

Ethionamide (ETH) needs to be activated by the mono-oxygenase EthA, which is regulated by EthR, in order to be active against Mycobacterium tuberculosis. The activated drug targets the enzyme InhA, which is involved in cell wall biosynthesis. Resistance to ETH has been reported to result from various mechanisms, including mutations altering EthA/EthR, InhA and its promoter, the NADH dehydrogenase encoded by ndh, and the MshA enzyme, involved in mycothiol biosynthesis. We searched for such mutations in 87 clinical isolates: 47 ETH-resistant (ETH(r)) isolates, 24 ETH-susceptible (ETH(s)) isolates, and 16 isolates susceptible to ETH but displaying an intermediate proportion of resistant cells (ETH(Sip); defined as ≥1% but <10% resistant cells). In 81% (38/47) of the ETH(r) isolates, we found mutations in ethA, ethR, or inhA or its promoter, which mostly corresponded to new alterations in ethA and ethR. The 9 ETH(r) isolates without a mutation in these three genes (9/47, 19%) had no mutation in ndh, and a single isolate had a mutation in mshA. Of the 16 ETH(Sip) isolates, 7 had a mutation in ethA, 8 had no detectable mutation, and 1 had a mutation in mshA. Finally, of the 24 ETH(s) isolates, 23 had no mutation in the studied genes and 1 displayed a yet unknown mutation in the inhA promoter. Globally, the mechanism of resistance to ETH remained unknown for 19% of the ETH(r) isolates, highlighting the complexity of the mechanisms of ETH resistance in M. tuberculosis.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry-based single nucleotide polymorphism genotyping assay using iPLEX gold technology for identification of Mycobacterium tuberculosis complex species and lineages.

The major goal of the present study was to investigate the potential use of a novel single nucleotide polymorphism (SNP) genotyping technology, called iPLEX Gold (Sequenom), for the simultaneous analysis of 16 SNPs that have been previously validated as useful for identification of Mycobacterium tuberculosis complex (MTBC) species and classification of MTBC isolates into distinct genetic lineages, known as principal genetic groups (PGGs) and SNP cluster groups (SCGs). In this context, we developed a 16-plex iPLEX assay based on an allele-specific-primer single-base-extension reaction using the iPLEX Gold kit (Sequenom), followed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis on the commercially available Sequenom MassARRAY platform. This assay was tested on a panel of 55 well-characterized MTBC strains that were also genotyped for the same loci using the previously reported SNaPshot assay, as well as 10 non-MTBC mycobacteria and 4 bacteria not belonging to the genus Mycobacterium. All MTBC samples were successfully analyzed with the iPLEX assay, which yielded clear allelic data for 99.9% of the SNPs (879 out of 880). No false-positive results were obtained with the negative controls. Compared to the SNaPshot assay, the newly developed 16-plex iPLEX assay produced fully concordant results that allowed reliable differentiation of MTBC species and recognition of lineages, thus demonstrating its potential value in diagnostic, epidemiological, and evolutionary applications. Compared to the SNaPshot approach, the implementation of the iPLEX technology could offer a higher throughput and could be a more flexible and cost-effective option for microbiology laboratories.

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.

Identification and genotyping of Mycobacterium tuberculosis complex species by use of a SNaPshot Minisequencing-based assay.

The aim of the present study was to investigate the use of the SNaPshot minisequencing method for the identification of Mycobacterium tuberculosis complex (MTBC) isolates to the species level and for further genotyping of M. tuberculosis isolates. We developed an innovative strategy based on two multiplex allele-specific minisequencing assays that allowed detection of eight species-specific and eight lineage-specific single nucleotide polymorphisms (SNPs). Each assay consisted of an eightplex PCR amplification, followed by an eightplex minisequencing reaction with the SNaPshot multiplex kit (Applied Biosystems) and, finally, analysis of the extension products by capillary electrophoresis. The whole strategy was developed with a panel of 56 MTBC strains and 15 negative controls. All MTBC strains tested except one M. africanum clinical isolate were accurately identified to the species level, and all M. tuberculosis isolates were successfully further genotyped. This two-step strategy based on SNaPshot minisequencing allows the simultaneous differentiation of closely related members of the MTBC, the distinction between principal genetic groups, and the characterization of M. tuberculosis isolates into one of the seven prominent SNP cluster groups (SCGs) and could be a useful tool for diagnostic and epidemiological purposes.

[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.

Performance of MTBDR plus for detecting high/low levels of Mycobacterium tuberculosis resistance to isoniazid.

SETTING: We recently evaluated the Genotype MTBDR test for assessing Mycobacterium tuberculosis resistance to rifampicin (RMP) and isoniazid (INH) by detecting mutations in rpoB (codons 511-533) and katG (codon 315). A new version of the test, MTBDR plus, has been designed to also detect mutations in the regulatory region of inhA. OBJECTIVE: To evaluate the performance of MTBDR plus over MTBDR. RESULTS: In 113 isolates, MTBDR plus detected all 76 RMP-resistant (RMP-R) strains and all 64 INH-resistant (INH-R) strains with KatG-315 mutations, 59 of which displayed a high level of INH resistance. It also identified 18 strains undetectable by MTBDR, without mutation in KatG-315 but with a -15 C-->T mutation in the regulatory region of inhA, of which 15 displayed a low level of INH resistance. Thirteen INH-R strains, which mainly harboured mutations in KatG at positions other than 315, were undetected by MTBDR plus. CONCLUSION: MTBDR plus retains the accuracy shown by MTBDR in detecting RMP resistance and is more sensitive in detecting INH resistance (86% vs. 67%), particularly at low levels (minimum inhibitory concentration<1 mg/l, 69% vs. 17%). The negative predictive value of the test (the probability of a strain with a wild-type test being susceptible to INH) is >98% when the rate of INH is <10%, as it is in France.

Cutaneous miliary resistant tuberculosis in a patient infected with human immunodeficiency virus: case report and literature review.

We report the case of a patient infected with human immunodeficiency virus who presented with fever and a disseminated papulous eruption, diagnosed as cutaneous miliary tuberculosis. The diagnosis was made by histological examination of a skin biopsy, which showed numerous acid-fast bacilli. A culture grown from a skin biopsy isolated a resistant Mycobacterium tuberculosis strain. The papules disappeared within a few days after starting treatment with pyrazinamide, isoniazid and moxifloxacin.

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.

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.

[Treatment of cutaneous infections due to Mycobacterium fortuitum: two cases]. / Traitement des infections cutanées àMycobacterium fortuitum : deux cas.

INTRODUCTION: Cutaneous infections due to Mycobacterium fortuitum, a rapidly growing environmental mycobacteria, are often iatrogenic, resulting from surgery or injection. We report two cases following plastic surgery and describe the outcome after surgery and antibiotics. CASE REPORTS: Two immunocompetent women underwent abdominal plastic surgery and liposuction, which were complicated with recurrent abscesses one and 13 months later respectively. Cultures of bacteriologic samples isolated M. fortuitum in the two patients. The two strains exhibited different antibiotic sensibility profiles. The initial antibiotic therapy consisted of combined amikacin and moxifloxacin in both patients plus imipenem in one, followed by oral doxycycline and clarithromycin in one and moxifloxacin in the other for a total duration of nine and five months, respectively. In both cases, surgical treatment was also given before, during and after antibiotic therapy. No new lesions had appeared six months after the end of antibiotic therapy. DISCUSSION: Cutaneous infections due to M. fortuitum are rare and secondary to iatrogenic skin wounds. The clinical appearance is not specific, accounting for delayed diagnosis. Treatment is difficult and there is no consensus. According to our experience, surgical treatment is essential whereas the efficacy of antibiotics, even involving multiple agents, seems more doubtful.

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.