Recovery of Mycobacterium haemophilum skin infection in an HIV-I-infected patient after the start of antiretroviral triple therapy

Constant Rate Thermal Analysis (CRTA) method implies controlling the temperature in such a way that the reaction rate is maintained constant all over the process. This method allows determining simultaneously both the kinetic parameters and the kinetic model from a single experiment as the shape of the CRTA α-T curves strongly depends on the kinetic model. CRTA method has been developed in the market only for thermogravimetric and thermodilatometric systems and, therefore, its use has been limited until now to the kinetic study of processes involving changes in mass or size of the samples, respectively. To overcome this obstacle, a method has been developed in this work for using the DSC signal for controlling the process rate in such a way that CRTA would be applied to the kinetic analysis of either phase transformations or crystallizations. The advantages of CRTA for performing the kinetics of crystallization processes have been here successfully demonstrated for the first time after selecting the crystallization of zirconia gel as test reaction.Ministerio de Economía y Competitividad CTQ2014-52763-C2-1-RJunta de Andalucía TEP-7858, TEP-1900FEDER CTQ2014-52763-C2-1-RFEDER TEP-7858 TEP-190

The ins and outs of mycobacterium tuberculosis drug susceptibility testing: Themed review 'Therapeutic efficiency in the presence of resistance mechanisms: (when) to give-or not to give?'

Clin Microbiol Infect ABSTRACT: Drug susceptibility testing of Mycobacterium tuberculosis in the diagnostic laboratory classifies clinical isolates as either drug-'resistant' or drug-'susceptible', on the basis of their ability to grow in the presence of a 'critical concentration' of the test compound. From knowledge of the mechanisms that underlie drug resistance, it has become evident that drug resistance in M. tuberculosis is quite heterogeneous and involves low-level, moderate-level and high-level drug resistance phenotypes. Different mutations are associated with different levels of phenotypic resistance, and the acquisition of a genetic alteration leading to a decrease in drug susceptibility does not inevitably exclude the affected compound from treatment regimens. As a result, the simple categorization of clinical M. tuberculosis isolates as 'resistant' on the basis of susceptibility testing at 'critical concentrations' may need to be revised and supplemented by quantitative measures of resistance testing to reflect the biological complexity of drug resistance, with the view of optimally exploiting the compounds available for treatment

Treatment of Nontuberculous Mycobacterial Pulmonary Disease: An Official ATS/ERS/ESCMID/IDSA Clinical Practice Guideline

Nontuberculous mycobacteria (NTM) represent over 190 species and subspecies, some of which can produce disease in humans of all ages and can affect both pulmonary and extrapulmonary sites. This guideline focuses on pulmonary disease in adults (without cystic fibrosis or human immunodeficiency virus infection) caused by the most common NTM pathogens such as Mycobacterium avium complex, Mycobacterium kansasii, and Mycobacterium xenopi among the slowly growing NTM and Mycobacterium abscessus among the rapidly growing NTM. A panel of experts was carefully selected by leading international respiratory medicine and infectious diseases societies (ATS, ERS, ESCMID, IDSA) and included specialists in pulmonary medicine, infectious diseases and clinical microbiology, laboratory medicine, and patient advocacy. Systematic reviews were conducted around each of 22 PICO (Population, Intervention, Comparator, Outcome) questions and the recommendations were formulated, written, and graded using the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach. Thirty-one evidence-based recommendations about treatment of NTM pulmonary disease are provided. This guideline is intended for use by healthcare professionals who care for patients with NTM pulmonary disease, including specialists in infectious diseases and pulmonary diseases

Evaluation of a diagnostic flow chart for detection and confirmation of extended spectrum β-lactamases (ESBL) in Enterobacteriaceae

Clin Microbiol Infect ABSTRACT: This study aimed to develop a modular, diagnostic algorithm for extended spectrum β-lactamase (ESBL) detection in Enterobacteriaceae. Clinical Enterobacteriaceae strains (n = 2518) were screened for ESBL production using Clinical and Laboratory Standards Institute (CLSI) breakpoints for third-generation cephalosporins and by synergy image detection (clavulanic acid/extended-spectrum cephalosporins). Isolates screening positive for ESBL (n = 242, 108 by critical CLSI diameters alone, five by double disk synergy test (DDST) alone, and 129 by both critical diameters and DDST) and 138 ESBL screening negative isolates (control group) were investigated by molecular methods considered to be the reference standard (multiplex CTX-M type PCR, TEM and SHV type sequence characterization). One hundred and twenty-four out of 242 Enterobacteriaceae isolates screening positive for ESBL were confirmed to be ESBL positive by the reference standard, the majority of them in E. coli, K. pneumoniae and E. cloacae (94, 17 and nine isolates, respectively). Prevalence of ESBL production ranged from <1% for P. mirabilis to 4.7%, 5.1% and 6.6%, for K. pneumoniae, E. cloacae and E. coli, respectively. Combining CLSI ceftriaxone and cefpodoxime critical ESBL diameters was found to be the most sensitive phenotypic screening method (sensitivity 99.2%). Combining critical diameters of cefpodoxime and ceftriaxone with DDST for cefpodoxime resulted in a sensitivity of 100%. For phenotypic confirmation, combining the CLSI recommended combined disk test (CDT) for ceftazidime and cefotaxime amended with a cefepime CDT was highly sensitive (100%) and specific (97.5%). With respect to the studied population, the diagnostic ESBL algorithm developed would have resulted in sensitivity and specificity of 100%. The corresponding flow chart is simple, easy to use, inexpensive and applicable in the routine diagnostic laboratory

Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country.

Immigrants from regions with a high incidence of tuberculosis (TB) are a risk group for TB in low-incidence countries such as Switzerland. In a previous analysis of a nationwide collection of 520 Mycobacterium tuberculosis isolates from 2000 to 2008, we identified 35 clusters comprising 90 patients based on standard genotyping (24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat [MIRU-VNTR] typing and spoligotyping). Here, we used whole-genome sequencing (WGS) to revisit these transmission clusters. Genome-based transmission clusters were defined as isolate pairs separated by ≤12 single nucleotide polymorphisms (SNPs). WGS confirmed 17/35 (49%) MIRU-VNTR typing clusters; the other 18 clusters contained pairs separated by &gt;12 SNPs. Most transmission clusters (3/4) of Swiss-born patients were confirmed by WGS, as opposed to 25% (4/16) of the clusters involving only foreign-born patients. The overall clustering proportion was 17% (90 patients; 95% confidence interval [CI], 14 to 21%) by standard genotyping but only 8% (43 patients; 95% CI, 6 to 11%) by WGS. The clustering proportion was 17% (67/401; 95% CI, 13 to 21%) by standard genotyping and 7% (26/401; 95% CI, 4 to 9%) by WGS among foreign-born patients and 19% (23/119; 95% CI, 13 to 28%) and 14% (17/119; 95% CI, 9 to 22%), respectively, among Swiss-born patients. Using weighted logistic regression, we found weak evidence of an association between birth origin and transmission (adjusted odds ratio of 2.2 and 95% CI of 0.9 to 5.5 comparing Swiss-born patients to others). In conclusion, standard genotyping overestimated recent TB transmission in Switzerland compared to WGS, particularly among immigrants from regions with a high TB incidence, where genetically closely related strains often predominate. We recommend the use of WGS to identify transmission clusters in settings with a low incidence of TB

Characterization of selected strains of mucorales using fatty acid profiles Caracterização de linhagens de mucorales através do perfil de ácidos graxos

The fatty acid profiles of several fungi of the order Mucorales (Zygomycetes), including Backusella lamprospora (Lendner) Benny and R.K. Benj., Benjaminiella youngii P.M. Kirk, Circinella simplex van Tieghem, Cunninghamella blakesleeana Lendner, Mortierella ramanniana (Möller) Linnem., Mucor circinelloides f. janssenii (Lendner) Schipper, Mycotypha microspora Fenner, Rhizomucor miehei (Cooney and R. Emerson) Schipper and Rhizomucor pusillus (Lindt) Schipper, and of Volutella sp. Fr., from the class Ascomycetes, were qualitatively analysed by gas-liquid chromatography in order to determine the taxonomic value of these chemotaxonomic markers. The fatty acids present in all strains were palmitic (16:0), oleic (18:1), linoleic (18:2) and <FONT FACE="Symbol">g</FONT>-linolenic (18:3) acid, with the exception that the latter was not found in Volutella sp. Chemotaxonomic markers for some species and genera were obtained, including a non-identified fatty acid, FAME8 (minimum and maximum retention times of 27.92 and 28.28 minutes) for Rhizomucor miehei CCT 2236 and Rhizomucor pusillus CCT 4133, and FAME3 (minimum and maximum of 16.53 and 16.61 minutes) for Benjaminiella youngii CCT 4121. The chemotaxonomic marker of the order Mucorales was the fatty acid 18:3<FONT FACE="Symbol">w</FONT>6, confirming previous data from literature. The results of the present study suggest that qualitative fatty acid analysis can be an important chemotaxonomic tool for the classification of fungi assigned to the order Mucorales (Zygomycetes).<br>O perfil de ácidos graxos de Backusella lamprospora (Lendner) Benny e R.K. Benj., Benjaminiella youngii P.M. Kirk, Circinella simplex van Tieghem, Cunninghamella blakesleeana Lendner, Mortierella ramanniana (Möller) Linnem., Mucor circinelloides f. janssenii (Lendner) Schipper, Mycotypha microspora Fenner, Rhizomucor miehei (Cooney e R. Emerson) Schipper e Rhizomucor pusillus (Lindt) Schipper, da ordem Mucorales (Zygomycetes), e Volutella sp. Fr., da classe Ascomycetes, foram analisados qualitativamente por cromatografia gás-líquida, tendo como objetivo determinar o valor taxonômico destes marcadores quimiotaxonômicos. Os ácidos palmítico (16:0), oléico (18:1), linoléico (18:2) e <FONT FACE="Symbol">g</FONT>-linolênico (18:3) foram encontrados em todas as linhagens, com exceção do último, o qual não foi encontrado na linhagem de Volutella analisada. Foram obtidos marcadores quimiotaxonômicos para algumas espécies e gêneros estudados, incluindo um ácido graxo não-identificado, FAME8 (tempos de retenção mínimo e máximo de 27,92 e 28,28 minutos) para Rhizomucor miehei CCT 2236 e Rhizomucor pusillus CCT 4133 e FAME3 (tempos de retenção mínimo e máximo de 16,53 e 16,61 minutos) para Benjaminiella youngii CCT 4121. Para a ordem Mucorales, o marcador quimiotaxonômico obtido foi o ácido graxo 18:3<FONT FACE="Symbol">w</FONT>6, confirmando dados da literatura. Os resultados do presente estudo sugerem que a análise qualitativa do perfil de ácidos graxos pode ser uma ferramenta importante na classificação de fungos da ordem Mucorales (Zygomycetes)

The critical influence of the intermediate category on interpretation errors in revised EUCAST and CLSI antimicrobial susceptibility testing guidelines

Erroneous assignments of clinical isolates to the interpretative categories susceptible, intermediate and resistant can deprive a patient of successful antimicrobial therapy. The rate of major errors (ME) and very major errors (vME) is dependent on: (i) the precision/standard deviation (σ) of the antibiotic susceptibility testing (AST) method, (ii) the diameter distributions, (iii) clinical breakpoints, and (iv) the width of the intermediate zone. The European Committee on AST (EUCAST) has abandoned or decreased the intermediate zone for several drug/species combinations. This study focused on the effects of discontinuing the intermediate category on the rate of interpretation errors. In total, 10 341 non-duplicate clinical isolates were included in the study. For susceptibility testing the disc diffusion method was used. Error probabilities were calculated separately for diameter values flanking the interpretative category borders. Error probabilities were then applied to the actual numbers of clinical isolates investigated and expected rates of ME and vME were calculated. Applying EUCAST AST guidelines, significant rates of ME/vME were demonstrated for all drug/species combinations without an intermediate range. Virtually all ME/vME expected were eliminated in CLSI guidelines that retained an intermediate zone. If wild-type and resistant isolates are not clearly separated in susceptibility distributions, the retaining of an intermediate zone will decrease the number of ME and vME. An intermediate zone of 2-3 mm avoids almost all ME/vME for most species/drug combinations depending on diameter distributions. Laboratories should know their epidemiology settings to be able to detect problems of individual species/drug/clinical breakpoint combinations and take measures to improve precision of diameter measurements