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  • 1
    Online Resource
    Online Resource
    Mycobacterium helveticum sp. nov., a novel slowly growing mycobacterial species associated with granulomatous lesions in adult swine
    Microbiology Society ; 2020
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 71, No. 1 ( 2020-12-23)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 71, No. 1 ( 2020-12-23)
    Abstract: The occurrence of nontuberculous mycobacteria in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. Mycobacteriosis in pigs is usually associated with members of the Mycobacterium avium complex and, in particular, with ‘ Mycobacterium avium subsp. hominissuis ’. Here we describe a novel slow-growing mycobacterial species isolated from lymph nodes obtained from two sows housed in different Swiss farms. The animals presented chronic inappetence and mild diarrhoea. Gross pathology revealed focal caseous lymphadenopathy of the mesenteric lymph nodes. Complete genome sequencing of the two isolates from the two sows was performed. The genomes comprised 5.76 Mb and an average nucleotide identity score of 99.97 %. Whole genome sequence, mycolic acid and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses revealed that the two isolates were not related to any previously described Mycobacterium species. The closest related species was Mycobacterium parmense , a slow-growing scotochromogenic mycobacterium first isolated from a cervical lymph node of a 3-year-old child. The name proposed for the new species is Mycobacterium helveticum sp. nov. and 16-83 T (=DSM 109965 T = LMG 2019-02457 T ) is the type strain.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004615
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2020
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    σ B and the σ B -Dependent arlRS and yabJ-spoVG Loci Affect Capsule Formation in Staphylococcus aureus
    American Society for Microbiology ; 2007
    In:  Infection and Immunity Vol. 75, No. 9 ( 2007-09), p. 4562-4571
    Details
    In: Infection and Immunity, American Society for Microbiology, Vol. 75, No. 9 ( 2007-09), p. 4562-4571
    Abstract: The alternative transcription factor σ B of Staphylococcus aureus affects the transcription of the cap gene cluster, required for the synthesis of capsular polysaccharide (CP), although this operon is lacking an apparent σ B -dependent promoter. Regulation of cap expression and CP production in S. aureus strain Newman was shown here to be influenced by σ B , the two-component signal transduction regulatory system ArlRS, and the yabJ-spoVG locus to different extents. Inactivation of arlR or deletion of the sigB operon strongly suppressed capA (CP synthesis enzyme A) transcription. Deletion of spoVG had a polar effect on yabJ-spoVG transcription and resulted in a two- to threefold decrease in capA transcription. Interestingly, immunofluorescence showed that CP production was strongly impaired in all three mutants, signaling that the yabJ-spoVG inactivation, despite its only partial effect on capA transcription, abolished capsule formation. trans -Complementation of the Δ spoVG mutant with yabJ-spoVG under the control of its native promoter restored CP-5 production and capA expression to levels seen in the wild type. Northern analyses revealed a strong impact of σ B on arlRS and yabJ-spoVG transcription. We hypothesize that ArlR and products of the yabJ-spoVG locus may serve as effectors that modulate σ B control over σ B -dependent genes lacking an apparent σ B promoter.
    Type of Medium: Online Resource
    ISSN: 0019-9567 , 1098-5522
    URL: Article
    DOI: 10.1128/IAI.00392-07
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2007
    detail.hit.zdb_id: 1483247-1
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  • 3
    Online Resource
    Online Resource
    In Vitro Bedaquiline and Clofazimine Susceptibility Testing in Mycobacterium abscessus
    American Society for Microbiology ; 2022
    In:  Antimicrobial Agents and Chemotherapy Vol. 66, No. 5 ( 2022-05-17)
    Details
    In: Antimicrobial Agents and Chemotherapy, American Society for Microbiology, Vol. 66, No. 5 ( 2022-05-17)
    Abstract: Bedaquiline and clofazimine are increasingly used to treat infections with Mycobacterium abscessus . We determined distributions of MICs by broth microdilution for bedaquiline and clofazimine for 61 M. abscessus clinical isolates using different media and incubation times. We show that incubation time and growth media critically influence the MIC. Our data will aid in defining future clinical breakpoints for in vitro susceptibility testing for bedaquiline and clofazimine in M. abscessus .
    Type of Medium: Online Resource
    ISSN: 0066-4804 , 1098-6596
    URL: Article
    DOI: 10.1128/aac.02346-21
    RVK:
    XA 24552
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 1496156-8
    SSG: 12
    SSG: 15,3
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  • 4
    Online Resource
    Online Resource
    Defining threshold values in microscopic examination and qPCR for optimal performance of line probe assays for resistance detection in Mycobacterium tuberculosis complex
    Elsevier BV ; 2019
    In:  Diagnostic Microbiology and Infectious Disease Vol. 95, No. 2 ( 2019-10), p. 159-161
    Details
    In: Diagnostic Microbiology and Infectious Disease, Elsevier BV, Vol. 95, No. 2 ( 2019-10), p. 159-161
    Type of Medium: Online Resource
    ISSN: 0732-8893
    URL: Article
    DOI: 10.1016/j.diagmicrobio.2019.06.001
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2019
    detail.hit.zdb_id: 2026024-6
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  • 5
    Online Resource
    Online Resource
    Functional Characterization of the σ B -Dependent yabJ - spoVG Operon in Staphylococcus aureus : Role in Methicillin and Glycopeptide Resistance
    American Society for Microbiology ; 2009
    In:  Antimicrobial Agents and Chemotherapy Vol. 53, No. 5 ( 2009-05), p. 1832-1839
    Details
    In: Antimicrobial Agents and Chemotherapy, American Society for Microbiology, Vol. 53, No. 5 ( 2009-05), p. 1832-1839
    Abstract: The alternative sigma factor σ B of Staphylococcus aureus controls the expression of multiple genes, including virulence determinants and global regulators; promotes capsule production; and increases the resistance levels of methicillin-resistant S. aureus (MRSA) and glycopeptide-intermediate-resistant S. aureus (GISA) strains. We show here that deletion of the σ B -controlled yabJ-spoVG operon, which codes for potential downstream regulators of σ B , abolished capsule synthesis and reduced resistance in MRSA and GISA to the same extent that σ B inactivation did. Introduction of the yabJ-spoVG operon in trans restored the original phenotype. By genetic manipulations, we show that SpoVG but not YabJ is required for complementation. We therefore postulate that SpoVG is the major factor of the yabJ-spoVG operon required in S. aureus for capsule formation and antibiotic resistance.
    Type of Medium: Online Resource
    ISSN: 0066-4804 , 1098-6596
    URL: Article
    DOI: 10.1128/AAC.01255-08
    RVK:
    XA 24552
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2009
    detail.hit.zdb_id: 1496156-8
    SSG: 12
    SSG: 15,3
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  • 6
    Online Resource
    Online Resource
    KatG as Counterselection Marker for Nontuberculous Mycobacteria
    American Society for Microbiology ; 2020
    In:  Antimicrobial Agents and Chemotherapy Vol. 64, No. 5 ( 2020-04-21)
    Details
    In: Antimicrobial Agents and Chemotherapy, American Society for Microbiology, Vol. 64, No. 5 ( 2020-04-21)
    Type of Medium: Online Resource
    ISSN: 0066-4804 , 1098-6596
    URL: Article
    DOI: 10.1128/AAC.02508-19
    RVK:
    XA 24552
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 1496156-8
    SSG: 12
    SSG: 15,3
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  • 7
    Online Resource
    Online Resource
    Use of the Bruker MALDI Biotyper for Identification of Molds in the Clinical Mycology Laboratory
    American Society for Microbiology ; 2014
    In:  Journal of Clinical Microbiology Vol. 52, No. 8 ( 2014-08), p. 2797-2803
    Details
    In: Journal of Clinical Microbiology, American Society for Microbiology, Vol. 52, No. 8 ( 2014-08), p. 2797-2803
    Abstract: Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is increasingly used for the identification of bacteria and fungi in the diagnostic laboratory. We evaluated the mold database of Bruker Daltonik (Bremen, Germany), the Filamentous Fungi Library 1.0. First, we studied 83 phenotypically and molecularly well-characterized, nondermatophyte, nondematiaceous molds from a clinical strain collection. Using the manufacturer-recommended interpretation criteria, genus and species identification rates were 78.3% and 54.2%, respectively. Reducing the species cutoff from 2.0 to 1.7 significantly increased species identification to 71.1% without increasing misidentifications. In a subsequent prospective study, 200 consecutive clinical mold isolates were identified by the MALDI Biotyper and our conventional identification algorithm. Discrepancies were resolved by ribosomal DNA (rDNA) internal transcribed spacer region sequence analysis. For the MALDI Biotyper, genus and species identification rates were 83.5% and 79.0%, respectively, when using a species cutoff of 1.7. Not identified were 16.5% of the isolates. Concordant genus and species assignments of MALDI-TOF MS and the conventional identification algorithm were observed for 98.2% and 64.2% of the isolates, respectively. Four erroneous species assignments were observed using the MALDI Biotyper. The MALDI Biotyper seems highly reliable for the identification of molds when using the Filamentous Fungi Library 1.0 and a species cutoff of 1.7. However, expansion of the database is required to reduce the number of nonidentified isolates.
    Type of Medium: Online Resource
    ISSN: 0095-1137 , 1098-660X
    URL: Article
    DOI: 10.1128/JCM.00049-14
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2014
    detail.hit.zdb_id: 1498353-9
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Streptococcus tigurinus, a Novel Member of the Streptococcus mitis Group, Causes Invasive Infections
    American Society for Microbiology ; 2012
    In:  Journal of Clinical Microbiology Vol. 50, No. 9 ( 2012-09), p. 2969-2973
    Details
    In: Journal of Clinical Microbiology, American Society for Microbiology, Vol. 50, No. 9 ( 2012-09), p. 2969-2973
    Abstract: We recently described the novel species Streptococcus tigurinus sp. nov. belonging to the Streptococcus mitis group. The type strain AZ_3a T of S. tigurinus was originally isolated from a patient with infective endocarditis. According to its phenotypic and molecular characteristics, S. tigurinus is most closely related to Streptococcus mitis , Streptococcus pneumoniae , Streptococcus pseudopneumoniae , Streptococcus oralis , and Streptococcus infantis . Accurate identification of S. tigurinus is facilitated by 16S rRNA gene analysis. We retrospectively analyzed our 16S rRNA gene molecular database, which contains sequences of all clinical samples obtained in our institute since 2003. We detected 17 16S rRNA gene sequences which were assigned to S. tigurinus , including sequences from the 3 S. tigurinus strains described previously. S. tigurinus originated from normally sterile body sites, such as blood, cerebrospinal fluid, or heart valves, of 14 patients and was initially detected by culture or broad-range 16S rRNA gene PCR, followed by sequencing. The 14 patients had serious invasive infections, i.e., infective endocarditis ( n = 6), spondylodiscitis ( n = 3), bacteremia ( n = 2), meningitis ( n = 1), prosthetic joint infection ( n = 1), and thoracic empyema ( n = 1). To evaluate the presence of Streptococcus tigurinus in the endogenous oral microbial flora, we screened saliva specimens of 31 volunteers. After selective growth, alpha-hemolytic growing colonies were analyzed by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and subsequent molecular methods. S. tigurinus was not identified among 608 strains analyzed. These data indicate that S. tigurinus is not widely distributed in the oral cavity. In conclusion, S. tigurinus is a novel agent of invasive infections, particularly infective endocarditis.
    Type of Medium: Online Resource
    ISSN: 0095-1137 , 1098-660X
    URL: Article
    DOI: 10.1128/JCM.00849-12
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2012
    detail.hit.zdb_id: 1498353-9
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Evaluation of the Bruker MALDI Biotyper for Identification of Gram-Positive Rods: Development of a Diagnostic Algorithm for the Clinical Laboratory
    American Society for Microbiology ; 2014
    In:  Journal of Clinical Microbiology Vol. 52, No. 4 ( 2014-04), p. 1089-1097
    Details
    In: Journal of Clinical Microbiology, American Society for Microbiology, Vol. 52, No. 4 ( 2014-04), p. 1089-1097
    Abstract: Reported matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) identification rates of Gram-positive rods (GPR) are low compared to identification rates of Gram-positive cocci. In this study, three sample preparation methods were compared for MALDI-TOF MS identification of 190 well-characterized GPR strains: direct transfer, direct transfer-formic acid preparation, and ethanol-formic acid extraction. Using the interpretation criteria recommended by the manufacturer, identification rates were significantly higher for direct transfer-formic acid preparation and ethanol-formic acid extraction than for direct transfer. Reducing the species cutoff from 2.0 to 1.7 significantly increased species identification rates. In a subsequent prospective study, 215 clinical GPR isolates were analyzed by MALDI-TOF MS, and the results were compared to those for identification using conventional methods, with discrepancies being resolved by 16S rRNA and rpoB gene analysis. Using the direct transfer-formic acid preparation and a species cutoff of 1.7, congruencies on the genus and species levels of 87.4% and 79.1%, respectively, were achieved. In addition, the rate of nonidentified isolates dropped from 12.1% to 5.6% when using an extended database, i.e., the Bruker database amended by reference spectra of the 190 GPR of the retrospective study. Our data demonstrate three ways to improve GPR identification by the Bruker MALDI Biotyper, (i) optimize sample preparation using formic acid, (ii) reduce cutoff scores for species identification, and (iii) expand the database. Based on our results, we suggest an identification algorithm for the clinical laboratory combining MALDI-TOF MS with nucleic acid sequencing.
    Type of Medium: Online Resource
    ISSN: 0095-1137 , 1098-660X
    URL: Article
    DOI: 10.1128/JCM.02399-13
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2014
    detail.hit.zdb_id: 1498353-9
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Evaluation of the Bruker MALDI Biotyper for Identification of Fastidious Gram-Negative Rods
    American Society for Microbiology ; 2016
    In:  Journal of Clinical Microbiology Vol. 54, No. 3 ( 2016-03), p. 543-548
    Details
    In: Journal of Clinical Microbiology, American Society for Microbiology, Vol. 54, No. 3 ( 2016-03), p. 543-548
    Abstract: Matrix-assisted laser desorption ionization−time of flight mass spectrometry (MALDI-TOF MS) has entered clinical laboratories, facilitating identification of bacteria. Here, we evaluated the MALDI Biotyper (Bruker Daltonics) for the identification of fastidious Gram-negative rods (GNR). Three sample preparation methods, direct colony transfer, direct transfer plus on-target formic acid preparation, and ethanol-formic acid extraction, were analyzed for 151 clinical isolates. Direct colony transfer applied with the manufacturer's interpretation criteria resulted in overall species and genus identification rates of 43.0% and 32.5%, respectively; 23.2% of the isolates were not identified, and two misidentifications (1.3%) were observed. The species identification rates increased to 46.4% and 53.7% for direct transfer plus formic acid preparation and ethanol-formic acid extraction, respectively. In addition, we evaluated score value cutoff alterations. The identification rates hardly increased by reducing the genus cutoff, while reducing the 2.0 species cutoff to 1.9 and to 1.8 increased the identification rates to up to 66.2% without increasing the rate of misidentifications. This study shows that fastidious GNR can reliably be identified using the MALDI Biotyper. However, the identification rates do not reach those of nonfastidious GNR such as the Enterobacteriaceae . In addition, two approaches optimizing the identification of fastidious GNR by the MALDI Biotyper were demonstrated: formic acid-based on-target sample treatment and reductions in cutoff scores to increase the species identification rates.
    Type of Medium: Online Resource
    ISSN: 0095-1137 , 1098-660X
    URL: Article
    DOI: 10.1128/JCM.03107-15
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2016
    detail.hit.zdb_id: 1498353-9
    SSG: 12
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