Multicenter Evaluation of the Bruker MALDI Biotyper CA System for the Identification of Clinically Important Bacteria and Yeasts

Wilson, Deborah A.; Young, Stephen; Timm, K. N.; Novak-Weekley, Susan; Marlowe, Elizabeth M.; Madisen, Neil; Lillie, Jennifer L.; Ledeboer, Nathan A.; Smith, Rebecca; Hyke, Josh; Griego-Fullbright, Christen; Jim, Patricia; Granato, Paul A.; Faron, Matthew L.; Cumpio, Joven; Buchan, Blake W.; Procop, Gary W.

doi:10.1093/ajcp/aqw225

Cited by 27 publications

(16 citation statements)

References 27 publications

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“…However, the non-genomic nature of this method limits the phylogenetic investigation of closely related species or strains. This method is also limited by the comprehensiveness of the database used to compare spectra, which to date are heavily biased towards medically relevant pathogens [42]. Classification using 16S rRNA sequences and ANI provided limited taxonomic resolution and thus, less confidence in species identification [43].…”

Section: Discussionmentioning

confidence: 99%

Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries

et al. 2020

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Background: Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes. In order to understand the genetic basis of these similarities, a comparative genomic approach was used to define the pan-, core, accessory, and unique coding sequences of a representative population of Salmonella and Citrobacter strains. Results: Analysis of the genomic content of 58 S. enterica strains and 37 Citrobacter strains revealed the presence of 31,130 and 1540 coding sequences within the pan-and core genome of this population. Amino acid sequences unique to either Salmonella (n = 1112) or Citrobacter (n = 195) were identified and revealed potential niche-specific adaptations. Phylogenetic network analysis of the protein families encoded by the pan-genome indicated that genetic exchange between Salmonella and Citrobacter may have led to the acquisition of similar traits and also diversification within the genera. Conclusions: Core genome analysis suggests that the Salmonella enterica and Citrobacter populations investigated here share a common evolutionary history. Comparative analysis of the core and pan-genomes was able to define the genetic features that distinguish Salmonella from Citrobacter and highlight niche specific adaptations.

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Section: Discussionmentioning

confidence: 99%

Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries

et al. 2020

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“…To investigate the broader utility of the NIH Mold Database beyond our institution, a multicenter study including eight US academic institutions was conducted. Unlike multicenter bacterial and yeast studies for which excellent inter- and intra-laboratory reproducibility has been demonstrated (Westblade et al, 2015; Wilson et al, 2017), this study has highlighted significant performance variability between instruments regardless of acquisition parameters and demonstrated that development of a specific mold standard is required for successful use of MALDI-TOF MS for mold identification.…”

Section: Introductionmentioning

confidence: 91%

Multicenter Study Demonstrates Standardization Requirements for Mold Identification by MALDI-TOF MS

et al. 2019

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ObjectivesRapid and accurate mold identification is critical for guiding therapy for mold infections. MALDI-TOF MS has been widely adopted for bacterial and yeast identification; however, few clinical laboratories have applied this technology for routine mold identification due to limited database availability and lack of standardized processes. Here, we evaluated the versatility of the NIH Mold Database in a multicenter evaluation.MethodsThe NIH Mold Database was evaluated by eight US academic centers using a solid media extraction method and a challenge set of 80 clinical mold isolates. Multiple instrument parameters important for spectra optimization were evaluated, leading to the development of two specialized acquisition programs (NIH method and the Alternate-B method).ResultsA wide range in performance (33–77%) was initially observed across the eight centers when routine spectral acquisition parameters were applied. Use of the NIH or the Alternate-B specialized acquisition programs, which are different than those used routinely for bacterial and yeast spectral acquisition (MBT_AutoX), in combination with optimized instrument maintenance, improved performance, illustrating that acquisition parameters may be one of the key limiting variable in achieving successful performance.ConclusionSuccessful mold identification using the NIH Database for MALDI-TOF MS on Biotyper systems was demonstrated across multiple institutions for the first time following identification of critical program parameters combined with instrument optimization. This significantly advances our potential to implement MALDI-TOF MS for mold identification across many institutions. Because instrument variability is inevitable, development of an instrument performance standard specific for mold spectral acquisition is suggested to improve reproducibility across instruments.

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“…Marucco et al compared identification of Candida species obtained by BD Phoenix (Becton Dickinson, Franklin Lakes, NJ, USA) and the Bruker system using 192 isolates from the strain collection of the Mycology Network of the Autonomous City of Buenos Aires, Argentina, reporting an observed concordance of 95%, with 5% of isolates not correctly identified by the BD Phoenix system [35]. Wilson et al reported results of a multicenter assessment of the Bruker MALDI Biotyper CA system for identification of clinically significant bacteria and yeasts, including 815 yeast isolates evaluated using three processing methods [36]. The percentage identified and the percentage identified with a high level of confidence were 98% and 88%, respectively, with the extended direct transfer method being superior to the direct transfer method (74% and 49% success, respectively) [36].…”

Section: Yeasts With a Focus On Candida And Cryptococcus Speciesmentioning

confidence: 99%

“…Wilson et al reported results of a multicenter assessment of the Bruker MALDI Biotyper CA system for identification of clinically significant bacteria and yeasts, including 815 yeast isolates evaluated using three processing methods [36]. The percentage identified and the percentage identified with a high level of confidence were 98% and 88%, respectively, with the extended direct transfer method being superior to the direct transfer method (74% and 49% success, respectively) [36]. Turhan et al assessed the Bruker system with 117 yeasts, including 115 candidemia-associated Candida species, reporting 98% and 87% identification to the genus- and species-level, respectively [37].…”

Section: Yeasts With a Focus On Candida And Cryptococcus Speciesmentioning

confidence: 99%

A Moldy Application of MALDI: MALDI-ToF Mass Spectrometry for Fungal Identification

Patel

2019

JoF

116

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As a result of its being inexpensive, easy to perform, fast and accurate, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) is quickly becoming the standard means of bacterial identification from cultures in clinical microbiology laboratories. Its adoption for routine identification of yeasts and even dimorphic and filamentous fungi in cultures, while slower, is now being realized, with many of the same benefits as have been recognized on the bacterial side. In this review, the use of MALDI-ToF MS for identification of yeasts, and dimorphic and filamentous fungi grown in culture will be reviewed, with strengths and limitations addressed.

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Multicenter Evaluation of the Bruker MALDI Biotyper CA System for the Identification of Clinically Important Bacteria and Yeasts

Abstract: The Bruker MALDI Biotyper CA System accurately identifies most clinically important bacteria and yeasts and has optional processing methods to improve isolate characterization.

Cited by 27 publications

References 27 publications

Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries

Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries

Multicenter Study Demonstrates Standardization Requirements for Mold Identification by MALDI-TOF MS

A Moldy Application of MALDI: MALDI-ToF Mass Spectrometry for Fungal Identification

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