Identification of airborne bacteria by 16S rDNA sequencing, MALDI-TOF MS and the MIDI microbial identification system

Fykse, Else Marie; Tjärnhage, Torbjörn; Humppi, Tarmo; Eggen, Vilde Sørvik; Ingebretsen, André; Skogan, Gunnar; Olofsson, G.; Wästerby, Pär; Gradmark, Per-Åke; Larsson, Anders; Dybwad, Marius; Blatny, Janet Martha

doi:10.1007/s10453-015-9363-9

Cited by 24 publications

(13 citation statements)

References 39 publications

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“…However, at the species level, only 15 (~35%) of the cultures identified coincided with those identified by 16S rRNA gene sequencing analysis. These findings are in contrast to previous studies of clinically important bacteria where concordant species identifications between MALDI BioTyper and 16S rRNA gene analysis were reported to be in the range 41–92.2% of samples (Mellmann et al, 2008 ; Bizzini et al, 2011 ; Schmitt et al, 2013 ; Cheng et al, 2015 ; Fykse et al, 2015 ; Schulthess et al, 2016 ). This discrepancy is most likely due to the insufficient coverage of bacterial species in the databases.…”

Section: Discussioncontrasting

confidence: 99%

Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates

et al. 2018

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Many ecological experiments are based on the extraction and downstream analyses of microorganisms from different environmental samples. Due to its high throughput, cost-effectiveness and rapid performance, Matrix Assisted Laser Desorption/Ionization Mass Spectrometry with Time-of-Flight detector (MALDI-TOF MS), which has been proposed as a promising tool for bacterial identification and classification, could be advantageously used for dereplication of recurrent bacterial isolates. In this study, we compared whole-cell MALDI-TOF MS-based analyses of 49 bacterial cultures to two well-established bacterial identification and classification methods based on nearly complete 16S rRNA gene sequence analyses: a phylotype-based approach, using a closest type strain assignment, and a sequence similarity-based approach involving a 98.65% sequence similarity threshold, which has been found to best delineate bacterial species. Culture classification using reference-based MALDI-TOF MS was comparable to that yielded by phylotype assignment up to the genus level. At the species level, agreement between 16S rRNA gene analysis and MALDI-TOF MS was found to be limited, potentially indicating that spectral reference databases need to be improved. We also evaluated the mass spectral similarity technique for species-level delineation which can be used independently of reference databases. We established optimal mass spectral similarity thresholds which group MALDI-TOF mass spectra of common environmental isolates analogically to phylotype- and sequence similarity-based approaches. When using a mass spectrum similarity approach, we recommend a mass range of 4–10 kDa for analysis, which is populated with stable mass signals and contains the majority of phylotype-determining peaks. We show that a cosine similarity (CS) threshold of 0.79 differentiate mass spectra analogously to 98.65% species-level delineation sequence similarity threshold, with corresponding precision and recall values of 0.70 and 0.73, respectively. When matched to species-level phylotype assignment, an optimal CS threshold of 0.92 was calculated, with associated precision and recall values of 0.83 and 0.64, respectively. Overall, our research indicates that a similarity-based MALDI-TOF MS approach can be routinely used for efficient dereplication of isolates for downstream analyses, with minimal loss of unique organisms. In addition, MALDI-TOF MS analysis has further improvement potential unlike 16S rRNA gene analysis, whose methodological limits have reached a plateau.

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Section: Discussioncontrasting

confidence: 99%

Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates

et al. 2018

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“…() and Fykse et al . (). The peak lists generated were used directly to obtain matches against the reference library (SARAMIS database).…”

Section: Methodsmentioning

confidence: 97%

“…Storage days with the different letter for the same bacterial group have means that are significantly different (P ≤ 0.05) (n = 72). and Fykse et al (2015). The peak lists generated were used directly to obtain matches against the reference library (SARAMIS database).…”

Section: Figurementioning

confidence: 99%

Bacillus and Paenibacillus species associated with extended shelf life milk during processing and storage

Mugadza

Buys

2017

Int J of Dairy Tech

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Characterisation of spore formers associated with extended shelf life milk was performed by analysing the bacteriological quality of milk samples collected at various processing stages and during storage. Isolates were identified with MALDI‐TOF‐MS. Milk had spore counts <2 log10 cfu/mL and 4 log10 cfu/mL during processing and storage, respectively. Bacillus pumilus dominated the bacterial population. Bacterial species were inoculated into sterile milk for a shelf life study, and the population change was observed over 42 days at 7 °C. Although the extended shelf life milk process was effective in reducing bacterial counts and species diversity, the presence of Bacillus cereus shows a potential safety problem in extended shelf life milk.

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“…In this study, matrix-assisted laser-desorption ionization time of flight (MALDI-TOF) mass spectrometry (MS) was used for identifying indoor airborne bacteria. Fykse et al (2015) used MALDI-TOF to identify indoor airborne bacteria, and Dybwad et al (2012Dybwad et al ( , 2014 investigated temporal variability of bacteria species in a subway station in Norway. Before MALDI-TOF analysis, colonies were picked with a toothpick and smeared on a steel target plate.…”

Section: Maldi-tof Analysismentioning

confidence: 99%

Assessment of indoor bioaerosols using a lab-made virtual impactor

Nasrabadi

Park

Kim

et al. 2016

Aerosol Science and Technology

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To assess indoor bioaerosols, a virtual impactor having 1 mm cutoff diameter was designed, fabricated, and evaluated with computational fluid dynamics simulation and also with laboratory test using polystyrene latex particles. Two other cutoff diameters of 635 nm and 1.5 mm were obtained by changing the inlet flow rate and the ratio of minor channel-to-inlet flow rates. In field test, the virtual impactor was operated with varying cutoff diameter and field-emission scanning electron microscope (FE-SEM) analysis was performed for each cutoff diameter to observe morphologies of indoor aerosol particles sampled at the major and minor outlet channels. Particles were sampled at both outlet channels using the SKC Button Aerosol sampler and subsequently cultured. By colony counting, it was found that 56% of cultured fungal particles and 63% of cultured bacterial particles had aerodynamic sizes smaller than 1 mm. MALDI-TOF analysis and visual inspection of culture samples were used to identify indoor bacterial and fungal species, respectively. Nearly same species of bacteria and fungi were detected both in the major and minor flow channels.

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Identification of airborne bacteria by 16S rDNA sequencing, MALDI-TOF MS and the MIDI microbial identification system

Cited by 24 publications

References 39 publications

Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates

Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates

Bacillus and Paenibacillus species associated with extended shelf life milk during processing and storage

Assessment of indoor bioaerosols using a lab-made virtual impactor

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